From 791b3bce00221c219a64bb09778eddc871b76d6a Mon Sep 17 00:00:00 2001 From: Daniel Burkhardt Date: Tue, 6 Apr 2021 08:20:55 -0400 Subject: [PATCH 0001/1233] Initial commit --- .gitignore | 2 + LICENSE | 674 +++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 2 + 3 files changed, 678 insertions(+) create mode 100644 .gitignore create mode 100644 LICENSE create mode 100644 README.md diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000..9c07d4ae98 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*.class +*.log diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000..f288702d2f --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 index 0000000000..112ad69621 --- /dev/null +++ b/README.md @@ -0,0 +1,2 @@ +# opsca-viash +Adapting Open Problems to use viash From ed3994ef8ec091acbc6d70c51dc171521243f3c2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 14:31:15 +0200 Subject: [PATCH 0002/1233] add viash Former-commit-id: 498ab3d6556d242eeb1382da7446be0369f2f175 --- bin/nextflow | 462 ++++++++++++++++++++ bin/project_build | 371 ++++++++++++++++ bin/project_clean | 173 ++++++++ bin/project_debug | 665 +++++++++++++++++++++++++++++ bin/project_push | 358 ++++++++++++++++ bin/project_test | 359 ++++++++++++++++ bin/viash | 1 + bin/viash-0.4.0-rc1.REMOVED.git-id | 1 + 8 files changed, 2390 insertions(+) create mode 100755 bin/nextflow create mode 100755 bin/project_build create mode 100755 bin/project_clean create mode 100755 bin/project_debug create mode 100755 bin/project_push create mode 100755 bin/project_test create mode 120000 bin/viash create mode 100644 bin/viash-0.4.0-rc1.REMOVED.git-id diff --git a/bin/nextflow b/bin/nextflow new file mode 100755 index 0000000000..a0e029b867 --- /dev/null +++ b/bin/nextflow @@ -0,0 +1,462 @@ +#!/bin/bash +# +# Copyright 2013-2019, Centre for Genomic Regulation (CRG) +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +[[ "$NXF_DEBUG" == 'x' ]] && set -x +NXF_VER=${NXF_VER:-'19.01.0'} +NXF_ORG=${NXF_ORG:-'nextflow-io'} +NXF_HOME=${NXF_HOME:-$HOME/.nextflow} +NXF_PROT=${NXF_PROT:-'https'} +NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases} +NXF_TEMP=${NXF_TEMP:-$TMPDIR} +NXF_DIST=${NXF_DIST:-$NXF_HOME/framework} +NXF_CLI="$0 $@" + +export NXF_CLI +export NXF_ORG +export NXF_HOME + +if [[ $TERM && $TERM != 'dumb' ]]; then +if command -v tput &>/dev/null; then +GREEN=$(tput setaf 2; tput bold) +YELLOW=$(tput setaf 3) +RED=$(tput setaf 1) +NORMAL=$(tput sgr0) +fi +fi + +function echo_red() { + >&2 echo -e "$RED$*$NORMAL" +} + +function echo_green() { + echo -e "$GREEN$*$NORMAL" +} + +function echo_yellow() { + >&2 echo -e "$YELLOW$*$NORMAL" +} + +function die() { + echo_red "$*" + exit 1 +} + +function get_abs_filename() { + echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")" +} + +function get() { + if command -v curl &>/dev/null; then + GET="curl -fsSL '$1' -o '$2'" + elif command -v wget &>/dev/null; then + GET="wget -q '$1' -O '$2'" + else + echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them" + exit 1 + fi + + printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. " + eval $GET; status=$? + printf "\r\033[K" + if [ $status -ne 0 ]; then + echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet" + echo "" + echo "Alternatively you can try to download this file:" + echo " $1" + echo "" + echo "and save it as:" + echo " ${3:-$2}" + echo "" + exit 1 + fi +} + +function make_temp() { + local base=${NXF_TEMP:=$PWD} + if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $? + else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $? + fi +} + +function resolve_link() { + [[ ! -f $1 ]] && exit 1 + if command -v realpath &>/dev/null; then + realpath "$1" + elif command -v readlink &>/dev/null; then + local target="$1" + cd $(dirname $target); target=$(basename $target) + while [ -L "$target" ]; do + target="$(readlink "$target")" + cd $(dirname $target); target=$(basename $target) + done + echo "$(cd "$(dirname "$target")"; pwd -P)/$target" + else + echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found" + exit 1 + fi +} + +function current_ver() { + [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest' +} + +function install() { + local tmpfile=$(make_temp) + local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver) + local action="a=${2:-default}" + get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $? + mv "$tmpfile" "$1" || exit $? + chmod +x "$1" || exit $? + bash "$1" -download || exit $? + echo '' + echo -e $'Nextflow installation completed. Please note:' + echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1) + if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then + echo -e $'- you may complete the installation by moving it to a directory in your $PATH' + fi + echo '' +} + +function launch_nextflow() { + # the launch command line + local cmdline=() + # remove leading and trailing double-quotes + for x in "${launcher[@]}"; do + x="${x%\"}" + x="${x#\"}" + cmdline+=("$x") + done + + if [[ $NXF_MPIRUN ]]; then + local rank='' + [[ $SLURM_PROCID ]] && rank=$SLURM_PROCID + [[ $OMPI_COMM_WORLD_RANK ]] && rank=$OMPI_COMM_WORLD_RANK + if [[ ! $rank ]]; then + echo_red 'It looks you are not running in a MPI enabled environment -- cannot find `$OMPI_COMM_WORLD_RANK` nor `$SLURM_PROCID` variable'; + exit 1; + fi + if [[ $SLURM_CPUS_PER_TASK && $SLURM_MEM_PER_CPU ]]; then + export NXF_CLUSTER_MAXCPUS=$SLURM_CPUS_PER_TASK + export NXF_CLUSTER_MAXMEMORY="$(($SLURM_MEM_PER_CPU*$SLURM_CPUS_PER_TASK))MB" + fi + if [[ $rank == 0 ]]; then + # sleep a few seconds in order to wait worker daemons to bootstrap + sleep ${NXF_SLEEP:-10} + export NXF_EXECUTOR='ignite' + export NXF_CLUSTER_SHUTDOWNONCOMPLETE='true' + else + args=(-log .nextflow_node_${rank}.log node ignite) + fi + # start in daemon mode + elif [[ "$bg" ]]; then + local pid_file="${NXF_PID_FILE:-.nextflow.pid}" + cmdline+=("${args[@]}") + exec "${cmdline[@]}" & + disown + echo $! > "$pid_file" + exit 0 + fi + + cmdline+=("${args[@]}") + exec "${cmdline[@]}" + exit 1 +} + +# check self-install +if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then + if [ -d nextflow ]; then + echo 'Please note:' + echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists." + echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder." + echo '' + exit 1 + fi + install "$PWD/nextflow" install + exit 0 +fi + + +# parse the command line +bg='' +dockerize='' +declare -a jvmopts=() +declare -a args=("$@") +declare -a commands=(clone config drop help history info ls pull run view node console kuberun) +cmd='' +while [[ $# != 0 ]]; do + case $1 in + -D*) + if [[ ! "$cmd" ]]; then + jvmopts+=("$1") + fi + ;; + -d|-dockerize) + if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then + dockerize=1 + fi + ;; + -bg) + if [[ ! -f /.nextflow/dockerized ]]; then + bg=1 + fi + ;; + -download) + if [[ ! "$cmd" ]]; then + rm -rf "$NXF_DIST/$NXF_VER" || exit $? + bash "$0" -version || exit $? + exit 0 + fi + ;; + -self-update|self-update) + if [[ ! "$cmd" ]]; then + [[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1 + unset NXF_VER + install "$0" update + exit 0 + fi + ;; + -process.executor|-executor.name) + if [[ $2 && $2 == 'ignite' ]]; then + NXF_MODE='ignite'; shift; + fi + ;; + -with-mpi) + NXF_MODE='ignite' + NXF_MPIRUN='true' + ;; + *) + [[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1 + ;; + esac + shift +done + +NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''} +if [[ "$dockerize" ]]; then + if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi + NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets} + mkdir -p "$NXF_ASSETS" + exec docker run $detach --rm --net host \ + -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \ + -v /var/run/docker.sock:/var/run/docker.sock \ + -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \ + nextflow/nextflow:$NXF_VER nextflow "${args[@]}" + exit 1 +fi + +CAPSULE_LOG=${CAPSULE_LOG:=''} +CAPSULE_RESET=${CAPSULE_RESET:=''} +CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"} + +NXF_PACK=one +NXF_MODE=${NXF_MODE:-''} +NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar} +NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR} +NXF_PATH=$(dirname "$NXF_BIN") +NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR} +NXF_GRAB=${NXF_GRAB:-''} +NXF_CLASSPATH=${NXF_CLASSPATH:-''} +NXF_MPIRUN=${NXF_MPIRUN:=''} +NXF_HOST=${HOSTNAME:-localhost} +[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST} + +[ ! $NXF_MODE ] && [[ $NXF_CLOUD_DRIVER == google ]] && NXF_MODE='google' +[ ! $NXF_MODE ] && [[ $GOOGLE_APPLICATION_CREDENTIALS ]] && NXF_MODE='google' + +if [[ $NXF_MODE == ignite ]]; then + # Fix JDK bug when there's a limit on the OS virtual memory + # https://bugs.openjdk.java.net/browse/JDK-8044054 + # https://issues.apache.org/jira/browse/HADOOP-7154 + export MALLOC_ARENA_MAX=4 +fi + +# Determine the path to this file +if [[ $NXF_PACK = all ]]; then + NXF_BIN=$(which "$0" 2>/dev/null) + [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0" +fi + +# use nextflow custom java home path +if [[ "$NXF_JAVA_HOME" ]]; then + JAVA_HOME="$NXF_JAVA_HOME" + unset JAVA_CMD +fi +# Determine the Java command to use to start the JVM. +if [ ! -x "$JAVA_CMD" ] ; then + if [ -d "$JAVA_HOME" ] ; then + if [ -x "$JAVA_HOME/jre/sh/java" ] ; then + # IBM's JDK on AIX uses strange locations for the executables + JAVA_CMD="$JAVA_HOME/jre/sh/java" + else + JAVA_CMD="$JAVA_HOME/bin/java" + fi + elif [ -x /usr/libexec/java_home ]; then + JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java" + else + JAVA_CMD="$(which java)" || JAVA_CMD=java + fi +fi + +# Retrieve the java version from a NF local file +JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')" +if [ -f "$JAVA_KEY" ]; then + JAVA_VER="$(cat "$JAVA_KEY")" +else + JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)" + if [ $? -ne 0 ]; then + echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}" + echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n" + exit 1 + fi + JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}') + # check NF version + if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then + echo_red "Not a valid Nextflow version: $NXF_VER" + exit 1 + fi + major=${BASH_REMATCH[1]} + minor=${BASH_REMATCH[2]} + version_check="^(1.8|9|10|11)" + version_message="Java 8" + # legacy version - Java 7/8 only + if [ $major -eq 0 ] && [ $minor -lt 26 ]; then + version_check="^(1.7|1.8)" + version_message="Java 7 or 8" + fi + if [[ ! $JAVA_VER =~ $version_check ]]; then + echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed" + if [[ "$NXF_JAVA_HOME" ]]; then + echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n" + else + echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n" + fi + exit 1 + fi + mkdir -p $(dirname "$JAVA_KEY") + [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY" +fi + +# Verify nextflow jar is available +if [ ! -f "$NXF_BIN" ]; then + [ -f "$NXF_PATH" ] && rm "$NXF_PATH" + mkdir -p "$NXF_PATH" || exit $? + tmpfile=$(make_temp) + get "$NXF_URL" "$tmpfile" "$NXF_BIN" + mv "$tmpfile" "$NXF_BIN" +fi + +[[ "$cmd" == "console" ]] && NXF_MODE='console' +[[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='ignite' + +COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`} +declare -a JAVA_OPTS=() +JAVA_OPTS+=(-Dfile.encoding=UTF-8 -noverify -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD") +if [[ $cmd == console ]]; then bg=1; +else JAVA_OPTS+=(-Djava.awt.headless=true) +fi + +[[ "$NXF_MODE" ]] && JAVA_OPTS+=(-Dcapsule.mode=$NXF_MODE) +[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME") +[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG) +[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true) +[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1) +[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS) +[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH +[[ "$NXF_GRAB" ]] && export NXF_GRAB +[[ "$COLUMNS" ]] && export COLUMNS +[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP") +[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}") +# use drip to speedup startup time -- https://github.com/ninjudd/drip +[[ "$NXF_DRIP" ]] && export DRIP_INIT='' && export DRIP_INIT_CLASS='nextflow.cli.DripMain' +export JAVA_CMD +export CAPSULE_CACHE_DIR + +# lookup the a `md5` command +if hash md5sum 2>/dev/null; then MD5=md5sum; +elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum; +elif hash md5 2>/dev/null; then MD5=md5; +else MD5='' +fi + +# when no md5 command is available fallback on default execution +if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then + launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")) + launch_nextflow + exit 1 +fi + +# creates a md5 unique for the given variables +env_md5() { +cat </dev/null; then + STR='' + for x in "${launcher[@]}"; do + [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$x " + done + printf "$STR">"$LAUNCH_FILE" + else + echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?" + fi + +fi + +# finally run it +launch_nextflow diff --git a/bin/project_build b/bin/project_build new file mode 100755 index 0000000000..cdf27a79bb --- /dev/null +++ b/bin/project_build @@ -0,0 +1,371 @@ +#!/usr/bin/env bash + +########################### +# project_build 0.1 # +########################### + +# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Build a project, usually in the context of a pipeline." + echo + echo "Options:" + echo " -m string, --mode=string" + echo " type: string, default: development" + echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." + echo "" + echo " -p string, --platforms=string" + echo " type: string, default: docker|nextflow" + echo " Which platforms to test, default is 'docker|nextflow'." + echo "" + echo " -q string, --query=string" + echo " type: string" + echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo "" + echo " -n string, --namespace=string" + echo " type: string" + echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo "" + echo " -v string, --version=string" + echo " type: string, default: dev" + echo " Which version of the pipeline to use." + echo "" + echo " -r string, --registry=string" + echo " type: string, default: " + echo " Docker registry to use, only used when using a registry." + echo "" + echo " -nc, --no-cache, --no_cache" + echo " type: boolean_true" + echo " Don't cache the docker build in development mode." + echo "" + echo " --log=file" + echo " type: file, default: log.txt" + echo " Log file" + echo "" + echo " --viash=file" + echo " type: file" + echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --mode) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --mode=*) + VIASH_PAR_MODE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -m) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --platforms) + VIASH_PAR_PLATFORMS="$2" + shift 2 + ;; + --platforms=*) + VIASH_PAR_PLATFORMS=$(ViashRemoveFlags "$1") + shift 1 + ;; + -p) + VIASH_PAR_PLATFORMS="$2" + shift 2 + ;; + --query) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --query=*) + VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -q) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --namespace) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --namespace=*) + VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -n) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --version) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --version=*) + VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --registry) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --registry=*) + VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -r) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --no_cache) + VIASH_PAR_NO_CACHE=true + shift 1 + ;; + -nc) + VIASH_PAR_NO_CACHE=true + shift 1 + ;; + --no-cache) + VIASH_PAR_NO_CACHE=true + shift 1 + ;; + --log) + VIASH_PAR_LOG="$2" + shift 2 + ;; + --log=*) + VIASH_PAR_LOG=$(ViashRemoveFlags "$1") + shift 1 + ;; + --viash) + VIASH_PAR_VIASH="$2" + shift 2 + ;; + --viash=*) + VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +if [ -z "$VIASH_PAR_MODE" ]; then + VIASH_PAR_MODE="development" +fi +if [ -z "$VIASH_PAR_PLATFORMS" ]; then + VIASH_PAR_PLATFORMS="docker|nextflow" +fi +if [ -z "$VIASH_PAR_VERSION" ]; then + VIASH_PAR_VERSION="dev" +fi +if [ -z "$VIASH_PAR_REGISTRY" ]; then + VIASH_PAR_REGISTRY="" +fi +if [ -z "$VIASH_PAR_NO_CACHE" ]; then + VIASH_PAR_NO_CACHE="false" +fi +if [ -z "$VIASH_PAR_LOG" ]; then + VIASH_PAR_LOG="log.txt" +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_build-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_mode='$VIASH_PAR_MODE' +par_platforms='$VIASH_PAR_PLATFORMS' +par_query='$VIASH_PAR_QUERY' +par_namespace='$VIASH_PAR_NAMESPACE' +par_version='$VIASH_PAR_VERSION' +par_registry='$VIASH_PAR_REGISTRY' +par_no_cache='$VIASH_PAR_NO_CACHE' +par_log='$VIASH_PAR_LOG' +par_viash='$VIASH_PAR_VIASH' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +# if not specified, default par_query to a catch-all regex +if [ -z "\$par_query" ]; then + par_query=".*" +fi + +# if not specified, default par_namespace to a catch-all regex +if [ -z "\$par_namespace" ]; then + par_namespace=".*" +fi + +# if not specified, default par_viash to look for 'viash' on the PATH +if [ -z "\$par_viash" ]; then + par_viash="viash" +fi + +if [ "\$par_mode" == "development" ]; then + echo "In development mode..." + + if [ "\$par_no_cache" == "true" ]; then + setup_strat="build" + else + setup_strat="cachedbuild" + fi + + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "dev"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "'\$setup_strat'"' \\ + -l -w \\ + --setup | tee "\$par_log" +elif [ "\$par_mode" == "integration" ]; then + echo "In integration mode..." + + if [ "\$par_no_cache" == "true" ]; then + echo "Warning: '--no_cache' only applies when '--mode=development'." + fi + + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l -w \\ + --setup | tee "\$par_log" +elif [ "\$par_mode" == "release" ]; then + echo "In release mode..." + + if [ "\$par_no_cache" == "true" ]; then + echo "Warning: '--no_cache' only applies when '--mode=development'." + fi + + if [ "\$par_version" == "dev" ]; then + echo "Error: For a release, you have to specify an explicit version using --version" + exit 1 + fi + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l -w \\ + --setup | tee "\$par_log" +else + echo "Not a valid mode argument" +fi +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_clean b/bin/project_clean new file mode 100755 index 0000000000..0b709a4128 --- /dev/null +++ b/bin/project_clean @@ -0,0 +1,173 @@ +#!/usr/bin/env bash + +########################### +# project_clean 0.1 # +########################### + +# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Clean a (nextflow) project directory" + echo + echo "Options:" + echo " file" + echo " type: file, default: ." + echo " Base directory" + echo "" + echo " -after string" + echo " type: string" + echo "" + echo " -before string" + echo " type: string" + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + -after) + VIASH_PAR_AFTER="$2" + shift 2 + ;; + -before) + VIASH_PAR_BEFORE="$2" + shift 2 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + +if [[ $# -gt 0 ]]; then + VIASH_PAR_DIR="$1" + shift 1 +fi + +if [ -z "$VIASH_PAR_DIR" ]; then + VIASH_PAR_DIR="." +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_clean-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_dir='$VIASH_PAR_DIR' +par_after='$VIASH_PAR_AFTER' +par_before='$VIASH_PAR_BEFORE' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +add="" + +if [ ! -z "\$par_after" ]; then + add="\$add -after \$par_after" +fi + +if [ ! -z "\$par_before" ]; then + add="\$add -before \$par_before" +fi + +nextflow clean -f "\$add" +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_debug b/bin/project_debug new file mode 100755 index 0000000000..70012aee84 --- /dev/null +++ b/bin/project_debug @@ -0,0 +1,665 @@ +#!/usr/bin/env bash + +########################### +# project_debug 0.1 # +########################### + +# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + : +} +# ViashDockerBuild: ... +function ViashDockerBuild { + ViashDockerPull $1 +} + +# ViashSetup: ... +function ViashSetup { + ViashDockerSetup dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_SETUP_STRATEGY +} + +# ViashPush: ... +function ViashPush { + ViashDockerPush dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_PUSH_STRATEGY +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Generate debugging report based on viash ns test output" + echo + echo "Options:" + echo " --input=file" + echo " type: file, required parameter" + echo " viasn ns test output file (tsv format)" + echo "" + echo " --tmp=file" + echo " type: file, default: /tmp" + echo " System temp dir if different from /tmp (e.g. on Mac use /private/tmp)" + echo "" + echo " --output=file" + echo " type: file, default: debug_report.md" + echo " Name/path of the output markdown file" + echo "" +} +######## Helper functions for setting up Docker images for viash ######## + + +# ViashDockerRemoteTagCheck: check whether a Docker image is available +# on a remote. Assumes `docker login` has been performed, if relevant. +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerRemoteTagCheck python:latest +# echo $? # returns '0' +# ViashDockerRemoteTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerRemoteTagCheck { + docker manifest inspect $1 > /dev/null 2> /dev/null +} + +# ViashDockerLocalTagCheck: check whether a Docker image is available locally +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# docker pull python:latest +# ViashDockerLocalTagCheck python:latest +# echo $? # returns '0' +# ViashDockerLocalTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerLocalTagCheck { + [ -n "$(docker images -q $1)" ] +} + +# ViashDockerPull: pull a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPull python:latest +# echo $? # returns '0' +# ViashDockerPull sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPull { + echo "> docker pull $1" + docker pull $1 && return 0 || return 1 +} + +# ViashDockerPullElseBuild: pull a Docker image, else build it +# +# $1 : image identifier with format `[registry/]image[:tag]` +# examples: +# ViashDockerPullElseBuild mynewcomponent +function ViashDockerPullElseBuild { + set +e + ViashDockerPull $1 + out=$? + set -e + if [ $out -ne 0 ]; then + ViashDockerBuild $@ + fi +} + +# ViashDockerSetup: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerSetupStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerSetup { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + echo "Skipping setup." + elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + ViashDockerLocalTagCheck $VSHD_ID + if [ $? -eq 0 ]; then + echo "Image $VSHD_ID already exists" + elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi +} + +# ViashDockerPush: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerPushStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerPush { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + set +e + docker push $1 + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "> $VSHD_ID force push ... ok" + else + echo "> $VSHD_ID force push ... error" + exit 1 + fi + elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + set +e + ViashDockerRemoteTagCheck $1 + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + echo "> $VSHD_ID exists, doing nothing" + else + echo -n "> $VSHD_ID does not exist, try pushing " + set +e + docker push $1 > /dev/null 2> /dev/null + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "... ok" + else + echo "... error" + fi + fi + else + echo "Unrecognised Docker push strategy: $VSHD_STRAT" + fi +} + +######## End of helper functions for setting up Docker images for viash ######## +# initialise variables +VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' +VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' +# ViashAbsolutePath: generate absolute path from relative path +# borrowed from https://stackoverflow.com/a/21951256 +# $1 : relative filename +# return : absolute path +# examples: +# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt +# ViashAbsolutePath /foo/bar/.. # returns /foo +function ViashAbsolutePath { + local thePath + if [[ ! "$1" =~ ^/ ]]; then + thePath="$PWD/$1" + else + thePath="$1" + fi + echo "$thePath" | ( + IFS=/ + read -a parr + declare -a outp + for i in "${parr[@]}"; do + case "$i" in + ''|.) continue ;; + ..) + len=${#outp[@]} + if ((len==0)); then + continue + else + unset outp[$((len-1))] + fi + ;; + *) + len=${#outp[@]} + outp[$len]="$i" + ;; + esac + done + echo /"${outp[*]}" + ) +} +# ViashAutodetectMount: auto configuring docker mounts from parameters +# $1 : The parameter value +# returns : New parameter +# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker +# examples: +# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' +# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' +function ViashAutodetectMount { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "$mount_target/$base_name" +} +function ViashAutodetectMountArg { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "-v \"$mount_source:$mount_target\"" +} +# ViashExtractFlags: Retain leading flag +# $1 : string with a possible leading flag +# return : leading flag +# examples: +# ViashExtractFlags --foo=bar # returns --foo +function ViashExtractFlags { + echo $1 | sed 's/=.*//' +} +# initialise variables +VIASH_EXTRA_MOUNTS='' + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --input) + VIASH_PAR_INPUT="$2" + shift 2 + ;; + --input=*) + VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + --tmp) + VIASH_PAR_TMP="$2" + shift 2 + ;; + --tmp=*) + VIASH_PAR_TMP=$(ViashRemoveFlags "$1") + shift 1 + ;; + --output) + VIASH_PAR_OUTPUT="$2" + shift 2 + ;; + --output=*) + VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + ---dss|---docker_setup_strategy) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY="$2" + shift 2 + ;; + ---docker_setup_strategy=*) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dps|---docker_push_strategy) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY="$2" + shift 2 + ;; + ---docker_push_strategy=*) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dockerfile) + ViashDockerfile + exit 0 + ;; + ---v|---volume) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" + shift 2 + ;; + ---volume=*) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" + shift 1 + ;; + ---debug) + echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1 + exit 0 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +# check whether required parameters exist +if [ -z "$VIASH_PAR_INPUT" ]; then + echo '--input' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_TMP" ]; then + VIASH_PAR_TMP="/tmp" +fi +if [ -z "$VIASH_PAR_OUTPUT" ]; then + VIASH_PAR_OUTPUT="debug_report.md" +fi + + +# detect volumes from file arguments +if [ ! -z "$VIASH_PAR_INPUT" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_INPUT")" + VIASH_PAR_INPUT=$(ViashAutodetectMount "$VIASH_PAR_INPUT") +fi +if [ ! -z "$VIASH_PAR_TMP" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_TMP")" + VIASH_PAR_TMP=$(ViashAutodetectMount "$VIASH_PAR_TMP") +fi +if [ ! -z "$VIASH_PAR_OUTPUT" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_OUTPUT")" + VIASH_PAR_OUTPUT=$(ViashAutodetectMount "$VIASH_PAR_OUTPUT") +fi + +# Always mount the resource directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" +VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") + +# Always mount the VIASH_TEMP directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" +VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") + +# change file ownership +function viash_perform_chown { + + if [ ! -z "$VIASH_PAR_OUTPUT" ]; then + eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" + fi +} +trap viash_perform_chown EXIT + + +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_debug-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_input='$VIASH_PAR_INPUT' +par_tmp='$VIASH_PAR_TMP' +par_output='$VIASH_PAR_OUTPUT' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +# set -ex + +function output { + echo "\$@" >> \$par_output +} + +echo "# Debug Report \`date\`" > \$par_output +output "" +output "This reports uses the provided tsv log file to retrieve components" +output "that gave errors during a \\\`viash ns test\\\` test run." + +output "" +output "In _append_ mode, additional test results are added to the tsv log file," +output "so an error may already be resolved but still represented here." + +output "" +output "In general, the following situations are possible:" +output "" +output "1. A component gives no errors, all builds and tests runs well for every platform" +output "2. A component fails for a given platform, either during build or test" +output " a. There is at least one failure in the tsv log file, but the last entry is a success." +output " b. The last run for this component failed." +output "" + +# Retrieve information about errors +cat \$par_input | grep ERROR > /dev/null +contains_errors=\$? +if [ \$contains_errors -eq 0 ]; then + errors=1 + cat \$par_input | grep ERROR > \$par_tmp/failed.tsv +else + errors=0 +fi + +# Retrieve information about missings +cat \$par_input | grep MISSING > /dev/null +contains_missings=\$? +if [ \$contains_missings -eq 0 ]; then + missings=1 + cat \$par_input | grep MISSING > \$par_tmp/missing.tsv +else + missings=0 +fi + +# Retrieve information about success +cat \$par_input | grep SUCCES > /dev/null +contains_success=\$? +if [ \$contains_success -eq 0 ]; then + success=1 + cat \$par_input | grep SUCCESS > \$par_tmp/success.tsv +else + success=0 +fi +# Start writing content +output "## Overview" +output "" + +output "Failed components:" +output "" +if [ \$errors -eq 1 ]; then + cat \$par_tmp/failed.tsv | cut -f1,2,3 | sort | uniq | while read f; do + ns=\`echo -n "\$f" | cut -f1\` + comp=\`echo -n "\$f" | cut -f2\` + platform=\`echo -n "\$f" | cut -f3\` + still_exec=\`cat \$par_input | grep -P "\$ns\\t\$comp\\t\$platform" | tail -1 | grep ERROR\` + still=\$? + if [ \$still -eq 0 ]; then + line="- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\` and is still open. See full report below." + else + line="- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\` but is resolved." + fi + output "\$line" + done + output "" +else + output "No failed components" + output "" +fi + +output "Missing components:" +output "" +if [ \$missings -eq 1 ]; then + cat \$par_tmp/missing.tsv | cut -f1,2,3 | sort | uniq | while read f; do + ns=\`echo -n "\$f" | cut -f1\` + comp=\`echo -n "\$f" | cut -f2\` + platform=\`echo -n "\$f" | cut -f3\` + output "- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\`" + done + output "" +else + output "No missing components" + output "" +fi + +# output "Working components:" +# output "" +# if [ \$success -eq 1 ]; then +# cat \$par_tmp/success.tsv | cut -f1,2,3 | sort | uniq | while read f; do +# ns=\`echo -n "\$f" | cut -f1\` +# comp=\`echo -n "\$f" | cut -f2\` +# platform=\`echo -n "\$f" | cut -f3\` +# output "- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\`" +# done +# output "" +# else +# output "No successfull components" +# output "" +# fi + +if [ \$errors -eq 1 ]; then + + output "" + output "## Error report" + output "" + + cat \$par_tmp/failed.tsv | cut -f1,2,3 | sort | uniq | while read f; do + ns=\`echo -n "\$f" | cut -f1\` + comp=\`echo -n "\$f" | cut -f2\` + platform=\`echo -n "\$f" | cut -f3\` + still_exec=\`cat \$par_input | grep -P "\$ns\\t\$comp\\t\$platform" | tail -1 | grep ERROR\` + still=\$? + root_test_dir=\`ls -ctd "\$par_tmp/viash_test_\$comp"* | head -1\` + + if [ \$still -eq 0 ]; then + + output "### \\\`\$comp\\\` Build" + output "" + output "Files:" + output "" + output '\`\`\`' + ls -alh "\$root_test_dir/build_executable" > \$par_tmp/list.log + cat \$par_tmp/list.log >> \$par_output + output '\`\`\`' + output "" + output "Build log:" + output "" + output '\`\`\`' + cat "\$root_test_dir/build_executable/_viash_build_log.txt" >> \$par_output + output '\`\`\`' + output "" + + output "### \\\`\$comp\\\` Test" + output "" + output "Files:" + output "" + output '\`\`\`' + ls -alh "\$root_test_dir/test_run"* > \$par_tmp/list.log + cat \$par_tmp/list.log >> \$par_output + output '\`\`\`' + output "" + output "Setup log:" + output "" + output '\`\`\`' + cat "\$root_test_dir/test_"*"/_viash_test_log.txt" >> \$par_output + output '\`\`\`' + output "" + fi + + done + +fi +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_push b/bin/project_push new file mode 100755 index 0000000000..0973473719 --- /dev/null +++ b/bin/project_push @@ -0,0 +1,358 @@ +#!/usr/bin/env bash + +########################## +# project_push 0.1 # +########################## + +# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Push a project, usually in the context of a pipeline." + echo + echo "Options:" + echo " -m string, --mode=string" + echo " type: string, default: development" + echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." + echo "" + echo " -q string, --query=string" + echo " type: string" + echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo "" + echo " -n string, --namespace=string" + echo " type: string" + echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo "" + echo " -v string, --version=string" + echo " type: string, default: dev" + echo " Which version of the pipeline to use." + echo "" + echo " -r string, --registry=string" + echo " type: string, default: itx-aiv.artifactrepo.jnj.com" + echo " Docker registry to use, only used when using a registry." + echo "" + echo " --force" + echo " type: boolean_true" + echo " Overwrite registry" + echo "" + echo " --log=file" + echo " type: file, default: log.txt" + echo " Log file" + echo "" + echo " --viash=file" + echo " type: file, default: bin/viash" + echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --mode) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --mode=*) + VIASH_PAR_MODE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -m) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --query) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --query=*) + VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -q) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --namespace) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --namespace=*) + VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -n) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --version) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --version=*) + VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --registry) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --registry=*) + VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -r) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --force) + VIASH_PAR_FORCE=true + shift 1 + ;; + --log) + VIASH_PAR_LOG="$2" + shift 2 + ;; + --log=*) + VIASH_PAR_LOG=$(ViashRemoveFlags "$1") + shift 1 + ;; + --viash) + VIASH_PAR_VIASH="$2" + shift 2 + ;; + --viash=*) + VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +if [ -z "$VIASH_PAR_MODE" ]; then + VIASH_PAR_MODE="development" +fi +if [ -z "$VIASH_PAR_VERSION" ]; then + VIASH_PAR_VERSION="dev" +fi +if [ -z "$VIASH_PAR_REGISTRY" ]; then + VIASH_PAR_REGISTRY="itx-aiv.artifactrepo.jnj.com" +fi +if [ -z "$VIASH_PAR_FORCE" ]; then + VIASH_PAR_FORCE="false" +fi +if [ -z "$VIASH_PAR_LOG" ]; then + VIASH_PAR_LOG="log.txt" +fi +if [ -z "$VIASH_PAR_VIASH" ]; then + VIASH_PAR_VIASH="bin/viash" +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_push-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_mode='$VIASH_PAR_MODE' +par_query='$VIASH_PAR_QUERY' +par_namespace='$VIASH_PAR_NAMESPACE' +par_version='$VIASH_PAR_VERSION' +par_registry='$VIASH_PAR_REGISTRY' +par_force='$VIASH_PAR_FORCE' +par_log='$VIASH_PAR_LOG' +par_viash='$VIASH_PAR_VIASH' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +if [ "\$par_mode" == "release" ]; then + echo "In release mode..." + if [ "\$par_version" == "dev" ]; then + echo "For a release, you have to specify an explicit version using --version" + exit 1 + else + echo "Using version \$par_version" to tag containers + fi +fi + +# if not specified, default par_query to a catch-all regex +if [ -z "\$par_query" ]; then + par_query=".*" +fi + +# if not specified, default par_namespace to a catch-all regex +if [ -z "\$par_namespace" ]; then + par_namespace=".*" +fi + +# if not specified, default par_viash to look for 'viash' on the PATH +if [ -z "\$par_viash" ]; then + par_viash="viash" +fi + +if [[ \$par_force == true ]]; then + echo "Force push... handle with care..." + if [ "\$par_mode" == "development" ]; then + echo "No container push can and should be performed in this mode" + elif [ "\$par_mode" == "integration" ]; then + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "docker" \\ + -q "\$par_query" \\ + -c '.functionality.version := "dev"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + --setup --push | tee "\$par_log" + elif [ "\$par_mode" == "release" ]; then + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "docker" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + --setup --push | tee "\$par_log" + else + echo "Not a valid mode argument" + fi +else + if [ "\$par_mode" == "development" ]; then + echo "No container push can and should be performed in this mode" + elif [ "\$par_mode" == "integration" ]; then + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "docker" \\ + -q "\$par_query" \\ + -c '.functionality.version := "dev"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + --setup --push | tee "\$par_log" + elif [ "\$par_mode" == "release" ]; then + "\$par_viash" ns build \\ + -n "\$par_namespace" \\ + -p "docker" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + --setup --push | tee "\$par_log" + else + echo "Not a valid mode argument" + fi +fi +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_test b/bin/project_test new file mode 100755 index 0000000000..c08d4482c2 --- /dev/null +++ b/bin/project_test @@ -0,0 +1,359 @@ +#!/usr/bin/env bash + +########################## +# project_test 0.1 # +########################## + +# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Test a project, usually in the context of a pipeline." + echo + echo "Options:" + echo " -m string, --mode=string" + echo " type: string, default: development" + echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." + echo "" + echo " -p string, --platforms=string" + echo " type: string, default: docker" + echo " Which platforms to test, default is 'docker'." + echo "" + echo " -q string, --query=string" + echo " type: string" + echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo "" + echo " -n string, --namespace=string" + echo " type: string" + echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo "" + echo " -v string, --version=string" + echo " type: string, default: dev" + echo " Which version of the pipeline to use." + echo "" + echo " -r string, --registry=string" + echo " type: string" + echo " Docker registry to use, only used when using a registry." + echo "" + echo " -l file, --log=file" + echo " type: file, default: log.tsv" + echo " Test log file" + echo "" + echo " --append=boolean" + echo " type: boolean, default: true" + echo " Append to the log file?" + echo "" + echo " --viash=file" + echo " type: file" + echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --mode) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --mode=*) + VIASH_PAR_MODE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -m) + VIASH_PAR_MODE="$2" + shift 2 + ;; + --platforms) + VIASH_PAR_PLATFORMS="$2" + shift 2 + ;; + --platforms=*) + VIASH_PAR_PLATFORMS=$(ViashRemoveFlags "$1") + shift 1 + ;; + -p) + VIASH_PAR_PLATFORMS="$2" + shift 2 + ;; + --query) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --query=*) + VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -q) + VIASH_PAR_QUERY="$2" + shift 2 + ;; + --namespace) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --namespace=*) + VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -n) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --version) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --version=*) + VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + shift 1 + ;; + -v) + VIASH_PAR_VERSION="$2" + shift 2 + ;; + --registry) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --registry=*) + VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -r) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --log) + VIASH_PAR_LOG="$2" + shift 2 + ;; + --log=*) + VIASH_PAR_LOG=$(ViashRemoveFlags "$1") + shift 1 + ;; + -l) + VIASH_PAR_LOG="$2" + shift 2 + ;; + --append) + VIASH_PAR_APPEND="$2" + shift 2 + ;; + --append=*) + VIASH_PAR_APPEND=$(ViashRemoveFlags "$1") + shift 1 + ;; + --viash) + VIASH_PAR_VIASH="$2" + shift 2 + ;; + --viash=*) + VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +if [ -z "$VIASH_PAR_MODE" ]; then + VIASH_PAR_MODE="development" +fi +if [ -z "$VIASH_PAR_PLATFORMS" ]; then + VIASH_PAR_PLATFORMS="docker" +fi +if [ -z "$VIASH_PAR_VERSION" ]; then + VIASH_PAR_VERSION="dev" +fi +if [ -z "$VIASH_PAR_LOG" ]; then + VIASH_PAR_LOG="log.tsv" +fi +if [ -z "$VIASH_PAR_APPEND" ]; then + VIASH_PAR_APPEND="true" +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_test-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_mode='$VIASH_PAR_MODE' +par_platforms='$VIASH_PAR_PLATFORMS' +par_query='$VIASH_PAR_QUERY' +par_namespace='$VIASH_PAR_NAMESPACE' +par_version='$VIASH_PAR_VERSION' +par_registry='$VIASH_PAR_REGISTRY' +par_log='$VIASH_PAR_LOG' +par_append='$VIASH_PAR_APPEND' +par_viash='$VIASH_PAR_VIASH' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +# if not specified, default par_query to a catch-all regex +if [ -z "\$par_query" ]; then + par_query=".*" +fi + +# if not specified, default par_namespace to a catch-all regex +if [ -z "\$par_namespace" ]; then + par_namespace=".*" +fi + +# if not specified, default par_viash to look for 'viash' on the PATH +if [ -z "\$par_viash" ]; then + par_viash="viash" +fi + +# if --append (-a) true is specified, add \`--append\` +if [ "\$par_append" == "true" ]; then + par_append_parsed="--append" +fi + +if [ "\$par_mode" == "development" ]; then + echo "In development mode..." + "\$par_viash" ns test \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "dev"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -l \\ + -t "\$par_log" \\ + \$par_append_parsed +elif [ "\$par_mode" == "integration" ]; then + echo "In integration mode..." + "\$par_viash" ns test \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + -t "\$par_log" \\ + \$par_append_parsed +elif [ "\$par_mode" == "release" ]; then + echo "In release mode..." + if [ "\$par_version" == "dev" ]; then + echo "For a release, you have to specify an explicit version using --version" + exit 1 + fi + "\$par_viash" ns test \\ + -n "\$par_namespace" \\ + -p "\$par_platforms" \\ + -q "\$par_query" \\ + -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "pull"' \\ + -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -l \\ + -t "\$par_log" \\ + \$par_append_parsed +else + echo "Not a valid mode argument" +fi +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/viash b/bin/viash new file mode 120000 index 0000000000..aff1be9f0f --- /dev/null +++ b/bin/viash @@ -0,0 +1 @@ +viash-0.4.0-rc1 \ No newline at end of file diff --git a/bin/viash-0.4.0-rc1.REMOVED.git-id b/bin/viash-0.4.0-rc1.REMOVED.git-id new file mode 100644 index 0000000000..5a44caa629 --- /dev/null +++ b/bin/viash-0.4.0-rc1.REMOVED.git-id @@ -0,0 +1 @@ +e6357d56ed905dbf85b4651b9f4ba502d8c6354e \ No newline at end of file From dd00bb6cbf9c3976666336d8eb00be5ec96d9085 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 15:56:26 +0200 Subject: [PATCH 0003/1233] add citeseq_cbmc component Former-commit-id: 275c5380f128ce0275261d37098db3d27000f6c1 --- .../datasets/citeseq_cbmc/config.vsh.yaml | 37 +++++++ .../datasets/citeseq_cbmc/script.py | 38 ++++++++ src/modality_alignment/resources/utils.py | 97 +++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml create mode 100644 src/modality_alignment/datasets/citeseq_cbmc/script.py create mode 100644 src/modality_alignment/resources/utils.py diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml new file mode 100644 index 0000000000..c1d79e5e4e --- /dev/null +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -0,0 +1,37 @@ +functionality: + name: "citeseq_cbmc" + namespace: "modality_alignment/datasets" + version: "dev" + description: "Download a modality alignment dataset from GEO" + arguments: + - name: "--input_rna" + type: "string" + default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" + description: "RNA file as a GZ-compressed csv file." + - name: "--input_adt" + type: "string" + default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" + description: "RNA file as a GZ-compressed csv file." + - name: "--test" + type: "boolean_true" + description: "Subset the dataset" + - name: "--output" + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing both RNA and ADT data" + resources: + - type: python_script + path: ./script.py + - path: "../../resources/utils.py" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - anndata # utils.py + - pandas # utils.py + - scanpy # utils.py + - numpy # utils.py diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py new file mode 100644 index 0000000000..df32682c64 --- /dev/null +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -0,0 +1,38 @@ +## VIASH START +par = { + "input_rna": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", + "input_adt": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", + "output": "output.h5ad", + "test": False +} +resources_dir = "..." +## VIASH END + +print("Running imports") +import sys +sys.path.append(resources_dir) +from utils import create_joint_adata +from utils import filter_joint_data_empty_cells +from utils import subset_joint_data +import scprep + +print("(Down)loading expression datasets from GEO") +sys.stdout.flush() + +rna_data = scprep.io.load_csv( + par["input_rna"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 +) +adt_data = scprep.io.load_csv( + par["input_adt"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 +) + +print("Transforming into adata") +adata = create_joint_adata(rna_data, adt_data) +adata = filter_joint_data_empty_cells(adata) + +if par["test"]: + print("Subsetting dataset") + adata = subset_joint_data(adata) + +print("Writing adata to file") +adata.write(par["output"]) \ No newline at end of file diff --git a/src/modality_alignment/resources/utils.py b/src/modality_alignment/resources/utils.py new file mode 100644 index 0000000000..2dd5f2cc9d --- /dev/null +++ b/src/modality_alignment/resources/utils.py @@ -0,0 +1,97 @@ +import anndata +import numpy as np +import pandas as pd +import scanpy as sc +import scprep + + +def subset_mode2_genes(adata, keep_genes): + """Randomly subset genes from adata.obsm["mode2"].""" + adata.obsm["mode2"] = adata.obsm["mode2"][:, keep_genes] + adata.uns["mode2_var"] = adata.uns["mode2_var"][keep_genes] + if "mode2_varnames" in adata.uns: + for varname in adata.uns["mode2_varnames"]: + adata.uns[varname] = adata.uns[varname][keep_genes] + return adata + + +def filter_joint_data_empty_cells(adata): + """Remove empty cells and genes from a multimodal dataset.""" + assert np.all(adata.uns["mode2_obs"] == adata.obs.index) + # filter cells + n_cells_mode1 = scprep.utils.toarray(adata.X.sum(axis=1)).flatten() + n_cells_mode2 = scprep.utils.toarray(adata.obsm["mode2"].sum(axis=1)).flatten() + keep_cells = np.minimum(n_cells_mode1, n_cells_mode2) > 1 + adata.uns["mode2_obs"] = adata.uns["mode2_obs"][keep_cells] + adata = adata[keep_cells, :].copy() + # filter genes + sc.pp.filter_genes(adata, min_counts=1) + n_genes_mode2 = scprep.utils.toarray(adata.obsm["mode2"].sum(axis=0)).flatten() + keep_genes_mode2 = n_genes_mode2 > 0 + adata = subset_mode2_genes(adata, keep_genes_mode2) + return adata + + +def create_joint_adata( + X, Y, X_index=None, X_columns=None, Y_index=None, Y_columns=None +): + """Create a multimodal dataset.""" + if X_index is None: + X_index = X.index + if X_columns is None: + X_columns = X.columns + if Y_index is None: + Y_index = Y.index + if Y_columns is None: + Y_columns = Y.columns + joint_index = np.sort(np.intersect1d(X_index, Y_index)) + try: + X = X.loc[joint_index] + Y = Y.loc[joint_index] + except AttributeError: + # keep only common observations + X_keep_idx = np.isin(X_index, joint_index) + Y_keep_idx = np.isin(Y_index, joint_index) + X = X[X_keep_idx] + Y = Y[Y_keep_idx] + + # reorder by alphabetical + X_index_sub = scprep.utils.toarray(X_index[X_keep_idx]) + Y_index_sub = scprep.utils.toarray(Y_index[Y_keep_idx]) + X = X[np.argsort(X_index_sub)] + Y = Y[np.argsort(Y_index_sub)] + + # check order is correct + assert (X_index_sub[np.argsort(X_index_sub)] == joint_index).all() + assert (Y_index_sub[np.argsort(Y_index_sub)] == joint_index).all() + adata = anndata.AnnData( + scprep.utils.to_array_or_spmatrix(X).tocsr(), + obs=pd.DataFrame(index=joint_index), + var=pd.DataFrame(index=X_columns), + ) + adata.obsm["mode2"] = scprep.utils.to_array_or_spmatrix(Y).tocsr() + adata.uns["mode2_obs"] = joint_index + adata.uns["mode2_var"] = scprep.utils.toarray(Y_columns) + return adata + + +def subset_joint_data(adata, n_cells=600, n_genes=1500): + """Randomly subset a multimodal dataset.""" + if adata.shape[0] > n_cells: + keep_cells = np.random.choice(adata.shape[0], n_cells, replace=False) + adata = adata[keep_cells].copy() + adata.uns["mode2_obs"] = adata.uns["mode2_obs"][keep_cells] + adata = filter_joint_data_empty_cells(adata) + + if adata.shape[1] > n_genes: + keep_mode1_genes = np.random.choice(adata.shape[1], n_genes, replace=False) + adata = adata[:, keep_mode1_genes].copy() + + if adata.obsm["mode2"].shape[1] > n_genes: + keep_genes_mode2 = np.random.choice( + adata.obsm["mode2"].shape[1], n_genes, replace=False + ) + adata = subset_mode2_genes(adata, keep_genes_mode2) + + adata = filter_joint_data_empty_cells(adata) + return adata \ No newline at end of file From 1b142143564df15b6c5d8385d7f4a39eb4d350d2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 20:01:23 +0200 Subject: [PATCH 0004/1233] change back to file Former-commit-id: 871446eaa800a4cf2d6a44a083c024546c54b7ba --- .../datasets/citeseq_cbmc/config.vsh.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index c1d79e5e4e..3c823f0620 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -5,13 +5,13 @@ functionality: description: "Download a modality alignment dataset from GEO" arguments: - name: "--input_rna" - type: "string" + type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" - description: "RNA file as a GZ-compressed csv file." + description: "RNA counts as a GZ-compressed csv file." - name: "--input_adt" - type: "string" + type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" - description: "RNA file as a GZ-compressed csv file." + description: "ADT counts as a GZ-compressed csv file." - name: "--test" type: "boolean_true" description: "Subset the dataset" From 9f2b99e8962bce1b38170d901c9e4e95b14e038e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 20:05:15 +0200 Subject: [PATCH 0005/1233] clean up cbmc script Former-commit-id: b34b28d8f811a7271c6ad5fd59877507c620d06a --- .../datasets/citeseq_cbmc/config.vsh.yaml | 4 ++-- .../datasets/citeseq_cbmc/script.py | 13 ++++++++++--- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index 3c823f0620..f3647fb3c1 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -7,11 +7,11 @@ functionality: - name: "--input_rna" type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" - description: "RNA counts as a GZ-compressed csv file." + description: "Path or URL to the RNA counts as a gzipped csv file." - name: "--input_adt" type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" - description: "ADT counts as a GZ-compressed csv file." + description: "Path or URL to the ADT counts as a gzipped csv file." - name: "--test" type: "boolean_true" description: "Subset the dataset" diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index df32682c64..f56e6a57be 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -1,24 +1,31 @@ ## VIASH START +# The code between the 'VIASH START' and 'VIASH END' gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. par = { "input_rna": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", "input_adt": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", "output": "output.h5ad", "test": False } -resources_dir = "..." +resources_dir = "../../resources/utils.py" ## VIASH END -print("Running imports") +print("Importing libraries") +import scprep + +# adding resources dir to system path import sys sys.path.append(resources_dir) + +# importing helper functions from common utils.py file in resources dir from utils import create_joint_adata from utils import filter_joint_data_empty_cells from utils import subset_joint_data -import scprep print("(Down)loading expression datasets from GEO") sys.stdout.flush() +# par["input_rna"] can be the path to a local file, or a url rna_data = scprep.io.load_csv( par["input_rna"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 ) From 0ea9ef222ee3b208750a2d585d0e8d234d930585 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 20:45:02 +0200 Subject: [PATCH 0006/1233] add comments Former-commit-id: cd0d9159052cdfab5b9312b6aa599cb3990e83cd --- .../datasets/citeseq_cbmc/config.vsh.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index f3647fb3c1..05213623bb 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -3,7 +3,7 @@ functionality: namespace: "modality_alignment/datasets" version: "dev" description: "Download a modality alignment dataset from GEO" - arguments: + arguments: - name: "--input_rna" type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" @@ -29,9 +29,9 @@ platforms: image: "python:3.8" setup: - type: python - packages: + packages: - scprep - - anndata # utils.py - - pandas # utils.py - - scanpy # utils.py - - numpy # utils.py + - anndata # needed by utils.py + - pandas # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py From 5e7320fa3e3e04775013decc8e1724368b901c12 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 20:45:29 +0200 Subject: [PATCH 0007/1233] implement mnn component Former-commit-id: b4777efd053bb757caeb4d8dd7880f074e84b183 --- .../methods/mnn/config.vsh.yaml | 35 +++++++++++++ src/modality_alignment/methods/mnn/script.R | 50 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 src/modality_alignment/methods/mnn/config.vsh.yaml create mode 100644 src/modality_alignment/methods/mnn/script.R diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/modality_alignment/methods/mnn/config.vsh.yaml new file mode 100644 index 0000000000..db5f56903e --- /dev/null +++ b/src/modality_alignment/methods/mnn/config.vsh.yaml @@ -0,0 +1,35 @@ +functionality: + name: "mnn" + namespace: "modality_alignment/methods" + version: "dev" + description: "Run Mutual Nearest Neighbours" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: "Input h5ad file containing at least `ad$X` and `ad$obsm['mode2']`." + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing both RNA and ADT data" + - name: "--n_svd" + type: "integer" + default: 100 + description: "Number of SVDs to use. Bounded by the number of columns in `ad$X` and `ad$obsm['mode2']`." + resources: + - type: r_script + path: ./script.R +platforms: + - type: docker + image: "dataintuitive/randpy:r4.0_bioc3.12" # already includes some R, bioconductor & anndata packages + setup: + - type: r + cran: + - anndata + - Matrix + - sparsesvd + bioc: + - batchelor diff --git a/src/modality_alignment/methods/mnn/script.R b/src/modality_alignment/methods/mnn/script.R new file mode 100644 index 0000000000..ff4158487c --- /dev/null +++ b/src/modality_alignment/methods/mnn/script.R @@ -0,0 +1,50 @@ +## VIASH START +par <- list( + input = "output.h5ad", + output = "output.mnn.h5ad", + n_svd = 100 +) +## VIASH END + +cat("Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) +requireNamespace("sparsesvd", quietly = TRUE) +requireNamespace("batchelor", quietly = TRUE) + +cat("Reading input h5ad file\n") +adata <- read_h5ad(par$input) + +# Convert data to friendly sparse format +mode1 <- as(adata$X, "CsparseMatrix") +mode2 <- as(adata$obsm[["mode2"]], "CsparseMatrix") + +# Check parameters +n_svd <- min( + par$n_svd, + ncol(mode1), + ncol(mode2) +) + +cat("Running SVD\n") +mode1_svd <- sparsesvd::sparsesvd(mode1, rank = n_svd) +mode1_svd_uv <- mode1_svd$u %*% diag(mode1_svd$d) +mode2_svd <- sparsesvd::sparsesvd(mode2, rank = n_svd) +mode2_svd_uv <- mode2_svd$u %*% diag(mode2_svd$d) + +cat("Running MNN\n") +sce_mnn <- batchelor::fastMNN( + t(mode1_svd_uv), + t(mode2_svd_uv) +) + +cat("Storing output\n") +combined_recons <- t(SummarizedExperiment::assay(sce_mnn, "reconstructed")) +mode1_recons <- combined_recons[seq_len(nrow(mode1_svd_uv)), , drop = FALSE] +mode2_recons <- combined_recons[-seq_len(nrow(mode1_svd_uv)), , drop = FALSE] + +adata$obsm[["aligned"]] <- as.matrix(mode1_recons) +adata$obsm[["mode2_aligned"]] <- as.matrix(mode2_recons) + +cat("Writing to file\n") +zzz <- adata$write_h5ad(par$output) From e03248cb12081d640b6d55a174e5f3213a72f109 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:05:05 +0200 Subject: [PATCH 0008/1233] update gitignore Former-commit-id: c3447534c5f51068a607a7647cb17b70d0133082 --- .gitignore | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.gitignore b/.gitignore index 9c07d4ae98..17b47ae49f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,7 @@ *.class *.log +.Rproj.user +*.Rproj +target +log.txt +out_bash From 3b810b3d0712fbf223e4213c44189cc97844ab43 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:05:52 +0200 Subject: [PATCH 0009/1233] fix script Former-commit-id: e87bec65c8c2716f63a10ebf1808dfadebf6f00d --- src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml | 4 ++-- src/modality_alignment/datasets/citeseq_cbmc/script.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index 05213623bb..649b16df68 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -5,11 +5,11 @@ functionality: description: "Download a modality alignment dataset from GEO" arguments: - name: "--input_rna" - type: "file" + type: "string" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" description: "Path or URL to the RNA counts as a gzipped csv file." - name: "--input_adt" - type: "file" + type: "string" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" description: "Path or URL to the ADT counts as a gzipped csv file." - name: "--test" diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index f56e6a57be..14db77400b 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -1,5 +1,5 @@ ## VIASH START -# The code between the 'VIASH START' and 'VIASH END' gets stripped away before +# The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. par = { "input_rna": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", From 330d48390207cc53d25ecb03da79fc5806e2bbfb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:05:57 +0200 Subject: [PATCH 0010/1233] add bash script Former-commit-id: 38ad17dbf0ce27418f4eecd5c64b2bc885a1a9f4 --- run_bash_pipeline.sh | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100755 run_bash_pipeline.sh diff --git a/run_bash_pipeline.sh b/run_bash_pipeline.sh new file mode 100755 index 0000000000..d4916e063c --- /dev/null +++ b/run_bash_pipeline.sh @@ -0,0 +1,40 @@ +#!/bin/bash + +# Run 'bin/project_build' prior to executing this script + +TARGET=target/docker/modality_alignment +OUTPUT=out_bash/modality_alignment + +mkdir -p $OUTPUT/datasets +mkdir -p $OUTPUT/methods +mkdir -p $OUTPUT/metrics + +if [ ! -f "$OUTPUT/dataset/citeseq_cbmc.h5ad" ]; then + "$TARGET/datasets/citeseq_cbmc/citeseq_cbmc" --output "$OUTPUT/dataset/citeseq_cbmc.h5ad" +fi + + +for meth in `ls "$TARGET/methods"`; do + for dat in `ls "$OUTPUT/datasets"`; do + dat_id="${dat%.*}" + input_h5ad="$OUTPUT/datasets/$dat_id.h5ad" + output_h5ad="$OUTPUT/methods/${dat_id}_$meth.h5ad" + if [ ! -f "$output_h5ad" ]; then + echo "> $TARGET/methods/$meth/$meth -i $input_h5ad -o $output_h5ad" + "$TARGET/methods/$meth/$meth" -i "$input_h5ad" -o "$output_h5ad" + fi + done +done + + +for met in `ls $TARGET/metrics`; do + for outp in `ls $OUTPUT/methods`; do + out_id="${outp%.*}" + input_h5ad="$OUTPUT/methods/$out_id.h5ad" + output_h5ad="$OUTPUT/metrics/${out_id}_$met.h5ad" + if [ ! -f "$output_h5ad" ]; then + echo "> $TARGET/metric/$met/$met" -i "$input_h5ad" -o "$output_h5ad" + "$TARGET/metric/$met/$met" -i "$input_h5ad" -o "$output_h5ad" + fi + done +done From 240acf3003e7db1e3108dfde3d646dca21704017 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:34:04 +0200 Subject: [PATCH 0011/1233] update bash pipeline Former-commit-id: 0d8351e31f0b48cfdff92cf6633879e1f4c15c18 --- .gitignore | 1 + run_bash_pipeline.sh | 16 +++++++++------- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index 17b47ae49f..5010075dba 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ target log.txt out_bash +.Rhistory diff --git a/run_bash_pipeline.sh b/run_bash_pipeline.sh index d4916e063c..c5500ec280 100755 --- a/run_bash_pipeline.sh +++ b/run_bash_pipeline.sh @@ -1,6 +1,7 @@ #!/bin/bash -# Run 'bin/project_build' prior to executing this script +# Run this prior to executing this script: +# bin/project_build TARGET=target/docker/modality_alignment OUTPUT=out_bash/modality_alignment @@ -9,11 +10,12 @@ mkdir -p $OUTPUT/datasets mkdir -p $OUTPUT/methods mkdir -p $OUTPUT/metrics -if [ ! -f "$OUTPUT/dataset/citeseq_cbmc.h5ad" ]; then - "$TARGET/datasets/citeseq_cbmc/citeseq_cbmc" --output "$OUTPUT/dataset/citeseq_cbmc.h5ad" +# generate datasets +if [ ! -f "$OUTPUT/datasets/citeseq_cbmc.h5ad" ]; then + "$TARGET/datasets/citeseq_cbmc/citeseq_cbmc" --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" fi - +# run all methods on all datasets for meth in `ls "$TARGET/methods"`; do for dat in `ls "$OUTPUT/datasets"`; do dat_id="${dat%.*}" @@ -26,15 +28,15 @@ for meth in `ls "$TARGET/methods"`; do done done - +# run all metrics on all outputs for met in `ls $TARGET/metrics`; do for outp in `ls $OUTPUT/methods`; do out_id="${outp%.*}" input_h5ad="$OUTPUT/methods/$out_id.h5ad" output_h5ad="$OUTPUT/metrics/${out_id}_$met.h5ad" if [ ! -f "$output_h5ad" ]; then - echo "> $TARGET/metric/$met/$met" -i "$input_h5ad" -o "$output_h5ad" - "$TARGET/metric/$met/$met" -i "$input_h5ad" -o "$output_h5ad" + echo "> $TARGET/metrics/$met/$met" -i "$input_h5ad" -o "$output_h5ad" + "$TARGET/metrics/$met/$met" -i "$input_h5ad" -o "$output_h5ad" fi done done From 6a5fd157bff8e037a4051de265beab6f3e65ec19 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:34:28 +0200 Subject: [PATCH 0012/1233] update datasets and methods components Former-commit-id: 448991b0318c4a6edc4bf96f4fbb56fd85eb4fed --- src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml | 1 + src/modality_alignment/datasets/citeseq_cbmc/script.py | 5 ++++- src/modality_alignment/methods/mnn/script.R | 1 + 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index 649b16df68..5005c20c5f 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -16,6 +16,7 @@ functionality: type: "boolean_true" description: "Subset the dataset" - name: "--output" + alternatives: ["-o"] type: "file" direction: "output" default: "output.h5ad" diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index 14db77400b..b491d8f2ab 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -22,7 +22,7 @@ from utils import filter_joint_data_empty_cells from utils import subset_joint_data -print("(Down)loading expression datasets from GEO") +print("Downloading expression datasets from GEO (this might take a while)") sys.stdout.flush() # par["input_rna"] can be the path to a local file, or a url @@ -37,9 +37,12 @@ adata = create_joint_adata(rna_data, adt_data) adata = filter_joint_data_empty_cells(adata) +adata.uns["dataset_name"] = "citeseq_cbmc" + if par["test"]: print("Subsetting dataset") adata = subset_joint_data(adata) + adata.uns["dataset_name"] = "citeseq_cbmc_test" print("Writing adata to file") adata.write(par["output"]) \ No newline at end of file diff --git a/src/modality_alignment/methods/mnn/script.R b/src/modality_alignment/methods/mnn/script.R index ff4158487c..a5472880a1 100644 --- a/src/modality_alignment/methods/mnn/script.R +++ b/src/modality_alignment/methods/mnn/script.R @@ -47,4 +47,5 @@ adata$obsm[["aligned"]] <- as.matrix(mode1_recons) adata$obsm[["mode2_aligned"]] <- as.matrix(mode2_recons) cat("Writing to file\n") +adata$uns["method_name"] = "mnn" zzz <- adata$write_h5ad(par$output) From d2c7f8a73b0499da3d5a9cba0fd6fcc61f23c71f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 21:34:56 +0200 Subject: [PATCH 0013/1233] add metric Former-commit-id: 7dbd01e1a5e82455c87f3c48fcfbcc23c851589a --- .../metrics/knn_auc/config.vsh.yaml | 40 ++++++++++++ .../metrics/knn_auc/script.py | 65 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 src/modality_alignment/metrics/knn_auc/config.vsh.yaml create mode 100644 src/modality_alignment/metrics/knn_auc/script.py diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml new file mode 100644 index 0000000000..01aca54a43 --- /dev/null +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -0,0 +1,40 @@ +functionality: + name: "knn_auc" + namespace: "modality_alignment/metrics" + version: "dev" + description: "Compute the kNN Area Under the Curve" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: | + File to input h5ad containing: + * ad.X + * ad.obsm["aligned"] + * ad.obsm["mode2_aligned"] + - name: "--output" + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing `ad.uns['metric_value']`" + - name: "--proportion_neighbors" + type: "double" + default: 0.1 + description: The propotion of neighbours to use in computing the KNN. + - name: "--n_svd" + type: integer + default: 100 + description: The maximum number of SVDs to use. + resources: + - type: python_script + path: ./script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - anndata + - numpy + - sklearn diff --git a/src/modality_alignment/metrics/knn_auc/script.py b/src/modality_alignment/metrics/knn_auc/script.py new file mode 100644 index 0000000000..145e327f2d --- /dev/null +++ b/src/modality_alignment/metrics/knn_auc/script.py @@ -0,0 +1,65 @@ +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input": "out_bash/modality_alignment/methods/citeseq_cbmc_mnn.h5ad", + "output": "out_bash/modality_alignment/metrics/citeseq_cbmc_mnn_knn_auc.h5ad", + "proportion_neighbors": 0.1, + "n_svd": 100 +} +## VIASH END + +print("Importing libraries") +import anndata +import numpy as np +import sklearn.decomposition +import sklearn.neighbors + +print("Reading adata file") +adata = anndata.read_h5ad(par["input"]) + +print("Checking parameters") +n_svd = min([par["n_svd"], min(adata.X.shape) - 1]) +n_neighbors = int(np.ceil(par["proportion_neighbors"] * adata.X.shape[0])) + +print("Performing PCA") +X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) + +print("Compute KNN on PCA") +_, indices_true = ( + sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) + .fit(X_pca) + .kneighbors(X_pca) +) + +print("Compute KNN on aligned matrix") +_, indices_pred = ( + sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) + .fit(adata.obsm["aligned"]) + .kneighbors(adata.obsm["mode2_aligned"]) +) + +print("Check which neighbours match") +neighbors_match = np.zeros(n_neighbors, dtype=int) +for i in range(adata.shape[0]): + _, pred_matches, true_matches = np.intersect1d( + indices_pred[i], indices_true[i], return_indices=True + ) + neighbors_match_idx = np.maximum(pred_matches, true_matches) + neighbors_match += np.sum( + np.arange(n_neighbors) >= neighbors_match_idx[:, None], + axis=0, + ) + +print("Compute area under neighbours match curve") +neighbors_match_curve = neighbors_match / ( + np.arange(1, n_neighbors + 1) * adata.shape[0] +) +area_under_curve = np.mean(neighbors_match_curve) + +print("Store metic value") +adata.uns["metric_name"] = "knn_auc" +adata.uns["metric_value"] = area_under_curve + +print("Writing adata to file") +adata.write(par["output"]) From ba82e85f0381208e7b1fde403291a169b54ea7b9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 22:00:37 +0200 Subject: [PATCH 0014/1233] output as gzip, add flag Former-commit-id: 9c752b9bf586a0af85be014aa96007f965d31add --- src/modality_alignment/datasets/citeseq_cbmc/script.py | 2 +- src/modality_alignment/methods/mnn/script.R | 2 +- src/modality_alignment/metrics/knn_auc/config.vsh.yaml | 1 + src/modality_alignment/metrics/knn_auc/script.py | 2 +- 4 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index b491d8f2ab..48cb84f71f 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -45,4 +45,4 @@ adata.uns["dataset_name"] = "citeseq_cbmc_test" print("Writing adata to file") -adata.write(par["output"]) \ No newline at end of file +adata.write(par["output"], compression = "gzip") \ No newline at end of file diff --git a/src/modality_alignment/methods/mnn/script.R b/src/modality_alignment/methods/mnn/script.R index a5472880a1..b875d05731 100644 --- a/src/modality_alignment/methods/mnn/script.R +++ b/src/modality_alignment/methods/mnn/script.R @@ -48,4 +48,4 @@ adata$obsm[["mode2_aligned"]] <- as.matrix(mode2_recons) cat("Writing to file\n") adata$uns["method_name"] = "mnn" -zzz <- adata$write_h5ad(par$output) +zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index 01aca54a43..bf2b623c96 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -14,6 +14,7 @@ functionality: * ad.obsm["aligned"] * ad.obsm["mode2_aligned"] - name: "--output" + alternatives: ["-o"] type: "file" direction: "output" default: "output.h5ad" diff --git a/src/modality_alignment/metrics/knn_auc/script.py b/src/modality_alignment/metrics/knn_auc/script.py index 145e327f2d..2403a62f36 100644 --- a/src/modality_alignment/metrics/knn_auc/script.py +++ b/src/modality_alignment/metrics/knn_auc/script.py @@ -62,4 +62,4 @@ adata.uns["metric_value"] = area_under_curve print("Writing adata to file") -adata.write(par["output"]) +adata.write(par["output"], compression = "gzip") From b931e8715cafaac91d8b182cf5e37136541b93d2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 22:00:52 +0200 Subject: [PATCH 0015/1233] add extract_scores module Former-commit-id: c2a1f868506c9009b83f3177d1f787f06ed236af --- run_bash_pipeline.sh | 8 ++++++-- src/utils/extract_scores/config.vsh.yaml | 24 ++++++++++++++++++++++++ src/utils/extract_scores/script.R | 20 ++++++++++++++++++++ 3 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 src/utils/extract_scores/config.vsh.yaml create mode 100644 src/utils/extract_scores/script.R diff --git a/run_bash_pipeline.sh b/run_bash_pipeline.sh index c5500ec280..5329d071c4 100755 --- a/run_bash_pipeline.sh +++ b/run_bash_pipeline.sh @@ -29,8 +29,8 @@ for meth in `ls "$TARGET/methods"`; do done # run all metrics on all outputs -for met in `ls $TARGET/metrics`; do - for outp in `ls $OUTPUT/methods`; do +for met in `ls "$TARGET/metrics"`; do + for outp in `ls "$OUTPUT/methods"`; do out_id="${outp%.*}" input_h5ad="$OUTPUT/methods/$out_id.h5ad" output_h5ad="$OUTPUT/metrics/${out_id}_$met.h5ad" @@ -40,3 +40,7 @@ for met in `ls $TARGET/metrics`; do fi done done + +# concatenate all scores into one tsv +INPUTS=$(ls -1 "$OUTPUT/metrics" | sed "s#.*#-i '$OUTPUT/metrics/&'#" | tr '\n' ' ') +eval "$TARGET/utils/docker/utils/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" \ No newline at end of file diff --git a/src/utils/extract_scores/config.vsh.yaml b/src/utils/extract_scores/config.vsh.yaml new file mode 100644 index 0000000000..f8e94982f3 --- /dev/null +++ b/src/utils/extract_scores/config.vsh.yaml @@ -0,0 +1,24 @@ +functionality: + name: "extract_scores" + namespace: "utils" + version: "dev" + description: "Extract evaluation data frame on output" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + multiple: true + default: "input.h5ad" + description: "Input h5ad files containing metadata and metrics in adata.uns" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.tsv" + description: "Output tsv" + resources: + - type: r_script + path: ./script.R +platforms: + - type: docker + image: "dataintuitive/randpy:r4.0_bioc3.12" # contains a few bioconductor and the 'anndata' package diff --git a/src/utils/extract_scores/script.R b/src/utils/extract_scores/script.R new file mode 100644 index 0000000000..b85de62613 --- /dev/null +++ b/src/utils/extract_scores/script.R @@ -0,0 +1,20 @@ +## VIASH START +par <- list( + input = list.files("out_bash/modality_alignment/metrics/", full.names = TRUE), + output = "out_bash/modality_alignment/scores.tsv" +) +inp <- par$input[[1]] +## VIASH END + +cat("Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +options(tidyverse.quiet = TRUE) +library(tidyverse) + +cat("Reading input h5ad files") +scores <- map_df(par$input, function(inp) { + ad <- read_h5ad(inp) + as_tibble(ad$uns[c("dataset_name", "method_name", "metric_name", "metric_value")]) +}) + +write_tsv(scores, par$output) From a35d37b04993ac7da20be22e5a4b72c05b5c8312 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 22:56:19 +0200 Subject: [PATCH 0016/1233] add nextflow platforms, fix description Former-commit-id: 6852ffa5523c1ad9ef91d1749f5d3abdd452337b --- .../datasets/citeseq_cbmc/config.vsh.yaml | 1 + src/modality_alignment/methods/mnn/config.vsh.yaml | 5 +++-- src/modality_alignment/metrics/knn_auc/config.vsh.yaml | 7 ++----- src/utils/extract_scores/config.vsh.yaml | 1 + 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index 5005c20c5f..d71f609eb1 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -36,3 +36,4 @@ platforms: - pandas # needed by utils.py - scanpy # needed by utils.py - numpy # needed by utils.py + - type: nextflow \ No newline at end of file diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/modality_alignment/methods/mnn/config.vsh.yaml index db5f56903e..a1f3f8faab 100644 --- a/src/modality_alignment/methods/mnn/config.vsh.yaml +++ b/src/modality_alignment/methods/mnn/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: alternatives: ["-i"] type: "file" default: "input.h5ad" - description: "Input h5ad file containing at least `ad$X` and `ad$obsm['mode2']`." + description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - name: "--output" alternatives: ["-o"] type: "file" @@ -18,7 +18,7 @@ functionality: - name: "--n_svd" type: "integer" default: 100 - description: "Number of SVDs to use. Bounded by the number of columns in `ad$X` and `ad$obsm['mode2']`." + description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." resources: - type: r_script path: ./script.R @@ -33,3 +33,4 @@ platforms: - sparsesvd bioc: - batchelor + - type: nextflow diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index bf2b623c96..204d98e812 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -8,11 +8,7 @@ functionality: alternatives: ["-i"] type: "file" default: "input.h5ad" - description: | - File to input h5ad containing: - * ad.X - * ad.obsm["aligned"] - * ad.obsm["mode2_aligned"] + description: "File to input h5ad containing: `ad.X`, `ad.obsm['aligned']`, `ad.obsm['mode2_aligned']`" - name: "--output" alternatives: ["-o"] type: "file" @@ -39,3 +35,4 @@ platforms: - anndata - numpy - sklearn + - type: nextflow diff --git a/src/utils/extract_scores/config.vsh.yaml b/src/utils/extract_scores/config.vsh.yaml index f8e94982f3..e4214aaec0 100644 --- a/src/utils/extract_scores/config.vsh.yaml +++ b/src/utils/extract_scores/config.vsh.yaml @@ -22,3 +22,4 @@ functionality: platforms: - type: docker image: "dataintuitive/randpy:r4.0_bioc3.12" # contains a few bioconductor and the 'anndata' package + - type: nextflow From 13ecad185712a8ba077b1762b1f552506a6d5e9e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 22:56:46 +0200 Subject: [PATCH 0017/1233] add nxf pipeline Former-commit-id: 94a76faaf581e3d0cf1cee3fc668dab05e94d390 --- main.nf | 45 +++++++++++++++++++++++++++++++++++++++++++++ nextflow.config | 22 ++++++++++++++++++++++ run_nxf_pipeline.sh | 7 +++++++ 3 files changed, 74 insertions(+) create mode 100644 main.nf create mode 100644 nextflow.config create mode 100755 run_nxf_pipeline.sh diff --git a/main.nf b/main.nf new file mode 100644 index 0000000000..1769277d48 --- /dev/null +++ b/main.nf @@ -0,0 +1,45 @@ +nextflow.preview.dsl=2 + +moduleRoot="./target/nextflow/modality_alignment/" + +include { citeseq_cbmc } from moduleRoot + 'datasets/citeseq_cbmc/main.nf' params(params) +include { mnn } from moduleRoot + 'methods/mnn/main.nf' params(params) +include { knn_auc } from moduleRoot + 'metrics/knn_auc/main.nf' params(params) + + +workflow { + // fetch datasets + data_citeseq_cbmc = Channel.fromPath( "dummy" ) \ + | map{ [ "dyngen", it, params] } \ + | citeseq_cbmc + + // add more datasets here + // data_... = ... + + // combine datasets in one channel + datasets = data_citeseq_cbmc + // when more datasets are available: + // datasets = data_citeseq_cbmc.mix(data_..., data_...) + + // apply methods to datasets + method_outputs = datasets \ + | mnn + /* + method_outputs = datasets \ + | (mnn & method2 & method3) \ + | mix + */ + + // apply metrics to outputs + method_evals = method_outputs \ + | knn_auc + /* + method_evals = method_outputs \ + | (knn_auc & metric2 & metric3) \ + | mix + */ + + // TODO: do something with 'method_evals' + method_evals \ + | view{ [ it[0], it[1] ] } +} diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000000..df80ce5d68 --- /dev/null +++ b/nextflow.config @@ -0,0 +1,22 @@ +manifest { + nextflowVersion = '!>=20.04.0-edge' +} + +includeConfig 'target/nextflow/modality_alignment/datasets/citeseq_cbmc/nextflow.config' +includeConfig 'target/nextflow/modality_alignment/methods/mnn/nextflow.config' +includeConfig 'target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config' + +docker { + runOptions = "-i -v ${baseDir}:${baseDir}" +} + +process { + maxForks = 30 + container = 'ubuntu' + errorStrategy='ignore' +} + +k8s { + pullPolicy = 'Always' + imagePullPolicy = 'Always' +} diff --git a/run_nxf_pipeline.sh b/run_nxf_pipeline.sh new file mode 100755 index 0000000000..d4cc3e9f83 --- /dev/null +++ b/run_nxf_pipeline.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/project_build + +NXF_VER=20.04.1-edge nextflow run main.nf -resume + From e67e589d6722bd5cc788d470feb7efe7efd9c6ef Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 22:56:55 +0200 Subject: [PATCH 0018/1233] update readme and gitignore Former-commit-id: e8445850bdebebe1ec92b91cc1248aa5c66f8d33 --- .gitignore | 15 +++++--- README.md | 100 ++++++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 110 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 5010075dba..c0ead2c50b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,15 @@ -*.class -*.log +# repo specific ignores +out_bash + +# R specific ignores +.Rhistory .Rproj.user *.Rproj + +# viash specific ignores target log.txt -out_bash -.Rhistory + +# nextflow specific ignores +.nextflow* +work diff --git a/README.md b/README.md index 112ad69621..f6107677d1 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,100 @@ # opsca-viash -Adapting Open Problems to use viash +Proof Of Concept in adapting Open Problems to use viash. + +## Requirements +To use this repository, make sure you have Bash, Java, and Docker installed. If you wish to use Nextflow, install that too. + +## Building the pipeline +To build all the components in `src` to `target`, run: + +```sh +bin/project_build +``` + +Note that this will also build docker containers for each of the components. The first time, this might take a while. + +## Running a simple pipeline with Bash + +Inspect the contents of the sample Bash pipeline in `run_bash_pipeline.sh`, then run it. + +```sh +./run_bash_pipeline.sh +``` + +Some components might take a while to run. In the end, the `out_bash/` folder will have been populated with a lot of h5ad files, and a `scores.tsv` file. + + +## Running a simple pipeline with Nextflow + +Inspect the contents of the sample bash pipeline in `run_nxf_pipeline.sh`, then run it. + +``` +$ ./run_nxf_pipeline.sh +N E X T F L O W ~ version 20.04.1-edge +Launching `main.nf` [suspicious_lavoisier] - revision: f6dca0e8d5 +WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE +executor > local (3) +[16/e727b4] process > citeseq_cbmc:citeseq_cbmc_process (dyngen) [100%] 1 of 1 ✔ +[85/88774c] process > mnn:mnn_process (dyngen) [100%] 1 of 1 ✔ +[1e/9593dd] process > knn_auc:knn_auc_process (dyngen) [100%] 1 of 1 ✔ +WARN: Access to undefined parameter `debug` -- Initialise it to a default value eg. `params.debug = some_value` +Completed at: 06-Apr-2021 22:52:43 +Duration : 2m 46s +CPU hours : (a few seconds) +Succeeded : 3 +``` + +Again, some components might take a while to run. + + +## Component development with viash + +You can run, build, or test a component individually with `bin/viash`. + +A tutorial on how to create components with viash can be found at +[github.com/data-intuitive/viash\_tutorial\_1](https://github.com/data-intuitive/viash_tutorial_1). + +More documentation is available at +[data-intuitive.com/viash\_docs](https://www.data-intuitive.com/viash_docs) (WIP). + +### Creating a new component + + + +Create a viash config file and write a script. + +### View help of a component + +``` bash +viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- -h +``` + +Or if you’ve already built the component (see below) + +``` bash +target/docker/modality_alignment/methods/mnn/mnn -h +``` + +### Build a component + +``` bash +viash build src/modality_alignment/methods/mnn/config.vsh.yaml -p docker -o target/docker/modality_alignment/methods/mnn --setup +``` + +### Test a component + +``` bash +viash test src/modality_alignment/methods/mnn/config.vsh.yaml +``` + +### Run a component + +``` bash +viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- [... arguments for the component ...] +``` + +Or if you’ve already built the component + +``` bash +target/docker/modality_alignment/methods/mnn/mnn [... arguments for the component ...] +``` From 08e90d5d47fec23a76e313151a6bd2549b1d5d61 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 23:04:41 +0200 Subject: [PATCH 0019/1233] clean up readme Former-commit-id: 85ff1a22a7afe877ad5e6e01b2215e679a2cd278 --- README.md | 30 +++++++++--------------------- 1 file changed, 9 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index f6107677d1..b3de316922 100644 --- a/README.md +++ b/README.md @@ -57,44 +57,32 @@ A tutorial on how to create components with viash can be found at More documentation is available at [data-intuitive.com/viash\_docs](https://www.data-intuitive.com/viash_docs) (WIP). -### Creating a new component +### Common commands +Create a new component by writing a viash config file and an R/Python script. - - -Create a viash config file and write a script. - -### View help of a component +View help of a component: ``` bash viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- -h ``` -Or if you’ve already built the component (see below) - -``` bash -target/docker/modality_alignment/methods/mnn/mnn -h -``` - -### Build a component +Run a component: ``` bash -viash build src/modality_alignment/methods/mnn/config.vsh.yaml -p docker -o target/docker/modality_alignment/methods/mnn --setup +viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- [... arguments for the component ...] ``` -### Test a component +Test a component (provided that you wrote tests, of course): ``` bash viash test src/modality_alignment/methods/mnn/config.vsh.yaml ``` -### Run a component +Build a component: ``` bash -viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- [... arguments for the component ...] -``` - -Or if you’ve already built the component +viash build src/modality_alignment/methods/mnn/config.vsh.yaml -p docker -o target/docker/modality_alignment/methods/mnn --setup -``` bash +target/docker/modality_alignment/methods/mnn/mnn -h target/docker/modality_alignment/methods/mnn/mnn [... arguments for the component ...] ``` From 336fa9fdfb92a2ab8d74916291013146b69cc920 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Apr 2021 23:09:25 +0200 Subject: [PATCH 0020/1233] add comment Former-commit-id: 2e16e148c5b4ebad3122955c7b452950d2189dd4 --- src/modality_alignment/datasets/citeseq_cbmc/script.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index 48cb84f71f..ab4e8ac919 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -14,6 +14,8 @@ import scprep # adding resources dir to system path +# the resources dir contains all files listed in the '.functionality.resources' part of the +# viash config, amongst which is the 'utils.py' file we need. import sys sys.path.append(resources_dir) From 1cdf9d7f74e9714b43eea0e28444667bb5ecfb6c Mon Sep 17 00:00:00 2001 From: Daniel Burkhardt Date: Wed, 7 Apr 2021 09:45:49 -0400 Subject: [PATCH 0021/1233] init scot Former-commit-id: f498a75a2ba5f8162a3ba3a2764bb3e39965abd6 --- output.h5ad.REMOVED.git-id | 1 + .../methods/scot/config.vsh.yaml | 42 ++++++++++++++++ src/modality_alignment/methods/scot/scot.py | 50 +++++++++++++++++++ .../resources/preprocessing.py | 42 ++++++++++++++++ 4 files changed, 135 insertions(+) create mode 100644 output.h5ad.REMOVED.git-id create mode 100644 src/modality_alignment/methods/scot/config.vsh.yaml create mode 100644 src/modality_alignment/methods/scot/scot.py create mode 100644 src/modality_alignment/resources/preprocessing.py diff --git a/output.h5ad.REMOVED.git-id b/output.h5ad.REMOVED.git-id new file mode 100644 index 0000000000..7b505ebadb --- /dev/null +++ b/output.h5ad.REMOVED.git-id @@ -0,0 +1 @@ +105ff533b3e0dc7c63342855c1579dae05885381 \ No newline at end of file diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml new file mode 100644 index 0000000000..13e8b8d6a3 --- /dev/null +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -0,0 +1,42 @@ +functionality: + name: "scot" + namespace: "modality_alignment/methods" + version: "dev" + description: "Run Single Cell Optimal Transport" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.scot.h5ad" + description: "Output h5ad file containing both RNA and ADT data" + - name: "--n_svd" + type: "integer" + default: 100 + description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." + - name: "--balanced" + type: "boolean_true" + description: "Determines whether balanced or unbalanced optimal transport. In the balanced case, the target and source distributions are assumed to have equal mass." + resources: + - type: python_script + path: ./scot.py + - path: "../../resources/preprocessing.py" + +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - anndata # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py + - scprep # needed by utils.py + - sklearn + - git+https://github.com/atong01/SCOT + - type: nextflow diff --git a/src/modality_alignment/methods/scot/scot.py b/src/modality_alignment/methods/scot/scot.py new file mode 100644 index 0000000000..4885015047 --- /dev/null +++ b/src/modality_alignment/methods/scot/scot.py @@ -0,0 +1,50 @@ +## VIASH START +par = { + input = "output.h5ad", + output = "output.scot.h5ad", + n_svd = 100, + balanced=False, +} +resources_dir = "../../resources/utils.py" +## VIASH END + +import scanpy as sc +import sklearn.decomposition +import sys +sys.path.append(resources_dir) + +# importing helper functions from common preprocessing.py file in resources dir +from preprocessing import log_cpm +from preprocessing import sqrt_cpm + +def _scot(adata, n_svd=100, balanced=False): + from SCOT import SCOT + + # PCA reduction + n_svd = min([n_svd, min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) + X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) + Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) + + # Initialize SCOT + scot = SCOT(X_pca, Y_pca) + + # call the unbalanced alignment + # From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 + X_new_unbal, y_new_unbal = scot.align( + k=50, e=1e-3, rho=0.0005, normalize=True, balanced=balanced + ) + adata.obsm["aligned"] = X_new_unbal + adata.obsm["mode2_aligned"] = y_new_unbal + + return adata + +if __name__ == "__main__": + adata = sc.read_h5ad(par["input"]) + # Normalize mode1 + sqrt_cpm(adata) + # Normalize mode2 + log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") + # run scot + _scot(adata, n_svd=par["n_svd"], balanced=par["balanced"]) + # Write output to file + adata.write_h5ad(par["output"], compression=9) diff --git a/src/modality_alignment/resources/preprocessing.py b/src/modality_alignment/resources/preprocessing.py new file mode 100644 index 0000000000..58f109f458 --- /dev/null +++ b/src/modality_alignment/resources/preprocessing.py @@ -0,0 +1,42 @@ +import scanpy as sc +import scprep + +#_scran = scprep.run.RFunction( +# setup="library('scran')", +# args="sce, min.mean=0.1", +# body=""" +# sce <- computeSumFactors(sce, min.mean=min.mean, assay.type="X") +# sizeFactors(sce) +# """, +#) +# +# +#def log_scran_pooling(adata): +# """Normalize data with scran via rpy2.""" +# scprep.run.install_bioconductor("scran") +# adata.obs["size_factors"] = _scran(adata) +# adata.X = scprep.utils.matrix_vector_elementwise_multiply( +# adata.X, adata.obs["size_factors"], axis=0 +# ) +# sc.pp.log1p(adata) + +def _cpm(adata): + adata.layers["counts"] = adata.X.copy() + sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") + + +def cpm(adata): + """Normalize data to counts per million.""" + _cpm(adata) + + +def log_cpm(adata): + """Normalize data to log counts per million.""" + _cpm(adata) + sc.pp.log1p(adata) + + +def sqrt_cpm(adata): + """Normalize data to sqrt counts per million.""" + _cpm(adata) + adata.X = scprep.transform.sqrt(adata.X) From 6f0d17bdc76e9050ce9164ca6586ab1c502f7dea Mon Sep 17 00:00:00 2001 From: Daniel Burkhardt Date: Wed, 7 Apr 2021 14:38:04 -0400 Subject: [PATCH 0022/1233] Update preprocessing Former-commit-id: 2799e7a97148443f412c09ae182b16da8a66ca53 --- .../resources/preprocessing.py | 52 +++++++++++-------- 1 file changed, 31 insertions(+), 21 deletions(-) diff --git a/src/modality_alignment/resources/preprocessing.py b/src/modality_alignment/resources/preprocessing.py index 58f109f458..1d660ca146 100644 --- a/src/modality_alignment/resources/preprocessing.py +++ b/src/modality_alignment/resources/preprocessing.py @@ -1,41 +1,51 @@ +import anndata +import functools import scanpy as sc import scprep -#_scran = scprep.run.RFunction( -# setup="library('scran')", -# args="sce, min.mean=0.1", -# body=""" -# sce <- computeSumFactors(sce, min.mean=min.mean, assay.type="X") -# sizeFactors(sce) -# """, -#) -# -# -#def log_scran_pooling(adata): -# """Normalize data with scran via rpy2.""" -# scprep.run.install_bioconductor("scran") -# adata.obs["size_factors"] = _scran(adata) -# adata.X = scprep.utils.matrix_vector_elementwise_multiply( -# adata.X, adata.obs["size_factors"], axis=0 -# ) -# sc.pp.log1p(adata) +def normalizer(func, *args, **kwargs): + """Decorate a normalization function.""" + + @functools.wraps(func) + def normalize(adata, *args, obsm=None, obs=None, var=None, **kwargs): + # log.debug("Running {} normalization".format(func.__name__)) + assert isinstance(adata, anndata.AnnData) + + if obsm is not None: + cache_name = "{}_{}".format(obsm, func.__name__) + if cache_name in adata.obsm: + adata.obsm[obsm] = adata.obsm[cache_name] + else: + obs = adata.uns[obs] if obs else adata.obs + var = adata.uns[var] if var else adata.var + adata_temp = anndata.AnnData(adata.obsm[obsm], obs=obs, var=var) + func(adata_temp, *args, **kwargs) + adata.obsm[obsm] = adata.obsm[cache_name] = adata_temp.X + else: + if func.__name__ in adata.layers: + adata.X = adata.layers[func.__name__] + else: + func(adata, *args, **kwargs) + adata.layers[func.__name__] = adata.X + + return normalize def _cpm(adata): adata.layers["counts"] = adata.X.copy() sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") - +@normalizer def cpm(adata): """Normalize data to counts per million.""" _cpm(adata) - +@normalizer def log_cpm(adata): """Normalize data to log counts per million.""" _cpm(adata) sc.pp.log1p(adata) - +@normalizer def sqrt_cpm(adata): """Normalize data to sqrt counts per million.""" _cpm(adata) From cc17927f7537e4cd5e86483963d830b530f43a21 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Apr 2021 03:57:26 +0200 Subject: [PATCH 0023/1233] remove accidental h5ad file in repo Former-commit-id: 29cb0f047aaf480a8c1489749a597ec642e8767e --- .gitignore | 1 + output.h5ad.REMOVED.git-id | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) delete mode 100644 output.h5ad.REMOVED.git-id diff --git a/.gitignore b/.gitignore index c0ead2c50b..408bc27ea5 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ # repo specific ignores out_bash +*.h5ad # R specific ignores .Rhistory diff --git a/output.h5ad.REMOVED.git-id b/output.h5ad.REMOVED.git-id deleted file mode 100644 index 7b505ebadb..0000000000 --- a/output.h5ad.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -105ff533b3e0dc7c63342855c1579dae05885381 \ No newline at end of file From 3dab4cb2ec4fe279bb7ad842d10ab7be21b40595 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 12 Apr 2021 14:49:37 +0200 Subject: [PATCH 0024/1233] add metadata to citeseq_cbmc Former-commit-id: 424e30b50b481adec3bdef68154ec1af6b19d282 --- .../datasets/citeseq_cbmc/config.vsh.yaml | 10 ++++++++-- src/modality_alignment/datasets/citeseq_cbmc/script.py | 2 +- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index d71f609eb1..fb958cefb2 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -2,7 +2,13 @@ functionality: name: "citeseq_cbmc" namespace: "modality_alignment/datasets" version: "dev" - description: "Download a modality alignment dataset from GEO" + description: "CITE-seq Cord Blood Mononuclear Cells" + info: + accession_id: "GSE100866" + doi: "10.1038/nmeth.4380" + organism: "human" + cell_types: "CL:2000001" # peripheral blood mononuclear cells + technology: "dropseq" arguments: - name: "--input_rna" type: "string" @@ -36,4 +42,4 @@ platforms: - pandas # needed by utils.py - scanpy # needed by utils.py - numpy # needed by utils.py - - type: nextflow \ No newline at end of file + - type: nextflow diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index ab4e8ac919..ad8d0beb2d 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -7,7 +7,7 @@ "output": "output.h5ad", "test": False } -resources_dir = "../../resources/utils.py" +resources_dir = "../../resources/" ## VIASH END print("Importing libraries") From eb1d188b9226b36c31734fa00ff1e6733ddedf93 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Apr 2021 16:55:28 +0200 Subject: [PATCH 0025/1233] update viash in bin Former-commit-id: e1454c2919237e07fa4017cf5da485a3d5c3f017 --- bin/project_build | 88 +++-- bin/project_clean | 318 ++++++++++++++++- bin/project_debug | 6 +- bin/project_doc | 545 +++++++++++++++++++++++++++++ bin/project_push | 104 ++++-- bin/project_test | 88 +++-- bin/skeleton | 536 ++++++++++++++++++++++++++++ bin/viash | 2 +- bin/viash-0.4.0-rc1.REMOVED.git-id | 1 - bin/viash-0.4.0.REMOVED.git-id | 1 + bin/vshtrafo | 331 ++++++++++++++++++ 11 files changed, 1922 insertions(+), 98 deletions(-) create mode 100755 bin/project_doc create mode 100755 bin/skeleton delete mode 100644 bin/viash-0.4.0-rc1.REMOVED.git-id create mode 100644 bin/viash-0.4.0.REMOVED.git-id create mode 100755 bin/vshtrafo diff --git a/bin/project_build b/bin/project_build index cdf27a79bb..16b85991f5 100755 --- a/bin/project_build +++ b/bin/project_build @@ -4,9 +4,9 @@ # project_build 0.1 # ########################### -# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -80,11 +80,15 @@ function ViashHelp { echo "" echo " -q string, --query=string" echo " type: string" - echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." echo "" - echo " -n string, --namespace=string" + echo " -n string, --query_namespace=string" echo " type: string" - echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." + echo "" + echo " --query_name=string" + echo " type: string" + echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." echo "" echo " -v string, --version=string" echo " type: string, default: dev" @@ -94,6 +98,10 @@ function ViashHelp { echo " type: string, default: " echo " Docker registry to use, only used when using a registry." echo "" + echo " --namespace_separator=string" + echo " type: string, default: _" + echo " The separator to use between the component name and namespace as the image name of a Docker container." + echo "" echo " -nc, --no-cache, --no_cache" echo " type: boolean_true" echo " Don't cache the docker build in development mode." @@ -160,18 +168,26 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY="$2" shift 2 ;; - --namespace) - VIASH_PAR_NAMESPACE="$2" + --query_namespace) + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; - --namespace=*) - VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + --query_namespace=*) + VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") shift 1 ;; -n) - VIASH_PAR_NAMESPACE="$2" + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; + --query_name) + VIASH_PAR_QUERY_NAME="$2" + shift 2 + ;; + --query_name=*) + VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") + shift 1 + ;; --version) VIASH_PAR_VERSION="$2" shift 2 @@ -196,6 +212,14 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGISTRY="$2" shift 2 ;; + --namespace_separator) + VIASH_PAR_NAMESPACE_SEPARATOR="$2" + shift 2 + ;; + --namespace_separator=*) + VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") + shift 1 + ;; --no_cache) VIASH_PAR_NO_CACHE=true shift 1 @@ -259,6 +283,9 @@ fi if [ -z "$VIASH_PAR_REGISTRY" ]; then VIASH_PAR_REGISTRY="" fi +if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then + VIASH_PAR_NAMESPACE_SEPARATOR="_" +fi if [ -z "$VIASH_PAR_NO_CACHE" ]; then VIASH_PAR_NO_CACHE="false" fi @@ -279,9 +306,11 @@ cat > "\$tempscript" << 'VIASHMAIN' par_mode='$VIASH_PAR_MODE' par_platforms='$VIASH_PAR_PLATFORMS' par_query='$VIASH_PAR_QUERY' -par_namespace='$VIASH_PAR_NAMESPACE' +par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' +par_query_name='$VIASH_PAR_QUERY_NAME' par_version='$VIASH_PAR_VERSION' par_registry='$VIASH_PAR_REGISTRY' +par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' par_no_cache='$VIASH_PAR_NO_CACHE' par_log='$VIASH_PAR_LOG' par_viash='$VIASH_PAR_VIASH' @@ -290,14 +319,15 @@ resources_dir="$VIASH_RESOURCES_DIR" #!/bin/bash -# if not specified, default par_query to a catch-all regex +# if not specified, default queries to a catch-all regexes if [ -z "\$par_query" ]; then par_query=".*" fi - -# if not specified, default par_namespace to a catch-all regex -if [ -z "\$par_namespace" ]; then - par_namespace=".*" +if [ -z "\$par_query_namespace" ]; then + par_query_namespace=".*" +fi +if [ -z "\$par_query_name" ]; then + par_query_name=".*" fi # if not specified, default par_viash to look for 'viash' on the PATH @@ -315,11 +345,13 @@ if [ "\$par_mode" == "development" ]; then fi "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "dev"' \\ -c '.platforms[.type == "docker"].setup_strategy := "'\$setup_strat'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l -w \\ --setup | tee "\$par_log" elif [ "\$par_mode" == "integration" ]; then @@ -330,13 +362,15 @@ elif [ "\$par_mode" == "integration" ]; then fi "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l -w \\ --setup | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then @@ -351,13 +385,15 @@ elif [ "\$par_mode" == "release" ]; then exit 1 fi "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l -w \\ --setup | tee "\$par_log" else diff --git a/bin/project_clean b/bin/project_clean index 0b709a4128..1213fdcde3 100755 --- a/bin/project_clean +++ b/bin/project_clean @@ -4,9 +4,9 @@ # project_clean 0.1 # ########################### -# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -60,8 +60,26 @@ function ViashSourceDir { VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` VIASH_EXEC_MODE="run" +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + : +} +# ViashDockerBuild: ... +function ViashDockerBuild { + ViashDockerPull $1 +} + +# ViashSetup: ... function ViashSetup { -: + ViashDockerSetup nextflow/nextflow:latest $VIASH_DOCKER_SETUP_STRATEGY +} + +# ViashPush: ... +function ViashPush { + ViashDockerPush nextflow/nextflow:latest $VIASH_DOCKER_PUSH_STRATEGY } @@ -81,6 +99,238 @@ function ViashHelp { echo " type: string" echo "" } +######## Helper functions for setting up Docker images for viash ######## + + +# ViashDockerRemoteTagCheck: check whether a Docker image is available +# on a remote. Assumes `docker login` has been performed, if relevant. +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerRemoteTagCheck python:latest +# echo $? # returns '0' +# ViashDockerRemoteTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerRemoteTagCheck { + docker manifest inspect $1 > /dev/null 2> /dev/null +} + +# ViashDockerLocalTagCheck: check whether a Docker image is available locally +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# docker pull python:latest +# ViashDockerLocalTagCheck python:latest +# echo $? # returns '0' +# ViashDockerLocalTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerLocalTagCheck { + [ -n "$(docker images -q $1)" ] +} + +# ViashDockerPull: pull a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPull python:latest +# echo $? # returns '0' +# ViashDockerPull sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPull { + echo "> docker pull $1" + docker pull $1 && return 0 || return 1 +} + +# ViashDockerPullElseBuild: pull a Docker image, else build it +# +# $1 : image identifier with format `[registry/]image[:tag]` +# examples: +# ViashDockerPullElseBuild mynewcomponent +function ViashDockerPullElseBuild { + set +e + ViashDockerPull $1 + out=$? + set -e + if [ $out -ne 0 ]; then + ViashDockerBuild $@ + fi +} + +# ViashDockerSetup: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerSetupStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerSetup { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + echo "Skipping setup." + elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + ViashDockerLocalTagCheck $VSHD_ID + if [ $? -eq 0 ]; then + echo "Image $VSHD_ID already exists" + elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi +} + +# ViashDockerPush: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerPushStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerPush { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + set +e + docker push $1 + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "> $VSHD_ID force push ... ok" + else + echo "> $VSHD_ID force push ... error" + exit 1 + fi + elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + set +e + ViashDockerRemoteTagCheck $1 + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + echo "> $VSHD_ID exists, doing nothing" + else + echo -n "> $VSHD_ID does not exist, try pushing " + set +e + docker push $1 > /dev/null 2> /dev/null + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "... ok" + else + echo "... error" + fi + fi + else + echo "Unrecognised Docker push strategy: $VSHD_STRAT" + fi +} + +######## End of helper functions for setting up Docker images for viash ######## +# initialise variables +VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' +VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' +# ViashAbsolutePath: generate absolute path from relative path +# borrowed from https://stackoverflow.com/a/21951256 +# $1 : relative filename +# return : absolute path +# examples: +# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt +# ViashAbsolutePath /foo/bar/.. # returns /foo +function ViashAbsolutePath { + local thePath + if [[ ! "$1" =~ ^/ ]]; then + thePath="$PWD/$1" + else + thePath="$1" + fi + echo "$thePath" | ( + IFS=/ + read -a parr + declare -a outp + for i in "${parr[@]}"; do + case "$i" in + ''|.) continue ;; + ..) + len=${#outp[@]} + if ((len==0)); then + continue + else + unset outp[$((len-1))] + fi + ;; + *) + len=${#outp[@]} + outp[$len]="$i" + ;; + esac + done + echo /"${outp[*]}" + ) +} +# ViashAutodetectMount: auto configuring docker mounts from parameters +# $1 : The parameter value +# returns : New parameter +# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker +# examples: +# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' +# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' +function ViashAutodetectMount { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "$mount_target/$base_name" +} +function ViashAutodetectMountArg { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "-v \"$mount_source:$mount_target\"" +} +# ViashExtractFlags: Retain leading flag +# $1 : string with a possible leading flag +# return : leading flag +# examples: +# ViashExtractFlags --foo=bar # returns --foo +function ViashExtractFlags { + echo $1 | sed 's/=.*//' +} +# initialise variables +VIASH_EXTRA_MOUNTS='' # initialise array VIASH_POSITIONAL_ARGS='' @@ -106,6 +356,43 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_BEFORE="$2" shift 2 ;; + ---dss|---docker_setup_strategy) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY="$2" + shift 2 + ;; + ---docker_setup_strategy=*) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dps|---docker_push_strategy) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY="$2" + shift 2 + ;; + ---docker_push_strategy=*) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dockerfile) + ViashDockerfile + exit 0 + ;; + ---v|---volume) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" + shift 2 + ;; + ---volume=*) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" + shift 1 + ;; + ---debug) + echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t nextflow/nextflow:latest" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t nextflow/nextflow:latest + exit 0 + ;; *) # positional arg or unknown option # since the positional args will be eval'd, can we always quote, instead of using ViashQuote VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" @@ -137,7 +424,28 @@ if [ -z "$VIASH_PAR_DIR" ]; then fi -cat << VIASHEOF | bash +# detect volumes from file arguments +if [ ! -z "$VIASH_PAR_DIR" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_DIR")" + VIASH_PAR_DIR=$(ViashAutodetectMount "$VIASH_PAR_DIR") +fi + +# Always mount the resource directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" +VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") + +# Always mount the VIASH_TEMP directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" +VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") + +# change file ownership +function viash_perform_chown { + : +} +trap viash_perform_chown EXIT + + +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS nextflow/nextflow:latest set -e tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_clean-XXXXXX") function clean_up { diff --git a/bin/project_debug b/bin/project_debug index 70012aee84..40620cde6c 100755 --- a/bin/project_debug +++ b/bin/project_debug @@ -4,9 +4,9 @@ # project_debug 0.1 # ########################### -# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. diff --git a/bin/project_doc b/bin/project_doc new file mode 100755 index 0000000000..0834de8f06 --- /dev/null +++ b/bin/project_doc @@ -0,0 +1,545 @@ +#!/usr/bin/env bash + +######################### +# project_doc 0.1 # +######################### + +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + : +} +# ViashDockerBuild: ... +function ViashDockerBuild { + ViashDockerPull $1 +} + +# ViashSetup: ... +function ViashSetup { + ViashDockerSetup dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_SETUP_STRATEGY +} + +# ViashPush: ... +function ViashPush { + ViashDockerPush dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_PUSH_STRATEGY +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Generate documentation" + echo + echo "Options:" + echo " file" + echo " type: file, default: ." + echo " Repository to generate documentation for" + echo "" + echo " -s string, --src=string" + echo " type: string, default: src" + echo " Folder to search for components, usually just src/" + echo "" + echo " -r file, --output=file" + echo " type: file, default: project_doc.md" + echo " Name/path of the output markdown file" + echo "" +} +######## Helper functions for setting up Docker images for viash ######## + + +# ViashDockerRemoteTagCheck: check whether a Docker image is available +# on a remote. Assumes `docker login` has been performed, if relevant. +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerRemoteTagCheck python:latest +# echo $? # returns '0' +# ViashDockerRemoteTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerRemoteTagCheck { + docker manifest inspect $1 > /dev/null 2> /dev/null +} + +# ViashDockerLocalTagCheck: check whether a Docker image is available locally +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# docker pull python:latest +# ViashDockerLocalTagCheck python:latest +# echo $? # returns '0' +# ViashDockerLocalTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerLocalTagCheck { + [ -n "$(docker images -q $1)" ] +} + +# ViashDockerPull: pull a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPull python:latest +# echo $? # returns '0' +# ViashDockerPull sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPull { + echo "> docker pull $1" + docker pull $1 && return 0 || return 1 +} + +# ViashDockerPullElseBuild: pull a Docker image, else build it +# +# $1 : image identifier with format `[registry/]image[:tag]` +# examples: +# ViashDockerPullElseBuild mynewcomponent +function ViashDockerPullElseBuild { + set +e + ViashDockerPull $1 + out=$? + set -e + if [ $out -ne 0 ]; then + ViashDockerBuild $@ + fi +} + +# ViashDockerSetup: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerSetupStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerSetup { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + echo "Skipping setup." + elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + ViashDockerLocalTagCheck $VSHD_ID + if [ $? -eq 0 ]; then + echo "Image $VSHD_ID already exists" + elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi + else + echo "Unrecognised Docker strategy: $VSHD_STRAT" + fi +} + +# ViashDockerPush: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerPushStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent alwaysbuild +function ViashDockerPush { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + set +e + docker push $1 + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "> $VSHD_ID force push ... ok" + else + echo "> $VSHD_ID force push ... error" + exit 1 + fi + elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + set +e + ViashDockerRemoteTagCheck $1 + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + echo "> $VSHD_ID exists, doing nothing" + else + echo -n "> $VSHD_ID does not exist, try pushing " + set +e + docker push $1 > /dev/null 2> /dev/null + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + echo "... ok" + else + echo "... error" + fi + fi + else + echo "Unrecognised Docker push strategy: $VSHD_STRAT" + fi +} + +######## End of helper functions for setting up Docker images for viash ######## +# initialise variables +VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' +VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' +# ViashAbsolutePath: generate absolute path from relative path +# borrowed from https://stackoverflow.com/a/21951256 +# $1 : relative filename +# return : absolute path +# examples: +# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt +# ViashAbsolutePath /foo/bar/.. # returns /foo +function ViashAbsolutePath { + local thePath + if [[ ! "$1" =~ ^/ ]]; then + thePath="$PWD/$1" + else + thePath="$1" + fi + echo "$thePath" | ( + IFS=/ + read -a parr + declare -a outp + for i in "${parr[@]}"; do + case "$i" in + ''|.) continue ;; + ..) + len=${#outp[@]} + if ((len==0)); then + continue + else + unset outp[$((len-1))] + fi + ;; + *) + len=${#outp[@]} + outp[$len]="$i" + ;; + esac + done + echo /"${outp[*]}" + ) +} +# ViashAutodetectMount: auto configuring docker mounts from parameters +# $1 : The parameter value +# returns : New parameter +# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker +# examples: +# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' +# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' +function ViashAutodetectMount { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "$mount_target/$base_name" +} +function ViashAutodetectMountArg { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "-v \"$mount_source:$mount_target\"" +} +# ViashExtractFlags: Retain leading flag +# $1 : string with a possible leading flag +# return : leading flag +# examples: +# ViashExtractFlags --foo=bar # returns --foo +function ViashExtractFlags { + echo $1 | sed 's/=.*//' +} +# initialise variables +VIASH_EXTRA_MOUNTS='' + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --src) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --src=*) + VIASH_PAR_SRC=$(ViashRemoveFlags "$1") + shift 1 + ;; + -s) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --output) + VIASH_PAR_OUTPUT="$2" + shift 2 + ;; + --output=*) + VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -r) + VIASH_PAR_OUTPUT="$2" + shift 2 + ;; + ---dss|---docker_setup_strategy) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY="$2" + shift 2 + ;; + ---docker_setup_strategy=*) + VIASH_EXEC_MODE="setup" + VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dps|---docker_push_strategy) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY="$2" + shift 2 + ;; + ---docker_push_strategy=*) + VIASH_EXEC_MODE="push" + VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") + shift 1 + ;; + ---dockerfile) + ViashDockerfile + exit 0 + ;; + ---v|---volume) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" + shift 2 + ;; + ---volume=*) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" + shift 1 + ;; + ---debug) + echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1 + exit 0 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + +if [[ $# -gt 0 ]]; then + VIASH_PAR_REPO="$1" + shift 1 +fi + +if [ -z "$VIASH_PAR_REPO" ]; then + VIASH_PAR_REPO="." +fi +if [ -z "$VIASH_PAR_SRC" ]; then + VIASH_PAR_SRC="src" +fi +if [ -z "$VIASH_PAR_OUTPUT" ]; then + VIASH_PAR_OUTPUT="project_doc.md" +fi + + +# detect volumes from file arguments +if [ ! -z "$VIASH_PAR_REPO" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_REPO")" + VIASH_PAR_REPO=$(ViashAutodetectMount "$VIASH_PAR_REPO") +fi +if [ ! -z "$VIASH_PAR_OUTPUT" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_OUTPUT")" + VIASH_PAR_OUTPUT=$(ViashAutodetectMount "$VIASH_PAR_OUTPUT") +fi + +# Always mount the resource directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" +VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") + +# Always mount the VIASH_TEMP directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" +VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") + +# change file ownership +function viash_perform_chown { + + if [ ! -z "$VIASH_PAR_OUTPUT" ]; then + eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" + fi +} +trap viash_perform_chown EXIT + + +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_doc-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_repo='$VIASH_PAR_REPO' +par_src='$VIASH_PAR_SRC' +par_output='$VIASH_PAR_OUTPUT' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +function output { + echo "\$@" >> \$par_output +} + +echo "# Repository Overview" > \$par_output +output "" + +namespaces=\`viash ns list -s \$par_repo/"\$par_src" | yq e '.[].functionality.namespace' - | uniq\` + +tempscript=\$(mktemp ".tmp_viash_config_view_XXXXXX") +function clean_up { + [[ -f "\$tempscript" ]] && rm "\$tempscript" +} +trap clean_up EXIT + +for ns in \$namespaces; do + echo "> Generating documentation for namespace \$ns" + output "## \$ns" + output "" + comp_files=\`viash ns list -n \$ns -s \$par_repo/\$par_src | yq e '.[].info.config' - | uniq\` + for comp_file in \$comp_files; do + viash config view "\$comp_file" > "\$tempscript" + + comp_name=\`yq e '.functionality.name' "\$tempscript"\` + comp_desc=\`yq e '.functionality.description' "\$tempscript"\` + echo " > Generating documentation for \$ns/\$comp_name" + output "### \$comp_name" + output "" + output \$comp_desc + output "" + output '\`\`\`sh' + output "\$ viash run \$comp_file -- -h" + viash run \$comp_file -- -h >> \$par_output + output '\`\`\`' + output "" + + clean_up + done +done + +output "# Tests" +output "" +output "__TODO__" +output "" +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_push b/bin/project_push index 0973473719..5c75d9f22a 100755 --- a/bin/project_push +++ b/bin/project_push @@ -4,9 +4,9 @@ # project_push 0.1 # ########################## -# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -76,20 +76,28 @@ function ViashHelp { echo "" echo " -q string, --query=string" echo " type: string" - echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." echo "" - echo " -n string, --namespace=string" + echo " -n string, --query_namespace=string" echo " type: string" - echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." + echo "" + echo " --query_name=string" + echo " type: string" + echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." echo "" echo " -v string, --version=string" echo " type: string, default: dev" echo " Which version of the pipeline to use." echo "" echo " -r string, --registry=string" - echo " type: string, default: itx-aiv.artifactrepo.jnj.com" + echo " type: string" echo " Docker registry to use, only used when using a registry." echo "" + echo " --namespace_separator=string" + echo " type: string, default: _" + echo " The separator to use between the component name and namespace as the image name of a Docker container." + echo "" echo " --force" echo " type: boolean_true" echo " Overwrite registry" @@ -99,7 +107,7 @@ function ViashHelp { echo " Log file" echo "" echo " --viash=file" - echo " type: file, default: bin/viash" + echo " type: file" echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." echo "" } @@ -144,18 +152,26 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY="$2" shift 2 ;; - --namespace) - VIASH_PAR_NAMESPACE="$2" + --query_namespace) + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; - --namespace=*) - VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + --query_namespace=*) + VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") shift 1 ;; -n) - VIASH_PAR_NAMESPACE="$2" + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; + --query_name) + VIASH_PAR_QUERY_NAME="$2" + shift 2 + ;; + --query_name=*) + VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") + shift 1 + ;; --version) VIASH_PAR_VERSION="$2" shift 2 @@ -180,6 +196,14 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGISTRY="$2" shift 2 ;; + --namespace_separator) + VIASH_PAR_NAMESPACE_SEPARATOR="$2" + shift 2 + ;; + --namespace_separator=*) + VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") + shift 1 + ;; --force) VIASH_PAR_FORCE=true shift 1 @@ -229,8 +253,8 @@ fi if [ -z "$VIASH_PAR_VERSION" ]; then VIASH_PAR_VERSION="dev" fi -if [ -z "$VIASH_PAR_REGISTRY" ]; then - VIASH_PAR_REGISTRY="itx-aiv.artifactrepo.jnj.com" +if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then + VIASH_PAR_NAMESPACE_SEPARATOR="_" fi if [ -z "$VIASH_PAR_FORCE" ]; then VIASH_PAR_FORCE="false" @@ -238,9 +262,6 @@ fi if [ -z "$VIASH_PAR_LOG" ]; then VIASH_PAR_LOG="log.txt" fi -if [ -z "$VIASH_PAR_VIASH" ]; then - VIASH_PAR_VIASH="bin/viash" -fi cat << VIASHEOF | bash @@ -254,9 +275,11 @@ cat > "\$tempscript" << 'VIASHMAIN' # The following code has been auto-generated by Viash. par_mode='$VIASH_PAR_MODE' par_query='$VIASH_PAR_QUERY' -par_namespace='$VIASH_PAR_NAMESPACE' +par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' +par_query_name='$VIASH_PAR_QUERY_NAME' par_version='$VIASH_PAR_VERSION' par_registry='$VIASH_PAR_REGISTRY' +par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' par_force='$VIASH_PAR_FORCE' par_log='$VIASH_PAR_LOG' par_viash='$VIASH_PAR_VIASH' @@ -275,14 +298,15 @@ if [ "\$par_mode" == "release" ]; then fi fi -# if not specified, default par_query to a catch-all regex +# if not specified, default queries to a catch-all regexes if [ -z "\$par_query" ]; then par_query=".*" fi - -# if not specified, default par_namespace to a catch-all regex -if [ -z "\$par_namespace" ]; then - par_namespace=".*" +if [ -z "\$par_query_namespace" ]; then + par_query_namespace=".*" +fi +if [ -z "\$par_query_name" ]; then + par_query_name=".*" fi # if not specified, default par_viash to look for 'viash' on the PATH @@ -296,26 +320,30 @@ if [[ \$par_force == true ]]; then echo "No container push can and should be performed in this mode" elif [ "\$par_mode" == "integration" ]; then "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "docker" \\ - -q "\$par_query" \\ + --platform "docker" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "dev"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ --setup --push | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "docker" \\ - -q "\$par_query" \\ + --platform "docker" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ --setup --push | tee "\$par_log" else @@ -326,24 +354,28 @@ else echo "No container push can and should be performed in this mode" elif [ "\$par_mode" == "integration" ]; then "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "docker" \\ - -q "\$par_query" \\ + --platform "docker" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "dev"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ --setup --push | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then "\$par_viash" ns build \\ - -n "\$par_namespace" \\ - -p "docker" \\ - -q "\$par_query" \\ + --platform "docker" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ --setup --push | tee "\$par_log" else diff --git a/bin/project_test b/bin/project_test index c08d4482c2..01d848d70c 100755 --- a/bin/project_test +++ b/bin/project_test @@ -4,9 +4,9 @@ # project_test 0.1 # ########################## -# This wrapper script is auto-generated by viash 0.4.0-rc1 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -80,11 +80,15 @@ function ViashHelp { echo "" echo " -q string, --query=string" echo " type: string" - echo " Filter which components get selected. Can be a regex. Example: '^cluster'." + echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." echo "" - echo " -n string, --namespace=string" + echo " -n string, --query_namespace=string" echo " type: string" - echo " Filter which namespaces get selected. Can be a regex. Example: 'build|run'." + echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." + echo "" + echo " --query_name=string" + echo " type: string" + echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." echo "" echo " -v string, --version=string" echo " type: string, default: dev" @@ -94,6 +98,10 @@ function ViashHelp { echo " type: string" echo " Docker registry to use, only used when using a registry." echo "" + echo " --namespace_separator=string" + echo " type: string, default: _" + echo " The separator to use between the component name and namespace as the image name of a Docker container." + echo "" echo " -l file, --log=file" echo " type: file, default: log.tsv" echo " Test log file" @@ -160,18 +168,26 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY="$2" shift 2 ;; - --namespace) - VIASH_PAR_NAMESPACE="$2" + --query_namespace) + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; - --namespace=*) - VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + --query_namespace=*) + VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") shift 1 ;; -n) - VIASH_PAR_NAMESPACE="$2" + VIASH_PAR_QUERY_NAMESPACE="$2" shift 2 ;; + --query_name) + VIASH_PAR_QUERY_NAME="$2" + shift 2 + ;; + --query_name=*) + VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") + shift 1 + ;; --version) VIASH_PAR_VERSION="$2" shift 2 @@ -196,6 +212,14 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_REGISTRY="$2" shift 2 ;; + --namespace_separator) + VIASH_PAR_NAMESPACE_SEPARATOR="$2" + shift 2 + ;; + --namespace_separator=*) + VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") + shift 1 + ;; --log) VIASH_PAR_LOG="$2" shift 2 @@ -256,6 +280,9 @@ fi if [ -z "$VIASH_PAR_VERSION" ]; then VIASH_PAR_VERSION="dev" fi +if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then + VIASH_PAR_NAMESPACE_SEPARATOR="_" +fi if [ -z "$VIASH_PAR_LOG" ]; then VIASH_PAR_LOG="log.tsv" fi @@ -276,9 +303,11 @@ cat > "\$tempscript" << 'VIASHMAIN' par_mode='$VIASH_PAR_MODE' par_platforms='$VIASH_PAR_PLATFORMS' par_query='$VIASH_PAR_QUERY' -par_namespace='$VIASH_PAR_NAMESPACE' +par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' +par_query_name='$VIASH_PAR_QUERY_NAME' par_version='$VIASH_PAR_VERSION' par_registry='$VIASH_PAR_REGISTRY' +par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' par_log='$VIASH_PAR_LOG' par_append='$VIASH_PAR_APPEND' par_viash='$VIASH_PAR_VIASH' @@ -287,14 +316,15 @@ resources_dir="$VIASH_RESOURCES_DIR" #!/bin/bash -# if not specified, default par_query to a catch-all regex +# if not specified, default queries to a catch-all regexes if [ -z "\$par_query" ]; then par_query=".*" fi - -# if not specified, default par_namespace to a catch-all regex -if [ -z "\$par_namespace" ]; then - par_namespace=".*" +if [ -z "\$par_query_namespace" ]; then + par_query_namespace=".*" +fi +if [ -z "\$par_query_name" ]; then + par_query_name=".*" fi # if not specified, default par_viash to look for 'viash' on the PATH @@ -310,24 +340,28 @@ fi if [ "\$par_mode" == "development" ]; then echo "In development mode..." "\$par_viash" ns test \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "dev"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ -t "\$par_log" \\ \$par_append_parsed elif [ "\$par_mode" == "integration" ]; then echo "In integration mode..." "\$par_viash" ns test \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ -t "\$par_log" \\ \$par_append_parsed @@ -338,13 +372,15 @@ elif [ "\$par_mode" == "release" ]; then exit 1 fi "\$par_viash" ns test \\ - -n "\$par_namespace" \\ - -p "\$par_platforms" \\ - -q "\$par_query" \\ + --platform "\$par_platforms" \\ + --query "\$par_query" \\ + --query_name "\$par_query_name" \\ + --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "'"\$par_version"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "pull"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ + -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ -l \\ -t "\$par_log" \\ \$par_append_parsed diff --git a/bin/skeleton b/bin/skeleton new file mode 100755 index 0000000000..513d657e02 --- /dev/null +++ b/bin/skeleton @@ -0,0 +1,536 @@ +#!/usr/bin/env bash + +###################### +# skeleton 0.1 # +###################### + +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Create a skeleton src component" + echo + echo "Options:" + echo " -n string, --name=string" + echo " type: string, required parameter" + echo " Name of the component" + echo "" + echo " -ns string, --namespace=string" + echo " type: string" + echo " Namespace of the component" + echo "" + echo " -l string, --language=string" + echo " type: string, default: bash" + echo " Which scripting language to use. Possible values are 'bash', 'r', and 'python'." + echo "" + echo " -p string1,string2,..., --platform=string1,string2,..." + echo " type: string, multiple values allowed, default: docker,native,nextflow" + echo " Which platforms to add. Possible values are 'native', 'docker', 'nextflow'. By default, all three will be added." + echo "" + echo " --src=file" + echo " type: file, default: src" + echo " Target directory if different from src/" + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --name) + VIASH_PAR_NAME="$2" + shift 2 + ;; + --name=*) + VIASH_PAR_NAME=$(ViashRemoveFlags "$1") + shift 1 + ;; + -n) + VIASH_PAR_NAME="$2" + shift 2 + ;; + --namespace) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --namespace=*) + VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -ns) + VIASH_PAR_NAMESPACE="$2" + shift 2 + ;; + --language) + VIASH_PAR_LANGUAGE="$2" + shift 2 + ;; + --language=*) + VIASH_PAR_LANGUAGE=$(ViashRemoveFlags "$1") + shift 1 + ;; + -l) + VIASH_PAR_LANGUAGE="$2" + shift 2 + ;; + --platform) + if [ -z "$VIASH_PAR_PLATFORM" ]; then + VIASH_PAR_PLATFORM="$2" + else + VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,""$2" + fi + shift 2 + ;; + --platform=*) + if [ -z "$VIASH_PAR_PLATFORM" ]; then + VIASH_PAR_PLATFORM=$(ViashRemoveFlags "$1") + else + VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + -p) + if [ -z "$VIASH_PAR_PLATFORM" ]; then + VIASH_PAR_PLATFORM="$2" + else + VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,""$2" + fi + shift 2 + ;; + --src) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --src=*) + VIASH_PAR_SRC=$(ViashRemoveFlags "$1") + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +# check whether required parameters exist +if [ -z "$VIASH_PAR_NAME" ]; then + echo '--name' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_LANGUAGE" ]; then + VIASH_PAR_LANGUAGE="bash" +fi +if [ -z "$VIASH_PAR_PLATFORM" ]; then + VIASH_PAR_PLATFORM="docker,native,nextflow" +fi +if [ -z "$VIASH_PAR_SRC" ]; then + VIASH_PAR_SRC="src" +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-skeleton-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_name='$VIASH_PAR_NAME' +par_namespace='$VIASH_PAR_NAMESPACE' +par_language='$VIASH_PAR_LANGUAGE' +par_platform='$VIASH_PAR_PLATFORM' +par_src='$VIASH_PAR_SRC' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + + +# check par_language +if [[ \$par_language =~ ^bash|sh|Bash\$ ]]; then + script_lang=bash +elif [[ \$par_language =~ ^r|R\$ ]]; then + script_lang=r +elif [[ \$par_language =~ ^py|python|Python\$ ]]; then + script_lang=python +else + echo "Unrecognised language: \$par_language; please specify one of 'python', 'r', or 'bash'" + exit 1 +fi + +# create output dir +out_dir="\$par_src/\$par_namespace/\$par_name" +mkdir -p "\$out_dir" + +################################################################################## +### FUNCTIONALITY ### +################################################################################## + +# write header +cat > "\$out_dir/config.vsh.yaml" << HERE +functionality: + name: "\$par_name" +HERE + +# write namespace, if need be +if [ ! -z "\$par_namespace" ]; then +cat >> "\$out_dir/config.vsh.yaml" << HERE + namespace: "\$par_namespace" +HERE +fi + +# write more metadata and initial arguments +cat >> "\$out_dir/config.vsh.yaml" << HERE + version: 0.0.1 + description: | + Replace this with a (multiline) description of your component. + arguments: + - name: "--input" + alternatives: [ "-i" ] + type: file + required: true + description: Describe the input file. + - name: "--output" + alternatives: [ "-o" ] + type: file + direction: output + required: true + description: Describe the output file. + - name: "--option" + type: string + description: Describe an optional parameter. + default: "default-" +HERE + +################################################################################## +### BASH SCRIPTS ### +################################################################################## +if [ \$script_lang == "bash" ]; then +cat >> "\$out_dir/config.vsh.yaml" << HERE + resources: + - type: bash_script + path: script.sh + tests: + - type: bash_script + path: test.sh +HERE + +cat >> "\$out_dir/script.sh" << 'HERE' +#!/bin/bash + +echo "This is a skeleton component" +echo "The arguments are:" +echo " - input: \$par_input" +echo " - output: \$par_output" +echo " - option: \$par_option" +echo + +echo "Writing output file" +cat "\$par_input" | sed "s#.*#\$par_option-&#" > "\$par_output" +HERE + +cat >> "\$out_dir/test.sh" << MAJORHERE +#!/bin/bash + +set -ex + +echo ">>> Creating dummy input file" +cat > input.txt << HERE +one +two +three +HERE + +echo ">>> Running executable" +./\$par_name --input input.txt --output output.txt --option FOO + +echo ">>> Checking whether output file exists" +[[ ! -f output.txt ]] && echo "Output file could not be found!" && exit 1 + +# create expected output file +cat > expected_output.txt << HERE +FOO-one +FOO-two +FOO-three +HERE + +echo ">>> Checking whether content matches expected content" +diff output.txt expected_output.txt +[ \\\$? -ne 0 ] && echo "Output file did not equal expected output" && exit 1 + +# print final message +echo ">>> Test finished successfully" + +# do not remove this +# as otherwise your test might exit with a different exit code +exit 0 +MAJORHERE + +################################################################################## +### RLANG SCRIPTS ### +################################################################################## +elif [ \$script_lang == "r" ]; then +cat >> "\$out_dir/config.vsh.yaml" << HERE + resources: + - type: r_script + path: script.R + tests: + - type: r_script + path: test.R +HERE +cat >> "\$out_dir/script.R" << 'HERE' +cat("This is a skeleton component\\n") +cat("The arguments are:\\n") +cat(" - input: ", par\$input, "\\n", sep = "") +cat(" - output: ", par\$output, "\\n", sep = "") +cat(" - option: ", par\$option, "\\n", sep = "") +cat("\\n") + +cat("Reading input file\\n") +lines <- readLines(par\$input) + +cat("Running output algorithm\\n") +new_lines <- paste0(par\$option, "-", lines) + +cat("Writing output file\\n") +writeLines(new_lines, con = par\$output) +HERE + +cat >> "\$out_dir/test.R" << HERE +library(testthat) + +# create dummy input file +old_lines <- c("one", "two", "three") +writeLines(old_lines, "input.txt") + +# run executable +system("./\$par_name --input input.txt --output output.txt --option FOO") + +# check whether output file exists +expect_true(file.exists("output.txt")) + +# check whether content matches expected content +expected_lines <- c("FOO-one", "FOO-two", "FOO-three") +new_lines <- readLines("output.txt") +expect_equal(new_lines, expected_lines) + +cat(">>> Test finished successfully!") +HERE + +################################################################################## +### PYTHON SCRIPTS ### +################################################################################## +elif [ \$script_lang == "python" ]; then +cat >> "\$out_dir/config.vsh.yaml" << HERE + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py +HERE + +cat >> "\$out_dir/script.py" << 'HERE' +print("This is a skeleton component") +print("The arguments are:") +print(" - input: ", par["input"]) +print(" - output: ", par["output"]) +print(" - option: ", par["option"]) +print("") + + +with open(par["input"], "r") as reader, open(par["output"], "w") as writer: + lines = reader.readlines() + + new_lines = [par["option"] + x for x in lines] + + writer.writelines(new_lines) +HERE + +cat >> "\$out_dir/test.py" << HERE +import unittest +import os +from os import path +import subprocess + + +with open("input.txt", "w") as writer: + writer.writelines(["one\\n", "two\\n", "three\\n"]) + + +class MyTest(unittest.TestCase): + def test_component(self): + out = subprocess.check_output(["./\$par_name", "--input", "input.txt", "--output", "output.txt", "--option", "FOO-"]).decode("utf-8") + + self.assertTrue(path.exists("output.txt")) + + with open("output.txt", "r") as reader: + lines = reader.readlines() + + self.assertEqual(lines, ["FOO-one\\n", "FOO-two\\n", "FOO-three\\n"]) + + +unittest.main() +HERE + +fi + +################################################################################## +### PLATFORMS ### +################################################################################## +# write platforms +cat >> "\$out_dir/config.vsh.yaml" << HERE +platforms: +HERE + +# iterate over different specified platforms +IFS=',' +set -f +for platform in \$par_platform; do + unset IFS + if [ \$platform == "docker" ]; then + + # choose different default docker image based on language + if [ \$script_lang == "bash" ]; then + cat >> "\$out_dir/config.vsh.yaml" << HERE + - type: docker + image: ubuntu:20.04 + setup: + - type: apt + packages: + - bash +HERE + + elif [ \$script_lang == "r" ]; then + cat >> "\$out_dir/config.vsh.yaml" << HERE + - type: docker + image: rocker/tidyverse:4.0.4 + setup: + - type: r + packages: + - princurve +HERE + + elif [ \$script_lang == "python" ]; then + cat >> "\$out_dir/config.vsh.yaml" << HERE + - type: docker + image: python:3.9.3-buster + setup: + - type: python + packages: + - numpy +HERE + fi + + elif [ \$platform == "native" ]; then + cat >> "\$out_dir/config.vsh.yaml" << HERE + - type: native +HERE + + elif [ \$platform == "nextflow" ]; then + cat >> "\$out_dir/config.vsh.yaml" << HERE + - type: nextflow +HERE + + fi +done +set +f + + + + +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/viash b/bin/viash index aff1be9f0f..649f03c7e2 120000 --- a/bin/viash +++ b/bin/viash @@ -1 +1 @@ -viash-0.4.0-rc1 \ No newline at end of file +viash-0.4.0 \ No newline at end of file diff --git a/bin/viash-0.4.0-rc1.REMOVED.git-id b/bin/viash-0.4.0-rc1.REMOVED.git-id deleted file mode 100644 index 5a44caa629..0000000000 --- a/bin/viash-0.4.0-rc1.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -e6357d56ed905dbf85b4651b9f4ba502d8c6354e \ No newline at end of file diff --git a/bin/viash-0.4.0.REMOVED.git-id b/bin/viash-0.4.0.REMOVED.git-id new file mode 100644 index 0000000000..54e7634593 --- /dev/null +++ b/bin/viash-0.4.0.REMOVED.git-id @@ -0,0 +1 @@ +f7e633e1ea26db7659361af2358f34db54fd2474 \ No newline at end of file diff --git a/bin/vshtrafo b/bin/vshtrafo new file mode 100755 index 0000000000..1372488be8 --- /dev/null +++ b/bin/vshtrafo @@ -0,0 +1,331 @@ +#!/usr/bin/env bash + +###################### +# vshtrafo 1.0 # +###################### + +# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VIASH_EXEC_MODE="run" + +function ViashSetup { +: +} + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "Transform viash formats." + echo + echo "Options:" + echo " -i file, --input=file" + echo " type: file, required parameter" + echo " Input file" + echo "" + echo " -o file, --output_dir=file" + echo " type: file, required parameter" + echo " Output directory" + echo "" + echo " -f string, --format=string" + echo " type: string, required parameter" + echo " Output format. Must be one of 'script', 'config'" + echo "" + echo " --rm" + echo " type: boolean_true" + echo " Remove the source files after use." + echo "" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit;; + ---setup) + VIASH_EXEC_MODE="setup" + shift 1 + ;; + ---push) + VIASH_EXEC_MODE="push" + shift 1 + ;; + --input) + VIASH_PAR_INPUT="$2" + shift 2 + ;; + --input=*) + VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -i) + VIASH_PAR_INPUT="$2" + shift 2 + ;; + --output_dir) + VIASH_PAR_OUTPUT_DIR="$2" + shift 2 + ;; + --output_dir=*) + VIASH_PAR_OUTPUT_DIR=$(ViashRemoveFlags "$1") + shift 1 + ;; + -o) + VIASH_PAR_OUTPUT_DIR="$2" + shift 2 + ;; + --format) + VIASH_PAR_FORMAT="$2" + shift 2 + ;; + --format=*) + VIASH_PAR_FORMAT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -f) + VIASH_PAR_FORMAT="$2" + shift 2 + ;; + --rm) + VIASH_PAR_RM=true + shift 1 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +if [ "$VIASH_EXEC_MODE" == "setup" ]; then + ViashSetup + exit 0 +fi + +if [ "$VIASH_EXEC_MODE" == "push" ]; then + ViashPush + exit 0 +fi + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +# check whether required parameters exist +if [ -z "$VIASH_PAR_INPUT" ]; then + echo '--input' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_OUTPUT_DIR" ]; then + echo '--output_dir' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_FORMAT" ]; then + echo '--format' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_RM" ]; then + VIASH_PAR_RM="false" +fi + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-vshtrafo-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_input='$VIASH_PAR_INPUT' +par_output_dir='$VIASH_PAR_OUTPUT_DIR' +par_format='$VIASH_PAR_FORMAT' +par_rm='$VIASH_PAR_RM' + +resources_dir="$VIASH_RESOURCES_DIR" + + +set -e + +# detect input type +input_dir=\$(dirname \$par_input) +if [[ "\$par_input" =~ ^.*\\.vsh\\.(sh|r|R|py)\$ ]]; then + input_type=script + input_ext=\`echo "\$par_input" | sed 's#.*\\.##'\` + + if [ "\$input_ext" = "sh" ]; then + script_type="bash" + elif [[ \$input_ext =~ ^[rR]\$ ]]; then + script_type="r" + elif [ "\$input_ext" = "py" ]; then + script_type="python" + else + echo "Unsupported format: \$input_ext!" + exit 1 + fi +elif [[ "\$par_input" =~ ^.*\\.vsh\\.(yaml|yml)\$ ]]; then + input_type=config +else + echo Input: unsupported format. + exit 1 +fi + +# create dir if it does not exist +[[ -d "\$par_output_dir" ]] || mkdir -p "\$par_output_dir" + +# check format +if [[ ! \$par_format =~ ^(script|config)\$ ]]; then + echo "Output: unsupported format. Must be one of 'script' or 'config'" + exit 1 +fi + +# ------------------------ X -> X ------------------------ +if [ \$input_type = \$par_format ]; then + echo Input type is equal to output type. + echo Just use cp, you son of a silly person. + cp "\$par_input" "\$par_output_dir/\$(basename \$par_input)" + +# ------------------------ SCRIPT -> CONFIG ------------------------ +elif [ \$input_type = "script" ] && [ \$par_format = "config" ]; then + echo "Converting from 'script' to 'config'" + + # determine output paths + config_yaml_relative="config.vsh.yaml" + config_yaml_path="\$par_output_dir/\$config_yaml_relative" + output_script_relative="\$(basename \$par_input | sed 's#\\.vsh\\.#.#')" + output_script_path="\$par_output_dir/\$output_script_relative" + + # WRITING CONFIG YAML + echo "> Writing config yaml to \$config_yaml_relative" + CONFIG_YAML=\$(cat "\$par_input" | grep "^#' " | sed "s/^#' //") + + # write yaml without resources + echo "\$CONFIG_YAML" | yq d - functionality.resources > "\$config_yaml_path" + + # add script to resources + printf "functionality:\\n resources:\\n - type: \${script_type}_script\\n path: \$output_script_relative\\n" | yq m "\$config_yaml_path" - -i + + # add other resources + has_resources=\`echo "\$CONFIG_YAML" | yq read - functionality.resources | head -1\` + if [ ! -z "\$has_resources" ]; then + echo "\$CONFIG_YAML" | yq read - functionality.resources | yq p - functionality.resources | yq m -a append "\$config_yaml_path" - -i + fi + + # WRITING SCRIPT + echo "> Writing script to \$output_script_relative" + cat "\$par_input" | grep -v "^#' " > "\$output_script_path" + + +# ------------------------ CONFIG -> SCRIPT ------------------------ +elif [ \$input_type = "config" ] && [ \$par_format = "script" ]; then + echo "Converting from 'config' to 'script'" + + # determine output paths + input_script_relative=\$(yq read "\$par_input" 'functionality.resources.[0].path') + input_script_path="\$input_dir/\$input_script_relative" + output_script_relative=\$(echo "\$input_script_relative" | sed 's#\\(\\.[^\\.]*\\)#.vsh\\1#') + output_script_path="\$par_output_dir/\$output_script_relative" + + # writing header + echo "> Writing script with header to \$output_script_relative" + yq delete "\$par_input" 'functionality.resources.[0]' | sed "s/^/#' /" > "\$output_script_path" + + # writing script + awk "/VIASH START/,/VIASH END/ { next; }; 1 {print; }" "\$input_script_path" >> "\$output_script_path" + awk "/VIASH START/,/VIASH END/ { next; }; 1 {print; }" "\$input_script_path" >> "\$output_script_path" + +# ------------------------ CONFIG -> SPLIT ------------------------ +elif [ \$input_type = "config" ] && [ \$par_format = "split" ]; then + echo "Converting from 'config' to 'split'" + + # determine output paths + funcionality_yaml_relative="functionality.yaml" + funcionality_yaml_path="\$par_output_dir/\$funcionality_yaml_relative" + + # WRITING FUNCTIONALITY YAML + echo "> Writing functionality yaml to \$funcionality_yaml_relative" + yq r "\$par_input" functionality > "\$funcionality_yaml_path" + + #### PLATFORM(S) + # create platform yamls + platforms=\$(yq read "\$par_input" platforms.*.type) + for plat in \$platforms; do + platform_yaml_relative="platform_\${plat}.yaml" + platform_yaml_path="\$par_output_dir/\$platform_yaml_relative" + echo "> Writing platform yaml to \$platform_yaml_relative" + yq read "\$par_input" platforms.[type==\$plat] > "\$platform_yaml_path" + done + + # copy script + input_script_relative=\$(yq read "\$par_input" 'functionality.resources.[0].path') + input_script_path="\$input_dir/\$input_script_relative" + output_script_path="\$par_output_dir/\$input_script_relative" + + if [ "\$input_script_path" != "\$output_script_path" ]; then + cp "\$input_script_path" "\$output_script_path" + fi + +fi +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF From 90a196989f5138b3f24530dfeb39d479fa3573f9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Apr 2021 16:55:50 +0200 Subject: [PATCH 0026/1233] refactor scot Former-commit-id: b1a1148f0ca1768711331149e50662e9a86d4e62 --- src/modality_alignment/methods/scot/scot.py | 69 +++++++++++---------- 1 file changed, 36 insertions(+), 33 deletions(-) diff --git a/src/modality_alignment/methods/scot/scot.py b/src/modality_alignment/methods/scot/scot.py index 4885015047..a30f3aaf69 100644 --- a/src/modality_alignment/methods/scot/scot.py +++ b/src/modality_alignment/methods/scot/scot.py @@ -8,43 +8,46 @@ resources_dir = "../../resources/utils.py" ## VIASH END +print("Loading dependencies") import scanpy as sc import sklearn.decomposition -import sys -sys.path.append(resources_dir) +from SCOT import SCOT # importing helper functions from common preprocessing.py file in resources dir +import sys +sys.path.append(resources_dir) from preprocessing import log_cpm from preprocessing import sqrt_cpm -def _scot(adata, n_svd=100, balanced=False): - from SCOT import SCOT - - # PCA reduction - n_svd = min([n_svd, min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) - X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) - Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) - - # Initialize SCOT - scot = SCOT(X_pca, Y_pca) - - # call the unbalanced alignment - # From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 - X_new_unbal, y_new_unbal = scot.align( - k=50, e=1e-3, rho=0.0005, normalize=True, balanced=balanced - ) - adata.obsm["aligned"] = X_new_unbal - adata.obsm["mode2_aligned"] = y_new_unbal - - return adata - -if __name__ == "__main__": - adata = sc.read_h5ad(par["input"]) - # Normalize mode1 - sqrt_cpm(adata) - # Normalize mode2 - log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") - # run scot - _scot(adata, n_svd=par["n_svd"], balanced=par["balanced"]) - # Write output to file - adata.write_h5ad(par["output"], compression=9) + +print("Reading input h5ad file") +adata = sc.read_h5ad(par["input"]) + +print("Normalising mode 1") +sqrt_cpm(adata) + +print("Normalising mode 2") +log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") + + +print("Performing PCA reduction") +n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) +X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) +Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) + +print("Initialize SCOT") +scot = SCOT(X_pca, Y_pca) + +print("Call the unbalanced alignment") +# From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 +X_new_unbal, y_new_unbal = scot.align( + k=50, e=1e-3, rho=0.0005, normalize=True, balanced=par["balanced"] +) + +print() +adata.obsm["aligned"] = X_new_unbal +adata.obsm["mode2_aligned"] = y_new_unbal + +print("Write output to file") +adata.uns["method_name"] = "scot" +adata.write(par["output"], compression="gzip") From 93dc754fa7bf09b8fbc4fb470e557a50c14a6886 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Apr 2021 16:55:59 +0200 Subject: [PATCH 0027/1233] refactor extract scores Former-commit-id: fc0ed288e74761922fef6aca3fdce0fbec494bd1 --- src/utils/extract_scores/config.vsh.yaml | 2 ++ src/utils/extract_scores/script.R | 12 ++++++++++-- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/src/utils/extract_scores/config.vsh.yaml b/src/utils/extract_scores/config.vsh.yaml index e4214aaec0..7f37b66c1b 100644 --- a/src/utils/extract_scores/config.vsh.yaml +++ b/src/utils/extract_scores/config.vsh.yaml @@ -23,3 +23,5 @@ platforms: - type: docker image: "dataintuitive/randpy:r4.0_bioc3.12" # contains a few bioconductor and the 'anndata' package - type: nextflow + publish: true + per_id: false diff --git a/src/utils/extract_scores/script.R b/src/utils/extract_scores/script.R index b85de62613..37636bb7fb 100644 --- a/src/utils/extract_scores/script.R +++ b/src/utils/extract_scores/script.R @@ -1,19 +1,27 @@ ## VIASH START par <- list( - input = list.files("out_bash/modality_alignment/metrics/", full.names = TRUE), + input = list.files("work", full.names = TRUE, pattern = "*.h5ad"), output = "out_bash/modality_alignment/scores.tsv" ) -inp <- par$input[[1]] +inp <- par$input[[2]] ## VIASH END cat("Loading dependencies\n") library(anndata, warn.conflicts = FALSE) options(tidyverse.quiet = TRUE) library(tidyverse) +library(assertthat) cat("Reading input h5ad files") scores <- map_df(par$input, function(inp) { + cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) + + assert_that("dataset_name" %in% names(ad$uns)) + assert_that("method_name" %in% names(ad$uns)) + assert_that("metric_name" %in% names(ad$uns)) + assert_that("metric_value" %in% names(ad$uns)) + as_tibble(ad$uns[c("dataset_name", "method_name", "metric_name", "metric_value")]) }) From 3f62a310d462c6c831cbfb13dc64b7e9a3cc7b03 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Apr 2021 16:56:26 +0200 Subject: [PATCH 0028/1233] rework nxf pipeline Former-commit-id: 2b6bf71fd6ed9a1330cde9e586f7171122d57d1f --- main.nf | 68 +++++++++++++++++++++++---------------------- nextflow.config | 2 ++ run_nxf_pipeline.sh | 2 +- 3 files changed, 38 insertions(+), 34 deletions(-) diff --git a/main.nf b/main.nf index 1769277d48..a85d2fc863 100644 --- a/main.nf +++ b/main.nf @@ -1,45 +1,47 @@ -nextflow.preview.dsl=2 +nextflow.enable.dsl=2 moduleRoot="./target/nextflow/modality_alignment/" -include { citeseq_cbmc } from moduleRoot + 'datasets/citeseq_cbmc/main.nf' params(params) -include { mnn } from moduleRoot + 'methods/mnn/main.nf' params(params) -include { knn_auc } from moduleRoot + 'metrics/knn_auc/main.nf' params(params) - +include { citeseq_cbmc } from moduleRoot + 'datasets/citeseq_cbmc/main.nf' params(params) +include { mnn } from moduleRoot + 'methods/mnn/main.nf' params(params) +include { scot } from moduleRoot + 'methods/scot/main.nf' params(params) +include { knn_auc } from moduleRoot + 'metrics/knn_auc/main.nf' params(params) +include { extract_scores } from './target/nextflow/utils/extract_scores/main.nf' params(params) workflow { + // helper functions + // set id of event to basename of input file + def updateID = { [ it[1].baseName, it[1], it[2] ] } + // turn list of triplets into triplet of list + def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } + + // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 + // fetch datasets - data_citeseq_cbmc = Channel.fromPath( "dummy" ) \ - | map{ [ "dyngen", it, params] } \ + data_citeseq_cbmc = Channel.fromPath( "citeseq_cbmc" ) \ + | map{ [ "citeseq_cbmc", it, params] } \ | citeseq_cbmc - // add more datasets here - // data_... = ... - // combine datasets in one channel datasets = data_citeseq_cbmc - // when more datasets are available: - // datasets = data_citeseq_cbmc.mix(data_..., data_...) - - // apply methods to datasets - method_outputs = datasets \ - | mnn - /* - method_outputs = datasets \ - | (mnn & method2 & method3) \ - | mix - */ - - // apply metrics to outputs - method_evals = method_outputs \ - | knn_auc - /* - method_evals = method_outputs \ - | (knn_auc & metric2 & metric3) \ - | mix - */ - // TODO: do something with 'method_evals' - method_evals \ - | view{ [ it[0], it[1] ] } + // when more datasets are available, replace the code above with: + // datasets = data_citeseq_cbmc.mix(data_2, data_3) + + datasets \ + | (mnn & scot) \ + | mix \ + | map(updateID) \ + | knn_auc \ + | map(updateID) \ + | toSortedList \ + | map( combineResults ) \ + | extract_scores + + + /* When more metrics become available, replace '| knn_auc \' with the following: + | (knn_auc & metric2 & metric3) \ + | mix \ + */ + } diff --git a/nextflow.config b/nextflow.config index df80ce5d68..035991fb41 100644 --- a/nextflow.config +++ b/nextflow.config @@ -4,7 +4,9 @@ manifest { includeConfig 'target/nextflow/modality_alignment/datasets/citeseq_cbmc/nextflow.config' includeConfig 'target/nextflow/modality_alignment/methods/mnn/nextflow.config' +includeConfig 'target/nextflow/modality_alignment/methods/scot/nextflow.config' includeConfig 'target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config' +includeConfig 'target/nextflow/utils/extract_scores/nextflow.config' docker { runOptions = "-i -v ${baseDir}:${baseDir}" diff --git a/run_nxf_pipeline.sh b/run_nxf_pipeline.sh index d4cc3e9f83..8ae032e532 100755 --- a/run_nxf_pipeline.sh +++ b/run_nxf_pipeline.sh @@ -3,5 +3,5 @@ # Run this prior to executing this script: # bin/project_build -NXF_VER=20.04.1-edge nextflow run main.nf -resume +NXF_VER=20.10.0 nextflow run main.nf -resume From 6c121871a23bc40e81d8df20970679f0fed55a25 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Apr 2021 20:48:18 +0200 Subject: [PATCH 0029/1233] add output folder to nextflow.config Former-commit-id: d5a0a64d5aaf536fb9cd2748d339ba5defd48380 --- .gitignore | 1 + nextflow.config | 2 ++ 2 files changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 408bc27ea5..66b27b7857 100644 --- a/.gitignore +++ b/.gitignore @@ -14,3 +14,4 @@ log.txt # nextflow specific ignores .nextflow* work +out_nxf diff --git a/nextflow.config b/nextflow.config index 035991fb41..a664ae77b3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,3 +22,5 @@ k8s { pullPolicy = 'Always' imagePullPolicy = 'Always' } + +params.output = "out_nxf" From 9559484af7a9e20e4bdcbb0e367d3bbf1db9f8cf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 15 Apr 2021 11:02:19 +0200 Subject: [PATCH 0030/1233] allow multiple datasets per dataset component Former-commit-id: db1b71485e25a1c384aca15766961b8826cfe0fa --- main.nf | 10 ++++++++-- .../datasets/citeseq_cbmc/config.vsh.yaml | 8 ++++---- .../datasets/citeseq_cbmc/script.py | 16 ++++++++-------- 3 files changed, 20 insertions(+), 14 deletions(-) diff --git a/main.nf b/main.nf index a85d2fc863..1cd275765b 100644 --- a/main.nf +++ b/main.nf @@ -18,8 +18,14 @@ workflow { // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 // fetch datasets - data_citeseq_cbmc = Channel.fromPath( "citeseq_cbmc" ) \ - | map{ [ "citeseq_cbmc", it, params] } \ + data_citeseq_cbmc = Channel.fromList( [ + [ + "citeseq_cbmc", + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" + ] + ] ) \ + | map { [ it[0], [ "input1": file(it[1]), "input2": file(it[2]) ], params ]} \ | citeseq_cbmc // combine datasets in one channel diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index fb958cefb2..7a933cecc5 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -10,12 +10,12 @@ functionality: cell_types: "CL:2000001" # peripheral blood mononuclear cells technology: "dropseq" arguments: - - name: "--input_rna" - type: "string" + - name: "--input1" + type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" description: "Path or URL to the RNA counts as a gzipped csv file." - - name: "--input_adt" - type: "string" + - name: "--input2" + type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" description: "Path or URL to the ADT counts as a gzipped csv file." - name: "--test" diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index ad8d0beb2d..4d4bc99795 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -2,8 +2,8 @@ # The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. par = { - "input_rna": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", - "input_adt": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", + "input1": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", + "input2": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", "output": "output.h5ad", "test": False } @@ -27,16 +27,16 @@ print("Downloading expression datasets from GEO (this might take a while)") sys.stdout.flush() -# par["input_rna"] can be the path to a local file, or a url -rna_data = scprep.io.load_csv( - par["input_rna"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 +# par["input1"] can be the path to a local file, or a url +adata1 = scprep.io.load_csv( + par["input1"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 ) -adt_data = scprep.io.load_csv( - par["input_adt"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 +adata2 = scprep.io.load_csv( + par["input2"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 ) print("Transforming into adata") -adata = create_joint_adata(rna_data, adt_data) +adata = create_joint_adata(adata1, adata2) adata = filter_joint_data_empty_cells(adata) adata.uns["dataset_name"] = "citeseq_cbmc" From 2891eb0e86dad7fb25b36d22ca34a5df9d4d08ab Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 15 Apr 2021 13:31:09 +0200 Subject: [PATCH 0031/1233] turn dataset id into a parameter Former-commit-id: 3a6d7a3ff000fa30969d1b0c3b4bbbfc5db7aa0d --- main.nf | 36 ++++++++++++++++--- .../datasets/citeseq_cbmc/config.vsh.yaml | 4 +++ .../datasets/citeseq_cbmc/script.py | 5 +-- 3 files changed, 38 insertions(+), 7 deletions(-) diff --git a/main.nf b/main.nf index 1cd275765b..2fd95ca814 100644 --- a/main.nf +++ b/main.nf @@ -8,12 +8,37 @@ include { scot } from moduleRoot + 'methods/scot/main.nf' include { knn_auc } from moduleRoot + 'metrics/knn_auc/main.nf' params(params) include { extract_scores } from './target/nextflow/utils/extract_scores/main.nf' params(params) +// helper functions +// set id of event to basename of input file +def updateID = { [ it[1].baseName, it[1], it[2] ] } +// turn list of triplets into triplet of list +def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } +// A functional approach to 'updating' a value for an option in the params Map. +def overrideOptionValue(triplet, _key, _option, _value) { + mapCopy = triplet[2].toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy + + return [ + triplet[0], + triplet[1], + triplet[2].collectEntries{ function, v1 -> + (function == _key) + ? [ (function) : v1.collectEntries{ k2, v2 -> + (k2 == "arguments") + ? [ (k2) : v2.collectEntries{ k3, v3 -> + (k3 == _option) + ? [ (k3) : v3 + [ "value" : _value ] ] + : [ (k3) : v3 ] + } ] + : [ (k2) : v2 ] + } ] + : [ (function), v1 ] + } + ] +} + + workflow { - // helper functions - // set id of event to basename of input file - def updateID = { [ it[1].baseName, it[1], it[2] ] } - // turn list of triplets into triplet of list - def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } + // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 @@ -26,6 +51,7 @@ workflow { ] ] ) \ | map { [ it[0], [ "input1": file(it[1]), "input2": file(it[2]) ], params ]} \ + | map { overrideOptionValue(it, "citeseq_cbmc", "id", it[0]) } \ | citeseq_cbmc // combine datasets in one channel diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml index 7a933cecc5..6d50bb0cb5 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml @@ -10,6 +10,10 @@ functionality: cell_types: "CL:2000001" # peripheral blood mononuclear cells technology: "dropseq" arguments: + - name: "--id" + type: "string" + default: "citeseq_cbmc" + description: "The id of the output dataset id" - name: "--input1" type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/citeseq_cbmc/script.py index 4d4bc99795..a94b193f57 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/citeseq_cbmc/script.py @@ -2,6 +2,7 @@ # The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. par = { + "id": "citeseq_cbmc", "input1": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", "input2": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", "output": "output.h5ad", @@ -39,12 +40,12 @@ adata = create_joint_adata(adata1, adata2) adata = filter_joint_data_empty_cells(adata) -adata.uns["dataset_name"] = "citeseq_cbmc" +adata.uns["dataset_name"] = par["id"] if par["test"]: print("Subsetting dataset") adata = subset_joint_data(adata) - adata.uns["dataset_name"] = "citeseq_cbmc_test" + adata.uns["dataset_name"] = par["id"] + "_test" print("Writing adata to file") adata.write(par["output"], compression = "gzip") \ No newline at end of file From 7864eb724c3987df1cf072bf0b751c978968d219 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 15 Apr 2021 15:49:10 +0200 Subject: [PATCH 0032/1233] add concept metadata for datasets as tsv Former-commit-id: b1af753b5d72c666ab797f44e3e9ba4ebd01e4a0 --- src/modality_alignment/datasets/datasets.tsv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 src/modality_alignment/datasets/datasets.tsv diff --git a/src/modality_alignment/datasets/datasets.tsv b/src/modality_alignment/datasets/datasets.tsv new file mode 100644 index 0000000000..5a4f891674 --- /dev/null +++ b/src/modality_alignment/datasets/datasets.tsv @@ -0,0 +1,2 @@ +id input1 input2 format compression accession_id doi organism cell_types technology +CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz csv gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq From 298703a1246b054f49cc0d12baa1f734f977710c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 11:17:07 +0200 Subject: [PATCH 0033/1233] rename dataset component Former-commit-id: 4505a28e2c7145545fa53b3e3e6fd554744a9799 --- .../config.vsh.yaml | 17 ++++++++--------- .../{citeseq_cbmc => scprep_csv}/script.py | 9 +++++---- 2 files changed, 13 insertions(+), 13 deletions(-) rename src/modality_alignment/datasets/{citeseq_cbmc => scprep_csv}/config.vsh.yaml (69%) rename src/modality_alignment/datasets/{citeseq_cbmc => scprep_csv}/script.py (84%) diff --git a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml similarity index 69% rename from src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml rename to src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 6d50bb0cb5..b6628c57b7 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -1,14 +1,8 @@ functionality: - name: "citeseq_cbmc" + name: "scprep_csv" namespace: "modality_alignment/datasets" version: "dev" - description: "CITE-seq Cord Blood Mononuclear Cells" - info: - accession_id: "GSE100866" - doi: "10.1038/nmeth.4380" - organism: "human" - cell_types: "CL:2000001" # peripheral blood mononuclear cells - technology: "dropseq" + description: "Create a modality alignment dataset from CSV using scprep." arguments: - name: "--id" type: "string" @@ -25,12 +19,17 @@ functionality: - name: "--test" type: "boolean_true" description: "Subset the dataset" + - name: "--compression" + type: "string" + default: "csv" + description: "For on-the-fly decompression of on-disk data. If 'infer' and filepath_or_buffer is path-like, then detect compression from the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise no decompression). If using 'zip', the ZIP file must contain only one data file to be read in. Set to None for no decompression." - name: "--output" alternatives: ["-o"] type: "file" direction: "output" default: "output.h5ad" - description: "Output h5ad file containing both RNA and ADT data" + description: "Output h5ad file containing both input matrices data" + required: true resources: - type: python_script path: ./script.py diff --git a/src/modality_alignment/datasets/citeseq_cbmc/script.py b/src/modality_alignment/datasets/scprep_csv/script.py similarity index 84% rename from src/modality_alignment/datasets/citeseq_cbmc/script.py rename to src/modality_alignment/datasets/scprep_csv/script.py index a94b193f57..651c6176bf 100644 --- a/src/modality_alignment/datasets/citeseq_cbmc/script.py +++ b/src/modality_alignment/datasets/scprep_csv/script.py @@ -6,7 +6,8 @@ "input1": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", "input2": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", "output": "output.h5ad", - "test": False + "test": False, + "compression" = "gzip" } resources_dir = "../../resources/" ## VIASH END @@ -30,10 +31,10 @@ # par["input1"] can be the path to a local file, or a url adata1 = scprep.io.load_csv( - par["input1"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 + par["input1"], cell_axis="col", compression=par["compression"], sparse=True, chunksize=1000 ) adata2 = scprep.io.load_csv( - par["input2"], cell_axis="col", compression="gzip", sparse=True, chunksize=1000 + par["input2"], cell_axis="col", compression=par["compression"], sparse=True, chunksize=1000 ) print("Transforming into adata") @@ -48,4 +49,4 @@ adata.uns["dataset_name"] = par["id"] + "_test" print("Writing adata to file") -adata.write(par["output"], compression = "gzip") \ No newline at end of file +adata.write(par["output"], compression = "gzip") From d6ad6aa0e95f4722d26e31d704352b822a27de49 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 11:45:19 +0200 Subject: [PATCH 0034/1233] move pipeline Former-commit-id: 0d50b9715385f62e212caf0ebffcaa657d669192 --- nextflow.config | 26 ------------------ run_nxf_pipeline.sh | 7 ----- .../modality_alignment/workflows/main.nf | 27 +++++++++++-------- .../workflows/nextflow.config | 24 +++++++++++++++++ .../modality_alignment/workflows/run_bash.sh | 15 ++++++++--- .../workflows/run_nextflow.sh | 15 +++++++++++ 6 files changed, 66 insertions(+), 48 deletions(-) delete mode 100644 nextflow.config delete mode 100755 run_nxf_pipeline.sh rename main.nf => src/modality_alignment/workflows/main.nf (70%) create mode 100644 src/modality_alignment/workflows/nextflow.config rename run_bash_pipeline.sh => src/modality_alignment/workflows/run_bash.sh (74%) create mode 100755 src/modality_alignment/workflows/run_nextflow.sh diff --git a/nextflow.config b/nextflow.config deleted file mode 100644 index a664ae77b3..0000000000 --- a/nextflow.config +++ /dev/null @@ -1,26 +0,0 @@ -manifest { - nextflowVersion = '!>=20.04.0-edge' -} - -includeConfig 'target/nextflow/modality_alignment/datasets/citeseq_cbmc/nextflow.config' -includeConfig 'target/nextflow/modality_alignment/methods/mnn/nextflow.config' -includeConfig 'target/nextflow/modality_alignment/methods/scot/nextflow.config' -includeConfig 'target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config' -includeConfig 'target/nextflow/utils/extract_scores/nextflow.config' - -docker { - runOptions = "-i -v ${baseDir}:${baseDir}" -} - -process { - maxForks = 30 - container = 'ubuntu' - errorStrategy='ignore' -} - -k8s { - pullPolicy = 'Always' - imagePullPolicy = 'Always' -} - -params.output = "out_nxf" diff --git a/run_nxf_pipeline.sh b/run_nxf_pipeline.sh deleted file mode 100755 index 8ae032e532..0000000000 --- a/run_nxf_pipeline.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/project_build - -NXF_VER=20.10.0 nextflow run main.nf -resume - diff --git a/main.nf b/src/modality_alignment/workflows/main.nf similarity index 70% rename from main.nf rename to src/modality_alignment/workflows/main.nf index 2fd95ca814..0ca99a21bd 100644 --- a/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -1,12 +1,17 @@ nextflow.enable.dsl=2 -moduleRoot="./target/nextflow/modality_alignment/" +opscaRoot = "../../../" +targetDir = opscaRoot + "target/nextflow/" +taskDir = targetDir + "modality_alignment/" -include { citeseq_cbmc } from moduleRoot + 'datasets/citeseq_cbmc/main.nf' params(params) -include { mnn } from moduleRoot + 'methods/mnn/main.nf' params(params) -include { scot } from moduleRoot + 'methods/scot/main.nf' params(params) -include { knn_auc } from moduleRoot + 'metrics/knn_auc/main.nf' params(params) -include { extract_scores } from './target/nextflow/utils/extract_scores/main.nf' params(params) +println(baseDir) + +include { scprep_csv } from '../../../target/nextflow/modality_alignment/datasets/scprep_csv/main.nf' params(params) +// include { scprep_csv } from taskDir + 'datasets/scprep_csv/main.nf' params(params) +include { mnn } from taskDir + 'methods/mnn/main.nf' params(params) +include { scot } from taskDir + 'methods/scot/main.nf' params(params) +include { knn_auc } from taskDir + 'metrics/knn_auc/main.nf' params(params) +include { extract_scores } from targetDir + 'utils/extract_scores/main.nf' params(params) // helper functions // set id of event to basename of input file @@ -43,19 +48,19 @@ workflow { // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 // fetch datasets - data_citeseq_cbmc = Channel.fromList( [ + data_scprep_csv = Channel.fromList( [ [ - "citeseq_cbmc", + "CBMC_8K_13AB_10x", "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" ] ] ) \ | map { [ it[0], [ "input1": file(it[1]), "input2": file(it[2]) ], params ]} \ - | map { overrideOptionValue(it, "citeseq_cbmc", "id", it[0]) } \ - | citeseq_cbmc + | map { overrideOptionValue(it, "scprep_csv", "id", it[0]) } \ + | scprep_csv // combine datasets in one channel - datasets = data_citeseq_cbmc + datasets = data_scprep_csv // when more datasets are available, replace the code above with: // datasets = data_citeseq_cbmc.mix(data_2, data_3) diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config new file mode 100644 index 0000000000..91b26ffd12 --- /dev/null +++ b/src/modality_alignment/workflows/nextflow.config @@ -0,0 +1,24 @@ +manifest { + nextflowVersion = '!>=20.10.0' +} + +includeConfig '../../../target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config' +includeConfig '../../../target/nextflow/modality_alignment/methods/mnn/nextflow.config' +includeConfig '../../../target/nextflow/modality_alignment/methods/scot/nextflow.config' +includeConfig '../../../target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config' +includeConfig '../../../target/nextflow/utils/extract_scores/nextflow.config' + +docker { + runOptions = "-i -v ${baseDir}:${baseDir}" +} + +process { + maxForks = 30 + container = 'ubuntu' + errorStrategy='ignore' +} + +k8s { + pullPolicy = 'Always' + imagePullPolicy = 'Always' +} diff --git a/run_bash_pipeline.sh b/src/modality_alignment/workflows/run_bash.sh similarity index 74% rename from run_bash_pipeline.sh rename to src/modality_alignment/workflows/run_bash.sh index 5329d071c4..ecc0f52dca 100755 --- a/run_bash_pipeline.sh +++ b/src/modality_alignment/workflows/run_bash.sh @@ -1,10 +1,16 @@ #!/bin/bash # Run this prior to executing this script: -# bin/project_build +# bin/project_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" TARGET=target/docker/modality_alignment -OUTPUT=out_bash/modality_alignment +OUTPUT=output_bash/modality_alignment mkdir -p $OUTPUT/datasets mkdir -p $OUTPUT/methods @@ -12,7 +18,8 @@ mkdir -p $OUTPUT/metrics # generate datasets if [ ! -f "$OUTPUT/datasets/citeseq_cbmc.h5ad" ]; then - "$TARGET/datasets/citeseq_cbmc/citeseq_cbmc" --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" + "$TARGET/datasets/data_scprep_csv/data_scprep_csv" \ + --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" fi # run all methods on all datasets @@ -43,4 +50,4 @@ done # concatenate all scores into one tsv INPUTS=$(ls -1 "$OUTPUT/metrics" | sed "s#.*#-i '$OUTPUT/metrics/&'#" | tr '\n' ' ') -eval "$TARGET/utils/docker/utils/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" \ No newline at end of file +eval "$TARGET/../utils/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh new file mode 100755 index 0000000000..16258e9dd3 --- /dev/null +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/project_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/main.nf \ + -resume \ + --output output/modality_alignment + From 80c7897c5f7f8b66a7c6bca17651b172e1d7aa38 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 13:56:54 +0200 Subject: [PATCH 0035/1233] fix default argument Former-commit-id: 3a90e2bc215a72b16a20d2c7947d423ae0bb35cf --- src/modality_alignment/datasets/scprep_csv/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index b6628c57b7..45ad125fb8 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -21,7 +21,7 @@ functionality: description: "Subset the dataset" - name: "--compression" type: "string" - default: "csv" + default: "gzip" description: "For on-the-fly decompression of on-disk data. If 'infer' and filepath_or_buffer is path-like, then detect compression from the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise no decompression). If using 'zip', the ZIP file must contain only one data file to be read in. Set to None for no decompression." - name: "--output" alternatives: ["-o"] From 4d8a93952393798d325db3b50421e8a569a13504 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 13:57:21 +0200 Subject: [PATCH 0036/1233] rework pipeline Former-commit-id: ed1b9f3344c88f4301861ffde00d98fd6821b1bb --- src/modality_alignment/workflows/main.nf | 51 +++++-------------- .../workflows/nextflow.config | 17 +++---- src/utils/workflows/utils.nf | 37 ++++++++++++++ 3 files changed, 55 insertions(+), 50 deletions(-) create mode 100644 src/utils/workflows/utils.nf diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 0ca99a21bd..84ee207cc3 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -1,50 +1,23 @@ nextflow.enable.dsl=2 -opscaRoot = "../../../" -targetDir = opscaRoot + "target/nextflow/" -taskDir = targetDir + "modality_alignment/" +println "projectDir : $projectDir" +println "launchDir : $launchDir" -println(baseDir) +targetDir = "$launchDir/target/nextflow" -include { scprep_csv } from '../../../target/nextflow/modality_alignment/datasets/scprep_csv/main.nf' params(params) -// include { scprep_csv } from taskDir + 'datasets/scprep_csv/main.nf' params(params) -include { mnn } from taskDir + 'methods/mnn/main.nf' params(params) -include { scot } from taskDir + 'methods/scot/main.nf' params(params) -include { knn_auc } from taskDir + 'metrics/knn_auc/main.nf' params(params) -include { extract_scores } from targetDir + 'utils/extract_scores/main.nf' params(params) +include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) +include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) +include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) +include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) + +// import helper functions +include { overrideOptionValue } from "../../../src/utils/workflows/utils.nf" -// helper functions -// set id of event to basename of input file def updateID = { [ it[1].baseName, it[1], it[2] ] } -// turn list of triplets into triplet of list def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } -// A functional approach to 'updating' a value for an option in the params Map. -def overrideOptionValue(triplet, _key, _option, _value) { - mapCopy = triplet[2].toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy - - return [ - triplet[0], - triplet[1], - triplet[2].collectEntries{ function, v1 -> - (function == _key) - ? [ (function) : v1.collectEntries{ k2, v2 -> - (k2 == "arguments") - ? [ (k2) : v2.collectEntries{ k3, v3 -> - (k3 == _option) - ? [ (k3) : v3 + [ "value" : _value ] ] - : [ (k3) : v3 ] - } ] - : [ (k2) : v2 ] - } ] - : [ (function), v1 ] - } - ] -} - workflow { - - // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 // fetch datasets @@ -81,4 +54,4 @@ workflow { | mix \ */ -} +} \ No newline at end of file diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index 91b26ffd12..d810cde8a0 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -2,14 +2,14 @@ manifest { nextflowVersion = '!>=20.10.0' } -includeConfig '../../../target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config' -includeConfig '../../../target/nextflow/modality_alignment/methods/mnn/nextflow.config' -includeConfig '../../../target/nextflow/modality_alignment/methods/scot/nextflow.config' -includeConfig '../../../target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config' -includeConfig '../../../target/nextflow/utils/extract_scores/nextflow.config' +includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/methods/mnn/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/methods/scot/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config" +includeConfig "$launchDir/target/nextflow/utils/extract_scores/nextflow.config" docker { - runOptions = "-i -v ${baseDir}:${baseDir}" + runOptions = "-v $launchDir:$launchDir" } process { @@ -17,8 +17,3 @@ process { container = 'ubuntu' errorStrategy='ignore' } - -k8s { - pullPolicy = 'Always' - imagePullPolicy = 'Always' -} diff --git a/src/utils/workflows/utils.nf b/src/utils/workflows/utils.nf new file mode 100644 index 0000000000..e943163163 --- /dev/null +++ b/src/utils/workflows/utils.nf @@ -0,0 +1,37 @@ +// helper functions +// set id of event to basename of input file +//def updateID = { [ it[1].baseName, it[1], it[2] ] } +def updateID(triplet) { + return [ triplet[1].baseName, triplet[1], triplet[2] ] + } + + +// turn list of triplets into triplet of list +//def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } +def combineResults(list) { + return [ "combined", list.collect{ a -> a[1] }, params ] + } + + +// A functional approach to 'updating' a value for an option in the params Map. +def overrideOptionValue(triplet, _key, _option, _value) { + mapCopy = triplet[2].toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy + + return [ + triplet[0], + triplet[1], + triplet[2].collectEntries{ function, v1 -> + (function == _key) + ? [ (function) : v1.collectEntries{ k2, v2 -> + (k2 == "arguments") + ? [ (k2) : v2.collectEntries{ k3, v3 -> + (k3 == _option) + ? [ (k3) : v3 + [ "value" : _value ] ] + : [ (k3) : v3 ] + } ] + : [ (k2) : v2 ] + } ] + : [ (function), v1 ] + } + ] +} From bc691d22b973559aba0a71e27c302f9877dfc29d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 13:57:27 +0200 Subject: [PATCH 0037/1233] update git ignores Former-commit-id: 2c83e757915ac83673794ef1bf118ee6a664d3aa --- .gitignore | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index 66b27b7857..ca0b3926c8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,5 @@ # repo specific ignores -out_bash +output_bash *.h5ad # R specific ignores @@ -14,4 +14,4 @@ log.txt # nextflow specific ignores .nextflow* work -out_nxf +output From aa473ffa5a359a8486e79bd25423012554683daa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 14:19:05 +0200 Subject: [PATCH 0038/1233] update readme Former-commit-id: 23a614b486510b4b804fbaf1f68afb9bb8583aad --- README.md | 175 +++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 127 insertions(+), 48 deletions(-) diff --git a/README.md b/README.md index b3de316922..af2903341f 100644 --- a/README.md +++ b/README.md @@ -4,85 +4,164 @@ Proof Of Concept in adapting Open Problems to use viash. ## Requirements To use this repository, make sure you have Bash, Java, and Docker installed. If you wish to use Nextflow, install that too. -## Building the pipeline -To build all the components in `src` to `target`, run: +## Quick start -```sh +Running the modality alignment pipeline requires two simple steps. + +First, by running the command below, viash will build all the components in the `src/` folder as executables in the `target/` folder. + +```bash bin/project_build ``` -Note that this will also build docker containers for each of the components. The first time, this might take a while. +Next, to run the pipeline with nextflow, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: -## Running a simple pipeline with Bash +``` +$ src/modality_alignment/workflows/run_nextflow.sh +[86/3d1927] process > scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[00/b3528e] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[75/bfdbb1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[bc/da3dce] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ +[b9/e083fe] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ +Completed at: 19-Apr-2021 13:18:26 +Duration : 3m 30s +CPU hours : 0.1 +Succeeded : 6 +``` -Inspect the contents of the sample Bash pipeline in `run_bash_pipeline.sh`, then run it. +## Project structure -```sh -./run_bash_pipeline.sh +``` +bin/ Helper scripts for building the project and developing a new component. +src/ Source files for each component in the pipeline. + modality_alignment/ Source files related to the 'Modality alignment' task. + datasets/ Dataset downloader components. + methods/ Modality alignment method components. + metrics/ Modality alignment metric components. + resources/ Helper files. + workflow/ The pipeline workflow for this task. + utils/ Helper files. +target/ Executables generated by viash based on the components listed under `src/`. + docker/ Bash executables which can be used from a terminal. + nextflow/ Nextflow modules which can be used in a Nextflow pipeline. +work/ A working directory used by Nextflow. +output/ Output generated by the pipeline. ``` -Some components might take a while to run. In the end, the `out_bash/` folder will have been populated with a lot of h5ad files, and a `scores.tsv` file. +## Adding a component with viash -## Running a simple pipeline with Nextflow +[`viash`](https://github.com/data-intuitive/viash) allows you to create pipelines +in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. -Inspect the contents of the sample bash pipeline in `run_nxf_pipeline.sh`, then run it. +### Create a skeleton component +You can start creating a new component using `bin/skeleton`. For example to create +a new Python-based viahs component in the `src/modality_alignment/methods/foo` folder, run: +You can start creating a new component by using the `bin/skeleton` command: -``` -$ ./run_nxf_pipeline.sh -N E X T F L O W ~ version 20.04.1-edge -Launching `main.nf` [suspicious_lavoisier] - revision: f6dca0e8d5 -WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE -executor > local (3) -[16/e727b4] process > citeseq_cbmc:citeseq_cbmc_process (dyngen) [100%] 1 of 1 ✔ -[85/88774c] process > mnn:mnn_process (dyngen) [100%] 1 of 1 ✔ -[1e/9593dd] process > knn_auc:knn_auc_process (dyngen) [100%] 1 of 1 ✔ -WARN: Access to undefined parameter `debug` -- Initialise it to a default value eg. `params.debug = some_value` -Completed at: 06-Apr-2021 22:52:43 -Duration : 2m 46s -CPU hours : (a few seconds) -Succeeded : 3 +```bash +bin/skeleton --name foo --namespace "modality_alignment/methods" --language python + +# or: +bin/skeleton -n foo -ns "modality_alignment/methods" -l python ``` -Again, some components might take a while to run. +This should create a few files in this folder: +``` +script.py A python script for you to edit. +config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. +test.py A python script with which you can start unit testing your component. +``` + +The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site +provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). -## Component development with viash +### Trying out the component -You can run, build, or test a component individually with `bin/viash`. +`viash` has several helper functions to help you quickly develop a component. -A tutorial on how to create components with viash can be found at -[github.com/data-intuitive/viash\_tutorial\_1](https://github.com/data-intuitive/viash_tutorial_1). +With **`viash build`**, you can turn the component into a standalone executable. +This standalone executable you can give to somebody else, and they will be able to +run it, provided that they have Bash and Docker installed. +``` +viash build src/modality_alignment/methods/foo/config.vsh.yaml \ + -o target/docker/modality_alignment/methods/foo \ + --setup +``` -More documentation is available at -[data-intuitive.com/viash\_docs](https://www.data-intuitive.com/viash_docs) (WIP). +**Command-line interface**: You can view the interface of the executable by running the executable with the `-h` parameter. +``` +$ target/docker/modality_alignment/methods/foo/foo -h +Replace this with a (multiline) description of your component. -### Common commands -Create a new component by writing a viash config file and an R/Python script. +Options: + -i file, --input=file + type: file, required parameter + Describe the input file. -View help of a component: + -o file, --output=file + type: file, required parameter + Describe the output file. -``` bash -viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- -h + --option=string + type: string, default: default- + Describe an optional parameter. ``` -Run a component: +You can **run the component** as follows: -``` bash -viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- [... arguments for the component ...] +``` +$ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o output.txt +This is a skeleton component +The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/output.txt + - option: default- +``` + +Alternatively, you can run the component straight from the viash config by using the **`viash run`** command: +``` +viash build src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o output.txt ``` -Test a component (provided that you wrote tests, of course): +Provided that you wrote a script that allows you to test the functionality of a component, +you can run the tests by using the **`viash test`** command. -``` bash -viash test src/modality_alignment/methods/mnn/config.vsh.yaml ``` +$ viash test src/modality_alignment/methods/foo/config.vsh.yaml +Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678' +==================================================================== ++/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678/build_executable/foo ---setup +> docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-RNMkfg +==================================================================== ++/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678/test_test.py/test.py +. +---------------------------------------------------------------------- +Ran 1 test in 0.016s + +OK +==================================================================== +SUCCESS! All 1 out of 1 test scripts succeeded! +Cleaning up temporary directory +``` + +## Frequently asked questions -Build a component: +### Running a component causes error 'Unable to find image' -``` bash -viash build src/modality_alignment/methods/mnn/config.vsh.yaml -p docker -o target/docker/modality_alignment/methods/mnn --setup +Depending on how an executable was created, a Docker container might not have been created. -target/docker/modality_alignment/methods/mnn/mnn -h -target/docker/modality_alignment/methods/mnn/mnn [... arguments for the component ...] +To solve this issue, run the executable with a `---setup` flag attached. This will +automatically build the Docker container for you. + +``` +$ target/docker/modality_alignment/methods/foo/foo ---setup +> docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-KeBjFs +``` + +Or when working with `viash run`: + +``` +$ viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- ---setup ``` From 22be31c20a0ccc63dcb8f2d39e67af0bbc374855 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 14:26:21 +0200 Subject: [PATCH 0039/1233] update readme Former-commit-id: 340fe65ada95ae780c4beee32995aa884cb8a496 --- README.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index af2903341f..fa484301da 100644 --- a/README.md +++ b/README.md @@ -77,20 +77,28 @@ test.py A python script with which you can start unit testing y The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). -### Trying out the component +### Building a component `viash` has several helper functions to help you quickly develop a component. With **`viash build`**, you can turn the component into a standalone executable. This standalone executable you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. + ``` viash build src/modality_alignment/methods/foo/config.vsh.yaml \ -o target/docker/modality_alignment/methods/foo \ --setup ``` -**Command-line interface**: You can view the interface of the executable by running the executable with the `-h` parameter. +Note that the `bin/project_build` component does a much better job of setting up +a collection of components. You can filter which components will be built by +providing a regex to the `-q` parameter, e.g. `bin/project_build -q 'utils|modality_alignment'`. + +### Running a component from CLI + +You can view the interface of the executable by running the executable with the `-h` parameter. + ``` $ target/docker/modality_alignment/methods/foo/foo -h Replace this with a (multiline) description of your component. @@ -125,6 +133,7 @@ Alternatively, you can run the component straight from the viash config by using viash build src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o output.txt ``` +### Unit testing a component Provided that you wrote a script that allows you to test the functionality of a component, you can run the tests by using the **`viash test`** command. @@ -146,6 +155,8 @@ SUCCESS! All 1 out of 1 test scripts succeeded! Cleaning up temporary directory ``` +To run all the unit tests of all the components in the repository, use `bin/project_test`. + ## Frequently asked questions ### Running a component causes error 'Unable to find image' From 485c46aea87d37da048fb1855363a85e44f14bd5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 14:27:33 +0200 Subject: [PATCH 0040/1233] update readme Former-commit-id: 487ec6dc100023cec6da6b7c62f5ba0674ba0870 --- README.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index fa484301da..5dd089235a 100644 --- a/README.md +++ b/README.md @@ -52,9 +52,7 @@ output/ Output generated by the pipeline. ## Adding a component with viash [`viash`](https://github.com/data-intuitive/viash) allows you to create pipelines -in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. - -### Create a skeleton component +in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. You can start creating a new component using `bin/skeleton`. For example to create a new Python-based viahs component in the `src/modality_alignment/methods/foo` folder, run: You can start creating a new component by using the `bin/skeleton` command: @@ -77,7 +75,7 @@ test.py A python script with which you can start unit testing y The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). -### Building a component +## Building a component `viash` has several helper functions to help you quickly develop a component. @@ -95,7 +93,7 @@ Note that the `bin/project_build` component does a much better job of setting up a collection of components. You can filter which components will be built by providing a regex to the `-q` parameter, e.g. `bin/project_build -q 'utils|modality_alignment'`. -### Running a component from CLI +## Running a component from CLI You can view the interface of the executable by running the executable with the `-h` parameter. @@ -133,7 +131,7 @@ Alternatively, you can run the component straight from the viash config by using viash build src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o output.txt ``` -### Unit testing a component +## Unit testing a component Provided that you wrote a script that allows you to test the functionality of a component, you can run the tests by using the **`viash test`** command. From 38f647ef72c50e576f76ca607677511196225696 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 16:32:06 +0200 Subject: [PATCH 0041/1233] use tsv to specify datasets Former-commit-id: 83e38c8db24af2d33704f94a26f54b6cd5a1431a --- src/modality_alignment/datasets/datasets.tsv | 4 +- src/modality_alignment/workflows/main.nf | 64 ++++++++++--------- .../workflows/run_nextflow.sh | 1 + src/utils/workflows/utils.nf | 20 ++++++ 4 files changed, 58 insertions(+), 31 deletions(-) diff --git a/src/modality_alignment/datasets/datasets.tsv b/src/modality_alignment/datasets/datasets.tsv index 5a4f891674..5b837c1d26 100644 --- a/src/modality_alignment/datasets/datasets.tsv +++ b/src/modality_alignment/datasets/datasets.tsv @@ -1,2 +1,2 @@ -id input1 input2 format compression accession_id doi organism cell_types technology -CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz csv gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq +processor id input1 input2 compression accession_id doi organism cell_types technology +scprep_csv CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 84ee207cc3..a52310e6cf 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -5,40 +5,52 @@ println "launchDir : $launchDir" targetDir = "$launchDir/target/nextflow" -include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { scprep_csv; scprep_csv as notscprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) // import helper functions -include { overrideOptionValue } from "../../../src/utils/workflows/utils.nf" +include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" def updateID = { [ it[1].baseName, it[1], it[2] ] } def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } +workflow scprep_csv_wrap { + take: + input_ + main: + output_ = input_ \ + | filter{ it[3].processor == "scprep_csv" } \ + | map { overrideOptionValue(it, it[3].processor, "compression", it[3].compression) } \ + | scprep_csv + emit: + output_ +} +workflow notscprep_csv_wrap { + take: + input_ + main: + output_ = input_ \ + | filter{ it[3].processor == "notscprep_csv" } \ + | notscprep_csv + emit: + output_ +} + workflow { - // idea: use tsv? -> https://github.com/biocorecrg/master_of_pores/blob/master/NanoMod/nanomod.nf#L80 - - // fetch datasets - data_scprep_csv = Channel.fromList( [ - [ - "CBMC_8K_13AB_10x", - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" - ] - ] ) \ - | map { [ it[0], [ "input1": file(it[1]), "input2": file(it[2]) ], params ]} \ - | map { overrideOptionValue(it, "scprep_csv", "id", it[0]) } \ - | scprep_csv - - // combine datasets in one channel - datasets = data_scprep_csv - - // when more datasets are available, replace the code above with: - // datasets = data_citeseq_cbmc.mix(data_2, data_3) - - datasets \ + dataset_info = Channel.fromPath(params.datasets) \ + | splitCsv(header: true, sep: "\t") \ + | map { row -> + files = [ "input1": file(row.input1), "input2": file(row.input2) ] + newParams = overrideParams(params, row.processor, "id", row.id) + [ row.id, files, newParams, row ] + } + + dataset_info \ + | (scprep_csv_wrap & notscprep_csv_wrap) \ + | mix \ | (mnn & scot) \ | mix \ | map(updateID) \ @@ -47,11 +59,5 @@ workflow { | toSortedList \ | map( combineResults ) \ | extract_scores - - - /* When more metrics become available, replace '| knn_auc \' with the following: - | (knn_auc & metric2 & metric3) \ - | mix \ - */ } \ No newline at end of file diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index 16258e9dd3..aec4e4dffe 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -11,5 +11,6 @@ cd "$REPO_ROOT" NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/main.nf \ -resume \ + --datasets src/modality_alignment/datasets/datasets.tsv \ --output output/modality_alignment diff --git a/src/utils/workflows/utils.nf b/src/utils/workflows/utils.nf index e943163163..b985fcdc3b 100644 --- a/src/utils/workflows/utils.nf +++ b/src/utils/workflows/utils.nf @@ -35,3 +35,23 @@ def overrideOptionValue(triplet, _key, _option, _value) { } ] } + +// A functional approach to 'updating' a value for an option in the params Map. +def overrideParams(params, _key, _option, _value) { + mapCopy = params.toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy + + return params.collectEntries{ function, v1 -> + (function == _key) + ? [ (function) : v1.collectEntries{ k2, v2 -> + (k2 == "arguments") + ? [ (k2) : v2.collectEntries{ k3, v3 -> + (k3 == _option) + ? [ (k3) : v3 + [ "value" : _value ] ] + : [ (k3) : v3 ] + } ] + : [ (k2) : v2 ] + } ] + : [ (function), v1 ] + } + +} \ No newline at end of file From 5855f4e004bc0768ecf9f3f211ef76ac3ae2b288 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 19:37:10 +0200 Subject: [PATCH 0042/1233] add mse metric Former-commit-id: f1edc6c6aa37ea86ea6c954f316f37a048754408 --- src/modality_alignment/datasets/datasets.tsv | 2 - .../metrics/mse/config.vsh.yaml | 31 ++++++++++++++ src/modality_alignment/metrics/mse/script.py | 40 +++++++++++++++++++ .../workflows/nextflow.config | 1 + 4 files changed, 72 insertions(+), 2 deletions(-) delete mode 100644 src/modality_alignment/datasets/datasets.tsv create mode 100644 src/modality_alignment/metrics/mse/config.vsh.yaml create mode 100644 src/modality_alignment/metrics/mse/script.py diff --git a/src/modality_alignment/datasets/datasets.tsv b/src/modality_alignment/datasets/datasets.tsv deleted file mode 100644 index 5b837c1d26..0000000000 --- a/src/modality_alignment/datasets/datasets.tsv +++ /dev/null @@ -1,2 +0,0 @@ -processor id input1 input2 compression accession_id doi organism cell_types technology -scprep_csv CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml new file mode 100644 index 0000000000..0cc8fa5668 --- /dev/null +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -0,0 +1,31 @@ +functionality: + name: "mse" + namespace: "modality_alignment/metrics" + version: "dev" + description: "Compute the mean squared error" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: "File to input h5ad containing: `ad.X`, `ad.obsm['aligned']`, `ad.obsm['mode2_aligned']`" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing `ad.uns['metric_value']`" + resources: + - type: python_script + path: ./script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - anndata + - numpy + - scipy + - scprep + - type: nextflow diff --git a/src/modality_alignment/metrics/mse/script.py b/src/modality_alignment/metrics/mse/script.py new file mode 100644 index 0000000000..18a9aafab5 --- /dev/null +++ b/src/modality_alignment/metrics/mse/script.py @@ -0,0 +1,40 @@ +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input": "out_bash/modality_alignment/methods/citeseq_cbmc_mnn.h5ad", + "output": "out_bash/modality_alignment/metrics/citeseq_cbmc_mnn_knn_auc.h5ad" +} +## VIASH END + +print("Importing libraries") +import anndata +import scprep +import numpy as np +from scipy import sparse + +print("Reading adata file") +adata = anndata.read_h5ad(par["input"]) + +print("Computing MSE") +def _square(X): + if sparse.issparse(X): + X.data = X.data ** 2 + return X + else: + return scprep.utils.toarray(X) ** 2 + +X = scprep.utils.toarray(adata.obsm["aligned"]) +Y = scprep.utils.toarray(adata.obsm["mode2_aligned"]) + +X_shuffled = X[np.random.permutation(np.arange(X.shape[0])), :] +error_random = np.mean(np.sum(_square(X_shuffled, Y))) +error_abs = np.mean(np.sum(_square(X - Y))) +metric_value = error_abs / error_random + +print("Store metic value") +adata.uns["metric_name"] = "mse" +adata.uns["metric_value"] = area_under_curve + +print("Writing adata to file") +adata.write(par["output"], compression = "gzip") diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index d810cde8a0..269e1e377d 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -6,6 +6,7 @@ includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/scprep_csv includeConfig "$launchDir/target/nextflow/modality_alignment/methods/mnn/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/scot/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/mse/nextflow.config" includeConfig "$launchDir/target/nextflow/utils/extract_scores/nextflow.config" docker { From 70d52bad470e88e54e13bcb33dd70088c2d67832 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 19:38:40 +0200 Subject: [PATCH 0043/1233] rework pipeline Former-commit-id: 7907ae21f6ab4bd53afc7412ae61c2da78cfee51 --- .../datasets/datasets_scprep_csv.tsv | 2 + src/modality_alignment/workflows/main.nf | 71 +++++++++++++------ 2 files changed, 51 insertions(+), 22 deletions(-) create mode 100644 src/modality_alignment/datasets/datasets_scprep_csv.tsv diff --git a/src/modality_alignment/datasets/datasets_scprep_csv.tsv b/src/modality_alignment/datasets/datasets_scprep_csv.tsv new file mode 100644 index 0000000000..5b837c1d26 --- /dev/null +++ b/src/modality_alignment/datasets/datasets_scprep_csv.tsv @@ -0,0 +1,2 @@ +processor id input1 input2 compression accession_id doi organism cell_types technology +scprep_csv CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index a52310e6cf..35d6e59229 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -9,6 +9,7 @@ include { scprep_csv; scprep_csv as notscprep_csv } from "$targetDir/modalit include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) +include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) // import helper functions @@ -17,47 +18,73 @@ include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workf def updateID = { [ it[1].baseName, it[1], it[2] ] } def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } -workflow scprep_csv_wrap { - take: +workflow multiMerge { + take: input_ main: output_ = input_ \ - | filter{ it[3].processor == "scprep_csv" } \ - | map { overrideOptionValue(it, it[3].processor, "compression", it[3].compression) } \ + | mix \ + | map{ [ it[1].baseName, it[1], it[2] ] } + emit: + output_ +} + +workflow get_scprep_csv_datasets { + main: + output_ = Channel.fromPath(file("$launchDir/src/modality_alignment/datasets/datasets_scprep_csv.tsv")) \ + | splitCsv(header: true, sep: "\t") \ + | map { row -> + files = [ "input1": file(row.input1), "input2": file(row.input2) ] + newParams = overrideParams(params, row.processor, "id", row.id) + [ row.id, files, newParams, row ] + } \ + | map{ overrideOptionValue(it, "scprep_csv", "compression", it[3].compression)} \ | scprep_csv emit: output_ } -workflow notscprep_csv_wrap { + +workflow processDatasets { take: - input_ + dataset_info_ main: - output_ = input_ \ - | filter{ it[3].processor == "notscprep_csv" } \ - | notscprep_csv + // read + datasets = dataset_info_ \ + | splitCsv(header: true, sep: "\t") \ + | map { row -> + files = [ "input1": file(row.input1), "input2": file(row.input2) ] + newParams = overrideParams(params, row.processor, "id", row.id) + [ row.id, files, newParams, row ] + } \ + | branch { + data_scprep_csv: it[3].processor == "scprep_csv" + data_notscprep_csv: it[3].processor == "notscprep_csv" + } + + // add extra scprep_csv parameters from tsv rows + out_scprep_csv = datasets.data_scprep_csv \ + | map{ overrideOptionValue(it, "scprep_csv", "compression", it[3].compression)} + | scprep_csv + + // process other data loaders + out_notscprep_csv = datasets.data_notscprep_csv | notscprep_csv + + // combine multiple data loaders into a single channel + output_ = out_scprep_csv.mix(out_notscprep_csv) emit: output_ } workflow { - dataset_info = Channel.fromPath(params.datasets) \ - | splitCsv(header: true, sep: "\t") \ - | map { row -> - files = [ "input1": file(row.input1), "input2": file(row.input2) ] - newParams = overrideParams(params, row.processor, "id", row.id) - [ row.id, files, newParams, row ] - } - - dataset_info \ - | (scprep_csv_wrap & notscprep_csv_wrap) \ - | mix \ + get_scprep_csv_datasets \ | (mnn & scot) \ | mix \ | map(updateID) \ - | knn_auc \ + | (knn_auc & mse) \ + | mix \ | map(updateID) \ | toSortedList \ - | map( combineResults ) \ + | map(combineResults) \ | extract_scores } \ No newline at end of file From 9f8a92b61368d6a0a0e63b24a3eed043f79da24f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 20:27:17 +0200 Subject: [PATCH 0044/1233] fix mse Former-commit-id: 2bb95b8bf26a896ddd2c85c2390ae6b613be8174 --- src/modality_alignment/metrics/mse/script.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/modality_alignment/metrics/mse/script.py b/src/modality_alignment/metrics/mse/script.py index 18a9aafab5..c5efa25811 100644 --- a/src/modality_alignment/metrics/mse/script.py +++ b/src/modality_alignment/metrics/mse/script.py @@ -28,13 +28,13 @@ def _square(X): Y = scprep.utils.toarray(adata.obsm["mode2_aligned"]) X_shuffled = X[np.random.permutation(np.arange(X.shape[0])), :] -error_random = np.mean(np.sum(_square(X_shuffled, Y))) +error_random = np.mean(np.sum(_square(X_shuffled - Y))) error_abs = np.mean(np.sum(_square(X - Y))) metric_value = error_abs / error_random print("Store metic value") adata.uns["metric_name"] = "mse" -adata.uns["metric_value"] = area_under_curve +adata.uns["metric_value"] = metric_value print("Writing adata to file") adata.write(par["output"], compression = "gzip") From aa1f42d45466579feb450bda09c9a96c6b091b0c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 20:27:26 +0200 Subject: [PATCH 0045/1233] clean up pipeline Former-commit-id: d99d6078d43e7ed06e2573bc7ca975e8454a7d70 --- src/modality_alignment/workflows/main.nf | 49 ++++-------------------- 1 file changed, 7 insertions(+), 42 deletions(-) diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 35d6e59229..d9ad3f9a9e 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -15,16 +15,15 @@ include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" // import helper functions include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" -def updateID = { [ it[1].baseName, it[1], it[2] ] } -def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } +def renameID = { [ it[1].baseName, it[1], it[2] ] } -workflow multiMerge { +workflow combineResults { take: input_ main: output_ = input_ \ - | mix \ - | map{ [ it[1].baseName, it[1], it[2] ] } + | toSortedList \ + | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } emit: output_ } @@ -44,47 +43,13 @@ workflow get_scprep_csv_datasets { output_ } -workflow processDatasets { - take: - dataset_info_ - main: - // read - datasets = dataset_info_ \ - | splitCsv(header: true, sep: "\t") \ - | map { row -> - files = [ "input1": file(row.input1), "input2": file(row.input2) ] - newParams = overrideParams(params, row.processor, "id", row.id) - [ row.id, files, newParams, row ] - } \ - | branch { - data_scprep_csv: it[3].processor == "scprep_csv" - data_notscprep_csv: it[3].processor == "notscprep_csv" - } - - // add extra scprep_csv parameters from tsv rows - out_scprep_csv = datasets.data_scprep_csv \ - | map{ overrideOptionValue(it, "scprep_csv", "compression", it[3].compression)} - | scprep_csv - - // process other data loaders - out_notscprep_csv = datasets.data_notscprep_csv | notscprep_csv - - // combine multiple data loaders into a single channel - output_ = out_scprep_csv.mix(out_notscprep_csv) - emit: - output_ -} - workflow { get_scprep_csv_datasets \ | (mnn & scot) \ - | mix \ - | map(updateID) \ + | mix | map(renameID) \ | (knn_auc & mse) \ - | mix \ - | map(updateID) \ - | toSortedList \ - | map(combineResults) \ + | mix | map(renameID) \ + | combineResults \ | extract_scores } \ No newline at end of file From bd9633fa8fc48e590ec4198d63749a43bb41ece0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 20:27:32 +0200 Subject: [PATCH 0046/1233] update readme Former-commit-id: 7deb243b0b24bcb2446f758a93c56724b12111c9 --- README.md | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) diff --git a/README.md b/README.md index 5dd089235a..f7b7df7286 100644 --- a/README.md +++ b/README.md @@ -174,3 +174,71 @@ Or when working with `viash run`: ``` $ viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- ---setup ``` + +### My component doesn't work! + +Debugging your component based on the output from a Nextflow pipeline is easier than you might realise. For example, the error message below tells you that the 'mse' component failed: + +``` +$ src/modality_alignment/workflows/run_nextflow.sh +N E X T F L O W ~ version 20.10.0 +[f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ +[00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ +[3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ +[22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ +[3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored +Completed at: 19-Apr-2021 20:09:22 +Duration : 3m 46s +CPU hours : 0.1 (2.7% failed) +Succeeded : 6 +Ignored : 2 +Failed : 2 +``` + +Looking at this output reveals in which step of the pipeline the 'mse' component failed, namely `3d/0d6afe`. This means we should check a folder called `work/3d/0d6afe...`: + +``` +$ ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ +total 28 +drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . +drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. +lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad +-rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin +-rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err +-rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log +-rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out +-rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run +-rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh +-rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode + +$ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err +Traceback (most recent call last): + File "/tmp/viash-run-mse-WausLu", line 39, in + adata.uns["metric_value"] = area_under_curve +NameError: name 'area_under_curve' is not defined +``` + +It seems that some error occurred within the Python script. Luckiky, the input file of this process is in this directory. We can manually run the component by running: + +``` +viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad +``` + +Alternatively, you can edit `src/modality_alignment/metrics/mse/script.py` and replace the header by: +```python +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input": "work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad", + "output": "test.h5ad" +} +## VIASH END + +## ... the rest of the script ... +``` + +Now you can work on the `script.py` file in your preferred editor (vim?). For easy prototyping, viash will automatically strip +away anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. \ No newline at end of file From 29469ee421049a0fd12bdee8eb61cd8b7bb7b7d8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 20:40:16 +0200 Subject: [PATCH 0047/1233] add comments to nextflow pipeline Former-commit-id: bf36d1ac9344fc4e54a7311d8ddb6f92f8f21bf5 --- src/modality_alignment/workflows/main.nf | 41 +++++++++++++++--------- 1 file changed, 25 insertions(+), 16 deletions(-) diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index d9ad3f9a9e..14167371e2 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -1,32 +1,36 @@ nextflow.enable.dsl=2 -println "projectDir : $projectDir" -println "launchDir : $launchDir" +// This workflow assumes that the directory from which the +// pipeline is launched is the root of the opsca repository. + +/******************************************************* +* Import viash modules * +*******************************************************/ targetDir = "$launchDir/target/nextflow" -include { scprep_csv; scprep_csv as notscprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) -// import helper functions include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" +// Helper function for redefining the ids of elements in a channel +// based on its files. def renameID = { [ it[1].baseName, it[1], it[2] ] } -workflow combineResults { - take: - input_ - main: - output_ = input_ \ - | toSortedList \ - | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } - emit: - output_ -} +/******************************************************* +* Dataset processor workflows * +*******************************************************/ +// This workflow reads in a tsv containing some metadata about each dataset. +// For each entry in the metadata, a dataset is generated, usually by downloading +// and processing some files. The end result of each of these workflows +// should be simply a channel of [id, h5adfile, params] triplets. +// +// If the need arises, these workflows could be split off into a separate file. workflow get_scprep_csv_datasets { main: @@ -43,13 +47,18 @@ workflow get_scprep_csv_datasets { output_ } +/******************************************************* +* Main workflow * +*******************************************************/ + workflow { get_scprep_csv_datasets \ | (mnn & scot) \ | mix | map(renameID) \ | (knn_auc & mse) \ | mix | map(renameID) \ - | combineResults \ + | toSortedList \ + | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } | extract_scores -} \ No newline at end of file +} From 50151691c625c9613ccf9caa292ce321e48b9eb5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Apr 2021 22:15:58 +0200 Subject: [PATCH 0048/1233] update readme Former-commit-id: 46c031bf40d74976d31cdc9cd4bec9516227ab15 --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index f7b7df7286..1a354ee6e2 100644 --- a/README.md +++ b/README.md @@ -8,13 +8,19 @@ To use this repository, make sure you have Bash, Java, and Docker installed. If Running the modality alignment pipeline requires two simple steps. -First, by running the command below, viash will build all the components in the `src/` folder as executables in the `target/` folder. +First, by running the command below, viash will **build all the components** in the `src/` folder as executables in the `target/` folder. ```bash -bin/project_build +$ bin/project_build +Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc +Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot +Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn +... ``` -Next, to run the pipeline with nextflow, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: +This might take a while. If you're interested in building only a subset of components, you can apply a regex to the selected components by for example using the `bin/project_build -q 'utils|modality_alignment'` command. + +Next, to **run the pipeline with nextflow**, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: ``` $ src/modality_alignment/workflows/run_nextflow.sh From 330916910f6067a74ada652cd44040eb9971eba5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 06:35:03 +0200 Subject: [PATCH 0049/1233] update requirements Former-commit-id: 4e13ed5061897557fd2a4283018833bbc28affc5 --- README.md | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1a354ee6e2..250a90346d 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,13 @@ # opsca-viash -Proof Of Concept in adapting Open Problems to use viash. +Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. ## Requirements -To use this repository, make sure you have Bash, Java, and Docker installed. If you wish to use Nextflow, install that too. + +To use this repository, please install the following dependencies: +* Bash +* Java (Java 8 or higher) +* Docker (Instructions [here](https://docs.docker.com/get-docker/)) +* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) ## Quick start From 07fc271631aa85a751e04bd7f4066c302efcb99e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 08:33:44 +0200 Subject: [PATCH 0050/1233] render readme with r markdown Former-commit-id: 19a163252252269fbdf7f43b672a076558af53cb --- README.Rmd | 249 +++++++++++++++++++++++++++++++++ README.md | 402 +++++++++++++++++++++++++++++++---------------------- 2 files changed, 481 insertions(+), 170 deletions(-) create mode 100644 README.Rmd diff --git a/README.Rmd b/README.Rmd new file mode 100644 index 0000000000..013ce16792 --- /dev/null +++ b/README.Rmd @@ -0,0 +1,249 @@ +--- +title: "opsca-viash" +output: + github_document: + toc: true + toc_depth: 2 + html_preview: false +--- + +```{r, setup, include=FALSE} +knitr::opts_chunk$set( + warning=FALSE, + message=FALSE, + error=FALSE, + comment="" +) +``` +Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. + +## Requirements + +To use this repository, please install the following dependencies: + +* Bash +* Java (Java 8 or higher) +* Docker (Instructions [here](https://docs.docker.com/get-docker/)) +* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) + +## Quick start + +The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. + +**Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. + +```bash +bin/project_build +``` + + Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc + Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot + Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn + ... + +These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. +The command might take a while to run, since it is building a docker container for each of the components. +If you're interested in building only a subset of components, you can apply a regex to the selected components. +For example: `bin/project_build -q 'utils|modality_alignment'`. + +**Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: + +```bash +src/modality_alignment/workflows/run_nextflow.sh +``` + + [15/84d27c] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [2f/318ad9] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [6f/dd22c1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [c6/6e0999] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [73/f6dffa] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [54/c89b95] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ + Completed at: 20-Apr-2021 06:52:19 + Duration : 3m 40s + CPU hours : 0.1 + Succeeded : 8 + +## Project structure + + bin/ Helper scripts for building the project and developing a new component. + src/ Source files for each component in the pipeline. + modality_alignment/ Source files related to the 'Modality alignment' task. + datasets/ Dataset downloader components. + methods/ Modality alignment method components. + metrics/ Modality alignment metric components. + resources/ Helper files. + workflow/ The pipeline workflow for this task. + utils/ Helper files. + target/ Executables generated by viash based on the components listed under `src/`. + docker/ Bash executables which can be used from a terminal. + nextflow/ Nextflow modules which can be used in a Nextflow pipeline. + work/ A working directory used by Nextflow. + output/ Output generated by the pipeline. + + +## Adding a viash component + +[`viash`](https://github.com/data-intuitive/viash) allows you to create pipelines +in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. +You can start creating a new component using `bin/skeleton`. For example to create +a new Python-based viash component in the `src/modality_alignment/methods/foo` folder, run: +You can start creating a new component by using the `bin/skeleton` command: + +```{bash} +bin/skeleton --name foo --namespace "modality_alignment/methods" --language python +``` + +This should create a few files in this folder: + + script.py A python script for you to edit. + config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. + test.py A python script with which you can start unit testing your component. + +The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site +provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). + +## Building a component + +`viash` has several helper functions to help you quickly develop a component. + +With **`viash build`**, you can turn the component into a standalone executable. +This standalone executable you can give to somebody else, and they will be able to +run it, provided that they have Bash and Docker installed. + +```{bash} +viash build src/modality_alignment/methods/foo/config.vsh.yaml \ + -o target/docker/modality_alignment/methods/foo \ + --setup +``` + +Note that the `bin/project_build` component does a much better job of setting up +a collection of components. You can filter which components will be built by +providing a regex to the `-q` parameter, e.g. `bin/project_build -q 'utils|modality_alignment'`. + +## Running a component from CLI + +You can view the interface of the executable by running the executable with the `-h` parameter. + +```{bash} +target/docker/modality_alignment/methods/foo/foo -h +``` + +You can **run the component** as follows: + +```{bash} +target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt +``` + +Alternatively, you can run the component straight from the viash config by using the **`viash run`** command: +```{bash} +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt +``` + +## Unit testing a component +Provided that you wrote a script that allows you to test the functionality of a component, +you can run the tests by using the **`viash test`** command. + +```{bash} +viash test src/modality_alignment/methods/foo/config.vsh.yaml +``` + +To run all the unit tests of all the components in the repository, use `bin/project_test`. + +## Frequently asked questions + +### Running a component causes error 'Unable to find image' + +Depending on how an executable was created, a Docker container might not have been created. + +To solve this issue, run the executable with a `---setup` flag attached. This will +automatically build the Docker container for you. + +```{bash} +target/docker/modality_alignment/methods/foo/foo ---setup +``` + +Or when working with `viash run`: + +```{bash} +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup +``` + +### My component doesn't work! + +Debugging your component based on the output from a Nextflow pipeline is easier than you might realise. For example, the error message below tells you that the 'mse' component failed: + +``` bash +src/modality_alignment/workflows/run_nextflow.sh +``` + + N E X T F L O W ~ version 20.10.0 + [f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ + [22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ + [3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored + Completed at: 19-Apr-2021 20:09:22 + Duration : 3m 46s + CPU hours : 0.1 (2.7% failed) + Succeeded : 6 + Ignored : 2 + Failed : 2 + + +Looking at this output reveals in which step of the pipeline the 'mse' component failed, namely `3d/0d6afe`. This means we should check a folder called `work/3d/0d6afe...`: + +``` bash +ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ +``` + + total 28 + drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . + drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. + lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad + -rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin + -rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err + -rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log + -rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out + -rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run + -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh + -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode + + $ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err + Traceback (most recent call last): + File "/tmp/viash-run-mse-WausLu", line 39, in + adata.uns["metric_value"] = area_under_curve + NameError: name 'area_under_curve' is not defined + +It seems that some error occurred within the Python script. Luckiky, the input file of this process is in this directory. We can manually run the component by running: + +``` bash +viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- \ + -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad +``` + +Alternatively, you can edit `src/modality_alignment/metrics/mse/script.py` and replace the header by: +```python +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input": "work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad", + "output": "test.h5ad" +} +## VIASH END + +## ... the rest of the script ... +``` + +Now you can work on the `script.py` file in your preferred editor (vim?). For easy prototyping, viash will automatically strip +away anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. + + + +```{bash, echo=FALSE} +# remove example files +rm -r src/modality_alignment/methods/foo target/docker/modality_alignment/methods/foo +rm foo_output.txt +``` \ No newline at end of file diff --git a/README.md b/README.md index 250a90346d..5c4237c8ed 100644 --- a/README.md +++ b/README.md @@ -1,244 +1,302 @@ -# opsca-viash -Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. +opsca-viash +================ + +- [Requirements](#requirements) +- [Quick start](#quick-start) +- [Project structure](#project-structure) +- [Adding a viash component](#adding-a-viash-component) +- [Building a component](#building-a-component) +- [Running a component from CLI](#running-a-component-from-cli) +- [Unit testing a component](#unit-testing-a-component) +- [Frequently asked questions](#frequently-asked-questions) + +Proof Of Concept in adapting [Open Problems for Single Cell Analysis +repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) +with Nextflow and viash. ## Requirements To use this repository, please install the following dependencies: -* Bash -* Java (Java 8 or higher) -* Docker (Instructions [here](https://docs.docker.com/get-docker/)) -* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) + +- Bash +- Java (Java 8 or higher) +- Docker (Instructions [here](https://docs.docker.com/get-docker/)) +- Nextflow (Optional, though [very easy to + install](https://www.nextflow.io/index.html#GetStarted)) ## Quick start -Running the modality alignment pipeline requires two simple steps. +The `src/` folder contains modular software components for running a +modality alignment benchmark. Running the full pipeline is quite easy. -First, by running the command below, viash will **build all the components** in the `src/` folder as executables in the `target/` folder. +**Step 1, build all the components:** in the `src/` folder as standalone +executables in the `target/` folder. -```bash -$ bin/project_build -Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc -Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot -Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn -... +``` bash +bin/project_build ``` -This might take a while. If you're interested in building only a subset of components, you can apply a regex to the selected components by for example using the `bin/project_build -q 'utils|modality_alignment'` command. + Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc + Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot + Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn + ... -Next, to **run the pipeline with nextflow**, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: +These standalone executables you can give to somebody else, and they +will be able to run it, provided that they have Bash and Docker +installed. The command might take a while to run, since it is building a +docker container for each of the components. If you’re interested in +building only a subset of components, you can apply a regex to the +selected components. For example: +`bin/project_build -q 'utils|modality_alignment'`. -``` -$ src/modality_alignment/workflows/run_nextflow.sh -[86/3d1927] process > scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[00/b3528e] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[75/bfdbb1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[bc/da3dce] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ -[b9/e083fe] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ -Completed at: 19-Apr-2021 13:18:26 -Duration : 3m 30s -CPU hours : 0.1 -Succeeded : 6 -``` - -## Project structure +**Step 2, run the pipeline with nextflow.** To do so, run the bash +script located at `src/modality_alignment/workflows/run_nextflow.sh`: +``` bash +src/modality_alignment/workflows/run_nextflow.sh ``` -bin/ Helper scripts for building the project and developing a new component. -src/ Source files for each component in the pipeline. - modality_alignment/ Source files related to the 'Modality alignment' task. - datasets/ Dataset downloader components. - methods/ Modality alignment method components. - metrics/ Modality alignment metric components. - resources/ Helper files. - workflow/ The pipeline workflow for this task. - utils/ Helper files. -target/ Executables generated by viash based on the components listed under `src/`. - docker/ Bash executables which can be used from a terminal. - nextflow/ Nextflow modules which can be used in a Nextflow pipeline. -work/ A working directory used by Nextflow. -output/ Output generated by the pipeline. -``` - -## Adding a component with viash + [15/84d27c] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [2f/318ad9] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [6f/dd22c1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [c6/6e0999] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [73/f6dffa] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [54/c89b95] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ + Completed at: 20-Apr-2021 06:52:19 + Duration : 3m 40s + CPU hours : 0.1 + Succeeded : 8 -[`viash`](https://github.com/data-intuitive/viash) allows you to create pipelines -in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. -You can start creating a new component using `bin/skeleton`. For example to create -a new Python-based viahs component in the `src/modality_alignment/methods/foo` folder, run: -You can start creating a new component by using the `bin/skeleton` command: +## Project structure -```bash + bin/ Helper scripts for building the project and developing a new component. + src/ Source files for each component in the pipeline. + modality_alignment/ Source files related to the 'Modality alignment' task. + datasets/ Dataset downloader components. + methods/ Modality alignment method components. + metrics/ Modality alignment metric components. + resources/ Helper files. + workflow/ The pipeline workflow for this task. + utils/ Helper files. + target/ Executables generated by viash based on the components listed under `src/`. + docker/ Bash executables which can be used from a terminal. + nextflow/ Nextflow modules which can be used in a Nextflow pipeline. + work/ A working directory used by Nextflow. + output/ Output generated by the pipeline. + +## Adding a viash component + +[`viash`](https://github.com/data-intuitive/viash) allows you to create +pipelines in Bash or Nextflow by wrapping Python, R, or Bash scripts +into reusable components. You can start creating a new component using +`bin/skeleton`. For example to create a new Python-based viash component +in the `src/modality_alignment/methods/foo` folder, run: You can start +creating a new component by using the `bin/skeleton` command: + +``` bash bin/skeleton --name foo --namespace "modality_alignment/methods" --language python - -# or: -bin/skeleton -n foo -ns "modality_alignment/methods" -l python ``` This should create a few files in this folder: -``` -script.py A python script for you to edit. -config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. -test.py A python script with which you can start unit testing your component. -``` + script.py A python script for you to edit. + config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. + test.py A python script with which you can start unit testing your component. -The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site -provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). +The [Getting started](http://www.data-intuitive.com/viash_docs/) page on +the viash documentation site provides some information on how a basic +viash component works, or on the specifications of the `config.vsh.yaml` +[config file](http://www.data-intuitive.com/viash_docs/config/). ## Building a component -`viash` has several helper functions to help you quickly develop a component. +`viash` has several helper functions to help you quickly develop a +component. -With **`viash build`**, you can turn the component into a standalone executable. -This standalone executable you can give to somebody else, and they will be able to -run it, provided that they have Bash and Docker installed. +With **`viash build`**, you can turn the component into a standalone +executable. This standalone executable you can give to somebody else, +and they will be able to run it, provided that they have Bash and Docker +installed. -``` +``` bash viash build src/modality_alignment/methods/foo/config.vsh.yaml \ -o target/docker/modality_alignment/methods/foo \ --setup ``` -Note that the `bin/project_build` component does a much better job of setting up -a collection of components. You can filter which components will be built by -providing a regex to the `-q` parameter, e.g. `bin/project_build -q 'utils|modality_alignment'`. + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-LkUMAr + +Note that the `bin/project_build` component does a much better job of +setting up a collection of components. You can filter which components +will be built by providing a regex to the `-q` parameter, +e.g. `bin/project_build -q 'utils|modality_alignment'`. ## Running a component from CLI -You can view the interface of the executable by running the executable with the `-h` parameter. +You can view the interface of the executable by running the executable +with the `-h` parameter. +``` bash +target/docker/modality_alignment/methods/foo/foo -h ``` -$ target/docker/modality_alignment/methods/foo/foo -h -Replace this with a (multiline) description of your component. -Options: - -i file, --input=file - type: file, required parameter - Describe the input file. + Replace this with a (multiline) description of your component. - -o file, --output=file - type: file, required parameter - Describe the output file. + Options: + -i file, --input=file + type: file, required parameter + Describe the input file. - --option=string - type: string, default: default- - Describe an optional parameter. -``` + -o file, --output=file + type: file, required parameter + Describe the output file. + + --option=string + type: string, default: default- + Describe an optional parameter. You can **run the component** as follows: -``` -$ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o output.txt -This is a skeleton component -The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/output.txt - - option: default- +``` bash +target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt ``` -Alternatively, you can run the component straight from the viash config by using the **`viash run`** command: -``` -viash build src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o output.txt + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + +Alternatively, you can run the component straight from the viash config +by using the **`viash run`** command: + +``` bash +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt ``` + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + ## Unit testing a component -Provided that you wrote a script that allows you to test the functionality of a component, -you can run the tests by using the **`viash test`** command. +Provided that you wrote a script that allows you to test the +functionality of a component, you can run the tests by using the +**`viash test`** command. + +``` bash +viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` -$ viash test src/modality_alignment/methods/foo/config.vsh.yaml -Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678' -==================================================================== -+/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678/build_executable/foo ---setup -> docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-RNMkfg -==================================================================== -+/home/rcannood/workspace/viash_temp/viash_test_foo8028146580425979678/test_test.py/test.py -. ----------------------------------------------------------------------- -Ran 1 test in 0.016s - -OK -==================================================================== -SUCCESS! All 1 out of 1 test scripts succeeded! -Cleaning up temporary directory -``` -To run all the unit tests of all the components in the repository, use `bin/project_test`. + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040' + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040/build_executable/foo ---setup + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-xcKqcl + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040/test_test.py/test.py + . + ---------------------------------------------------------------------- + Ran 1 test in 0.016s + + OK + ==================================================================== + SUCCESS! All 1 out of 1 test scripts succeeded! + Cleaning up temporary directory + +To run all the unit tests of all the components in the repository, use +`bin/project_test`. ## Frequently asked questions -### Running a component causes error 'Unable to find image' +### Running a component causes error ‘Unable to find image’ -Depending on how an executable was created, a Docker container might not have been created. +Depending on how an executable was created, a Docker container might not +have been created. -To solve this issue, run the executable with a `---setup` flag attached. This will -automatically build the Docker container for you. +To solve this issue, run the executable with a `---setup` flag attached. +This will automatically build the Docker container for you. -``` -$ target/docker/modality_alignment/methods/foo/foo ---setup -> docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-KeBjFs +``` bash +target/docker/modality_alignment/methods/foo/foo ---setup ``` + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-wmpR2g + Or when working with `viash run`: -``` -$ viash run src/modality_alignment/methods/mnn/config.vsh.yaml -- ---setup +``` bash +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup ``` -### My component doesn't work! + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Ku7ZNt -Debugging your component based on the output from a Nextflow pipeline is easier than you might realise. For example, the error message below tells you that the 'mse' component failed: +### My component doesn’t work! -``` -$ src/modality_alignment/workflows/run_nextflow.sh -N E X T F L O W ~ version 20.10.0 -[f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ -[00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ -[3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ -[22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ -[3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored -Completed at: 19-Apr-2021 20:09:22 -Duration : 3m 46s -CPU hours : 0.1 (2.7% failed) -Succeeded : 6 -Ignored : 2 -Failed : 2 -``` +Debugging your component based on the output from a Nextflow pipeline is +easier than you might realise. For example, the error message below +tells you that the ‘mse’ component failed: -Looking at this output reveals in which step of the pipeline the 'mse' component failed, namely `3d/0d6afe`. This means we should check a folder called `work/3d/0d6afe...`: - -``` -$ ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ -total 28 -drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . -drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. -lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad --rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin --rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err --rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log --rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out --rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run --rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh --rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode - -$ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err -Traceback (most recent call last): - File "/tmp/viash-run-mse-WausLu", line 39, in - adata.uns["metric_value"] = area_under_curve -NameError: name 'area_under_curve' is not defined +``` bash +src/modality_alignment/workflows/run_nextflow.sh ``` -It seems that some error occurred within the Python script. Luckiky, the input file of this process is in this directory. We can manually run the component by running: - + N E X T F L O W ~ version 20.10.0 + [f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ + [00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ + [3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ + [22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ + [3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored + Completed at: 19-Apr-2021 20:09:22 + Duration : 3m 46s + CPU hours : 0.1 (2.7% failed) + Succeeded : 6 + Ignored : 2 + Failed : 2 + +Looking at this output reveals in which step of the pipeline the ‘mse’ +component failed, namely `3d/0d6afe`. This means we should check a +folder called `work/3d/0d6afe...`: + +``` bash +ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ ``` -viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad + + total 28 + drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . + drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. + lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad + -rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin + -rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err + -rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log + -rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out + -rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run + -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh + -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode + + $ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err + Traceback (most recent call last): + File "/tmp/viash-run-mse-WausLu", line 39, in + adata.uns["metric_value"] = area_under_curve + NameError: name 'area_under_curve' is not defined + +It seems that some error occurred within the Python script. Luckiky, the +input file of this process is in this directory. We can manually run the +component by running: + +``` bash +viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- \ + -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad ``` -Alternatively, you can edit `src/modality_alignment/metrics/mse/script.py` and replace the header by: -```python +Alternatively, you can edit +`src/modality_alignment/metrics/mse/script.py` and replace the header +by: + +``` python ## VIASH START # The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. @@ -251,5 +309,9 @@ par = { ## ... the rest of the script ... ``` -Now you can work on the `script.py` file in your preferred editor (vim?). For easy prototyping, viash will automatically strip -away anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. \ No newline at end of file +Now you can work on the `script.py` file in your preferred editor +(vim?). For easy prototyping, viash will automatically strip away +anything between the `## VIASH START` and `## VIASH END` codeblock at +runtime. + + From 6b392084207280be4927ad9d9bfb044ed7a46d89 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 09:37:33 +0200 Subject: [PATCH 0051/1233] Update readme Former-commit-id: 5e5303516c1e6ab958157aa12f9a6c1adb871d09 --- README.Rmd | 18 +++++++++++++++++- README.md | 36 ++++++++++++++++++++++++++++-------- 2 files changed, 45 insertions(+), 9 deletions(-) diff --git a/README.Rmd b/README.Rmd index 013ce16792..b7e3f8f036 100644 --- a/README.Rmd +++ b/README.Rmd @@ -210,7 +210,10 @@ ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode - $ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err +```bash +cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err +``` + Traceback (most recent call last): File "/tmp/viash-run-mse-WausLu", line 39, in adata.uns["metric_value"] = area_under_curve @@ -240,6 +243,19 @@ par = { Now you can work on the `script.py` file in your preferred editor (vim?). For easy prototyping, viash will automatically strip away anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. + +## Benefits of using Nextflow + viash + +### The pipeline is **language-agnostic** + +This means that each component can be written in whatever scripting language the user desires. +Here are examples of a [Python](src/modality_alignment/methods/scot/) and an [R](src/modality_alignment/methods/mnn) component. + +By default, viash supports wrapping the following scripting languages: Bash, Python, R, JavaScript, and Scala. +If viash doesn't support your preferred scripting language, feel free to ask the developers to [add it](https://github.com/data-intuitive/viash/issues). +Alternatively, you can write a Bash script which calls your desired programming language. + + ```{bash, echo=FALSE} diff --git a/README.md b/README.md index 5c4237c8ed..47e86552e9 100644 --- a/README.md +++ b/README.md @@ -9,6 +9,8 @@ opsca-viash - [Running a component from CLI](#running-a-component-from-cli) - [Unit testing a component](#unit-testing-a-component) - [Frequently asked questions](#frequently-asked-questions) +- [Benefits of using Nextflow + + viash](#benefits-of-using-nextflow--viash) Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) @@ -124,7 +126,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ --setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-LkUMAr + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-MDmQNu Note that the `bin/project_build` component does a much better job of setting up a collection of components. You can filter which components @@ -190,12 +192,12 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040/build_executable/foo ---setup - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-xcKqcl + +/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780/build_executable/foo ---setup + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-58B3Jr ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo10681448973463170040/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780/test_test.py/test.py . ---------------------------------------------------------------------- Ran 1 test in 0.016s @@ -222,7 +224,7 @@ This will automatically build the Docker container for you. target/docker/modality_alignment/methods/foo/foo ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-wmpR2g + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-KFChia Or when working with `viash run`: @@ -230,7 +232,7 @@ Or when working with `viash run`: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Ku7ZNt + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-YpI0FX ### My component doesn’t work! @@ -277,7 +279,10 @@ ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode - $ cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err +``` bash +cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err +``` + Traceback (most recent call last): File "/tmp/viash-run-mse-WausLu", line 39, in adata.uns["metric_value"] = area_under_curve @@ -314,4 +319,19 @@ Now you can work on the `script.py` file in your preferred editor anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. +## Benefits of using Nextflow + viash + +### The pipeline is **language-agnostic** + +This means that each component can be written in whatever scripting +language the user desires. Here are examples of a +[Python](src/modality_alignment/methods/scot/) and an +[R](src/modality_alignment/methods/mnn) component. + +By default, viash supports wrapping the following scripting languages: +Bash, Python, R, JavaScript, and Scala. If viash doesn’t support your +preferred scripting language, feel free to ask the developers to [add +it](https://github.com/data-intuitive/viash/issues). Alternatively, you +can write a Bash script which calls your desired programming language. + From d274f7c8483a5eaba97bbc7a02ea47d77475c22e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 09:45:25 +0200 Subject: [PATCH 0052/1233] update nxf script Former-commit-id: 8fcd488fa6de3511e3c91e5833b24b995a9922e2 --- src/modality_alignment/workflows/run_nextflow.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index aec4e4dffe..16258e9dd3 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -11,6 +11,5 @@ cd "$REPO_ROOT" NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/main.nf \ -resume \ - --datasets src/modality_alignment/datasets/datasets.tsv \ --output output/modality_alignment From dba8838547944a8282ee315ecf1a9ec2c3f0bd9d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 11:19:30 +0200 Subject: [PATCH 0053/1233] Update readme Former-commit-id: d09b9ca337e0cf73138a516b0792ce1813058b10 --- README.Rmd | 62 ++++++++++++++++++++++++++++- README.md | 112 +++++++++++++++++++++++++++++++++++++++++++++++++---- 2 files changed, 165 insertions(+), 9 deletions(-) diff --git a/README.Rmd b/README.Rmd index b7e3f8f036..eb740d5c09 100644 --- a/README.Rmd +++ b/README.Rmd @@ -255,11 +255,71 @@ By default, viash supports wrapping the following scripting languages: Bash, Pyt If viash doesn't support your preferred scripting language, feel free to ask the developers to [add it](https://github.com/data-intuitive/viash/issues). Alternatively, you can write a Bash script which calls your desired programming language. +### One Docker container per component +By running the `bin/project_build` command, viash will build one Docker container per component. While this results in some initial computational overhead, +this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with those of other components. + +### Reproducible components + +A component built by viash is meant to be reproducible. If you send the `target/docker/modality_alignment/methods/foo/foo` file to someone, +they can run `./foo ---setup` and then will be able to use the `foo` component however they like. + +```{bash} +# pretend to send the component to someone through 'cp' +cp target/docker/modality_alignment/methods/foo/foo foo_by_email + +# build container +./foo_by_email ---setup + +# view help +./foo_by_email -h + +# run component +./foo_by_email -i LICENSE -o foo_output.txt +``` + +### Reprodicible components on Docker Hub +You might notice that the `---setup` builds the docker container from scratch, rather than pulling it from Docker hub. + +With `bin/project_build`, you can build a versioned release of all the components in the repository and push it to Docker hub. + +```bash +bin/project_build -m release -v '0.1.0' -r singlecellopenproblems +``` + + In release mode... + Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn + Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot + Exporting src/utils/extract_scores/ (utils) =docker=> target/docker/utils/extract_scores + Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc + Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv + Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse + > docker build -t singlecellopenproblems/utils_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS + > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO + > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 + > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 + > docker build -t singlecellopenproblems/modality_alignment/methods_scot:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scot-xUKof3 + > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc + +The images themselves can be pushed to Docker Hub with the `bin/project_push` command. I'd have to make a small change to viash to ensure that the component names don't contain any slashes because the images listed above can't be pushed to Docker hub. However, the output would look something like this: + +```bash +bin/project_push -m release -v '0.1.0' -r singlecellopenproblems +In release mode... +Using version 0.1.0 to tag containers +``` + > singlecellopenproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! + ```{bash, echo=FALSE} # remove example files rm -r src/modality_alignment/methods/foo target/docker/modality_alignment/methods/foo -rm foo_output.txt +rm foo_output.txt foo_by_email ``` \ No newline at end of file diff --git a/README.md b/README.md index 47e86552e9..0a3ef13cd9 100644 --- a/README.md +++ b/README.md @@ -126,7 +126,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ --setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-MDmQNu + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-0Cq825 Note that the `bin/project_build` component does a much better job of setting up a collection of components. You can filter which components @@ -192,15 +192,15 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780/build_executable/foo ---setup - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-58B3Jr + +/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777/build_executable/foo ---setup + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-otrw1O ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo5732704703787235780/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777/test_test.py/test.py . ---------------------------------------------------------------------- - Ran 1 test in 0.016s + Ran 1 test in 0.018s OK ==================================================================== @@ -224,7 +224,7 @@ This will automatically build the Docker container for you. target/docker/modality_alignment/methods/foo/foo ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-KFChia + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-NroSjh Or when working with `viash run`: @@ -232,7 +232,7 @@ Or when working with `viash run`: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-YpI0FX + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-tnOQs8 ### My component doesn’t work! @@ -334,4 +334,100 @@ preferred scripting language, feel free to ask the developers to [add it](https://github.com/data-intuitive/viash/issues). Alternatively, you can write a Bash script which calls your desired programming language. +### One Docker container per component + +By running the `bin/project_build` command, viash will build one Docker +container per component. While this results in some initial +computational overhead, this makes it a lot easier to add a new +component to the pipeline with dependencies which might conflict with +those of other components. + +### Reproducible components + +A component built by viash is meant to be reproducible. If you send the +`target/docker/modality_alignment/methods/foo/foo` file to someone, they +can run `./foo ---setup` and then will be able to use the `foo` +component however they like. + +``` bash +# pretend to send the component to someone through 'cp' +cp target/docker/modality_alignment/methods/foo/foo foo_by_email + +# build container +./foo_by_email ---setup + +# view help +./foo_by_email -h + +# run component +./foo_by_email -i LICENSE -o foo_output.txt +``` + + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-201YUb + Replace this with a (multiline) description of your component. + + Options: + -i file, --input=file + type: file, required parameter + Describe the input file. + + -o file, --output=file + type: file, required parameter + Describe the output file. + + --option=string + type: string, default: default- + Describe an optional parameter. + + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + +### Reprodicible components on Docker Hub + +You might notice that the `---setup` builds the docker container from +scratch, rather than pulling it from Docker hub. + +With `bin/project_build`, you can build a versioned release of all the +components in the repository and push it to Docker hub. + +``` bash +bin/project_build -m release -v '0.1.0' -r singlecellopenproblems +``` + + In release mode... + Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn + Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot + Exporting src/utils/extract_scores/ (utils) =docker=> target/docker/utils/extract_scores + Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc + Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv + Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse + > docker build -t singlecellopenproblems/utils_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS + > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO + > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 + > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 + > docker build -t singlecellopenproblems/modality_alignment/methods_scot:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scot-xUKof3 + > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc + +The images themselves can be pushed to Docker Hub with the +`bin/project_push` command. I’d have to make a small change to viash to +ensure that the component names don’t contain any slashes because the +images listed above can’t be pushed to Docker hub. However, the output +would look something like this: + +``` bash +bin/project_push -m release -v '0.1.0' -r singlecellopenproblems +In release mode... +Using version 0.1.0 to tag containers +``` + + > singlecellopenproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > singlecellopenproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! + From 23aafb942ed2a23951f10986859bbd2bbd0cee06 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 20 Apr 2021 11:21:38 +0200 Subject: [PATCH 0054/1233] fix codeblock Former-commit-id: ed5994c0aa9eba953bfcd398963c26506f1937dd --- README.Rmd | 6 +++++- README.md | 29 +++++++++++++++++------------ 2 files changed, 22 insertions(+), 13 deletions(-) diff --git a/README.Rmd b/README.Rmd index eb740d5c09..fd084e24de 100644 --- a/README.Rmd +++ b/README.Rmd @@ -271,10 +271,14 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email # build container ./foo_by_email ---setup +``` +```{bash} # view help ./foo_by_email -h +``` +```{bash} # run component ./foo_by_email -i LICENSE -o foo_output.txt ``` @@ -315,7 +319,7 @@ Using version 0.1.0 to tag containers > singlecellopenproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! > singlecellopenproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! > singlecellopenproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! - + ```{bash, echo=FALSE} diff --git a/README.md b/README.md index 0a3ef13cd9..dcc89a8688 100644 --- a/README.md +++ b/README.md @@ -126,7 +126,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ --setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-0Cq825 + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-eH7f4N Note that the `bin/project_build` component does a much better job of setting up a collection of components. You can filter which components @@ -192,15 +192,15 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777/build_executable/foo ---setup - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-otrw1O + +/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571/build_executable/foo ---setup + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-9YuZJq ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo13438869660876872777/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571/test_test.py/test.py . ---------------------------------------------------------------------- - Ran 1 test in 0.018s + Ran 1 test in 0.017s OK ==================================================================== @@ -224,7 +224,7 @@ This will automatically build the Docker container for you. target/docker/modality_alignment/methods/foo/foo ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-NroSjh + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-AXbMHW Or when working with `viash run`: @@ -232,7 +232,7 @@ Or when working with `viash run`: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-tnOQs8 + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Rwww1W ### My component doesn’t work! @@ -355,15 +355,15 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email # build container ./foo_by_email ---setup +``` + + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-M31xzb +``` bash # view help ./foo_by_email -h - -# run component -./foo_by_email -i LICENSE -o foo_output.txt ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-201YUb Replace this with a (multiline) description of your component. Options: @@ -379,6 +379,11 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email type: string, default: default- Describe an optional parameter. +``` bash +# run component +./foo_by_email -i LICENSE -o foo_output.txt +``` + This is a skeleton component The arguments are: - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE From bcc816aa70117d6d0e068f6d5c0de19fd3c03ba1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 13:33:47 +0200 Subject: [PATCH 0055/1233] rename folder Former-commit-id: 0d253e77c23dfd978d918253fc95ca214082fbdb --- README.Rmd | 4 +-- README.md | 36 ++++++++++++++----- .../datasets/scprep_csv/config.vsh.yaml | 2 +- .../datasets/scprep_csv/script.py | 2 +- .../methods/scot/config.vsh.yaml | 2 +- src/modality_alignment/methods/scot/scot.py | 2 +- .../{resources => utils}/preprocessing.py | 0 .../{resources => utils}/utils.py | 0 8 files changed, 33 insertions(+), 15 deletions(-) rename src/modality_alignment/{resources => utils}/preprocessing.py (100%) rename src/modality_alignment/{resources => utils}/utils.py (100%) diff --git a/README.Rmd b/README.Rmd index fd084e24de..49d700a67d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -71,7 +71,7 @@ src/modality_alignment/workflows/run_nextflow.sh datasets/ Dataset downloader components. methods/ Modality alignment method components. metrics/ Modality alignment metric components. - resources/ Helper files. + utils/ Utils functions. workflow/ The pipeline workflow for this task. utils/ Helper files. target/ Executables generated by viash based on the components listed under `src/`. @@ -326,4 +326,4 @@ Using version 0.1.0 to tag containers # remove example files rm -r src/modality_alignment/methods/foo target/docker/modality_alignment/methods/foo rm foo_output.txt foo_by_email -``` \ No newline at end of file +``` diff --git a/README.md b/README.md index dcc89a8688..f01d1513ed 100644 --- a/README.md +++ b/README.md @@ -77,7 +77,7 @@ src/modality_alignment/workflows/run_nextflow.sh datasets/ Dataset downloader components. methods/ Modality alignment method components. metrics/ Modality alignment metric components. - resources/ Helper files. + utils/ Utils functions. workflow/ The pipeline workflow for this task. utils/ Helper files. target/ Executables generated by viash based on the components listed under `src/`. @@ -126,7 +126,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ --setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-eH7f4N + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-6uqKl4 Note that the `bin/project_build` component does a much better job of setting up a collection of components. You can filter which components @@ -169,6 +169,12 @@ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + Alternatively, you can run the component straight from the viash config by using the **`viash run`** command: @@ -182,6 +188,12 @@ viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o fo - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + ## Unit testing a component Provided that you wrote a script that allows you to test the @@ -192,12 +204,12 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571/build_executable/foo ---setup - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-9YuZJq + +/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208/build_executable/foo ---setup + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Md2dPC ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo2584360881202159571/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208/test_test.py/test.py . ---------------------------------------------------------------------- Ran 1 test in 0.017s @@ -224,7 +236,7 @@ This will automatically build the Docker container for you. target/docker/modality_alignment/methods/foo/foo ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-AXbMHW + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-E9IAUq Or when working with `viash run`: @@ -232,7 +244,7 @@ Or when working with `viash run`: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Rwww1W + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-fZUT3j ### My component doesn’t work! @@ -357,7 +369,7 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email ./foo_by_email ---setup ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-M31xzb + > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-cgD19k ``` bash # view help @@ -390,6 +402,12 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - option: default- + ### Reprodicible components on Docker Hub You might notice that the `---setup` builds the docker container from diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 45ad125fb8..a3d64b60e7 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: resources: - type: python_script path: ./script.py - - path: "../../resources/utils.py" + - path: "../../utils/utils.py" platforms: - type: docker image: "python:3.8" diff --git a/src/modality_alignment/datasets/scprep_csv/script.py b/src/modality_alignment/datasets/scprep_csv/script.py index 651c6176bf..ff2aab8de6 100644 --- a/src/modality_alignment/datasets/scprep_csv/script.py +++ b/src/modality_alignment/datasets/scprep_csv/script.py @@ -9,7 +9,7 @@ "test": False, "compression" = "gzip" } -resources_dir = "../../resources/" +resources_dir = "../../utils/" ## VIASH END print("Importing libraries") diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml index 13e8b8d6a3..768f80ef86 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: resources: - type: python_script path: ./scot.py - - path: "../../resources/preprocessing.py" + - path: "../../utils/preprocessing.py" platforms: - type: docker diff --git a/src/modality_alignment/methods/scot/scot.py b/src/modality_alignment/methods/scot/scot.py index a30f3aaf69..d6d107bad2 100644 --- a/src/modality_alignment/methods/scot/scot.py +++ b/src/modality_alignment/methods/scot/scot.py @@ -5,7 +5,7 @@ n_svd = 100, balanced=False, } -resources_dir = "../../resources/utils.py" +resources_dir = "../../utils/" ## VIASH END print("Loading dependencies") diff --git a/src/modality_alignment/resources/preprocessing.py b/src/modality_alignment/utils/preprocessing.py similarity index 100% rename from src/modality_alignment/resources/preprocessing.py rename to src/modality_alignment/utils/preprocessing.py diff --git a/src/modality_alignment/resources/utils.py b/src/modality_alignment/utils/utils.py similarity index 100% rename from src/modality_alignment/resources/utils.py rename to src/modality_alignment/utils/utils.py From 05516d034c2c48a287733a88b22735da3400bd31 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 13:37:41 +0200 Subject: [PATCH 0056/1233] add API readme Former-commit-id: c1c1982f9f212526a9e66b5b5075519a2f32689e --- src/modality_alignment/README.md | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 src/modality_alignment/README.md diff --git a/src/modality_alignment/README.md b/src/modality_alignment/README.md new file mode 100644 index 0000000000..3964a719b5 --- /dev/null +++ b/src/modality_alignment/README.md @@ -0,0 +1,11 @@ +# Modality alignment + +Modality alignment refers to the task of combining together two datasets of different modalities of measurements (e.g., single-cell RNA sequencing and single-cell ATAC sequencing) on different observations of the same biological system. Integrating such measurements allows us to analyze the interaction between the different modalities, without requiring an explicitly joint measurement like [sci-CAR](https://doi.org/10.1126/science.aau0730) or [CITE-seq](https://doi.org/10.1038/nmeth.4380). + +## API + +Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. The dataset identifier should be stored in `adata.uns["dataset_name"]`. + +Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. The method identifier should be stored in `adata.uns["method_name"]`. + +Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. The metric identifier should be stored in `adata.uns["metric_name"]`. The metric value should be stored in `adata.uns["metric_value"]`. From 3424f11e3ea1b738ddaf3fad7881e9737e5d10c2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 13:57:21 +0200 Subject: [PATCH 0057/1233] add more metadata Former-commit-id: ced8878717ec1d83889194d677b90fb21d181deb --- .../datasets/scprep_csv/config.vsh.yaml | 6 +++++- src/modality_alignment/methods/mnn/config.vsh.yaml | 12 ++++++++++++ src/modality_alignment/methods/scot/config.vsh.yaml | 12 ++++++++++++ .../metrics/knn_auc/config.vsh.yaml | 8 ++++++++ src/modality_alignment/metrics/mse/config.vsh.yaml | 8 ++++++++ 5 files changed, 45 insertions(+), 1 deletion(-) diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index a3d64b60e7..91837664fa 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -3,7 +3,11 @@ functionality: namespace: "modality_alignment/datasets" version: "dev" description: "Create a modality alignment dataset from CSV using scprep." - arguments: + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + arguments: - name: "--id" type: "string" default: "citeseq_cbmc" diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/modality_alignment/methods/mnn/config.vsh.yaml index a1f3f8faab..d73b2b741b 100644 --- a/src/modality_alignment/methods/mnn/config.vsh.yaml +++ b/src/modality_alignment/methods/mnn/config.vsh.yaml @@ -3,6 +3,18 @@ functionality: namespace: "modality_alignment/methods" version: "dev" description: "Run Mutual Nearest Neighbours" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + info: + method_label: "MNN" + method_name: "Mutual Nearest Neighbors" + paper_name: "Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors" + paper_doi: "10.1038/nbt.4091" + paper_year: "2018" + code_url: "https://github.com/LTLA/batchelor" + code_version: "1.7.14" arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml index 768f80ef86..8bd4f3d907 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -3,6 +3,18 @@ functionality: namespace: "modality_alignment/methods" version: "dev" description: "Run Single Cell Optimal Transport" + authors: + - name: "Alex Tong" + roles: [ maintainer, author ] + props: { github: atong01 } + info: + method_label: "SCOT" + method_name: "Single Cell Optimal Transport" + paper_name: "Gromov-Wasserstein optimal transport to align single-cell multi-omics data" + paper_doi: "10.1101/2020.04.28.066787" + paper_year: "2020" + code_url: "https://github.com/rsinghlab/SCOT" + code_version: "0.2.0" arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index 204d98e812..f19c1f05ac 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -3,6 +3,14 @@ functionality: namespace: "modality_alignment/metrics" version: "dev" description: "Compute the kNN Area Under the Curve" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + info: + method_label: "KNN-AUC" + metric_name: "kNN Area Under the Curve" + maximise: true arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml index 0cc8fa5668..94f4249698 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -3,6 +3,14 @@ functionality: namespace: "modality_alignment/metrics" version: "dev" description: "Compute the mean squared error" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + info: + method_label: "MSE" + metric_name: "Mean Squared Error" + maximise: true arguments: - name: "--input" alternatives: ["-i"] From 324c5f89a6a1f53ad7fe13f9e360e0c74d3b53ca Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 14:00:54 +0200 Subject: [PATCH 0058/1233] rename scot script Former-commit-id: e457580314995dc6aee442ac6c4f6d48acd1f694 --- src/modality_alignment/methods/scot/config.vsh.yaml | 2 +- src/modality_alignment/methods/scot/{scot.py => script.py} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename src/modality_alignment/methods/scot/{scot.py => script.py} (100%) diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml index 8bd4f3d907..8523e6077b 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: description: "Determines whether balanced or unbalanced optimal transport. In the balanced case, the target and source distributions are assumed to have equal mass." resources: - type: python_script - path: ./scot.py + path: ./script.py - path: "../../utils/preprocessing.py" platforms: diff --git a/src/modality_alignment/methods/scot/scot.py b/src/modality_alignment/methods/scot/script.py similarity index 100% rename from src/modality_alignment/methods/scot/scot.py rename to src/modality_alignment/methods/scot/script.py From 9cc539e1277dfc3d08ddd4734fd321f9e51d46f1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 14:15:03 +0200 Subject: [PATCH 0059/1233] fix configs Former-commit-id: 52aeb01bc8f4044fbf86273de93724152cd5291d --- src/modality_alignment/datasets/scprep_csv/config.vsh.yaml | 2 +- src/modality_alignment/metrics/knn_auc/config.vsh.yaml | 2 +- src/modality_alignment/metrics/mse/config.vsh.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 91837664fa..0b17c05ef5 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - name: "Scott Gigante" roles: [ maintainer, author ] props: { github: scottgigante } - arguments: + arguments: - name: "--id" type: "string" default: "citeseq_cbmc" diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index f19c1f05ac..3dc08fc260 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: info: method_label: "KNN-AUC" metric_name: "kNN Area Under the Curve" - maximise: true + maximise: "true" arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml index 94f4249698..7e8d17575f 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: info: method_label: "MSE" metric_name: "Mean Squared Error" - maximise: true + maximise: "true" arguments: - name: "--input" alternatives: ["-i"] From 55fa0a0694bc9d13d655749a4a0a76599b960954 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 14:51:16 +0200 Subject: [PATCH 0060/1233] add nicer error message Former-commit-id: de49b3b8806c20479a6940eee5b3da4363bdbdeb --- src/utils/extract_scores/script.R | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/utils/extract_scores/script.R b/src/utils/extract_scores/script.R index 37636bb7fb..1b81f3569c 100644 --- a/src/utils/extract_scores/script.R +++ b/src/utils/extract_scores/script.R @@ -17,10 +17,12 @@ scores <- map_df(par$input, function(inp) { cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) - assert_that("dataset_name" %in% names(ad$uns)) - assert_that("method_name" %in% names(ad$uns)) - assert_that("metric_name" %in% names(ad$uns)) - assert_that("metric_value" %in% names(ad$uns)) + for (uns_name in c("dataset_name", "method_name", "metric_name", "metric_value")) { + assert_that( + uns_name %in% names(ad$uns), + msg = paste0("File ", inp, " must contain `uns['", uns_name, "']`") + ) + } as_tibble(ad$uns[c("dataset_name", "method_name", "metric_name", "metric_value")]) }) From 73fb7441e9a38647006db13ace86be1b124213f4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 15:06:23 +0200 Subject: [PATCH 0061/1233] add harmonic alignment component Former-commit-id: d31e2aa0b0875c6c82bf81e3752bba6e3129a941 --- .../harmonic_alignment/config.vsh.yaml | 57 ++++++++++++++++++ .../methods/harmonic_alignment/script.py | 59 +++++++++++++++++++ src/modality_alignment/workflows/main.nf | 25 ++++---- .../workflows/nextflow.config | 1 + 4 files changed, 130 insertions(+), 12 deletions(-) create mode 100644 src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml create mode 100644 src/modality_alignment/methods/harmonic_alignment/script.py diff --git a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml new file mode 100644 index 0000000000..6e84f92c5e --- /dev/null +++ b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml @@ -0,0 +1,57 @@ +functionality: + name: "harmonic_alignment" + namespace: "modality_alignment/methods" + version: "dev" + description: "Run Harmonic Alignment" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + info: + method_name: "Harmonic Alignment" + paper_name: "Harmonic Alignment" + paper_doi: "10.1137/1.9781611976236.36" + paper_year: "2020" + code_url: "https://github.com/KrishnaswamyLab/harmonic-alignment" + code_version: "0.0" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing both RNA and ADT data" + - name: "--n_svd" + type: "integer" + default: 100 + description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." + - name: "--n_pca_XY" + type: "integer" + default: 100 + description: "Default number of principal components on which to build graph." + - name: "--n_eigenvectors" + type: "integer" + default: 100 + description: "Number of eigenvectors of the normalized Laplacian on which to perform alignment." + resources: + - type: python_script + path: ./script.py + - path: "../../utils/preprocessing.py" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - anndata # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py + - scprep # needed by utils.py + - sklearn + - git+https://github.com/KrishnaswamyLab/harmonic-alignment#subdirectory=python + - type: nextflow diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/modality_alignment/methods/harmonic_alignment/script.py new file mode 100644 index 0000000000..d43288ef55 --- /dev/null +++ b/src/modality_alignment/methods/harmonic_alignment/script.py @@ -0,0 +1,59 @@ +## VIASH START +par = { + input = "output.h5ad", + output = "output.scot.h5ad", + n_svd = 100, + n_pca_XY = 100 + eigenvectors = 100 +} +resources_dir = "../../utils/" +## VIASH END + +print("Loading dependencies") +import scanpy as sc +import harmonicalignment +import sklearn.decomposition + +# importing helper functions from common preprocessing.py file in resources dir +import sys +sys.path.append(resources_dir) +from preprocessing import log_cpm +from preprocessing import sqrt_cpm + +print("Reading input h5ad file") +adata = sc.read_h5ad(par["input"]) + +print("Check parameters") +n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) +n_eigenvectors = par["n_eigenvectors"] +n_pca_XY = par["n_pca_XY"] + +if adata.X.shape[0] <= n_eigenvectors: + n_eigenvectors = None +if adata.X.shape[0] <= n_pca_XY: + n_pca_XY = None + +print("Normalising mode 1") +sqrt_cpm(adata) + +print("Normalising mode 2") +log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") + +print("Performing PCA reduction") +X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) +Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) + +print("Running Harmonic Alignment") +ha_op = harmonicalignment.HarmonicAlignment( + n_filters=8, n_pca_XY=n_pca_XY, n_eigenvectors=n_eigenvectors +) +ha_op.align(X_pca, Y_pca) +XY_aligned = ha_op.diffusion_map(n_eigenvectors=n_eigenvectors) + +print("Storing output data structures") +adata.obsm["aligned"] = XY_aligned[: X_pca.shape[0]] +adata.obsm["mode2_aligned"] = XY_aligned[X_pca.shape[0] :] + +print("Write output to file") +adata.uns["method_name"] = "harmonic_alignment" +adata.write(par["output"], compression="gzip") diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 14167371e2..c6c936f7fe 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -1,6 +1,6 @@ nextflow.enable.dsl=2 -// This workflow assumes that the directory from which the +// This workflow assumes that the directory from which the // pipeline is launched is the root of the opsca repository. /******************************************************* @@ -9,16 +9,17 @@ nextflow.enable.dsl=2 targetDir = "$launchDir/target/nextflow" -include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) -include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) -include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) -include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) -include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) -include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) +include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) +include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) +include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) +include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) +include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) +include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" -// Helper function for redefining the ids of elements in a channel +// Helper function for redefining the ids of elements in a channel // based on its files. def renameID = { [ it[1].baseName, it[1], it[2] ] } @@ -36,10 +37,10 @@ workflow get_scprep_csv_datasets { main: output_ = Channel.fromPath(file("$launchDir/src/modality_alignment/datasets/datasets_scprep_csv.tsv")) \ | splitCsv(header: true, sep: "\t") \ - | map { row -> + | map { row -> files = [ "input1": file(row.input1), "input2": file(row.input2) ] newParams = overrideParams(params, row.processor, "id", row.id) - [ row.id, files, newParams, row ] + [ row.id, files, newParams, row ] } \ | map{ overrideOptionValue(it, "scprep_csv", "compression", it[3].compression)} \ | scprep_csv @@ -53,12 +54,12 @@ workflow get_scprep_csv_datasets { workflow { get_scprep_csv_datasets \ - | (mnn & scot) \ + | (mnn & scot & harmonic_alignment) \ | mix | map(renameID) \ | (knn_auc & mse) \ | mix | map(renameID) \ | toSortedList \ | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } | extract_scores - + } diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index 269e1e377d..63ecba799c 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -5,6 +5,7 @@ manifest { includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/mnn/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/scot/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/methods/harmonic_alignment/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/mse/nextflow.config" includeConfig "$launchDir/target/nextflow/utils/extract_scores/nextflow.config" From 36192593276a4a91ccd8ad7fd11320d029c35b18 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 20:49:10 +0200 Subject: [PATCH 0062/1233] rename name to id Former-commit-id: 566e2ddcc1c12b9df1df890785570e2a482b42ff --- src/modality_alignment/README.md | 6 +++--- src/modality_alignment/datasets/scprep_csv/script.py | 4 ++-- src/modality_alignment/methods/harmonic_alignment/script.py | 2 +- src/modality_alignment/methods/mnn/script.R | 2 +- src/modality_alignment/methods/scot/script.py | 2 +- src/modality_alignment/metrics/knn_auc/script.py | 2 +- src/modality_alignment/metrics/mse/script.py | 2 +- src/utils/extract_scores/script.R | 6 +++--- 8 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/modality_alignment/README.md b/src/modality_alignment/README.md index 3964a719b5..93c41615fe 100644 --- a/src/modality_alignment/README.md +++ b/src/modality_alignment/README.md @@ -4,8 +4,8 @@ Modality alignment refers to the task of combining together two datasets of diff ## API -Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. The dataset identifier should be stored in `adata.uns["dataset_name"]`. +Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. The dataset identifier should be stored in `adata.uns["dataset_id"]`. -Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. The method identifier should be stored in `adata.uns["method_name"]`. +Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. The method identifier should be stored in `adata.uns["method_id"]`. -Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. The metric identifier should be stored in `adata.uns["metric_name"]`. The metric value should be stored in `adata.uns["metric_value"]`. +Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. The metric identifier should be stored in `adata.uns["metric_id"]`. The metric value should be stored in `adata.uns["metric_value"]`. diff --git a/src/modality_alignment/datasets/scprep_csv/script.py b/src/modality_alignment/datasets/scprep_csv/script.py index ff2aab8de6..78de2926fb 100644 --- a/src/modality_alignment/datasets/scprep_csv/script.py +++ b/src/modality_alignment/datasets/scprep_csv/script.py @@ -41,12 +41,12 @@ adata = create_joint_adata(adata1, adata2) adata = filter_joint_data_empty_cells(adata) -adata.uns["dataset_name"] = par["id"] +adata.uns["dataset_id"] = par["id"] if par["test"]: print("Subsetting dataset") adata = subset_joint_data(adata) - adata.uns["dataset_name"] = par["id"] + "_test" + adata.uns["dataset_id"] = par["id"] + "_test" print("Writing adata to file") adata.write(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/modality_alignment/methods/harmonic_alignment/script.py index d43288ef55..78a2e2a1cb 100644 --- a/src/modality_alignment/methods/harmonic_alignment/script.py +++ b/src/modality_alignment/methods/harmonic_alignment/script.py @@ -55,5 +55,5 @@ adata.obsm["mode2_aligned"] = XY_aligned[X_pca.shape[0] :] print("Write output to file") -adata.uns["method_name"] = "harmonic_alignment" +adata.uns["method_id"] = "harmonic_alignment" adata.write(par["output"], compression="gzip") diff --git a/src/modality_alignment/methods/mnn/script.R b/src/modality_alignment/methods/mnn/script.R index b875d05731..c7f127d578 100644 --- a/src/modality_alignment/methods/mnn/script.R +++ b/src/modality_alignment/methods/mnn/script.R @@ -47,5 +47,5 @@ adata$obsm[["aligned"]] <- as.matrix(mode1_recons) adata$obsm[["mode2_aligned"]] <- as.matrix(mode2_recons) cat("Writing to file\n") -adata$uns["method_name"] = "mnn" +adata$uns["method_id"] = "mnn" zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/modality_alignment/methods/scot/script.py b/src/modality_alignment/methods/scot/script.py index d6d107bad2..5a27f79084 100644 --- a/src/modality_alignment/methods/scot/script.py +++ b/src/modality_alignment/methods/scot/script.py @@ -49,5 +49,5 @@ adata.obsm["mode2_aligned"] = y_new_unbal print("Write output to file") -adata.uns["method_name"] = "scot" +adata.uns["method_id"] = "scot" adata.write(par["output"], compression="gzip") diff --git a/src/modality_alignment/metrics/knn_auc/script.py b/src/modality_alignment/metrics/knn_auc/script.py index 2403a62f36..594a749365 100644 --- a/src/modality_alignment/metrics/knn_auc/script.py +++ b/src/modality_alignment/metrics/knn_auc/script.py @@ -58,7 +58,7 @@ area_under_curve = np.mean(neighbors_match_curve) print("Store metic value") -adata.uns["metric_name"] = "knn_auc" +adata.uns["metric_id"] = "knn_auc" adata.uns["metric_value"] = area_under_curve print("Writing adata to file") diff --git a/src/modality_alignment/metrics/mse/script.py b/src/modality_alignment/metrics/mse/script.py index c5efa25811..59dee3c81e 100644 --- a/src/modality_alignment/metrics/mse/script.py +++ b/src/modality_alignment/metrics/mse/script.py @@ -33,7 +33,7 @@ def _square(X): metric_value = error_abs / error_random print("Store metic value") -adata.uns["metric_name"] = "mse" +adata.uns["metric_id"] = "mse" adata.uns["metric_value"] = metric_value print("Writing adata to file") diff --git a/src/utils/extract_scores/script.R b/src/utils/extract_scores/script.R index 1b81f3569c..dbfcdc7f99 100644 --- a/src/utils/extract_scores/script.R +++ b/src/utils/extract_scores/script.R @@ -17,14 +17,14 @@ scores <- map_df(par$input, function(inp) { cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) - for (uns_name in c("dataset_name", "method_name", "metric_name", "metric_value")) { + for (uns_name in c("dataset_id", "method_id", "metric_id", "metric_value")) { assert_that( - uns_name %in% names(ad$uns), + uns_name %in% names(ad$uns), msg = paste0("File ", inp, " must contain `uns['", uns_name, "']`") ) } - as_tibble(ad$uns[c("dataset_name", "method_name", "metric_name", "metric_value")]) + as_tibble(ad$uns[c("dataset_id", "method_id", "metric_id", "metric_value")]) }) write_tsv(scores, par$output) From 8abc53b09ecdd35524d371a7e6829fad4b34ab88 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 21:09:30 +0200 Subject: [PATCH 0063/1233] add simple unit test Former-commit-id: 98c71ddfab6c1e0707fcf0356e8d63981d81bf8d --- .../datasets/scprep_csv/config.vsh.yaml | 5 ++- .../datasets/scprep_csv/test.py | 43 +++++++++++++++++++ 2 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 src/modality_alignment/datasets/scprep_csv/test.py diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 0b17c05ef5..8e27d93096 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -36,8 +36,11 @@ functionality: required: true resources: - type: python_script - path: ./script.py + path: script.py - path: "../../utils/utils.py" + tests: + - type: python_script + path: test.py platforms: - type: docker image: "python:3.8" diff --git a/src/modality_alignment/datasets/scprep_csv/test.py b/src/modality_alignment/datasets/scprep_csv/test.py new file mode 100644 index 0000000000..622612381a --- /dev/null +++ b/src/modality_alignment/datasets/scprep_csv/test.py @@ -0,0 +1,43 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import pandas +import numpy as np + +import urllib.request + +print(">> Downloading input file") +# need to download file manually for now; viash docker platform tries to auto-mount them +urllib.request.urlretrieve("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100866/suppl/GSE100866%5FCD8%5Fmerged%2DADT%5Fumi%2Ecsv%2Egz", "adt_umi.csv.gz") + +print(">> Running scprep_csv") + +out = subprocess.check_output([ + "./scprep_csv", + "--id", "footest", + "--input1", "adt_umi.csv.gz", + "--input2", "adt_umi.csv.gz", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") +assert "mode2" in adata.obsm +assert "mode2_obs" in adata.uns +assert "mode2_var" in adata.uns +assert np.all(adata.obs.index == adata.uns["mode2_obs"]) +assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] + +# since same file was used for both datasets +assert adata.shape == adata.obsm["mode2"].shape + +# check dataset id +assert "dataset_id" in adata.uns +assert adata.uns["dataset_id"] == "footest" + +print(">> All tests passed successfully") From ee2bdfa28fa6234db69da7af61147d5bdfdabc2b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 21:28:37 +0200 Subject: [PATCH 0064/1233] remove compression param Former-commit-id: 148f7128af174d30df6c1bd2dcdf84741e38d6a9 --- src/modality_alignment/datasets/scprep_csv/config.vsh.yaml | 4 ---- src/modality_alignment/methods/harmonic_alignment/script.py | 2 +- src/modality_alignment/methods/scot/script.py | 2 +- 3 files changed, 2 insertions(+), 6 deletions(-) diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 8e27d93096..1ceb8a4863 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -23,10 +23,6 @@ functionality: - name: "--test" type: "boolean_true" description: "Subset the dataset" - - name: "--compression" - type: "string" - default: "gzip" - description: "For on-the-fly decompression of on-disk data. If 'infer' and filepath_or_buffer is path-like, then detect compression from the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise no decompression). If using 'zip', the ZIP file must contain only one data file to be read in. Set to None for no decompression." - name: "--output" alternatives: ["-o"] type: "file" diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/modality_alignment/methods/harmonic_alignment/script.py index 78a2e2a1cb..cdf29c75e9 100644 --- a/src/modality_alignment/methods/harmonic_alignment/script.py +++ b/src/modality_alignment/methods/harmonic_alignment/script.py @@ -56,4 +56,4 @@ print("Write output to file") adata.uns["method_id"] = "harmonic_alignment" -adata.write(par["output"], compression="gzip") +adata.write(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/scot/script.py b/src/modality_alignment/methods/scot/script.py index 5a27f79084..58fa078cea 100644 --- a/src/modality_alignment/methods/scot/script.py +++ b/src/modality_alignment/methods/scot/script.py @@ -50,4 +50,4 @@ print("Write output to file") adata.uns["method_id"] = "scot" -adata.write(par["output"], compression="gzip") +adata.write(par["output"], compression = "gzip") From 3dc8d68cca3afad03f21647f09f1320748465954 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 21:29:50 +0200 Subject: [PATCH 0065/1233] add sample component Former-commit-id: b917f59cb143055a330b3e4a7e31d6853c0a95d8 --- .../datasets/sample_dataset/config.vsh.yaml | 36 ++++++++ .../datasets/sample_dataset/script.py | 84 +++++++++++++++++++ .../datasets/sample_dataset/test.py | 30 +++++++ 3 files changed, 150 insertions(+) create mode 100644 src/modality_alignment/datasets/sample_dataset/config.vsh.yaml create mode 100644 src/modality_alignment/datasets/sample_dataset/script.py create mode 100644 src/modality_alignment/datasets/sample_dataset/test.py diff --git a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml new file mode 100644 index 0000000000..88626828a3 --- /dev/null +++ b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml @@ -0,0 +1,36 @@ +functionality: + name: "sample_dataset" + namespace: "modality_alignment/datasets" + version: "dev" + description: "Sample dataset for testing purposes" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + arguments: + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing both input matrices data" + required: true + resources: + - type: python_script + path: script.py + - path: "../../utils/utils.py" + tests: + - type: python_script + path: test.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - anndata # needed by utils.py + - pandas # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py + - type: nextflow diff --git a/src/modality_alignment/datasets/sample_dataset/script.py b/src/modality_alignment/datasets/sample_dataset/script.py new file mode 100644 index 0000000000..6794760c6b --- /dev/null +++ b/src/modality_alignment/datasets/sample_dataset/script.py @@ -0,0 +1,84 @@ +print("Importing libraries") +import scprep +import pandas as pd +import numpy as np +import scipy.sparse + +# adding resources dir to system path +# the resources dir contains all files listed in the '.functionality.resources' part of the +# viash config, amongst which is the 'utils.py' file we need. +import sys +sys.path.append(resources_dir) + +# importing helper functions from common utils.py file in resources dir +from utils import create_joint_adata +from utils import filter_joint_data_empty_cells +from utils import subset_joint_data + + +rna_cells_url = ( + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271044" + "&format=file&file=GSM3271044%5FRNA%5Fmouse%5Fkidney%5Fcell.txt.gz" +) +rna_genes_url = ( + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271044" + "&format=file&file=GSM3271044%5FRNA%5Fmouse%5Fkidney%5Fgene.txt.gz" +) +atac_cells_url = ( + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271045" + "&format=file&file=GSM3271045%5FATAC%5Fmouse%5Fkidney%5Fcell.txt.gz" +) +atac_genes_url = ( + "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271045" + "&format=file&file=GSM3271045%5FATAC%5Fmouse%5Fkidney%5Fpeak.txt.gz" +) + +print("Downloading input files") +sys.stdout.flush() +rna_genes = pd.read_csv(rna_genes_url, low_memory=False, index_col=0) +atac_genes = pd.read_csv(atac_genes_url, low_memory=False, index_col=1) +rna_cells = pd.read_csv(rna_cells_url, low_memory=False, index_col=0) +atac_cells = pd.read_csv(atac_cells_url, low_memory=False, index_col=0) + +print("Creating joint adata object") +keep_cells = np.intersect1d(rna_cells.index, atac_cells.index)[:200] +rna_cells = rna_cells.loc[keep_cells] +atac_cells = atac_cells.loc[keep_cells] + +rna_data = scipy.sparse.csr_matrix((len(keep_cells), len(rna_genes))) +atac_data = scipy.sparse.csr_matrix((len(keep_cells), len(atac_genes))) + +adata = create_joint_adata( + rna_data, + atac_data, + X_index=rna_cells.index, + X_columns=rna_genes.index, + Y_index=atac_cells.index, + Y_columns=atac_genes.index, +) + +print("Merging obs and var") +adata.obs = rna_cells.loc[adata.obs.index] +adata.var = rna_genes +for key in atac_cells.columns: + adata.obs[key] = atac_cells[key] +adata.uns["mode2_varnames"] = [] +for key in atac_genes.columns: + varname = "mode2_var_{}".format(key) + adata.uns[varname] = atac_genes[key].values + adata.uns["mode2_varnames"].append(varname) + +adata.X = scipy.sparse.csr_matrix(np.random.poisson(0.1, adata.X.shape)).astype(np.float64) +adata.obsm["mode2"] = scipy.sparse.csr_matrix( + np.random.poisson(0.1, adata.obsm["mode2"].shape) +).astype(np.float64) + +adata = filter_joint_data_empty_cells(adata) + +print("Subsetting dataset") +adata = subset_joint_data(adata) + +adata.uns["dataset_id"] = "sample_dataset_test" + +print("Writing adata to file") +adata.write(par["output"], compression = "gzip") diff --git a/src/modality_alignment/datasets/sample_dataset/test.py b/src/modality_alignment/datasets/sample_dataset/test.py new file mode 100644 index 0000000000..24541064e5 --- /dev/null +++ b/src/modality_alignment/datasets/sample_dataset/test.py @@ -0,0 +1,30 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import pandas +import numpy as np + +print(">> Running sample_dataset") + +out = subprocess.check_output([ + "./sample_dataset", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") +assert "mode2" in adata.obsm +assert "mode2_obs" in adata.uns +assert "mode2_var" in adata.uns +assert np.all(adata.obs.index == adata.uns["mode2_obs"]) +assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] + +# check dataset id +assert "dataset_id" in adata.uns + +print(">> All tests passed successfully") From 52b385727b0a8177a73fa04e0a07c75aabe8372f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 22:05:52 +0200 Subject: [PATCH 0066/1233] fix scprep_csv Former-commit-id: 97239cca1e0da70ff1010017dd68ab5e2445fb62 --- src/modality_alignment/datasets/scprep_csv/config.vsh.yaml | 4 ++++ src/modality_alignment/datasets/scprep_csv/test.py | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index 1ceb8a4863..e8efc7423c 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -20,6 +20,10 @@ functionality: type: "file" default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" description: "Path or URL to the ADT counts as a gzipped csv file." + - name: "--compression" + type: "string" + default: "gzip" + description: "For on-the-fly decompression of on-disk data. If 'infer' and filepath_or_buffer is path-like, then detect compression from the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise no decompression). If using 'zip', the ZIP file must contain only one data file to be read in. Set to None for no decompression." - name: "--test" type: "boolean_true" description: "Subset the dataset" diff --git a/src/modality_alignment/datasets/scprep_csv/test.py b/src/modality_alignment/datasets/scprep_csv/test.py index 622612381a..6b7af2d6c4 100644 --- a/src/modality_alignment/datasets/scprep_csv/test.py +++ b/src/modality_alignment/datasets/scprep_csv/test.py @@ -17,7 +17,7 @@ out = subprocess.check_output([ "./scprep_csv", "--id", "footest", - "--input1", "adt_umi.csv.gz", + "--input1", "adt_umi.csv.gz", "--input2", "adt_umi.csv.gz", "--output", "output.h5ad" ]).decode("utf-8") From fc382c854720571fb3a969881a3c074ad867b2d8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 22:06:56 +0200 Subject: [PATCH 0067/1233] add sample methods and unit tests Former-commit-id: 4e8c0b166f6a902be781ca789ae011a071a01e52 --- .gitignore | 1 - .../datasets/sample_dataset/config.vsh.yaml | 8 ++++ .../datasets/sample_dataset/script.py | 2 +- .../datasets/sample_dataset/test.py | 31 +++++++++++++- .../harmonic_alignment/config.vsh.yaml | 4 ++ .../methods/harmonic_alignment/test.py | 30 +++++++++++++ .../methods/mnn/config.vsh.yaml | 9 +++- src/modality_alignment/methods/mnn/test.py | 30 +++++++++++++ .../methods/sample_method/config.vsh.yaml | 40 ++++++++++++++++++ .../methods/sample_method/script.py | 15 +++++++ .../methods/sample_method/test.py | 30 +++++++++++++ .../methods/scot/config.vsh.yaml | 7 ++- src/modality_alignment/methods/scot/test.py | 31 ++++++++++++++ .../resources/sample_dataset.h5ad | Bin 0 -> 137726 bytes .../resources/sample_output.h5ad | Bin 0 -> 159452 bytes 15 files changed, 232 insertions(+), 6 deletions(-) create mode 100644 src/modality_alignment/methods/harmonic_alignment/test.py create mode 100644 src/modality_alignment/methods/mnn/test.py create mode 100644 src/modality_alignment/methods/sample_method/config.vsh.yaml create mode 100644 src/modality_alignment/methods/sample_method/script.py create mode 100644 src/modality_alignment/methods/sample_method/test.py create mode 100644 src/modality_alignment/methods/scot/test.py create mode 100644 src/modality_alignment/resources/sample_dataset.h5ad create mode 100644 src/modality_alignment/resources/sample_output.h5ad diff --git a/.gitignore b/.gitignore index ca0b3926c8..2187195d87 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,5 @@ # repo specific ignores output_bash -*.h5ad # R specific ignores .Rhistory diff --git a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml index 88626828a3..8d388d82b2 100644 --- a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml +++ b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml @@ -15,6 +15,14 @@ functionality: default: "output.h5ad" description: "Output h5ad file containing both input matrices data" required: true + - name: "--n_cells" + type: "integer" + default: 600 + description: "Number of cells" + - name: "--n_genes" + type: "integer" + default: 1500 + description: "Number of genes" resources: - type: python_script path: script.py diff --git a/src/modality_alignment/datasets/sample_dataset/script.py b/src/modality_alignment/datasets/sample_dataset/script.py index 6794760c6b..c81093b0df 100644 --- a/src/modality_alignment/datasets/sample_dataset/script.py +++ b/src/modality_alignment/datasets/sample_dataset/script.py @@ -76,7 +76,7 @@ adata = filter_joint_data_empty_cells(adata) print("Subsetting dataset") -adata = subset_joint_data(adata) +adata = subset_joint_data(adata, n_cells = par["n_cells"], n_genes = par["n_genes"]) adata.uns["dataset_id"] = "sample_dataset_test" diff --git a/src/modality_alignment/datasets/sample_dataset/test.py b/src/modality_alignment/datasets/sample_dataset/test.py index 24541064e5..e53f2d61bf 100644 --- a/src/modality_alignment/datasets/sample_dataset/test.py +++ b/src/modality_alignment/datasets/sample_dataset/test.py @@ -7,7 +7,6 @@ import numpy as np print(">> Running sample_dataset") - out = subprocess.check_output([ "./sample_dataset", "--output", "output.h5ad" @@ -27,4 +26,34 @@ # check dataset id assert "dataset_id" in adata.uns + + + +print(">> Running sample_dataset with different args") +out = subprocess.check_output([ + "./sample_dataset", + "--output", "output.h5ad", + "--n_cells", "100", + "--n_genes", "200" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") +assert "mode2" in adata.obsm +assert "mode2_obs" in adata.uns +assert "mode2_var" in adata.uns +assert np.all(adata.obs.index == adata.uns["mode2_obs"]) +assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] + +# check shape based on args +assert adata.shape == (100, 200) + +# check dataset id +assert "dataset_id" in adata.uns + + + print(">> All tests passed successfully") diff --git a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml index 6e84f92c5e..4cb6eadc62 100644 --- a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml +++ b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml @@ -42,6 +42,10 @@ functionality: - type: python_script path: ./script.py - path: "../../utils/preprocessing.py" + tests: + - type: python_script + path: test.py + - path: "../../resources/sample_dataset.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/modality_alignment/methods/harmonic_alignment/test.py b/src/modality_alignment/methods/harmonic_alignment/test.py new file mode 100644 index 0000000000..dbb722af9d --- /dev/null +++ b/src/modality_alignment/methods/harmonic_alignment/test.py @@ -0,0 +1,30 @@ +import os +from os import path +import subprocess + +import scanpy as sc + +print(">> Running harmonic_alignment") +out = subprocess.check_output([ + "./harmonic_alignment", + "--input", "sample_dataset.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") + +assert "aligned" in adata.obsm +assert "mode2_aligned" in adata.obsm +assert adata.obsm["aligned"].shape[0] == adata.shape[0] +assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] +assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] + +# check dataset id +assert "method_id" in adata.uns +assert adata.uns["method_id"] == "harmonic_alignment" + +print(">> All tests passed successfully") diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/modality_alignment/methods/mnn/config.vsh.yaml index d73b2b741b..58acdcf477 100644 --- a/src/modality_alignment/methods/mnn/config.vsh.yaml +++ b/src/modality_alignment/methods/mnn/config.vsh.yaml @@ -34,9 +34,13 @@ functionality: resources: - type: r_script path: ./script.R + tests: + - type: python_script + path: test.py + - path: "../../resources/sample_dataset.h5ad" platforms: - type: docker - image: "dataintuitive/randpy:r4.0_bioc3.12" # already includes some R, bioconductor & anndata packages + image: "dataintuitive/randpy:r4.0_py3.8_bioc3.12" # already includes some R, bioconductor & anndata packages setup: - type: r cran: @@ -45,4 +49,7 @@ platforms: - sparsesvd bioc: - batchelor + - type: python + packages: + - scanpy # needed by tests - type: nextflow diff --git a/src/modality_alignment/methods/mnn/test.py b/src/modality_alignment/methods/mnn/test.py new file mode 100644 index 0000000000..ac7448a2d7 --- /dev/null +++ b/src/modality_alignment/methods/mnn/test.py @@ -0,0 +1,30 @@ +import os +from os import path +import subprocess + +import scanpy as sc + +print(">> Running mnn") +out = subprocess.check_output([ + "./mnn", + "--input", "sample_dataset.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") + +assert "aligned" in adata.obsm +assert "mode2_aligned" in adata.obsm +assert adata.obsm["aligned"].shape[0] == adata.shape[0] +assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] +assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] + +# check dataset id +assert "method_id" in adata.uns +assert adata.uns["method_id"] == "mnn" + +print(">> All tests passed successfully") diff --git a/src/modality_alignment/methods/sample_method/config.vsh.yaml b/src/modality_alignment/methods/sample_method/config.vsh.yaml new file mode 100644 index 0000000000..21a4f1ef32 --- /dev/null +++ b/src/modality_alignment/methods/sample_method/config.vsh.yaml @@ -0,0 +1,40 @@ +functionality: + name: "sample_method" + namespace: "modality_alignment/methods" + version: "dev" + description: "Sample method" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + info: + method_name: "Sample method" + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + default: "input.h5ad" + description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing both RNA and ADT data" + resources: + - type: python_script + path: ./script.py + tests: + - type: python_script + path: test.py + - path: "../../resources/sample_dataset.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - anndata # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py + - type: nextflow diff --git a/src/modality_alignment/methods/sample_method/script.py b/src/modality_alignment/methods/sample_method/script.py new file mode 100644 index 0000000000..5a75ad7614 --- /dev/null +++ b/src/modality_alignment/methods/sample_method/script.py @@ -0,0 +1,15 @@ +print("Loading dependencies") +import scanpy as sc +import numpy as np + +print("Reading input h5ad file") +adata = sc.read_h5ad(par["input"]) + +print("Check parameters") +new_shape = (adata.X.shape[0], 10) +adata.obsm["aligned"] = np.random.normal(0, 0.1, new_shape) +adata.obsm["mode2_aligned"] = np.random.normal(0, 0.1, new_shape) + +print("Write output to file") +adata.uns["method_id"] = "sample_method" +adata.write(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/sample_method/test.py b/src/modality_alignment/methods/sample_method/test.py new file mode 100644 index 0000000000..01d5e95fc4 --- /dev/null +++ b/src/modality_alignment/methods/sample_method/test.py @@ -0,0 +1,30 @@ +import os +from os import path +import subprocess + +import scanpy as sc + +print(">> Running sample_method") +out = subprocess.check_output([ + "./sample_method", + "--input", "sample_dataset.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") + +assert "aligned" in adata.obsm +assert "mode2_aligned" in adata.obsm +assert adata.obsm["aligned"].shape[0] == adata.shape[0] +assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] +assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] + +# check dataset id +assert "method_id" in adata.uns +assert adata.uns["method_id"] == "sample_method" + +print(">> All tests passed successfully") diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml index 8523e6077b..f4b193ead1 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -36,9 +36,12 @@ functionality: description: "Determines whether balanced or unbalanced optimal transport. In the balanced case, the target and source distributions are assumed to have equal mass." resources: - type: python_script - path: ./script.py + path: script.py - path: "../../utils/preprocessing.py" - + tests: + - type: python_script + path: test.py + - path: "../../resources/sample_dataset.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/modality_alignment/methods/scot/test.py b/src/modality_alignment/methods/scot/test.py new file mode 100644 index 0000000000..7bb7b08720 --- /dev/null +++ b/src/modality_alignment/methods/scot/test.py @@ -0,0 +1,31 @@ +import os +from os import path +import subprocess + +import scanpy as sc + + +print(">> Running scot") +out = subprocess.check_output([ + "./scot", + "--input", "sample_dataset.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset output fits expected API") +adata = sc.read_h5ad("output.h5ad") + +assert 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zF4~t~u~GT}@2ttEZ!9|+9zWv3p}kf9(DhFfM*Z0}z-!z6rtitY_Y&5gYP7NECw}X< zpUtXNt5wRHt7#E0It5({4R|uXXw#`d`7)l4>)df{$9&y>QDe4@8}BVmz4+zMZ+0Jh zUconW|E`D`EiW_(emdfVb9rV4mR@u1x9AHiE|!R?+3`l+!t&-CEth`ao!X`Q+^S8J z#{SsCcgLV;(Muyk z9~VmbwdbOIy*B;vh_BnX`HjtagkPRCx_N46ff_Ns?+&Ed5zfL~nITuXL@ztgnimGWt`hlU-G8JrOKD1SZKe(~o= zhrNp3s_cJv^n)7#%X>UX9~RR(YehnlluduM?e7Jc2 z>aPXwjoWsl;ohiC4caU&{@LBzS%q^SwwXU~_OD%V|6v{b2i1E@^!f+XdvdCuoXO$5 z>~I%P{p26!(jIj@7VucWV*!r^JQnyLw}89+$^7|P^ZLK=_wKtGe_Nh3S;RDe^}VBx z=B@wMYfkx7l^j~RT|4^?(@svsv)}f7^H{)R0gnYd7VucWV}XBx1#;mxrIPor%@9@wv(FXeVfc++?zCQq&@#;*p+o=I5qplSaoD|YVS*E|<~TVyLks|!Ba>q~!C i)_i-sM618Y4K*Hot>@q4#u~Wh1O6WOS3Uk|-~S7 Date: Mon, 26 Apr 2021 22:16:38 +0200 Subject: [PATCH 0068/1233] add and fix unit tests Former-commit-id: 4ea95dd1f784f5d24d5002442d798bcc4cc10bdf --- .../datasets/sample_dataset/test.py | 4 +-- .../datasets/scprep_csv/test.py | 2 +- .../methods/harmonic_alignment/test.py | 2 +- src/modality_alignment/methods/mnn/test.py | 2 +- .../methods/sample_method/test.py | 2 +- src/modality_alignment/methods/scot/test.py | 3 +-- .../metrics/knn_auc/config.vsh.yaml | 7 ++++- .../metrics/knn_auc/test.py | 27 +++++++++++++++++++ .../metrics/mse/config.vsh.yaml | 5 ++++ src/modality_alignment/metrics/mse/test.py | 27 +++++++++++++++++++ 10 files changed, 72 insertions(+), 9 deletions(-) create mode 100644 src/modality_alignment/metrics/knn_auc/test.py create mode 100644 src/modality_alignment/metrics/mse/test.py diff --git a/src/modality_alignment/datasets/sample_dataset/test.py b/src/modality_alignment/datasets/sample_dataset/test.py index e53f2d61bf..ca12a259dc 100644 --- a/src/modality_alignment/datasets/sample_dataset/test.py +++ b/src/modality_alignment/datasets/sample_dataset/test.py @@ -15,7 +15,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns @@ -40,7 +40,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns diff --git a/src/modality_alignment/datasets/scprep_csv/test.py b/src/modality_alignment/datasets/scprep_csv/test.py index 6b7af2d6c4..ff07391c6b 100644 --- a/src/modality_alignment/datasets/scprep_csv/test.py +++ b/src/modality_alignment/datasets/scprep_csv/test.py @@ -25,7 +25,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns diff --git a/src/modality_alignment/methods/harmonic_alignment/test.py b/src/modality_alignment/methods/harmonic_alignment/test.py index dbb722af9d..aa8324b3e5 100644 --- a/src/modality_alignment/methods/harmonic_alignment/test.py +++ b/src/modality_alignment/methods/harmonic_alignment/test.py @@ -14,7 +14,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm diff --git a/src/modality_alignment/methods/mnn/test.py b/src/modality_alignment/methods/mnn/test.py index ac7448a2d7..00d8db5b15 100644 --- a/src/modality_alignment/methods/mnn/test.py +++ b/src/modality_alignment/methods/mnn/test.py @@ -14,7 +14,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm diff --git a/src/modality_alignment/methods/sample_method/test.py b/src/modality_alignment/methods/sample_method/test.py index 01d5e95fc4..473ea8541e 100644 --- a/src/modality_alignment/methods/sample_method/test.py +++ b/src/modality_alignment/methods/sample_method/test.py @@ -14,7 +14,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that dataset fits expected API") adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm diff --git a/src/modality_alignment/methods/scot/test.py b/src/modality_alignment/methods/scot/test.py index 7bb7b08720..492c50743c 100644 --- a/src/modality_alignment/methods/scot/test.py +++ b/src/modality_alignment/methods/scot/test.py @@ -4,7 +4,6 @@ import scanpy as sc - print(">> Running scot") out = subprocess.check_output([ "./scot", @@ -15,7 +14,7 @@ print(">> Checking whether file exists") assert path.exists("output.h5ad") -print(">> Check that dataset output fits expected API") +print(">> Check that output fits expected API") adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index 3dc08fc260..e96966dd7f 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -33,7 +33,11 @@ functionality: description: The maximum number of SVDs to use. resources: - type: python_script - path: ./script.py + path: script.py + tests: + - type: python_script + path: test.py + - path: ../../resources/sample_output.h5ad platforms: - type: docker image: "python:3.8" @@ -43,4 +47,5 @@ platforms: - anndata - numpy - sklearn + - scanpy - type: nextflow diff --git a/src/modality_alignment/metrics/knn_auc/test.py b/src/modality_alignment/metrics/knn_auc/test.py new file mode 100644 index 0000000000..d4bd11a563 --- /dev/null +++ b/src/modality_alignment/metrics/knn_auc/test.py @@ -0,0 +1,27 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import numpy as np + +print(">> Running knn_auc") +out = subprocess.check_output([ + "./knn_auc", + "--input", "sample_output.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that dataset fits expected API") +adata = sc.read_h5ad("output.h5ad") + +# check id +assert "metric_id" in adata.uns +assert adata.uns["metric_id"] == "knn_auc" +assert "metric_value" in adata.uns +assert type(adata.uns["metric_value"]) is np.float64 + +print(">> All tests passed successfully") diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml index 7e8d17575f..6c7eecd29c 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -26,6 +26,10 @@ functionality: resources: - type: python_script path: ./script.py + tests: + - type: python_script + path: test.py + - path: ../../resources/sample_output.h5ad platforms: - type: docker image: "python:3.8" @@ -36,4 +40,5 @@ platforms: - numpy - scipy - scprep + - scanpy - type: nextflow diff --git a/src/modality_alignment/metrics/mse/test.py b/src/modality_alignment/metrics/mse/test.py new file mode 100644 index 0000000000..3bdf2899be --- /dev/null +++ b/src/modality_alignment/metrics/mse/test.py @@ -0,0 +1,27 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import numpy as np + +print(">> Running mse") +out = subprocess.check_output([ + "./mse", + "--input", "sample_output.h5ad", + "--output", "output.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.h5ad") + +print(">> Check that output fits expected API") +adata = sc.read_h5ad("output.h5ad") + +# check id +assert "metric_id" in adata.uns +assert adata.uns["metric_id"] == "mse" +assert "metric_value" in adata.uns +assert type(adata.uns["metric_value"]) is np.float64 + +print(">> All tests passed successfully") From 60f0b6188e4671604a72f1d93201f05a0cae1243 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 22:34:37 +0200 Subject: [PATCH 0069/1233] add integration workflow for quick testing Former-commit-id: 00f7c97216aa716e290a1c3d2e04acb4703dbc7f --- src/modality_alignment/workflows/main.nf | 15 ++++++- .../workflows/nextflow.config | 2 + .../workflows/run_integration_test.sh | 15 +++++++ src/modality_alignment/workflows/test.nf | 40 +++++++++++++++++++ 4 files changed, 70 insertions(+), 2 deletions(-) create mode 100755 src/modality_alignment/workflows/run_integration_test.sh create mode 100644 src/modality_alignment/workflows/test.nf diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index c6c936f7fe..3820f2556f 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -9,7 +9,9 @@ nextflow.enable.dsl=2 targetDir = "$launchDir/target/nextflow" +include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) @@ -48,13 +50,22 @@ workflow get_scprep_csv_datasets { output_ } +workflow get_sample_datasets { + main: + output_ = Channel.fromList( [[ "sample_dataset", [], params]] ) \ + | sample_dataset + emit: + output_ +} + /******************************************************* * Main workflow * *******************************************************/ workflow { - get_scprep_csv_datasets \ - | (mnn & scot & harmonic_alignment) \ + (get_sample_datasets & get_scprep_csv_datasets) \ + | mix \ + | (sample_method & mnn & scot & harmonic_alignment) \ | mix | map(renameID) \ | (knn_auc & mse) \ | mix | map(renameID) \ diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index 63ecba799c..ad0766514c 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -3,9 +3,11 @@ manifest { } includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/sample_dataset/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/mnn/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/scot/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/methods/harmonic_alignment/nextflow.config" +includeConfig "$launchDir/target/nextflow/modality_alignment/methods/sample_method/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config" includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/mse/nextflow.config" includeConfig "$launchDir/target/nextflow/utils/extract_scores/nextflow.config" diff --git a/src/modality_alignment/workflows/run_integration_test.sh b/src/modality_alignment/workflows/run_integration_test.sh new file mode 100755 index 0000000000..aec1d2fa85 --- /dev/null +++ b/src/modality_alignment/workflows/run_integration_test.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/project_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/test.nf \ + -resume \ + --output output/modality_alignment/test + diff --git a/src/modality_alignment/workflows/test.nf b/src/modality_alignment/workflows/test.nf new file mode 100644 index 0000000000..c85a19f392 --- /dev/null +++ b/src/modality_alignment/workflows/test.nf @@ -0,0 +1,40 @@ +nextflow.enable.dsl=2 + +// This workflow assumes that the directory from which the +// pipeline is launched is the root of the opsca repository. + +/******************************************************* +* Import viash modules * +*******************************************************/ + +targetDir = "$launchDir/target/nextflow" + +include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) +include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) +include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) +include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) +include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) + +include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" + +// Helper function for redefining the ids of elements in a channel +// based on its files. +def renameID = { [ it[1].baseName, it[1], it[2] ] } + + +/******************************************************* +* Main workflow * +*******************************************************/ + +workflow { + Channel.fromList( [[ "sample_dataset", [], params]] ) \ + | sample_dataset \ + | sample_method \ + | map(renameID) \ + | (knn_auc & mse) \ + | mix | map(renameID) \ + | toSortedList \ + | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } + | extract_scores + +} From 2bd9ffd3b46171964defda9b3bd6a376a34d7746 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 23:01:35 +0200 Subject: [PATCH 0070/1233] update bash script Former-commit-id: ba56dde6bc2e1b9da81053cce8ec8a344a871d2c --- src/modality_alignment/workflows/run_bash.sh | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/modality_alignment/workflows/run_bash.sh b/src/modality_alignment/workflows/run_bash.sh index ecc0f52dca..8913cc4c19 100755 --- a/src/modality_alignment/workflows/run_bash.sh +++ b/src/modality_alignment/workflows/run_bash.sh @@ -18,7 +18,11 @@ mkdir -p $OUTPUT/metrics # generate datasets if [ ! -f "$OUTPUT/datasets/citeseq_cbmc.h5ad" ]; then - "$TARGET/datasets/data_scprep_csv/data_scprep_csv" \ + wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz' -O "$OUTPUT/datasets/citeseq_cbmc_input1.csv.gz" + wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz' -O "$OUTPUT/datasets/citeseq_cbmc_input2.csv.gz" + "$TARGET/datasets/scprep_csv/scprep_csv" \ + --input1 "$OUTPUT/datasets/citeseq_cbmc_input1.csv.gz" \ + --input2 "$OUTPUT/datasets/citeseq_cbmc_input2.csv.gz" \ --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" fi @@ -50,4 +54,4 @@ done # concatenate all scores into one tsv INPUTS=$(ls -1 "$OUTPUT/metrics" | sed "s#.*#-i '$OUTPUT/metrics/&'#" | tr '\n' ' ') -eval "$TARGET/../utils/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" +eval "$TARGET/../utils/extract_scores/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" From b084ea88422d729ffd2e41edb738706c79a09de9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Apr 2021 23:04:07 +0200 Subject: [PATCH 0071/1233] update bash script Former-commit-id: f6c0bd49df0c9ceb2bb86ecfe904d96e073b0b15 --- src/modality_alignment/workflows/run_bash.sh | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/modality_alignment/workflows/run_bash.sh b/src/modality_alignment/workflows/run_bash.sh index 8913cc4c19..f76481f750 100755 --- a/src/modality_alignment/workflows/run_bash.sh +++ b/src/modality_alignment/workflows/run_bash.sh @@ -18,12 +18,15 @@ mkdir -p $OUTPUT/metrics # generate datasets if [ ! -f "$OUTPUT/datasets/citeseq_cbmc.h5ad" ]; then - wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz' -O "$OUTPUT/datasets/citeseq_cbmc_input1.csv.gz" - wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz' -O "$OUTPUT/datasets/citeseq_cbmc_input2.csv.gz" + tmp1=`tempfile` + tmp2=`tempfile` + wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz' -O "$tmp1" + wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz' -O "$tmp2" "$TARGET/datasets/scprep_csv/scprep_csv" \ - --input1 "$OUTPUT/datasets/citeseq_cbmc_input1.csv.gz" \ - --input2 "$OUTPUT/datasets/citeseq_cbmc_input2.csv.gz" \ + --input1 "$tmp1" \ + --input2 "$tmp2" \ --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" + rm "$tmp1" "$tmp2" fi # run all methods on all datasets From b85a647b3f898772bbf9aeb24fee7e79657ef385 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 27 Apr 2021 08:34:44 +0200 Subject: [PATCH 0072/1233] use nextflow in repo Former-commit-id: d6c8fbb65bd2d27a1e62f87358feae7065674fe8 --- src/modality_alignment/workflows/run_integration_test.sh | 2 +- src/modality_alignment/workflows/run_nextflow.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/modality_alignment/workflows/run_integration_test.sh b/src/modality_alignment/workflows/run_integration_test.sh index aec1d2fa85..5832cf2e1b 100755 --- a/src/modality_alignment/workflows/run_integration_test.sh +++ b/src/modality_alignment/workflows/run_integration_test.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/test.nf \ +NXF_VER=20.10.0 bin/nextflow run src/modality_alignment/workflows/test.nf \ -resume \ --output output/modality_alignment/test diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index 16258e9dd3..4aa3bebb2b 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -NXF_VER=20.10.0 nextflow run src/modality_alignment/workflows/main.nf \ +NXF_VER=20.10.0 bin/nextflow run src/modality_alignment/workflows/main.nf \ -resume \ --output output/modality_alignment From dfb994ff846708b7eb52e002f5e317e749acff18 Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Wed, 12 May 2021 14:45:13 +0200 Subject: [PATCH 0073/1233] Prototype script & config for downloading dynverse datasets Former-commit-id: 3559fc690ec63ed2e2847caebd559fcb9c662dc3 --- .../datasets/config.vsh.yml | 29 ++++++++++ .../trajectory_inference/datasets/script.R | 55 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml create mode 100644 src/cellular_dynamics/trajectory_inference/datasets/script.R diff --git a/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml b/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml new file mode 100644 index 0000000000..9d0d3dd650 --- /dev/null +++ b/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml @@ -0,0 +1,29 @@ +functionality: + name: "download datasets" + namespace: "cellular_dynamics/trajectory_inference/datasets" + version: "dev" + description: "Download datasets to use for TI, mix of real and synthetic" + authors: + - name: "Louise Deconinck" + roles: [ maintainer, author ] + props: { github: LouiseDck } + arguments: + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file containing input matrices data" + required: true + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: "rocker/tidyverse:4.0.4" + setup: + - type: R + packages: + - httr + - anndata # needed by utils.py + - type: nextflow \ No newline at end of file diff --git a/src/cellular_dynamics/trajectory_inference/datasets/script.R b/src/cellular_dynamics/trajectory_inference/datasets/script.R new file mode 100644 index 0000000000..7c001109ee --- /dev/null +++ b/src/cellular_dynamics/trajectory_inference/datasets/script.R @@ -0,0 +1,55 @@ +## VIASH START +par <- list( + output = "datasets" +) +## VIASH END + + +library(httr) +library(tidyverse) + +output_dir <- tempfile() +dir.create(output_dir) + +# config +deposit_id <- 1443566 + +print("Retrieveing metadata") + +# retrieve file metadata from zenodo +files <- + GET(glue::glue("https://zenodo.org/api/records/{deposit_id}")) %>% + httr::content() %>% + .$files %>% + map_df(function(l) { + as_tibble(t(unlist(l))) + }) %>% + filter(grepl("^real/", filename)) %>% + mutate( + name = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), + url = paste0("https://github.com/dynverse/dyngen/raw/data_files/", name, ".rds"), + local_out = paste0(output_dir, "/", name, ".rds") + ) + +print("Downloading datasets & converting to AnnData & writing to file") + +# iterate over rows +pbapply::pblapply( + seq_len(nrow(files)), + cl = 8, + function(i) { + tmp <- tempfile() + on.exit(file.remove(tmp)) + + # download file + download.file(files$links.download[[i]], tmp, quiet = TRUE) + + # read counts + ds <- read_rds(tmp) + ad <- to_h5ad(ds) + ad$uns["dataset_id"] = ds$id + + write_h5ad(ad, paste0(par$output + "/" + ad$uns["dataset_id"])) + } +) + From e70a28ad7f4d1f89c5ee257cbb8c17c4d2088118 Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Wed, 12 May 2021 16:09:33 +0200 Subject: [PATCH 0074/1233] Provide dataset .tsv & component to download one of these datasets Former-commit-id: aeab42ea99ed09069cb134ac9d1237a6e5ce0c85 --- .../datasets/datasets.tsv | 111 ++++++++++++++++++ .../trajectory_inference/datasets/script.R | 50 ++------ .../datasets/write_dataset_table.R | 27 +++++ 3 files changed, 147 insertions(+), 41 deletions(-) create mode 100644 src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv create mode 100644 src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R diff --git 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"/tmp/RtmpZdE7os/file4d89176a3c47a/zenodo_1443566_real_silver_trophoblast-stem-cell-trophoblast-differentiation_mca.rds" diff --git a/src/cellular_dynamics/trajectory_inference/datasets/script.R b/src/cellular_dynamics/trajectory_inference/datasets/script.R index 7c001109ee..9a3548aedf 100644 --- a/src/cellular_dynamics/trajectory_inference/datasets/script.R +++ b/src/cellular_dynamics/trajectory_inference/datasets/script.R @@ -1,55 +1,23 @@ ## VIASH START par <- list( - output = "datasets" + output = "datasets", + download_link = "" ) ## VIASH END - library(httr) library(tidyverse) output_dir <- tempfile() dir.create(output_dir) -# config -deposit_id <- 1443566 - -print("Retrieveing metadata") +tmp <- tempfile() +on.exit(file.remove(tmp)) +download.file(files$links.download[[i]], tmp, quiet = TRUE) -# retrieve file metadata from zenodo -files <- - GET(glue::glue("https://zenodo.org/api/records/{deposit_id}")) %>% - httr::content() %>% - .$files %>% - map_df(function(l) { - as_tibble(t(unlist(l))) - }) %>% - filter(grepl("^real/", filename)) %>% - mutate( - name = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), - url = paste0("https://github.com/dynverse/dyngen/raw/data_files/", name, ".rds"), - local_out = paste0(output_dir, "/", name, ".rds") - ) +ds <- read_rds(tmp) +ad <- to_h5ad(ds) +ad$uns["dataset_id"] <- ds$id -print("Downloading datasets & converting to AnnData & writing to file") - -# iterate over rows -pbapply::pblapply( - seq_len(nrow(files)), - cl = 8, - function(i) { - tmp <- tempfile() - on.exit(file.remove(tmp)) - - # download file - download.file(files$links.download[[i]], tmp, quiet = TRUE) - - # read counts - ds <- read_rds(tmp) - ad <- to_h5ad(ds) - ad$uns["dataset_id"] = ds$id - - write_h5ad(ad, paste0(par$output + "/" + ad$uns["dataset_id"])) - } -) +write_h5ad(ad, paste0(par$output + "/" + ad$uns["dataset_id"])) diff --git a/src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R b/src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R new file mode 100644 index 0000000000..e51b591d43 --- /dev/null +++ b/src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R @@ -0,0 +1,27 @@ +library(httr) +library(tidyverse) + +output_dir <- tempfile() +dir.create(output_dir) + +# config +deposit_id <- 1443566 + +print("Retrieveing metadata") + +# retrieve file metadata from zenodo +files <- + GET(glue::glue("https://zenodo.org/api/records/{deposit_id}")) %>% + httr::content() %>% + .$files %>% + map_df(function(l) { + as_tibble(t(unlist(l))) + }) %>% + filter(grepl("^real/", filename)) %>% + mutate( + name = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), + url = paste0("https://github.com/dynverse/dyngen/raw/data_files/", name, ".rds"), + local_out = paste0(output_dir, "/", name, ".rds") + ) + +write.table(files, "src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv") From 3efd9fd7506626202dd07ed9fb6c1b4e05760697 Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Wed, 12 May 2021 16:14:26 +0200 Subject: [PATCH 0075/1233] Adapt .yaml Former-commit-id: 5b4c784a6a2de3e77ed9af3fe66b41c08f77ce4f --- .../trajectory_inference/datasets/config.vsh.yml | 7 +++++++ .../trajectory_inference/datasets/script.R | 3 ++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml b/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml index 9d0d3dd650..24547c7df6 100644 --- a/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml +++ b/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml @@ -8,6 +8,13 @@ functionality: roles: [ maintainer, author ] props: { github: LouiseDck } arguments: + - name: "--download_link" + alternatives: ["-d"] + type: "string" + direction: "input" + default: "" + description: "Input download link for the dataset" + required: true - name: "--output" alternatives: ["-o"] type: "file" diff --git a/src/cellular_dynamics/trajectory_inference/datasets/script.R b/src/cellular_dynamics/trajectory_inference/datasets/script.R index 9a3548aedf..bba091365e 100644 --- a/src/cellular_dynamics/trajectory_inference/datasets/script.R +++ b/src/cellular_dynamics/trajectory_inference/datasets/script.R @@ -13,7 +13,8 @@ dir.create(output_dir) tmp <- tempfile() on.exit(file.remove(tmp)) -download.file(files$links.download[[i]], tmp, quiet = TRUE) + +download.file(download_link, tmp, quiet = TRUE) ds <- read_rds(tmp) ad <- to_h5ad(ds) From 3b33282d21a7e45d22a360598fb3c3ba23fd184e Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Thu, 20 May 2021 15:45:56 +0200 Subject: [PATCH 0076/1233] nextflow config for downloading dynverse datasets Former-commit-id: 3f13b9a0a59942778dffec315d3b190bea29d8b4 --- src/test_comp/config.vsh.yaml | 36 +++++++++++++++++++ src/test_comp/script.sh | 11 ++++++ src/test_comp/test.sh | 34 ++++++++++++++++++ .../datasets/config.vsh.yml | 8 +++-- .../datasets/datasets.tsv | 0 .../trajectory_inference/datasets/script.R | 0 .../datasets/write_dataset_table.R | 0 src/trajectory_inference/workflows/main.nf | 33 +++++++++++++++++ 8 files changed, 120 insertions(+), 2 deletions(-) create mode 100755 src/test_comp/config.vsh.yaml create mode 100755 src/test_comp/script.sh create mode 100755 src/test_comp/test.sh rename src/{cellular_dynamics => }/trajectory_inference/datasets/config.vsh.yml (84%) rename src/{cellular_dynamics => }/trajectory_inference/datasets/datasets.tsv (100%) rename src/{cellular_dynamics => }/trajectory_inference/datasets/script.R (100%) rename src/{cellular_dynamics => }/trajectory_inference/datasets/write_dataset_table.R (100%) create mode 100644 src/trajectory_inference/workflows/main.nf diff --git a/src/test_comp/config.vsh.yaml b/src/test_comp/config.vsh.yaml new file mode 100755 index 0000000000..3ee4bb7bae --- /dev/null +++ b/src/test_comp/config.vsh.yaml @@ -0,0 +1,36 @@ +functionality: + name: "test_comp" + version: 0.0.1 + description: | + Replace this with a (multiline) description of your component. + arguments: + - name: "--input" + alternatives: [ "-i" ] + type: file + required: true + description: Describe the input file. + - name: "--output" + alternatives: [ "-o" ] + type: file + direction: output + required: true + description: Describe the output file. + - name: "--option" + type: string + description: Describe an optional parameter. + default: "default-" + resources: + - type: bash_script + path: script.sh + tests: + - type: bash_script + path: test.sh +platforms: + - type: docker + image: ubuntu:20.04 + setup: + - type: apt + packages: + - bash + - type: native + - type: nextflow diff --git a/src/test_comp/script.sh b/src/test_comp/script.sh new file mode 100755 index 0000000000..6e84fe75d0 --- /dev/null +++ b/src/test_comp/script.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +echo "This is a skeleton component" +echo "The arguments are:" +echo " - input: $par_input" +echo " - output: $par_output" +echo " - option: $par_option" +echo + +echo "Writing output file" +cat "$par_input" | sed "s#.*#$par_option-&#" > "$par_output" diff --git a/src/test_comp/test.sh b/src/test_comp/test.sh new file mode 100755 index 0000000000..fcb958a72c --- /dev/null +++ b/src/test_comp/test.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +set -ex + +echo ">>> Creating dummy input file" +cat > input.txt << HERE +one +two +three +HERE + +echo ">>> Running executable" +./test_comp --input input.txt --output output.txt --option FOO + +echo ">>> Checking whether output file exists" +[[ ! -f output.txt ]] && echo "Output file could not be found!" && exit 1 + +# create expected output file +cat > expected_output.txt << HERE +FOO-one +FOO-two +FOO-three +HERE + +echo ">>> Checking whether content matches expected content" +diff output.txt expected_output.txt +[ $? -ne 0 ] && echo "Output file did not equal expected output" && exit 1 + +# print final message +echo ">>> Test finished successfully" + +# do not remove this +# as otherwise your test might exit with a different exit code +exit 0 diff --git a/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml b/src/trajectory_inference/datasets/config.vsh.yml similarity index 84% rename from src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml rename to src/trajectory_inference/datasets/config.vsh.yml index 24547c7df6..9abb24ada3 100644 --- a/src/cellular_dynamics/trajectory_inference/datasets/config.vsh.yml +++ b/src/trajectory_inference/datasets/config.vsh.yml @@ -1,5 +1,5 @@ functionality: - name: "download datasets" + name: "download_datasets" namespace: "cellular_dynamics/trajectory_inference/datasets" version: "dev" description: "Download datasets to use for TI, mix of real and synthetic" @@ -8,6 +8,10 @@ functionality: roles: [ maintainer, author ] props: { github: LouiseDck } arguments: + - name: "--id" + type: "string" + default: "ti_dataset" + description: "The id of the output dataset id" - name: "--download_link" alternatives: ["-d"] type: "string" @@ -29,7 +33,7 @@ platforms: - type: docker image: "rocker/tidyverse:4.0.4" setup: - - type: R + - type: r packages: - httr - anndata # needed by utils.py diff --git a/src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv b/src/trajectory_inference/datasets/datasets.tsv similarity index 100% rename from src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv rename to src/trajectory_inference/datasets/datasets.tsv diff --git a/src/cellular_dynamics/trajectory_inference/datasets/script.R b/src/trajectory_inference/datasets/script.R similarity index 100% rename from src/cellular_dynamics/trajectory_inference/datasets/script.R rename to src/trajectory_inference/datasets/script.R diff --git a/src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R b/src/trajectory_inference/datasets/write_dataset_table.R similarity index 100% rename from src/cellular_dynamics/trajectory_inference/datasets/write_dataset_table.R rename to src/trajectory_inference/datasets/write_dataset_table.R diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf new file mode 100644 index 0000000000..8bff826bcf --- /dev/null +++ b/src/trajectory_inference/workflows/main.nf @@ -0,0 +1,33 @@ +nextflow.enable.dsl=2 + +targetDir = "$launchDir/target/nextflow" + +include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" + +include { download_datasets } from "$targetDir/cellular_dynamics/trajectory_inference/datasets/main.nf" params(params) + + + +/******************************************************* +* Dataset processor workflows * +*******************************************************/ +// This workflow reads in a tsv containing some metadata about each dataset. +// For each entry in the metadata, a dataset is generated, usually by downloading +// and processing some files. The end result of each of these workflows +// should be simply a channel of [id, h5adfile, params] triplets. +// +// If the need arises, these workflows could be split off into a separate file. + +workflow get_dynverse_datasets { + main: + output_ = Channel.fromPath(file("$launchDir/src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv")) \ + | splitCsv(header: true, sep: "\t") \ + | map { row -> + files = file(row.links.download) + newParams = overrideParams(params, "download_datasets", "id", row.id) + [ row.id, files, newParams ] + } \ + | download_datasets + emit: + output_ +} \ No newline at end of file From 1773b69236913f1c671227ae6e755cb9a91abc6b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 15:51:21 +0200 Subject: [PATCH 0077/1233] fix moving refactor, add script Former-commit-id: b9aadea8dafb57b242371e6bde1e88642d7a26ea --- .../{ => download_datasets}/config.vsh.yml | 4 ++-- .../datasets/{ => download_datasets}/datasets.tsv | 0 .../datasets/{ => download_datasets}/script.R | 0 .../{ => download_datasets}/write_dataset_table.R | 0 src/trajectory_inference/workflows/main.nf | 6 +++--- .../workflows/nextflow.config | 15 +++++++++++++++ .../workflows/run_nextflow.sh | 15 +++++++++++++++ 7 files changed, 35 insertions(+), 5 deletions(-) rename src/trajectory_inference/datasets/{ => download_datasets}/config.vsh.yml (92%) rename src/trajectory_inference/datasets/{ => download_datasets}/datasets.tsv (100%) rename src/trajectory_inference/datasets/{ => download_datasets}/script.R (100%) rename src/trajectory_inference/datasets/{ => download_datasets}/write_dataset_table.R (100%) create mode 100644 src/trajectory_inference/workflows/nextflow.config create mode 100755 src/trajectory_inference/workflows/run_nextflow.sh diff --git a/src/trajectory_inference/datasets/config.vsh.yml b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml similarity index 92% rename from src/trajectory_inference/datasets/config.vsh.yml rename to src/trajectory_inference/datasets/download_datasets/config.vsh.yml index 9abb24ada3..1e41a7c49f 100644 --- a/src/trajectory_inference/datasets/config.vsh.yml +++ b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml @@ -1,6 +1,6 @@ functionality: name: "download_datasets" - namespace: "cellular_dynamics/trajectory_inference/datasets" + namespace: "trajectory_inference/datasets" version: "dev" description: "Download datasets to use for TI, mix of real and synthetic" authors: @@ -37,4 +37,4 @@ platforms: packages: - httr - anndata # needed by utils.py - - type: nextflow \ No newline at end of file + - type: nextflow diff --git a/src/trajectory_inference/datasets/datasets.tsv b/src/trajectory_inference/datasets/download_datasets/datasets.tsv similarity index 100% rename from src/trajectory_inference/datasets/datasets.tsv rename to src/trajectory_inference/datasets/download_datasets/datasets.tsv diff --git a/src/trajectory_inference/datasets/script.R b/src/trajectory_inference/datasets/download_datasets/script.R similarity index 100% rename from src/trajectory_inference/datasets/script.R rename to src/trajectory_inference/datasets/download_datasets/script.R diff --git a/src/trajectory_inference/datasets/write_dataset_table.R b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R similarity index 100% rename from src/trajectory_inference/datasets/write_dataset_table.R rename to src/trajectory_inference/datasets/download_datasets/write_dataset_table.R diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index 8bff826bcf..5443038b28 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -4,7 +4,7 @@ targetDir = "$launchDir/target/nextflow" include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" -include { download_datasets } from "$targetDir/cellular_dynamics/trajectory_inference/datasets/main.nf" params(params) +include { download_datasets } from "$targetDir/trajectory_inference/datasets/download_datasets/main.nf" params(params) @@ -20,7 +20,7 @@ include { download_datasets } from "$targetDir/cellular_dynamics/trajector workflow get_dynverse_datasets { main: - output_ = Channel.fromPath(file("$launchDir/src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv")) \ + output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/datasets.tsv")) \ | splitCsv(header: true, sep: "\t") \ | map { row -> files = file(row.links.download) @@ -30,4 +30,4 @@ workflow get_dynverse_datasets { | download_datasets emit: output_ -} \ No newline at end of file +} diff --git a/src/trajectory_inference/workflows/nextflow.config b/src/trajectory_inference/workflows/nextflow.config new file mode 100644 index 0000000000..371b3c88ea --- /dev/null +++ b/src/trajectory_inference/workflows/nextflow.config @@ -0,0 +1,15 @@ +manifest { + nextflowVersion = '!>=20.10.0' +} + +includeConfig "$launchDir/target/nextflow/trajectory_inference/datasets/download_datasets/nextflow.config" + +docker { + runOptions = "-v $launchDir:$launchDir" +} + +process { + maxForks = 30 + container = 'ubuntu' + errorStrategy='ignore' +} diff --git a/src/trajectory_inference/workflows/run_nextflow.sh b/src/trajectory_inference/workflows/run_nextflow.sh new file mode 100755 index 0000000000..7e2baa325e --- /dev/null +++ b/src/trajectory_inference/workflows/run_nextflow.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/project_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +NXF_VER=20.10.0 bin/nextflow run src/trajectory_inference/workflows/main.nf \ + -resume \ + --output output/trajectory_inference + From dc0a9ca124a379f6b06489760fef50a99d52b6dd Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Thu, 20 May 2021 16:09:56 +0200 Subject: [PATCH 0078/1233] improve tsv Former-commit-id: 9a949d0c431866a670a16cd0e183cdf1ca9e9abb --- .../datasets/download_datasets/datasets.tsv | 222 +++++++++--------- .../download_datasets/write_dataset_table.R | 3 +- src/trajectory_inference/workflows/main.nf | 9 +- 3 files changed, 118 insertions(+), 116 deletions(-) diff --git a/src/trajectory_inference/datasets/download_datasets/datasets.tsv b/src/trajectory_inference/datasets/download_datasets/datasets.tsv index 2b2d10b959..70be7492bd 100644 --- a/src/trajectory_inference/datasets/download_datasets/datasets.tsv +++ b/src/trajectory_inference/datasets/download_datasets/datasets.tsv @@ -1,111 +1,111 @@ -"checksum" "filename" "filesize" "id" "links.download" "links.self" "name" "url" "local_out" -"1" "b889d9e24abbd1c6cbd603a8bfbb73c5" "real/gold/aging-hsc-old_kowalczyk.rds" "7068624" 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/tmp/RtmpNEhZTL/file149b868eba365/zenodo_1443566_real_silver_trophoblast-stem-cell-trophoblast-differentiation_mca.rds diff --git a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R index e51b591d43..726235793a 100644 --- a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R +++ b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R @@ -24,4 +24,5 @@ files <- local_out = paste0(output_dir, "/", name, ".rds") ) -write.table(files, "src/cellular_dynamics/trajectory_inference/datasets/datasets.tsv") +# TODO rename links.download as heasder to links_download +write_tsv(files, "src/trajectory_inference/datasets/download_datasets/datasets.tsv") \ No newline at end of file diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index 5443038b28..8644f65df7 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -18,16 +18,17 @@ include { download_datasets } from "$targetDir/trajectory_inference/datase // // If the need arises, these workflows could be split off into a separate file. -workflow get_dynverse_datasets { +workflow { main: - output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/datasets.tsv")) \ + output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/download_datasets/datasets.tsv")) \ | splitCsv(header: true, sep: "\t") \ | map { row -> - files = file(row.links.download) - newParams = overrideParams(params, "download_datasets", "id", row.id) + files = file(row.links_download) + newParams = overrideParams(params, "download_datasets", "id", row.name) [ row.id, files, newParams ] } \ | download_datasets emit: output_ } + From 66a7105a05f6603191b3300e3a12fd755c599601 Mon Sep 17 00:00:00 2001 From: Louise Deconinck Date: Thu, 20 May 2021 18:49:01 +0200 Subject: [PATCH 0079/1233] WIP, fixing dataset pipeline bugs Former-commit-id: 308c0d0c669ec7e466ccc13345e4ed26a82e3f71 --- .../datasets/download_datasets/config.vsh.yml | 9 +- .../datasets/download_datasets/datasets.tsv | 111 +----------------- .../datasets/download_datasets/script.R | 30 +++-- .../download_datasets/write_dataset_table.R | 4 +- src/trajectory_inference/workflows/main.nf | 4 +- 5 files changed, 33 insertions(+), 125 deletions(-) diff --git a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml index 1e41a7c49f..d42263cda3 100644 --- a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml +++ b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml @@ -12,13 +12,12 @@ functionality: type: "string" default: "ti_dataset" description: "The id of the output dataset id" - - name: "--download_link" + - name: "--input1" alternatives: ["-d"] - type: 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https://github.com/dynverse/dyngen/raw/data_files/zenodo_1443566_real_gold_aging-hsc-old_kowalczyk.rds /tmp/RtmpJ8Znre/file221c93a99ffe2/zenodo_1443566_real_gold_aging-hsc-old_kowalczyk.rds diff --git a/src/trajectory_inference/datasets/download_datasets/script.R b/src/trajectory_inference/datasets/download_datasets/script.R index bba091365e..060bd46b79 100644 --- a/src/trajectory_inference/datasets/download_datasets/script.R +++ b/src/trajectory_inference/datasets/download_datasets/script.R @@ -1,24 +1,36 @@ ## VIASH START par <- list( - output = "datasets", - download_link = "" + id = "ti_dataset", + output = "dataset", + input1 = "https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/silver/placenta-trophoblast-differentiation-invasive_mca.rds" ) ## VIASH END +print("1") + library(httr) library(tidyverse) +library(dynio) +library(anndata) output_dir <- tempfile() dir.create(output_dir) -tmp <- tempfile() -on.exit(file.remove(tmp)) +print("2") -download.file(download_link, tmp, quiet = TRUE) +if(par$input1 %>% startsWith("http://") || par$input1 %>% startsWith("https://")){ + # Check if link or local file + tmp <- tempfile() + on.exit(file.remove(tmp)) + + download.file(par$input1, tmp, quiet = TRUE) + +} else { + print("3") + tmp <- par$input1 +} ds <- read_rds(tmp) ad <- to_h5ad(ds) -ad$uns["dataset_id"] <- ds$id - -write_h5ad(ad, paste0(par$output + "/" + ad$uns["dataset_id"])) - +print("Here") +ad$write_h5ad(paste0(par$output)) diff --git a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R index 726235793a..5b7e4ba1cb 100644 --- a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R +++ b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R @@ -24,5 +24,7 @@ files <- local_out = paste0(output_dir, "/", name, ".rds") ) +files <- files[1,] + # TODO rename links.download as heasder to links_download -write_tsv(files, "src/trajectory_inference/datasets/download_datasets/datasets.tsv") \ No newline at end of file +write_tsv(files, "src/trajectory_inference/datasets/download_datasets/datasets.tsv") diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index 8644f65df7..0aa1952316 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -23,9 +23,9 @@ workflow { output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/download_datasets/datasets.tsv")) \ | splitCsv(header: true, sep: "\t") \ | map { row -> - files = file(row.links_download) + files = [ "input1": file(row.links_download)] newParams = overrideParams(params, "download_datasets", "id", row.name) - [ row.id, files, newParams ] + [ row.name, files, newParams] } \ | download_datasets emit: From 53726c3334f9759043affa5284d17ad369de81d3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 22:11:35 +0200 Subject: [PATCH 0080/1233] remove old component Former-commit-id: 56e0f028fc30b79b803a025ce5ea150ec1c08765 --- src/test_comp/config.vsh.yaml | 36 ----------------------------------- src/test_comp/script.sh | 11 ----------- src/test_comp/test.sh | 34 --------------------------------- 3 files changed, 81 deletions(-) delete mode 100755 src/test_comp/config.vsh.yaml delete mode 100755 src/test_comp/script.sh delete mode 100755 src/test_comp/test.sh diff --git a/src/test_comp/config.vsh.yaml b/src/test_comp/config.vsh.yaml deleted file mode 100755 index 3ee4bb7bae..0000000000 --- a/src/test_comp/config.vsh.yaml +++ /dev/null @@ -1,36 +0,0 @@ -functionality: - name: "test_comp" - version: 0.0.1 - description: | - Replace this with a (multiline) description of your component. - arguments: - - name: "--input" - alternatives: [ "-i" ] - type: file - required: true - description: Describe the input file. - - name: "--output" - alternatives: [ "-o" ] - type: file - direction: output - required: true - description: Describe the output file. - - name: "--option" - type: string - description: Describe an optional parameter. - default: "default-" - resources: - - type: bash_script - path: script.sh - tests: - - type: bash_script - path: test.sh -platforms: - - type: docker - image: ubuntu:20.04 - setup: - - type: apt - packages: - - bash - - type: native - - type: nextflow diff --git a/src/test_comp/script.sh b/src/test_comp/script.sh deleted file mode 100755 index 6e84fe75d0..0000000000 --- a/src/test_comp/script.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -echo "This is a skeleton component" -echo "The arguments are:" -echo " - input: $par_input" -echo " - output: $par_output" -echo " - option: $par_option" -echo - -echo "Writing output file" -cat "$par_input" | sed "s#.*#$par_option-&#" > "$par_output" diff --git a/src/test_comp/test.sh b/src/test_comp/test.sh deleted file mode 100755 index fcb958a72c..0000000000 --- a/src/test_comp/test.sh +++ /dev/null @@ -1,34 +0,0 @@ -#!/bin/bash - -set -ex - -echo ">>> Creating dummy input file" -cat > input.txt << HERE -one -two -three -HERE - -echo ">>> Running executable" -./test_comp --input input.txt --output output.txt --option FOO - -echo ">>> Checking whether output file exists" -[[ ! -f output.txt ]] && echo "Output file could not be found!" && exit 1 - -# create expected output file -cat > expected_output.txt << HERE -FOO-one -FOO-two -FOO-three -HERE - -echo ">>> Checking whether content matches expected content" -diff output.txt expected_output.txt -[ $? -ne 0 ] && echo "Output file did not equal expected output" && exit 1 - -# print final message -echo ">>> Test finished successfully" - -# do not remove this -# as otherwise your test might exit with a different exit code -exit 0 From 6008a6da58bc543b713fbc7bbada290a60a93498 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 22:11:51 +0200 Subject: [PATCH 0081/1233] rework dataset tsv fetcher 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https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/germline-human-both_guo.rds ff530a2b5f5e86c48fc88fb1c44df2c5 7171704 +zenodo_1443566_real_gold_germline-human-female_guo https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/germline-human-female_guo.rds b3c42c7c86a27468faea9e072dd6abae 2471628 diff --git a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R index 5b7e4ba1cb..99c747a88d 100644 --- a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R +++ b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R @@ -7,7 +7,7 @@ dir.create(output_dir) # config deposit_id <- 1443566 -print("Retrieveing metadata") +cat("Retrieving metadata\n") # retrieve file metadata from zenodo files <- @@ -17,14 +17,15 @@ files <- map_df(function(l) { as_tibble(t(unlist(l))) }) %>% - filter(grepl("^real/", filename)) %>% - mutate( - name = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), - url = paste0("https://github.com/dynverse/dyngen/raw/data_files/", name, ".rds"), - local_out = paste0(output_dir, "/", name, ".rds") + transmute( + id = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), + url = links.download, + checksum, + filesize ) -files <- files[1,] +# subsample dataset +files <- files %>% slice(1:10) -# TODO rename links.download as heasder to links_download +# TODO rename links.download as header to links_download write_tsv(files, "src/trajectory_inference/datasets/download_datasets/datasets.tsv") From 747d16269ca88e978fc529479ca2b82c020219c2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 22:12:10 +0200 Subject: [PATCH 0082/1233] rename input argument and fix dockerfile recipe Former-commit-id: 868d30ba71ccc577991dfb9a35895810fa530542 --- .../datasets/download_datasets/config.vsh.yml | 11 ++++++++--- src/trajectory_inference/workflows/main.nf | 5 ++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml index d42263cda3..f2ddd551ef 100644 --- a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml +++ b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml @@ -12,8 +12,8 @@ functionality: type: "string" default: "ti_dataset" description: "The id of the output dataset id" - - name: "--input1" - alternatives: ["-d"] + - name: "--input" + alternatives: ["-i"] type: "file" direction: "input" default: "" @@ -38,6 +38,11 @@ platforms: - anndata # needed by utils.py github: - dynverse/dynio + - type: apt + packages: + - python3 + - pip - type: python - + packages: + - anndata - type: nextflow diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index 0aa1952316..fdfd97088e 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -23,9 +23,8 @@ workflow { output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/download_datasets/datasets.tsv")) \ | splitCsv(header: true, sep: "\t") \ | map { row -> - files = [ "input1": file(row.links_download)] - newParams = overrideParams(params, "download_datasets", "id", row.name) - [ row.name, files, newParams] + newParams = overrideParams(params, "download_datasets", "id", row.id) + [ row.name, file(row.url), newParams] } \ | download_datasets emit: From ea48ec5505267880dd2539853bdb9996dc8707c6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 22:12:16 +0200 Subject: [PATCH 0083/1233] clean up script Former-commit-id: c876006b9668959ed1dbfba33975af6dabc81b42 --- .../datasets/download_datasets/script.R | 46 ++++++++++--------- 1 file changed, 25 insertions(+), 21 deletions(-) diff --git a/src/trajectory_inference/datasets/download_datasets/script.R b/src/trajectory_inference/datasets/download_datasets/script.R index 060bd46b79..4b0805c190 100644 --- a/src/trajectory_inference/datasets/download_datasets/script.R +++ b/src/trajectory_inference/datasets/download_datasets/script.R @@ -6,31 +6,35 @@ par <- list( ) ## VIASH END -print("1") +print("> Loading dependencies") -library(httr) +options(tidyverse.quiet = TRUE) # make sure tidyverse is quiet library(tidyverse) -library(dynio) -library(anndata) +requireNamespace("dynio", quietly = TRUE) +requireNamespace("anndata", quietly = TRUE) output_dir <- tempfile() dir.create(output_dir) -print("2") - -if(par$input1 %>% startsWith("http://") || par$input1 %>% startsWith("https://")){ - # Check if link or local file - tmp <- tempfile() - on.exit(file.remove(tmp)) - - download.file(par$input1, tmp, quiet = TRUE) - -} else { - print("3") - tmp <- par$input1 -} - -ds <- read_rds(tmp) -ad <- to_h5ad(ds) -print("Here") +cat("> Checking input parameter\n") + +input_path <- + if (grepl("^https?://", par$input)) { + cat("> Downloading file from remote\n") + # Check if link or local file + tmp <- tempfile() + on.exit(file.remove(tmp)) + utils::download.file(par$input, tmp, quiet = TRUE) + tmp + } else { + par$input + } + +cat("> Reading file\n") +ds <- read_rds(input_path) + +cat("> Converting RDS to h5ad\n") +ad <- dynio::to_h5ad(ds) + +cat("> Writing to h5ad\n") ad$write_h5ad(paste0(par$output)) From e3c0df08331eb1d703374cd0d8601fa7a9ca92ba Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 20 May 2021 22:13:44 +0200 Subject: [PATCH 0084/1233] fix rename bug Former-commit-id: 4c56ea103a374642455573b82b2822248f6b7899 --- src/trajectory_inference/workflows/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index fdfd97088e..3a2264c988 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -24,7 +24,7 @@ workflow { | splitCsv(header: true, sep: "\t") \ | map { row -> newParams = overrideParams(params, "download_datasets", "id", row.id) - [ row.name, file(row.url), newParams] + [ row.id, file(row.url), newParams] } \ | download_datasets emit: From eb2ddec86861c95f0dbd5ca191cb5e1a029bd984 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 14:41:45 +0200 Subject: [PATCH 0085/1233] add GitHub Actions workflows for building and testing the components Former-commit-id: 975e3449ffaf7c88b51c60b0889bd005ab3bab06 --- .github/workflows/viash-build.yml | 39 +++++++++++++++++++++++++++++++ .github/workflows/viash-test.yml | 37 +++++++++++++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 .github/workflows/viash-build.yml create mode 100644 .github/workflows/viash-test.yml diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml new file mode 100644 index 0000000000..d02fc258f5 --- /dev/null +++ b/.github/workflows/viash-build.yml @@ -0,0 +1,39 @@ +name: viash build CI + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + viash-build: + runs-on: ${{ matrix.config.os }} + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + config: + - {name: 'main', os: ubuntu-latest } + + steps: + - uses: actions/checkout@v2 + + - name: Build components + run: | + # allow publishing the target folder + sed -i '/^target\/$/d' .gitignore + + # skip docker builds + bin/project_build -c '.platforms[.type == "docker"].setup_strategy := "donothing"' + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: target_main + +# todo: add build for tag +# https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-create-git-tag diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml new file mode 100644 index 0000000000..c3b6b84435 --- /dev/null +++ b/.github/workflows/viash-test.yml @@ -0,0 +1,37 @@ +name: viash test CI + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + viash-test: + runs-on: ${{ matrix.config.os }} + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + config: + - {name: 'main', os: ubuntu-latest } + + steps: + - uses: actions/checkout@v2 + + - name: Run tests + run: | + # allow publishing the check_results folder + sed -i '/^check_results\/$/d' .gitignore + + # run tests and output results to check_results directory + mkdir check_results + bin/project_test --append=false --log=check_results/results.tsv + + - name: Upload check results + uses: actions/upload-artifact@master + with: + name: ${{ matrix.config.name }}_results + path: check_results + From 2074903c7e14140276995a8ed67fa4611465ac51 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 14:45:01 +0200 Subject: [PATCH 0086/1233] build before testing Former-commit-id: 3c74475a23cc95744b7bcd6112d69df3556a3814 --- .github/workflows/viash-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index c3b6b84435..8db70253f5 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -27,6 +27,7 @@ jobs: # run tests and output results to check_results directory mkdir check_results + bin/project_build bin/project_test --append=false --log=check_results/results.tsv - name: Upload check results From 18a1ef4e61ffaf92a65e60ff0fd309785eecd8b9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 14:45:43 +0200 Subject: [PATCH 0087/1233] extend gitignore Former-commit-id: 07600c88fd21520e2d75542689f3f8c4c3769cec --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 2187195d87..bdcfd61ec9 100644 --- a/.gitignore +++ b/.gitignore @@ -7,7 +7,8 @@ output_bash *.Rproj # viash specific ignores -target +target/ +check_results/ log.txt # nextflow specific ignores From 59c1a266b8336374cd8dccfb7460a831e37839a6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 15:10:46 +0200 Subject: [PATCH 0088/1233] try caching layers Former-commit-id: 8f47c92c69046317d2d3be210d617ef53c4f4d05 --- .github/workflows/viash-build.yml | 39 ------------------- .../{viash-test.yml => viash-ci.yml} | 22 ++++++++++- 2 files changed, 20 insertions(+), 41 deletions(-) delete mode 100644 .github/workflows/viash-build.yml rename .github/workflows/{viash-test.yml => viash-ci.yml} (61%) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml deleted file mode 100644 index d02fc258f5..0000000000 --- a/.github/workflows/viash-build.yml +++ /dev/null @@ -1,39 +0,0 @@ -name: viash build CI - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - viash-build: - runs-on: ${{ matrix.config.os }} - if: "!contains(github.event.head_commit.message, 'ci skip')" - - strategy: - fail-fast: false - matrix: - config: - - {name: 'main', os: ubuntu-latest } - - steps: - - uses: actions/checkout@v2 - - - name: Build components - run: | - # allow publishing the target folder - sed -i '/^target\/$/d' .gitignore - - # skip docker builds - bin/project_build -c '.platforms[.type == "docker"].setup_strategy := "donothing"' - - - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: . - publish_branch: target_main - -# todo: add build for tag -# https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-create-git-tag diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-ci.yml similarity index 61% rename from .github/workflows/viash-test.yml rename to .github/workflows/viash-ci.yml index 8db70253f5..9ea3a6b016 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-ci.yml @@ -1,4 +1,4 @@ -name: viash test CI +name: viash CI on: push: @@ -7,7 +7,7 @@ on: branches: [ main ] jobs: - viash-test: + viash-ci: runs-on: ${{ matrix.config.os }} if: "!contains(github.event.head_commit.message, 'ci skip')" @@ -19,6 +19,17 @@ jobs: steps: - uses: actions/checkout@v2 + + - uses: satackey/action-docker-layer-caching@v0.0.11 + continue-on-error: true + + - name: Build components + run: | + # allow publishing the target folder + sed -i '/^target\/$/d' .gitignore + + # skip docker builds + bin/project_build - name: Run tests run: | @@ -30,6 +41,13 @@ jobs: bin/project_build bin/project_test --append=false --log=check_results/results.tsv + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: target_main + - name: Upload check results uses: actions/upload-artifact@master with: From dbf227efccfe3d2c6cb15263ee882d9293884b46 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 16:56:57 +0200 Subject: [PATCH 0089/1233] WIP trajectory inference readme Former-commit-id: e4694824e42817ceff002c715869ef5f80d36dbb --- src/trajectory_inference/README.md | 27 ++++++++++++++++++ .../docs/images/trajectory_inference.png | Bin 0 -> 676367 bytes 2 files changed, 27 insertions(+) create mode 100644 src/trajectory_inference/README.md create mode 100644 src/trajectory_inference/docs/images/trajectory_inference.png diff --git a/src/trajectory_inference/README.md b/src/trajectory_inference/README.md new file mode 100644 index 0000000000..10942dd76f --- /dev/null +++ b/src/trajectory_inference/README.md @@ -0,0 +1,27 @@ +# Trajectory inference + +## Task description +Trajectory inference (TI) is a computational analysis used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression through the process. +A trajectory is a graph where the nodes represent noteworthy cellular states, and each cell is predicted to be progressing along transitions between the different states (Figure 1A). +Main applications of TI are identifying branch points, end states, predicting the topology of the dynamic process, or identifying genes whose expression varies gradually along the topology (Figure 1B). + +| ![](docs/images/trajectory_inference.png) | +|:--:| +| **Figure 1**: Trajectory inference for single-cell omics data. Image borrowed from [1]. **A**: During a dynamic process cells pass through several transitional states, characterized by different waves of transcriptional, morphological, epigenomic and/or surface marker changes [2]. TI methods provide an unbiased approach to identifying and correctly ordering different transitional stages. **B**: By overlaying gene expression levels on a dimensionality reduction, the milestones can be annotated to allow better interpretation of the cellular heterogeneity. | + +A comparison of 45 TI methods on 110 real and 229 synthetic datasets found that the different methods are very complementary when comparing different types of input datasets, and that performance of a method can be highly variable even in multiple runs on the same input dataset [3]. + +A persisting issue amongst TI methods is the usage of a standard definition of the task and usage of well-defined input and output data structures in order to make results comparable between methods. This task uses more restrictive version of the data structures proposed by Saelens et al. [3], but updated to make use of the anndata file format as used in the rest of the openproblems project. + +## Metrics + +## API + + + +## References +1. Robrecht Cannoodt. “Modelling single-cell dynamics with trajectories and gene regulatory networks“. Doctoral dissertation, Ghent University (2019). URL: [cannoodt.dev/files/phdthesis.pdf](https://cannoodt.dev/files/phdthesis.pdf). + +2. Tariq Enver et al. “Stem Cell States, Fates, and the Rules of Attraction”. In: Cell Stem Cell 4.5 (May 8, 2009), pp. 387–397. ISSN: 1875-9777. DOI: [10.1016/j.stem.2009.04.011](https://doi.org/10.1016/j.stem.2009.04.011). pmid: 19427289. + +3. Wouter Saelens, Cannoodt Robrecht et al. “A Comparison of Single-Cell Trajectory Inference Methods“. In: Nature Biotechnology 37 (May 2019). ISSN: 15461696. 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HcmV?d00001 From 4ecd79110398b9450933c05f50d549a5a3cad556 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 May 2021 17:12:51 +0200 Subject: [PATCH 0090/1233] add api discussion script Former-commit-id: f97aaa86ec618696a80bb58acc0854de77729d52 --- .../docs/api_discussion.R | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 src/trajectory_inference/docs/api_discussion.R diff --git a/src/trajectory_inference/docs/api_discussion.R b/src/trajectory_inference/docs/api_discussion.R new file mode 100644 index 0000000000..378202db7f --- /dev/null +++ b/src/trajectory_inference/docs/api_discussion.R @@ -0,0 +1,56 @@ +library(tidyverse) + +# example from: https://github.com/rcannood/phdthesis/blob/master/ch3_dynbenchmark/fig/snote1fig_1.pdf + +cell_ids <- c("a", "b", "c", "d", "e") +milestone_ids <- c("W", "X", "Y", "Z") + +milestone_network <- tribble( + ~from, ~to, ~length, ~directed, + "W", "X", 2, FALSE, + "X", "Y", 3, FALSE, + "X", "Z", 4, FALSE +) + +milestone_percentages <- tribble( + ~cell_id, ~milestone_id, ~percentage, + "a", "W", 0.9, + "a", "X", 0.1, + "b", "W", 0.2, + "b", "X", 0.8, + "c", "X", 0.8, + "c", "Z", 0.2, + "d", "X", 0.2, + "d", "Y", 0.7, + "d", "Z", 0.1, + "e", "X", 0.3, + "e", "Y", 0.2, + "e", "Z", 0.5 +) + +divergence_regions <- tribble( + ~divergence_id, ~milestone_id, ~is_start, + "XYZ", "X", TRUE, + "XYZ", "Y", FALSE, + "XYZ", "Z", FALSE +) + +library(dynwrap) + +convert_milestone_percentages_to_progressions( + cell_ids = cell_ids, + milestone_ids = milestone_ids, + milestone_network = milestone_network, + milestone_percentages = milestone_percentages +) + +traj <- + wrap_data(cell_ids = cell_ids) %>% + add_trajectory( + milestone_ids = milestone_ids, + milestone_network = milestone_network, + milestone_percentages = milestone_percentages, + divergence_regions = divergence_regions + ) + +plot_graph(traj) From b6ac83936ae35ea53c8dd3b009ac5cd8f7684c34 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 28 May 2021 07:17:14 +0200 Subject: [PATCH 0091/1233] fix script Former-commit-id: c5686c52bcb6d9a315dd34870b23ccf64f86fec1 --- src/trajectory_inference/docs/api_discussion.R | 1 + 1 file changed, 1 insertion(+) diff --git a/src/trajectory_inference/docs/api_discussion.R b/src/trajectory_inference/docs/api_discussion.R index 378202db7f..de2ee5fab9 100644 --- a/src/trajectory_inference/docs/api_discussion.R +++ b/src/trajectory_inference/docs/api_discussion.R @@ -36,6 +36,7 @@ divergence_regions <- tribble( ) library(dynwrap) +library(dynplot) convert_milestone_percentages_to_progressions( cell_ids = cell_ids, From a61a65c1ded75389e23a8d83a227dca1ee8b2c8c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 31 May 2021 20:57:35 +0200 Subject: [PATCH 0092/1233] extend readme Former-commit-id: e77b770f6ded412b276d0044351f294e0f2dc218 --- src/trajectory_inference/README.md | 56 +- .../docs/images/format.svg | 698 ++++++++++++++ .../docs/images/format_delayed.svg | 885 ++++++++++++++++++ 3 files changed, 1632 insertions(+), 7 deletions(-) create mode 100644 src/trajectory_inference/docs/images/format.svg create mode 100644 src/trajectory_inference/docs/images/format_delayed.svg diff --git a/src/trajectory_inference/README.md b/src/trajectory_inference/README.md index 10942dd76f..77e4526e04 100644 --- a/src/trajectory_inference/README.md +++ b/src/trajectory_inference/README.md @@ -5,23 +5,65 @@ Trajectory inference (TI) is a computational analysis used in single-cell transc A trajectory is a graph where the nodes represent noteworthy cellular states, and each cell is predicted to be progressing along transitions between the different states (Figure 1A). Main applications of TI are identifying branch points, end states, predicting the topology of the dynamic process, or identifying genes whose expression varies gradually along the topology (Figure 1B). -| ![](docs/images/trajectory_inference.png) | -|:--:| -| **Figure 1**: Trajectory inference for single-cell omics data. Image borrowed from [1]. **A**: During a dynamic process cells pass through several transitional states, characterized by different waves of transcriptional, morphological, epigenomic and/or surface marker changes [2]. TI methods provide an unbiased approach to identifying and correctly ordering different transitional stages. **B**: By overlaying gene expression levels on a dimensionality reduction, the milestones can be annotated to allow better interpretation of the cellular heterogeneity. | +![](docs/images/trajectory_inference.png) +**Figure 1**: Trajectory inference for single-cell omics data. Image borrowed from [1]. **A**: During a dynamic process cells pass through several transitional states, characterized by different waves of transcriptional, morphological, epigenomic and/or surface marker changes [2]. TI methods provide an unbiased approach to identifying and correctly ordering different transitional stages. **B**: By overlaying gene expression levels on a dimensionality reduction, the milestones can be annotated to allow better interpretation of the cellular heterogeneity. A comparison of 45 TI methods on 110 real and 229 synthetic datasets found that the different methods are very complementary when comparing different types of input datasets, and that performance of a method can be highly variable even in multiple runs on the same input dataset [3]. -A persisting issue amongst TI methods is the usage of a standard definition of the task and usage of well-defined input and output data structures in order to make results comparable between methods. This task uses more restrictive version of the data structures proposed by Saelens et al. [3], but updated to make use of the anndata file format as used in the rest of the openproblems project. +A persisting issue amongst TI methods is the usage of a standard definition of the task and usage of well-defined input and output data structures in order to make results comparable between methods. +This task assumes a trajectory consists of two data structures: the milestone network and the cell progressions (Figure 2). The milestone network is a data frame that must contain the columns 'from' (milestones), 'to' (milestones) and 'length' (> 0). The progressions is a data frame that must contain the columns 'cell_id' (name of the cell), 'from' and 'to' (transition it is located on), and 'percentage' (its' percentual progression along the transition). -## Metrics +![](docs/images/format.svg) +**Figure 2**: The data structure for a trajectory. -## API +These data structures first used in a the comparison of 45 TI methods [3]. It was also used in a TopCoder competition for Trajectory inference [4]. +## API via anndata +The interface of the following files are as follows: + +### Dataset generator + +**--output** is a dataset h5ad-file containing: + +* `ad.uns["dataset_id"]`: A unique identifier for the dataset. +* `ad.X`: a normalised expression matrix (Required). A sparse, double/numeric, M-by-N matrix, where M is the number of cells and N is the number of features. +* `ad.obsm["dimred"]`: a dimensionality reduction matrix (Optional). A dense, double/numeric, M-by-P matrix, where P << N. +* `ad.obs["clustering"]`: a clustering vector (Optional). an integer vector of length M. +* `ad.uns["traj_milestone_network"]`: Gold standard network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. +* `ad.uns["traj_progressions"]`: Gold standard cell progressions (Required). A data frame with columns 'cell_id', 'from', 'to', 'percentage'. + +### Method + +**--input** is a dataset h5ad file containing the objets `ad.uns["dataset_id"]` and `ad.X`, and may require `ad.obsm["dimred"]` and `"ad.obs["clustering"]`. Note that, a method should run successfully, **whether or not** a dimensionality reduction or clustering object is passed. + +**--output** is a prediction h5ad file containing: + +* `ad.uns["dataset_id"]`: The unique identifier for the dataset. +* `ad.uns["method"]`: A unique identifier for the method. +* `ad.uns["traj_milestone_network"]`: Predicted standard network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. +* `ad.uns["traj_progressions"]`: Predicted cell progressions (Required). A data frame with columns 'cell_id', 'from', 'to', 'percentage'. + + +## Metric + +**--dataset** is a dataset h5ad file. + +**--prediction** is a prediction h5ad file. + +**--output** is an evaluation h5ad file containing: + +* `ad.uns["evaluation"]`: A data frame containing columns `dataset_id`, `method_id`, `metric_id`, `value`. May contain one or more rows. + +## API via HDF5 + +This description can be provided if necessary, create an issue and mention @LouiseDck and @rcannood. ## References 1. Robrecht Cannoodt. “Modelling single-cell dynamics with trajectories and gene regulatory networks“. Doctoral dissertation, Ghent University (2019). URL: [cannoodt.dev/files/phdthesis.pdf](https://cannoodt.dev/files/phdthesis.pdf). 2. Tariq Enver et al. “Stem Cell States, Fates, and the Rules of Attraction”. In: Cell Stem Cell 4.5 (May 8, 2009), pp. 387–397. ISSN: 1875-9777. DOI: [10.1016/j.stem.2009.04.011](https://doi.org/10.1016/j.stem.2009.04.011). pmid: 19427289. -3. Wouter Saelens, Cannoodt Robrecht et al. “A Comparison of Single-Cell Trajectory Inference Methods“. In: Nature Biotechnology 37 (May 2019). ISSN: 15461696. DOI: [10.1038/s41587-019-0071-9](https://doi.org/10.1038/s41587-019-0071-9). \ No newline at end of file +3. Wouter Saelens, Cannoodt Robrecht et al. “A Comparison of Single-Cell Trajectory Inference Methods“. In: Nature Biotechnology 37 (May 2019). ISSN: 15461696. DOI: [10.1038/s41587-019-0071-9](https://doi.org/10.1038/s41587-019-0071-9). + +4. Luca Pinello et al. “TopCoder Challenge: Single-Cell Trajectory Inference Methods“. URL: [topcoder.com/lp/single-cell](https://www.topcoder.com/lp/single-cell). \ No newline at end of file diff --git a/src/trajectory_inference/docs/images/format.svg b/src/trajectory_inference/docs/images/format.svg new file mode 100644 index 0000000000..e9fbe39e2a --- /dev/null +++ b/src/trajectory_inference/docs/images/format.svg @@ -0,0 +1,698 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + Cell progressions + + + cell_idabcde + fromWWXXX + percentage0.10.80.20.80.7 + toXXZYZ + + + + + + + + + + + + + + + + + + + d + e + b + a + W + X + Y + Z + 2 + 3 + 4 + + c + + + + + Milestone network + fromWXX + toXYZ + length234 + + + + + + diff --git a/src/trajectory_inference/docs/images/format_delayed.svg b/src/trajectory_inference/docs/images/format_delayed.svg new file mode 100644 index 0000000000..141177ea31 --- /dev/null +++ b/src/trajectory_inference/docs/images/format_delayed.svg @@ -0,0 +1,885 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + d + e + b + a + W + X + Y + Z + 2 + 3 + 4 + + c + + + + Milestone network + fromWXX + toXYZ + length234 + + + Cell progressions + + + + Regions of delayedcommitment + + regionXYZXYZXYZ + toXYZ + is_beginTRUEFALSEFALSE + + + cell_idabcddee + fromWWXXXXX + percentage0.10.80.20.70.10.20.5 + toXXZYZYZ + + + From d9a79bfe75e616644a0228069dedd8b46f18b8dd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 31 May 2021 20:59:43 +0200 Subject: [PATCH 0093/1233] fix description Former-commit-id: 6ac7149d9920bf33f96b090fb177bf79f31e5816 --- src/trajectory_inference/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/trajectory_inference/README.md b/src/trajectory_inference/README.md index 77e4526e04..2e6fd4f283 100644 --- a/src/trajectory_inference/README.md +++ b/src/trajectory_inference/README.md @@ -26,7 +26,7 @@ The interface of the following files are as follows: **--output** is a dataset h5ad-file containing: -* `ad.uns["dataset_id"]`: A unique identifier for the dataset. +* `ad.uns["dataset_id"]`: A unique identifier for the dataset (Required). * `ad.X`: a normalised expression matrix (Required). A sparse, double/numeric, M-by-N matrix, where M is the number of cells and N is the number of features. * `ad.obsm["dimred"]`: a dimensionality reduction matrix (Optional). A dense, double/numeric, M-by-P matrix, where P << N. * `ad.obs["clustering"]`: a clustering vector (Optional). an integer vector of length M. @@ -39,9 +39,9 @@ The interface of the following files are as follows: **--output** is a prediction h5ad file containing: -* `ad.uns["dataset_id"]`: The unique identifier for the dataset. -* `ad.uns["method"]`: A unique identifier for the method. -* `ad.uns["traj_milestone_network"]`: Predicted standard network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. +* `ad.uns["dataset_id"]`: The unique identifier for the dataset (Required). +* `ad.uns["method"]`: A unique identifier for the method (Required). +* `ad.uns["traj_milestone_network"]`: Predicted network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. * `ad.uns["traj_progressions"]`: Predicted cell progressions (Required). A data frame with columns 'cell_id', 'from', 'to', 'percentage'. From b1442d31194062ccf33fa843c2888e675249f0f1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:36:23 +0200 Subject: [PATCH 0094/1233] update executables Former-commit-id: d97628184a335270375916c62d05d3f9dba19d9b --- bin/.gitignore | 2 + bin/README.md | 7 + bin/viash | 29 +- bin/viash-0.4.0.REMOVED.git-id | 1 - bin/viash_bootstrap | 761 +++++++++++++++++++++++++ bin/{project_build => viash_build} | 372 +++++++++--- bin/{project_clean => viash_clean_nxf} | 312 ++++++---- bin/{project_doc => viash_gendoc} | 320 +++++++---- bin/{project_debug => viash_genrep} | 321 +++++++---- bin/{project_push => viash_push} | 354 +++++++++--- bin/{skeleton => viash_skeleton} | 208 +++++-- bin/{project_test => viash_test} | 361 +++++++++--- bin/{vshtrafo => viash_trafo} | 175 ++++-- 13 files changed, 2502 insertions(+), 721 deletions(-) create mode 100644 bin/.gitignore create mode 100644 bin/README.md mode change 120000 => 100755 bin/viash delete mode 100644 bin/viash-0.4.0.REMOVED.git-id create mode 100755 bin/viash_bootstrap rename bin/{project_build => viash_build} (51%) rename bin/{project_clean => viash_clean_nxf} (64%) rename bin/{project_doc => viash_gendoc} (67%) rename bin/{project_debug => viash_genrep} (72%) rename bin/{project_push => viash_push} (54%) rename bin/{skeleton => viash_skeleton} (72%) rename bin/{project_test => viash_test} (52%) rename bin/{vshtrafo => viash_trafo} (69%) diff --git a/bin/.gitignore b/bin/.gitignore new file mode 100644 index 0000000000..48a23c5be0 --- /dev/null +++ b/bin/.gitignore @@ -0,0 +1,2 @@ +fetch +viash-* diff --git a/bin/README.md b/bin/README.md new file mode 100644 index 0000000000..9dcffa21a8 --- /dev/null +++ b/bin/README.md @@ -0,0 +1,7 @@ +These executables were generated by running: +``` +curl -s https://get.nextflow.io | bash + +# todo: use https://get.viash.io +viash_bootstrap -t 0.5.0-rc2 --log check_results/results.tsv +``` diff --git a/bin/viash b/bin/viash deleted file mode 120000 index 649f03c7e2..0000000000 --- a/bin/viash +++ /dev/null @@ -1 +0,0 @@ -viash-0.4.0 \ No newline at end of file diff --git a/bin/viash b/bin/viash new file mode 100755 index 0000000000..f9adcabc0c --- /dev/null +++ b/bin/viash @@ -0,0 +1,28 @@ +#!/bin/bash + +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} + + +VIASH_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` +VERSION="0.5.0-rc3" + +VIASH_EXEC="$VIASH_DIR/viash-$VERSION" + +if [[ ! -f $VIASH_EXEC ]]; then + wget https://github.com/data-intuitive/viash/releases/download/$VERSION/viash -O "$VIASH_EXEC" + chmod +x "$VIASH_EXEC" +fi + +$VIASH_EXEC "$@" diff --git a/bin/viash-0.4.0.REMOVED.git-id b/bin/viash-0.4.0.REMOVED.git-id deleted file mode 100644 index 54e7634593..0000000000 --- a/bin/viash-0.4.0.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -f7e633e1ea26db7659361af2358f34db54fd2474 \ No newline at end of file diff --git a/bin/viash_bootstrap b/bin/viash_bootstrap new file mode 100755 index 0000000000..4476b637e1 --- /dev/null +++ b/bin/viash_bootstrap @@ -0,0 +1,761 @@ +#!/usr/bin/env bash + +############################# +# viash_bootstrap 0.1 # +############################# + +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different +# license. The authors of this component should specify the license in the +# header of such files, or include a separate license file detailing the +# licenses of all included files. + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ +} + +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "viash_bootstrap 0.1" +echo "Bootstrap or update a viash project's CI/CD artefacts" + echo + echo "Options:" + +echo " --bin" +echo " type: file, output" +echo " default: bin" +echo " Target dir for viash scripts and tools" +echo "" + + +echo " -r, --registry" +echo " type: string" +echo " default: " +echo " Docker registry to use, only used when using a registry." +echo "" + + +echo " --namespace_separator" +echo " type: string" +echo " default: _" +echo " The separator to use between the component name and namespace as the image name of a Docker container." +echo "" + + +echo " -c, --config_mod" +echo " type: string, multiple values allowed" +echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." +echo "" + + +echo " -t, --tag" +echo " type: string" +echo " Which tag/version of viash to use, leave blank for the latest release" +echo "" + + +echo " --log" +echo " type: file" +echo " default: log.tsv" +echo " Path to write the test logs to." +echo "" + + +echo " --viash" +echo " type: file" +echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." +echo "" + +} +######## Helper functions for setting up Docker images for viash ######## + + +# ViashDockerRemoteTagCheck: check whether a Docker image is available +# on a remote. Assumes `docker login` has been performed, if relevant. +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerRemoteTagCheck python:latest +# echo $? # returns '0' +# ViashDockerRemoteTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerRemoteTagCheck { + docker manifest inspect $1 > /dev/null 2> /dev/null +} + +# ViashDockerLocalTagCheck: check whether a Docker image is available locally +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# docker pull python:latest +# ViashDockerLocalTagCheck python:latest +# echo $? # returns '0' +# ViashDockerLocalTagCheck sdaizudceahifu +# echo $? # returns '1' +function ViashDockerLocalTagCheck { + [ -n "$(docker images -q $1)" ] +} + +# ViashDockerPull: pull a Docker image +# +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was found +# examples: +# ViashDockerPull python:latest +# echo $? # returns '0' +# ViashDockerPull sdaizudceahifu +# echo $? # returns '1' +function ViashDockerPull { + ViashNotice "Running 'docker pull $1'" + docker pull $1 && return 0 || return 1 +} + +# ViashDockerPullElseBuild: pull a Docker image, else build it +# +# $1 : image identifier with format `[registry/]image[:tag]` +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerPullElseBuild mynewcomponent +function ViashDockerPullElseBuild { + set +e + ViashDockerPull $1 + out=$? + set -e + if [ $out -ne 0 ]; then + ViashDockerBuild $@ + fi +} + +# ViashDockerSetup: create a Docker image, according to specified docker setup strategy +# +# $1 : image identifier with format `[registry/]image[:tag]` +# $2 : docker setup strategy, see DockerSetupStrategy.scala +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. +# examples: +# ViashDockerSetup mynewcomponent alwaysbuild +function ViashDockerSetup { + VSHD_ID="$1" + VSHD_STRAT="$2" + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then + ViashDockerBuild $VSHD_ID + elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + set +e + ViashDockerLocalTagCheck $VSHD_ID + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + ViashInfo "Image $VSHD_ID already exists" + elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then + ViashDockerBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then + ViashDockerBuild $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then + ViashDockerPull $VSHD_ID + elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then + ViashDockerPullElseBuild $VSHD_ID --no-cache + elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then + ViashDockerPullElseBuild $VSHD_ID + else + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 + fi + elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then + set +e + docker push $VSHD_ID + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + ViashNotice "Container '$VSHD_ID' push succeeded." + else + ViashError "Container '$VSHD_ID' push errored." + exit 1 + fi + elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then + set +e + ViashDockerRemoteTagCheck $VSHD_ID + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + ViashNotice "Container '$VSHD_ID' exists, doing nothing." + else + ViashNotice "Container '$VSHD_ID' does not yet exist." + set +e + docker push $1 > /dev/null 2> /dev/null + outPush=$? + set -e + if [ $outPush -eq 0 ]; then + ViashNotice "Container '$VSHD_ID' push succeeded." + else + ViashError "Container '$VSHD_ID' push errored." + exit 1 + fi + fi + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + ViashNotice "Skipping setup." + else + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 + fi +} + + +######## End of helper functions for setting up Docker images for viash ######## + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + cat << 'VIASHDOCKER' +FROM dataintuitive/viash:latest + +RUN curl -sSLfo /usr/local/bin/fetch https://github.com/gruntwork-io/fetch/releases/download/v0.4.2/fetch_linux_amd64 +RUN chmod +x /usr/local/bin/fetch +VIASHDOCKER +} + +# ViashDockerBuild: build a docker container +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was built +function ViashDockerBuild { + + # create temporary directory to store dockerfile & optional resources in + tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_bootstrap-XXXXXX") + function clean_up { + rm -rf "$tmpdir" + } + trap clean_up EXIT + + # store dockerfile and resources + ViashDockerfile > $tmpdir/Dockerfile + cp -r $VIASH_RESOURCES_DIR/* $tmpdir + + # Build the container + ViashNotice "Running 'docker build -t $@ $tmpdir'" + set +e + if [ $VIASH_VERBOSITY -ge 6 ]; then + docker build -t $@ $tmpdir + else + docker build -t $@ $tmpdir &> $tmpdir/docker_build.log + fi + out=$? + set -e + if [ ! $out -eq 0 ]; then + ViashError "Error occurred while building the container $@." + if [ ! $VIASH_VERBOSITY -ge 6 ]; then + ViashError "Transcript: --------------------------------" + cat "$tmpdir/docker_build.log" + ViashError "End of transcript --------------------------" + fi + exit 1 + fi +} +# ViashAbsolutePath: generate absolute path from relative path +# borrowed from https://stackoverflow.com/a/21951256 +# $1 : relative filename +# return : absolute path +# examples: +# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt +# ViashAbsolutePath /foo/bar/.. # returns /foo +function ViashAbsolutePath { + local thePath + if [[ ! "$1" =~ ^/ ]]; then + thePath="$PWD/$1" + else + thePath="$1" + fi + echo "$thePath" | ( + IFS=/ + read -a parr + declare -a outp + for i in "${parr[@]}"; do + case "$i" in + ''|.) continue ;; + ..) + len=${#outp[@]} + if ((len==0)); then + continue + else + unset outp[$((len-1))] + fi + ;; + *) + len=${#outp[@]} + outp[$len]="$i" + ;; + esac + done + echo /"${outp[*]}" + ) +} +# ViashAutodetectMount: auto configuring docker mounts from parameters +# $1 : The parameter value +# returns : New parameter +# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker +# examples: +# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' +# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' +function ViashAutodetectMount { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "$mount_target/$base_name" +} +function ViashAutodetectMountArg { + abs_path=$(ViashAbsolutePath "$1") + if [ -d "$abs_path" ]; then + mount_source="$abs_path" + base_name="" + else + mount_source=`dirname "$abs_path"` + base_name=`basename "$abs_path"` + fi + mount_target="/viash_automount$mount_source" + echo "-v \"$mount_source:$mount_target\"" +} +# ViashExtractFlags: Retain leading flag +# $1 : string with a possible leading flag +# return : leading flag +# examples: +# ViashExtractFlags --foo=bar # returns --foo +function ViashExtractFlags { + echo $1 | sed 's/=.*//' +} +# initialise variables +VIASH_EXTRA_MOUNTS='' + +# initialise array +VIASH_POSITIONAL_ARGS='' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" + shift 1 + ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_bootstrap 0.1" + exit + ;; + --bin) + VIASH_PAR_BIN="$2" + shift 2 + ;; + --bin=*) + VIASH_PAR_BIN=$(ViashRemoveFlags "$1") + shift 1 + ;; + --registry) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --registry=*) + VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") + shift 1 + ;; + -r) + VIASH_PAR_REGISTRY="$2" + shift 2 + ;; + --namespace_separator) + VIASH_PAR_NAMESPACE_SEPARATOR="$2" + shift 2 + ;; + --namespace_separator=*) + VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") + shift 1 + ;; + --config_mod) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; + --config_mod=*) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + -c) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; + --tag) + VIASH_PAR_TAG="$2" + shift 2 + ;; + --tag=*) + VIASH_PAR_TAG=$(ViashRemoveFlags "$1") + shift 1 + ;; + -t) + VIASH_PAR_TAG="$2" + shift 2 + ;; + --log) + VIASH_PAR_LOG="$2" + shift 2 + ;; + --log=*) + VIASH_PAR_LOG=$(ViashRemoveFlags "$1") + shift 1 + ;; + --viash) + VIASH_PAR_VIASH="$2" + shift 2 + ;; + --viash=*) + VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") + shift 1 + ;; + ---setup) + ViashDockerSetup 'viash_viash_bootstrap:0.1' "$2" + exit 0 + ;; + ---setup=*) + ViashDockerSetup 'viash_viash_bootstrap:0.1' "$(ViashRemoveFlags "$1")" + exit 0 + ;; + ---dockerfile) + ViashDockerfile + exit 0 + ;; + ---v|---volume) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" + shift 2 + ;; + ---volume=*) + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" + shift 1 + ;; + ---debug) + ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_bootstrap:0.1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_bootstrap:0.1 + exit 0 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + +if [ -z "$VIASH_PAR_BIN" ]; then + VIASH_PAR_BIN="bin" +fi +if [ -z "$VIASH_PAR_REGISTRY" ]; then + VIASH_PAR_REGISTRY="" +fi +if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then + VIASH_PAR_NAMESPACE_SEPARATOR="_" +fi +if [ -z "$VIASH_PAR_LOG" ]; then + VIASH_PAR_LOG="log.tsv" +fi + +ViashDockerSetup 'viash_viash_bootstrap:0.1' ifneedbepullelsecachedbuild + +# detect volumes from file arguments +if [ ! -z "$VIASH_PAR_BIN" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_BIN")" + VIASH_PAR_BIN=$(ViashAutodetectMount "$VIASH_PAR_BIN") +fi +if [ ! -z "$VIASH_PAR_LOG" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_LOG")" + VIASH_PAR_LOG=$(ViashAutodetectMount "$VIASH_PAR_LOG") +fi +if [ ! -z "$VIASH_PAR_VIASH" ]; then + VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_VIASH")" + VIASH_PAR_VIASH=$(ViashAutodetectMount "$VIASH_PAR_VIASH") +fi + +# Always mount the resource directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" +VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") + +# Always mount the VIASH_TEMP directory +VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" +VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") + +# change file ownership +function viash_perform_chown { + + if [ ! -z "$VIASH_PAR_BIN" ]; then + eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_bootstrap:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_BIN" + fi +} +trap viash_perform_chown EXIT + + +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_bootstrap:0.1 +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_bootstrap-XXXXXX") +function clean_up { + rm "\$tempscript" +} +trap clean_up EXIT +cat > "\$tempscript" << 'VIASHMAIN' +# The following code has been auto-generated by Viash. +par_bin='$VIASH_PAR_BIN' +par_registry='$VIASH_PAR_REGISTRY' +par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' +par_config_mod='$VIASH_PAR_CONFIG_MOD' +par_tag='$VIASH_PAR_TAG' +par_log='$VIASH_PAR_LOG' +par_viash='$VIASH_PAR_VIASH' + +resources_dir="$VIASH_RESOURCES_DIR" + +#!/bin/bash + +# get the root of the repository +REPO_ROOT=\`pwd\` + +if [ ! -d "\$par_bin" ]; then + echo "> Creating \$par_bin" + mkdir "\$par_bin" +fi + +cd "\$par_bin" + +# Retrieving version +viash_version=\`viash -v | sed -E 's/^viash ([v0-9.]+[\\-rc0-9]*).*/\\1/'\` +if [ -z \$par_tag ]; then + par_tag="\$viash_version" + same_version=1 +else + same_version=0 +fi +echo "> Using tag \$par_tag" + +# remove previous binaries +echo "> Cleanup" +if [ -f viash ]; then + echo " > Removing previous versions of viash and recent project binaries" + rm viash* +fi +if [ -f project_update ]; then + echo " > Removing previous versions of project binaries" + rm project_* +fi +if [ -f skeleton ]; then + echo " > Removing previous versions of skeleton binary" + rm skeleton +fi + +# build helper components +build_dir=\$(mktemp -d) +function clean_up { + [[ -d "\$build_dir" ]] && rm -r "\$build_dir" +} +trap clean_up EXIT + +# Install viash itself +echo "> Install viash \$par_tag under \$par_bin" +if [ \$same_version = 1 ];then + cp \`which viash\` . +elif [ \$par_tag == "develop" ]; then + cd \$build_dir + git clone --branch develop https://github.com/viash-io/viash + cd \$build_dir/viash + ls + ./configure + make bin/viash + cp bin/viash \$par_bin + cd .. + rm -r viash + cd \$par_bin +else + wget -nv "https://github.com/viash-io/viash/releases/download/\$par_tag/viash" + chmod +x viash +fi + +# download viash components +echo "> Fetching components sources (version \$par_tag)" +fetch --repo="https://github.com/viash-io/viash" --branch="\$par_tag" --source-path="/src/viash" "\$build_dir" + +# build components +echo "> Building components" +./viash ns build \\ + -s "\$build_dir" \\ + -t . \\ + --flatten \\ + -c '.functionality.arguments[.name == "--registry"].default := "'\$par_registry'"' \\ + -c '.functionality.arguments[.name == "--viash"].default := "'\$par_viash'"' \\ + -c '.functionality.arguments[.name == "--log" && root.functionality.name == "project_test"].default := "'\$par_log'"' \\ + -c '.functionality.arguments[.name == "--namespace_separator"].default := "'\$par_namespace_separator'"' + +echo "> Done, happy viash-ing!" +VIASHMAIN +PATH="$VIASH_RESOURCES_DIR:\$PATH" + +bash "\$tempscript" + +VIASHEOF diff --git a/bin/project_build b/bin/viash_build similarity index 51% rename from bin/project_build rename to bin/viash_build index 16b85991f5..9eeb76b527 100755 --- a/bin/project_build +++ b/bin/viash_build @@ -1,12 +1,12 @@ #!/usr/bin/env bash -########################### -# project_build 0.1 # -########################### +######################### +# viash_build 0.1 # +######################### -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,65 +55,182 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} -function ViashSetup { -: +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ } +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Build a project, usually in the context of a pipeline." + echo "viash_build 0.1" +echo "Build a project, usually in the context of a pipeline." echo echo "Options:" - echo " -m string, --mode=string" - echo " type: string, default: development" - echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." - echo "" - echo " -p string, --platforms=string" - echo " type: string, default: docker|nextflow" - echo " Which platforms to test, default is 'docker|nextflow'." - echo "" - echo " -q string, --query=string" - echo " type: string" - echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." - echo "" - echo " -n string, --query_namespace=string" - echo " type: string" - echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." - echo "" - echo " --query_name=string" - echo " type: string" - echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." - echo "" - echo " -v string, --version=string" - echo " type: string, default: dev" - echo " Which version of the pipeline to use." - echo "" - echo " -r string, --registry=string" - echo " type: string, default: " - echo " Docker registry to use, only used when using a registry." - echo "" - echo " --namespace_separator=string" - echo " type: string, default: _" - echo " The separator to use between the component name and namespace as the image name of a Docker container." - echo "" - echo " -nc, --no-cache, --no_cache" - echo " type: boolean_true" - echo " Don't cache the docker build in development mode." - echo "" - echo " --log=file" - echo " type: file, default: log.txt" - echo " Log file" - echo "" - echo " --viash=file" - echo " type: file" - echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." - echo "" + +echo " -s, --src" +echo " type: file" +echo " default: src" +echo " Directory for sources if different from src/" +echo "" + + +echo " -m, --mode" +echo " type: string" +echo " default: development" +echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." +echo "" + + +echo " -p, --platforms" +echo " type: string" +echo " default: docker|nextflow" +echo " Which platforms to test, default is 'docker|nextflow'." +echo "" + + +echo " -q, --query" +echo " type: string" +echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." +echo "" + + +echo " -n, --query_namespace" +echo " type: string" +echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." +echo "" + + +echo " --query_name" +echo " type: string" +echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." +echo "" + + +echo " -t, --tag" +echo " type: string" +echo " default: dev" +echo " The tag/version to be used." +echo "" + + +echo " -r, --registry" +echo " type: string" +echo " default: " +echo " Docker registry to use, only used when using a registry." +echo "" + + +echo " --namespace_separator" +echo " type: string" +echo " default: _" +echo " The separator to use between the component name and namespace as the image name of a Docker container." +echo "" + + +echo " --max_threads" +echo " type: integer" +echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." +echo "" + + +echo " -c, --config_mod" +echo " type: string, multiple values allowed" +echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." +echo "" + + +echo " -nc, --no-cache, --no_cache" +echo " type: boolean_true" +echo " Don't cache the docker build in development mode." +echo "" + + +echo " --log" +echo " type: file, output" +echo " default: log.txt" +echo " Log file" +echo "" + + +echo " --viash" +echo " type: file" +echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." +echo "" + } # initialise array @@ -123,15 +240,40 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" + shift 1 + ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + --version) + echo "viash_build 0.1" + exit + ;; + --src) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --src=*) + VIASH_PAR_SRC=$(ViashRemoveFlags "$1") shift 1 ;; + -s) + VIASH_PAR_SRC="$2" + shift 2 + ;; --mode) VIASH_PAR_MODE="$2" shift 2 @@ -188,16 +330,16 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") shift 1 ;; - --version) - VIASH_PAR_VERSION="$2" + --tag) + VIASH_PAR_TAG="$2" shift 2 ;; - --version=*) - VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + --tag=*) + VIASH_PAR_TAG=$(ViashRemoveFlags "$1") shift 1 ;; - -v) - VIASH_PAR_VERSION="$2" + -t) + VIASH_PAR_TAG="$2" shift 2 ;; --registry) @@ -220,6 +362,38 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") shift 1 ;; + --max_threads) + VIASH_PAR_MAX_THREADS="$2" + shift 2 + ;; + --max_threads=*) + VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --config_mod) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; + --config_mod=*) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + -c) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; --no_cache) VIASH_PAR_NO_CACHE=true shift 1 @@ -256,29 +430,22 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS +if [ -z "$VIASH_PAR_SRC" ]; then + VIASH_PAR_SRC="src" +fi if [ -z "$VIASH_PAR_MODE" ]; then VIASH_PAR_MODE="development" fi if [ -z "$VIASH_PAR_PLATFORMS" ]; then VIASH_PAR_PLATFORMS="docker|nextflow" fi -if [ -z "$VIASH_PAR_VERSION" ]; then - VIASH_PAR_VERSION="dev" +if [ -z "$VIASH_PAR_TAG" ]; then + VIASH_PAR_TAG="dev" fi if [ -z "$VIASH_PAR_REGISTRY" ]; then VIASH_PAR_REGISTRY="" @@ -296,21 +463,24 @@ fi cat << VIASHEOF | bash set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_build-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_build-XXXXXX") function clean_up { rm "\$tempscript" } trap clean_up EXIT cat > "\$tempscript" << 'VIASHMAIN' # The following code has been auto-generated by Viash. +par_src='$VIASH_PAR_SRC' par_mode='$VIASH_PAR_MODE' par_platforms='$VIASH_PAR_PLATFORMS' par_query='$VIASH_PAR_QUERY' par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' par_query_name='$VIASH_PAR_QUERY_NAME' -par_version='$VIASH_PAR_VERSION' +par_tag='$VIASH_PAR_TAG' par_registry='$VIASH_PAR_REGISTRY' par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' +par_max_threads='$VIASH_PAR_MAX_THREADS' +par_config_mod='$VIASH_PAR_CONFIG_MOD' par_no_cache='$VIASH_PAR_NO_CACHE' par_log='$VIASH_PAR_LOG' par_viash='$VIASH_PAR_VIASH' @@ -335,6 +505,20 @@ if [ -z "\$par_viash" ]; then par_viash="viash" fi + +# if specified, use par_max_threads as a java argument +if [ ! -z "\$par_max_threads" ]; then + export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" +fi + +if [ "\$par_mode" == "release" ]; then + echo "In release mode with tag '\$par_tag'." + if [ "\$par_tag" == "dev" ]; then + echo "For a release, you have to specify an explicit version using --tag" + exit 1 + fi +fi + if [ "\$par_mode" == "development" ]; then echo "In development mode..." @@ -345,15 +529,16 @@ if [ "\$par_mode" == "development" ]; then fi "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ -c '.functionality.version := "dev"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "'\$setup_strat'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l -w \\ - --setup | tee "\$par_log" + --setup "\$setup_strat" | tee "\$par_log" elif [ "\$par_mode" == "integration" ]; then echo "In integration mode..." @@ -362,40 +547,39 @@ elif [ "\$par_mode" == "integration" ]; then fi "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "ifneedbepullelsecachedbuild"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l -w \\ - --setup | tee "\$par_log" + --setup "build" | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then - echo "In release mode..." if [ "\$par_no_cache" == "true" ]; then echo "Warning: '--no_cache' only applies when '--mode=development'." fi - if [ "\$par_version" == "dev" ]; then - echo "Error: For a release, you have to specify an explicit version using --version" - exit 1 - fi "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "build"' \\ + -c '.platforms[.type == "docker"].setup_strategy := "ifneedbepullelsecachedbuild"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l -w \\ - --setup | tee "\$par_log" + --setup "build" | tee "\$par_log" else echo "Not a valid mode argument" fi diff --git a/bin/project_clean b/bin/viash_clean_nxf similarity index 64% rename from bin/project_clean rename to bin/viash_clean_nxf index 1213fdcde3..b40704df66 100755 --- a/bin/project_clean +++ b/bin/viash_clean_nxf @@ -1,12 +1,12 @@ #!/usr/bin/env bash -########################### -# project_clean 0.1 # -########################### +############################# +# viash_clean_nxf 0.1 # +############################# -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,49 +55,108 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - : +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ } -# ViashDockerBuild: ... -function ViashDockerBuild { - ViashDockerPull $1 + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ +} + +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ } -# ViashSetup: ... -function ViashSetup { - ViashDockerSetup nextflow/nextflow:latest $VIASH_DOCKER_SETUP_STRATEGY +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ } -# ViashPush: ... -function ViashPush { - ViashDockerPush nextflow/nextflow:latest $VIASH_DOCKER_PUSH_STRATEGY +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ } +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Clean a (nextflow) project directory" + echo "viash_clean_nxf 0.1" +echo "Clean a (nextflow) project directory" echo echo "Options:" - echo " file" - echo " type: file, default: ." - echo " Base directory" - echo "" - echo " -after string" - echo " type: string" - echo "" - echo " -before string" - echo " type: string" - echo "" + +echo " dir" +echo " type: file" +echo " default: ." +echo " Base directory" +echo "" + + +echo " -after" +echo " type: string" +echo "" + + +echo " -before" +echo " type: string" +echo "" + } ######## Helper functions for setting up Docker images for viash ######## @@ -140,13 +199,14 @@ function ViashDockerLocalTagCheck { # ViashDockerPull sdaizudceahifu # echo $? # returns '1' function ViashDockerPull { - echo "> docker pull $1" + ViashNotice "Running 'docker pull $1'" docker pull $1 && return 0 || return 1 } # ViashDockerPullElseBuild: pull a Docker image, else build it # # $1 : image identifier with format `[registry/]image[:tag]` +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: # ViashDockerPullElseBuild mynewcomponent function ViashDockerPullElseBuild { @@ -165,26 +225,27 @@ function ViashDockerPullElseBuild { # $2 : docker setup strategy, see DockerSetupStrategy.scala # ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild +# ViashDockerSetup mynewcomponent alwaysbuild function ViashDockerSetup { VSHD_ID="$1" VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then ViashDockerPull $VSHD_ID elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then ViashDockerPullElseBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - echo "Skipping setup." elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + set +e ViashDockerLocalTagCheck $VSHD_ID - if [ $? -eq 0 ]; then - echo "Image $VSHD_ID already exists" + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + ViashInfo "Image $VSHD_ID already exists" elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then ViashDockerBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then @@ -196,62 +257,99 @@ function ViashDockerSetup { elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID else - echo "Unrecognised Docker strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi - else - echo "Unrecognised Docker strategy: $VSHD_STRAT" - fi -} - -# ViashDockerPush: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerPushStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild -function ViashDockerPush { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then set +e - docker push $1 + docker push $VSHD_ID outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "> $VSHD_ID force push ... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "> $VSHD_ID force push ... error" + ViashError "Container '$VSHD_ID' push errored." exit 1 fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then set +e - ViashDockerRemoteTagCheck $1 + ViashDockerRemoteTagCheck $VSHD_ID outCheck=$? set -e if [ $outCheck -eq 0 ]; then - echo "> $VSHD_ID exists, doing nothing" + ViashNotice "Container '$VSHD_ID' exists, doing nothing." else - echo -n "> $VSHD_ID does not exist, try pushing " + ViashNotice "Container '$VSHD_ID' does not yet exist." set +e docker push $1 > /dev/null 2> /dev/null outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "... error" + ViashError "Container '$VSHD_ID' push errored." + exit 1 fi fi + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + ViashNotice "Skipping setup." else - echo "Unrecognised Docker push strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi } + ######## End of helper functions for setting up Docker images for viash ######## -# initialise variables -VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' -VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + cat << 'VIASHDOCKER' +FROM nextflow/nextflow:latest + +RUN : +VIASHDOCKER +} + +# ViashDockerBuild: build a docker container +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was built +function ViashDockerBuild { + + # create temporary directory to store dockerfile & optional resources in + tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_clean_nxf-XXXXXX") + function clean_up { + rm -rf "$tmpdir" + } + trap clean_up EXIT + + # store dockerfile and resources + ViashDockerfile > $tmpdir/Dockerfile + cp -r $VIASH_RESOURCES_DIR/* $tmpdir + + # Build the container + ViashNotice "Running 'docker build -t $@ $tmpdir'" + set +e + if [ $VIASH_VERBOSITY -ge 6 ]; then + docker build -t $@ $tmpdir + else + docker build -t $@ $tmpdir &> $tmpdir/docker_build.log + fi + out=$? + set -e + if [ ! $out -eq 0 ]; then + ViashError "Error occurred while building the container $@." + if [ ! $VIASH_VERBOSITY -ge 6 ]; then + ViashError "Transcript: --------------------------------" + cat "$tmpdir/docker_build.log" + ViashError "End of transcript --------------------------" + fi + exit 1 + fi +} # ViashAbsolutePath: generate absolute path from relative path # borrowed from https://stackoverflow.com/a/21951256 # $1 : relative filename @@ -339,15 +437,28 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_clean_nxf 0.1" + exit + ;; -after) VIASH_PAR_AFTER="$2" shift 2 @@ -356,25 +467,13 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_BEFORE="$2" shift 2 ;; - ---dss|---docker_setup_strategy) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY="$2" - shift 2 - ;; - ---docker_setup_strategy=*) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 - ;; - ---dps|---docker_push_strategy) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY="$2" - shift 2 + ---setup) + ViashDockerSetup 'viash_viash_clean_nxf:0.1' "$2" + exit 0 ;; - ---docker_push_strategy=*) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 + ---setup=*) + ViashDockerSetup 'viash_viash_clean_nxf:0.1' "$(ViashRemoveFlags "$1")" + exit 0 ;; ---dockerfile) ViashDockerfile @@ -389,8 +488,8 @@ while [[ $# -gt 0 ]]; do shift 1 ;; ---debug) - echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t nextflow/nextflow:latest" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t nextflow/nextflow:latest + ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_clean_nxf:0.1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_clean_nxf:0.1 exit 0 ;; *) # positional arg or unknown option @@ -401,16 +500,6 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS @@ -423,6 +512,7 @@ if [ -z "$VIASH_PAR_DIR" ]; then VIASH_PAR_DIR="." fi +ViashDockerSetup 'viash_viash_clean_nxf:0.1' ifneedbepullelsecachedbuild # detect volumes from file arguments if [ ! -z "$VIASH_PAR_DIR" ]; then @@ -445,9 +535,9 @@ function viash_perform_chown { trap viash_perform_chown EXIT -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS nextflow/nextflow:latest +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_clean_nxf:0.1 set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_clean-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_clean_nxf-XXXXXX") function clean_up { rm "\$tempscript" } diff --git a/bin/project_doc b/bin/viash_gendoc similarity index 67% rename from bin/project_doc rename to bin/viash_gendoc index 0834de8f06..18c79bc6c1 100755 --- a/bin/project_doc +++ b/bin/viash_gendoc @@ -1,12 +1,12 @@ #!/usr/bin/env bash -######################### -# project_doc 0.1 # -######################### +########################## +# viash_gendoc 0.1 # +########################## -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,51 +55,112 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - : +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ } -# ViashDockerBuild: ... -function ViashDockerBuild { - ViashDockerPull $1 + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ } -# ViashSetup: ... -function ViashSetup { - ViashDockerSetup dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_SETUP_STRATEGY +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ } -# ViashPush: ... -function ViashPush { - ViashDockerPush dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_PUSH_STRATEGY +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ } +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Generate documentation" + echo "viash_gendoc 0.1" +echo "Generate documentation" echo echo "Options:" - echo " file" - echo " type: file, default: ." - echo " Repository to generate documentation for" - echo "" - echo " -s string, --src=string" - echo " type: string, default: src" - echo " Folder to search for components, usually just src/" - echo "" - echo " -r file, --output=file" - echo " type: file, default: project_doc.md" - echo " Name/path of the output markdown file" - echo "" + +echo " repo" +echo " type: file" +echo " default: ." +echo " Repository to generate documentation for" +echo "" + + +echo " -s, --src" +echo " type: string" +echo " default: src" +echo " Folder to search for components, usually just src/" +echo "" + + +echo " -r, --output" +echo " type: file, output" +echo " default: project_doc.md" +echo " Name/path of the output markdown file" +echo "" + } ######## Helper functions for setting up Docker images for viash ######## @@ -142,13 +203,14 @@ function ViashDockerLocalTagCheck { # ViashDockerPull sdaizudceahifu # echo $? # returns '1' function ViashDockerPull { - echo "> docker pull $1" + ViashNotice "Running 'docker pull $1'" docker pull $1 && return 0 || return 1 } # ViashDockerPullElseBuild: pull a Docker image, else build it # # $1 : image identifier with format `[registry/]image[:tag]` +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: # ViashDockerPullElseBuild mynewcomponent function ViashDockerPullElseBuild { @@ -167,26 +229,27 @@ function ViashDockerPullElseBuild { # $2 : docker setup strategy, see DockerSetupStrategy.scala # ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild +# ViashDockerSetup mynewcomponent alwaysbuild function ViashDockerSetup { VSHD_ID="$1" VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then ViashDockerPull $VSHD_ID elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then ViashDockerPullElseBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - echo "Skipping setup." elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + set +e ViashDockerLocalTagCheck $VSHD_ID - if [ $? -eq 0 ]; then - echo "Image $VSHD_ID already exists" + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + ViashInfo "Image $VSHD_ID already exists" elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then ViashDockerBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then @@ -198,62 +261,99 @@ function ViashDockerSetup { elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID else - echo "Unrecognised Docker strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi - else - echo "Unrecognised Docker strategy: $VSHD_STRAT" - fi -} - -# ViashDockerPush: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerPushStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild -function ViashDockerPush { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then set +e - docker push $1 + docker push $VSHD_ID outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "> $VSHD_ID force push ... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "> $VSHD_ID force push ... error" + ViashError "Container '$VSHD_ID' push errored." exit 1 fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then set +e - ViashDockerRemoteTagCheck $1 + ViashDockerRemoteTagCheck $VSHD_ID outCheck=$? set -e if [ $outCheck -eq 0 ]; then - echo "> $VSHD_ID exists, doing nothing" + ViashNotice "Container '$VSHD_ID' exists, doing nothing." else - echo -n "> $VSHD_ID does not exist, try pushing " + ViashNotice "Container '$VSHD_ID' does not yet exist." set +e docker push $1 > /dev/null 2> /dev/null outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "... error" + ViashError "Container '$VSHD_ID' push errored." + exit 1 fi fi + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + ViashNotice "Skipping setup." else - echo "Unrecognised Docker push strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi } + ######## End of helper functions for setting up Docker images for viash ######## -# initialise variables -VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' -VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + cat << 'VIASHDOCKER' +FROM dataintuitive/viash:0.4.0-rc1 + +RUN : +VIASHDOCKER +} + +# ViashDockerBuild: build a docker container +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was built +function ViashDockerBuild { + + # create temporary directory to store dockerfile & optional resources in + tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_gendoc-XXXXXX") + function clean_up { + rm -rf "$tmpdir" + } + trap clean_up EXIT + + # store dockerfile and resources + ViashDockerfile > $tmpdir/Dockerfile + cp -r $VIASH_RESOURCES_DIR/* $tmpdir + + # Build the container + ViashNotice "Running 'docker build -t $@ $tmpdir'" + set +e + if [ $VIASH_VERBOSITY -ge 6 ]; then + docker build -t $@ $tmpdir + else + docker build -t $@ $tmpdir &> $tmpdir/docker_build.log + fi + out=$? + set -e + if [ ! $out -eq 0 ]; then + ViashError "Error occurred while building the container $@." + if [ ! $VIASH_VERBOSITY -ge 6 ]; then + ViashError "Transcript: --------------------------------" + cat "$tmpdir/docker_build.log" + ViashError "End of transcript --------------------------" + fi + exit 1 + fi +} # ViashAbsolutePath: generate absolute path from relative path # borrowed from https://stackoverflow.com/a/21951256 # $1 : relative filename @@ -341,15 +441,28 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_gendoc 0.1" + exit + ;; --src) VIASH_PAR_SRC="$2" shift 2 @@ -374,25 +487,13 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_OUTPUT="$2" shift 2 ;; - ---dss|---docker_setup_strategy) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY="$2" - shift 2 - ;; - ---docker_setup_strategy=*) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 - ;; - ---dps|---docker_push_strategy) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY="$2" - shift 2 + ---setup) + ViashDockerSetup 'viash_viash_gendoc:0.1' "$2" + exit 0 ;; - ---docker_push_strategy=*) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 + ---setup=*) + ViashDockerSetup 'viash_viash_gendoc:0.1' "$(ViashRemoveFlags "$1")" + exit 0 ;; ---dockerfile) ViashDockerfile @@ -407,8 +508,8 @@ while [[ $# -gt 0 ]]; do shift 1 ;; ---debug) - echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1 + ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_gendoc:0.1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_gendoc:0.1 exit 0 ;; *) # positional arg or unknown option @@ -419,16 +520,6 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS @@ -447,6 +538,7 @@ if [ -z "$VIASH_PAR_OUTPUT" ]; then VIASH_PAR_OUTPUT="project_doc.md" fi +ViashDockerSetup 'viash_viash_gendoc:0.1' ifneedbepullelsecachedbuild # detect volumes from file arguments if [ ! -z "$VIASH_PAR_REPO" ]; then @@ -470,15 +562,15 @@ VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") function viash_perform_chown { if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" + eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_gendoc:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" fi } trap viash_perform_chown EXIT -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_gendoc:0.1 set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_doc-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_gendoc-XXXXXX") function clean_up { rm "\$tempscript" } diff --git a/bin/project_debug b/bin/viash_genrep similarity index 72% rename from bin/project_debug rename to bin/viash_genrep index 40620cde6c..44fc5d7f28 100755 --- a/bin/project_debug +++ b/bin/viash_genrep @@ -1,12 +1,12 @@ #!/usr/bin/env bash -########################### -# project_debug 0.1 # -########################### +########################## +# viash_genrep 0.1 # +########################## -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,51 +55,111 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - : +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ } -# ViashDockerBuild: ... -function ViashDockerBuild { - ViashDockerPull $1 + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ } -# ViashSetup: ... -function ViashSetup { - ViashDockerSetup dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_SETUP_STRATEGY +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ } -# ViashPush: ... -function ViashPush { - ViashDockerPush dataintuitive/viash:0.4.0-rc1 $VIASH_DOCKER_PUSH_STRATEGY +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ } +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Generate debugging report based on viash ns test output" + echo "viash_genrep 0.1" +echo "Generate a test report based on viash ns test output" echo echo "Options:" - echo " --input=file" - echo " type: file, required parameter" - echo " viasn ns test output file (tsv format)" - echo "" - echo " --tmp=file" - echo " type: file, default: /tmp" - echo " System temp dir if different from /tmp (e.g. on Mac use /private/tmp)" - echo "" - echo " --output=file" - echo " type: file, default: debug_report.md" - echo " Name/path of the output markdown file" - echo "" + +echo " --input" +echo " type: file, required parameter" +echo " viasn ns test output file (tsv format)" +echo "" + + +echo " --tmp" +echo " type: file" +echo " default: /tmp" +echo " System temp dir if different from /tmp (e.g. on Mac use /private/tmp)" +echo "" + + +echo " --output" +echo " type: file, output" +echo " default: debug_report.md" +echo " Name/path of the output markdown file" +echo "" + } ######## Helper functions for setting up Docker images for viash ######## @@ -142,13 +202,14 @@ function ViashDockerLocalTagCheck { # ViashDockerPull sdaizudceahifu # echo $? # returns '1' function ViashDockerPull { - echo "> docker pull $1" + ViashNotice "Running 'docker pull $1'" docker pull $1 && return 0 || return 1 } # ViashDockerPullElseBuild: pull a Docker image, else build it # # $1 : image identifier with format `[registry/]image[:tag]` +# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: # ViashDockerPullElseBuild mynewcomponent function ViashDockerPullElseBuild { @@ -167,26 +228,27 @@ function ViashDockerPullElseBuild { # $2 : docker setup strategy, see DockerSetupStrategy.scala # ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. # examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild +# ViashDockerSetup mynewcomponent alwaysbuild function ViashDockerSetup { VSHD_ID="$1" VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" ]; then + if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" ]; then + elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then ViashDockerPull $VSHD_ID elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then ViashDockerPullElseBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" ]; then + elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - echo "Skipping setup." elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then + set +e ViashDockerLocalTagCheck $VSHD_ID - if [ $? -eq 0 ]; then - echo "Image $VSHD_ID already exists" + outCheck=$? + set -e + if [ $outCheck -eq 0 ]; then + ViashInfo "Image $VSHD_ID already exists" elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then ViashDockerBuild $VSHD_ID --no-cache elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then @@ -198,62 +260,99 @@ function ViashDockerSetup { elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then ViashDockerPullElseBuild $VSHD_ID else - echo "Unrecognised Docker strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi - else - echo "Unrecognised Docker strategy: $VSHD_STRAT" - fi -} - -# ViashDockerPush: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerPushStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent alwaysbuild -function ViashDockerPush { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwayspush" -o "$VSHD_STRAT" == "force" ]; then + elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then set +e - docker push $1 + docker push $VSHD_ID outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "> $VSHD_ID force push ... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "> $VSHD_ID force push ... error" + ViashError "Container '$VSHD_ID' push errored." exit 1 fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" ]; then + elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then set +e - ViashDockerRemoteTagCheck $1 + ViashDockerRemoteTagCheck $VSHD_ID outCheck=$? set -e if [ $outCheck -eq 0 ]; then - echo "> $VSHD_ID exists, doing nothing" + ViashNotice "Container '$VSHD_ID' exists, doing nothing." else - echo -n "> $VSHD_ID does not exist, try pushing " + ViashNotice "Container '$VSHD_ID' does not yet exist." set +e docker push $1 > /dev/null 2> /dev/null outPush=$? set -e if [ $outPush -eq 0 ]; then - echo "... ok" + ViashNotice "Container '$VSHD_ID' push succeeded." else - echo "... error" + ViashError "Container '$VSHD_ID' push errored." + exit 1 fi fi + elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then + ViashNotice "Skipping setup." else - echo "Unrecognised Docker push strategy: $VSHD_STRAT" + ViashError "Unrecognised Docker strategy: $VSHD_STRAT" + exit 1 fi } + ######## End of helper functions for setting up Docker images for viash ######## -# initialise variables -VIASH_DOCKER_SETUP_STRATEGY='alwayscachedbuild' -VIASH_DOCKER_PUSH_STRATEGY='pushifnotpresent' + +# ViashDockerFile: print the dockerfile to stdout +# return : dockerfile required to run this component +# examples: +# ViashDockerFile +function ViashDockerfile { + cat << 'VIASHDOCKER' +FROM dataintuitive/viash:0.4.0-rc1 + +RUN : +VIASHDOCKER +} + +# ViashDockerBuild: build a docker container +# $1 : image identifier with format `[registry/]image[:tag]` +# exit code $? : whether or not the image was built +function ViashDockerBuild { + + # create temporary directory to store dockerfile & optional resources in + tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_genrep-XXXXXX") + function clean_up { + rm -rf "$tmpdir" + } + trap clean_up EXIT + + # store dockerfile and resources + ViashDockerfile > $tmpdir/Dockerfile + cp -r $VIASH_RESOURCES_DIR/* $tmpdir + + # Build the container + ViashNotice "Running 'docker build -t $@ $tmpdir'" + set +e + if [ $VIASH_VERBOSITY -ge 6 ]; then + docker build -t $@ $tmpdir + else + docker build -t $@ $tmpdir &> $tmpdir/docker_build.log + fi + out=$? + set -e + if [ ! $out -eq 0 ]; then + ViashError "Error occurred while building the container $@." + if [ ! $VIASH_VERBOSITY -ge 6 ]; then + ViashError "Transcript: --------------------------------" + cat "$tmpdir/docker_build.log" + ViashError "End of transcript --------------------------" + fi + exit 1 + fi +} # ViashAbsolutePath: generate absolute path from relative path # borrowed from https://stackoverflow.com/a/21951256 # $1 : relative filename @@ -341,15 +440,28 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_genrep 0.1" + exit + ;; --input) VIASH_PAR_INPUT="$2" shift 2 @@ -374,25 +486,13 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") shift 1 ;; - ---dss|---docker_setup_strategy) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY="$2" - shift 2 - ;; - ---docker_setup_strategy=*) - VIASH_EXEC_MODE="setup" - VIASH_DOCKER_SETUP_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 - ;; - ---dps|---docker_push_strategy) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY="$2" - shift 2 + ---setup) + ViashDockerSetup 'viash_viash_genrep:0.1' "$2" + exit 0 ;; - ---docker_push_strategy=*) - VIASH_EXEC_MODE="push" - VIASH_DOCKER_PUSH_STRATEGY=$(ViashRemoveFlags "$2") - shift 1 + ---setup=*) + ViashDockerSetup 'viash_viash_genrep:0.1' "$(ViashRemoveFlags "$1")" + exit 0 ;; ---dockerfile) ViashDockerfile @@ -407,8 +507,8 @@ while [[ $# -gt 0 ]]; do shift 1 ;; ---debug) - echo "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t dataintuitive/viash:0.4.0-rc1 + ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_genrep:0.1" + docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_genrep:0.1 exit 0 ;; *) # positional arg or unknown option @@ -419,16 +519,6 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS @@ -436,7 +526,7 @@ eval set -- $VIASH_POSITIONAL_ARGS # check whether required parameters exist if [ -z "$VIASH_PAR_INPUT" ]; then - echo '--input' is a required argument. Use "--help" to get more information on the parameters. + ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi if [ -z "$VIASH_PAR_TMP" ]; then @@ -446,6 +536,7 @@ if [ -z "$VIASH_PAR_OUTPUT" ]; then VIASH_PAR_OUTPUT="debug_report.md" fi +ViashDockerSetup 'viash_viash_genrep:0.1' ifneedbepullelsecachedbuild # detect volumes from file arguments if [ ! -z "$VIASH_PAR_INPUT" ]; then @@ -473,15 +564,15 @@ VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") function viash_perform_chown { if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" + eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_genrep:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" fi } trap viash_perform_chown EXIT -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS dataintuitive/viash:0.4.0-rc1 +cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_genrep:0.1 set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_debug-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_genrep-XXXXXX") function clean_up { rm "\$tempscript" } diff --git a/bin/project_push b/bin/viash_push similarity index 54% rename from bin/project_push rename to bin/viash_push index 5c75d9f22a..5d16628776 100755 --- a/bin/project_push +++ b/bin/viash_push @@ -1,12 +1,12 @@ #!/usr/bin/env bash -########################## -# project_push 0.1 # -########################## +######################## +# viash_push 0.1 # +######################## -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,61 +55,174 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} -function ViashSetup { -: +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ } +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Push a project, usually in the context of a pipeline." + echo "viash_push 0.1" +echo "Push a project, usually in the context of a pipeline." echo echo "Options:" - echo " -m string, --mode=string" - echo " type: string, default: development" - echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." - echo "" - echo " -q string, --query=string" - echo " type: string" - echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." - echo "" - echo " -n string, --query_namespace=string" - echo " type: string" - echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." - echo "" - echo " --query_name=string" - echo " type: string" - echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." - echo "" - echo " -v string, --version=string" - echo " type: string, default: dev" - echo " Which version of the pipeline to use." - echo "" - echo " -r string, --registry=string" - echo " type: string" - echo " Docker registry to use, only used when using a registry." - echo "" - echo " --namespace_separator=string" - echo " type: string, default: _" - echo " The separator to use between the component name and namespace as the image name of a Docker container." - echo "" - echo " --force" - echo " type: boolean_true" - echo " Overwrite registry" - echo "" - echo " --log=file" - echo " type: file, default: log.txt" - echo " Log file" - echo "" - echo " --viash=file" - echo " type: file" - echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." - echo "" + +echo " -s, --src" +echo " type: file" +echo " default: src" +echo " Directory for sources if different from src/" +echo "" + + +echo " -m, --mode" +echo " type: string" +echo " default: development" +echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." +echo "" + + +echo " -q, --query" +echo " type: string" +echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." +echo "" + + +echo " -n, --query_namespace" +echo " type: string" +echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." +echo "" + + +echo " --query_name" +echo " type: string" +echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." +echo "" + + +echo " -t, --tag" +echo " type: string" +echo " default: dev" +echo " The tag/version to be used." +echo "" + + +echo " -r, --registry" +echo " type: string" +echo " Docker registry to use, only used when using a registry." +echo "" + + +echo " --namespace_separator" +echo " type: string" +echo " default: _" +echo " The separator to use between the component name and namespace as the image name of a Docker container." +echo "" + + +echo " --force" +echo " type: boolean_true" +echo " Overwrite registry" +echo "" + + +echo " --max_threads" +echo " type: integer" +echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." +echo "" + + +echo " -c, --config_mod" +echo " type: string, multiple values allowed" +echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." +echo "" + + +echo " --log" +echo " type: file" +echo " default: log.txt" +echo " Log file" +echo "" + + +echo " --viash" +echo " type: file" +echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." +echo "" + } # initialise array @@ -119,15 +232,40 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_push 0.1" + exit + ;; + --src) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --src=*) + VIASH_PAR_SRC=$(ViashRemoveFlags "$1") shift 1 ;; + -s) + VIASH_PAR_SRC="$2" + shift 2 + ;; --mode) VIASH_PAR_MODE="$2" shift 2 @@ -172,16 +310,16 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") shift 1 ;; - --version) - VIASH_PAR_VERSION="$2" + --tag) + VIASH_PAR_TAG="$2" shift 2 ;; - --version=*) - VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + --tag=*) + VIASH_PAR_TAG=$(ViashRemoveFlags "$1") shift 1 ;; - -v) - VIASH_PAR_VERSION="$2" + -t) + VIASH_PAR_TAG="$2" shift 2 ;; --registry) @@ -208,6 +346,38 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_FORCE=true shift 1 ;; + --max_threads) + VIASH_PAR_MAX_THREADS="$2" + shift 2 + ;; + --max_threads=*) + VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --config_mod) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; + --config_mod=*) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + -c) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; --log) VIASH_PAR_LOG="$2" shift 2 @@ -232,26 +402,19 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS +if [ -z "$VIASH_PAR_SRC" ]; then + VIASH_PAR_SRC="src" +fi if [ -z "$VIASH_PAR_MODE" ]; then VIASH_PAR_MODE="development" fi -if [ -z "$VIASH_PAR_VERSION" ]; then - VIASH_PAR_VERSION="dev" +if [ -z "$VIASH_PAR_TAG" ]; then + VIASH_PAR_TAG="dev" fi if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then VIASH_PAR_NAMESPACE_SEPARATOR="_" @@ -266,21 +429,24 @@ fi cat << VIASHEOF | bash set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_push-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_push-XXXXXX") function clean_up { rm "\$tempscript" } trap clean_up EXIT cat > "\$tempscript" << 'VIASHMAIN' # The following code has been auto-generated by Viash. +par_src='$VIASH_PAR_SRC' par_mode='$VIASH_PAR_MODE' par_query='$VIASH_PAR_QUERY' par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' par_query_name='$VIASH_PAR_QUERY_NAME' -par_version='$VIASH_PAR_VERSION' +par_tag='$VIASH_PAR_TAG' par_registry='$VIASH_PAR_REGISTRY' par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' par_force='$VIASH_PAR_FORCE' +par_max_threads='$VIASH_PAR_MAX_THREADS' +par_config_mod='$VIASH_PAR_CONFIG_MOD' par_log='$VIASH_PAR_LOG' par_viash='$VIASH_PAR_VIASH' @@ -289,12 +455,10 @@ resources_dir="$VIASH_RESOURCES_DIR" #!/bin/bash if [ "\$par_mode" == "release" ]; then - echo "In release mode..." - if [ "\$par_version" == "dev" ]; then - echo "For a release, you have to specify an explicit version using --version" + echo "In release mode with tag '\$par_tag'." + if [ "\$par_tag" == "dev" ]; then + echo "For a release, you have to specify an explicit version using --tag" exit 1 - else - echo "Using version \$par_version" to tag containers fi fi @@ -314,12 +478,19 @@ if [ -z "\$par_viash" ]; then par_viash="viash" fi + +# if specified, use par_max_threads as a java argument +if [ ! -z "\$par_max_threads" ]; then + export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" +fi + if [[ \$par_force == true ]]; then echo "Force push... handle with care..." if [ "\$par_mode" == "development" ]; then echo "No container push can and should be performed in this mode" elif [ "\$par_mode" == "integration" ]; then "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "docker" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ @@ -330,22 +501,25 @@ if [[ \$par_force == true ]]; then -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ - --setup --push | tee "\$par_log" + --setup "push" | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "docker" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ - --setup --push | tee "\$par_log" + --setup "push" | tee "\$par_log" else echo "Not a valid mode argument" fi @@ -354,6 +528,7 @@ else echo "No container push can and should be performed in this mode" elif [ "\$par_mode" == "integration" ]; then "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "docker" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ @@ -363,21 +538,24 @@ else -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ - --setup --push | tee "\$par_log" + --setup "push" | tee "\$par_log" elif [ "\$par_mode" == "release" ]; then "\$par_viash" ns build \\ + -s "\$par_src" \\ --platform "docker" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ - --setup --push | tee "\$par_log" + --setup "push" | tee "\$par_log" else echo "Not a valid mode argument" fi diff --git a/bin/skeleton b/bin/viash_skeleton similarity index 72% rename from bin/skeleton rename to bin/viash_skeleton index 513d657e02..ae2df8e195 100755 --- a/bin/skeleton +++ b/bin/viash_skeleton @@ -1,12 +1,12 @@ #!/usr/bin/env bash -###################### -# skeleton 0.1 # -###################### +############################ +# viash_skeleton 0.1 # +############################ -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,41 +55,124 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ +} -function ViashSetup { -: +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ } +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Create a skeleton src component" + echo "viash_skeleton 0.1" +echo "Create a skeleton src component" echo echo "Options:" - echo " -n string, --name=string" - echo " type: string, required parameter" - echo " Name of the component" - echo "" - echo " -ns string, --namespace=string" - echo " type: string" - echo " Namespace of the component" - echo "" - echo " -l string, --language=string" - echo " type: string, default: bash" - echo " Which scripting language to use. Possible values are 'bash', 'r', and 'python'." - echo "" - echo " -p string1,string2,..., --platform=string1,string2,..." - echo " type: string, multiple values allowed, default: docker,native,nextflow" - echo " Which platforms to add. Possible values are 'native', 'docker', 'nextflow'. By default, all three will be added." - echo "" - echo " --src=file" - echo " type: file, default: src" - echo " Target directory if different from src/" - echo "" + +echo " -n, --name" +echo " type: string, required parameter" +echo " Name of the component" +echo "" + + +echo " -ns, --namespace" +echo " type: string" +echo " Namespace of the component" +echo "" + + +echo " -l, --language" +echo " type: string" +echo " default: bash" +echo " Which scripting language to use. Possible values are 'bash', 'r', and 'python'." +echo "" + + +echo " -p, --platform" +echo " type: string, multiple values allowed" +echo " default: docker,native,nextflow" +echo " Which platforms to add. Possible values are 'native', 'docker', 'nextflow'. By default, all three will be added." +echo "" + + +echo " --src" +echo " type: file, output" +echo " default: src" +echo " Target directory if different from src/" +echo "" + } # initialise array @@ -99,15 +182,28 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" shift 1 ;; + --version) + echo "viash_skeleton 0.1" + exit + ;; --name) VIASH_PAR_NAME="$2" shift 2 @@ -184,16 +280,6 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS @@ -201,7 +287,7 @@ eval set -- $VIASH_POSITIONAL_ARGS # check whether required parameters exist if [ -z "$VIASH_PAR_NAME" ]; then - echo '--name' is a required argument. Use "--help" to get more information on the parameters. + ViashError '--name' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi if [ -z "$VIASH_PAR_LANGUAGE" ]; then @@ -217,7 +303,7 @@ fi cat << VIASHEOF | bash set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-skeleton-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_skeleton-XXXXXX") function clean_up { rm "\$tempscript" } @@ -442,24 +528,22 @@ import os from os import path import subprocess - +print(">> Writing test file") with open("input.txt", "w") as writer: writer.writelines(["one\\n", "two\\n", "three\\n"]) +print(">> Running component") +out = subprocess.check_output(["./\$par_name", "--input", "input.txt", "--output", "output.txt", "--option", "FOO-"]).decode("utf-8") -class MyTest(unittest.TestCase): - def test_component(self): - out = subprocess.check_output(["./\$par_name", "--input", "input.txt", "--output", "output.txt", "--option", "FOO-"]).decode("utf-8") +print(">> Checking whether output file exists") +assert path.exists("output.txt") - self.assertTrue(path.exists("output.txt")) - - with open("output.txt", "r") as reader: - lines = reader.readlines() - - self.assertEqual(lines, ["FOO-one\\n", "FOO-two\\n", "FOO-three\\n"]) - - -unittest.main() +print(">> Checking contents of output file") +with open("output.txt", "r") as reader: + lines = reader.readlines() +assert lines == ["FOO-one\\n", "FOO-two\\n", "FOO-three\\n"] + +print(">> All tests succeeded successfully!") HERE fi diff --git a/bin/project_test b/bin/viash_test similarity index 52% rename from bin/project_test rename to bin/viash_test index 01d848d70c..a6627080aa 100755 --- a/bin/project_test +++ b/bin/viash_test @@ -1,12 +1,12 @@ #!/usr/bin/env bash -########################## -# project_test 0.1 # -########################## +######################## +# viash_test 0.1 # +######################## -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,65 +55,182 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} -function ViashSetup { -: +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ } +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Test a project, usually in the context of a pipeline." + echo "viash_test 0.1" +echo "Test a project, usually in the context of a pipeline." echo echo "Options:" - echo " -m string, --mode=string" - echo " type: string, default: development" - echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." - echo "" - echo " -p string, --platforms=string" - echo " type: string, default: docker" - echo " Which platforms to test, default is 'docker'." - echo "" - echo " -q string, --query=string" - echo " type: string" - echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." - echo "" - echo " -n string, --query_namespace=string" - echo " type: string" - echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." - echo "" - echo " --query_name=string" - echo " type: string" - echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." - echo "" - echo " -v string, --version=string" - echo " type: string, default: dev" - echo " Which version of the pipeline to use." - echo "" - echo " -r string, --registry=string" - echo " type: string" - echo " Docker registry to use, only used when using a registry." - echo "" - echo " --namespace_separator=string" - echo " type: string, default: _" - echo " The separator to use between the component name and namespace as the image name of a Docker container." - echo "" - echo " -l file, --log=file" - echo " type: file, default: log.tsv" - echo " Test log file" - echo "" - echo " --append=boolean" - echo " type: boolean, default: true" - echo " Append to the log file?" - echo "" - echo " --viash=file" - echo " type: file" - echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." - echo "" + +echo " -s, --src" +echo " type: file" +echo " default: src" +echo " Directory for sources if different from src/" +echo "" + + +echo " -m, --mode" +echo " type: string" +echo " default: development" +echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." +echo "" + + +echo " -p, --platforms" +echo " type: string" +echo " default: docker" +echo " Which platforms to test, default is 'docker'." +echo "" + + +echo " -q, --query" +echo " type: string" +echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." +echo "" + + +echo " -n, --query_namespace" +echo " type: string" +echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." +echo "" + + +echo " --query_name" +echo " type: string" +echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." +echo "" + + +echo " -t, --tag" +echo " type: string" +echo " default: dev" +echo " Which tag/version of the pipeline to use." +echo "" + + +echo " -r, --registry" +echo " type: string" +echo " Docker registry to use, only used when using a registry." +echo "" + + +echo " --namespace_separator" +echo " type: string" +echo " default: _" +echo " The separator to use between the component name and namespace as the image name of a Docker container." +echo "" + + +echo " --max_threads" +echo " type: integer" +echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." +echo "" + + +echo " -c, --config_mod" +echo " type: string, multiple values allowed" +echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." +echo "" + + +echo " -l, --log" +echo " type: file" +echo " default: log.tsv" +echo " Test log file" +echo "" + + +echo " --append" +echo " type: boolean" +echo " default: true" +echo " Append to the log file?" +echo "" + + +echo " --viash" +echo " type: file" +echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." +echo "" + } # initialise array @@ -123,15 +240,40 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" + shift 1 + ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + --version) + echo "viash_test 0.1" + exit + ;; + --src) + VIASH_PAR_SRC="$2" + shift 2 + ;; + --src=*) + VIASH_PAR_SRC=$(ViashRemoveFlags "$1") shift 1 ;; + -s) + VIASH_PAR_SRC="$2" + shift 2 + ;; --mode) VIASH_PAR_MODE="$2" shift 2 @@ -188,16 +330,16 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") shift 1 ;; - --version) - VIASH_PAR_VERSION="$2" + --tag) + VIASH_PAR_TAG="$2" shift 2 ;; - --version=*) - VIASH_PAR_VERSION=$(ViashRemoveFlags "$1") + --tag=*) + VIASH_PAR_TAG=$(ViashRemoveFlags "$1") shift 1 ;; - -v) - VIASH_PAR_VERSION="$2" + -t) + VIASH_PAR_TAG="$2" shift 2 ;; --registry) @@ -220,6 +362,38 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") shift 1 ;; + --max_threads) + VIASH_PAR_MAX_THREADS="$2" + shift 2 + ;; + --max_threads=*) + VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") + shift 1 + ;; + --config_mod) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; + --config_mod=*) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") + fi + shift 1 + ;; + -c) + if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then + VIASH_PAR_CONFIG_MOD="$2" + else + VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" + fi + shift 2 + ;; --log) VIASH_PAR_LOG="$2" shift 2 @@ -256,29 +430,22 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS +if [ -z "$VIASH_PAR_SRC" ]; then + VIASH_PAR_SRC="src" +fi if [ -z "$VIASH_PAR_MODE" ]; then VIASH_PAR_MODE="development" fi if [ -z "$VIASH_PAR_PLATFORMS" ]; then VIASH_PAR_PLATFORMS="docker" fi -if [ -z "$VIASH_PAR_VERSION" ]; then - VIASH_PAR_VERSION="dev" +if [ -z "$VIASH_PAR_TAG" ]; then + VIASH_PAR_TAG="dev" fi if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then VIASH_PAR_NAMESPACE_SEPARATOR="_" @@ -293,21 +460,24 @@ fi cat << VIASHEOF | bash set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-project_test-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_test-XXXXXX") function clean_up { rm "\$tempscript" } trap clean_up EXIT cat > "\$tempscript" << 'VIASHMAIN' # The following code has been auto-generated by Viash. +par_src='$VIASH_PAR_SRC' par_mode='$VIASH_PAR_MODE' par_platforms='$VIASH_PAR_PLATFORMS' par_query='$VIASH_PAR_QUERY' par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' par_query_name='$VIASH_PAR_QUERY_NAME' -par_version='$VIASH_PAR_VERSION' +par_tag='$VIASH_PAR_TAG' par_registry='$VIASH_PAR_REGISTRY' par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' +par_max_threads='$VIASH_PAR_MAX_THREADS' +par_config_mod='$VIASH_PAR_CONFIG_MOD' par_log='$VIASH_PAR_LOG' par_append='$VIASH_PAR_APPEND' par_viash='$VIASH_PAR_VIASH' @@ -337,9 +507,24 @@ if [ "\$par_append" == "true" ]; then par_append_parsed="--append" fi + +# if specified, use par_max_threads as a java argument +if [ ! -z "\$par_max_threads" ]; then + export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" +fi + +if [ "\$par_mode" == "release" ]; then + echo "In release mode with tag '\$par_tag'." + if [ "\$par_tag" == "dev" ]; then + echo "For a release, you have to specify an explicit version using --tag" + exit 1 + fi +fi + if [ "\$par_mode" == "development" ]; then echo "In development mode..." "\$par_viash" ns test \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ @@ -347,40 +532,40 @@ if [ "\$par_mode" == "development" ]; then -c '.functionality.version := "dev"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ -t "\$par_log" \\ \$par_append_parsed elif [ "\$par_mode" == "integration" ]; then echo "In integration mode..." "\$par_viash" ns test \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ -t "\$par_log" \\ \$par_append_parsed elif [ "\$par_mode" == "release" ]; then - echo "In release mode..." - if [ "\$par_version" == "dev" ]; then - echo "For a release, you have to specify an explicit version using --version" - exit 1 - fi "\$par_viash" ns test \\ + -s "\$par_src" \\ --platform "\$par_platforms" \\ --query "\$par_query" \\ --query_name "\$par_query_name" \\ --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_version"'"' \\ + -c '.functionality.version := "'"\$par_tag"'"' \\ -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker"].setup_strategy := "pull"' \\ -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ + -c "\$par_config_mod" \\ -l \\ -t "\$par_log" \\ \$par_append_parsed diff --git a/bin/vshtrafo b/bin/viash_trafo similarity index 69% rename from bin/vshtrafo rename to bin/viash_trafo index 1372488be8..fc0086969f 100755 --- a/bin/vshtrafo +++ b/bin/viash_trafo @@ -1,12 +1,12 @@ #!/usr/bin/env bash -###################### -# vshtrafo 1.0 # -###################### +######################### +# viash_trafo 1.0 # +######################### -# This wrapper script is auto-generated by viash 0.4.0 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. The component may contain files which fall under a different +# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a +# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from +# Data Intuitive. The component may contain files which fall under a different # license. The authors of this component should specify the license in the # header of such files, or include a separate license file detailing the # licenses of all included files. @@ -55,37 +55,115 @@ function ViashSourceDir { done cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd } +VIASH_VERBOSITY=5 + +# see https://en.wikipedia.org/wiki/Syslog#Severity_level + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VIASH_EXEC_MODE="run" +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog 0 emergency $@ +} -function ViashSetup { -: +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog 1 alert $@ } +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog 2 critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog 3 error $@ +} + +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog 4 warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog 5 notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog 6 info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog 7 debug $@ +} + +# find source folder of this component +VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "Transform viash formats." + echo "viash_trafo 1.0" +echo "Transform viash formats." echo echo "Options:" - echo " -i file, --input=file" - echo " type: file, required parameter" - echo " Input file" - echo "" - echo " -o file, --output_dir=file" - echo " type: file, required parameter" - echo " Output directory" - echo "" - echo " -f string, --format=string" - echo " type: string, required parameter" - echo " Output format. Must be one of 'script', 'config'" - echo "" - echo " --rm" - echo " type: boolean_true" - echo " Remove the source files after use." - echo "" + +echo " -i, --input" +echo " type: file, required parameter" +echo " Input file" +echo "" + + +echo " -o, --output_dir" +echo " type: file, required parameter, output" +echo " Output directory" +echo "" + + +echo " -f, --format" +echo " type: string, required parameter" +echo " Output format. Must be one of 'script', 'config'" +echo "" + + +echo " --rm" +echo " type: boolean_true" +echo " Remove the source files after use." +echo "" + } # initialise array @@ -95,15 +173,28 @@ while [[ $# -gt 0 ]]; do case "$1" in -h|--help) ViashHelp - exit;; - ---setup) - VIASH_EXEC_MODE="setup" + exit + ;; + -v|--verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" shift 1 ;; - ---push) - VIASH_EXEC_MODE="push" + -vv) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" shift 1 ;; + --verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + --verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "viash_trafo 1.0" + exit + ;; --input) VIASH_PAR_INPUT="$2" shift 2 @@ -152,16 +243,6 @@ while [[ $# -gt 0 ]]; do esac done -if [ "$VIASH_EXEC_MODE" == "setup" ]; then - ViashSetup - exit 0 -fi - -if [ "$VIASH_EXEC_MODE" == "push" ]; then - ViashPush - exit 0 -fi - # parse positional parameters eval set -- $VIASH_POSITIONAL_ARGS @@ -169,15 +250,15 @@ eval set -- $VIASH_POSITIONAL_ARGS # check whether required parameters exist if [ -z "$VIASH_PAR_INPUT" ]; then - echo '--input' is a required argument. Use "--help" to get more information on the parameters. + ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi if [ -z "$VIASH_PAR_OUTPUT_DIR" ]; then - echo '--output_dir' is a required argument. Use "--help" to get more information on the parameters. + ViashError '--output_dir' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi if [ -z "$VIASH_PAR_FORMAT" ]; then - echo '--format' is a required argument. Use "--help" to get more information on the parameters. + ViashError '--format' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi if [ -z "$VIASH_PAR_RM" ]; then @@ -187,7 +268,7 @@ fi cat << VIASHEOF | bash set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-vshtrafo-XXXXXX") +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_trafo-XXXXXX") function clean_up { rm "\$tempscript" } From da094f1a71dd1c34646708fdabc80882462c17d4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:41:54 +0200 Subject: [PATCH 0095/1233] update readme to reflect bin changes Former-commit-id: 26a1d688d68c9e3b749c85a296cf1f7c9fd0e04e --- README.Rmd | 74 +++++++++----------- README.md | 202 ++++++++++++++++++++++++++--------------------------- 2 files changed, 130 insertions(+), 146 deletions(-) diff --git a/README.Rmd b/README.Rmd index 49d700a67d..4f2d4aed64 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( comment="" ) ``` -Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. +Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. Documentation for viash is available at [viash.io](https://viash.io). ## Requirements @@ -33,7 +33,7 @@ The `src/` folder contains modular software components for running a modality al **Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. ```bash -bin/project_build +bin/viash_build ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -44,7 +44,7 @@ bin/project_build These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. The command might take a while to run, since it is building a docker container for each of the components. If you're interested in building only a subset of components, you can apply a regex to the selected components. -For example: `bin/project_build -q 'utils|modality_alignment'`. +For example: `bin/viash_build -q 'utils|modality_alignment'`. **Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: @@ -90,7 +90,7 @@ a new Python-based viash component in the `src/modality_alignment/methods/foo` f You can start creating a new component by using the `bin/skeleton` command: ```{bash} -bin/skeleton --name foo --namespace "modality_alignment/methods" --language python +bin/viash_skeleton --name foo --namespace "modality_alignment/methods" --language python ``` This should create a few files in this folder: @@ -102,6 +102,20 @@ This should create a few files in this folder: The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). +## Running a component from CLI + +You can view the interface of the executable by running the executable with the `-h` parameter. + +```{bash} +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -h +``` + +You can **run the component** as follows: + +```{bash} +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt +``` + ## Building a component `viash` has several helper functions to help you quickly develop a component. @@ -112,32 +126,25 @@ run it, provided that they have Bash and Docker installed. ```{bash} viash build src/modality_alignment/methods/foo/config.vsh.yaml \ - -o target/docker/modality_alignment/methods/foo \ - --setup + -o target/docker/modality_alignment/methods/foo ``` -Note that the `bin/project_build` component does a much better job of setting up +Note that the `bin/viash_build` component does a much better job of setting up a collection of components. You can filter which components will be built by -providing a regex to the `-q` parameter, e.g. `bin/project_build -q 'utils|modality_alignment'`. - -## Running a component from CLI +providing a regex to the `-q` parameter, e.g. `bin/viash_build -q 'utils|modality_alignment'`. -You can view the interface of the executable by running the executable with the `-h` parameter. +You can now view the same interface of the executable by running the executable with the `-h` parameter. ```{bash} target/docker/modality_alignment/methods/foo/foo -h ``` -You can **run the component** as follows: +Or **run the component** as follows: ```{bash} target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt ``` -Alternatively, you can run the component straight from the viash config by using the **`viash run`** command: -```{bash} -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt -``` ## Unit testing a component Provided that you wrote a script that allows you to test the functionality of a component, @@ -147,27 +154,10 @@ you can run the tests by using the **`viash test`** command. viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` -To run all the unit tests of all the components in the repository, use `bin/project_test`. +To run all the unit tests of all the components in the repository, use `bin/viash_test`. ## Frequently asked questions -### Running a component causes error 'Unable to find image' - -Depending on how an executable was created, a Docker container might not have been created. - -To solve this issue, run the executable with a `---setup` flag attached. This will -automatically build the Docker container for you. - -```{bash} -target/docker/modality_alignment/methods/foo/foo ---setup -``` - -Or when working with `viash run`: - -```{bash} -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup -``` - ### My component doesn't work! Debugging your component based on the output from a Nextflow pipeline is easier than you might realise. For example, the error message below tells you that the 'mse' component failed: @@ -257,20 +247,20 @@ Alternatively, you can write a Bash script which calls your desired programming ### One Docker container per component -By running the `bin/project_build` command, viash will build one Docker container per component. While this results in some initial computational overhead, +By running the `bin/viash_build` command, viash will build one Docker container per component. While this results in some initial computational overhead, this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with those of other components. ### Reproducible components A component built by viash is meant to be reproducible. If you send the `target/docker/modality_alignment/methods/foo/foo` file to someone, -they can run `./foo ---setup` and then will be able to use the `foo` component however they like. +they can run `./foo ---setup cachedbuild` and then will be able to use the `foo` component however they like. ```{bash} # pretend to send the component to someone through 'cp' cp target/docker/modality_alignment/methods/foo/foo foo_by_email # build container -./foo_by_email ---setup +./foo_by_email ---setup cachedbuild ``` ```{bash} @@ -284,12 +274,12 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email ``` ### Reprodicible components on Docker Hub -You might notice that the `---setup` builds the docker container from scratch, rather than pulling it from Docker hub. +You might notice that the `---setup cachedbuild` builds the docker container from scratch, rather than pulling it from Docker hub. -With `bin/project_build`, you can build a versioned release of all the components in the repository and push it to Docker hub. +With `bin/viash_build`, you can build a versioned release of all the components in the repository and push it to Docker hub. ```bash -bin/project_build -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems ``` In release mode... @@ -306,10 +296,10 @@ bin/project_build -m release -v '0.1.0' -r singlecellopenproblems > docker build -t singlecellopenproblems/modality_alignment/methods_scot:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scot-xUKof3 > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc -The images themselves can be pushed to Docker Hub with the `bin/project_push` command. I'd have to make a small change to viash to ensure that the component names don't contain any slashes because the images listed above can't be pushed to Docker hub. However, the output would look something like this: +The images themselves can be pushed to Docker Hub with the `bin/viash_push` command. I'd have to make a small change to viash to ensure that the component names don't contain any slashes because the images listed above can't be pushed to Docker hub. However, the output would look something like this: ```bash -bin/project_push -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_push -m release -v '0.1.0' -r singlecellopenproblems In release mode... Using version 0.1.0 to tag containers ``` diff --git a/README.md b/README.md index f01d1513ed..af757029de 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,8 @@ opsca-viash - [Quick start](#quick-start) - [Project structure](#project-structure) - [Adding a viash component](#adding-a-viash-component) -- [Building a component](#building-a-component) - [Running a component from CLI](#running-a-component-from-cli) +- [Building a component](#building-a-component) - [Unit testing a component](#unit-testing-a-component) - [Frequently asked questions](#frequently-asked-questions) - [Benefits of using Nextflow + @@ -14,7 +14,8 @@ opsca-viash Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) -with Nextflow and viash. +with Nextflow and viash. Documentation for viash is available at +[viash.io](https://viash.io). ## Requirements @@ -35,7 +36,7 @@ modality alignment benchmark. Running the full pipeline is quite easy. executables in the `target/` folder. ``` bash -bin/project_build +bin/viash_build ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -49,7 +50,7 @@ installed. The command might take a while to run, since it is building a docker container for each of the components. If you’re interested in building only a subset of components, you can apply a regex to the selected components. For example: -`bin/project_build -q 'utils|modality_alignment'`. +`bin/viash_build -q 'utils|modality_alignment'`. **Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: @@ -96,7 +97,7 @@ in the `src/modality_alignment/methods/foo` folder, run: You can start creating a new component by using the `bin/skeleton` command: ``` bash -bin/skeleton --name foo --namespace "modality_alignment/methods" --language python +bin/viash_skeleton --name foo --namespace "modality_alignment/methods" --language python ``` This should create a few files in this folder: @@ -110,6 +111,44 @@ the viash documentation site provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). +## Running a component from CLI + +You can view the interface of the executable by running the executable +with the `-h` parameter. + +``` bash +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -h +``` + + foo 0.0.1 + Replace this with a (multiline) description of your component. + + Options: + -i, --input + type: file, required parameter + Describe the input file. + + -o, --output + type: file, required parameter, output + Describe the output file. + + --option + type: string + default: default- + Describe an optional parameter. + +You can **run the component** as follows: + +``` bash +viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt +``` + + This is a skeleton component + The arguments are: + - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt + - option: default- + ## Building a component `viash` has several helper functions to help you quickly develop a @@ -122,42 +161,39 @@ installed. ``` bash viash build src/modality_alignment/methods/foo/config.vsh.yaml \ - -o target/docker/modality_alignment/methods/foo \ - --setup + -o target/docker/modality_alignment/methods/foo ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-6uqKl4 - -Note that the `bin/project_build` component does a much better job of +Note that the `bin/viash_build` component does a much better job of setting up a collection of components. You can filter which components will be built by providing a regex to the `-q` parameter, -e.g. `bin/project_build -q 'utils|modality_alignment'`. +e.g. `bin/viash_build -q 'utils|modality_alignment'`. -## Running a component from CLI - -You can view the interface of the executable by running the executable -with the `-h` parameter. +You can now view the same interface of the executable by running the +executable with the `-h` parameter. ``` bash target/docker/modality_alignment/methods/foo/foo -h ``` + foo 0.0.1 Replace this with a (multiline) description of your component. Options: - -i file, --input=file + -i, --input type: file, required parameter Describe the input file. - -o file, --output=file - type: file, required parameter + -o, --output + type: file, required parameter, output Describe the output file. - --option=string - type: string, default: default- + --option + type: string + default: default- Describe an optional parameter. -You can **run the component** as follows: +Or **run the component** as follows: ``` bash target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt @@ -165,33 +201,8 @@ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - - option: default- - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - - option: default- - -Alternatively, you can run the component straight from the viash config -by using the **`viash run`** command: - -``` bash -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt -``` - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - - option: default- - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt - option: default- ## Unit testing a component @@ -204,48 +215,35 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208/build_executable/foo ---setup - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-Md2dPC + +/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654/build_executable/foo --verbosity 6 ---setup cachedbuild + [notice] Running 'docker build -t modality_alignment/methods_foo:9rREBVaKbQTM /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-k8Idnc' + Sending build context to Docker daemon 22.53kB + + Step 1/2 : FROM python:3.9.3-buster + ---> 05034335a2e3 + Step 2/2 : RUN pip install --upgrade pip && pip install --no-cache-dir "numpy" + ---> Using cache + ---> 45db33ebb9de + Successfully built 45db33ebb9de + Successfully tagged modality_alignment/methods_foo:9rREBVaKbQTM ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo10112285657605906208/test_test.py/test.py - . - ---------------------------------------------------------------------- - Ran 1 test in 0.017s - - OK + +/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654/test_test.py/test.py + >> Writing test file + >> Running component + >> Checking whether output file exists + >> Checking contents of output file + >> All tests succeeded successfully! ==================================================================== SUCCESS! All 1 out of 1 test scripts succeeded! Cleaning up temporary directory To run all the unit tests of all the components in the repository, use -`bin/project_test`. +`bin/viash_test`. ## Frequently asked questions -### Running a component causes error ‘Unable to find image’ - -Depending on how an executable was created, a Docker container might not -have been created. - -To solve this issue, run the executable with a `---setup` flag attached. -This will automatically build the Docker container for you. - -``` bash -target/docker/modality_alignment/methods/foo/foo ---setup -``` - - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-E9IAUq - -Or when working with `viash run`: - -``` bash -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- ---setup -``` - - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-fZUT3j - ### My component doesn’t work! Debugging your component based on the output from a Nextflow pipeline is @@ -348,7 +346,7 @@ can write a Bash script which calls your desired programming language. ### One Docker container per component -By running the `bin/project_build` command, viash will build one Docker +By running the `bin/viash_build` command, viash will build one Docker container per component. While this results in some initial computational overhead, this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with @@ -358,37 +356,39 @@ those of other components. A component built by viash is meant to be reproducible. If you send the `target/docker/modality_alignment/methods/foo/foo` file to someone, they -can run `./foo ---setup` and then will be able to use the `foo` -component however they like. +can run `./foo ---setup cachedbuild` and then will be able to use the +`foo` component however they like. ``` bash # pretend to send the component to someone through 'cp' cp target/docker/modality_alignment/methods/foo/foo foo_by_email # build container -./foo_by_email ---setup +./foo_by_email ---setup cachedbuild ``` - > docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-cgD19k + [notice] Running 'docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-kZ7Cn8' ``` bash # view help ./foo_by_email -h ``` + foo 0.0.1 Replace this with a (multiline) description of your component. Options: - -i file, --input=file + -i, --input type: file, required parameter Describe the input file. - -o file, --output=file - type: file, required parameter + -o, --output + type: file, required parameter, output Describe the output file. - --option=string - type: string, default: default- + --option + type: string + default: default- Describe an optional parameter. ``` bash @@ -398,26 +398,20 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - - option: default- - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt - option: default- ### Reprodicible components on Docker Hub -You might notice that the `---setup` builds the docker container from -scratch, rather than pulling it from Docker hub. +You might notice that the `---setup cachedbuild` builds the docker +container from scratch, rather than pulling it from Docker hub. -With `bin/project_build`, you can build a versioned release of all the +With `bin/viash_build`, you can build a versioned release of all the components in the repository and push it to Docker hub. ``` bash -bin/project_build -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems ``` In release mode... @@ -435,13 +429,13 @@ bin/project_build -m release -v '0.1.0' -r singlecellopenproblems > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc The images themselves can be pushed to Docker Hub with the -`bin/project_push` command. I’d have to make a small change to viash to +`bin/viash_push` command. I’d have to make a small change to viash to ensure that the component names don’t contain any slashes because the images listed above can’t be pushed to Docker hub. However, the output would look something like this: ``` bash -bin/project_push -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_push -m release -v '0.1.0' -r singlecellopenproblems In release mode... Using version 0.1.0 to tag containers ``` From 5a5ea2272f88c4bcae891209d0640985cf534523 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:42:12 +0200 Subject: [PATCH 0096/1233] update workflow Former-commit-id: 56f057ce5d41268f94bfa9b8682a9cf39ebaa640 --- src/modality_alignment/workflows/main.nf | 22 ++++++---- .../workflows/nextflow.config | 39 ++++++++++++------ .../workflows/run_integration_test.sh | 15 ------- .../workflows/run_nextflow.sh | 7 +++- src/modality_alignment/workflows/test.nf | 40 ------------------- src/trajectory_inference/workflows/main.nf | 15 ++++++- .../workflows/nextflow.config | 22 ++++++++-- 7 files changed, 78 insertions(+), 82 deletions(-) delete mode 100755 src/modality_alignment/workflows/run_integration_test.sh delete mode 100644 src/modality_alignment/workflows/test.nf diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 3820f2556f..54f2cceaed 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -1,25 +1,31 @@ nextflow.enable.dsl=2 -// This workflow assumes that the directory from which the -// pipeline is launched is the root of the opsca repository. +/* For now, you need to manually specify the + * root directory of this repository as follows. + * (it's a nextflow limitation I'm trying to figure out + * how to resolve.) */ +rootDir = "$projectDir/../../.." -/******************************************************* -* Import viash modules * -*******************************************************/ - -targetDir = "$launchDir/target/nextflow" +// target dir containing the nxf modules generated by viash +targetDir = "$rootDir/target/nextflow" +// import dataset loaders include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) + +// import methods include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) + +// import metrics include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) -include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) +// import helper functions include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" +include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) // Helper function for redefining the ids of elements in a channel // based on its files. diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index ad0766514c..0efbded3cf 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -1,23 +1,38 @@ manifest { - nextflowVersion = '!>=20.10.0' + nextflowVersion = '!>=20.12.1-edge' } -includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/scprep_csv/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/datasets/sample_dataset/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/methods/mnn/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/methods/scot/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/methods/harmonic_alignment/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/methods/sample_method/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/knn_auc/nextflow.config" -includeConfig "$launchDir/target/nextflow/modality_alignment/metrics/mse/nextflow.config" -includeConfig "$launchDir/target/nextflow/utils/extract_scores/nextflow.config" +rootDir = "$projectDir/../.." +targetDir = "$rootDir/target/nextflow" docker { - runOptions = "-v $launchDir:$launchDir" + runOptions = "-v $rootDir:$rootDir" } process { maxForks = 30 - container = 'ubuntu' + cpus = 2 errorStrategy='ignore' + container = 'nextflow/bash:latest' + + pod = [ [ nodeSelector: 'worker-group = m5s' ] ] + + withLabel: highmem { memory = 50.Gb } + withLabel: highcpu { cpus = 20 } + withLabel: highmem_highcpu { + cpus = 20 + memory = 128.Gb + } } + +// additional includes +includeConfig "$targetDir/modality_alignment/datasets/scprep_csv/nextflow.config" +includeConfig "$targetDir/modality_alignment/datasets/sample_dataset/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/mnn/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/scot/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/harmonic_alignment/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/sample_method/nextflow.config" +includeConfig "$targetDir/modality_alignment/metrics/knn_auc/nextflow.config" +includeConfig "$targetDir/modality_alignment/metrics/mse/nextflow.config" +includeConfig "$targetDir/utils/extract_scores/nextflow.config" + diff --git a/src/modality_alignment/workflows/run_integration_test.sh b/src/modality_alignment/workflows/run_integration_test.sh deleted file mode 100755 index 5832cf2e1b..0000000000 --- a/src/modality_alignment/workflows/run_integration_test.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/project_build -q 'modality_alignment|utils' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -NXF_VER=20.10.0 bin/nextflow run src/modality_alignment/workflows/test.nf \ - -resume \ - --output output/modality_alignment/test - diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index 4aa3bebb2b..bedd6c8864 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -9,7 +9,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -NXF_VER=20.10.0 bin/nextflow run src/modality_alignment/workflows/main.nf \ +# choose a particular version of nextflow +export NXF_VER=21.04.1 + +bin/nextflow \ + run . \ + -main-script src/modality_alignment/workflows/main.nf \ -resume \ --output output/modality_alignment diff --git a/src/modality_alignment/workflows/test.nf b/src/modality_alignment/workflows/test.nf deleted file mode 100644 index c85a19f392..0000000000 --- a/src/modality_alignment/workflows/test.nf +++ /dev/null @@ -1,40 +0,0 @@ -nextflow.enable.dsl=2 - -// This workflow assumes that the directory from which the -// pipeline is launched is the root of the opsca repository. - -/******************************************************* -* Import viash modules * -*******************************************************/ - -targetDir = "$launchDir/target/nextflow" - -include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) -include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) -include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) -include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) -include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) - -include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" - -// Helper function for redefining the ids of elements in a channel -// based on its files. -def renameID = { [ it[1].baseName, it[1], it[2] ] } - - -/******************************************************* -* Main workflow * -*******************************************************/ - -workflow { - Channel.fromList( [[ "sample_dataset", [], params]] ) \ - | sample_dataset \ - | sample_method \ - | map(renameID) \ - | (knn_auc & mse) \ - | mix | map(renameID) \ - | toSortedList \ - | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } - | extract_scores - -} diff --git a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf index 3a2264c988..d8a5e3a367 100644 --- a/src/trajectory_inference/workflows/main.nf +++ b/src/trajectory_inference/workflows/main.nf @@ -1,12 +1,23 @@ nextflow.enable.dsl=2 -targetDir = "$launchDir/target/nextflow" +/* for now, you need to manually specify the + * root directory of this repository as follows. + * (it's a nextflow limitation I'm trying to figure out + * how to resolve.) */ +rootDir = "$projectDir/../../.." -include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" +// target dir containing the nxf modules generated by viash +targetDir = "$rootDir/target/nextflow" +// import dataset loaders include { download_datasets } from "$targetDir/trajectory_inference/datasets/download_datasets/main.nf" params(params) +// import methods + +// import metrics +// import helper functions +include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" /******************************************************* * Dataset processor workflows * diff --git a/src/trajectory_inference/workflows/nextflow.config b/src/trajectory_inference/workflows/nextflow.config index 371b3c88ea..01d97273ca 100644 --- a/src/trajectory_inference/workflows/nextflow.config +++ b/src/trajectory_inference/workflows/nextflow.config @@ -1,15 +1,29 @@ manifest { - nextflowVersion = '!>=20.10.0' + nextflowVersion = '!>=20.12.1-edge' } -includeConfig "$launchDir/target/nextflow/trajectory_inference/datasets/download_datasets/nextflow.config" +rootDir = "$projectDir/../.." +targetDir = "$rootDir/target/nextflow" docker { - runOptions = "-v $launchDir:$launchDir" + runOptions = "-v $rootDir:$rootDir" } process { maxForks = 30 - container = 'ubuntu' + cpus = 2 errorStrategy='ignore' + container = 'nextflow/bash:latest' + + pod = [ [ nodeSelector: 'worker-group = m5s' ] ] + + withLabel: highmem { memory = 50.Gb } + withLabel: highcpu { cpus = 20 } + withLabel: highmem_highcpu { + cpus = 20 + memory = 128.Gb + } } + +// additional includes +includeConfig "$targetDir/trajectory_inference/datasets/download_datasets/nextflow.config" From 0b96acc167e06c686b348a0c71987ad78087ece0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:42:21 +0200 Subject: [PATCH 0097/1233] rename docs to resources Former-commit-id: 1b9c06da0896afcd8fcc86df8b3e1b11f0718b06 --- src/trajectory_inference/README.md | 6 +++--- .../{docs => resources}/api_discussion.R | 11 +++++++++++ .../{docs => resources}/images/format.svg | 0 .../{docs => resources}/images/format_delayed.svg | 0 .../images/trajectory_inference.png | Bin 5 files changed, 14 insertions(+), 3 deletions(-) rename src/trajectory_inference/{docs => resources}/api_discussion.R (97%) rename src/trajectory_inference/{docs => resources}/images/format.svg (100%) rename src/trajectory_inference/{docs => resources}/images/format_delayed.svg (100%) rename src/trajectory_inference/{docs => resources}/images/trajectory_inference.png (100%) diff --git a/src/trajectory_inference/README.md b/src/trajectory_inference/README.md index 2e6fd4f283..4899d697d0 100644 --- a/src/trajectory_inference/README.md +++ b/src/trajectory_inference/README.md @@ -5,7 +5,7 @@ Trajectory inference (TI) is a computational analysis used in single-cell transc A trajectory is a graph where the nodes represent noteworthy cellular states, and each cell is predicted to be progressing along transitions between the different states (Figure 1A). Main applications of TI are identifying branch points, end states, predicting the topology of the dynamic process, or identifying genes whose expression varies gradually along the topology (Figure 1B). -![](docs/images/trajectory_inference.png) +![](resources/images/trajectory_inference.png) **Figure 1**: Trajectory inference for single-cell omics data. Image borrowed from [1]. **A**: During a dynamic process cells pass through several transitional states, characterized by different waves of transcriptional, morphological, epigenomic and/or surface marker changes [2]. TI methods provide an unbiased approach to identifying and correctly ordering different transitional stages. **B**: By overlaying gene expression levels on a dimensionality reduction, the milestones can be annotated to allow better interpretation of the cellular heterogeneity. A comparison of 45 TI methods on 110 real and 229 synthetic datasets found that the different methods are very complementary when comparing different types of input datasets, and that performance of a method can be highly variable even in multiple runs on the same input dataset [3]. @@ -13,7 +13,7 @@ A comparison of 45 TI methods on 110 real and 229 synthetic datasets found that A persisting issue amongst TI methods is the usage of a standard definition of the task and usage of well-defined input and output data structures in order to make results comparable between methods. This task assumes a trajectory consists of two data structures: the milestone network and the cell progressions (Figure 2). The milestone network is a data frame that must contain the columns 'from' (milestones), 'to' (milestones) and 'length' (> 0). The progressions is a data frame that must contain the columns 'cell_id' (name of the cell), 'from' and 'to' (transition it is located on), and 'percentage' (its' percentual progression along the transition). -![](docs/images/format.svg) +![](resources/images/format.svg) **Figure 2**: The data structure for a trajectory. @@ -66,4 +66,4 @@ This description can be provided if necessary, create an issue and mention @Loui 3. Wouter Saelens, Cannoodt Robrecht et al. “A Comparison of Single-Cell Trajectory Inference Methods“. In: Nature Biotechnology 37 (May 2019). ISSN: 15461696. DOI: [10.1038/s41587-019-0071-9](https://doi.org/10.1038/s41587-019-0071-9). -4. Luca Pinello et al. “TopCoder Challenge: Single-Cell Trajectory Inference Methods“. URL: [topcoder.com/lp/single-cell](https://www.topcoder.com/lp/single-cell). \ No newline at end of file +4. Luca Pinello et al. “TopCoder Challenge: Single-Cell Trajectory Inference Methods“. URL: [topcoder.com/lp/single-cell](https://www.topcoder.com/lp/single-cell). diff --git a/src/trajectory_inference/docs/api_discussion.R b/src/trajectory_inference/resources/api_discussion.R similarity index 97% rename from src/trajectory_inference/docs/api_discussion.R rename to src/trajectory_inference/resources/api_discussion.R index de2ee5fab9..3d8faaeb6e 100644 --- a/src/trajectory_inference/docs/api_discussion.R +++ b/src/trajectory_inference/resources/api_discussion.R @@ -55,3 +55,14 @@ traj <- ) plot_graph(traj) + +traj$progressions + + + + + + + + + diff --git a/src/trajectory_inference/docs/images/format.svg b/src/trajectory_inference/resources/images/format.svg similarity index 100% rename from src/trajectory_inference/docs/images/format.svg rename to src/trajectory_inference/resources/images/format.svg diff --git a/src/trajectory_inference/docs/images/format_delayed.svg b/src/trajectory_inference/resources/images/format_delayed.svg similarity index 100% rename from src/trajectory_inference/docs/images/format_delayed.svg rename to src/trajectory_inference/resources/images/format_delayed.svg diff --git a/src/trajectory_inference/docs/images/trajectory_inference.png b/src/trajectory_inference/resources/images/trajectory_inference.png similarity index 100% rename from src/trajectory_inference/docs/images/trajectory_inference.png rename to src/trajectory_inference/resources/images/trajectory_inference.png From 6cb95a5dbe2ac5e4aba3a83a3c51029da52e6546 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:44:53 +0200 Subject: [PATCH 0098/1233] fix ci script Former-commit-id: 6edaa39f78b8c8b342513e3bb99d4f929769716e --- .github/workflows/viash-build.yml | 39 +++++++++++++++++++++ .github/workflows/viash-ci.yml | 56 ------------------------------- .github/workflows/viash-test.yml | 41 ++++++++++++++++++++++ 3 files changed, 80 insertions(+), 56 deletions(-) create mode 100644 .github/workflows/viash-build.yml delete mode 100644 .github/workflows/viash-ci.yml create mode 100644 .github/workflows/viash-test.yml diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml new file mode 100644 index 0000000000..90a35f87dd --- /dev/null +++ b/.github/workflows/viash-build.yml @@ -0,0 +1,39 @@ +name: viash build CI + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + viash-build: + runs-on: ${{ matrix.config.os }} + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + config: + - {name: 'main', os: ubuntu-latest } + + steps: + - uses: actions/checkout@v2 + + - name: Build components + run: | + # allow publishing the target folder + sed -i '/^target\/$/d' .gitignore + + # skip docker builds + bin/viash_build -c '.platforms[.type == "docker"].setup_strategy := "donothing"' + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: main_build + +# todo: add build for tag +# https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-create-git-tag diff --git a/.github/workflows/viash-ci.yml b/.github/workflows/viash-ci.yml deleted file mode 100644 index 9ea3a6b016..0000000000 --- a/.github/workflows/viash-ci.yml +++ /dev/null @@ -1,56 +0,0 @@ -name: viash CI - -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -jobs: - viash-ci: - runs-on: ${{ matrix.config.os }} - if: "!contains(github.event.head_commit.message, 'ci skip')" - - strategy: - fail-fast: false - matrix: - config: - - {name: 'main', os: ubuntu-latest } - - steps: - - uses: actions/checkout@v2 - - - uses: satackey/action-docker-layer-caching@v0.0.11 - continue-on-error: true - - - name: Build components - run: | - # allow publishing the target folder - sed -i '/^target\/$/d' .gitignore - - # skip docker builds - bin/project_build - - - name: Run tests - run: | - # allow publishing the check_results folder - sed -i '/^check_results\/$/d' .gitignore - - # run tests and output results to check_results directory - mkdir check_results - bin/project_build - bin/project_test --append=false --log=check_results/results.tsv - - - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: . - publish_branch: target_main - - - name: Upload check results - uses: actions/upload-artifact@master - with: - name: ${{ matrix.config.name }}_results - path: check_results - diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml new file mode 100644 index 0000000000..56cb21b68c --- /dev/null +++ b/.github/workflows/viash-test.yml @@ -0,0 +1,41 @@ +name: viash test CI + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + viash-test: + runs-on: ${{ matrix.config.os }} + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + config: + - {name: 'main', os: ubuntu-latest } + + steps: + - uses: actions/checkout@v2 + + - name: Run build + run: | + bin/viash_build + + - name: Run tests + run: | + # create check_results folder + sed -i '/^check_results\/$/d' .gitignore + mkdir check_results + + # run tests + bin/viash_test --append=false --log=check_results/results.tsv + + - name: Upload check results + uses: actions/upload-artifact@master + with: + name: ${{ matrix.config.name }}_results + path: check_results + From 02d7985fd50f1f8da57ff44362337bddb147bc85 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 11:57:17 +0200 Subject: [PATCH 0099/1233] only build nextflow targets Former-commit-id: fcf024bd4f746451cab6aca5903fd8f0e9c72039 --- .github/workflows/viash-build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index 90a35f87dd..b84175c2cd 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -25,8 +25,8 @@ jobs: # allow publishing the target folder sed -i '/^target\/$/d' .gitignore - # skip docker builds - bin/viash_build -c '.platforms[.type == "docker"].setup_strategy := "donothing"' + # only build nextflow targets + bin/viash_build -m release -t latest -p nextflow - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 From 2b8c6d9cc4b70feb8704860946c783e6913ef129 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 12:12:36 +0200 Subject: [PATCH 0100/1233] fetch viash separately Former-commit-id: 0894d1910debe8aeacd6bf2d9e5593c07adfc5b6 --- .github/workflows/viash-build.yml | 3 +++ .github/workflows/viash-test.yml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index b84175c2cd..84994bd841 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -20,6 +20,9 @@ jobs: steps: - uses: actions/checkout@v2 + - name: Fetch viash + run: bin/viash -h + - name: Build components run: | # allow publishing the target folder diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 56cb21b68c..f8b21f75c6 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -20,6 +20,9 @@ jobs: steps: - uses: actions/checkout@v2 + - name: Fetch viash + run: bin/viash -h + - name: Run build run: | bin/viash_build From 27b5a9b1694f1590de92f6686e091d864a435943 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 1 Jun 2021 12:47:14 +0200 Subject: [PATCH 0101/1233] fix config orders Former-commit-id: ea8d592674b5892144ad549ab14fa99d7d16e866 --- src/modality_alignment/workflows/main.nf | 3 +-- .../workflows/nextflow.config | 24 ++++++++++--------- src/modality_alignment/workflows/run_bash.sh | 2 +- .../workflows/run_nextflow.sh | 6 +++-- .../workflows/nextflow.config | 9 ++++--- 5 files changed, 25 insertions(+), 19 deletions(-) diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index 54f2cceaed..d1a5911d55 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -4,9 +4,8 @@ nextflow.enable.dsl=2 * root directory of this repository as follows. * (it's a nextflow limitation I'm trying to figure out * how to resolve.) */ + rootDir = "$projectDir/../../.." - -// target dir containing the nxf modules generated by viash targetDir = "$rootDir/target/nextflow" // import dataset loaders diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index 0efbded3cf..defdc73055 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -2,9 +2,21 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } -rootDir = "$projectDir/../.." +rootDir = "$projectDir/../../.." targetDir = "$rootDir/target/nextflow" +// custom includes +includeConfig "$targetDir/modality_alignment/datasets/scprep_csv/nextflow.config" +includeConfig "$targetDir/modality_alignment/datasets/sample_dataset/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/mnn/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/scot/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/harmonic_alignment/nextflow.config" +includeConfig "$targetDir/modality_alignment/methods/sample_method/nextflow.config" +includeConfig "$targetDir/modality_alignment/metrics/knn_auc/nextflow.config" +includeConfig "$targetDir/modality_alignment/metrics/mse/nextflow.config" +includeConfig "$targetDir/utils/extract_scores/nextflow.config" + +// other configs docker { runOptions = "-v $rootDir:$rootDir" } @@ -25,14 +37,4 @@ process { } } -// additional includes -includeConfig "$targetDir/modality_alignment/datasets/scprep_csv/nextflow.config" -includeConfig "$targetDir/modality_alignment/datasets/sample_dataset/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/mnn/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/scot/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/harmonic_alignment/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/sample_method/nextflow.config" -includeConfig "$targetDir/modality_alignment/metrics/knn_auc/nextflow.config" -includeConfig "$targetDir/modality_alignment/metrics/mse/nextflow.config" -includeConfig "$targetDir/utils/extract_scores/nextflow.config" diff --git a/src/modality_alignment/workflows/run_bash.sh b/src/modality_alignment/workflows/run_bash.sh index f76481f750..b40e389ee8 100755 --- a/src/modality_alignment/workflows/run_bash.sh +++ b/src/modality_alignment/workflows/run_bash.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/project_build -q 'modality_alignment|utils' +# bin/viash_build -q 'modality_alignment|utils' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index bedd6c8864..bcc1170bdf 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/project_build -q 'modality_alignment|utils' +# bin/viash_build -q 'modality_alignment|utils' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -15,6 +15,8 @@ export NXF_VER=21.04.1 bin/nextflow \ run . \ -main-script src/modality_alignment/workflows/main.nf \ - -resume \ + -c src/modality_alignment/workflows/nextflow.config \ --output output/modality_alignment + +# -resume \ diff --git a/src/trajectory_inference/workflows/nextflow.config b/src/trajectory_inference/workflows/nextflow.config index 01d97273ca..630f1b79b0 100644 --- a/src/trajectory_inference/workflows/nextflow.config +++ b/src/trajectory_inference/workflows/nextflow.config @@ -2,9 +2,13 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } -rootDir = "$projectDir/../.." +rootDir = "$projectDir/../../.." targetDir = "$rootDir/target/nextflow" +// additional includes +includeConfig "$targetDir/trajectory_inference/datasets/download_datasets/nextflow.config" + +// other configs docker { runOptions = "-v $rootDir:$rootDir" } @@ -25,5 +29,4 @@ process { } } -// additional includes -includeConfig "$targetDir/trajectory_inference/datasets/download_datasets/nextflow.config" + From e6ce7e9b75505174b6b58c2e43328ec9a5da2b69 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 08:36:56 +0200 Subject: [PATCH 0102/1233] remove old binaries Former-commit-id: 32241f8fcc2e582d96e75a5aaa5e9989f7f38cf7 --- bin/.gitignore | 2 - bin/README.md | 7 - bin/nextflow | 462 --------------------------- bin/viash | 28 -- bin/viash_bootstrap | 761 -------------------------------------------- bin/viash_build | 591 ---------------------------------- bin/viash_clean_nxf | 571 --------------------------------- bin/viash_gendoc | 637 ------------------------------------ bin/viash_genrep | 756 ------------------------------------------- bin/viash_push | 568 --------------------------------- bin/viash_skeleton | 620 ------------------------------------ bin/viash_test | 580 --------------------------------- bin/viash_trafo | 412 ------------------------ 13 files changed, 5995 deletions(-) delete mode 100644 bin/.gitignore delete mode 100644 bin/README.md delete mode 100755 bin/nextflow delete mode 100755 bin/viash delete mode 100755 bin/viash_bootstrap delete mode 100755 bin/viash_build delete mode 100755 bin/viash_clean_nxf delete mode 100755 bin/viash_gendoc delete mode 100755 bin/viash_genrep delete mode 100755 bin/viash_push delete mode 100755 bin/viash_skeleton delete mode 100755 bin/viash_test delete mode 100755 bin/viash_trafo diff --git a/bin/.gitignore b/bin/.gitignore deleted file mode 100644 index 48a23c5be0..0000000000 --- a/bin/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -fetch -viash-* diff --git a/bin/README.md b/bin/README.md deleted file mode 100644 index 9dcffa21a8..0000000000 --- a/bin/README.md +++ /dev/null @@ -1,7 +0,0 @@ -These executables were generated by running: -``` -curl -s https://get.nextflow.io | bash - -# todo: use https://get.viash.io -viash_bootstrap -t 0.5.0-rc2 --log check_results/results.tsv -``` diff --git a/bin/nextflow b/bin/nextflow deleted file mode 100755 index a0e029b867..0000000000 --- a/bin/nextflow +++ /dev/null @@ -1,462 +0,0 @@ -#!/bin/bash -# -# Copyright 2013-2019, Centre for Genomic Regulation (CRG) -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. - -[[ "$NXF_DEBUG" == 'x' ]] && set -x -NXF_VER=${NXF_VER:-'19.01.0'} -NXF_ORG=${NXF_ORG:-'nextflow-io'} -NXF_HOME=${NXF_HOME:-$HOME/.nextflow} -NXF_PROT=${NXF_PROT:-'https'} -NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases} -NXF_TEMP=${NXF_TEMP:-$TMPDIR} -NXF_DIST=${NXF_DIST:-$NXF_HOME/framework} -NXF_CLI="$0 $@" - -export NXF_CLI -export NXF_ORG -export NXF_HOME - -if [[ $TERM && $TERM != 'dumb' ]]; then -if command -v tput &>/dev/null; then -GREEN=$(tput setaf 2; tput bold) -YELLOW=$(tput setaf 3) -RED=$(tput setaf 1) -NORMAL=$(tput sgr0) -fi -fi - -function echo_red() { - >&2 echo -e "$RED$*$NORMAL" -} - -function echo_green() { - echo -e "$GREEN$*$NORMAL" -} - -function echo_yellow() { - >&2 echo -e "$YELLOW$*$NORMAL" -} - -function die() { - echo_red "$*" - exit 1 -} - -function get_abs_filename() { - echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")" -} - -function get() { - if command -v curl &>/dev/null; then - GET="curl -fsSL '$1' -o '$2'" - elif command -v wget &>/dev/null; then - GET="wget -q '$1' -O '$2'" - else - echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them" - exit 1 - fi - - printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. " - eval $GET; status=$? - printf "\r\033[K" - if [ $status -ne 0 ]; then - echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet" - echo "" - echo "Alternatively you can try to download this file:" - echo " $1" - echo "" - echo "and save it as:" - echo " ${3:-$2}" - echo "" - exit 1 - fi -} - -function make_temp() { - local base=${NXF_TEMP:=$PWD} - if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $? - else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $? - fi -} - -function resolve_link() { - [[ ! -f $1 ]] && exit 1 - if command -v realpath &>/dev/null; then - realpath "$1" - elif command -v readlink &>/dev/null; then - local target="$1" - cd $(dirname $target); target=$(basename $target) - while [ -L "$target" ]; do - target="$(readlink "$target")" - cd $(dirname $target); target=$(basename $target) - done - echo "$(cd "$(dirname "$target")"; pwd -P)/$target" - else - echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found" - exit 1 - fi -} - -function current_ver() { - [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest' -} - -function install() { - local tmpfile=$(make_temp) - local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver) - local action="a=${2:-default}" - get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $? - mv "$tmpfile" "$1" || exit $? - chmod +x "$1" || exit $? - bash "$1" -download || exit $? - echo '' - echo -e $'Nextflow installation completed. Please note:' - echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1) - if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then - echo -e $'- you may complete the installation by moving it to a directory in your $PATH' - fi - echo '' -} - -function launch_nextflow() { - # the launch command line - local cmdline=() - # remove leading and trailing double-quotes - for x in "${launcher[@]}"; do - x="${x%\"}" - x="${x#\"}" - cmdline+=("$x") - done - - if [[ $NXF_MPIRUN ]]; then - local rank='' - [[ $SLURM_PROCID ]] && rank=$SLURM_PROCID - [[ $OMPI_COMM_WORLD_RANK ]] && rank=$OMPI_COMM_WORLD_RANK - if [[ ! $rank ]]; then - echo_red 'It looks you are not running in a MPI enabled environment -- cannot find `$OMPI_COMM_WORLD_RANK` nor `$SLURM_PROCID` variable'; - exit 1; - fi - if [[ $SLURM_CPUS_PER_TASK && $SLURM_MEM_PER_CPU ]]; then - export NXF_CLUSTER_MAXCPUS=$SLURM_CPUS_PER_TASK - export NXF_CLUSTER_MAXMEMORY="$(($SLURM_MEM_PER_CPU*$SLURM_CPUS_PER_TASK))MB" - fi - if [[ $rank == 0 ]]; then - # sleep a few seconds in order to wait worker daemons to bootstrap - sleep ${NXF_SLEEP:-10} - export NXF_EXECUTOR='ignite' - export NXF_CLUSTER_SHUTDOWNONCOMPLETE='true' - else - args=(-log .nextflow_node_${rank}.log node ignite) - fi - # start in daemon mode - elif [[ "$bg" ]]; then - local pid_file="${NXF_PID_FILE:-.nextflow.pid}" - cmdline+=("${args[@]}") - exec "${cmdline[@]}" & - disown - echo $! > "$pid_file" - exit 0 - fi - - cmdline+=("${args[@]}") - exec "${cmdline[@]}" - exit 1 -} - -# check self-install -if [ "$0" = "bash" ] || [ "$0" = "/bin/bash" ]; then - if [ -d nextflow ]; then - echo 'Please note:' - echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists." - echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder." - echo '' - exit 1 - fi - install "$PWD/nextflow" install - exit 0 -fi - - -# parse the command line -bg='' -dockerize='' -declare -a jvmopts=() -declare -a args=("$@") -declare -a commands=(clone config drop help history info ls pull run view node console kuberun) -cmd='' -while [[ $# != 0 ]]; do - case $1 in - -D*) - if [[ ! "$cmd" ]]; then - jvmopts+=("$1") - fi - ;; - -d|-dockerize) - if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then - dockerize=1 - fi - ;; - -bg) - if [[ ! -f /.nextflow/dockerized ]]; then - bg=1 - fi - ;; - -download) - if [[ ! "$cmd" ]]; then - rm -rf "$NXF_DIST/$NXF_VER" || exit $? - bash "$0" -version || exit $? - exit 0 - fi - ;; - -self-update|self-update) - if [[ ! "$cmd" ]]; then - [[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1 - unset NXF_VER - install "$0" update - exit 0 - fi - ;; - -process.executor|-executor.name) - if [[ $2 && $2 == 'ignite' ]]; then - NXF_MODE='ignite'; shift; - fi - ;; - -with-mpi) - NXF_MODE='ignite' - NXF_MPIRUN='true' - ;; - *) - [[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1 - ;; - esac - shift -done - -NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''} -if [[ "$dockerize" ]]; then - if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi - NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets} - mkdir -p "$NXF_ASSETS" - exec docker run $detach --rm --net host \ - -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \ - -v /var/run/docker.sock:/var/run/docker.sock \ - -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \ - nextflow/nextflow:$NXF_VER nextflow "${args[@]}" - exit 1 -fi - -CAPSULE_LOG=${CAPSULE_LOG:=''} -CAPSULE_RESET=${CAPSULE_RESET:=''} -CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"} - -NXF_PACK=one -NXF_MODE=${NXF_MODE:-''} -NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar} -NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR} -NXF_PATH=$(dirname "$NXF_BIN") -NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR} -NXF_GRAB=${NXF_GRAB:-''} -NXF_CLASSPATH=${NXF_CLASSPATH:-''} -NXF_MPIRUN=${NXF_MPIRUN:=''} -NXF_HOST=${HOSTNAME:-localhost} -[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST} - -[ ! $NXF_MODE ] && [[ $NXF_CLOUD_DRIVER == google ]] && NXF_MODE='google' -[ ! $NXF_MODE ] && [[ $GOOGLE_APPLICATION_CREDENTIALS ]] && NXF_MODE='google' - -if [[ $NXF_MODE == ignite ]]; then - # Fix JDK bug when there's a limit on the OS virtual memory - # https://bugs.openjdk.java.net/browse/JDK-8044054 - # https://issues.apache.org/jira/browse/HADOOP-7154 - export MALLOC_ARENA_MAX=4 -fi - -# Determine the path to this file -if [[ $NXF_PACK = all ]]; then - NXF_BIN=$(which "$0" 2>/dev/null) - [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0" -fi - -# use nextflow custom java home path -if [[ "$NXF_JAVA_HOME" ]]; then - JAVA_HOME="$NXF_JAVA_HOME" - unset JAVA_CMD -fi -# Determine the Java command to use to start the JVM. -if [ ! -x "$JAVA_CMD" ] ; then - if [ -d "$JAVA_HOME" ] ; then - if [ -x "$JAVA_HOME/jre/sh/java" ] ; then - # IBM's JDK on AIX uses strange locations for the executables - JAVA_CMD="$JAVA_HOME/jre/sh/java" - else - JAVA_CMD="$JAVA_HOME/bin/java" - fi - elif [ -x /usr/libexec/java_home ]; then - JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java" - else - JAVA_CMD="$(which java)" || JAVA_CMD=java - fi -fi - -# Retrieve the java version from a NF local file -JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')" -if [ -f "$JAVA_KEY" ]; then - JAVA_VER="$(cat "$JAVA_KEY")" -else - JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)" - if [ $? -ne 0 ]; then - echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}" - echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n" - exit 1 - fi - JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}') - # check NF version - if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then - echo_red "Not a valid Nextflow version: $NXF_VER" - exit 1 - fi - major=${BASH_REMATCH[1]} - minor=${BASH_REMATCH[2]} - version_check="^(1.8|9|10|11)" - version_message="Java 8" - # legacy version - Java 7/8 only - if [ $major -eq 0 ] && [ $minor -lt 26 ]; then - version_check="^(1.7|1.8)" - version_message="Java 7 or 8" - fi - if [[ ! $JAVA_VER =~ $version_check ]]; then - echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed" - if [[ "$NXF_JAVA_HOME" ]]; then - echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n" - else - echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n" - fi - exit 1 - fi - mkdir -p $(dirname "$JAVA_KEY") - [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY" -fi - -# Verify nextflow jar is available -if [ ! -f "$NXF_BIN" ]; then - [ -f "$NXF_PATH" ] && rm "$NXF_PATH" - mkdir -p "$NXF_PATH" || exit $? - tmpfile=$(make_temp) - get "$NXF_URL" "$tmpfile" "$NXF_BIN" - mv "$tmpfile" "$NXF_BIN" -fi - -[[ "$cmd" == "console" ]] && NXF_MODE='console' -[[ "$cmd" == "node" && ! "$NXF_MODE" ]] && NXF_MODE='ignite' - -COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`} -declare -a JAVA_OPTS=() -JAVA_OPTS+=(-Dfile.encoding=UTF-8 -noverify -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD") -if [[ $cmd == console ]]; then bg=1; -else JAVA_OPTS+=(-Djava.awt.headless=true) -fi - -[[ "$NXF_MODE" ]] && JAVA_OPTS+=(-Dcapsule.mode=$NXF_MODE) -[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME") -[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG) -[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true) -[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1) -[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS) -[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH -[[ "$NXF_GRAB" ]] && export NXF_GRAB -[[ "$COLUMNS" ]] && export COLUMNS -[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP") -[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}") -# use drip to speedup startup time -- https://github.com/ninjudd/drip -[[ "$NXF_DRIP" ]] && export DRIP_INIT='' && export DRIP_INIT_CLASS='nextflow.cli.DripMain' -export JAVA_CMD -export CAPSULE_CACHE_DIR - -# lookup the a `md5` command -if hash md5sum 2>/dev/null; then MD5=md5sum; -elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum; -elif hash md5 2>/dev/null; then MD5=md5; -else MD5='' -fi - -# when no md5 command is available fallback on default execution -if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then - launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN")) - launch_nextflow - exit 1 -fi - -# creates a md5 unique for the given variables -env_md5() { -cat </dev/null; then - STR='' - for x in "${launcher[@]}"; do - [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$x " - done - printf "$STR">"$LAUNCH_FILE" - else - echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?" - fi - -fi - -# finally run it -launch_nextflow diff --git a/bin/viash b/bin/viash deleted file mode 100755 index f9adcabc0c..0000000000 --- a/bin/viash +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} - - -VIASH_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` -VERSION="0.5.0-rc3" - -VIASH_EXEC="$VIASH_DIR/viash-$VERSION" - -if [[ ! -f $VIASH_EXEC ]]; then - wget https://github.com/data-intuitive/viash/releases/download/$VERSION/viash -O "$VIASH_EXEC" - chmod +x "$VIASH_EXEC" -fi - -$VIASH_EXEC "$@" diff --git a/bin/viash_bootstrap b/bin/viash_bootstrap deleted file mode 100755 index 4476b637e1..0000000000 --- a/bin/viash_bootstrap +++ /dev/null @@ -1,761 +0,0 @@ -#!/usr/bin/env bash - -############################# -# viash_bootstrap 0.1 # -############################# - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_bootstrap 0.1" -echo "Bootstrap or update a viash project's CI/CD artefacts" - echo - echo "Options:" - -echo " --bin" -echo " type: file, output" -echo " default: bin" -echo " Target dir for viash scripts and tools" -echo "" - - -echo " -r, --registry" -echo " type: string" -echo " default: " -echo " Docker registry to use, only used when using a registry." -echo "" - - -echo " --namespace_separator" -echo " type: string" -echo " default: _" -echo " The separator to use between the component name and namespace as the image name of a Docker container." -echo "" - - -echo " -c, --config_mod" -echo " type: string, multiple values allowed" -echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." -echo "" - - -echo " -t, --tag" -echo " type: string" -echo " Which tag/version of viash to use, leave blank for the latest release" -echo "" - - -echo " --log" -echo " type: file" -echo " default: log.tsv" -echo " Path to write the test logs to." -echo "" - - -echo " --viash" -echo " type: file" -echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." -echo "" - -} -######## Helper functions for setting up Docker images for viash ######## - - -# ViashDockerRemoteTagCheck: check whether a Docker image is available -# on a remote. Assumes `docker login` has been performed, if relevant. -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerRemoteTagCheck python:latest -# echo $? # returns '0' -# ViashDockerRemoteTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerRemoteTagCheck { - docker manifest inspect $1 > /dev/null 2> /dev/null -} - -# ViashDockerLocalTagCheck: check whether a Docker image is available locally -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# docker pull python:latest -# ViashDockerLocalTagCheck python:latest -# echo $? # returns '0' -# ViashDockerLocalTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerLocalTagCheck { - [ -n "$(docker images -q $1)" ] -} - -# ViashDockerPull: pull a Docker image -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerPull python:latest -# echo $? # returns '0' -# ViashDockerPull sdaizudceahifu -# echo $? # returns '1' -function ViashDockerPull { - ViashNotice "Running 'docker pull $1'" - docker pull $1 && return 0 || return 1 -} - -# ViashDockerPullElseBuild: pull a Docker image, else build it -# -# $1 : image identifier with format `[registry/]image[:tag]` -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent -function ViashDockerPullElseBuild { - set +e - ViashDockerPull $1 - out=$? - set -e - if [ $out -ne 0 ]; then - ViashDockerBuild $@ - fi -} - -# ViashDockerSetup: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerSetupStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerSetup mynewcomponent alwaysbuild -function ViashDockerSetup { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then - ViashDockerBuild $VSHD_ID - elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then - set +e - ViashDockerLocalTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashInfo "Image $VSHD_ID already exists" - elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then - ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi - elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then - set +e - docker push $VSHD_ID - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then - set +e - ViashDockerRemoteTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' exists, doing nothing." - else - ViashNotice "Container '$VSHD_ID' does not yet exist." - set +e - docker push $1 > /dev/null 2> /dev/null - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - fi - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - ViashNotice "Skipping setup." - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi -} - - -######## End of helper functions for setting up Docker images for viash ######## - -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - cat << 'VIASHDOCKER' -FROM dataintuitive/viash:latest - -RUN curl -sSLfo /usr/local/bin/fetch https://github.com/gruntwork-io/fetch/releases/download/v0.4.2/fetch_linux_amd64 -RUN chmod +x /usr/local/bin/fetch -VIASHDOCKER -} - -# ViashDockerBuild: build a docker container -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was built -function ViashDockerBuild { - - # create temporary directory to store dockerfile & optional resources in - tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_bootstrap-XXXXXX") - function clean_up { - rm -rf "$tmpdir" - } - trap clean_up EXIT - - # store dockerfile and resources - ViashDockerfile > $tmpdir/Dockerfile - cp -r $VIASH_RESOURCES_DIR/* $tmpdir - - # Build the container - ViashNotice "Running 'docker build -t $@ $tmpdir'" - set +e - if [ $VIASH_VERBOSITY -ge 6 ]; then - docker build -t $@ $tmpdir - else - docker build -t $@ $tmpdir &> $tmpdir/docker_build.log - fi - out=$? - set -e - if [ ! $out -eq 0 ]; then - ViashError "Error occurred while building the container $@." - if [ ! $VIASH_VERBOSITY -ge 6 ]; then - ViashError "Transcript: --------------------------------" - cat "$tmpdir/docker_build.log" - ViashError "End of transcript --------------------------" - fi - exit 1 - fi -} -# ViashAbsolutePath: generate absolute path from relative path -# borrowed from https://stackoverflow.com/a/21951256 -# $1 : relative filename -# return : absolute path -# examples: -# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt -# ViashAbsolutePath /foo/bar/.. # returns /foo -function ViashAbsolutePath { - local thePath - if [[ ! "$1" =~ ^/ ]]; then - thePath="$PWD/$1" - else - thePath="$1" - fi - echo "$thePath" | ( - IFS=/ - read -a parr - declare -a outp - for i in "${parr[@]}"; do - case "$i" in - ''|.) continue ;; - ..) - len=${#outp[@]} - if ((len==0)); then - continue - else - unset outp[$((len-1))] - fi - ;; - *) - len=${#outp[@]} - outp[$len]="$i" - ;; - esac - done - echo /"${outp[*]}" - ) -} -# ViashAutodetectMount: auto configuring docker mounts from parameters -# $1 : The parameter value -# returns : New parameter -# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker -# examples: -# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' -# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' -function ViashAutodetectMount { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "$mount_target/$base_name" -} -function ViashAutodetectMountArg { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "-v \"$mount_source:$mount_target\"" -} -# ViashExtractFlags: Retain leading flag -# $1 : string with a possible leading flag -# return : leading flag -# examples: -# ViashExtractFlags --foo=bar # returns --foo -function ViashExtractFlags { - echo $1 | sed 's/=.*//' -} -# initialise variables -VIASH_EXTRA_MOUNTS='' - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_bootstrap 0.1" - exit - ;; - --bin) - VIASH_PAR_BIN="$2" - shift 2 - ;; - --bin=*) - VIASH_PAR_BIN=$(ViashRemoveFlags "$1") - shift 1 - ;; - --registry) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --registry=*) - VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -r) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --namespace_separator) - VIASH_PAR_NAMESPACE_SEPARATOR="$2" - shift 2 - ;; - --namespace_separator=*) - VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --config_mod) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --config_mod=*) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - -c) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --tag) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --tag=*) - VIASH_PAR_TAG=$(ViashRemoveFlags "$1") - shift 1 - ;; - -t) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --log) - VIASH_PAR_LOG="$2" - shift 2 - ;; - --log=*) - VIASH_PAR_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --viash) - VIASH_PAR_VIASH="$2" - shift 2 - ;; - --viash=*) - VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") - shift 1 - ;; - ---setup) - ViashDockerSetup 'viash_viash_bootstrap:0.1' "$2" - exit 0 - ;; - ---setup=*) - ViashDockerSetup 'viash_viash_bootstrap:0.1' "$(ViashRemoveFlags "$1")" - exit 0 - ;; - ---dockerfile) - ViashDockerfile - exit 0 - ;; - ---v|---volume) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" - shift 2 - ;; - ---volume=*) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" - shift 1 - ;; - ---debug) - ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_bootstrap:0.1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_bootstrap:0.1 - exit 0 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -if [ -z "$VIASH_PAR_BIN" ]; then - VIASH_PAR_BIN="bin" -fi -if [ -z "$VIASH_PAR_REGISTRY" ]; then - VIASH_PAR_REGISTRY="" -fi -if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then - VIASH_PAR_NAMESPACE_SEPARATOR="_" -fi -if [ -z "$VIASH_PAR_LOG" ]; then - VIASH_PAR_LOG="log.tsv" -fi - -ViashDockerSetup 'viash_viash_bootstrap:0.1' ifneedbepullelsecachedbuild - -# detect volumes from file arguments -if [ ! -z "$VIASH_PAR_BIN" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_BIN")" - VIASH_PAR_BIN=$(ViashAutodetectMount "$VIASH_PAR_BIN") -fi -if [ ! -z "$VIASH_PAR_LOG" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_LOG")" - VIASH_PAR_LOG=$(ViashAutodetectMount "$VIASH_PAR_LOG") -fi -if [ ! -z "$VIASH_PAR_VIASH" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_VIASH")" - VIASH_PAR_VIASH=$(ViashAutodetectMount "$VIASH_PAR_VIASH") -fi - -# Always mount the resource directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" -VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") - -# Always mount the VIASH_TEMP directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" -VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") - -# change file ownership -function viash_perform_chown { - - if [ ! -z "$VIASH_PAR_BIN" ]; then - eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_bootstrap:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_BIN" - fi -} -trap viash_perform_chown EXIT - - -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_bootstrap:0.1 -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_bootstrap-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_bin='$VIASH_PAR_BIN' -par_registry='$VIASH_PAR_REGISTRY' -par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' -par_config_mod='$VIASH_PAR_CONFIG_MOD' -par_tag='$VIASH_PAR_TAG' -par_log='$VIASH_PAR_LOG' -par_viash='$VIASH_PAR_VIASH' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -# get the root of the repository -REPO_ROOT=\`pwd\` - -if [ ! -d "\$par_bin" ]; then - echo "> Creating \$par_bin" - mkdir "\$par_bin" -fi - -cd "\$par_bin" - -# Retrieving version -viash_version=\`viash -v | sed -E 's/^viash ([v0-9.]+[\\-rc0-9]*).*/\\1/'\` -if [ -z \$par_tag ]; then - par_tag="\$viash_version" - same_version=1 -else - same_version=0 -fi -echo "> Using tag \$par_tag" - -# remove previous binaries -echo "> Cleanup" -if [ -f viash ]; then - echo " > Removing previous versions of viash and recent project binaries" - rm viash* -fi -if [ -f project_update ]; then - echo " > Removing previous versions of project binaries" - rm project_* -fi -if [ -f skeleton ]; then - echo " > Removing previous versions of skeleton binary" - rm skeleton -fi - -# build helper components -build_dir=\$(mktemp -d) -function clean_up { - [[ -d "\$build_dir" ]] && rm -r "\$build_dir" -} -trap clean_up EXIT - -# Install viash itself -echo "> Install viash \$par_tag under \$par_bin" -if [ \$same_version = 1 ];then - cp \`which viash\` . -elif [ \$par_tag == "develop" ]; then - cd \$build_dir - git clone --branch develop https://github.com/viash-io/viash - cd \$build_dir/viash - ls - ./configure - make bin/viash - cp bin/viash \$par_bin - cd .. - rm -r viash - cd \$par_bin -else - wget -nv "https://github.com/viash-io/viash/releases/download/\$par_tag/viash" - chmod +x viash -fi - -# download viash components -echo "> Fetching components sources (version \$par_tag)" -fetch --repo="https://github.com/viash-io/viash" --branch="\$par_tag" --source-path="/src/viash" "\$build_dir" - -# build components -echo "> Building components" -./viash ns build \\ - -s "\$build_dir" \\ - -t . \\ - --flatten \\ - -c '.functionality.arguments[.name == "--registry"].default := "'\$par_registry'"' \\ - -c '.functionality.arguments[.name == "--viash"].default := "'\$par_viash'"' \\ - -c '.functionality.arguments[.name == "--log" && root.functionality.name == "project_test"].default := "'\$par_log'"' \\ - -c '.functionality.arguments[.name == "--namespace_separator"].default := "'\$par_namespace_separator'"' - -echo "> Done, happy viash-ing!" -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_build b/bin/viash_build deleted file mode 100755 index 9eeb76b527..0000000000 --- a/bin/viash_build +++ /dev/null @@ -1,591 +0,0 @@ -#!/usr/bin/env bash - -######################### -# viash_build 0.1 # -######################### - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_build 0.1" -echo "Build a project, usually in the context of a pipeline." - echo - echo "Options:" - -echo " -s, --src" -echo " type: file" -echo " default: src" -echo " Directory for sources if different from src/" -echo "" - - -echo " -m, --mode" -echo " type: string" -echo " default: development" -echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." -echo "" - - -echo " -p, --platforms" -echo " type: string" -echo " default: docker|nextflow" -echo " Which platforms to test, default is 'docker|nextflow'." -echo "" - - -echo " -q, --query" -echo " type: string" -echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." -echo "" - - -echo " -n, --query_namespace" -echo " type: string" -echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." -echo "" - - -echo " --query_name" -echo " type: string" -echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." -echo "" - - -echo " -t, --tag" -echo " type: string" -echo " default: dev" -echo " The tag/version to be used." -echo "" - - -echo " -r, --registry" -echo " type: string" -echo " default: " -echo " Docker registry to use, only used when using a registry." -echo "" - - -echo " --namespace_separator" -echo " type: string" -echo " default: _" -echo " The separator to use between the component name and namespace as the image name of a Docker container." -echo "" - - -echo " --max_threads" -echo " type: integer" -echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." -echo "" - - -echo " -c, --config_mod" -echo " type: string, multiple values allowed" -echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." -echo "" - - -echo " -nc, --no-cache, --no_cache" -echo " type: boolean_true" -echo " Don't cache the docker build in development mode." -echo "" - - -echo " --log" -echo " type: file, output" -echo " default: log.txt" -echo " Log file" -echo "" - - -echo " --viash" -echo " type: file" -echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." -echo "" - -} - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_build 0.1" - exit - ;; - --src) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --src=*) - VIASH_PAR_SRC=$(ViashRemoveFlags "$1") - shift 1 - ;; - -s) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --mode) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --mode=*) - VIASH_PAR_MODE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -m) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --platforms) - VIASH_PAR_PLATFORMS="$2" - shift 2 - ;; - --platforms=*) - VIASH_PAR_PLATFORMS=$(ViashRemoveFlags "$1") - shift 1 - ;; - -p) - VIASH_PAR_PLATFORMS="$2" - shift 2 - ;; - --query) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query=*) - VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -q) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query_namespace) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_namespace=*) - VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -n) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_name) - VIASH_PAR_QUERY_NAME="$2" - shift 2 - ;; - --query_name=*) - VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tag) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --tag=*) - VIASH_PAR_TAG=$(ViashRemoveFlags "$1") - shift 1 - ;; - -t) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --registry) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --registry=*) - VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -r) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --namespace_separator) - VIASH_PAR_NAMESPACE_SEPARATOR="$2" - shift 2 - ;; - --namespace_separator=*) - VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --max_threads) - VIASH_PAR_MAX_THREADS="$2" - shift 2 - ;; - --max_threads=*) - VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --config_mod) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --config_mod=*) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - -c) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --no_cache) - VIASH_PAR_NO_CACHE=true - shift 1 - ;; - -nc) - VIASH_PAR_NO_CACHE=true - shift 1 - ;; - --no-cache) - VIASH_PAR_NO_CACHE=true - shift 1 - ;; - --log) - VIASH_PAR_LOG="$2" - shift 2 - ;; - --log=*) - VIASH_PAR_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --viash) - VIASH_PAR_VIASH="$2" - shift 2 - ;; - --viash=*) - VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -if [ -z "$VIASH_PAR_SRC" ]; then - VIASH_PAR_SRC="src" -fi -if [ -z "$VIASH_PAR_MODE" ]; then - VIASH_PAR_MODE="development" -fi -if [ -z "$VIASH_PAR_PLATFORMS" ]; then - VIASH_PAR_PLATFORMS="docker|nextflow" -fi -if [ -z "$VIASH_PAR_TAG" ]; then - VIASH_PAR_TAG="dev" -fi -if [ -z "$VIASH_PAR_REGISTRY" ]; then - VIASH_PAR_REGISTRY="" -fi -if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then - VIASH_PAR_NAMESPACE_SEPARATOR="_" -fi -if [ -z "$VIASH_PAR_NO_CACHE" ]; then - VIASH_PAR_NO_CACHE="false" -fi -if [ -z "$VIASH_PAR_LOG" ]; then - VIASH_PAR_LOG="log.txt" -fi - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_build-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_src='$VIASH_PAR_SRC' -par_mode='$VIASH_PAR_MODE' -par_platforms='$VIASH_PAR_PLATFORMS' -par_query='$VIASH_PAR_QUERY' -par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' -par_query_name='$VIASH_PAR_QUERY_NAME' -par_tag='$VIASH_PAR_TAG' -par_registry='$VIASH_PAR_REGISTRY' -par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' -par_max_threads='$VIASH_PAR_MAX_THREADS' -par_config_mod='$VIASH_PAR_CONFIG_MOD' -par_no_cache='$VIASH_PAR_NO_CACHE' -par_log='$VIASH_PAR_LOG' -par_viash='$VIASH_PAR_VIASH' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -# if not specified, default queries to a catch-all regexes -if [ -z "\$par_query" ]; then - par_query=".*" -fi -if [ -z "\$par_query_namespace" ]; then - par_query_namespace=".*" -fi -if [ -z "\$par_query_name" ]; then - par_query_name=".*" -fi - -# if not specified, default par_viash to look for 'viash' on the PATH -if [ -z "\$par_viash" ]; then - par_viash="viash" -fi - - -# if specified, use par_max_threads as a java argument -if [ ! -z "\$par_max_threads" ]; then - export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" -fi - -if [ "\$par_mode" == "release" ]; then - echo "In release mode with tag '\$par_tag'." - if [ "\$par_tag" == "dev" ]; then - echo "For a release, you have to specify an explicit version using --tag" - exit 1 - fi -fi - -if [ "\$par_mode" == "development" ]; then - echo "In development mode..." - - if [ "\$par_no_cache" == "true" ]; then - setup_strat="build" - else - setup_strat="cachedbuild" - fi - - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "dev"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l -w \\ - --setup "\$setup_strat" | tee "\$par_log" -elif [ "\$par_mode" == "integration" ]; then - echo "In integration mode..." - - if [ "\$par_no_cache" == "true" ]; then - echo "Warning: '--no_cache' only applies when '--mode=development'." - fi - - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "ifneedbepullelsecachedbuild"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l -w \\ - --setup "build" | tee "\$par_log" -elif [ "\$par_mode" == "release" ]; then - - if [ "\$par_no_cache" == "true" ]; then - echo "Warning: '--no_cache' only applies when '--mode=development'." - fi - - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "ifneedbepullelsecachedbuild"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l -w \\ - --setup "build" | tee "\$par_log" -else - echo "Not a valid mode argument" -fi -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_clean_nxf b/bin/viash_clean_nxf deleted file mode 100755 index b40704df66..0000000000 --- a/bin/viash_clean_nxf +++ /dev/null @@ -1,571 +0,0 @@ -#!/usr/bin/env bash - -############################# -# viash_clean_nxf 0.1 # -############################# - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_clean_nxf 0.1" -echo "Clean a (nextflow) project directory" - echo - echo "Options:" - -echo " dir" -echo " type: file" -echo " default: ." -echo " Base directory" -echo "" - - -echo " -after" -echo " type: string" -echo "" - - -echo " -before" -echo " type: string" -echo "" - -} -######## Helper functions for setting up Docker images for viash ######## - - -# ViashDockerRemoteTagCheck: check whether a Docker image is available -# on a remote. Assumes `docker login` has been performed, if relevant. -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerRemoteTagCheck python:latest -# echo $? # returns '0' -# ViashDockerRemoteTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerRemoteTagCheck { - docker manifest inspect $1 > /dev/null 2> /dev/null -} - -# ViashDockerLocalTagCheck: check whether a Docker image is available locally -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# docker pull python:latest -# ViashDockerLocalTagCheck python:latest -# echo $? # returns '0' -# ViashDockerLocalTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerLocalTagCheck { - [ -n "$(docker images -q $1)" ] -} - -# ViashDockerPull: pull a Docker image -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerPull python:latest -# echo $? # returns '0' -# ViashDockerPull sdaizudceahifu -# echo $? # returns '1' -function ViashDockerPull { - ViashNotice "Running 'docker pull $1'" - docker pull $1 && return 0 || return 1 -} - -# ViashDockerPullElseBuild: pull a Docker image, else build it -# -# $1 : image identifier with format `[registry/]image[:tag]` -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent -function ViashDockerPullElseBuild { - set +e - ViashDockerPull $1 - out=$? - set -e - if [ $out -ne 0 ]; then - ViashDockerBuild $@ - fi -} - -# ViashDockerSetup: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerSetupStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerSetup mynewcomponent alwaysbuild -function ViashDockerSetup { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then - ViashDockerBuild $VSHD_ID - elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then - set +e - ViashDockerLocalTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashInfo "Image $VSHD_ID already exists" - elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then - ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi - elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then - set +e - docker push $VSHD_ID - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then - set +e - ViashDockerRemoteTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' exists, doing nothing." - else - ViashNotice "Container '$VSHD_ID' does not yet exist." - set +e - docker push $1 > /dev/null 2> /dev/null - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - fi - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - ViashNotice "Skipping setup." - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi -} - - -######## End of helper functions for setting up Docker images for viash ######## - -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - cat << 'VIASHDOCKER' -FROM nextflow/nextflow:latest - -RUN : -VIASHDOCKER -} - -# ViashDockerBuild: build a docker container -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was built -function ViashDockerBuild { - - # create temporary directory to store dockerfile & optional resources in - tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_clean_nxf-XXXXXX") - function clean_up { - rm -rf "$tmpdir" - } - trap clean_up EXIT - - # store dockerfile and resources - ViashDockerfile > $tmpdir/Dockerfile - cp -r $VIASH_RESOURCES_DIR/* $tmpdir - - # Build the container - ViashNotice "Running 'docker build -t $@ $tmpdir'" - set +e - if [ $VIASH_VERBOSITY -ge 6 ]; then - docker build -t $@ $tmpdir - else - docker build -t $@ $tmpdir &> $tmpdir/docker_build.log - fi - out=$? - set -e - if [ ! $out -eq 0 ]; then - ViashError "Error occurred while building the container $@." - if [ ! $VIASH_VERBOSITY -ge 6 ]; then - ViashError "Transcript: --------------------------------" - cat "$tmpdir/docker_build.log" - ViashError "End of transcript --------------------------" - fi - exit 1 - fi -} -# ViashAbsolutePath: generate absolute path from relative path -# borrowed from https://stackoverflow.com/a/21951256 -# $1 : relative filename -# return : absolute path -# examples: -# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt -# ViashAbsolutePath /foo/bar/.. # returns /foo -function ViashAbsolutePath { - local thePath - if [[ ! "$1" =~ ^/ ]]; then - thePath="$PWD/$1" - else - thePath="$1" - fi - echo "$thePath" | ( - IFS=/ - read -a parr - declare -a outp - for i in "${parr[@]}"; do - case "$i" in - ''|.) continue ;; - ..) - len=${#outp[@]} - if ((len==0)); then - continue - else - unset outp[$((len-1))] - fi - ;; - *) - len=${#outp[@]} - outp[$len]="$i" - ;; - esac - done - echo /"${outp[*]}" - ) -} -# ViashAutodetectMount: auto configuring docker mounts from parameters -# $1 : The parameter value -# returns : New parameter -# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker -# examples: -# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' -# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' -function ViashAutodetectMount { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "$mount_target/$base_name" -} -function ViashAutodetectMountArg { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "-v \"$mount_source:$mount_target\"" -} -# ViashExtractFlags: Retain leading flag -# $1 : string with a possible leading flag -# return : leading flag -# examples: -# ViashExtractFlags --foo=bar # returns --foo -function ViashExtractFlags { - echo $1 | sed 's/=.*//' -} -# initialise variables -VIASH_EXTRA_MOUNTS='' - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_clean_nxf 0.1" - exit - ;; - -after) - VIASH_PAR_AFTER="$2" - shift 2 - ;; - -before) - VIASH_PAR_BEFORE="$2" - shift 2 - ;; - ---setup) - ViashDockerSetup 'viash_viash_clean_nxf:0.1' "$2" - exit 0 - ;; - ---setup=*) - ViashDockerSetup 'viash_viash_clean_nxf:0.1' "$(ViashRemoveFlags "$1")" - exit 0 - ;; - ---dockerfile) - ViashDockerfile - exit 0 - ;; - ---v|---volume) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" - shift 2 - ;; - ---volume=*) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" - shift 1 - ;; - ---debug) - ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_clean_nxf:0.1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_clean_nxf:0.1 - exit 0 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - -if [[ $# -gt 0 ]]; then - VIASH_PAR_DIR="$1" - shift 1 -fi - -if [ -z "$VIASH_PAR_DIR" ]; then - VIASH_PAR_DIR="." -fi - -ViashDockerSetup 'viash_viash_clean_nxf:0.1' ifneedbepullelsecachedbuild - -# detect volumes from file arguments -if [ ! -z "$VIASH_PAR_DIR" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_DIR")" - VIASH_PAR_DIR=$(ViashAutodetectMount "$VIASH_PAR_DIR") -fi - -# Always mount the resource directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" -VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") - -# Always mount the VIASH_TEMP directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" -VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") - -# change file ownership -function viash_perform_chown { - : -} -trap viash_perform_chown EXIT - - -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_clean_nxf:0.1 -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_clean_nxf-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_dir='$VIASH_PAR_DIR' -par_after='$VIASH_PAR_AFTER' -par_before='$VIASH_PAR_BEFORE' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -add="" - -if [ ! -z "\$par_after" ]; then - add="\$add -after \$par_after" -fi - -if [ ! -z "\$par_before" ]; then - add="\$add -before \$par_before" -fi - -nextflow clean -f "\$add" -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_gendoc b/bin/viash_gendoc deleted file mode 100755 index 18c79bc6c1..0000000000 --- a/bin/viash_gendoc +++ /dev/null @@ -1,637 +0,0 @@ -#!/usr/bin/env bash - -########################## -# viash_gendoc 0.1 # -########################## - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_gendoc 0.1" -echo "Generate documentation" - echo - echo "Options:" - -echo " repo" -echo " type: file" -echo " default: ." -echo " Repository to generate documentation for" -echo "" - - -echo " -s, --src" -echo " type: string" -echo " default: src" -echo " Folder to search for components, usually just src/" -echo "" - - -echo " -r, --output" -echo " type: file, output" -echo " default: project_doc.md" -echo " Name/path of the output markdown file" -echo "" - -} -######## Helper functions for setting up Docker images for viash ######## - - -# ViashDockerRemoteTagCheck: check whether a Docker image is available -# on a remote. Assumes `docker login` has been performed, if relevant. -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerRemoteTagCheck python:latest -# echo $? # returns '0' -# ViashDockerRemoteTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerRemoteTagCheck { - docker manifest inspect $1 > /dev/null 2> /dev/null -} - -# ViashDockerLocalTagCheck: check whether a Docker image is available locally -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# docker pull python:latest -# ViashDockerLocalTagCheck python:latest -# echo $? # returns '0' -# ViashDockerLocalTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerLocalTagCheck { - [ -n "$(docker images -q $1)" ] -} - -# ViashDockerPull: pull a Docker image -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerPull python:latest -# echo $? # returns '0' -# ViashDockerPull sdaizudceahifu -# echo $? # returns '1' -function ViashDockerPull { - ViashNotice "Running 'docker pull $1'" - docker pull $1 && return 0 || return 1 -} - -# ViashDockerPullElseBuild: pull a Docker image, else build it -# -# $1 : image identifier with format `[registry/]image[:tag]` -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent -function ViashDockerPullElseBuild { - set +e - ViashDockerPull $1 - out=$? - set -e - if [ $out -ne 0 ]; then - ViashDockerBuild $@ - fi -} - -# ViashDockerSetup: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerSetupStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerSetup mynewcomponent alwaysbuild -function ViashDockerSetup { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then - ViashDockerBuild $VSHD_ID - elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then - set +e - ViashDockerLocalTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashInfo "Image $VSHD_ID already exists" - elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then - ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi - elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then - set +e - docker push $VSHD_ID - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then - set +e - ViashDockerRemoteTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' exists, doing nothing." - else - ViashNotice "Container '$VSHD_ID' does not yet exist." - set +e - docker push $1 > /dev/null 2> /dev/null - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - fi - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - ViashNotice "Skipping setup." - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi -} - - -######## End of helper functions for setting up Docker images for viash ######## - -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - cat << 'VIASHDOCKER' -FROM dataintuitive/viash:0.4.0-rc1 - -RUN : -VIASHDOCKER -} - -# ViashDockerBuild: build a docker container -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was built -function ViashDockerBuild { - - # create temporary directory to store dockerfile & optional resources in - tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_gendoc-XXXXXX") - function clean_up { - rm -rf "$tmpdir" - } - trap clean_up EXIT - - # store dockerfile and resources - ViashDockerfile > $tmpdir/Dockerfile - cp -r $VIASH_RESOURCES_DIR/* $tmpdir - - # Build the container - ViashNotice "Running 'docker build -t $@ $tmpdir'" - set +e - if [ $VIASH_VERBOSITY -ge 6 ]; then - docker build -t $@ $tmpdir - else - docker build -t $@ $tmpdir &> $tmpdir/docker_build.log - fi - out=$? - set -e - if [ ! $out -eq 0 ]; then - ViashError "Error occurred while building the container $@." - if [ ! $VIASH_VERBOSITY -ge 6 ]; then - ViashError "Transcript: --------------------------------" - cat "$tmpdir/docker_build.log" - ViashError "End of transcript --------------------------" - fi - exit 1 - fi -} -# ViashAbsolutePath: generate absolute path from relative path -# borrowed from https://stackoverflow.com/a/21951256 -# $1 : relative filename -# return : absolute path -# examples: -# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt -# ViashAbsolutePath /foo/bar/.. # returns /foo -function ViashAbsolutePath { - local thePath - if [[ ! "$1" =~ ^/ ]]; then - thePath="$PWD/$1" - else - thePath="$1" - fi - echo "$thePath" | ( - IFS=/ - read -a parr - declare -a outp - for i in "${parr[@]}"; do - case "$i" in - ''|.) continue ;; - ..) - len=${#outp[@]} - if ((len==0)); then - continue - else - unset outp[$((len-1))] - fi - ;; - *) - len=${#outp[@]} - outp[$len]="$i" - ;; - esac - done - echo /"${outp[*]}" - ) -} -# ViashAutodetectMount: auto configuring docker mounts from parameters -# $1 : The parameter value -# returns : New parameter -# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker -# examples: -# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' -# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' -function ViashAutodetectMount { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "$mount_target/$base_name" -} -function ViashAutodetectMountArg { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "-v \"$mount_source:$mount_target\"" -} -# ViashExtractFlags: Retain leading flag -# $1 : string with a possible leading flag -# return : leading flag -# examples: -# ViashExtractFlags --foo=bar # returns --foo -function ViashExtractFlags { - echo $1 | sed 's/=.*//' -} -# initialise variables -VIASH_EXTRA_MOUNTS='' - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_gendoc 0.1" - exit - ;; - --src) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --src=*) - VIASH_PAR_SRC=$(ViashRemoveFlags "$1") - shift 1 - ;; - -s) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --output) - VIASH_PAR_OUTPUT="$2" - shift 2 - ;; - --output=*) - VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - -r) - VIASH_PAR_OUTPUT="$2" - shift 2 - ;; - ---setup) - ViashDockerSetup 'viash_viash_gendoc:0.1' "$2" - exit 0 - ;; - ---setup=*) - ViashDockerSetup 'viash_viash_gendoc:0.1' "$(ViashRemoveFlags "$1")" - exit 0 - ;; - ---dockerfile) - ViashDockerfile - exit 0 - ;; - ---v|---volume) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" - shift 2 - ;; - ---volume=*) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" - shift 1 - ;; - ---debug) - ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_gendoc:0.1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_gendoc:0.1 - exit 0 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - -if [[ $# -gt 0 ]]; then - VIASH_PAR_REPO="$1" - shift 1 -fi - -if [ -z "$VIASH_PAR_REPO" ]; then - VIASH_PAR_REPO="." -fi -if [ -z "$VIASH_PAR_SRC" ]; then - VIASH_PAR_SRC="src" -fi -if [ -z "$VIASH_PAR_OUTPUT" ]; then - VIASH_PAR_OUTPUT="project_doc.md" -fi - -ViashDockerSetup 'viash_viash_gendoc:0.1' ifneedbepullelsecachedbuild - -# detect volumes from file arguments -if [ ! -z "$VIASH_PAR_REPO" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_REPO")" - VIASH_PAR_REPO=$(ViashAutodetectMount "$VIASH_PAR_REPO") -fi -if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_OUTPUT")" - VIASH_PAR_OUTPUT=$(ViashAutodetectMount "$VIASH_PAR_OUTPUT") -fi - -# Always mount the resource directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" -VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") - -# Always mount the VIASH_TEMP directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" -VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") - -# change file ownership -function viash_perform_chown { - - if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_gendoc:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" - fi -} -trap viash_perform_chown EXIT - - -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_gendoc:0.1 -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_gendoc-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_repo='$VIASH_PAR_REPO' -par_src='$VIASH_PAR_SRC' -par_output='$VIASH_PAR_OUTPUT' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -function output { - echo "\$@" >> \$par_output -} - -echo "# Repository Overview" > \$par_output -output "" - -namespaces=\`viash ns list -s \$par_repo/"\$par_src" | yq e '.[].functionality.namespace' - | uniq\` - -tempscript=\$(mktemp ".tmp_viash_config_view_XXXXXX") -function clean_up { - [[ -f "\$tempscript" ]] && rm "\$tempscript" -} -trap clean_up EXIT - -for ns in \$namespaces; do - echo "> Generating documentation for namespace \$ns" - output "## \$ns" - output "" - comp_files=\`viash ns list -n \$ns -s \$par_repo/\$par_src | yq e '.[].info.config' - | uniq\` - for comp_file in \$comp_files; do - viash config view "\$comp_file" > "\$tempscript" - - comp_name=\`yq e '.functionality.name' "\$tempscript"\` - comp_desc=\`yq e '.functionality.description' "\$tempscript"\` - echo " > Generating documentation for \$ns/\$comp_name" - output "### \$comp_name" - output "" - output \$comp_desc - output "" - output '\`\`\`sh' - output "\$ viash run \$comp_file -- -h" - viash run \$comp_file -- -h >> \$par_output - output '\`\`\`' - output "" - - clean_up - done -done - -output "# Tests" -output "" -output "__TODO__" -output "" -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_genrep b/bin/viash_genrep deleted file mode 100755 index 44fc5d7f28..0000000000 --- a/bin/viash_genrep +++ /dev/null @@ -1,756 +0,0 @@ -#!/usr/bin/env bash - -########################## -# viash_genrep 0.1 # -########################## - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_genrep 0.1" -echo "Generate a test report based on viash ns test output" - echo - echo "Options:" - -echo " --input" -echo " type: file, required parameter" -echo " viasn ns test output file (tsv format)" -echo "" - - -echo " --tmp" -echo " type: file" -echo " default: /tmp" -echo " System temp dir if different from /tmp (e.g. on Mac use /private/tmp)" -echo "" - - -echo " --output" -echo " type: file, output" -echo " default: debug_report.md" -echo " Name/path of the output markdown file" -echo "" - -} -######## Helper functions for setting up Docker images for viash ######## - - -# ViashDockerRemoteTagCheck: check whether a Docker image is available -# on a remote. Assumes `docker login` has been performed, if relevant. -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerRemoteTagCheck python:latest -# echo $? # returns '0' -# ViashDockerRemoteTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerRemoteTagCheck { - docker manifest inspect $1 > /dev/null 2> /dev/null -} - -# ViashDockerLocalTagCheck: check whether a Docker image is available locally -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# docker pull python:latest -# ViashDockerLocalTagCheck python:latest -# echo $? # returns '0' -# ViashDockerLocalTagCheck sdaizudceahifu -# echo $? # returns '1' -function ViashDockerLocalTagCheck { - [ -n "$(docker images -q $1)" ] -} - -# ViashDockerPull: pull a Docker image -# -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was found -# examples: -# ViashDockerPull python:latest -# echo $? # returns '0' -# ViashDockerPull sdaizudceahifu -# echo $? # returns '1' -function ViashDockerPull { - ViashNotice "Running 'docker pull $1'" - docker pull $1 && return 0 || return 1 -} - -# ViashDockerPullElseBuild: pull a Docker image, else build it -# -# $1 : image identifier with format `[registry/]image[:tag]` -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerPullElseBuild mynewcomponent -function ViashDockerPullElseBuild { - set +e - ViashDockerPull $1 - out=$? - set -e - if [ $out -ne 0 ]; then - ViashDockerBuild $@ - fi -} - -# ViashDockerSetup: create a Docker image, according to specified docker setup strategy -# -# $1 : image identifier with format `[registry/]image[:tag]` -# $2 : docker setup strategy, see DockerSetupStrategy.scala -# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument. -# examples: -# ViashDockerSetup mynewcomponent alwaysbuild -function ViashDockerSetup { - VSHD_ID="$1" - VSHD_STRAT="$2" - if [ "$VSHD_STRAT" == "alwaysbuild" -o "$VSHD_STRAT" == "build" -o "$VSHD_STRAT" == "b" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspull" -o "$VSHD_STRAT" == "pull" -o "$VSHD_STRAT" == "p" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayspullelsebuild" -o "$VSHD_STRAT" == "pullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "alwayspullelsecachedbuild" -o "$VSHD_STRAT" == "pullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "alwayscachedbuild" -o "$VSHD_STRAT" == "cachedbuild" -o "$VSHD_STRAT" == "cb" ]; then - ViashDockerBuild $VSHD_ID - elif [[ "$VSHD_STRAT" =~ ^ifneedbe ]]; then - set +e - ViashDockerLocalTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashInfo "Image $VSHD_ID already exists" - elif [ "$VSHD_STRAT" == "ifneedbebuild" ]; then - ViashDockerBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbecachedbuild" ]; then - ViashDockerBuild $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepull" ]; then - ViashDockerPull $VSHD_ID - elif [ "$VSHD_STRAT" == "ifneedbepullelsebuild" ]; then - ViashDockerPullElseBuild $VSHD_ID --no-cache - elif [ "$VSHD_STRAT" == "ifneedbepullelsecachedbuild" ]; then - ViashDockerPullElseBuild $VSHD_ID - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi - elif [ "$VSHD_STRAT" == "push" -o "$VSHD_STRAT" == "forcepush" -o "$VSHD_STRAT" == "alwayspush" ]; then - set +e - docker push $VSHD_ID - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - elif [ "$VSHD_STRAT" == "pushifnotpresent" -o "$VSHD_STRAT" == "gentlepush" -o "$VSHD_STRAT" == "maybepush" ]; then - set +e - ViashDockerRemoteTagCheck $VSHD_ID - outCheck=$? - set -e - if [ $outCheck -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' exists, doing nothing." - else - ViashNotice "Container '$VSHD_ID' does not yet exist." - set +e - docker push $1 > /dev/null 2> /dev/null - outPush=$? - set -e - if [ $outPush -eq 0 ]; then - ViashNotice "Container '$VSHD_ID' push succeeded." - else - ViashError "Container '$VSHD_ID' push errored." - exit 1 - fi - fi - elif [ "$VSHD_STRAT" == "donothing" -o "$VSHD_STRAT" == "meh" ]; then - ViashNotice "Skipping setup." - else - ViashError "Unrecognised Docker strategy: $VSHD_STRAT" - exit 1 - fi -} - - -######## End of helper functions for setting up Docker images for viash ######## - -# ViashDockerFile: print the dockerfile to stdout -# return : dockerfile required to run this component -# examples: -# ViashDockerFile -function ViashDockerfile { - cat << 'VIASHDOCKER' -FROM dataintuitive/viash:0.4.0-rc1 - -RUN : -VIASHDOCKER -} - -# ViashDockerBuild: build a docker container -# $1 : image identifier with format `[registry/]image[:tag]` -# exit code $? : whether or not the image was built -function ViashDockerBuild { - - # create temporary directory to store dockerfile & optional resources in - tmpdir=$(mktemp -d "$VIASH_TEMP/viashsetupdocker-viash_genrep-XXXXXX") - function clean_up { - rm -rf "$tmpdir" - } - trap clean_up EXIT - - # store dockerfile and resources - ViashDockerfile > $tmpdir/Dockerfile - cp -r $VIASH_RESOURCES_DIR/* $tmpdir - - # Build the container - ViashNotice "Running 'docker build -t $@ $tmpdir'" - set +e - if [ $VIASH_VERBOSITY -ge 6 ]; then - docker build -t $@ $tmpdir - else - docker build -t $@ $tmpdir &> $tmpdir/docker_build.log - fi - out=$? - set -e - if [ ! $out -eq 0 ]; then - ViashError "Error occurred while building the container $@." - if [ ! $VIASH_VERBOSITY -ge 6 ]; then - ViashError "Transcript: --------------------------------" - cat "$tmpdir/docker_build.log" - ViashError "End of transcript --------------------------" - fi - exit 1 - fi -} -# ViashAbsolutePath: generate absolute path from relative path -# borrowed from https://stackoverflow.com/a/21951256 -# $1 : relative filename -# return : absolute path -# examples: -# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt -# ViashAbsolutePath /foo/bar/.. # returns /foo -function ViashAbsolutePath { - local thePath - if [[ ! "$1" =~ ^/ ]]; then - thePath="$PWD/$1" - else - thePath="$1" - fi - echo "$thePath" | ( - IFS=/ - read -a parr - declare -a outp - for i in "${parr[@]}"; do - case "$i" in - ''|.) continue ;; - ..) - len=${#outp[@]} - if ((len==0)); then - continue - else - unset outp[$((len-1))] - fi - ;; - *) - len=${#outp[@]} - outp[$len]="$i" - ;; - esac - done - echo /"${outp[*]}" - ) -} -# ViashAutodetectMount: auto configuring docker mounts from parameters -# $1 : The parameter value -# returns : New parameter -# $VIASH_EXTRA_MOUNTS : Added another parameter to be passed to docker -# examples: -# ViashAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar' -# ViashAutodetectMountArg /path/to/bar # returns '-v /path/to:/viash_automount/path/to' -function ViashAutodetectMount { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "$mount_target/$base_name" -} -function ViashAutodetectMountArg { - abs_path=$(ViashAbsolutePath "$1") - if [ -d "$abs_path" ]; then - mount_source="$abs_path" - base_name="" - else - mount_source=`dirname "$abs_path"` - base_name=`basename "$abs_path"` - fi - mount_target="/viash_automount$mount_source" - echo "-v \"$mount_source:$mount_target\"" -} -# ViashExtractFlags: Retain leading flag -# $1 : string with a possible leading flag -# return : leading flag -# examples: -# ViashExtractFlags --foo=bar # returns --foo -function ViashExtractFlags { - echo $1 | sed 's/=.*//' -} -# initialise variables -VIASH_EXTRA_MOUNTS='' - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_genrep 0.1" - exit - ;; - --input) - VIASH_PAR_INPUT="$2" - shift 2 - ;; - --input=*) - VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tmp) - VIASH_PAR_TMP="$2" - shift 2 - ;; - --tmp=*) - VIASH_PAR_TMP=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output) - VIASH_PAR_OUTPUT="$2" - shift 2 - ;; - --output=*) - VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - ---setup) - ViashDockerSetup 'viash_viash_genrep:0.1' "$2" - exit 0 - ;; - ---setup=*) - ViashDockerSetup 'viash_viash_genrep:0.1' "$(ViashRemoveFlags "$1")" - exit 0 - ;; - ---dockerfile) - ViashDockerfile - exit 0 - ;; - ---v|---volume) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v "$2"" - shift 2 - ;; - ---volume=*) - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS -v $(ViashRemoveFlags "$2")" - shift 1 - ;; - ---debug) - ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_genrep:0.1" - docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t viash_viash_genrep:0.1 - exit 0 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -# check whether required parameters exist -if [ -z "$VIASH_PAR_INPUT" ]; then - ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_TMP" ]; then - VIASH_PAR_TMP="/tmp" -fi -if [ -z "$VIASH_PAR_OUTPUT" ]; then - VIASH_PAR_OUTPUT="debug_report.md" -fi - -ViashDockerSetup 'viash_viash_genrep:0.1' ifneedbepullelsecachedbuild - -# detect volumes from file arguments -if [ ! -z "$VIASH_PAR_INPUT" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_INPUT")" - VIASH_PAR_INPUT=$(ViashAutodetectMount "$VIASH_PAR_INPUT") -fi -if [ ! -z "$VIASH_PAR_TMP" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_TMP")" - VIASH_PAR_TMP=$(ViashAutodetectMount "$VIASH_PAR_TMP") -fi -if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_PAR_OUTPUT")" - VIASH_PAR_OUTPUT=$(ViashAutodetectMount "$VIASH_PAR_OUTPUT") -fi - -# Always mount the resource directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_RESOURCES_DIR")" -VIASH_RESOURCES_DIR=$(ViashAutodetectMount "$VIASH_RESOURCES_DIR") - -# Always mount the VIASH_TEMP directory -VIASH_EXTRA_MOUNTS="$VIASH_EXTRA_MOUNTS $(ViashAutodetectMountArg "$VIASH_TEMP")" -VIASH_TEMP=$(ViashAutodetectMount "$VIASH_TEMP") - -# change file ownership -function viash_perform_chown { - - if [ ! -z "$VIASH_PAR_OUTPUT" ]; then - eval docker run --entrypoint=chown -i --rm $VIASH_EXTRA_MOUNTS viash_viash_genrep:0.1 "$(id -u):$(id -g)" -R "$VIASH_PAR_OUTPUT" - fi -} -trap viash_perform_chown EXIT - - -cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm $VIASH_EXTRA_MOUNTS viash_viash_genrep:0.1 -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_genrep-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_input='$VIASH_PAR_INPUT' -par_tmp='$VIASH_PAR_TMP' -par_output='$VIASH_PAR_OUTPUT' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -# set -ex - -function output { - echo "\$@" >> \$par_output -} - -echo "# Debug Report \`date\`" > \$par_output -output "" -output "This reports uses the provided tsv log file to retrieve components" -output "that gave errors during a \\\`viash ns test\\\` test run." - -output "" -output "In _append_ mode, additional test results are added to the tsv log file," -output "so an error may already be resolved but still represented here." - -output "" -output "In general, the following situations are possible:" -output "" -output "1. A component gives no errors, all builds and tests runs well for every platform" -output "2. A component fails for a given platform, either during build or test" -output " a. There is at least one failure in the tsv log file, but the last entry is a success." -output " b. The last run for this component failed." -output "" - -# Retrieve information about errors -cat \$par_input | grep ERROR > /dev/null -contains_errors=\$? -if [ \$contains_errors -eq 0 ]; then - errors=1 - cat \$par_input | grep ERROR > \$par_tmp/failed.tsv -else - errors=0 -fi - -# Retrieve information about missings -cat \$par_input | grep MISSING > /dev/null -contains_missings=\$? -if [ \$contains_missings -eq 0 ]; then - missings=1 - cat \$par_input | grep MISSING > \$par_tmp/missing.tsv -else - missings=0 -fi - -# Retrieve information about success -cat \$par_input | grep SUCCES > /dev/null -contains_success=\$? -if [ \$contains_success -eq 0 ]; then - success=1 - cat \$par_input | grep SUCCESS > \$par_tmp/success.tsv -else - success=0 -fi -# Start writing content -output "## Overview" -output "" - -output "Failed components:" -output "" -if [ \$errors -eq 1 ]; then - cat \$par_tmp/failed.tsv | cut -f1,2,3 | sort | uniq | while read f; do - ns=\`echo -n "\$f" | cut -f1\` - comp=\`echo -n "\$f" | cut -f2\` - platform=\`echo -n "\$f" | cut -f3\` - still_exec=\`cat \$par_input | grep -P "\$ns\\t\$comp\\t\$platform" | tail -1 | grep ERROR\` - still=\$? - if [ \$still -eq 0 ]; then - line="- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\` and is still open. See full report below." - else - line="- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\` but is resolved." - fi - output "\$line" - done - output "" -else - output "No failed components" - output "" -fi - -output "Missing components:" -output "" -if [ \$missings -eq 1 ]; then - cat \$par_tmp/missing.tsv | cut -f1,2,3 | sort | uniq | while read f; do - ns=\`echo -n "\$f" | cut -f1\` - comp=\`echo -n "\$f" | cut -f2\` - platform=\`echo -n "\$f" | cut -f3\` - output "- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\`" - done - output "" -else - output "No missing components" - output "" -fi - -# output "Working components:" -# output "" -# if [ \$success -eq 1 ]; then -# cat \$par_tmp/success.tsv | cut -f1,2,3 | sort | uniq | while read f; do -# ns=\`echo -n "\$f" | cut -f1\` -# comp=\`echo -n "\$f" | cut -f2\` -# platform=\`echo -n "\$f" | cut -f3\` -# output "- \\\`\$comp\\\` in \\\`\$ns\\\`, platform \\\`\$platform\\\`" -# done -# output "" -# else -# output "No successfull components" -# output "" -# fi - -if [ \$errors -eq 1 ]; then - - output "" - output "## Error report" - output "" - - cat \$par_tmp/failed.tsv | cut -f1,2,3 | sort | uniq | while read f; do - ns=\`echo -n "\$f" | cut -f1\` - comp=\`echo -n "\$f" | cut -f2\` - platform=\`echo -n "\$f" | cut -f3\` - still_exec=\`cat \$par_input | grep -P "\$ns\\t\$comp\\t\$platform" | tail -1 | grep ERROR\` - still=\$? - root_test_dir=\`ls -ctd "\$par_tmp/viash_test_\$comp"* | head -1\` - - if [ \$still -eq 0 ]; then - - output "### \\\`\$comp\\\` Build" - output "" - output "Files:" - output "" - output '\`\`\`' - ls -alh "\$root_test_dir/build_executable" > \$par_tmp/list.log - cat \$par_tmp/list.log >> \$par_output - output '\`\`\`' - output "" - output "Build log:" - output "" - output '\`\`\`' - cat "\$root_test_dir/build_executable/_viash_build_log.txt" >> \$par_output - output '\`\`\`' - output "" - - output "### \\\`\$comp\\\` Test" - output "" - output "Files:" - output "" - output '\`\`\`' - ls -alh "\$root_test_dir/test_run"* > \$par_tmp/list.log - cat \$par_tmp/list.log >> \$par_output - output '\`\`\`' - output "" - output "Setup log:" - output "" - output '\`\`\`' - cat "\$root_test_dir/test_"*"/_viash_test_log.txt" >> \$par_output - output '\`\`\`' - output "" - fi - - done - -fi -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_push b/bin/viash_push deleted file mode 100755 index 5d16628776..0000000000 --- a/bin/viash_push +++ /dev/null @@ -1,568 +0,0 @@ -#!/usr/bin/env bash - -######################## -# viash_push 0.1 # -######################## - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_push 0.1" -echo "Push a project, usually in the context of a pipeline." - echo - echo "Options:" - -echo " -s, --src" -echo " type: file" -echo " default: src" -echo " Directory for sources if different from src/" -echo "" - - -echo " -m, --mode" -echo " type: string" -echo " default: development" -echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." -echo "" - - -echo " -q, --query" -echo " type: string" -echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." -echo "" - - -echo " -n, --query_namespace" -echo " type: string" -echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." -echo "" - - -echo " --query_name" -echo " type: string" -echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." -echo "" - - -echo " -t, --tag" -echo " type: string" -echo " default: dev" -echo " The tag/version to be used." -echo "" - - -echo " -r, --registry" -echo " type: string" -echo " Docker registry to use, only used when using a registry." -echo "" - - -echo " --namespace_separator" -echo " type: string" -echo " default: _" -echo " The separator to use between the component name and namespace as the image name of a Docker container." -echo "" - - -echo " --force" -echo " type: boolean_true" -echo " Overwrite registry" -echo "" - - -echo " --max_threads" -echo " type: integer" -echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." -echo "" - - -echo " -c, --config_mod" -echo " type: string, multiple values allowed" -echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." -echo "" - - -echo " --log" -echo " type: file" -echo " default: log.txt" -echo " Log file" -echo "" - - -echo " --viash" -echo " type: file" -echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." -echo "" - -} - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_push 0.1" - exit - ;; - --src) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --src=*) - VIASH_PAR_SRC=$(ViashRemoveFlags "$1") - shift 1 - ;; - -s) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --mode) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --mode=*) - VIASH_PAR_MODE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -m) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --query) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query=*) - VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -q) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query_namespace) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_namespace=*) - VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -n) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_name) - VIASH_PAR_QUERY_NAME="$2" - shift 2 - ;; - --query_name=*) - VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tag) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --tag=*) - VIASH_PAR_TAG=$(ViashRemoveFlags "$1") - shift 1 - ;; - -t) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --registry) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --registry=*) - VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -r) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --namespace_separator) - VIASH_PAR_NAMESPACE_SEPARATOR="$2" - shift 2 - ;; - --namespace_separator=*) - VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --force) - VIASH_PAR_FORCE=true - shift 1 - ;; - --max_threads) - VIASH_PAR_MAX_THREADS="$2" - shift 2 - ;; - --max_threads=*) - VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --config_mod) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --config_mod=*) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - -c) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --log) - VIASH_PAR_LOG="$2" - shift 2 - ;; - --log=*) - VIASH_PAR_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - --viash) - VIASH_PAR_VIASH="$2" - shift 2 - ;; - --viash=*) - VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -if [ -z "$VIASH_PAR_SRC" ]; then - VIASH_PAR_SRC="src" -fi -if [ -z "$VIASH_PAR_MODE" ]; then - VIASH_PAR_MODE="development" -fi -if [ -z "$VIASH_PAR_TAG" ]; then - VIASH_PAR_TAG="dev" -fi -if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then - VIASH_PAR_NAMESPACE_SEPARATOR="_" -fi -if [ -z "$VIASH_PAR_FORCE" ]; then - VIASH_PAR_FORCE="false" -fi -if [ -z "$VIASH_PAR_LOG" ]; then - VIASH_PAR_LOG="log.txt" -fi - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_push-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_src='$VIASH_PAR_SRC' -par_mode='$VIASH_PAR_MODE' -par_query='$VIASH_PAR_QUERY' -par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' -par_query_name='$VIASH_PAR_QUERY_NAME' -par_tag='$VIASH_PAR_TAG' -par_registry='$VIASH_PAR_REGISTRY' -par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' -par_force='$VIASH_PAR_FORCE' -par_max_threads='$VIASH_PAR_MAX_THREADS' -par_config_mod='$VIASH_PAR_CONFIG_MOD' -par_log='$VIASH_PAR_LOG' -par_viash='$VIASH_PAR_VIASH' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -if [ "\$par_mode" == "release" ]; then - echo "In release mode with tag '\$par_tag'." - if [ "\$par_tag" == "dev" ]; then - echo "For a release, you have to specify an explicit version using --tag" - exit 1 - fi -fi - -# if not specified, default queries to a catch-all regexes -if [ -z "\$par_query" ]; then - par_query=".*" -fi -if [ -z "\$par_query_namespace" ]; then - par_query_namespace=".*" -fi -if [ -z "\$par_query_name" ]; then - par_query_name=".*" -fi - -# if not specified, default par_viash to look for 'viash' on the PATH -if [ -z "\$par_viash" ]; then - par_viash="viash" -fi - - -# if specified, use par_max_threads as a java argument -if [ ! -z "\$par_max_threads" ]; then - export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" -fi - -if [[ \$par_force == true ]]; then - echo "Force push... handle with care..." - if [ "\$par_mode" == "development" ]; then - echo "No container push can and should be performed in this mode" - elif [ "\$par_mode" == "integration" ]; then - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "docker" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "dev"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - --setup "push" | tee "\$par_log" - elif [ "\$par_mode" == "release" ]; then - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "docker" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "docker"].push_strategy := "alwayspush"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - --setup "push" | tee "\$par_log" - else - echo "Not a valid mode argument" - fi -else - if [ "\$par_mode" == "development" ]; then - echo "No container push can and should be performed in this mode" - elif [ "\$par_mode" == "integration" ]; then - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "docker" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "dev"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - --setup "push" | tee "\$par_log" - elif [ "\$par_mode" == "release" ]; then - "\$par_viash" ns build \\ - -s "\$par_src" \\ - --platform "docker" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - --setup "push" | tee "\$par_log" - else - echo "Not a valid mode argument" - fi -fi -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_skeleton b/bin/viash_skeleton deleted file mode 100755 index ae2df8e195..0000000000 --- a/bin/viash_skeleton +++ /dev/null @@ -1,620 +0,0 @@ -#!/usr/bin/env bash - -############################ -# viash_skeleton 0.1 # -############################ - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_skeleton 0.1" -echo "Create a skeleton src component" - echo - echo "Options:" - -echo " -n, --name" -echo " type: string, required parameter" -echo " Name of the component" -echo "" - - -echo " -ns, --namespace" -echo " type: string" -echo " Namespace of the component" -echo "" - - -echo " -l, --language" -echo " type: string" -echo " default: bash" -echo " Which scripting language to use. Possible values are 'bash', 'r', and 'python'." -echo "" - - -echo " -p, --platform" -echo " type: string, multiple values allowed" -echo " default: docker,native,nextflow" -echo " Which platforms to add. Possible values are 'native', 'docker', 'nextflow'. By default, all three will be added." -echo "" - - -echo " --src" -echo " type: file, output" -echo " default: src" -echo " Target directory if different from src/" -echo "" - -} - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_skeleton 0.1" - exit - ;; - --name) - VIASH_PAR_NAME="$2" - shift 2 - ;; - --name=*) - VIASH_PAR_NAME=$(ViashRemoveFlags "$1") - shift 1 - ;; - -n) - VIASH_PAR_NAME="$2" - shift 2 - ;; - --namespace) - VIASH_PAR_NAMESPACE="$2" - shift 2 - ;; - --namespace=*) - VIASH_PAR_NAMESPACE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -ns) - VIASH_PAR_NAMESPACE="$2" - shift 2 - ;; - --language) - VIASH_PAR_LANGUAGE="$2" - shift 2 - ;; - --language=*) - VIASH_PAR_LANGUAGE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -l) - VIASH_PAR_LANGUAGE="$2" - shift 2 - ;; - --platform) - if [ -z "$VIASH_PAR_PLATFORM" ]; then - VIASH_PAR_PLATFORM="$2" - else - VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,""$2" - fi - shift 2 - ;; - --platform=*) - if [ -z "$VIASH_PAR_PLATFORM" ]; then - VIASH_PAR_PLATFORM=$(ViashRemoveFlags "$1") - else - VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - -p) - if [ -z "$VIASH_PAR_PLATFORM" ]; then - VIASH_PAR_PLATFORM="$2" - else - VIASH_PAR_PLATFORM="$VIASH_PAR_PLATFORM,""$2" - fi - shift 2 - ;; - --src) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --src=*) - VIASH_PAR_SRC=$(ViashRemoveFlags "$1") - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -# check whether required parameters exist -if [ -z "$VIASH_PAR_NAME" ]; then - ViashError '--name' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_LANGUAGE" ]; then - VIASH_PAR_LANGUAGE="bash" -fi -if [ -z "$VIASH_PAR_PLATFORM" ]; then - VIASH_PAR_PLATFORM="docker,native,nextflow" -fi -if [ -z "$VIASH_PAR_SRC" ]; then - VIASH_PAR_SRC="src" -fi - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_skeleton-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_name='$VIASH_PAR_NAME' -par_namespace='$VIASH_PAR_NAMESPACE' -par_language='$VIASH_PAR_LANGUAGE' -par_platform='$VIASH_PAR_PLATFORM' -par_src='$VIASH_PAR_SRC' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - - -# check par_language -if [[ \$par_language =~ ^bash|sh|Bash\$ ]]; then - script_lang=bash -elif [[ \$par_language =~ ^r|R\$ ]]; then - script_lang=r -elif [[ \$par_language =~ ^py|python|Python\$ ]]; then - script_lang=python -else - echo "Unrecognised language: \$par_language; please specify one of 'python', 'r', or 'bash'" - exit 1 -fi - -# create output dir -out_dir="\$par_src/\$par_namespace/\$par_name" -mkdir -p "\$out_dir" - -################################################################################## -### FUNCTIONALITY ### -################################################################################## - -# write header -cat > "\$out_dir/config.vsh.yaml" << HERE -functionality: - name: "\$par_name" -HERE - -# write namespace, if need be -if [ ! -z "\$par_namespace" ]; then -cat >> "\$out_dir/config.vsh.yaml" << HERE - namespace: "\$par_namespace" -HERE -fi - -# write more metadata and initial arguments -cat >> "\$out_dir/config.vsh.yaml" << HERE - version: 0.0.1 - description: | - Replace this with a (multiline) description of your component. - arguments: - - name: "--input" - alternatives: [ "-i" ] - type: file - required: true - description: Describe the input file. - - name: "--output" - alternatives: [ "-o" ] - type: file - direction: output - required: true - description: Describe the output file. - - name: "--option" - type: string - description: Describe an optional parameter. - default: "default-" -HERE - -################################################################################## -### BASH SCRIPTS ### -################################################################################## -if [ \$script_lang == "bash" ]; then -cat >> "\$out_dir/config.vsh.yaml" << HERE - resources: - - type: bash_script - path: script.sh - tests: - - type: bash_script - path: test.sh -HERE - -cat >> "\$out_dir/script.sh" << 'HERE' -#!/bin/bash - -echo "This is a skeleton component" -echo "The arguments are:" -echo " - input: \$par_input" -echo " - output: \$par_output" -echo " - option: \$par_option" -echo - -echo "Writing output file" -cat "\$par_input" | sed "s#.*#\$par_option-&#" > "\$par_output" -HERE - -cat >> "\$out_dir/test.sh" << MAJORHERE -#!/bin/bash - -set -ex - -echo ">>> Creating dummy input file" -cat > input.txt << HERE -one -two -three -HERE - -echo ">>> Running executable" -./\$par_name --input input.txt --output output.txt --option FOO - -echo ">>> Checking whether output file exists" -[[ ! -f output.txt ]] && echo "Output file could not be found!" && exit 1 - -# create expected output file -cat > expected_output.txt << HERE -FOO-one -FOO-two -FOO-three -HERE - -echo ">>> Checking whether content matches expected content" -diff output.txt expected_output.txt -[ \\\$? -ne 0 ] && echo "Output file did not equal expected output" && exit 1 - -# print final message -echo ">>> Test finished successfully" - -# do not remove this -# as otherwise your test might exit with a different exit code -exit 0 -MAJORHERE - -################################################################################## -### RLANG SCRIPTS ### -################################################################################## -elif [ \$script_lang == "r" ]; then -cat >> "\$out_dir/config.vsh.yaml" << HERE - resources: - - type: r_script - path: script.R - tests: - - type: r_script - path: test.R -HERE -cat >> "\$out_dir/script.R" << 'HERE' -cat("This is a skeleton component\\n") -cat("The arguments are:\\n") -cat(" - input: ", par\$input, "\\n", sep = "") -cat(" - output: ", par\$output, "\\n", sep = "") -cat(" - option: ", par\$option, "\\n", sep = "") -cat("\\n") - -cat("Reading input file\\n") -lines <- readLines(par\$input) - -cat("Running output algorithm\\n") -new_lines <- paste0(par\$option, "-", lines) - -cat("Writing output file\\n") -writeLines(new_lines, con = par\$output) -HERE - -cat >> "\$out_dir/test.R" << HERE -library(testthat) - -# create dummy input file -old_lines <- c("one", "two", "three") -writeLines(old_lines, "input.txt") - -# run executable -system("./\$par_name --input input.txt --output output.txt --option FOO") - -# check whether output file exists -expect_true(file.exists("output.txt")) - -# check whether content matches expected content -expected_lines <- c("FOO-one", "FOO-two", "FOO-three") -new_lines <- readLines("output.txt") -expect_equal(new_lines, expected_lines) - -cat(">>> Test finished successfully!") -HERE - -################################################################################## -### PYTHON SCRIPTS ### -################################################################################## -elif [ \$script_lang == "python" ]; then -cat >> "\$out_dir/config.vsh.yaml" << HERE - resources: - - type: python_script - path: script.py - tests: - - type: python_script - path: test.py -HERE - -cat >> "\$out_dir/script.py" << 'HERE' -print("This is a skeleton component") -print("The arguments are:") -print(" - input: ", par["input"]) -print(" - output: ", par["output"]) -print(" - option: ", par["option"]) -print("") - - -with open(par["input"], "r") as reader, open(par["output"], "w") as writer: - lines = reader.readlines() - - new_lines = [par["option"] + x for x in lines] - - writer.writelines(new_lines) -HERE - -cat >> "\$out_dir/test.py" << HERE -import unittest -import os -from os import path -import subprocess - -print(">> Writing test file") -with open("input.txt", "w") as writer: - writer.writelines(["one\\n", "two\\n", "three\\n"]) - -print(">> Running component") -out = subprocess.check_output(["./\$par_name", "--input", "input.txt", "--output", "output.txt", "--option", "FOO-"]).decode("utf-8") - -print(">> Checking whether output file exists") -assert path.exists("output.txt") - -print(">> Checking contents of output file") -with open("output.txt", "r") as reader: - lines = reader.readlines() -assert lines == ["FOO-one\\n", "FOO-two\\n", "FOO-three\\n"] - -print(">> All tests succeeded successfully!") -HERE - -fi - -################################################################################## -### PLATFORMS ### -################################################################################## -# write platforms -cat >> "\$out_dir/config.vsh.yaml" << HERE -platforms: -HERE - -# iterate over different specified platforms -IFS=',' -set -f -for platform in \$par_platform; do - unset IFS - if [ \$platform == "docker" ]; then - - # choose different default docker image based on language - if [ \$script_lang == "bash" ]; then - cat >> "\$out_dir/config.vsh.yaml" << HERE - - type: docker - image: ubuntu:20.04 - setup: - - type: apt - packages: - - bash -HERE - - elif [ \$script_lang == "r" ]; then - cat >> "\$out_dir/config.vsh.yaml" << HERE - - type: docker - image: rocker/tidyverse:4.0.4 - setup: - - type: r - packages: - - princurve -HERE - - elif [ \$script_lang == "python" ]; then - cat >> "\$out_dir/config.vsh.yaml" << HERE - - type: docker - image: python:3.9.3-buster - setup: - - type: python - packages: - - numpy -HERE - fi - - elif [ \$platform == "native" ]; then - cat >> "\$out_dir/config.vsh.yaml" << HERE - - type: native -HERE - - elif [ \$platform == "nextflow" ]; then - cat >> "\$out_dir/config.vsh.yaml" << HERE - - type: nextflow -HERE - - fi -done -set +f - - - - -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_test b/bin/viash_test deleted file mode 100755 index a6627080aa..0000000000 --- a/bin/viash_test +++ /dev/null @@ -1,580 +0,0 @@ -#!/usr/bin/env bash - -######################## -# viash_test 0.1 # -######################## - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_test 0.1" -echo "Test a project, usually in the context of a pipeline." - echo - echo "Options:" - -echo " -s, --src" -echo " type: file" -echo " default: src" -echo " Directory for sources if different from src/" -echo "" - - -echo " -m, --mode" -echo " type: string" -echo " default: development" -echo " The mode to run in. Possible values are: 'development', 'integration', 'release'." -echo "" - - -echo " -p, --platforms" -echo " type: string" -echo " default: docker" -echo " Which platforms to test, default is 'docker'." -echo "" - - -echo " -q, --query" -echo " type: string" -echo " Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1\$'." -echo "" - - -echo " -n, --query_namespace" -echo " type: string" -echo " Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace\$'." -echo "" - - -echo " --query_name" -echo " type: string" -echo " Filter which components get selected by name. Can be a regex. Example: '^component1'." -echo "" - - -echo " -t, --tag" -echo " type: string" -echo " default: dev" -echo " Which tag/version of the pipeline to use." -echo "" - - -echo " -r, --registry" -echo " type: string" -echo " Docker registry to use, only used when using a registry." -echo "" - - -echo " --namespace_separator" -echo " type: string" -echo " default: _" -echo " The separator to use between the component name and namespace as the image name of a Docker container." -echo "" - - -echo " --max_threads" -echo " type: integer" -echo " The maximum number of threads viash will use when \`--parallell\` during parallel tasks." -echo "" - - -echo " -c, --config_mod" -echo " type: string, multiple values allowed" -echo " Modify a viash config at runtime using a custom DSL. For more information, see the online documentation." -echo "" - - -echo " -l, --log" -echo " type: file" -echo " default: log.tsv" -echo " Test log file" -echo "" - - -echo " --append" -echo " type: boolean" -echo " default: true" -echo " Append to the log file?" -echo "" - - -echo " --viash" -echo " type: file" -echo " A path to the viash executable. If not specified, this component will look for 'viash' on the \$PATH." -echo "" - -} - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_test 0.1" - exit - ;; - --src) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --src=*) - VIASH_PAR_SRC=$(ViashRemoveFlags "$1") - shift 1 - ;; - -s) - VIASH_PAR_SRC="$2" - shift 2 - ;; - --mode) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --mode=*) - VIASH_PAR_MODE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -m) - VIASH_PAR_MODE="$2" - shift 2 - ;; - --platforms) - VIASH_PAR_PLATFORMS="$2" - shift 2 - ;; - --platforms=*) - VIASH_PAR_PLATFORMS=$(ViashRemoveFlags "$1") - shift 1 - ;; - -p) - VIASH_PAR_PLATFORMS="$2" - shift 2 - ;; - --query) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query=*) - VIASH_PAR_QUERY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -q) - VIASH_PAR_QUERY="$2" - shift 2 - ;; - --query_namespace) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_namespace=*) - VIASH_PAR_QUERY_NAMESPACE=$(ViashRemoveFlags "$1") - shift 1 - ;; - -n) - VIASH_PAR_QUERY_NAMESPACE="$2" - shift 2 - ;; - --query_name) - VIASH_PAR_QUERY_NAME="$2" - shift 2 - ;; - --query_name=*) - VIASH_PAR_QUERY_NAME=$(ViashRemoveFlags "$1") - shift 1 - ;; - --tag) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --tag=*) - VIASH_PAR_TAG=$(ViashRemoveFlags "$1") - shift 1 - ;; - -t) - VIASH_PAR_TAG="$2" - shift 2 - ;; - --registry) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --registry=*) - VIASH_PAR_REGISTRY=$(ViashRemoveFlags "$1") - shift 1 - ;; - -r) - VIASH_PAR_REGISTRY="$2" - shift 2 - ;; - --namespace_separator) - VIASH_PAR_NAMESPACE_SEPARATOR="$2" - shift 2 - ;; - --namespace_separator=*) - VIASH_PAR_NAMESPACE_SEPARATOR=$(ViashRemoveFlags "$1") - shift 1 - ;; - --max_threads) - VIASH_PAR_MAX_THREADS="$2" - shift 2 - ;; - --max_threads=*) - VIASH_PAR_MAX_THREADS=$(ViashRemoveFlags "$1") - shift 1 - ;; - --config_mod) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --config_mod=*) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD=$(ViashRemoveFlags "$1") - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;"$(ViashRemoveFlags "$1") - fi - shift 1 - ;; - -c) - if [ -z "$VIASH_PAR_CONFIG_MOD" ]; then - VIASH_PAR_CONFIG_MOD="$2" - else - VIASH_PAR_CONFIG_MOD="$VIASH_PAR_CONFIG_MOD;""$2" - fi - shift 2 - ;; - --log) - VIASH_PAR_LOG="$2" - shift 2 - ;; - --log=*) - VIASH_PAR_LOG=$(ViashRemoveFlags "$1") - shift 1 - ;; - -l) - VIASH_PAR_LOG="$2" - shift 2 - ;; - --append) - VIASH_PAR_APPEND="$2" - shift 2 - ;; - --append=*) - VIASH_PAR_APPEND=$(ViashRemoveFlags "$1") - shift 1 - ;; - --viash) - VIASH_PAR_VIASH="$2" - shift 2 - ;; - --viash=*) - VIASH_PAR_VIASH=$(ViashRemoveFlags "$1") - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -if [ -z "$VIASH_PAR_SRC" ]; then - VIASH_PAR_SRC="src" -fi -if [ -z "$VIASH_PAR_MODE" ]; then - VIASH_PAR_MODE="development" -fi -if [ -z "$VIASH_PAR_PLATFORMS" ]; then - VIASH_PAR_PLATFORMS="docker" -fi -if [ -z "$VIASH_PAR_TAG" ]; then - VIASH_PAR_TAG="dev" -fi -if [ -z "$VIASH_PAR_NAMESPACE_SEPARATOR" ]; then - VIASH_PAR_NAMESPACE_SEPARATOR="_" -fi -if [ -z "$VIASH_PAR_LOG" ]; then - VIASH_PAR_LOG="log.tsv" -fi -if [ -z "$VIASH_PAR_APPEND" ]; then - VIASH_PAR_APPEND="true" -fi - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_test-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_src='$VIASH_PAR_SRC' -par_mode='$VIASH_PAR_MODE' -par_platforms='$VIASH_PAR_PLATFORMS' -par_query='$VIASH_PAR_QUERY' -par_query_namespace='$VIASH_PAR_QUERY_NAMESPACE' -par_query_name='$VIASH_PAR_QUERY_NAME' -par_tag='$VIASH_PAR_TAG' -par_registry='$VIASH_PAR_REGISTRY' -par_namespace_separator='$VIASH_PAR_NAMESPACE_SEPARATOR' -par_max_threads='$VIASH_PAR_MAX_THREADS' -par_config_mod='$VIASH_PAR_CONFIG_MOD' -par_log='$VIASH_PAR_LOG' -par_append='$VIASH_PAR_APPEND' -par_viash='$VIASH_PAR_VIASH' - -resources_dir="$VIASH_RESOURCES_DIR" - -#!/bin/bash - -# if not specified, default queries to a catch-all regexes -if [ -z "\$par_query" ]; then - par_query=".*" -fi -if [ -z "\$par_query_namespace" ]; then - par_query_namespace=".*" -fi -if [ -z "\$par_query_name" ]; then - par_query_name=".*" -fi - -# if not specified, default par_viash to look for 'viash' on the PATH -if [ -z "\$par_viash" ]; then - par_viash="viash" -fi - -# if --append (-a) true is specified, add \`--append\` -if [ "\$par_append" == "true" ]; then - par_append_parsed="--append" -fi - - -# if specified, use par_max_threads as a java argument -if [ ! -z "\$par_max_threads" ]; then - export JAVA_ARGS="\$JAVA_ARGS -Dscala.concurrent.context.maxThreads=\$par_max_threads" -fi - -if [ "\$par_mode" == "release" ]; then - echo "In release mode with tag '\$par_tag'." - if [ "\$par_tag" == "dev" ]; then - echo "For a release, you have to specify an explicit version using --tag" - exit 1 - fi -fi - -if [ "\$par_mode" == "development" ]; then - echo "In development mode..." - "\$par_viash" ns test \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "dev"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - -t "\$par_log" \\ - \$par_append_parsed -elif [ "\$par_mode" == "integration" ]; then - echo "In integration mode..." - "\$par_viash" ns test \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "donothing"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - -t "\$par_log" \\ - \$par_append_parsed -elif [ "\$par_mode" == "release" ]; then - "\$par_viash" ns test \\ - -s "\$par_src" \\ - --platform "\$par_platforms" \\ - --query "\$par_query" \\ - --query_name "\$par_query_name" \\ - --query_namespace "\$par_query_namespace" \\ - -c '.functionality.version := "'"\$par_tag"'"' \\ - -c '.platforms[.type == "docker"].target_registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker"].setup_strategy := "pull"' \\ - -c '.platforms[.type == "nextflow"].registry := "'"\$par_registry"'"' \\ - -c '.platforms[.type == "docker" || .type == "nextflow"].namespace_separator := "'\$par_namespace_separator'"' \\ - -c "\$par_config_mod" \\ - -l \\ - -t "\$par_log" \\ - \$par_append_parsed -else - echo "Not a valid mode argument" -fi -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF diff --git a/bin/viash_trafo b/bin/viash_trafo deleted file mode 100755 index fc0086969f..0000000000 --- a/bin/viash_trafo +++ /dev/null @@ -1,412 +0,0 @@ -#!/usr/bin/env bash - -######################### -# viash_trafo 1.0 # -######################### - -# This wrapper script is auto-generated by viash 0.5.0-rc2 and is thus a -# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from -# Data Intuitive. The component may contain files which fall under a different -# license. The authors of this component should specify the license in the -# header of such files, or include a separate license file detailing the -# licenses of all included files. - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -VIASH_VERBOSITY=5 - -# see https://en.wikipedia.org/wiki/Syslog#Severity_level - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog 0 emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog 1 alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog 2 critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog 3 error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog 4 warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog 5 notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog 6 info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog 7 debug $@ -} - -# find source folder of this component -VIASH_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "viash_trafo 1.0" -echo "Transform viash formats." - echo - echo "Options:" - -echo " -i, --input" -echo " type: file, required parameter" -echo " Input file" -echo "" - - -echo " -o, --output_dir" -echo " type: file, required parameter, output" -echo " Output directory" -echo "" - - -echo " -f, --format" -echo " type: string, required parameter" -echo " Output format. Must be one of 'script', 'config'" -echo "" - - -echo " --rm" -echo " type: boolean_true" -echo " Remove the source files after use." -echo "" - -} - -# initialise array -VIASH_POSITIONAL_ARGS='' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - -v|--verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - -vv) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+2" - shift 1 - ;; - --verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - --verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "viash_trafo 1.0" - exit - ;; - --input) - VIASH_PAR_INPUT="$2" - shift 2 - ;; - --input=*) - VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - -i) - VIASH_PAR_INPUT="$2" - shift 2 - ;; - --output_dir) - VIASH_PAR_OUTPUT_DIR="$2" - shift 2 - ;; - --output_dir=*) - VIASH_PAR_OUTPUT_DIR=$(ViashRemoveFlags "$1") - shift 1 - ;; - -o) - VIASH_PAR_OUTPUT_DIR="$2" - shift 2 - ;; - --format) - VIASH_PAR_FORMAT="$2" - shift 2 - ;; - --format=*) - VIASH_PAR_FORMAT=$(ViashRemoveFlags "$1") - shift 1 - ;; - -f) - VIASH_PAR_FORMAT="$2" - shift 2 - ;; - --rm) - VIASH_PAR_RM=true - shift 1 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - -# check whether required parameters exist -if [ -z "$VIASH_PAR_INPUT" ]; then - ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_OUTPUT_DIR" ]; then - ViashError '--output_dir' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_FORMAT" ]; then - ViashError '--format' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_RM" ]; then - VIASH_PAR_RM="false" -fi - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-viash_trafo-XXXXXX") -function clean_up { - rm "\$tempscript" -} -trap clean_up EXIT -cat > "\$tempscript" << 'VIASHMAIN' -# The following code has been auto-generated by Viash. -par_input='$VIASH_PAR_INPUT' -par_output_dir='$VIASH_PAR_OUTPUT_DIR' -par_format='$VIASH_PAR_FORMAT' -par_rm='$VIASH_PAR_RM' - -resources_dir="$VIASH_RESOURCES_DIR" - - -set -e - -# detect input type -input_dir=\$(dirname \$par_input) -if [[ "\$par_input" =~ ^.*\\.vsh\\.(sh|r|R|py)\$ ]]; then - input_type=script - input_ext=\`echo "\$par_input" | sed 's#.*\\.##'\` - - if [ "\$input_ext" = "sh" ]; then - script_type="bash" - elif [[ \$input_ext =~ ^[rR]\$ ]]; then - script_type="r" - elif [ "\$input_ext" = "py" ]; then - script_type="python" - else - echo "Unsupported format: \$input_ext!" - exit 1 - fi -elif [[ "\$par_input" =~ ^.*\\.vsh\\.(yaml|yml)\$ ]]; then - input_type=config -else - echo Input: unsupported format. - exit 1 -fi - -# create dir if it does not exist -[[ -d "\$par_output_dir" ]] || mkdir -p "\$par_output_dir" - -# check format -if [[ ! \$par_format =~ ^(script|config)\$ ]]; then - echo "Output: unsupported format. Must be one of 'script' or 'config'" - exit 1 -fi - -# ------------------------ X -> X ------------------------ -if [ \$input_type = \$par_format ]; then - echo Input type is equal to output type. - echo Just use cp, you son of a silly person. - cp "\$par_input" "\$par_output_dir/\$(basename \$par_input)" - -# ------------------------ SCRIPT -> CONFIG ------------------------ -elif [ \$input_type = "script" ] && [ \$par_format = "config" ]; then - echo "Converting from 'script' to 'config'" - - # determine output paths - config_yaml_relative="config.vsh.yaml" - config_yaml_path="\$par_output_dir/\$config_yaml_relative" - output_script_relative="\$(basename \$par_input | sed 's#\\.vsh\\.#.#')" - output_script_path="\$par_output_dir/\$output_script_relative" - - # WRITING CONFIG YAML - echo "> Writing config yaml to \$config_yaml_relative" - CONFIG_YAML=\$(cat "\$par_input" | grep "^#' " | sed "s/^#' //") - - # write yaml without resources - echo "\$CONFIG_YAML" | yq d - functionality.resources > "\$config_yaml_path" - - # add script to resources - printf "functionality:\\n resources:\\n - type: \${script_type}_script\\n path: \$output_script_relative\\n" | yq m "\$config_yaml_path" - -i - - # add other resources - has_resources=\`echo "\$CONFIG_YAML" | yq read - functionality.resources | head -1\` - if [ ! -z "\$has_resources" ]; then - echo "\$CONFIG_YAML" | yq read - functionality.resources | yq p - functionality.resources | yq m -a append "\$config_yaml_path" - -i - fi - - # WRITING SCRIPT - echo "> Writing script to \$output_script_relative" - cat "\$par_input" | grep -v "^#' " > "\$output_script_path" - - -# ------------------------ CONFIG -> SCRIPT ------------------------ -elif [ \$input_type = "config" ] && [ \$par_format = "script" ]; then - echo "Converting from 'config' to 'script'" - - # determine output paths - input_script_relative=\$(yq read "\$par_input" 'functionality.resources.[0].path') - input_script_path="\$input_dir/\$input_script_relative" - output_script_relative=\$(echo "\$input_script_relative" | sed 's#\\(\\.[^\\.]*\\)#.vsh\\1#') - output_script_path="\$par_output_dir/\$output_script_relative" - - # writing header - echo "> Writing script with header to \$output_script_relative" - yq delete "\$par_input" 'functionality.resources.[0]' | sed "s/^/#' /" > "\$output_script_path" - - # writing script - awk "/VIASH START/,/VIASH END/ { next; }; 1 {print; }" "\$input_script_path" >> "\$output_script_path" - awk "/VIASH START/,/VIASH END/ { next; }; 1 {print; }" "\$input_script_path" >> "\$output_script_path" - -# ------------------------ CONFIG -> SPLIT ------------------------ -elif [ \$input_type = "config" ] && [ \$par_format = "split" ]; then - echo "Converting from 'config' to 'split'" - - # determine output paths - funcionality_yaml_relative="functionality.yaml" - funcionality_yaml_path="\$par_output_dir/\$funcionality_yaml_relative" - - # WRITING FUNCTIONALITY YAML - echo "> Writing functionality yaml to \$funcionality_yaml_relative" - yq r "\$par_input" functionality > "\$funcionality_yaml_path" - - #### PLATFORM(S) - # create platform yamls - platforms=\$(yq read "\$par_input" platforms.*.type) - for plat in \$platforms; do - platform_yaml_relative="platform_\${plat}.yaml" - platform_yaml_path="\$par_output_dir/\$platform_yaml_relative" - echo "> Writing platform yaml to \$platform_yaml_relative" - yq read "\$par_input" platforms.[type==\$plat] > "\$platform_yaml_path" - done - - # copy script - input_script_relative=\$(yq read "\$par_input" 'functionality.resources.[0].path') - input_script_path="\$input_dir/\$input_script_relative" - output_script_path="\$par_output_dir/\$input_script_relative" - - if [ "\$input_script_path" != "\$output_script_path" ]; then - cp "\$input_script_path" "\$output_script_path" - fi - -fi -VIASHMAIN -PATH="$VIASH_RESOURCES_DIR:\$PATH" - -bash "\$tempscript" - -VIASHEOF From 7217f5a56bbf5037dea4284038c43b9104da166c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 08:43:41 +0200 Subject: [PATCH 0103/1233] update github actions Former-commit-id: 638a2978a85de971476dcf120f657a2d5c7353c3 --- .github/workflows/viash-build.yml | 10 +++++++++- .github/workflows/viash-test.yml | 16 ++++++++++++---- bin/.gitignore | 3 +++ bin/README.md | 10 ++++++++++ bin/init | 13 +++++++++++++ 5 files changed, 47 insertions(+), 5 deletions(-) create mode 100644 bin/.gitignore create mode 100644 bin/README.md create mode 100755 bin/init diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index 84994bd841..199cb68a3d 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -20,8 +20,16 @@ jobs: steps: - uses: actions/checkout@v2 + - name: Cache executables + uses: actions/cache@v2 + with: + path: bin + key: executable-caching-${{ github.workflow }}-${{ matrix.config.name }} + - name: Fetch viash - run: bin/viash -h + run: | + bin/init + bin/viash -h - name: Build components run: | diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f8b21f75c6..5385b9e522 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -20,19 +20,27 @@ jobs: steps: - uses: actions/checkout@v2 + - name: Cache executables + uses: actions/cache@v2 + with: + path: bin + key: executable-caching-${{ github.workflow }}-${{ matrix.config.name }} + - name: Fetch viash - run: bin/viash -h + run: | + bin/init + bin/viash -h - name: Run build run: | bin/viash_build - + - name: Run tests run: | # create check_results folder - sed -i '/^check_results\/$/d' .gitignore + sed -i '/^check_results\/$/d' .gitignore mkdir check_results - + # run tests bin/viash_test --append=false --log=check_results/results.tsv diff --git a/bin/.gitignore b/bin/.gitignore new file mode 100644 index 0000000000..d00b90146a --- /dev/null +++ b/bin/.gitignore @@ -0,0 +1,3 @@ +fetch +viash* +nextflow diff --git a/bin/README.md b/bin/README.md new file mode 100644 index 0000000000..35f41588de --- /dev/null +++ b/bin/README.md @@ -0,0 +1,10 @@ +These executables were generated by running the `bin/init` executable. + +``` +$ bin/init +curl -fsSL get.viash.io | bash -s -- --registry openpipeline --tag 0.5.0-rc3 --log check_results/results.tsv + +cd bin + +curl -s https://get.nextflow.io | bash +``` diff --git a/bin/init b/bin/init new file mode 100755 index 0000000000..885f8e7ca6 --- /dev/null +++ b/bin/init @@ -0,0 +1,13 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +curl -fsSL get.viash.io | bash -s -- --registry openpipeline --tag develop --log check_results/results.tsv + +cd bin + +curl -s https://get.nextflow.io | bash From 86f1aff50e9647f225714f8b8800385ef113ac20 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 08:52:43 +0200 Subject: [PATCH 0104/1233] add baseline main.nf and nextflow.config, add script from release Former-commit-id: 44a277e80a8f53cb50541c53064322e9cbb2b72c --- main.nf | 5 +++ nextflow.config | 32 +++++++++++++++++++ .../workflows/run_nextflow.sh | 5 ++- .../workflows/run_nextflow_from_repo.sh | 22 +++++++++++++ 4 files changed, 61 insertions(+), 3 deletions(-) create mode 100644 main.nf create mode 100644 nextflow.config create mode 100755 src/modality_alignment/workflows/run_nextflow_from_repo.sh diff --git a/main.nf b/main.nf new file mode 100644 index 0000000000..28839dad42 --- /dev/null +++ b/main.nf @@ -0,0 +1,5 @@ +nextflow.enable.dsl=2 + +workflow { + print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.") +} diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000000..ab0869fbae --- /dev/null +++ b/nextflow.config @@ -0,0 +1,32 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT +rootDir = "$projectDir" +targetDir = "$rootDir/target/nextflow" + +// INSERT CUSTOM IMPORTS HERE + +// END INSERT + +docker { + runOptions = "-v $rootDir:$rootDir" +} + +process { + maxForks = 30 + cpus = 2 + errorStrategy='ignore' + container = 'nextflow/bash:latest' + + pod = [ [ nodeSelector: 'worker-group = m5s' ] ] + + withLabel: highmem { memory = 50.Gb } + withLabel: highcpu { cpus = 20 } + withLabel: highmem_highcpu { + cpus = 20 + memory = 128.Gb + } +} + diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run_nextflow.sh index bcc1170bdf..9c6e7d8b8c 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run_nextflow.sh @@ -16,7 +16,6 @@ bin/nextflow \ run . \ -main-script src/modality_alignment/workflows/main.nf \ -c src/modality_alignment/workflows/nextflow.config \ - --output output/modality_alignment - -# -resume \ + --output output/modality_alignment \ + -resume diff --git a/src/modality_alignment/workflows/run_nextflow_from_repo.sh b/src/modality_alignment/workflows/run_nextflow_from_repo.sh new file mode 100755 index 0000000000..fa9039a758 --- /dev/null +++ b/src/modality_alignment/workflows/run_nextflow_from_repo.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +# choose a particular version of nextflow +export NXF_VER=21.04.1 + +bin/nextflow \ + run https://github.com/openproblems-bio/opsca-viash.git \ + -r main_build \ + -main-script src/modality_alignment/workflows/main.nf \ + -c src/modality_alignment/workflows/nextflow.config \ + --output output/modality_alignment \ + -resume + From 3750187ec7df81b47f9fc32139bdcd9678e91a28 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 09:47:10 +0200 Subject: [PATCH 0105/1233] update readme Former-commit-id: 2b1cbbc283c6b0736bb0b1659bf648995fe8e84f --- README.Rmd | 34 ++++++++++++++++++++--------- README.md | 63 +++++++++++++++++++++++++++++++++--------------------- 2 files changed, 63 insertions(+), 34 deletions(-) diff --git a/README.Rmd b/README.Rmd index 4f2d4aed64..3071d88684 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( comment="" ) ``` -Proof Of Concept in adapting [Open Problems for Single Cell Analysis repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) with Nextflow and viash. Documentation for viash is available at [viash.io](https://viash.io). +Proof Of Concept in adapting [Open Problems repository](https://github.com/openproblems-bio/openproblems) with Nextflow and viash. Documentation for viash is available at [viash.io](https://viash.io). ## Requirements @@ -30,10 +30,24 @@ To use this repository, please install the following dependencies: The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. -**Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. +**Step 0, fetch viash and nextflow:** run the `bin/init` executable. ```bash -bin/viash_build +bin/init +``` + + > Using tag develop + > Cleanup + > Install viash develop under /viash_automount/home/rcannood/workspace/opsca/opsca-viash/bin/ + > Fetching components sources (version develop) + > Building components + > Done, happy viash-ing! + > Nextflow installation completed. + +**Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. + +```bash +bin/viash_build -q 'modality_alignment|utils' ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -299,16 +313,16 @@ bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems The images themselves can be pushed to Docker Hub with the `bin/viash_push` command. I'd have to make a small change to viash to ensure that the component names don't contain any slashes because the images listed above can't be pushed to Docker hub. However, the output would look something like this: ```bash -bin/viash_push -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_push -m release -v '0.1.0' -r openproblems In release mode... Using version 0.1.0 to tag containers ``` - > singlecellopenproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! + > openproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! diff --git a/README.md b/README.md index af757029de..22f6b215fe 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,9 @@ opsca-viash - [Benefits of using Nextflow + viash](#benefits-of-using-nextflow--viash) -Proof Of Concept in adapting [Open Problems for Single Cell Analysis -repository](https://github.com/singlecellopenproblems/SingleCellOpenProblems) -with Nextflow and viash. Documentation for viash is available at +Proof Of Concept in adapting [Open Problems +repository](https://github.com/openproblems-bio/openproblems) with +Nextflow and viash. Documentation for viash is available at [viash.io](https://viash.io). ## Requirements @@ -32,11 +32,26 @@ To use this repository, please install the following dependencies: The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. +**Step 0, fetch viash and nextflow:** run the `bin/init` executable. + +``` bash +bin/init +``` + + > Using tag develop + > Cleanup + > Install viash develop under /viash_automount/home/rcannood/workspace/opsca/opsca-viash/bin/ + > Fetching components sources (version develop) + > Building components + > Done, happy viash-ing! + > Nextflow installation completed. + **Step 1, build all the components:** in the `src/` folder as standalone -executables in the `target/` folder. +executables in the `target/` folder. Use the `-q 'xxx'` parameter to +build only several components of the repository. ``` bash -bin/viash_build +bin/viash_build -q 'modality_alignment|utils' ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -145,8 +160,8 @@ viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o fo This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- ## Building a component @@ -201,8 +216,8 @@ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- ## Unit testing a component @@ -215,10 +230,10 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654/build_executable/foo --verbosity 6 ---setup cachedbuild - [notice] Running 'docker build -t modality_alignment/methods_foo:9rREBVaKbQTM /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-k8Idnc' + +/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711/build_executable/foo --verbosity 6 ---setup cachedbuild + [notice] Running 'docker build -t modality_alignment/methods_foo:da7Qhr5nLi6A /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-4h6urx' Sending build context to Docker daemon 22.53kB Step 1/2 : FROM python:3.9.3-buster @@ -227,9 +242,9 @@ viash test src/modality_alignment/methods/foo/config.vsh.yaml ---> Using cache ---> 45db33ebb9de Successfully built 45db33ebb9de - Successfully tagged modality_alignment/methods_foo:9rREBVaKbQTM + Successfully tagged modality_alignment/methods_foo:da7Qhr5nLi6A ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo8067684801221966654/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711/test_test.py/test.py >> Writing test file >> Running component >> Checking whether output file exists @@ -367,7 +382,7 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email ./foo_by_email ---setup cachedbuild ``` - [notice] Running 'docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-kZ7Cn8' + [notice] Running 'docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-TsNVGL' ``` bash # view help @@ -398,8 +413,8 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/vib/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/vib/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE + - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt - option: default- ### Reprodicible components on Docker Hub @@ -435,16 +450,16 @@ images listed above can’t be pushed to Docker hub. However, the output would look something like this: ``` bash -bin/viash_push -m release -v '0.1.0' -r singlecellopenproblems +bin/viash_push -m release -v '0.1.0' -r openproblems In release mode... Using version 0.1.0 to tag containers ``` - > singlecellopenproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! - > singlecellopenproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! + > openproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! From 8acc9619546fbcb75febfc1ff0ffcbd81cff401a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 09:51:30 +0200 Subject: [PATCH 0106/1233] let build push to docker hub, run tests on all branches Former-commit-id: 721d35f07ab3f9f7d80d5da3c484859eee349d34 --- .github/workflows/viash-build.yml | 30 +++++++++++++++++++++++++++++- .github/workflows/viash-test.yml | 4 ++-- 2 files changed, 31 insertions(+), 3 deletions(-) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index 199cb68a3d..c180ab46a2 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -37,7 +37,16 @@ jobs: sed -i '/^target\/$/d' .gitignore # only build nextflow targets - bin/viash_build -m release -t latest -p nextflow + bin/viash_build -m release -t main_build + + - name: Run tests + run: | + # create check_results folder + sed -i '/^check_results\/$/d' .gitignore + mkdir check_results + + # run tests + bin/viash_test -m release -t main_build --append=false --log=check_results/results.tsv - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -45,6 +54,25 @@ jobs: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . publish_branch: main_build + + - name: Login to Docker Hub + if: false + uses: docker/login-action@v1 + with: + username: ${{ secrets.DOCKER_USERNAME }} + password: ${{ secrets.DOCKER_PASSWORD }} + + - name: Push containers + if: false + run: | + bin/viash_push -m release -t main_build + + - name: Upload check results + uses: actions/upload-artifact@master + with: + name: ${{ matrix.config.name }}_results + path: check_results + # todo: add build for tag # https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-create-git-tag diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 5385b9e522..7ed2499a33 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -2,9 +2,9 @@ name: viash test CI on: push: - branches: [ main ] + branches: [ * ] pull_request: - branches: [ main ] + branches: [ * ] jobs: viash-test: From 2606e01b2fe5b6e9cf7c8be02913cce48b80865e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 3 Jun 2021 09:53:05 +0200 Subject: [PATCH 0107/1233] fix github actions Former-commit-id: a73bcd940759292415bc0ff591951a95e611175c --- .github/workflows/viash-build.yml | 4 +--- .github/workflows/viash-test.yml | 4 ++-- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index c180ab46a2..c712c720b4 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -3,8 +3,6 @@ name: viash build CI on: push: branches: [ main ] - pull_request: - branches: [ main ] jobs: viash-build: @@ -12,7 +10,7 @@ jobs: if: "!contains(github.event.head_commit.message, 'ci skip')" strategy: - fail-fast: false + fail-fast: true matrix: config: - {name: 'main', os: ubuntu-latest } diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 7ed2499a33..f00da08fb1 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -2,9 +2,9 @@ name: viash test CI on: push: - branches: [ * ] + branches: [ '*' ] pull_request: - branches: [ * ] + branches: [ '*' ] jobs: viash-test: From f5c61eec27c0b4a6e4d934fcb3b151e48452e25a Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 17 Jun 2021 11:18:46 +0200 Subject: [PATCH 0108/1233] added first data loader script, adapted from openproblems repo Former-commit-id: 18d9df8ca8cbde2d60e15600c917d408b89be795 --- .gitignore | 6 ++++ src/data_loader/config.vsh.yaml | 32 +++++++++++++++++++++ src/data_loader/script.py | 44 +++++++++++++++++++++++++++++ src/data_loader/test.py | 27 ++++++++++++++++++ src/data_loader/utils/utils.py | 49 +++++++++++++++++++++++++++++++++ 5 files changed, 158 insertions(+) create mode 100644 src/data_loader/config.vsh.yaml create mode 100644 src/data_loader/script.py create mode 100644 src/data_loader/test.py create mode 100644 src/data_loader/utils/utils.py diff --git a/.gitignore b/.gitignore index bdcfd61ec9..8855a1b0d7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,9 @@ +*__pycache__ +*.h5ad + +# IDE ignores +.idea/ + # repo specific ignores output_bash diff --git a/src/data_loader/config.vsh.yaml b/src/data_loader/config.vsh.yaml new file mode 100644 index 0000000000..0eed8a1b67 --- /dev/null +++ b/src/data_loader/config.vsh.yaml @@ -0,0 +1,32 @@ +functionality: + name: "data_loader" + namespace: "data_loader" + version: "dev" + description: "Load datasets" + arguments: + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + description: "Output h5ad file of the cleaned dataset" + required: true + - name: "--url" + type: "string" + description: "URL of dataset" + resources: + - type: python_script + path: script.py + - path: "./utils/utils.py" + tests: + - type: python_script + path: test.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - type: native + - type: nextflow diff --git a/src/data_loader/script.py b/src/data_loader/script.py new file mode 100644 index 0000000000..ca6824756a --- /dev/null +++ b/src/data_loader/script.py @@ -0,0 +1,44 @@ +## VIASH START +par = { + "url": "https://ndownloader.figshare.com/files/24974582", # PBMC data + "output": "test_data.h5ad" +} +resources_dir = "./utils/" +## VIASH END + +print("Importing libraries") +import scanpy as sc +import tempfile +import os +import scprep + +# # adding resources dir to system path +# # the resources dir contains all files listed in the '.functionality.resources' part of the +# # viash config, amongst which is the 'utils.py' file we need. +import sys + +sys.path.append(resources_dir) +# # importing helper functions from common utils.py file in resources dir +from utils import filter_genes_cells + +with tempfile.TemporaryDirectory() as tempdir: + URL = par['url'] + print("Downloading", URL) + sys.stdout.flush() + filepath = os.path.join(tempdir, "pancreas.h5ad") + scprep.io.download.download_url(URL, filepath) + + print("Read file") + adata = sc.read(filepath) + + # Remove preprocessing + if "counts" in adata.layers: + adata.X = adata.layers["counts"] + del adata.layers["counts"] + + # Ensure there are no cells or genes with 0 counts + filter_genes_cells(adata) + + +print("Writing adata to file") +adata.write(par["output"], compression="gzip") diff --git a/src/data_loader/test.py b/src/data_loader/test.py new file mode 100644 index 0000000000..4549a03ffd --- /dev/null +++ b/src/data_loader/test.py @@ -0,0 +1,27 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import pandas +import numpy as np + +import urllib.request + +anndata_file = "pcmc.h5ad" + +print(">> Running script") +out = subprocess.check_output([ + "./data_loader", + "--url", "https://ndownloader.figshare.com/files/24974582", + "--output", anndata_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(anndata_file) + +print(">> Check that output fits expected API") +adata = sc.read_h5ad(anndata_file) +# TODO: complete with API checks + +print(">> All tests passed successfully") diff --git a/src/data_loader/utils/utils.py b/src/data_loader/utils/utils.py new file mode 100644 index 0000000000..4f3cf95867 --- /dev/null +++ b/src/data_loader/utils/utils.py @@ -0,0 +1,49 @@ +import tempfile +import hashlib +import logging +import os +import scanpy as sc + +log = logging.getLogger("openproblems") + + +def _make_tempdir(): + tempdir = os.path.join(tempfile.gettempdir(), "openproblems_cache") + try: + os.mkdir(tempdir) + log.debug("Created data cache directory") + except OSError: + log.debug("Data cache directory exists") + return tempdir + + +TEMPDIR = _make_tempdir() + + +def _func_to_bytes(func): + return bytes(".".join([func.__module__, func.__name__]), encoding="utf-8") + + +def _obj_to_bytes(obj): + return bytes(str(obj), encoding="utf-8") + + +def _hash_function(func, *args, **kwargs): + hash = hashlib.sha256() + hash.update(_func_to_bytes(func)) + hash.update(_obj_to_bytes(args)) + hash.update(_obj_to_bytes(kwargs)) + return hash.hexdigest() + + +def _cache_path(func, *args, **kwargs): + if hasattr(func, "__wrapped__"): + func = func.__wrapped__ + filename = "openproblems_{}.h5ad".format(_hash_function(func, *args, **kwargs)) + return os.path.join(TEMPDIR, filename) + + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) From 72b607c5ab2618a2a2ffe10404802c507511b5a1 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 24 Jun 2021 09:59:09 +0200 Subject: [PATCH 0109/1233] moved data loaders to subdirectory Former-commit-id: 93e132ac85ba9dde94becb2f324c08342622f73c --- src/data_loader/anndata_loader.tsv | 5 +++++ src/data_loader/{ => anndata_loader}/config.vsh.yaml | 2 +- src/data_loader/{ => anndata_loader}/script.py | 0 src/data_loader/{ => anndata_loader}/test.py | 0 4 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 src/data_loader/anndata_loader.tsv rename src/data_loader/{ => anndata_loader}/config.vsh.yaml (95%) rename src/data_loader/{ => anndata_loader}/script.py (100%) rename src/data_loader/{ => anndata_loader}/test.py (100%) diff --git a/src/data_loader/anndata_loader.tsv b/src/data_loader/anndata_loader.tsv new file mode 100644 index 0000000000..bfa73d8704 --- /dev/null +++ b/src/data_loader/anndata_loader.tsv @@ -0,0 +1,5 @@ +processor name url +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 +anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 +anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 +anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 diff --git a/src/data_loader/config.vsh.yaml b/src/data_loader/anndata_loader/config.vsh.yaml similarity index 95% rename from src/data_loader/config.vsh.yaml rename to src/data_loader/anndata_loader/config.vsh.yaml index 0eed8a1b67..170322ae14 100644 --- a/src/data_loader/config.vsh.yaml +++ b/src/data_loader/anndata_loader/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: resources: - type: python_script path: script.py - - path: "./utils/utils.py" + - path: "../utils/utils.py" tests: - type: python_script path: test.py diff --git a/src/data_loader/script.py b/src/data_loader/anndata_loader/script.py similarity index 100% rename from src/data_loader/script.py rename to src/data_loader/anndata_loader/script.py diff --git a/src/data_loader/test.py b/src/data_loader/anndata_loader/test.py similarity index 100% rename from src/data_loader/test.py rename to src/data_loader/anndata_loader/test.py From 4d6ed8d42f32107021f81d46992f94c88eaf4ac7 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 24 Jun 2021 10:25:56 +0200 Subject: [PATCH 0110/1233] include name in anndata Former-commit-id: 8c2838732bcca9eff29606d65277323abe9ed9ea --- src/data_loader/anndata_loader/config.vsh.yaml | 9 +++++++++ src/data_loader/anndata_loader/script.py | 4 +++- src/data_loader/anndata_loader/test.py | 10 ++++------ 3 files changed, 16 insertions(+), 7 deletions(-) diff --git a/src/data_loader/anndata_loader/config.vsh.yaml b/src/data_loader/anndata_loader/config.vsh.yaml index 170322ae14..2b9fb74244 100644 --- a/src/data_loader/anndata_loader/config.vsh.yaml +++ b/src/data_loader/anndata_loader/config.vsh.yaml @@ -3,6 +3,10 @@ functionality: namespace: "data_loader" version: "dev" description: "Load datasets" + authors: + - name: "Michaela Mueller " + roles: [ maintainer, author ] + props: { github: mumichae } arguments: - name: "--output" alternatives: ["-o"] @@ -13,6 +17,11 @@ functionality: - name: "--url" type: "string" description: "URL of dataset" + required: true + - name: "--name" + type: "string" + description: "Name of dataset" + required: true resources: - type: python_script path: script.py diff --git a/src/data_loader/anndata_loader/script.py b/src/data_loader/anndata_loader/script.py index ca6824756a..74d07108c3 100644 --- a/src/data_loader/anndata_loader/script.py +++ b/src/data_loader/anndata_loader/script.py @@ -1,9 +1,10 @@ ## VIASH START par = { "url": "https://ndownloader.figshare.com/files/24974582", # PBMC data + "name": "pbmc", "output": "test_data.h5ad" } -resources_dir = "./utils/" +resources_dir = "../utils/" ## VIASH END print("Importing libraries") @@ -30,6 +31,7 @@ print("Read file") adata = sc.read(filepath) + adata.uns["name"] = par["name"] # Remove preprocessing if "counts" in adata.layers: diff --git a/src/data_loader/anndata_loader/test.py b/src/data_loader/anndata_loader/test.py index 4549a03ffd..7e36071407 100644 --- a/src/data_loader/anndata_loader/test.py +++ b/src/data_loader/anndata_loader/test.py @@ -1,19 +1,15 @@ -import os from os import path import subprocess - import scanpy as sc -import pandas -import numpy as np - -import urllib.request +name = "pbmc" anndata_file = "pcmc.h5ad" print(">> Running script") out = subprocess.check_output([ "./data_loader", "--url", "https://ndownloader.figshare.com/files/24974582", + "--name", name, "--output", anndata_file ]).decode("utf-8") @@ -23,5 +19,7 @@ print(">> Check that output fits expected API") adata = sc.read_h5ad(anndata_file) # TODO: complete with API checks +assert "counts" not in adata.layers +assert adata.uns["name"] == name print(">> All tests passed successfully") From 1255b99dabf91282eca757f00b71a73b97a734bf Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 24 Jun 2021 11:18:16 +0200 Subject: [PATCH 0111/1233] selective build Former-commit-id: 71872ec20fde225f15e1bb345fbca8d9d09e28ff --- .github/workflows/viash-build.yml | 2 +- .gitignore | 1 + src/data_loader/utils/utils.py | 49 ------------------------------- 3 files changed, 2 insertions(+), 50 deletions(-) delete mode 100644 src/data_loader/utils/utils.py diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index c712c720b4..8baeadde6f 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -35,7 +35,7 @@ jobs: sed -i '/^target\/$/d' .gitignore # only build nextflow targets - bin/viash_build -m release -t main_build + bin/viash_build -m release -t main_build -q 'utils|data_loader' - name: Run tests run: | diff --git a/.gitignore b/.gitignore index 8855a1b0d7..724755c0c9 100644 --- a/.gitignore +++ b/.gitignore @@ -13,6 +13,7 @@ output_bash *.Rproj # viash specific ignores +docker_output/ target/ check_results/ log.txt diff --git a/src/data_loader/utils/utils.py b/src/data_loader/utils/utils.py deleted file mode 100644 index 4f3cf95867..0000000000 --- a/src/data_loader/utils/utils.py +++ /dev/null @@ -1,49 +0,0 @@ -import tempfile -import hashlib -import logging -import os -import scanpy as sc - -log = logging.getLogger("openproblems") - - -def _make_tempdir(): - tempdir = os.path.join(tempfile.gettempdir(), "openproblems_cache") - try: - os.mkdir(tempdir) - log.debug("Created data cache directory") - except OSError: - log.debug("Data cache directory exists") - return tempdir - - -TEMPDIR = _make_tempdir() - - -def _func_to_bytes(func): - return bytes(".".join([func.__module__, func.__name__]), encoding="utf-8") - - -def _obj_to_bytes(obj): - return bytes(str(obj), encoding="utf-8") - - -def _hash_function(func, *args, **kwargs): - hash = hashlib.sha256() - hash.update(_func_to_bytes(func)) - hash.update(_obj_to_bytes(args)) - hash.update(_obj_to_bytes(kwargs)) - return hash.hexdigest() - - -def _cache_path(func, *args, **kwargs): - if hasattr(func, "__wrapped__"): - func = func.__wrapped__ - filename = "openproblems_{}.h5ad".format(_hash_function(func, *args, **kwargs)) - return os.path.join(TEMPDIR, filename) - - -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) From 2bf72e38f2de0eb1bf5959114b153aaecf87776e Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 24 Jun 2021 11:18:35 +0200 Subject: [PATCH 0112/1233] simplified data loaders Former-commit-id: e4b7e5e2d10affaef9bcd20946bb4104fbd6270e --- .../{anndata_loader => }/config.vsh.yaml | 1 - src/data_loader/{anndata_loader => }/script.py | 13 +++---------- src/data_loader/{anndata_loader => }/test.py | 0 3 files changed, 3 insertions(+), 11 deletions(-) rename src/data_loader/{anndata_loader => }/config.vsh.yaml (96%) rename src/data_loader/{anndata_loader => }/script.py (68%) rename src/data_loader/{anndata_loader => }/test.py (100%) diff --git a/src/data_loader/anndata_loader/config.vsh.yaml b/src/data_loader/config.vsh.yaml similarity index 96% rename from src/data_loader/anndata_loader/config.vsh.yaml rename to src/data_loader/config.vsh.yaml index 2b9fb74244..dbd64be8fd 100644 --- a/src/data_loader/anndata_loader/config.vsh.yaml +++ b/src/data_loader/config.vsh.yaml @@ -25,7 +25,6 @@ functionality: resources: - type: python_script path: script.py - - path: "../utils/utils.py" tests: - type: python_script path: test.py diff --git a/src/data_loader/anndata_loader/script.py b/src/data_loader/script.py similarity index 68% rename from src/data_loader/anndata_loader/script.py rename to src/data_loader/script.py index 74d07108c3..dcd1c95848 100644 --- a/src/data_loader/anndata_loader/script.py +++ b/src/data_loader/script.py @@ -4,23 +4,15 @@ "name": "pbmc", "output": "test_data.h5ad" } -resources_dir = "../utils/" ## VIASH END print("Importing libraries") +import sys import scanpy as sc import tempfile import os import scprep -# # adding resources dir to system path -# # the resources dir contains all files listed in the '.functionality.resources' part of the -# # viash config, amongst which is the 'utils.py' file we need. -import sys - -sys.path.append(resources_dir) -# # importing helper functions from common utils.py file in resources dir -from utils import filter_genes_cells with tempfile.TemporaryDirectory() as tempdir: URL = par['url'] @@ -39,7 +31,8 @@ del adata.layers["counts"] # Ensure there are no cells or genes with 0 counts - filter_genes_cells(adata) + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) print("Writing adata to file") diff --git a/src/data_loader/anndata_loader/test.py b/src/data_loader/test.py similarity index 100% rename from src/data_loader/anndata_loader/test.py rename to src/data_loader/test.py From b3f4cd0777016e23319122cd96e268aa3e3cd57c Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 24 Jun 2021 11:23:17 +0200 Subject: [PATCH 0113/1233] selective build for running tests Former-commit-id: ef761c9db94065d8fd0841d1269ed5beab79a2f1 --- .github/workflows/viash-build.yml | 2 +- .github/workflows/viash-test.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index 8baeadde6f..c712c720b4 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -35,7 +35,7 @@ jobs: sed -i '/^target\/$/d' .gitignore # only build nextflow targets - bin/viash_build -m release -t main_build -q 'utils|data_loader' + bin/viash_build -m release -t main_build - name: Run tests run: | diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f00da08fb1..9fcfd528d6 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -33,7 +33,7 @@ jobs: - name: Run build run: | - bin/viash_build + bin/viash_build -q 'utils|data_loader' - name: Run tests run: | From eaab51cf57fc250b16d7c77ad4edda95f2ee968f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Jun 2021 13:55:30 +0200 Subject: [PATCH 0114/1233] move utils to common, move dataloader to common Former-commit-id: bdd35b210216447982075db9b8e0b2c205425785 --- README.Rmd | 14 +++++++------- README.md | 14 +++++++------- src/{ => common}/data_loader/anndata_loader.tsv | 0 src/{ => common}/data_loader/config.vsh.yaml | 2 +- src/{ => common}/data_loader/script.py | 0 src/{ => common}/data_loader/test.py | 0 .../extract_scores/config.vsh.yaml | 2 +- src/{utils => common}/extract_scores/script.R | 0 src/{utils => common}/workflows/utils.nf | 0 src/modality_alignment/workflows/main.nf | 4 ++-- src/modality_alignment/workflows/nextflow.config | 2 +- src/modality_alignment/workflows/run_bash.sh | 4 ++-- .../workflows/run_nextflow_from_repo.sh | 2 +- src/trajectory_inference/workflows/run_nextflow.sh | 2 +- 14 files changed, 23 insertions(+), 23 deletions(-) rename src/{ => common}/data_loader/anndata_loader.tsv (100%) rename src/{ => common}/data_loader/config.vsh.yaml (97%) rename src/{ => common}/data_loader/script.py (100%) rename src/{ => common}/data_loader/test.py (100%) rename src/{utils => common}/extract_scores/config.vsh.yaml (97%) rename src/{utils => common}/extract_scores/script.R (100%) rename src/{utils => common}/workflows/utils.nf (100%) diff --git a/README.Rmd b/README.Rmd index 3071d88684..c0d00878c9 100644 --- a/README.Rmd +++ b/README.Rmd @@ -47,7 +47,7 @@ bin/init **Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. ```bash -bin/viash_build -q 'modality_alignment|utils' +bin/viash_build -q 'modality_alignment|common' ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -58,7 +58,7 @@ bin/viash_build -q 'modality_alignment|utils' These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. The command might take a while to run, since it is building a docker container for each of the components. If you're interested in building only a subset of components, you can apply a regex to the selected components. -For example: `bin/viash_build -q 'utils|modality_alignment'`. +For example: `bin/viash_build -q 'common|modality_alignment'`. **Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: @@ -87,7 +87,7 @@ src/modality_alignment/workflows/run_nextflow.sh metrics/ Modality alignment metric components. utils/ Utils functions. workflow/ The pipeline workflow for this task. - utils/ Helper files. + common/ Helper files. target/ Executables generated by viash based on the components listed under `src/`. docker/ Bash executables which can be used from a terminal. nextflow/ Nextflow modules which can be used in a Nextflow pipeline. @@ -145,7 +145,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ Note that the `bin/viash_build` component does a much better job of setting up a collection of components. You can filter which components will be built by -providing a regex to the `-q` parameter, e.g. `bin/viash_build -q 'utils|modality_alignment'`. +providing a regex to the `-q` parameter, e.g. `bin/viash_build -q 'common|modality_alignment'`. You can now view the same interface of the executable by running the executable with the `-h` parameter. @@ -299,11 +299,11 @@ bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems In release mode... Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot - Exporting src/utils/extract_scores/ (utils) =docker=> target/docker/utils/extract_scores + Exporting src/common/extract_scores/ (common) =docker=> target/docker/common/extract_scores Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse - > docker build -t singlecellopenproblems/utils_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS + > docker build -t singlecellopenproblems/common_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 @@ -321,7 +321,7 @@ Using version 0.1.0 to tag containers > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > openproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > openproblems/common_extract_scores:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! diff --git a/README.md b/README.md index 22f6b215fe..7ad2466921 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. ``` bash -bin/viash_build -q 'modality_alignment|utils' +bin/viash_build -q 'modality_alignment|common' ``` Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc @@ -65,7 +65,7 @@ installed. The command might take a while to run, since it is building a docker container for each of the components. If you’re interested in building only a subset of components, you can apply a regex to the selected components. For example: -`bin/viash_build -q 'utils|modality_alignment'`. +`bin/viash_build -q 'common|modality_alignment'`. **Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: @@ -95,7 +95,7 @@ src/modality_alignment/workflows/run_nextflow.sh metrics/ Modality alignment metric components. utils/ Utils functions. workflow/ The pipeline workflow for this task. - utils/ Helper files. + common/ Helper files. target/ Executables generated by viash based on the components listed under `src/`. docker/ Bash executables which can be used from a terminal. nextflow/ Nextflow modules which can be used in a Nextflow pipeline. @@ -182,7 +182,7 @@ viash build src/modality_alignment/methods/foo/config.vsh.yaml \ Note that the `bin/viash_build` component does a much better job of setting up a collection of components. You can filter which components will be built by providing a regex to the `-q` parameter, -e.g. `bin/viash_build -q 'utils|modality_alignment'`. +e.g. `bin/viash_build -q 'common|modality_alignment'`. You can now view the same interface of the executable by running the executable with the `-h` parameter. @@ -432,11 +432,11 @@ bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems In release mode... Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot - Exporting src/utils/extract_scores/ (utils) =docker=> target/docker/utils/extract_scores + Exporting src/common/extract_scores/ (common) =docker=> target/docker/common/extract_scores Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse - > docker build -t singlecellopenproblems/utils_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS + > docker build -t singlecellopenproblems/common_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 @@ -459,7 +459,7 @@ Using version 0.1.0 to tag containers > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > openproblems/utils_extract_scores:0.1.0 does not exist, try pushing ... OK! + > openproblems/common_extract_scores:0.1.0 does not exist, try pushing ... OK! > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! diff --git a/src/data_loader/anndata_loader.tsv b/src/common/data_loader/anndata_loader.tsv similarity index 100% rename from src/data_loader/anndata_loader.tsv rename to src/common/data_loader/anndata_loader.tsv diff --git a/src/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml similarity index 97% rename from src/data_loader/config.vsh.yaml rename to src/common/data_loader/config.vsh.yaml index dbd64be8fd..c12a4f11c5 100644 --- a/src/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "data_loader" - namespace: "data_loader" + namespace: "common" version: "dev" description: "Load datasets" authors: diff --git a/src/data_loader/script.py b/src/common/data_loader/script.py similarity index 100% rename from src/data_loader/script.py rename to src/common/data_loader/script.py diff --git a/src/data_loader/test.py b/src/common/data_loader/test.py similarity index 100% rename from src/data_loader/test.py rename to src/common/data_loader/test.py diff --git a/src/utils/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml similarity index 97% rename from src/utils/extract_scores/config.vsh.yaml rename to src/common/extract_scores/config.vsh.yaml index 7f37b66c1b..b79716ddc8 100644 --- a/src/utils/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "extract_scores" - namespace: "utils" + namespace: "common" version: "dev" description: "Extract evaluation data frame on output" arguments: diff --git a/src/utils/extract_scores/script.R b/src/common/extract_scores/script.R similarity index 100% rename from src/utils/extract_scores/script.R rename to src/common/extract_scores/script.R diff --git a/src/utils/workflows/utils.nf b/src/common/workflows/utils.nf similarity index 100% rename from src/utils/workflows/utils.nf rename to src/common/workflows/utils.nf diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index d1a5911d55..2319d4c603 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -23,8 +23,8 @@ include { knn_auc } from "$targetDir/modality_alignment/metrics/knn include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) // import helper functions -include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" -include { extract_scores } from "$targetDir/utils/extract_scores/main.nf" params(params) +include { overrideOptionValue; overrideParams } from "$launchDir/src/common/workflows/utils.nf" +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) // Helper function for redefining the ids of elements in a channel // based on its files. diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index defdc73055..72e899b34e 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -14,7 +14,7 @@ includeConfig "$targetDir/modality_alignment/methods/harmonic_alignment/nextflow includeConfig "$targetDir/modality_alignment/methods/sample_method/nextflow.config" includeConfig "$targetDir/modality_alignment/metrics/knn_auc/nextflow.config" includeConfig "$targetDir/modality_alignment/metrics/mse/nextflow.config" -includeConfig "$targetDir/utils/extract_scores/nextflow.config" +includeConfig "$targetDir/common/extract_scores/nextflow.config" // other configs docker { diff --git a/src/modality_alignment/workflows/run_bash.sh b/src/modality_alignment/workflows/run_bash.sh index b40e389ee8..4745e7c776 100755 --- a/src/modality_alignment/workflows/run_bash.sh +++ b/src/modality_alignment/workflows/run_bash.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|utils' +# bin/viash_build -q 'modality_alignment|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -57,4 +57,4 @@ done # concatenate all scores into one tsv INPUTS=$(ls -1 "$OUTPUT/metrics" | sed "s#.*#-i '$OUTPUT/metrics/&'#" | tr '\n' ' ') -eval "$TARGET/../utils/extract_scores/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" +eval "$TARGET/../common/extract_scores/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" diff --git a/src/modality_alignment/workflows/run_nextflow_from_repo.sh b/src/modality_alignment/workflows/run_nextflow_from_repo.sh index fa9039a758..7bf0016560 100755 --- a/src/modality_alignment/workflows/run_nextflow_from_repo.sh +++ b/src/modality_alignment/workflows/run_nextflow_from_repo.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|utils' +# bin/viash_build -q 'modality_alignment|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) diff --git a/src/trajectory_inference/workflows/run_nextflow.sh b/src/trajectory_inference/workflows/run_nextflow.sh index 7e2baa325e..9e2da87cce 100755 --- a/src/trajectory_inference/workflows/run_nextflow.sh +++ b/src/trajectory_inference/workflows/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/project_build -q 'modality_alignment|utils' +# bin/project_build -q 'modality_alignment|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) From f9b87003469f6ff80d7dd7dd8d8acefaef061ce9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Jun 2021 13:55:48 +0200 Subject: [PATCH 0115/1233] add builds per namespace Former-commit-id: c91771927ba6ba5227fd3dd1cd3683f466572cc0 --- .github/workflows/viash-test.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 9fcfd528d6..dfe69b4c25 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -15,7 +15,9 @@ jobs: fail-fast: false matrix: config: - - {name: 'main', os: ubuntu-latest } + - {name: 'main_only_utils', os: ubuntu-latest, query: 'utils' } + - {name: 'main_only_MA', os: ubuntu-latest, query: 'modality_alignment' } + - {name: 'main_only_TI', os: ubuntu-latest, query: 'trajectory_inference' } steps: - uses: actions/checkout@v2 @@ -33,7 +35,7 @@ jobs: - name: Run build run: | - bin/viash_build -q 'utils|data_loader' + bin/viash_build -q '${{ matrix.config.query }}' - name: Run tests run: | @@ -42,7 +44,7 @@ jobs: mkdir check_results # run tests - bin/viash_test --append=false --log=check_results/results.tsv + bin/viash_test -q '${{ matrix.config.query }}' --append=false --log=check_results/results.tsv - name: Upload check results uses: actions/upload-artifact@master From 63a26dd14fd93b34c8676062565d2f84b0a5f115 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Jun 2021 14:07:12 +0200 Subject: [PATCH 0116/1233] fix github actions Former-commit-id: 697a5b0c8401f6caf8abfb3b98e6590972033d9a --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index dfe69b4c25..9eb1b29543 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -15,7 +15,7 @@ jobs: fail-fast: false matrix: config: - - {name: 'main_only_utils', os: ubuntu-latest, query: 'utils' } + - {name: 'main_only_common', os: ubuntu-latest, query: 'common' } - {name: 'main_only_MA', os: ubuntu-latest, query: 'modality_alignment' } - {name: 'main_only_TI', os: ubuntu-latest, query: 'trajectory_inference' } From ca20c88f6b7b54dbeffe02e8a3c0f673162d29ed Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 8 Jul 2021 11:23:17 +0200 Subject: [PATCH 0117/1233] Started with data loaders for Batch integration component Former-commit-id: 735244d9f225aa102a0093fa731aa60a070b0794 --- src/batch_integration/datasets/README.md | 0 .../datasets/config.vsh.yaml | 64 +++++++++++++++++++ src/batch_integration/datasets/params.tsv | 3 + src/batch_integration/datasets/script.py | 64 +++++++++++++++++++ src/batch_integration/datasets/test.py | 25 ++++++++ 5 files changed, 156 insertions(+) create mode 100644 src/batch_integration/datasets/README.md create mode 100644 src/batch_integration/datasets/config.vsh.yaml create mode 100644 src/batch_integration/datasets/params.tsv create mode 100644 src/batch_integration/datasets/script.py create mode 100644 src/batch_integration/datasets/test.py diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/batch_integration/datasets/config.vsh.yaml b/src/batch_integration/datasets/config.vsh.yaml new file mode 100644 index 0000000000..74691c7ac8 --- /dev/null +++ b/src/batch_integration/datasets/config.vsh.yaml @@ -0,0 +1,64 @@ +functionality: + name: datasets + namespace: batch_integration + version: dev + description: Preprocess adata object for data integration + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output h5ad file of the cleaned dataset + required: true + - name: --adata + type: file + description: Anndata HDF5 file + required: true + - name: --name + type: string + description: Name of dataset + required: true + - name: --label + type: string + description: Cell annotation label in adata.obs + required: true + - name: --batch + type: string + description: Batch assignment in adata.obs + required: true + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + required: false + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + - path: '../../common/utils/preprocessing.py' + tests: + - type: python_script + path: test.py +platforms: + - type: docker + image: mambaorg/micromamba:0.14.0 + setup: + - type: docker + run: + - ls -la + - micromamba install -y -c conda-forge -c bioconda \ + python=3.9.5 scprep scanpy r-base rpy2 +# - micromamba install -y -n base -f /root/env.yaml + - micromamba clean --all --yes +# resources: +# - envs/py_r.yaml /root/env.yaml + - type: native + - type: nextflow diff --git a/src/batch_integration/datasets/params.tsv b/src/batch_integration/datasets/params.tsv new file mode 100644 index 0000000000..37251ea0bf --- /dev/null +++ b/src/batch_integration/datasets/params.tsv @@ -0,0 +1,3 @@ +name label batch hvgs +pancreas celltype tech 2000 +immune_cells final_annotation batch 2000 diff --git a/src/batch_integration/datasets/script.py b/src/batch_integration/datasets/script.py new file mode 100644 index 0000000000..5a898fe60a --- /dev/null +++ b/src/batch_integration/datasets/script.py @@ -0,0 +1,64 @@ +## VIASH START +par = { + 'adata': '../resources/pancreas.h5ad', + 'name': 'pancreas', + 'label': 'celltype', + 'batch': 'tech', + 'hvgs': 2000, + 'output': 'adata_out.h5ad', + 'debug': True +} +resources_dir = '../../common/utils/' +## VIASH END + +print('Importing libraries') +import scanpy as sc +import sys +import os + +sys.path.append(os.path.abspath(resources_dir)) + +from preprocessing import log_scran_pooling + +if par['debug']: + import pprint + + pprint.pprint(par) + +adata_file = par['adata'] +name = par['name'] +label = par['label'] +batch = par['batch'] +hvgs = par['hvgs'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +assert name == adata.uns['name'] + +# Rename columns +adata.obs['labels'] = adata.obs[label] +adata.obs['batch'] = adata.obs[batch] +adata.layers['counts'] = adata.X + +print(f'Select {hvgs} highly variable genes') +if adata.n_obs > hvgs: + sc.pp.subsample(adata, n_obs=hvgs) + +print('Normalisation with scran') +log_scran_pooling(adata) +adata.layers['logcounts'] = adata.X + +print('Transformation: PCA') +sc.tl.pca( + adata, + svd_solver='arpack', + return_info=True, +) +adata.obsm['X_uni'] = adata.obsm['X_pca'] + +print('Transformation: kNN') +sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') + +print('Writing adata to file') +adata.write(output, compression='gzip') diff --git a/src/batch_integration/datasets/test.py b/src/batch_integration/datasets/test.py new file mode 100644 index 0000000000..7e36071407 --- /dev/null +++ b/src/batch_integration/datasets/test.py @@ -0,0 +1,25 @@ +from os import path +import subprocess +import scanpy as sc + +name = "pbmc" +anndata_file = "pcmc.h5ad" + +print(">> Running script") +out = subprocess.check_output([ + "./data_loader", + "--url", "https://ndownloader.figshare.com/files/24974582", + "--name", name, + "--output", anndata_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(anndata_file) + +print(">> Check that output fits expected API") +adata = sc.read_h5ad(anndata_file) +# TODO: complete with API checks +assert "counts" not in adata.layers +assert adata.uns["name"] == name + +print(">> All tests passed successfully") From 9092859882513a177d493d870adb466eabb3e1ed Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 8 Jul 2021 11:25:21 +0200 Subject: [PATCH 0118/1233] added Dockerfiles for base images Former-commit-id: cae7af41d7d7755a4f80e8c5981eb02dacc105e8 --- .../base_images/scanpy-r-micromamba/Dockerfile | 5 +++++ src/common/base_images/scanpy-r-micromamba/env.yaml | 13 +++++++++++++ src/common/base_images/scib-base/Dockerfile | 7 +++++++ src/common/base_images/scib-base/env.yaml | 13 +++++++++++++ 4 files changed, 38 insertions(+) create mode 100644 src/common/base_images/scanpy-r-micromamba/Dockerfile create mode 100644 src/common/base_images/scanpy-r-micromamba/env.yaml create mode 100644 src/common/base_images/scib-base/Dockerfile create mode 100644 src/common/base_images/scib-base/env.yaml diff --git a/src/common/base_images/scanpy-r-micromamba/Dockerfile b/src/common/base_images/scanpy-r-micromamba/Dockerfile new file mode 100644 index 0000000000..e5e88f71fa --- /dev/null +++ b/src/common/base_images/scanpy-r-micromamba/Dockerfile @@ -0,0 +1,5 @@ +FROM mambaorg/micromamba:0.14.0 +COPY env.yaml /tmp/env.yaml +RUN micromamba install -y -n base -f /tmp/env.yaml && \ + micromamba clean --all --yes +WORKDIR /home/micromamba diff --git a/src/common/base_images/scanpy-r-micromamba/env.yaml b/src/common/base_images/scanpy-r-micromamba/env.yaml new file mode 100644 index 0000000000..acb74d2642 --- /dev/null +++ b/src/common/base_images/scanpy-r-micromamba/env.yaml @@ -0,0 +1,13 @@ +name: base +channels: + - conda-forge +dependencies: + - python=3.8 + - pip=21.1 + - rpy2=3.4.5 + - scanpy=1.8 + - r-base=4 + - anndata=0.7.6 + - git + - pip: + - anndata2ri=1.0.6 diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile new file mode 100644 index 0000000000..418a418234 --- /dev/null +++ b/src/common/base_images/scib-base/Dockerfile @@ -0,0 +1,7 @@ +FROM scanpy-r-micromamba:latest +COPY env.yaml /tmp/env.yaml +RUN micromamba install -y -n base -f /tmp/env.yaml +RUN git clone https://github.com/theislab/scib.git +RUN cd scib && \ + pip install . +RUN micromamba clean --all --yes diff --git a/src/common/base_images/scib-base/env.yaml b/src/common/base_images/scib-base/env.yaml new file mode 100644 index 0000000000..acb74d2642 --- /dev/null +++ b/src/common/base_images/scib-base/env.yaml @@ -0,0 +1,13 @@ +name: base +channels: + - conda-forge +dependencies: + - python=3.8 + - pip=21.1 + - rpy2=3.4.5 + - scanpy=1.8 + - r-base=4 + - anndata=0.7.6 + - git + - pip: + - anndata2ri=1.0.6 From 7cb5358144df09595fc36ff0a518833d38216654 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 8 Jul 2021 15:25:40 +0200 Subject: [PATCH 0119/1233] added ARI for feature output Former-commit-id: 3a263a24ff110c0aa2360132125260488f458a0e --- .../metrics/feature/ari/config.vsh.yaml | 41 ++++++++++++++ .../metrics/feature/ari/script.py | 54 +++++++++++++++++++ .../metrics/feature/ari/test.py | 25 +++++++++ 3 files changed, 120 insertions(+) create mode 100644 src/batch_integration/metrics/feature/ari/config.vsh.yaml create mode 100644 src/batch_integration/metrics/feature/ari/script.py create mode 100644 src/batch_integration/metrics/feature/ari/test.py diff --git a/src/batch_integration/metrics/feature/ari/config.vsh.yaml b/src/batch_integration/metrics/feature/ari/config.vsh.yaml new file mode 100644 index 0000000000..c95c0cab8f --- /dev/null +++ b/src/batch_integration/metrics/feature/ari/config.vsh.yaml @@ -0,0 +1,41 @@ +functionality: + name: ari + namespace: feature + version: dev + description: Adjusted rand index (ARI) + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file + required: true + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/metrics/feature/ari/script.py b/src/batch_integration/metrics/feature/ari/script.py new file mode 100644 index 0000000000..39d6346924 --- /dev/null +++ b/src/batch_integration/metrics/feature/ari/script.py @@ -0,0 +1,54 @@ +## VIASH START +par = { + 'adata': '../resources/mnn.h5ad', + 'hvgs': 2000, + 'output': 'metrics.tsv', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.preprocessing import reduce_data +from scIB.clustering import opt_louvain +from scIB.metrics import ari + +if par['debug']: + pprint.pprint(par) + +adata_file = par['adata'] +n_hvgs = par['hvgs'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +name = adata.uns['name'] + +# preprocess adata object +print('preprocess adata') +reduce_data( + adata, + n_top_genes=n_hvgs, + neighbors=True, + use_rep='X_pca', + pca=True, + umap=False +) + +print('Clustering') +opt_louvain( + adata, + label_key='label', + cluster_key='cluster', + plot=False, + inplace=True, + force=True +) +score = ari(adata, group1='cluster', group2='label') + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] + entry = [name, 'feature', n_hvgs, 'ARI', score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/metrics/feature/ari/test.py b/src/batch_integration/metrics/feature/ari/test.py new file mode 100644 index 0000000000..6efc5f0498 --- /dev/null +++ b/src/batch_integration/metrics/feature/ari/test.py @@ -0,0 +1,25 @@ +from os import path +import subprocess +import pandas as pd + +metric = 'ari.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./ari", + "--adata", 'mnn.h5ad', + '--hvgs', '2000', + "--output", metric +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric) + +print(">> Check that score makes sense") +result = pd.read_table(metric) +assert result.shape == (1, 5) +ari = result.loc[0, 'value'] +assert 0 < ari < 1 +assert ari == 0.2459195865045752 + +print(">> All tests passed successfully") From 109d4051083bd98b2fe2f2866c867aea2aaa6900 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Jul 2021 09:45:34 +0200 Subject: [PATCH 0120/1233] add batch integration to GA Former-commit-id: cef8eb6283f7d5bd110cb1ae95b058d61c6fc6a6 --- .github/workflows/viash-test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 9eb1b29543..bbb0310f15 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -18,6 +18,7 @@ jobs: - {name: 'main_only_common', os: ubuntu-latest, query: 'common' } - {name: 'main_only_MA', os: ubuntu-latest, query: 'modality_alignment' } - {name: 'main_only_TI', os: ubuntu-latest, query: 'trajectory_inference' } + - {name: 'main_only_BI', os: ubuntu-latest, query: 'batch_integration' } steps: - uses: actions/checkout@v2 From d09f12bf0b998c3bf430ed0ce2db3f95c93632eb Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Jul 2021 09:46:26 +0200 Subject: [PATCH 0121/1233] generalised ARI, added random seed Former-commit-id: cf5c0f1b36f5008c8f183f72f6a5e2a0fb2aa403 --- .../metrics/feature/ari/script.py | 3 ++- .../metrics/feature/ari/test.py | 22 ++++++++++++------- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/src/batch_integration/metrics/feature/ari/script.py b/src/batch_integration/metrics/feature/ari/script.py index 39d6346924..ce097d73f5 100644 --- a/src/batch_integration/metrics/feature/ari/script.py +++ b/src/batch_integration/metrics/feature/ari/script.py @@ -17,6 +17,7 @@ if par['debug']: pprint.pprint(par) +METRIC = 'ari' adata_file = par['adata'] n_hvgs = par['hvgs'] output = par['output'] @@ -49,6 +50,6 @@ with open(output, 'w') as file: header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] - entry = [name, 'feature', n_hvgs, 'ARI', score] + entry = [name, 'feature', n_hvgs, METRIC, score] file.write('\t'.join(header) + '\n') file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/metrics/feature/ari/test.py b/src/batch_integration/metrics/feature/ari/test.py index 6efc5f0498..96a622f874 100644 --- a/src/batch_integration/metrics/feature/ari/test.py +++ b/src/batch_integration/metrics/feature/ari/test.py @@ -1,25 +1,31 @@ from os import path import subprocess import pandas as pd +import numpy as np -metric = 'ari.tsv' +np.random.seed(42) + +metric = 'ari' +metric_file = metric + '.tsv' print(">> Running script") out = subprocess.check_output([ - "./ari", + "./" + metric, "--adata", 'mnn.h5ad', '--hvgs', '2000', - "--output", metric + "--output", metric_file ]).decode("utf-8") print(">> Checking whether file exists") -assert path.exists(metric) +assert path.exists(metric_file) +result = pd.read_table(metric_file) print(">> Check that score makes sense") -result = pd.read_table(metric) assert result.shape == (1, 5) -ari = result.loc[0, 'value'] -assert 0 < ari < 1 -assert ari == 0.2459195865045752 +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.2459195865045752 print(">> All tests passed successfully") From 245770444ad816cae1cb763ef8b98de23f38f0ee Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Jul 2021 09:48:11 +0200 Subject: [PATCH 0122/1233] added NMI component Former-commit-id: 7ef2716223f9673cefdee8a18e1d0a04d30b7bbc --- .../metrics/feature/nmi/config.vsh.yaml | 41 ++++++++++++++ .../metrics/feature/nmi/script.py | 55 +++++++++++++++++++ .../metrics/feature/nmi/test.py | 31 +++++++++++ 3 files changed, 127 insertions(+) create mode 100644 src/batch_integration/metrics/feature/nmi/config.vsh.yaml create mode 100644 src/batch_integration/metrics/feature/nmi/script.py create mode 100644 src/batch_integration/metrics/feature/nmi/test.py diff --git a/src/batch_integration/metrics/feature/nmi/config.vsh.yaml b/src/batch_integration/metrics/feature/nmi/config.vsh.yaml new file mode 100644 index 0000000000..afae13cb93 --- /dev/null +++ b/src/batch_integration/metrics/feature/nmi/config.vsh.yaml @@ -0,0 +1,41 @@ +functionality: + name: nmi + namespace: feature + version: dev + description: Normalized mutual information (NMI) + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file + required: true + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/metrics/feature/nmi/script.py b/src/batch_integration/metrics/feature/nmi/script.py new file mode 100644 index 0000000000..11f246fc11 --- /dev/null +++ b/src/batch_integration/metrics/feature/nmi/script.py @@ -0,0 +1,55 @@ +## VIASH START +par = { + 'adata': '../resources/mnn.h5ad', + 'hvgs': 2000, + 'output': 'nmi.tsv', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.preprocessing import reduce_data +from scIB.clustering import opt_louvain +from scIB.metrics import nmi + +if par['debug']: + pprint.pprint(par) + +METRIC = 'nmi' +adata_file = par['adata'] +n_hvgs = par['hvgs'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +name = adata.uns['name'] + +# preprocess adata object +print('preprocess adata') +reduce_data( + adata, + n_top_genes=n_hvgs, + neighbors=True, + use_rep='X_pca', + pca=True, + umap=False +) + +print('Clustering') +opt_louvain( + adata, + label_key='label', + cluster_key='cluster', + plot=False, + inplace=True, + force=True +) +score = nmi(adata, group1='cluster', group2='label') + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] + entry = [name, 'feature', n_hvgs, METRIC, score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/metrics/feature/nmi/test.py b/src/batch_integration/metrics/feature/nmi/test.py new file mode 100644 index 0000000000..da47719a10 --- /dev/null +++ b/src/batch_integration/metrics/feature/nmi/test.py @@ -0,0 +1,31 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'nmi' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'mnn.h5ad', + '--hvgs', '2000', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) + +print(">> Check that score makes sense") +result = pd.read_table(metric_file) +assert result.shape == (1, 5) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.4871368591999889 + +print(">> All tests passed successfully") From 54cffe91a938449ac742112e0786450c4f5b854d Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Jul 2021 10:22:53 +0200 Subject: [PATCH 0123/1233] added ASW batch score Former-commit-id: 39b9b8c15309f0c89159752cddcd38009d11458f --- .../metrics/feature/ari/script.py | 9 ++- .../metrics/feature/asw_batch/config.vsh.yaml | 41 ++++++++++++++ .../metrics/feature/asw_batch/script.py | 56 +++++++++++++++++++ .../metrics/feature/asw_batch/test.py | 31 ++++++++++ .../metrics/feature/nmi/script.py | 9 ++- 5 files changed, 142 insertions(+), 4 deletions(-) create mode 100644 src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml create mode 100644 src/batch_integration/metrics/feature/asw_batch/script.py create mode 100644 src/batch_integration/metrics/feature/asw_batch/test.py diff --git a/src/batch_integration/metrics/feature/ari/script.py b/src/batch_integration/metrics/feature/ari/script.py index ce097d73f5..f51e3ed539 100644 --- a/src/batch_integration/metrics/feature/ari/script.py +++ b/src/batch_integration/metrics/feature/ari/script.py @@ -18,8 +18,11 @@ pprint.pprint(par) METRIC = 'ari' +EMBEDDING = 'X_pca' + adata_file = par['adata'] n_hvgs = par['hvgs'] +n_hvgs = n_hvgs if n_hvgs > 0 else None output = par['output'] print('Read adata') @@ -32,12 +35,12 @@ adata, n_top_genes=n_hvgs, neighbors=True, - use_rep='X_pca', + use_rep=EMBEDDING, pca=True, umap=False ) -print('Clustering') +print('clustering') opt_louvain( adata, label_key='label', @@ -46,6 +49,8 @@ inplace=True, force=True ) + +print('compute score') score = ari(adata, group1='cluster', group2='label') with open(output, 'w') as file: diff --git a/src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml new file mode 100644 index 0000000000..acf284256d --- /dev/null +++ b/src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml @@ -0,0 +1,41 @@ +functionality: + name: asw_batch + namespace: feature + version: dev + description: Average silhouette of batches per label + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file before integration + required: true + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/metrics/feature/asw_batch/script.py b/src/batch_integration/metrics/feature/asw_batch/script.py new file mode 100644 index 0000000000..90e74f5380 --- /dev/null +++ b/src/batch_integration/metrics/feature/asw_batch/script.py @@ -0,0 +1,56 @@ +## VIASH START +par = { + 'adata': '../resources/mnn.h5ad', + 'hvgs': 2000, + 'output': 'asw_batch.tsv', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.preprocessing import reduce_data +from scIB.metrics import silhouette_batch + +if par['debug']: + pprint.pprint(par) + +METRIC = 'asw_batch' +EMBEDDING = 'X_pca' + +adata_file = par['adata'] +n_hvgs = par['hvgs'] +n_hvgs = n_hvgs if n_hvgs > 0 else None +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +name = adata.uns['name'] + +# preprocess adata object +print('preprocess adata') +reduce_data( + adata, + n_top_genes=n_hvgs, + pca=True, + neighbors=False, + use_rep=EMBEDDING, + umap=False +) + +print('compute score') +_, sil_clus = silhouette_batch( + adata, + batch_key='batch', + group_key='label', + embed=EMBEDDING, + verbose=False +) +score = sil_clus['silhouette_score'].mean() + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] + entry = [name, 'feature', n_hvgs, METRIC, score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/metrics/feature/asw_batch/test.py b/src/batch_integration/metrics/feature/asw_batch/test.py new file mode 100644 index 0000000000..16104dce0b --- /dev/null +++ b/src/batch_integration/metrics/feature/asw_batch/test.py @@ -0,0 +1,31 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'asw_batch' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'mnn.h5ad', + '--hvgs', '2000', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) + +print(">> Check that score makes sense") +result = pd.read_table(metric_file) +assert result.shape == (1, 5) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.8778942688412869 + +print(">> All tests passed successfully") diff --git a/src/batch_integration/metrics/feature/nmi/script.py b/src/batch_integration/metrics/feature/nmi/script.py index 11f246fc11..a46344ae2e 100644 --- a/src/batch_integration/metrics/feature/nmi/script.py +++ b/src/batch_integration/metrics/feature/nmi/script.py @@ -18,8 +18,11 @@ pprint.pprint(par) METRIC = 'nmi' +EMBEDDING = 'X_pca' + adata_file = par['adata'] n_hvgs = par['hvgs'] +n_hvgs = n_hvgs if n_hvgs > 0 else None output = par['output'] print('Read adata') @@ -32,12 +35,12 @@ adata, n_top_genes=n_hvgs, neighbors=True, - use_rep='X_pca', + use_rep=EMBEDDING, pca=True, umap=False ) -print('Clustering') +print('clustering') opt_louvain( adata, label_key='label', @@ -46,6 +49,8 @@ inplace=True, force=True ) + +print('compute score') score = nmi(adata, group1='cluster', group2='label') with open(output, 'w') as file: From ad2c19c7d947c9ac4352c13931a6e3f7aac37dcd Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Jul 2021 10:25:28 +0200 Subject: [PATCH 0124/1233] removed redundant preprocessing script from config Former-commit-id: e00cd18b74326e3d010301ee54d7bbb7776e38db --- src/batch_integration/datasets/config.vsh.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/batch_integration/datasets/config.vsh.yaml b/src/batch_integration/datasets/config.vsh.yaml index 74691c7ac8..6cd157eeec 100644 --- a/src/batch_integration/datasets/config.vsh.yaml +++ b/src/batch_integration/datasets/config.vsh.yaml @@ -43,7 +43,6 @@ functionality: resources: - type: python_script path: script.py - - path: '../../common/utils/preprocessing.py' tests: - type: python_script path: test.py From 885a4238f96209bdc7e2772ae075a2551b4e815e Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Sun, 18 Jul 2021 19:41:51 +0200 Subject: [PATCH 0125/1233] properly added anndata2ri to docker image Former-commit-id: adcdb6c93b1280ae323e2daadf5200d4540a38ad --- src/common/base_images/scanpy-r-micromamba/Dockerfile | 1 + src/common/base_images/scanpy-r-micromamba/env.yaml | 2 -- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/common/base_images/scanpy-r-micromamba/Dockerfile b/src/common/base_images/scanpy-r-micromamba/Dockerfile index e5e88f71fa..f5429f256c 100644 --- a/src/common/base_images/scanpy-r-micromamba/Dockerfile +++ b/src/common/base_images/scanpy-r-micromamba/Dockerfile @@ -2,4 +2,5 @@ FROM mambaorg/micromamba:0.14.0 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml && \ micromamba clean --all --yes +RUN pip install anndata2ri==1.0.6 WORKDIR /home/micromamba diff --git a/src/common/base_images/scanpy-r-micromamba/env.yaml b/src/common/base_images/scanpy-r-micromamba/env.yaml index acb74d2642..d266b2a582 100644 --- a/src/common/base_images/scanpy-r-micromamba/env.yaml +++ b/src/common/base_images/scanpy-r-micromamba/env.yaml @@ -9,5 +9,3 @@ dependencies: - r-base=4 - anndata=0.7.6 - git - - pip: - - anndata2ri=1.0.6 From dbbd06690839b4d93a12dceec43131bf74d5ccc2 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Sun, 18 Jul 2021 19:52:03 +0200 Subject: [PATCH 0126/1233] fixed dataset preparation and fixed test Former-commit-id: f263479094f73da44d39c75e969d161b4a03c6c3 --- src/batch_integration/datasets/README.md | 19 +++++++++ .../datasets/config.vsh.yaml | 10 ++--- src/batch_integration/datasets/script.py | 34 +++++++++++----- src/batch_integration/datasets/test.py | 39 ++++++++++++------- 4 files changed, 70 insertions(+), 32 deletions(-) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index e69de29bb2..33734f455a 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -0,0 +1,19 @@ +# Datasets + +Viash component for preparing data **before** running data integration methods. + +## API + +This script will write an adata object that contains: + +* `adata.obs['batch']`: batch covariate +* `adata.obs['label']`: cell identity label +* `adata.layers['counts']`: raw, integer UMI count data +* `adata.X`: log-normalized data + +And transformations of the data: + +* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` diff --git a/src/batch_integration/datasets/config.vsh.yaml b/src/batch_integration/datasets/config.vsh.yaml index 6cd157eeec..528887075e 100644 --- a/src/batch_integration/datasets/config.vsh.yaml +++ b/src/batch_integration/datasets/config.vsh.yaml @@ -18,10 +18,6 @@ functionality: type: file description: Anndata HDF5 file required: true - - name: --name - type: string - description: Name of dataset - required: true - name: --label type: string description: Cell annotation label in adata.obs @@ -46,15 +42,15 @@ functionality: tests: - type: python_script path: test.py + - path: '../resources/data_loader_pancreas.h5ad' platforms: - type: docker - image: mambaorg/micromamba:0.14.0 + image: mumichae/scanpy-r-micromamba:0.1.1 setup: - type: docker run: - ls -la - - micromamba install -y -c conda-forge -c bioconda \ - python=3.9.5 scprep scanpy r-base rpy2 + - micromamba install -y -c conda-forge -c bioconda scprep bioconductor-scran # - micromamba install -y -n base -f /root/env.yaml - micromamba clean --all --yes # resources: diff --git a/src/batch_integration/datasets/script.py b/src/batch_integration/datasets/script.py index 5a898fe60a..9a28d31533 100644 --- a/src/batch_integration/datasets/script.py +++ b/src/batch_integration/datasets/script.py @@ -1,24 +1,40 @@ ## VIASH START +import os +print(os.getcwd()) par = { - 'adata': '../resources/pancreas.h5ad', - 'name': 'pancreas', + 'adata': './src/batch_integration/resources/data_loader_pancreas.h5ad', 'label': 'celltype', 'batch': 'tech', 'hvgs': 2000, 'output': 'adata_out.h5ad', 'debug': True } -resources_dir = '../../common/utils/' ## VIASH END print('Importing libraries') import scanpy as sc -import sys -import os +import scprep + -sys.path.append(os.path.abspath(resources_dir)) +def log_scran_pooling(adata): + """Normalize data with scran via rpy2.""" + _scran = scprep.run.RFunction( + setup="library('scran')", + args="sce, min.mean=0.1", + body=""" + sce <- computeSumFactors( + sce, min.mean=min.mean, + assay.type="X" + ) + sizeFactors(sce) + """, + ) + adata.obs["size_factors"] = _scran(adata) + adata.X = scprep.utils.matrix_vector_elementwise_multiply( + adata.X, adata.obs["size_factors"], axis=0 + ) + sc.pp.log1p(adata) -from preprocessing import log_scran_pooling if par['debug']: import pprint @@ -26,7 +42,6 @@ pprint.pprint(par) adata_file = par['adata'] -name = par['name'] label = par['label'] batch = par['batch'] hvgs = par['hvgs'] @@ -34,10 +49,9 @@ print('Read adata') adata = sc.read(adata_file) -assert name == adata.uns['name'] # Rename columns -adata.obs['labels'] = adata.obs[label] +adata.obs['label'] = adata.obs[label] adata.obs['batch'] = adata.obs[batch] adata.layers['counts'] = adata.X diff --git a/src/batch_integration/datasets/test.py b/src/batch_integration/datasets/test.py index 7e36071407..cfd6295329 100644 --- a/src/batch_integration/datasets/test.py +++ b/src/batch_integration/datasets/test.py @@ -2,24 +2,33 @@ import subprocess import scanpy as sc -name = "pbmc" -anndata_file = "pcmc.h5ad" +name = 'pancreas' +anndata_in = 'data_loader_pancreas.h5ad' +anndata_out = 'data_loader_pancreas.h5ad' -print(">> Running script") +print('>> Running script') out = subprocess.check_output([ - "./data_loader", - "--url", "https://ndownloader.figshare.com/files/24974582", - "--name", name, - "--output", anndata_file -]).decode("utf-8") + './datasets', + '--adata', anndata_in, + '--label', 'celltype', + '--batch', 'tech', + '--hvgs', '2000', + '--output', anndata_out +]).decode('utf-8') -print(">> Checking whether file exists") -assert path.exists(anndata_file) +print('>> Checking whether file exists') +assert path.exists(anndata_in) -print(">> Check that output fits expected API") -adata = sc.read_h5ad(anndata_file) +print('>> Check that output fits expected API') +adata = sc.read_h5ad(anndata_in) # TODO: complete with API checks -assert "counts" not in adata.layers -assert adata.uns["name"] == name +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'logcounts' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp -print(">> All tests passed successfully") +print('>> All tests passed successfully') From 9f72e288dea0841abba8e784b4296fe8d2409b6c Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Sun, 18 Jul 2021 20:57:26 +0200 Subject: [PATCH 0127/1233] added testing dataset Former-commit-id: cfec15267ccf1bcb7f31ec3d7c3dda40dfd0fef2 --- .../resources/data_loader_pancreas.h5ad | Bin 0 -> 110520 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 src/batch_integration/resources/data_loader_pancreas.h5ad diff --git a/src/batch_integration/resources/data_loader_pancreas.h5ad b/src/batch_integration/resources/data_loader_pancreas.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..144a187d715970c669bb1dbbb035ce0ce3140ef8 GIT binary patch literal 110520 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wG9a&uR`>r?m0s#{=mknAnEYJgg6gJTCw}g8uNmI;+A$kwB Date: Mon, 19 Jul 2021 18:42:20 +0200 Subject: [PATCH 0128/1233] changed folder structure for metrics Former-commit-id: 0f82e4001f88bd5194f01a8560183d6a88a01059 --- .../feature => embedding/metrics}/asw_batch/config.vsh.yaml | 0 .../{metrics/feature => embedding/metrics}/asw_batch/script.py | 0 .../{metrics/feature => embedding/metrics}/asw_batch/test.py | 0 .../{metrics/feature => graph/metrics}/ari/config.vsh.yaml | 0 .../{metrics/feature => graph/metrics}/ari/script.py | 0 .../{metrics/feature => graph/metrics}/ari/test.py | 2 +- .../{metrics/feature => graph/metrics}/nmi/config.vsh.yaml | 0 .../{metrics/feature => graph/metrics}/nmi/script.py | 0 .../{metrics/feature => graph/metrics}/nmi/test.py | 0 9 files changed, 1 insertion(+), 1 deletion(-) rename src/batch_integration/{metrics/feature => embedding/metrics}/asw_batch/config.vsh.yaml (100%) rename src/batch_integration/{metrics/feature => embedding/metrics}/asw_batch/script.py (100%) rename src/batch_integration/{metrics/feature => embedding/metrics}/asw_batch/test.py (100%) rename src/batch_integration/{metrics/feature => graph/metrics}/ari/config.vsh.yaml (100%) rename src/batch_integration/{metrics/feature => graph/metrics}/ari/script.py (100%) rename src/batch_integration/{metrics/feature => graph/metrics}/ari/test.py (96%) rename src/batch_integration/{metrics/feature => graph/metrics}/nmi/config.vsh.yaml (100%) rename src/batch_integration/{metrics/feature => graph/metrics}/nmi/script.py (100%) rename src/batch_integration/{metrics/feature => graph/metrics}/nmi/test.py (100%) diff --git a/src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/feature/asw_batch/config.vsh.yaml rename to src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml diff --git a/src/batch_integration/metrics/feature/asw_batch/script.py b/src/batch_integration/embedding/metrics/asw_batch/script.py similarity index 100% rename from src/batch_integration/metrics/feature/asw_batch/script.py rename to src/batch_integration/embedding/metrics/asw_batch/script.py diff --git a/src/batch_integration/metrics/feature/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py similarity index 100% rename from src/batch_integration/metrics/feature/asw_batch/test.py rename to src/batch_integration/embedding/metrics/asw_batch/test.py diff --git a/src/batch_integration/metrics/feature/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/feature/ari/config.vsh.yaml rename to src/batch_integration/graph/metrics/ari/config.vsh.yaml diff --git a/src/batch_integration/metrics/feature/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py similarity index 100% rename from src/batch_integration/metrics/feature/ari/script.py rename to src/batch_integration/graph/metrics/ari/script.py diff --git a/src/batch_integration/metrics/feature/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py similarity index 96% rename from src/batch_integration/metrics/feature/ari/test.py rename to src/batch_integration/graph/metrics/ari/test.py index 96a622f874..ecd125e95a 100644 --- a/src/batch_integration/metrics/feature/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -12,7 +12,7 @@ out = subprocess.check_output([ "./" + metric, "--adata", 'mnn.h5ad', - '--hvgs', '2000', + '--hvgs', '100', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/metrics/feature/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/feature/nmi/config.vsh.yaml rename to src/batch_integration/graph/metrics/nmi/config.vsh.yaml diff --git a/src/batch_integration/metrics/feature/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py similarity index 100% rename from src/batch_integration/metrics/feature/nmi/script.py rename to src/batch_integration/graph/metrics/nmi/script.py diff --git a/src/batch_integration/metrics/feature/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py similarity index 100% rename from src/batch_integration/metrics/feature/nmi/test.py rename to src/batch_integration/graph/metrics/nmi/test.py From 1335eabd94f2bf2080b262a2d084a82145af921b Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 19 Jul 2021 19:48:07 +0200 Subject: [PATCH 0129/1233] dataset preparation specific to pancreas Former-commit-id: 87ec9549203961fd7ba098a7338020d2cc779418 --- src/batch_integration/datasets/{ => pancreas}/config.vsh.yaml | 0 src/batch_integration/datasets/{ => pancreas}/script.py | 1 + src/batch_integration/datasets/{ => pancreas}/test.py | 1 - 3 files changed, 1 insertion(+), 1 deletion(-) rename src/batch_integration/datasets/{ => pancreas}/config.vsh.yaml (100%) rename src/batch_integration/datasets/{ => pancreas}/script.py (97%) rename src/batch_integration/datasets/{ => pancreas}/test.py (96%) diff --git a/src/batch_integration/datasets/config.vsh.yaml b/src/batch_integration/datasets/pancreas/config.vsh.yaml similarity index 100% rename from src/batch_integration/datasets/config.vsh.yaml rename to src/batch_integration/datasets/pancreas/config.vsh.yaml diff --git a/src/batch_integration/datasets/script.py b/src/batch_integration/datasets/pancreas/script.py similarity index 97% rename from src/batch_integration/datasets/script.py rename to src/batch_integration/datasets/pancreas/script.py index 9a28d31533..bb376237a6 100644 --- a/src/batch_integration/datasets/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -60,6 +60,7 @@ def log_scran_pooling(adata): sc.pp.subsample(adata, n_obs=hvgs) print('Normalisation with scran') +# only if "lognorm" exists in adata.layers log_scran_pooling(adata) adata.layers['logcounts'] = adata.X diff --git a/src/batch_integration/datasets/test.py b/src/batch_integration/datasets/pancreas/test.py similarity index 96% rename from src/batch_integration/datasets/test.py rename to src/batch_integration/datasets/pancreas/test.py index cfd6295329..37950f2783 100644 --- a/src/batch_integration/datasets/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -21,7 +21,6 @@ print('>> Check that output fits expected API') adata = sc.read_h5ad(anndata_in) -# TODO: complete with API checks assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'logcounts' in adata.layers From a7737a4bd681b4e2a9d2b834b1cc2136f50002a0 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 19 Jul 2021 19:49:08 +0200 Subject: [PATCH 0130/1233] added READMEs Former-commit-id: 6dbe50b3bc01bd38f7863b1bf31f07fe78264646 --- src/batch_integration/README.md | 13 +++++++ src/batch_integration/embedding/README.md | 37 ++++++++++++++++++ .../embedding/metrics/README.md | 23 +++++++++++ src/batch_integration/graph/README.md | 38 +++++++++++++++++++ src/batch_integration/graph/metrics/README.md | 22 +++++++++++ 5 files changed, 133 insertions(+) create mode 100644 src/batch_integration/README.md create mode 100644 src/batch_integration/embedding/README.md create mode 100644 src/batch_integration/embedding/metrics/README.md create mode 100644 src/batch_integration/graph/README.md create mode 100644 src/batch_integration/graph/metrics/README.md diff --git a/src/batch_integration/README.md b/src/batch_integration/README.md new file mode 100644 index 0000000000..1693cf2231 --- /dev/null +++ b/src/batch_integration/README.md @@ -0,0 +1,13 @@ +# Batch integration + +Batch (or data) integration methods integrate datasets across batches that arise from various biological (e.g., tissue, location, individual, species) and technical (e.g., ambient RNA, lab, protocol) sources. The goal of a batch integration method is to remove unwanted batch effects in the data, while retaining biologically-meaningful variation that can help us to detect cell identities, fit cellular trajectories, or understand patterns of gene or pathway activity. + +Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have divided the batch integration task into three subtasks. These subtasks are: + +* [Batch integration graphs](graph/), +* [Batch integration embeddings](embedding/), and +* [Batch integrated feature matrices](feature/) + +These subtasks collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. Information on the task API for datasets, methods, and metrics can be found in the individual subtask pages. + +Metrics for this task either assess the removal of batch effects or assess the conservation of biological variation. This can be a helpful distinction when devising new metrics. This task, including the subtask structure, was taken from a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2), which is a useful reference for more background reading on this task and the above concepts. diff --git a/src/batch_integration/embedding/README.md b/src/batch_integration/embedding/README.md new file mode 100644 index 0000000000..47bfeb94f5 --- /dev/null +++ b/src/batch_integration/embedding/README.md @@ -0,0 +1,37 @@ +# Batch Integration with Embedding Output + +This sub-task focuses on all methods that can output integrated embeddings. +Additionally, metrics can also be applied to PCA embeddings of the feature matrix output. +Other sub-tasks for batch integration can be found for: + +* [graph](../graph/), and +* [corrected features](../feature/) + +This sub-task was taken from +a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2). + +## API + +Datasets should contain the following attributes: + +* `adata.obs['batch']` with the batch covariate, +* `adata.obs['label']` with the cell identity label, +* `adata.layers['counts']` with raw, integer UMI count data, and +* `adata.X` with log-normalized data + +Methods should assign output to: + +* `adata.obsm['X_emb']` + +Methods are run in four different scenarios that include scaling and highly variable gene selection: + +* `full_unscaled` +* `hvg_unscaled` +* `full_scaled` +* `hvg_scaled` + +Metrics can compare: + +* `adata.obsm['X_emb']` to `adata.obsm['X_pca']` +* `adata.obsm['X_emb']` to `adata.obs['label']` +* `adata.obsm['X_emb']` to `adata.obs['batch']` diff --git a/src/batch_integration/embedding/metrics/README.md b/src/batch_integration/embedding/metrics/README.md new file mode 100644 index 0000000000..f54ac388a8 --- /dev/null +++ b/src/batch_integration/embedding/metrics/README.md @@ -0,0 +1,23 @@ +# Evaluation of Batch Integration with Embedding Output + +Metrics on embedding output include: + +* Average silhouette width on batches ASW_batch +* Average silhouette width on labels ASW_label +* Cell cycle conservation +* Principle component regression PCR + +## API + +All datasets should contain the following attributes: + +* `adata.obs['batch']`: the batch covariate +* `adata.obs['label']`: the cell identity label +* `adata.obsm['X_pca']`: the PCA embedding before integration +* `adata.obsm['X_emb']`: the embedding after integration + +Metrics compare: + +* `adata.obsm['X_emb']` to `adata.obsm['X_pca']` +* `adata.obsm['X_emb']` to `adata.obs['label']` +* `adata.obsm['X_emb']` to `adata.obs['batch']` diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md new file mode 100644 index 0000000000..60ac5135bc --- /dev/null +++ b/src/batch_integration/graph/README.md @@ -0,0 +1,38 @@ +# Batch Integration with Graph Output + +The output of all batch integration tasks can be represented as a graph. This sub-task focuses on all methods that can +output integrated graphs, and includes methods that canonically output the other two data formats with subsequent +postprocessing to generate a graph. Other sub-tasks for batch integration can be found for: + +* [embeddings](../embedding/), and +* [corrected features](../feature/) + +This sub-task was taken from +a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2). + +## API + +Datasets should contain the following attributes: + +* `adata.obs['batch']` with the batch covariate, +* `adata.obs['label']` with the cell identity label, +* `adata.layers['counts']` with raw, integer UMI count data, and +* `adata.X` with log-normalized data + +Methods should assign output to: + +* `adata.obsp['connectivities']` and `adata.obsp['distances']`, or +* `adata.uns['neighbors']['connectivities']` and `adata.uns['neighbors']['distances']`, and + +Methods are run in four different scenarios that include scaling and highly variable gene selection: + +* `full_unscaled` +* `hvg_unscaled` +* `full_scaled` +* `hvg_scaled` + +Metrics can compare: + +* `adata.obsp['connectivities']` to `adata.obs['uni_connectivies']`, +* `adata.obsp['connectivities']` to `adata.obs['label']`, and/or +* `adata.obsp['connectivities']` to `adata.obs['batch']`. diff --git a/src/batch_integration/graph/metrics/README.md b/src/batch_integration/graph/metrics/README.md new file mode 100644 index 0000000000..1d57dc6520 --- /dev/null +++ b/src/batch_integration/graph/metrics/README.md @@ -0,0 +1,22 @@ +# Evaluation of Batch Integration with Graph Output + +Metrics on graph output include: + +* adjusted rand index ARI +* normalized mutual information NMI + +## API + +All datasets should contain the following attributes: + +* `adata.obs['batch']`: the batch covariate +* `adata.obs['label']`: the cell identity label +* `adata.obs['uni_connectivies']`: graph connectivities before integration +* `adata.obsp['connectivities']`: graph connectivities after integration +* `adata.obsp['distances']`: graph distances after integration + +Metrics compare: + +* `adata.obsp['connectivities']` to `adata.obs['uni_connectivies']`, +* `adata.obsp['connectivities']` to `adata.obs['label']`, and/or +* `adata.obsp['connectivities']` to `adata.obs['batch']`. From f86f067bf7a00b1c92ce6341d5b006f64cdac51f Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 19 Jul 2021 19:53:49 +0200 Subject: [PATCH 0131/1233] fixed pancreas dataset script Former-commit-id: d3a3d94d5588ecd083875b8752eeb24c6e26e895 --- .../datasets/pancreas/config.vsh.yaml | 5 ++-- .../datasets/pancreas/script.py | 28 ++++--------------- .../datasets/pancreas/test.py | 2 +- src/batch_integration/datasets/utils.py | 22 +++++++++++++++ 4 files changed, 31 insertions(+), 26 deletions(-) create mode 100644 src/batch_integration/datasets/utils.py diff --git a/src/batch_integration/datasets/pancreas/config.vsh.yaml b/src/batch_integration/datasets/pancreas/config.vsh.yaml index 528887075e..ae4741c13a 100644 --- a/src/batch_integration/datasets/pancreas/config.vsh.yaml +++ b/src/batch_integration/datasets/pancreas/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: - name: datasets - namespace: batch_integration + name: pancreas + namespace: batch_integration/datasets version: dev description: Preprocess adata object for data integration authors: @@ -39,6 +39,7 @@ functionality: resources: - type: python_script path: script.py + - path: "../utils.py" tests: - type: python_script path: test.py diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index bb376237a6..22352ade27 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -1,5 +1,6 @@ ## VIASH START import os + print(os.getcwd()) par = { 'adata': './src/batch_integration/resources/data_loader_pancreas.h5ad', @@ -9,32 +10,14 @@ 'output': 'adata_out.h5ad', 'debug': True } +resources_dir = '../' ## VIASH END print('Importing libraries') import scanpy as sc -import scprep - - -def log_scran_pooling(adata): - """Normalize data with scran via rpy2.""" - _scran = scprep.run.RFunction( - setup="library('scran')", - args="sce, min.mean=0.1", - body=""" - sce <- computeSumFactors( - sce, min.mean=min.mean, - assay.type="X" - ) - sizeFactors(sce) - """, - ) - adata.obs["size_factors"] = _scran(adata) - adata.X = scprep.utils.matrix_vector_elementwise_multiply( - adata.X, adata.obs["size_factors"], axis=0 - ) - sc.pp.log1p(adata) - +import sys +sys.path.append(resources_dir) +from utils import log_scran_pooling if par['debug']: import pprint @@ -60,7 +43,6 @@ def log_scran_pooling(adata): sc.pp.subsample(adata, n_obs=hvgs) print('Normalisation with scran') -# only if "lognorm" exists in adata.layers log_scran_pooling(adata) adata.layers['logcounts'] = adata.X diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index 37950f2783..7d3f306189 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -8,7 +8,7 @@ print('>> Running script') out = subprocess.check_output([ - './datasets', + './pancreas', '--adata', anndata_in, '--label', 'celltype', '--batch', 'tech', diff --git a/src/batch_integration/datasets/utils.py b/src/batch_integration/datasets/utils.py new file mode 100644 index 0000000000..93e0cc3f73 --- /dev/null +++ b/src/batch_integration/datasets/utils.py @@ -0,0 +1,22 @@ +import scanpy as sc +import scprep + + +def log_scran_pooling(adata): + """Normalize data with scran via rpy2.""" + _scran = scprep.run.RFunction( + setup="library('scran')", + args="sce, min.mean=0.1", + body=""" + sce <- computeSumFactors( + sce, min.mean=min.mean, + assay.type="X" + ) + sizeFactors(sce) + """, + ) + adata.obs["size_factors"] = _scran(adata) + adata.X = scprep.utils.matrix_vector_elementwise_multiply( + adata.X, adata.obs["size_factors"], axis=0 + ) + sc.pp.log1p(adata) From 838759bca7c4e219b9dca5608d077ebf5f9c348f Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 19 Jul 2021 19:54:41 +0200 Subject: [PATCH 0132/1233] moved pancreas test data Former-commit-id: 66a5daa98d86c5cc4da80cea8ed9b3f2c6ad9cd6 --- .../resources/data_loader_pancreas.h5ad | Bin 1 file changed, 0 insertions(+), 0 deletions(-) rename src/batch_integration/{ => datasets}/resources/data_loader_pancreas.h5ad (100%) diff --git a/src/batch_integration/resources/data_loader_pancreas.h5ad b/src/batch_integration/datasets/resources/data_loader_pancreas.h5ad similarity index 100% rename from src/batch_integration/resources/data_loader_pancreas.h5ad rename to src/batch_integration/datasets/resources/data_loader_pancreas.h5ad From 52a17c506b7acb5ed5367f2c5ca709013182fc4d Mon Sep 17 00:00:00 2001 From: Michaela Mueller <51025211+mumichae@users.noreply.github.com> Date: Mon, 19 Jul 2021 19:56:51 +0200 Subject: [PATCH 0133/1233] Remove old neighbors location Former-commit-id: 6331245d7b5672926fbaa45cbafb788d06f13753 --- src/batch_integration/graph/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index 60ac5135bc..840c3799e1 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -21,8 +21,7 @@ Datasets should contain the following attributes: Methods should assign output to: -* `adata.obsp['connectivities']` and `adata.obsp['distances']`, or -* `adata.uns['neighbors']['connectivities']` and `adata.uns['neighbors']['distances']`, and +* `adata.obsp['connectivities']` and `adata.obsp['distances']` Methods are run in four different scenarios that include scaling and highly variable gene selection: From fb0145533c9acd85d35fdb0cd514a1a5a92479e3 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 12:35:35 +0200 Subject: [PATCH 0134/1233] adapted data loader to accept existing log-normalized counts Former-commit-id: 85da605c05931e17b812a5464dbf3a41af575935 --- src/common/data_loader/README.md | 9 +++++++++ src/common/data_loader/anndata_loader.tsv | 10 +++++----- src/common/data_loader/config.vsh.yaml | 5 ++++- src/common/data_loader/script.py | 13 +++++++++---- src/common/data_loader/test.py | 7 ++++--- 5 files changed, 31 insertions(+), 13 deletions(-) create mode 100644 src/common/data_loader/README.md diff --git a/src/common/data_loader/README.md b/src/common/data_loader/README.md new file mode 100644 index 0000000000..7670fafd6e --- /dev/null +++ b/src/common/data_loader/README.md @@ -0,0 +1,9 @@ +# Universal Data Loader + +Download data from URL and ensure that matrices are stored as expected. + +## API +Downloaded datasets contain: + +* `adata.X`: raw counts +* `adata.layers['lognorm']`: log-normalized counts, only if available diff --git a/src/common/data_loader/anndata_loader.tsv b/src/common/data_loader/anndata_loader.tsv index bfa73d8704..60a68770b5 100644 --- a/src/common/data_loader/anndata_loader.tsv +++ b/src/common/data_loader/anndata_loader.tsv @@ -1,5 +1,5 @@ -processor name url -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 -anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 -anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 +name url lognorm_available +pancreas https://ndownloader.figshare.com/files/24539828 adata.X +immune_cells https://ndownloader.figshare.com/files/25717328 adata.X +pbmc https://ndownloader.figshare.com/files/24974582 +tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml index c12a4f11c5..ddd84774df 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: props: { github: mumichae } arguments: - name: "--output" - alternatives: ["-o"] + alternatives: [ "-o" ] type: "file" direction: "output" description: "Output h5ad file of the cleaned dataset" @@ -21,6 +21,9 @@ functionality: - name: "--name" type: "string" description: "Name of dataset" + - name: "--lognorm_available" + type: "string" + description: "Location of lognorm counts if exists, else empty" required: true resources: - type: python_script diff --git a/src/common/data_loader/script.py b/src/common/data_loader/script.py index dcd1c95848..e7de7d7635 100644 --- a/src/common/data_loader/script.py +++ b/src/common/data_loader/script.py @@ -1,8 +1,9 @@ ## VIASH START par = { - "url": "https://ndownloader.figshare.com/files/24974582", # PBMC data - "name": "pbmc", - "output": "test_data.h5ad" + "url": "https://ndownloader.figshare.com/files/24539828", # pancreas data + "name": "pancreas", + "output": "./src/common/data_loader/resources/pancreas.h5ad", + "lognorm_available": "adata.X" } ## VIASH END @@ -25,7 +26,11 @@ adata = sc.read(filepath) adata.uns["name"] = par["name"] - # Remove preprocessing + # Rearrange preprocessing + if par['lognorm_available'] == 'adata.X': + # save lognorm counts + adata.layers['logcounts'] = adata.X + if "counts" in adata.layers: adata.X = adata.layers["counts"] del adata.layers["counts"] diff --git a/src/common/data_loader/test.py b/src/common/data_loader/test.py index 7e36071407..056c63a373 100644 --- a/src/common/data_loader/test.py +++ b/src/common/data_loader/test.py @@ -10,16 +10,17 @@ "./data_loader", "--url", "https://ndownloader.figshare.com/files/24974582", "--name", name, + "--lognorm_available", "adata.X", "--output", anndata_file -]).decode("utf-8") +], stderr=subprocess.STDOUT).decode("utf-8") print(">> Checking whether file exists") assert path.exists(anndata_file) print(">> Check that output fits expected API") adata = sc.read_h5ad(anndata_file) -# TODO: complete with API checks -assert "counts" not in adata.layers assert adata.uns["name"] == name +assert "counts" not in adata.layers +assert "logcounts" in adata.layers print(">> All tests passed successfully") From 96dcd781440c1e8c34e139381b41d39973135d3b Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 12:36:48 +0200 Subject: [PATCH 0135/1233] proper subsetting of test data (preserving cell-cycle genes) Former-commit-id: c60f09d26ab28293ef146dac1b9341603d8d899f --- .../resources/data_loader_pancreas.h5ad | Bin 110520 -> 314909 bytes .../resources/g2m_genes_tirosh_hm.txt | 54 ++++++++++++++++++ .../datasets/resources/s_genes_tirosh_hm.txt | 43 ++++++++++++++ .../datasets/resources/subset_data.py | 32 +++++++++++ 4 files changed, 129 insertions(+) create mode 100644 src/batch_integration/datasets/resources/g2m_genes_tirosh_hm.txt create mode 100644 src/batch_integration/datasets/resources/s_genes_tirosh_hm.txt create mode 100644 src/batch_integration/datasets/resources/subset_data.py diff --git a/src/batch_integration/datasets/resources/data_loader_pancreas.h5ad b/src/batch_integration/datasets/resources/data_loader_pancreas.h5ad index 144a187d715970c669bb1dbbb035ce0ce3140ef8..80505ec1d887720a6ccac2a9be17addae88cccfb 100644 GIT binary patch literal 314909 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V^BL{ZN5L>nALO>H8ir(e007sTRuBLH literal 0 HcmV?d00001 From bbd66311fdc6f59ae495a4dc0415d9adf89d90fb Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 22:07:48 +0200 Subject: [PATCH 0138/1233] include name as mandatory field Former-commit-id: bbe87842831cfbb1a86b283de132b60dcbcf818a --- src/batch_integration/datasets/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index 33734f455a..a4fbbc84cb 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -6,6 +6,7 @@ Viash component for preparing data **before** running data integration methods. This script will write an adata object that contains: +* `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: batch covariate * `adata.obs['label']`: cell identity label * `adata.layers['counts']`: raw, integer UMI count data From 387636e0fef068e90e6b84034f70429636a9ee8c Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 22:08:27 +0200 Subject: [PATCH 0139/1233] updated namespace Former-commit-id: 45b270dbb5a1bee06bbb5ff237ad204e2671f2a5 --- .../embedding/metrics/asw_batch/config.vsh.yaml | 2 +- src/batch_integration/graph/metrics/ari/config.vsh.yaml | 2 +- src/batch_integration/graph/metrics/nmi/config.vsh.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index b2503be2e6..df8d8642be 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: asw_batch - namespace: feature + namespace: batch_integration version: dev description: Average silhouette of batches per label authors: diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index b5c8f2f418..79b0561c6e 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: ari - namespace: feature + namespace: batch_integration version: dev description: Adjusted rand index (ARI) authors: diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 158668d019..c988dc1af8 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: nmi - namespace: feature + namespace: batch_integration version: dev description: Normalized mutual information (NMI) authors: From 9830586f120d7440c0044a65e7e158c5e8ba6a47 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 22:22:34 +0200 Subject: [PATCH 0140/1233] added asw_label Former-commit-id: 991dc274080eebdd45bf5922d2a2f64f9a39ced0 --- .../metrics/asw_batch/config.vsh.yaml | 2 +- .../metrics/asw_label/config.vsh.yaml | 37 +++++++++++++++++++ .../embedding/metrics/asw_label/script.py | 34 +++++++++++++++++ .../embedding/metrics/asw_label/test.py | 30 +++++++++++++++ .../graph/metrics/ari/config.vsh.yaml | 2 +- .../graph/metrics/nmi/config.vsh.yaml | 2 +- 6 files changed, 104 insertions(+), 3 deletions(-) create mode 100644 src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml create mode 100644 src/batch_integration/embedding/metrics/asw_label/script.py create mode 100644 src/batch_integration/embedding/metrics/asw_label/test.py diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index df8d8642be..5cc2e597f4 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: asw_batch - namespace: batch_integration + namespace: batch_integration/graph/metrics version: dev description: Average silhouette of batches per label authors: diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml new file mode 100644 index 0000000000..fa95ddb307 --- /dev/null +++ b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml @@ -0,0 +1,37 @@ +functionality: + name: asw_label + namespace: batch_integration/embedding/metrics + version: dev + description: Average silhouette of batches per label + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file before integration + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/pancreas_mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/embedding/metrics/asw_label/script.py new file mode 100644 index 0000000000..4e77344df6 --- /dev/null +++ b/src/batch_integration/embedding/metrics/asw_label/script.py @@ -0,0 +1,34 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/embedding/resources/asw_batch_pancreas_mnn.tsv', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.metrics import silhouette + +if par['debug']: + pprint.pprint(par) + +OUTPUT_TYPE = 'embedding' +METRIC = 'asw_label' + +adata_file = par['adata'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +name = adata.uns['name'] + +print('compute score') +score = silhouette(adata, group_key='label', embed='X_emb') + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py new file mode 100644 index 0000000000..4fc1ee63b5 --- /dev/null +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -0,0 +1,30 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'asw_label' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'pancreas_mnn.h5ad', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) + +print(">> Check that score makes sense") +result = pd.read_table(metric_file) +assert result.shape == (1, 4) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.6171182170510292 + +print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 79b0561c6e..939c4dd296 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: ari - namespace: batch_integration + namespace: batch_integration/embedding/metrics version: dev description: Adjusted rand index (ARI) authors: diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index c988dc1af8..6f61f74051 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: nmi - namespace: batch_integration + namespace: batch_integration/graph/metrics version: dev description: Normalized mutual information (NMI) authors: From 885dce1f2c6b6dcac9c58b91da2b88e1c30ac4b6 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 22:58:04 +0200 Subject: [PATCH 0141/1233] added cell cycle score Former-commit-id: 420a8bd2f923929027aee6ee541c9cd8ce5f2f6c --- src/batch_integration/embedding/README.md | 1 + .../embedding/metrics/README.md | 1 + .../metrics/asw_batch/config.vsh.yaml | 2 +- .../metrics/asw_label/config.vsh.yaml | 4 +- .../embedding/metrics/asw_label/script.py | 2 +- .../cell_cycle_conservation/config.vsh.yaml | 41 ++++++++++++++++++ .../metrics/cell_cycle_conservation/script.py | 43 +++++++++++++++++++ .../metrics/cell_cycle_conservation/test.py | 31 +++++++++++++ src/batch_integration/graph/README.md | 1 + src/batch_integration/graph/metrics/README.md | 1 + .../graph/metrics/ari/config.vsh.yaml | 2 +- .../graph/metrics/nmi/config.vsh.yaml | 2 +- 12 files changed, 125 insertions(+), 6 deletions(-) create mode 100644 src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml create mode 100644 src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py create mode 100644 src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py diff --git a/src/batch_integration/embedding/README.md b/src/batch_integration/embedding/README.md index 47bfeb94f5..90a25de046 100644 --- a/src/batch_integration/embedding/README.md +++ b/src/batch_integration/embedding/README.md @@ -14,6 +14,7 @@ a [benchmarking study of data integration methods](https://www.biorxiv.org/conte Datasets should contain the following attributes: +* `adata.uns['name']`: name of the dataset * `adata.obs['batch']` with the batch covariate, * `adata.obs['label']` with the cell identity label, * `adata.layers['counts']` with raw, integer UMI count data, and diff --git a/src/batch_integration/embedding/metrics/README.md b/src/batch_integration/embedding/metrics/README.md index f54ac388a8..5fc16ca7b2 100644 --- a/src/batch_integration/embedding/metrics/README.md +++ b/src/batch_integration/embedding/metrics/README.md @@ -11,6 +11,7 @@ Metrics on embedding output include: All datasets should contain the following attributes: +* `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: the batch covariate * `adata.obs['label']`: the cell identity label * `adata.obsm['X_pca']`: the PCA embedding before integration diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index 5cc2e597f4..91fd23a4dc 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: required: true - name: --adata type: file - description: Anndata HDF5 file before integration + description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] required: true - name: --debug type: boolean diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml index fa95ddb307..7b8df766f8 100644 --- a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: asw_label namespace: batch_integration/embedding/metrics version: dev - description: Average silhouette of batches per label + description: Average silhouette of labels authors: - name: Michaela Mueller roles: [ maintainer, author ] @@ -16,7 +16,7 @@ functionality: required: true - name: --adata type: file - description: Anndata HDF5 file before integration + description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] required: true - name: --debug type: boolean diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/embedding/metrics/asw_label/script.py index 4e77344df6..2c878a7c6c 100644 --- a/src/batch_integration/embedding/metrics/asw_label/script.py +++ b/src/batch_integration/embedding/metrics/asw_label/script.py @@ -1,7 +1,7 @@ ## VIASH START par = { 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/asw_batch_pancreas_mnn.tsv', + 'output': './src/batch_integration/embedding/resources/asw_label_pancreas_mnn.tsv', 'debug': True } ## VIASH END diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml new file mode 100644 index 0000000000..bd11ba8461 --- /dev/null +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml @@ -0,0 +1,41 @@ +functionality: + name: cell_cycle_conservation + namespace: batch_integration/embedding/metrics + version: dev + description: Cell cycle conservation score based on cell cycle gene scoring + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] + required: true + - name: --organism + type: string + description: Name of organism to compute cell cycle scores on + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/pancreas_mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py new file mode 100644 index 0000000000..498e24863b --- /dev/null +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py @@ -0,0 +1,43 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', + 'organism': 'human', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.metrics import cell_cycle + +if par['debug']: + pprint.pprint(par) + +OUTPUT_TYPE = 'embedding' +METRIC = 'cell_cycle_conservation' + +adata_file = par['adata'] +organism = par['organism'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +adata_int = adata.copy() +name = adata.uns['name'] + +print('compute score') +score = cell_cycle( + adata, + adata_int, + batch_key='batch', + embed='X_emb', + organism=organism +) + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py new file mode 100644 index 0000000000..7962d6fb13 --- /dev/null +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -0,0 +1,31 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'cell_cycle_conservation' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'pancreas_mnn.h5ad', + "--organism", "human", + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) + +print(">> Check that score makes sense") +result = pd.read_table(metric_file) +assert result.shape == (1, 4) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert 0.9380807 <= score <= 0.938081 + +print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index 840c3799e1..379735d439 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -14,6 +14,7 @@ a [benchmarking study of data integration methods](https://www.biorxiv.org/conte Datasets should contain the following attributes: +* `adata.uns['name']`: name of the dataset * `adata.obs['batch']` with the batch covariate, * `adata.obs['label']` with the cell identity label, * `adata.layers['counts']` with raw, integer UMI count data, and diff --git a/src/batch_integration/graph/metrics/README.md b/src/batch_integration/graph/metrics/README.md index 1d57dc6520..1701dd23da 100644 --- a/src/batch_integration/graph/metrics/README.md +++ b/src/batch_integration/graph/metrics/README.md @@ -9,6 +9,7 @@ Metrics on graph output include: All datasets should contain the following attributes: +* `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: the batch covariate * `adata.obs['label']`: the cell identity label * `adata.obs['uni_connectivies']`: graph connectivities before integration diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 939c4dd296..537709e71b 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: required: true - name: --adata type: file - description: Anndata HDF5 file + description: Anndata HDF5 file with graph in adata.obsp['connectivities'] required: true - name: --debug type: boolean diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 6f61f74051..e9cabc8313 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: required: true - name: --adata type: file - description: Anndata HDF5 file + description: Anndata HDF5 file with graph in adata.obsp['connectivities'] required: true - name: --debug type: boolean From 1a99227c20369f7f8ce1f112890b7063ce7ae2dd Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 23:30:49 +0200 Subject: [PATCH 0142/1233] added PCR Former-commit-id: 245778883f6f91a409757bcf448f1333118a9b69 --- .../embedding/metrics/pcr/config.vsh.yaml | 37 +++++++++++++++++ .../embedding/metrics/pcr/script.py | 41 +++++++++++++++++++ .../embedding/metrics/pcr/test.py | 30 ++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 src/batch_integration/embedding/metrics/pcr/config.vsh.yaml create mode 100644 src/batch_integration/embedding/metrics/pcr/script.py create mode 100644 src/batch_integration/embedding/metrics/pcr/test.py diff --git a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml new file mode 100644 index 0000000000..60265425e8 --- /dev/null +++ b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml @@ -0,0 +1,37 @@ +functionality: + name: pcr + namespace: batch_integration/embedding/metrics + version: dev + description: PCA regression + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + - name: --adata + type: file + description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../resources/pancreas_mnn.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + - type: native + - type: nextflow diff --git a/src/batch_integration/embedding/metrics/pcr/script.py b/src/batch_integration/embedding/metrics/pcr/script.py new file mode 100644 index 0000000000..5d2e0da2c7 --- /dev/null +++ b/src/batch_integration/embedding/metrics/pcr/script.py @@ -0,0 +1,41 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.metrics import pcr_comparison + +if par['debug']: + pprint.pprint(par) + +OUTPUT_TYPE = 'embedding' +METRIC = 'pcr' + +adata_file = par['adata'] +output = par['output'] + +print('Read adata') +adata = sc.read(adata_file) +adata_int = adata.copy() +name = adata.uns['name'] + +print('compute score') +score = pcr_comparison( + adata, + adata_int, + embed='X_emb', + covariate='batch', + verbose=False +) + +with open(output, 'w') as file: + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] + file.write('\t'.join(header) + '\n') + file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/embedding/metrics/pcr/test.py b/src/batch_integration/embedding/metrics/pcr/test.py new file mode 100644 index 0000000000..d900fae98c --- /dev/null +++ b/src/batch_integration/embedding/metrics/pcr/test.py @@ -0,0 +1,30 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'pcr' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'pancreas_mnn.h5ad', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) + +print(">> Check that score makes sense") +result = pd.read_table(metric_file) +assert result.shape == (1, 4) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.0356482252608894 + +print(">> All tests passed successfully") From b280138b5e7e368947f2f5e28a268f36c972619f Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 2 Aug 2021 14:04:13 +0200 Subject: [PATCH 0143/1233] fixed namespace for ARI Former-commit-id: fa1545f906d17cd7f8aecb04954abebfede8afaa --- src/batch_integration/graph/metrics/ari/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 537709e71b..328ea8344e 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: ari - namespace: batch_integration/embedding/metrics + namespace: batch_integration/graph/metrics version: dev description: Adjusted rand index (ARI) authors: From 964ff1b158c793318efc6b4cb9c962adb846a643 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 2 Aug 2021 14:24:50 +0200 Subject: [PATCH 0144/1233] added BBKNN Former-commit-id: 91eeb228a70441d3b9b8210bed10173ab72c2cc1 --- .../graph/methods/bbknn/config.vsh.yaml | 53 +++++++++++++++++++ .../graph/methods/bbknn/script.py | 43 +++++++++++++++ .../graph/methods/bbknn/test.py | 32 +++++++++++ .../graph/methods/bbknn/test_scaled_hvg.py | 34 ++++++++++++ 4 files changed, 162 insertions(+) create mode 100644 src/batch_integration/graph/methods/bbknn/config.vsh.yaml create mode 100644 src/batch_integration/graph/methods/bbknn/script.py create mode 100644 src/batch_integration/graph/methods/bbknn/test.py create mode 100644 src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml new file mode 100644 index 0000000000..7c979f4f2e --- /dev/null +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -0,0 +1,53 @@ +functionality: + name: bbknn + namespace: batch_integration/graph/methods + version: dev + description: Run BBKNN on adata object + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --adata + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: integer + description: | + Number of highly variable genes to select by. + If 0, no HVG selection will be performed. + required: true + - name: --scaling + type: boolean + description: Whether to scale the data or not + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - type: python_script + path: test_scaled_hvg.py + - path: '../../../resources/datasets_pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:0.1 + setup: + - type: python + packages: + - bbknn + - type: native + - type: nextflow diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py new file mode 100644 index 0000000000..627a291b39 --- /dev/null +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -0,0 +1,43 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': 100, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +import pprint +import scanpy as sc +from scIB.integration import runBBKNN +from scIB.preprocessing import hvg_batch +from scIB.preprocessing import scale_batch + +if par['debug']: + pprint.pprint(par) + +adata_file = par['adata'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read(adata_file) + +print('Prepare data') +if hvg > 0: + # TODO: check that hvg value makes sense on dataset + adata = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=True) + +if scaling: + adata = scale_batch(adata, batch='batch') + +print('Integrate') +adata = runBBKNN(adata, batch='batch') + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling +adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py new file mode 100644 index 0000000000..114341059f --- /dev/null +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -0,0 +1,32 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'bbknn' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", '0', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == 0 +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py new file mode 100644 index 0000000000..27aaa6af7a --- /dev/null +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -0,0 +1,34 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'bbknn' +output_file = method + '_scaled_hvg.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", '100', + "--scaling", 'True', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == 100 +assert 'scaled' in adata.uns +print(isinstance(adata.uns['scaled'], bool)) +print(type(adata.uns['scaled']).__name__()) +assert adata.uns['scaled'] == True + +print(">> All tests passed successfully") From ba9f0f972295176de6f7d5cf32f2d7ee937b9db4 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 2 Aug 2021 14:44:47 +0200 Subject: [PATCH 0145/1233] fixed HVG Former-commit-id: 536708d2a960deeadeaedfbe53488512968735f6 --- src/batch_integration/graph/methods/bbknn/script.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 627a291b39..f8245d30ec 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -26,12 +26,14 @@ print('Read adata') adata = sc.read(adata_file) -print('Prepare data') if hvg > 0: + print('Select HVGs') # TODO: check that hvg value makes sense on dataset - adata = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=True) + hvgs_list = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=False) + adata = adata[:, hvgs_list].copy() if scaling: + print('Scale') adata = scale_batch(adata, batch='batch') print('Integrate') From be3a58b79680371cb3c0a507140db426ebc7f4b7 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 2 Aug 2021 14:49:04 +0200 Subject: [PATCH 0146/1233] API for methods added Former-commit-id: 8bac7ad2d331319865e67bcb701492339ae47f59 --- src/batch_integration/graph/methods/README.md | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 src/batch_integration/graph/methods/README.md diff --git a/src/batch_integration/graph/methods/README.md b/src/batch_integration/graph/methods/README.md new file mode 100644 index 0000000000..cea477ff1e --- /dev/null +++ b/src/batch_integration/graph/methods/README.md @@ -0,0 +1,23 @@ +# Run Graph Integration Methods + +Viash component for running integration methods. + +## API + +### Input data formats + +The components before integration must contain: + +* `adata.uns['name']`: name of the dataset +* `adata.obs['batch']`: batch covariate +* `adata.X`: log-normalized expression + +Whether a dataset is scaled or selected for highly-variable genes before integration is passed by parameters to the +script. + +### Output data formats + +* `adata.obsp['connectivities']`: Integrated graph connectivities +* `adata.obsp['distances']`: Integrated graph distances +* `adata.uns['hvg']`: Number of highly variable genes selected before integration (0 meaning that no HVG selection was performed) +* `adata.uns['scaled']`: Boolean entry whether scaling was performed before integration From 30bdb98887d42d954b4312a5eb1a901a9e6fdb2c Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 20 Aug 2021 10:23:56 +0200 Subject: [PATCH 0147/1233] updated images Former-commit-id: b9cfff09ffc09d6853c476e1f11b3ef4a2c6cda0 --- src/common/base_images/scanpy-r-micromamba/Dockerfile | 2 +- src/common/base_images/scanpy-r-micromamba/env.yaml | 2 ++ src/common/base_images/scib-base/Dockerfile | 3 ++- src/common/base_images/scib-base/env.yaml | 2 -- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/common/base_images/scanpy-r-micromamba/Dockerfile b/src/common/base_images/scanpy-r-micromamba/Dockerfile index f5429f256c..ad4f117162 100644 --- a/src/common/base_images/scanpy-r-micromamba/Dockerfile +++ b/src/common/base_images/scanpy-r-micromamba/Dockerfile @@ -1,6 +1,6 @@ +# version 0.1.2 FROM mambaorg/micromamba:0.14.0 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml && \ micromamba clean --all --yes -RUN pip install anndata2ri==1.0.6 WORKDIR /home/micromamba diff --git a/src/common/base_images/scanpy-r-micromamba/env.yaml b/src/common/base_images/scanpy-r-micromamba/env.yaml index d266b2a582..9b8ac434b2 100644 --- a/src/common/base_images/scanpy-r-micromamba/env.yaml +++ b/src/common/base_images/scanpy-r-micromamba/env.yaml @@ -9,3 +9,5 @@ dependencies: - r-base=4 - anndata=0.7.6 - git + - pip: + - anndata2ri==1.0.6 diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile index 418a418234..12f43c8a5f 100644 --- a/src/common/base_images/scib-base/Dockerfile +++ b/src/common/base_images/scib-base/Dockerfile @@ -1,4 +1,5 @@ -FROM scanpy-r-micromamba:latest +# version 0.1.2 +FROM mumichae/scanpy-r-micromamba:0.1.2 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml RUN git clone https://github.com/theislab/scib.git diff --git a/src/common/base_images/scib-base/env.yaml b/src/common/base_images/scib-base/env.yaml index acb74d2642..d266b2a582 100644 --- a/src/common/base_images/scib-base/env.yaml +++ b/src/common/base_images/scib-base/env.yaml @@ -9,5 +9,3 @@ dependencies: - r-base=4 - anndata=0.7.6 - git - - pip: - - anndata2ri=1.0.6 From 4a66a1fdbdbf5a9e25d31e09b83d583aa4405bc6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 21 Oct 2021 10:58:56 +0200 Subject: [PATCH 0148/1233] simplify ci Former-commit-id: d49720560b67298097496bd2023fe200158f60cf --- .github/workflows/viash-test.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f00da08fb1..50c56c05e8 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -1,10 +1,6 @@ name: viash test CI -on: - push: - branches: [ '*' ] - pull_request: - branches: [ '*' ] +on: [ push, pull_request ] jobs: viash-test: From 689ee86dce143915711e6b70410343a8ad784ec0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 21 Oct 2021 10:59:42 +0200 Subject: [PATCH 0149/1233] rework rootdir Former-commit-id: db94bef10f3efd53054e7b66f82099c358855749 --- src/modality_alignment/workflows/main.nf | 3 +-- src/modality_alignment/workflows/nextflow.config | 9 ++++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/main.nf index d1a5911d55..d0d843d79c 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/main.nf @@ -5,8 +5,7 @@ nextflow.enable.dsl=2 * (it's a nextflow limitation I'm trying to figure out * how to resolve.) */ -rootDir = "$projectDir/../../.." -targetDir = "$rootDir/target/nextflow" +targetDir = "${params.rootDir}/target/nextflow" // import dataset loaders include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config index defdc73055..4b7b0e269d 100644 --- a/src/modality_alignment/workflows/nextflow.config +++ b/src/modality_alignment/workflows/nextflow.config @@ -2,8 +2,11 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } -rootDir = "$projectDir/../../.." -targetDir = "$rootDir/target/nextflow" +// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT +params{ + rootDir = "$projectDir/../../.." +} +targetDir = "${params.rootDir}/target/nextflow" // custom includes includeConfig "$targetDir/modality_alignment/datasets/scprep_csv/nextflow.config" @@ -18,7 +21,7 @@ includeConfig "$targetDir/utils/extract_scores/nextflow.config" // other configs docker { - runOptions = "-v $rootDir:$rootDir" + runOptions = "-v \$(realpath --no-symlinks ${params.rootDir}):\$(realpath --no-symlinks ${params.rootDir})" } process { From b1cceccfcbb7ec84fca5342630afcf436b718163 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 26 Oct 2021 14:07:29 +0200 Subject: [PATCH 0150/1233] using scib version 1.0.0 from pip Former-commit-id: 71e368cf6982a0e67f063613ea7247f133773875 --- src/common/base_images/scib-base/Dockerfile | 5 +---- src/common/base_images/scib-base/env.yaml | 2 ++ 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile index 12f43c8a5f..e21cedb076 100644 --- a/src/common/base_images/scib-base/Dockerfile +++ b/src/common/base_images/scib-base/Dockerfile @@ -1,8 +1,5 @@ -# version 0.1.2 +# version 1.0.0 FROM mumichae/scanpy-r-micromamba:0.1.2 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml -RUN git clone https://github.com/theislab/scib.git -RUN cd scib && \ - pip install . RUN micromamba clean --all --yes diff --git a/src/common/base_images/scib-base/env.yaml b/src/common/base_images/scib-base/env.yaml index d266b2a582..a6f706feff 100644 --- a/src/common/base_images/scib-base/env.yaml +++ b/src/common/base_images/scib-base/env.yaml @@ -9,3 +9,5 @@ dependencies: - r-base=4 - anndata=0.7.6 - git + - pip: + - scib==1.0.0 From e1a86da21577f3f5938eea48db90bec8a3ab08d9 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 16:25:20 +0100 Subject: [PATCH 0151/1233] add scaling and HVG Former-commit-id: 1b56490d7e1004367189e1a1d53e5f26c0593f69 --- src/batch_integration/datasets/README.md | 14 +++--- .../datasets/pancreas/config.vsh.yaml | 6 +-- .../datasets/pancreas/run_example.sh | 12 +++++ .../datasets/pancreas/script.py | 44 +++++++++---------- src/batch_integration/datasets/utils.py | 23 ++++++++++ src/batch_integration/graph/README.md | 37 ++++++++++++---- .../graph/methods/bbknn/config.vsh.yaml | 10 ++--- .../graph/methods/bbknn/run_example.sh | 14 ++++++ .../graph/methods/bbknn/script.py | 26 ++++++----- .../graph/methods/params.tsv | 10 +++++ 10 files changed, 132 insertions(+), 64 deletions(-) create mode 100644 src/batch_integration/datasets/pancreas/run_example.sh create mode 100644 src/batch_integration/graph/methods/bbknn/run_example.sh create mode 100644 src/batch_integration/graph/methods/params.tsv diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index a4fbbc84cb..e6c36f15f8 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -4,17 +4,13 @@ Viash component for preparing data **before** running data integration methods. ## API -This script will write an adata object that contains: +This module creates Anndata objects that contain: * `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: batch covariate * `adata.obs['label']`: cell identity label +* `adata.vars['hvg']`: label whether a gene is identified as highly variable * `adata.layers['counts']`: raw, integer UMI count data -* `adata.X`: log-normalized data - -And transformations of the data: - -* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts -* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` +* `adata.layers['logcounts']`: log-normalized count data +* `adata.layers['logcounts_scaled']`: scaled log-normalized count data +* `adata.X`: same as in `adata.layers['logcounts']` diff --git a/src/batch_integration/datasets/pancreas/config.vsh.yaml b/src/batch_integration/datasets/pancreas/config.vsh.yaml index ae4741c13a..757be32f6f 100644 --- a/src/batch_integration/datasets/pancreas/config.vsh.yaml +++ b/src/batch_integration/datasets/pancreas/config.vsh.yaml @@ -46,15 +46,11 @@ functionality: - path: '../resources/data_loader_pancreas.h5ad' platforms: - type: docker - image: mumichae/scanpy-r-micromamba:0.1.1 + image: mumichae/scib-base:1.0.0 setup: - type: docker run: - - ls -la - micromamba install -y -c conda-forge -c bioconda scprep bioconductor-scran -# - micromamba install -y -n base -f /root/env.yaml - micromamba clean --all --yes -# resources: -# - envs/py_r.yaml /root/env.yaml - type: native - type: nextflow diff --git a/src/batch_integration/datasets/pancreas/run_example.sh b/src/batch_integration/datasets/pancreas/run_example.sh new file mode 100644 index 0000000000..1c8734a83c --- /dev/null +++ b/src/batch_integration/datasets/pancreas/run_example.sh @@ -0,0 +1,12 @@ +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata ${SCRIPTPATH}/../resources/data_loader_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvgs 100 \ + --output ${SCRIPTPATH}/../resources/datasets_pancreas.h5ad \ + --debug diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index 48c1df190a..95eb7857b7 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -15,14 +15,13 @@ print('Importing libraries') import scanpy as sc -# import sys -# sys.path.append(resources_dir) -# from utils import log_scran_pooling +from pprint import pprint +import sys +sys.path.append(resources_dir) +from utils import scale_batch, hvg_batch if par['debug']: - import pprint - - pprint.pprint(par) + pprint(par) adata_file = par['adata'] label = par['label'] @@ -38,23 +37,22 @@ adata.layers['counts'] = adata.X print(f'Select {hvgs} highly variable genes') -if adata.n_obs > hvgs: - sc.pp.subsample(adata, n_obs=hvgs) - -#print('Normalisation with scran') -#log_scran_pooling(adata) -#adata.layers['logcounts'] = adata.X - -print('Transformation: PCA') -sc.tl.pca( - adata, - svd_solver='arpack', - return_info=True, -) -adata.obsm['X_uni'] = adata.obsm['X_pca'] - -print('Transformation: kNN') -sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') +hvg_list = hvg_batch(adata, 'batch', n_hvg=hvgs) +adata.var['hvg'] = adata.var_names.isin(hvg_list) + +print('Scaling') +adata.layers['logcounts_scaled'] = scale_batch(adata, 'batch').X + +# print('Transformation: PCA') +# sc.tl.pca( +# adata, +# svd_solver='arpack', +# return_info=True, +# ) +# adata.obsm['X_uni'] = adata.obsm['X_pca'] +# +# print('Transformation: kNN') +# sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') print('Writing adata to file') adata.write(output, compression='gzip') diff --git a/src/batch_integration/datasets/utils.py b/src/batch_integration/datasets/utils.py index 93e0cc3f73..f0891790d6 100644 --- a/src/batch_integration/datasets/utils.py +++ b/src/batch_integration/datasets/utils.py @@ -1,5 +1,6 @@ import scanpy as sc import scprep +import scib def log_scran_pooling(adata): @@ -20,3 +21,25 @@ def log_scran_pooling(adata): adata.X, adata.obs["size_factors"], axis=0 ) sc.pp.log1p(adata) + + +def scale_batch(adata, batch_key): + """ + Scale count matrix by batch + """ + return scib.pp.scale_batch(adata, batch=batch_key) + + +# TODO: HVG by batch +def hvg_batch(adata, batch_key, n_hvg): + """ + Compute highly variable genes by batch + """ + if n_hvg > adata.n_vars: + return adata.var_names.tolist() + return scib.pp.hvg_batch( + adata, + batch_key=batch_key, + target_genes=n_hvg, + adataOut=False + ) diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index 379735d439..feb6951d97 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -12,24 +12,43 @@ a [benchmarking study of data integration methods](https://www.biorxiv.org/conte ## API +### Input + Datasets should contain the following attributes: * `adata.uns['name']`: name of the dataset * `adata.obs['batch']` with the batch covariate, * `adata.obs['label']` with the cell identity label, -* `adata.layers['counts']` with raw, integer UMI count data, and -* `adata.X` with log-normalized data +* `adata.layers['counts']` with raw, integer UMI count data +* `adata.layers['logcounts']`: log-normalized count data +* `adata.layers['logcounts_scaled']`: scaled log-normalized count data -Methods should assign output to: +The default count matrix in `adata.X` is assumed to contain the log normalised counts from `adata.layers['logcounts']`. -* `adata.obsp['connectivities']` and `adata.obsp['distances']` +### Output + +For each integration method, the count matrix can be used as-is, feature selected for highly variable genes (HVGs) +and/or scaled between 0 and 1. As a result, there are four different preprocessing scenarios per dataset and method that +include scaling and HVG selection: + +* `full_unscaled`: no HVG selection or scaling +* `hvg_unscaled`: HVG selected +* `full_scaled`: scaled +* `hvg_scaled`: HVG selected and scaled -Methods are run in four different scenarios that include scaling and highly variable gene selection: +The user should be able to specify which of the four scenarios to run the method with. -* `full_unscaled` -* `hvg_unscaled` -* `full_scaled` -* `hvg_scaled` +In order to be able to compare the integrated with the unintegrated data, embeddings of the unintegrated data should be +stored prior to integration: + +* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` + +Methods should assign integration output to: + +* `adata.obsp['connectivities']` and `adata.obsp['distances']` Metrics can compare: diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index 7c979f4f2e..67717e6d83 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -18,11 +18,9 @@ functionality: type: file description: Unintegrated anndata HDF5 file required: true - - name: --hvg - type: integer - description: | - Number of highly variable genes to select by. - If 0, no HVG selection will be performed. + - name: --hvgs + type: boolean + description: Whether to subset to highly variable genes required: true - name: --scaling type: boolean @@ -44,7 +42,7 @@ functionality: - path: '../../../resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:0.1 + image: mumichae/scib-base:1.0.0 setup: - type: python packages: diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh new file mode 100644 index 0000000000..90eb28421c --- /dev/null +++ b/src/batch_integration/graph/methods/bbknn/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvgs true \ + --scaling true \ + --output src/batch_integration/resources/graph_bbknn_pancreas.h5ad \ + --debug true diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index f8245d30ec..398d329e63 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -2,44 +2,46 @@ par = { 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', - 'hvg': 100, + 'hvgs': True, 'scaling': True, 'debug': True } ## VIASH END print('Importing libraries') -import pprint +from pprint import pprint import scanpy as sc -from scIB.integration import runBBKNN -from scIB.preprocessing import hvg_batch -from scIB.preprocessing import scale_batch +from scib.integration import bbknn if par['debug']: - pprint.pprint(par) + pprint(par) adata_file = par['adata'] output = par['output'] -hvg = par['hvg'] +hvg = par['hvgs'] scaling = par['scaling'] print('Read adata') adata = sc.read(adata_file) -if hvg > 0: +if hvg: print('Select HVGs') # TODO: check that hvg value makes sense on dataset - hvgs_list = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=False) - adata = adata[:, hvgs_list].copy() + #hvgs_list = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=False) + adata = adata[:, adata.var['hvg']] + if scaling: print('Scale') - adata = scale_batch(adata, batch='batch') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] print('Integrate') -adata = runBBKNN(adata, batch='batch') +adata = bbknn(adata, batch='batch') print('Save HDF5') adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling + adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/params.tsv b/src/batch_integration/graph/methods/params.tsv new file mode 100644 index 0000000000..21a3ad4e50 --- /dev/null +++ b/src/batch_integration/graph/methods/params.tsv @@ -0,0 +1,10 @@ +# HVG, scaling preprocessing setupts for integration methods +hvg scaling method +2000 True bbknn +2000 True bbknn +2000 False bbknn +2000 False bbknn +0 True bbknn +0 True bbknn +0 False bbknn +0 False bbknn From 6032f4464ab754b3b6ce1e53d797a98ea5bb7f96 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 17:48:26 +0100 Subject: [PATCH 0152/1233] add kBET installation to docker image Former-commit-id: 09012abecb69225d342a665631a38edbae6102d5 --- src/common/base_images/scib-base/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile index e21cedb076..214d9a25bc 100644 --- a/src/common/base_images/scib-base/Dockerfile +++ b/src/common/base_images/scib-base/Dockerfile @@ -2,4 +2,5 @@ FROM mumichae/scanpy-r-micromamba:0.1.2 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml +RUN Rscript -e "devtools::install_github('theislab/kBET')" RUN micromamba clean --all --yes From f9be51957cee6c7cade6ffe13d44351fdd05f300 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 18:14:25 +0100 Subject: [PATCH 0153/1233] reactivate data transformations for dataset module Former-commit-id: eefed891c20d7c92029d2b6067a91ab5fb6e59be --- src/batch_integration/datasets/README.md | 9 ++++++++- .../datasets/pancreas/script.py | 20 +++++++++---------- .../datasets/pancreas/test.py | 3 +++ 3 files changed, 21 insertions(+), 11 deletions(-) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index e6c36f15f8..584bc7181a 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -9,8 +9,15 @@ This module creates Anndata objects that contain: * `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: batch covariate * `adata.obs['label']`: cell identity label -* `adata.vars['hvg']`: label whether a gene is identified as highly variable +* `adata.var['hvg']`: label whether a gene is identified as highly variable * `adata.layers['counts']`: raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data * `adata.layers['logcounts_scaled']`: scaled log-normalized count data * `adata.X`: same as in `adata.layers['logcounts']` + +And transformations of the data: + +* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index 95eb7857b7..9f17549137 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -43,16 +43,16 @@ print('Scaling') adata.layers['logcounts_scaled'] = scale_batch(adata, 'batch').X -# print('Transformation: PCA') -# sc.tl.pca( -# adata, -# svd_solver='arpack', -# return_info=True, -# ) -# adata.obsm['X_uni'] = adata.obsm['X_pca'] -# -# print('Transformation: kNN') -# sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') +print('Transformation: PCA') +sc.tl.pca( + adata, + svd_solver='arpack', + return_info=True, +) +adata.obsm['X_uni'] = adata.obsm['X_pca'] + +print('Transformation: kNN') +sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') print('Writing adata to file') adata.write(output, compression='gzip') diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index 7d3f306189..d5a94e4be9 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -23,7 +23,10 @@ adata = sc.read_h5ad(anndata_in) assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns +assert 'hvg' in adata.var +assert 'counts' in adata.layers assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers assert 'X_pca' in adata.obsm assert 'X_uni' in adata.obsm assert 'uni' in adata.uns From 71cc4a8f56ec631057c8ce1a8b8afd1faba509cf Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 18:25:34 +0100 Subject: [PATCH 0154/1233] fix tests Former-commit-id: e2ec3b6cc26230f6bea4e083c0338a0ee2bf36d1 --- src/batch_integration/graph/methods/bbknn/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/bbknn/run_example.sh | 2 +- src/batch_integration/graph/methods/bbknn/script.py | 4 ++-- src/batch_integration/graph/methods/bbknn/test.py | 4 ++-- .../graph/methods/bbknn/test_scaled_hvg.py | 6 ++---- 5 files changed, 9 insertions(+), 11 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index 67717e6d83..055564dc85 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: type: file description: Unintegrated anndata HDF5 file required: true - - name: --hvgs + - name: --hvg type: boolean description: Whether to subset to highly variable genes required: true @@ -39,7 +39,7 @@ functionality: path: test.py - type: python_script path: test_scaled_hvg.py - - path: '../../../resources/datasets_pancreas.h5ad' + - path: '../../../datasets/resources/datasets_pancreas.h5ad' platforms: - type: docker image: mumichae/scib-base:1.0.0 diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh index 90eb28421c..b45a408729 100644 --- a/src/batch_integration/graph/methods/bbknn/run_example.sh +++ b/src/batch_integration/graph/methods/bbknn/run_example.sh @@ -8,7 +8,7 @@ bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --label celltype \ --batch tech \ - --hvgs true \ + --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_bbknn_pancreas.h5ad \ --debug true diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 398d329e63..36f774fc3e 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -2,7 +2,7 @@ par = { 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', - 'hvgs': True, + 'hvg': True, 'scaling': True, 'debug': True } @@ -18,7 +18,7 @@ adata_file = par['adata'] output = par['output'] -hvg = par['hvgs'] +hvg = par['hvg'] scaling = par['scaling'] print('Read adata') diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index 114341059f..68f78225a0 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -12,7 +12,7 @@ out = subprocess.check_output([ "./" + method, "--adata", 'datasets_pancreas.h5ad', - "--hvg", '0', + "--hvg", 'False', "--scaling", 'False', "--output", output_file ]).decode("utf-8") @@ -25,7 +25,7 @@ assert 'connectivities' in adata.obsp assert 'distances' in adata.obsp assert 'hvg' in adata.uns -assert adata.uns['hvg'] == 0 +assert adata.uns['hvg'] == False assert 'scaled' in adata.uns assert adata.uns['scaled'] == False diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 27aaa6af7a..6768c42f57 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -12,7 +12,7 @@ out = subprocess.check_output([ "./" + method, "--adata", 'datasets_pancreas.h5ad', - "--hvg", '100', + "--hvg", 'True', "--scaling", 'True', "--output", output_file ]).decode("utf-8") @@ -25,10 +25,8 @@ assert 'connectivities' in adata.obsp assert 'distances' in adata.obsp assert 'hvg' in adata.uns -assert adata.uns['hvg'] == 100 +assert adata.uns['hvg'] == True assert 'scaled' in adata.uns -print(isinstance(adata.uns['scaled'], bool)) -print(type(adata.uns['scaled']).__name__()) assert adata.uns['scaled'] == True print(">> All tests passed successfully") From 88c9030dff96b3a837f6d6ad4609e84f82e5afc6 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 19:04:32 +0100 Subject: [PATCH 0155/1233] add tests for scaling and HVG values Former-commit-id: 7a99d7e735ba6bbbfa9a2759af8f99dfb7dad265 --- src/batch_integration/datasets/README.md | 2 +- .../datasets/pancreas/run_example.sh | 6 +++--- src/batch_integration/datasets/pancreas/test.py | 8 +++++++- src/batch_integration/graph/README.md | 17 +++++++---------- .../graph/methods/bbknn/script.py | 3 --- .../graph/methods/bbknn/test_scaled_hvg.py | 3 +++ 6 files changed, 21 insertions(+), 18 deletions(-) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index 584bc7181a..0ab3dcc4c2 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -12,7 +12,7 @@ This module creates Anndata objects that contain: * `adata.var['hvg']`: label whether a gene is identified as highly variable * `adata.layers['counts']`: raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data -* `adata.layers['logcounts_scaled']`: scaled log-normalized count data +* `adata.layers['logcounts_scaled']`: log-normalized count data scaled to unit variance and zero mean * `adata.X`: same as in `adata.layers['logcounts']` And transformations of the data: diff --git a/src/batch_integration/datasets/pancreas/run_example.sh b/src/batch_integration/datasets/pancreas/run_example.sh index 1c8734a83c..1976744536 100644 --- a/src/batch_integration/datasets/pancreas/run_example.sh +++ b/src/batch_integration/datasets/pancreas/run_example.sh @@ -4,9 +4,9 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata ${SCRIPTPATH}/../resources/data_loader_pancreas.h5ad \ + --adata src/batch_integration/datasets/resources/data_loader_pancreas.h5ad \ --label celltype \ --batch tech \ --hvgs 100 \ - --output ${SCRIPTPATH}/../resources/datasets_pancreas.h5ad \ - --debug + --output src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --debug true diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index d5a94e4be9..b10d5408bc 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -1,6 +1,7 @@ from os import path import subprocess import scanpy as sc +import numpy as np name = 'pancreas' anndata_in = 'data_loader_pancreas.h5ad' @@ -12,7 +13,7 @@ '--adata', anndata_in, '--label', 'celltype', '--batch', 'tech', - '--hvgs', '2000', + '--hvgs', '100', '--output', anndata_out ]).decode('utf-8') @@ -33,4 +34,9 @@ assert 'uni_distances' in adata.obsp assert 'uni_connectivities' in adata.obsp +assert adata.var['hvg'].dtype == 'bool' +assert adata.var['hvg'].sum() == 100 +assert -0.0000001 <= np.mean(adata.layers['logcounts_scaled']) <= 0.0000001 +assert 0.8 <= np.var(adata.layers['logcounts_scaled']) <= 1 + print('>> All tests passed successfully') diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index feb6951d97..aacf69dbaf 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -22,14 +22,19 @@ Datasets should contain the following attributes: * `adata.layers['counts']` with raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data * `adata.layers['logcounts_scaled']`: scaled log-normalized count data +* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` The default count matrix in `adata.X` is assumed to contain the log normalised counts from `adata.layers['logcounts']`. ### Output For each integration method, the count matrix can be used as-is, feature selected for highly variable genes (HVGs) -and/or scaled between 0 and 1. As a result, there are four different preprocessing scenarios per dataset and method that -include scaling and HVG selection: +and/or scaled to unit variance and zero mean. +As a result, there are four different preprocessing scenarios per dataset +and method that include scaling and HVG selection: * `full_unscaled`: no HVG selection or scaling * `hvg_unscaled`: HVG selected @@ -38,14 +43,6 @@ include scaling and HVG selection: The user should be able to specify which of the four scenarios to run the method with. -In order to be able to compare the integrated with the unintegrated data, embeddings of the unintegrated data should be -stored prior to integration: - -* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts -* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` - Methods should assign integration output to: * `adata.obsp['connectivities']` and `adata.obsp['distances']` diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 36f774fc3e..6c10f0a488 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -26,11 +26,8 @@ if hvg: print('Select HVGs') - # TODO: check that hvg value makes sense on dataset - #hvgs_list = hvg_batch(adata, batch_key='batch', target_genes=hvg, adataOut=False) adata = adata[:, adata.var['hvg']] - if scaling: print('Scale') adata.X = adata.layers['logcounts_scaled'] diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 6768c42f57..4d7992886d 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -26,7 +26,10 @@ assert 'distances' in adata.obsp assert 'hvg' in adata.uns assert adata.uns['hvg'] == True +assert adata.n_vars == 100 assert 'scaled' in adata.uns assert adata.uns['scaled'] == True +assert -0.0000001 <= np.mean(adata.X) <= 0.0000001 +assert 0.8 <= np.var(adata.X) <= 1 print(">> All tests passed successfully") From 897c61bcbe5793fe5d786c9b166629ddb8243e3a Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 19:27:45 +0100 Subject: [PATCH 0156/1233] check all dataset keys in bbknn run Former-commit-id: 0f887ef41d9a67fb72bc0df6ec154eb3abafde80 --- src/batch_integration/datasets/pancreas/test.py | 1 + .../graph/methods/bbknn/run_example.sh | 2 +- src/batch_integration/graph/methods/bbknn/test.py | 14 ++++++++++++++ .../graph/methods/bbknn/test_scaled_hvg.py | 14 ++++++++++++++ 4 files changed, 30 insertions(+), 1 deletion(-) diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index b10d5408bc..8c44c7d41c 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -22,6 +22,7 @@ print('>> Check that output fits expected API') adata = sc.read_h5ad(anndata_in) +assert 'name' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'hvg' in adata.var diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh index b45a408729..45d2126cdc 100644 --- a/src/batch_integration/graph/methods/bbknn/run_example.sh +++ b/src/batch_integration/graph/methods/bbknn/run_example.sh @@ -10,5 +10,5 @@ bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --batch tech \ --hvg true \ --scaling true \ - --output src/batch_integration/resources/graph_bbknn_pancreas.h5ad \ + --output src/batch_integration/resources/graph_pancreas_bbknn.h5ad \ --debug true diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index 68f78225a0..526732b32e 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -22,6 +22,20 @@ print('>> Checking API') adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'hvg' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + assert 'connectivities' in adata.obsp assert 'distances' in adata.obsp assert 'hvg' in adata.uns diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 4d7992886d..5d14d7f872 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -22,6 +22,20 @@ print('>> Checking API') adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'hvg' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + assert 'connectivities' in adata.obsp assert 'distances' in adata.obsp assert 'hvg' in adata.uns From 389c6d9bdffc435a1d1c29b690a0c03299479751 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 19:28:40 +0100 Subject: [PATCH 0157/1233] fix ARI to scib 1.0.0 and method output Former-commit-id: 2d043bd70706c4c87920ed0ffb5928dae8954ff5 --- src/batch_integration/graph/methods/params.tsv | 16 ++++++++-------- .../graph/metrics/ari/config.vsh.yaml | 4 ++-- .../graph/metrics/ari/script.py | 4 ++-- src/batch_integration/graph/metrics/ari/test.py | 4 ++-- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/batch_integration/graph/methods/params.tsv b/src/batch_integration/graph/methods/params.tsv index 21a3ad4e50..ca79eb3d39 100644 --- a/src/batch_integration/graph/methods/params.tsv +++ b/src/batch_integration/graph/methods/params.tsv @@ -1,10 +1,10 @@ # HVG, scaling preprocessing setupts for integration methods hvg scaling method -2000 True bbknn -2000 True bbknn -2000 False bbknn -2000 False bbknn -0 True bbknn -0 True bbknn -0 False bbknn -0 False bbknn +True True bbknn +True False bbknn +False True bbknn +False False bbknn +True True combat +True False combat +False True combat +False False combat diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 328ea8344e..755934c975 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -29,9 +29,9 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: '../../../resources/graph_pancreas_bbknn.h5ad' platforms: - type: docker - image: mumichae/scib-base:0.1 + image: mumichae/scib-base:1.0.0 - type: native - type: nextflow diff --git a/src/batch_integration/graph/metrics/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py index 39d5add64f..217f663031 100644 --- a/src/batch_integration/graph/metrics/ari/script.py +++ b/src/batch_integration/graph/metrics/ari/script.py @@ -9,8 +9,8 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.clustering import opt_louvain -from scIB.metrics import ari +from scib.metrics.clustering import opt_louvain +from scib.metrics import ari if par['debug']: pprint.pprint(par) diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index bdb3053201..cdd69ed538 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'graph_pancreas_bbknn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.9341303589103552 +assert score == 0.2097653589001798 print(">> All tests passed successfully") From 7123271dd3a379e4df9d8b3294b79ef3a743652d Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 19:31:58 +0100 Subject: [PATCH 0158/1233] fix NMI Former-commit-id: 17a5acb31714cf0947d452100f39130a03053257 --- src/batch_integration/graph/metrics/nmi/config.vsh.yaml | 4 ++-- src/batch_integration/graph/metrics/nmi/script.py | 5 ++--- src/batch_integration/graph/metrics/nmi/test.py | 4 ++-- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index e9cabc8313..20445b6e4b 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -29,9 +29,9 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: '../../../resources/graph_pancreas_bbknn.h5ad' platforms: - type: docker - image: mumichae/scib-base:0.1 + image: mumichae/scib-base:1.0.0 - type: native - type: nextflow diff --git a/src/batch_integration/graph/metrics/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py index 8f05831734..994c287378 100644 --- a/src/batch_integration/graph/metrics/nmi/script.py +++ b/src/batch_integration/graph/metrics/nmi/script.py @@ -9,9 +9,8 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.preprocessing import reduce_data -from scIB.clustering import opt_louvain -from scIB.metrics import nmi +from scib.metrics.clustering import opt_louvain +from scib.metrics import nmi if par['debug']: pprint.pprint(par) diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index 91a17338c8..eb31d5fc8b 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'graph_pancreas_bbknn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.8589185688918367 +assert score == 0.2179112948125749 print(">> All tests passed successfully") From 3e9ee8a3df045de2702be24d2856375a4d8e654c Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:15:54 +0100 Subject: [PATCH 0159/1233] slimmed down pancreas dataset & use highly_variable instead of hvg key Former-commit-id: 4b5d5457a9259d9c96decbe072bbdfea44b764f5 --- src/batch_integration/datasets/README.md | 2 +- .../datasets/pancreas/config.vsh.yaml | 7 +----- .../datasets/pancreas/script.py | 7 +++--- .../datasets/pancreas/test.py | 6 ++--- .../datasets/utils/_hvg_batch.py | 15 ++++++++++++ .../{utils.py => utils/_log_scran_pooling.py} | 23 ------------------- 6 files changed, 24 insertions(+), 36 deletions(-) create mode 100644 src/batch_integration/datasets/utils/_hvg_batch.py rename src/batch_integration/datasets/{utils.py => utils/_log_scran_pooling.py} (54%) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index 0ab3dcc4c2..3cc1c9c160 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -9,7 +9,7 @@ This module creates Anndata objects that contain: * `adata.uns['name']`: name of the dataset * `adata.obs['batch']`: batch covariate * `adata.obs['label']`: cell identity label -* `adata.var['hvg']`: label whether a gene is identified as highly variable +* `adata.var['highly_variable']`: label whether a gene is identified as highly variable * `adata.layers['counts']`: raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data * `adata.layers['logcounts_scaled']`: log-normalized count data scaled to unit variance and zero mean diff --git a/src/batch_integration/datasets/pancreas/config.vsh.yaml b/src/batch_integration/datasets/pancreas/config.vsh.yaml index 757be32f6f..3869b12913 100644 --- a/src/batch_integration/datasets/pancreas/config.vsh.yaml +++ b/src/batch_integration/datasets/pancreas/config.vsh.yaml @@ -39,7 +39,7 @@ functionality: resources: - type: python_script path: script.py - - path: "../utils.py" + - path: "../utils/_hvg_batch.py" tests: - type: python_script path: test.py @@ -47,10 +47,5 @@ functionality: platforms: - type: docker image: mumichae/scib-base:1.0.0 - setup: - - type: docker - run: - - micromamba install -y -c conda-forge -c bioconda scprep bioconductor-scran - - micromamba clean --all --yes - type: native - type: nextflow diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index 9f17549137..84f6edc300 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -15,10 +15,11 @@ print('Importing libraries') import scanpy as sc +import scib from pprint import pprint import sys sys.path.append(resources_dir) -from utils import scale_batch, hvg_batch +from _hvg_batch import hvg_batch if par['debug']: pprint(par) @@ -38,10 +39,10 @@ print(f'Select {hvgs} highly variable genes') hvg_list = hvg_batch(adata, 'batch', n_hvg=hvgs) -adata.var['hvg'] = adata.var_names.isin(hvg_list) +adata.var['highly_variable'] = adata.var_names.isin(hvg_list) print('Scaling') -adata.layers['logcounts_scaled'] = scale_batch(adata, 'batch').X +adata.layers['logcounts_scaled'] = scib.pp.scale_batch(adata, 'batch').X print('Transformation: PCA') sc.tl.pca( diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index 8c44c7d41c..c064440282 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -25,7 +25,7 @@ assert 'name' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns -assert 'hvg' in adata.var +assert 'highly_variable' in adata.var assert 'counts' in adata.layers assert 'logcounts' in adata.layers assert 'logcounts_scaled' in adata.layers @@ -35,8 +35,8 @@ assert 'uni_distances' in adata.obsp assert 'uni_connectivities' in adata.obsp -assert adata.var['hvg'].dtype == 'bool' -assert adata.var['hvg'].sum() == 100 +assert adata.var['highly_variable'].dtype == 'bool' +assert adata.var['highly_variable'].sum() == 100 assert -0.0000001 <= np.mean(adata.layers['logcounts_scaled']) <= 0.0000001 assert 0.8 <= np.var(adata.layers['logcounts_scaled']) <= 1 diff --git a/src/batch_integration/datasets/utils/_hvg_batch.py b/src/batch_integration/datasets/utils/_hvg_batch.py new file mode 100644 index 0000000000..3cede619c4 --- /dev/null +++ b/src/batch_integration/datasets/utils/_hvg_batch.py @@ -0,0 +1,15 @@ +import scib + + +def hvg_batch(adata, batch_key, n_hvg): + """ + Compute highly variable genes by batch + """ + if n_hvg > adata.n_vars: + return adata.var_names.tolist() + return scib.pp.hvg_batch( + adata, + batch_key=batch_key, + target_genes=n_hvg, + adataOut=False + ) diff --git a/src/batch_integration/datasets/utils.py b/src/batch_integration/datasets/utils/_log_scran_pooling.py similarity index 54% rename from src/batch_integration/datasets/utils.py rename to src/batch_integration/datasets/utils/_log_scran_pooling.py index f0891790d6..93e0cc3f73 100644 --- a/src/batch_integration/datasets/utils.py +++ b/src/batch_integration/datasets/utils/_log_scran_pooling.py @@ -1,6 +1,5 @@ import scanpy as sc import scprep -import scib def log_scran_pooling(adata): @@ -21,25 +20,3 @@ def log_scran_pooling(adata): adata.X, adata.obs["size_factors"], axis=0 ) sc.pp.log1p(adata) - - -def scale_batch(adata, batch_key): - """ - Scale count matrix by batch - """ - return scib.pp.scale_batch(adata, batch=batch_key) - - -# TODO: HVG by batch -def hvg_batch(adata, batch_key, n_hvg): - """ - Compute highly variable genes by batch - """ - if n_hvg > adata.n_vars: - return adata.var_names.tolist() - return scib.pp.hvg_batch( - adata, - batch_key=batch_key, - target_genes=n_hvg, - adataOut=False - ) From b9c64978e81a10ba699b48cfd080e1fd01a4c80d Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:30:28 +0100 Subject: [PATCH 0160/1233] change hvg to highly_variable Former-commit-id: 94af54b34b7b26c0119bc4cee35c05f1f0e65055 --- src/batch_integration/graph/README.md | 5 +++-- src/batch_integration/graph/methods/bbknn/script.py | 2 +- src/batch_integration/graph/methods/bbknn/test.py | 2 +- src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index aacf69dbaf..0a98da398b 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -17,8 +17,9 @@ a [benchmarking study of data integration methods](https://www.biorxiv.org/conte Datasets should contain the following attributes: * `adata.uns['name']`: name of the dataset -* `adata.obs['batch']` with the batch covariate, -* `adata.obs['label']` with the cell identity label, +* `adata.obs['batch']` with the batch covariate +* `adata.obs['label']` with the cell identity label + * `adata.var['highly_variable']`: label whether a gene is identified as highly variable * `adata.layers['counts']` with raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data * `adata.layers['logcounts_scaled']`: scaled log-normalized count data diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 6c10f0a488..3d5cd08318 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -26,7 +26,7 @@ if hvg: print('Select HVGs') - adata = adata[:, adata.var['hvg']] + adata = adata[:, adata.var['highly_variable']] if scaling: print('Scale') diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index 526732b32e..f5b4d27f5a 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -26,7 +26,7 @@ assert 'name' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns -assert 'hvg' in adata.var +assert 'highly_variable' in adata.var assert 'counts' in adata.layers assert 'logcounts' in adata.layers assert 'logcounts_scaled' in adata.layers diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 5d14d7f872..87b4d91039 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -26,7 +26,7 @@ assert 'name' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns -assert 'hvg' in adata.var +assert 'highly_variable' in adata.var assert 'counts' in adata.layers assert 'logcounts' in adata.layers assert 'logcounts_scaled' in adata.layers From d45bba062c91d07c87edbf156c85e84be038dbad Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:30:39 +0100 Subject: [PATCH 0161/1233] add Combat Former-commit-id: 54f55e81629e70ddb5091a89c5b9a94f603120c7 --- .../graph/methods/combat/config.vsh.yaml | 45 ++++++++++++++++ .../graph/methods/combat/run_example.sh | 14 +++++ .../graph/methods/combat/script.py | 54 +++++++++++++++++++ .../graph/methods/combat/test.py | 46 ++++++++++++++++ 4 files changed, 159 insertions(+) create mode 100644 src/batch_integration/graph/methods/combat/config.vsh.yaml create mode 100644 src/batch_integration/graph/methods/combat/run_example.sh create mode 100644 src/batch_integration/graph/methods/combat/script.py create mode 100644 src/batch_integration/graph/methods/combat/test.py diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml new file mode 100644 index 0000000000..9c5615f98a --- /dev/null +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -0,0 +1,45 @@ +functionality: + name: combat + namespace: batch_integration/embedding/methods + version: dev + description: Run Combat + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --adata + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + required: true + - name: --scaling + type: boolean + description: Whether to scale the data or not + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../datasets/resources/datasets_pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:1.0.0 + - type: native + - type: nextflow diff --git a/src/batch_integration/graph/methods/combat/run_example.sh b/src/batch_integration/graph/methods/combat/run_example.sh new file mode 100644 index 0000000000..298b44396b --- /dev/null +++ b/src/batch_integration/graph/methods/combat/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvg true \ + --scaling true \ + --output src/batch_integration/resources/graph_pancreas_combat.h5ad \ + --debug true diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py new file mode 100644 index 0000000000..ae88261e71 --- /dev/null +++ b/src/batch_integration/graph/methods/combat/script.py @@ -0,0 +1,54 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': True, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +from pprint import pprint +import scanpy as sc +from scib.integration import combat + +if par['debug']: + pprint(par) + +adata_file = par['adata'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read(adata_file) + +if hvg: + print('Select HVGs') + adata = adata[:, adata.var['highly_variable']] + +if scaling: + print('Scale') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] + +print('Integrate') +adata = combat(adata, batch='batch') + +print('Postprocess data') +sc.pp.pca( + adata, + n_comps=50, + use_highly_variable=True, + svd_solver='arpack', + return_info=True +) +sc.pp.neighbors(adata, use_rep='X_pca') + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/combat/test.py b/src/batch_integration/graph/methods/combat/test.py new file mode 100644 index 0000000000..8347702971 --- /dev/null +++ b/src/batch_integration/graph/methods/combat/test.py @@ -0,0 +1,46 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'combat' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", 'False', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'highly_variable' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == False +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +print(">> All tests passed successfully") From f5a4c4414f8e1682423b74107d662a93336555e9 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:36:27 +0100 Subject: [PATCH 0162/1233] add test for graph metrics after combat correction Former-commit-id: 91c30b04d92fddef1184fdeea60cdea32ffb14ad --- .../graph/metrics/ari/config.vsh.yaml | 3 ++ .../graph/metrics/ari/test_combat.py | 30 +++++++++++++++++++ .../graph/metrics/nmi/config.vsh.yaml | 3 ++ .../graph/metrics/nmi/test_combat.py | 30 +++++++++++++++++++ 4 files changed, 66 insertions(+) create mode 100644 src/batch_integration/graph/metrics/ari/test_combat.py create mode 100644 src/batch_integration/graph/metrics/nmi/test_combat.py diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 755934c975..9e470e5feb 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -30,6 +30,9 @@ functionality: - type: python_script path: test.py - path: '../../../resources/graph_pancreas_bbknn.h5ad' + - type: python_script + path: test_combat.py + - path: '../../../resources/graph_pancreas_combat.h5ad' platforms: - type: docker image: mumichae/scib-base:1.0.0 diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py new file mode 100644 index 0000000000..7ce87cb116 --- /dev/null +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -0,0 +1,30 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'ari' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'graph_pancreas_combat.h5ad', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) +result = pd.read_table(metric_file) + +print(">> Check that score makes sense") +assert result.shape == (1, 4) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.5808883769609893 + +print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 20445b6e4b..950f7da7f9 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -30,6 +30,9 @@ functionality: - type: python_script path: test.py - path: '../../../resources/graph_pancreas_bbknn.h5ad' + - type: python_script + path: test_combat.py + - path: '../../../resources/graph_pancreas_combat.h5ad' platforms: - type: docker image: mumichae/scib-base:1.0.0 diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py new file mode 100644 index 0000000000..059194871f --- /dev/null +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -0,0 +1,30 @@ +from os import path +import subprocess +import pandas as pd +import numpy as np + +np.random.seed(42) + +metric = 'nmi' +metric_file = metric + '.tsv' + +print(">> Running script") +out = subprocess.check_output([ + "./" + metric, + "--adata", 'graph_pancreas_combat.h5ad', + "--output", metric_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(metric_file) +result = pd.read_table(metric_file) + +print(">> Check that score makes sense") +assert result.shape == (1, 4) +score = result.loc[0, 'value'] +print(score) + +assert 0 < score < 1 +assert score == 0.4240058744404366 + +print(">> All tests passed successfully") From 52d117f94502ae02f1bc940866197173f9db1474 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:46:58 +0100 Subject: [PATCH 0163/1233] add scVI Former-commit-id: 6ffde447f9456f98f01a4e293401303668336e0f --- .../graph/methods/scvi/config.vsh.yaml | 49 +++++++++++++++++++ .../graph/methods/scvi/run_example.sh | 14 ++++++ .../graph/methods/scvi/script.py | 47 ++++++++++++++++++ .../graph/methods/scvi/test.py | 46 +++++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 src/batch_integration/graph/methods/scvi/config.vsh.yaml create mode 100644 src/batch_integration/graph/methods/scvi/run_example.sh create mode 100644 src/batch_integration/graph/methods/scvi/script.py create mode 100644 src/batch_integration/graph/methods/scvi/test.py diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml new file mode 100644 index 0000000000..3dfd7e5cbf --- /dev/null +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -0,0 +1,49 @@ +functionality: + name: scvi + namespace: batch_integration/graph/methods + version: dev + description: Run scVI on adata object + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --adata + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + required: true + - name: --scaling + type: boolean + description: Whether to scale the data or not + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../datasets/resources/datasets_pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:1.0.0 + setup: + - type: python + packages: + - scvi + - type: native + - type: nextflow diff --git a/src/batch_integration/graph/methods/scvi/run_example.sh b/src/batch_integration/graph/methods/scvi/run_example.sh new file mode 100644 index 0000000000..68025e89ce --- /dev/null +++ b/src/batch_integration/graph/methods/scvi/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvg true \ + --scaling true \ + --output src/batch_integration/resources/graph_pancreas_scvi.h5ad \ + --debug true diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/graph/methods/scvi/script.py new file mode 100644 index 0000000000..b202ca9daa --- /dev/null +++ b/src/batch_integration/graph/methods/scvi/script.py @@ -0,0 +1,47 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': True, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +from pprint import pprint +import scanpy as sc +from scib.integration import scvi + +if par['debug']: + pprint(par) + +adata_file = par['adata'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read(adata_file) + +if hvg: + print('Select HVGs') + adata = adata[:, adata.var['highly_variable']] + +if scaling: + print('Scale') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] + +print('Integrate') +adata = scvi(adata, batch='batch') + +print('Postprocess data') +sc.pp.neighbors(adata, use_rep='X_emb') + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/scvi/test.py b/src/batch_integration/graph/methods/scvi/test.py new file mode 100644 index 0000000000..1ae0c44ed7 --- /dev/null +++ b/src/batch_integration/graph/methods/scvi/test.py @@ -0,0 +1,46 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'scvi' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", 'False', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'highly_variable' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == False +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +print(">> All tests passed successfully") From d8c424e8181a038804a802b01691a7496c5378c1 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 16 Dec 2021 20:52:47 +0100 Subject: [PATCH 0164/1233] add scanorama feature Former-commit-id: 72b87c5bf106f78832e331ab4b5f543b58c4dff1 --- .../methods/scanorama_feature/config.vsh.yaml | 49 +++++++++++++++++ .../methods/scanorama_feature/run_example.sh | 14 +++++ .../graph/methods/scanorama_feature/script.py | 54 +++++++++++++++++++ .../graph/methods/scanorama_feature/test.py | 46 ++++++++++++++++ 4 files changed, 163 insertions(+) create mode 100644 src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml create mode 100644 src/batch_integration/graph/methods/scanorama_feature/run_example.sh create mode 100644 src/batch_integration/graph/methods/scanorama_feature/script.py create mode 100644 src/batch_integration/graph/methods/scanorama_feature/test.py diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml new file mode 100644 index 0000000000..b15a655535 --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -0,0 +1,49 @@ +functionality: + name: scanorama + namespace: batch_integration/graph/methods + version: dev + description: Run Scanorama on adata object + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --adata + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + required: true + - name: --scaling + type: boolean + description: Whether to scale the data or not + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../datasets/resources/datasets_pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:1.0.0 + setup: + - type: python + packages: + - scanorama + - type: native + - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh new file mode 100644 index 0000000000..dc2fa27c9c --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvg true \ + --scaling true \ + --output src/batch_integration/resources/graph_pancreas_scanorama.h5ad \ + --debug true diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py new file mode 100644 index 0000000000..c9818adb93 --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -0,0 +1,54 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': True, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +from pprint import pprint +import scanpy as sc +from scib.integration import scanorama + +if par['debug']: + pprint(par) + +adata_file = par['adata'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read(adata_file) + +if hvg: + print('Select HVGs') + adata = adata[:, adata.var['highly_variable']] + +if scaling: + print('Scale') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] + +print('Integrate') +adata.X = scanorama(adata, batch='batch').X + +print('Postprocess data') +sc.pp.pca( + adata, + n_comps=50, + use_highly_variable=True, + svd_solver='arpack', + return_info=True +) +sc.pp.neighbors(adata, use_rep='X_pca') + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/scanorama_feature/test.py b/src/batch_integration/graph/methods/scanorama_feature/test.py new file mode 100644 index 0000000000..f01c1172f3 --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_feature/test.py @@ -0,0 +1,46 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'scanorama' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", 'False', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'highly_variable' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == False +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +print(">> All tests passed successfully") From 3fa8530b7c1f7ea71e702d5177aced50e4e2fb6f Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 20 Dec 2021 20:19:22 +0100 Subject: [PATCH 0165/1233] fix scanorama Former-commit-id: 4be17ac1cec3ab635fcf28ea80ff7f480b049435 --- .../methods/scanorama_embed/config.vsh.yaml | 49 +++++++++++++++++++ .../methods/scanorama_embed/run_example.sh | 14 ++++++ .../graph/methods/scanorama_embed/script.py | 47 ++++++++++++++++++ .../graph/methods/scanorama_embed/test.py | 46 +++++++++++++++++ .../methods/scanorama_feature/config.vsh.yaml | 4 +- .../methods/scanorama_feature/run_example.sh | 2 +- .../graph/methods/scanorama_feature/test.py | 2 +- 7 files changed, 160 insertions(+), 4 deletions(-) create mode 100644 src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml create mode 100644 src/batch_integration/graph/methods/scanorama_embed/run_example.sh create mode 100644 src/batch_integration/graph/methods/scanorama_embed/script.py create mode 100644 src/batch_integration/graph/methods/scanorama_embed/test.py diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml new file mode 100644 index 0000000000..77ced015b5 --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -0,0 +1,49 @@ +functionality: + name: scanorama_embed + namespace: batch_integration/graph/methods + version: dev + description: Run Scanorama on adata object, use embedding output + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --adata + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + required: true + - name: --scaling + type: boolean + description: Whether to scale the data or not + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test.py + - path: '../../../datasets/resources/datasets_pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:1.0.0 + setup: + - type: python + packages: + - scanorama + - type: native + - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh new file mode 100644 index 0000000000..da3352ce5c --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch tech \ + --hvg true \ + --scaling true \ + --output src/batch_integration/resources/graph_pancreas_scanorama_embed.h5ad \ + --debug true diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/graph/methods/scanorama_embed/script.py new file mode 100644 index 0000000000..08b1017bba --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_embed/script.py @@ -0,0 +1,47 @@ +## VIASH START +par = { + 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': True, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +from pprint import pprint +import scanpy as sc +from scib.integration import scanorama + +if par['debug']: + pprint(par) + +adata_file = par['adata'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read(adata_file) + +if hvg: + print('Select HVGs') + adata = adata[:, adata.var['highly_variable']] + +if scaling: + print('Scale') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] + +print('Integrate') +adata.obsm['X_emb'] = scanorama(adata, batch='batch').obsm['X_emb'] + +print('Postprocess data') +sc.pp.neighbors(adata, use_rep='X_emb') + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/graph/methods/scanorama_embed/test.py b/src/batch_integration/graph/methods/scanorama_embed/test.py new file mode 100644 index 0000000000..488bdfde11 --- /dev/null +++ b/src/batch_integration/graph/methods/scanorama_embed/test.py @@ -0,0 +1,46 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'scanorama_embed' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--adata", 'datasets_pancreas.h5ad', + "--hvg", 'False', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) + +assert 'name' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'highly_variable' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns +assert 'uni_distances' in adata.obsp +assert 'uni_connectivities' in adata.obsp + +assert 'connectivities' in adata.obsp +assert 'distances' in adata.obsp +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == False +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index b15a655535..980a9510c2 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -1,8 +1,8 @@ functionality: - name: scanorama + name: scanorama_feature namespace: batch_integration/graph/methods version: dev - description: Run Scanorama on adata object + description: Run Scanorama on adata object, use full feature output authors: - name: Michaela Mueller roles: [ maintainer, author ] diff --git a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh index dc2fa27c9c..c8a7ccf8fc 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh +++ b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh @@ -10,5 +10,5 @@ bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --batch tech \ --hvg true \ --scaling true \ - --output src/batch_integration/resources/graph_pancreas_scanorama.h5ad \ + --output src/batch_integration/resources/graph_pancreas_scanorama_feature.h5ad \ --debug true diff --git a/src/batch_integration/graph/methods/scanorama_feature/test.py b/src/batch_integration/graph/methods/scanorama_feature/test.py index f01c1172f3..cb6676df11 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/test.py +++ b/src/batch_integration/graph/methods/scanorama_feature/test.py @@ -5,7 +5,7 @@ np.random.seed(42) -method = 'scanorama' +method = 'scanorama_feature' output_file = method + '.h5ad' print(">> Running script") From 03218e87a3380d028c53b392e40b5fd39609a80b Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 20 Dec 2021 21:04:14 +0100 Subject: [PATCH 0166/1233] fix run example command Former-commit-id: 9a3f706c0790e06a58d7a9543e8b6ee68c704434 --- src/batch_integration/graph/methods/bbknn/run_example.sh | 2 -- src/batch_integration/graph/methods/combat/run_example.sh | 2 +- .../graph/methods/scanorama_embed/run_example.sh | 2 -- .../graph/methods/scanorama_feature/run_example.sh | 2 -- src/batch_integration/graph/methods/scanorama_feature/script.py | 2 +- src/batch_integration/graph/methods/scvi/run_example.sh | 2 -- 6 files changed, 2 insertions(+), 10 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh index 45d2126cdc..b89da943c8 100644 --- a/src/batch_integration/graph/methods/bbknn/run_example.sh +++ b/src/batch_integration/graph/methods/bbknn/run_example.sh @@ -6,8 +6,6 @@ SCRIPTPATH="$( bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch tech \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_bbknn.h5ad \ diff --git a/src/batch_integration/graph/methods/combat/run_example.sh b/src/batch_integration/graph/methods/combat/run_example.sh index 298b44396b..6db4a0f885 100644 --- a/src/batch_integration/graph/methods/combat/run_example.sh +++ b/src/batch_integration/graph/methods/combat/run_example.sh @@ -7,7 +7,7 @@ SCRIPTPATH="$( bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --label celltype \ - --batch tech \ + --batch batch \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_combat.h5ad \ diff --git a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh index da3352ce5c..1495b11ae8 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh +++ b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh @@ -6,8 +6,6 @@ SCRIPTPATH="$( bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch tech \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scanorama_embed.h5ad \ diff --git a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh index c8a7ccf8fc..afac7b5393 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh +++ b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh @@ -6,8 +6,6 @@ SCRIPTPATH="$( bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch tech \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scanorama_feature.h5ad \ diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index c9818adb93..c730684f01 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -35,7 +35,7 @@ adata.X = adata.layers['logcounts'] print('Integrate') -adata.X = scanorama(adata, batch='batch').X +adata.X = scanorama(adata, batch='batch').X.todense() print('Postprocess data') sc.pp.pca( diff --git a/src/batch_integration/graph/methods/scvi/run_example.sh b/src/batch_integration/graph/methods/scvi/run_example.sh index 68025e89ce..6e86cf3aaa 100644 --- a/src/batch_integration/graph/methods/scvi/run_example.sh +++ b/src/batch_integration/graph/methods/scvi/run_example.sh @@ -6,8 +6,6 @@ SCRIPTPATH="$( bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch tech \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scvi.h5ad \ From ff7e8917d29b06e645d13b2aaa081acaf98a913a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 23 May 2022 14:27:48 +0200 Subject: [PATCH 0167/1233] wip update modality alignment Former-commit-id: 7856d6228a515d0557901dc4cfd152e58990658f --- src/common/extract_scores/config.vsh.yaml | 9 ++- .../workflows/nextflow.config | 43 ------------- .../workflows/{ => run}/main.nf | 37 +++++------- .../workflows/run/nextflow.config | 16 +++++ .../workflows/{ => run}/run_nextflow.sh | 8 +-- src/modality_alignment/workflows/run_bash.sh | 60 ------------------- .../workflows/run_nextflow_from_repo.sh | 22 ------- 7 files changed, 42 insertions(+), 153 deletions(-) delete mode 100644 src/modality_alignment/workflows/nextflow.config rename src/modality_alignment/workflows/{ => run}/main.nf (67%) create mode 100644 src/modality_alignment/workflows/run/nextflow.config rename src/modality_alignment/workflows/{ => run}/run_nextflow.sh (71%) delete mode 100755 src/modality_alignment/workflows/run_bash.sh delete mode 100755 src/modality_alignment/workflows/run_nextflow_from_repo.sh diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index b79716ddc8..5dd81f7ae3 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -21,7 +21,10 @@ functionality: path: ./script.R platforms: - type: docker - image: "dataintuitive/randpy:r4.0_bioc3.12" # contains a few bioconductor and the 'anndata' package + image: "ghcr.io/data-intuitive/randpy:r4.1_py3.10" + setup: + - type: r + cran: anndata + - type: python + pypi: anndata - type: nextflow - publish: true - per_id: false diff --git a/src/modality_alignment/workflows/nextflow.config b/src/modality_alignment/workflows/nextflow.config deleted file mode 100644 index b5cdffca16..0000000000 --- a/src/modality_alignment/workflows/nextflow.config +++ /dev/null @@ -1,43 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT -params{ - rootDir = "$projectDir/../../.." -} -targetDir = "${params.rootDir}/target/nextflow" - -// custom includes -includeConfig "$targetDir/modality_alignment/datasets/scprep_csv/nextflow.config" -includeConfig "$targetDir/modality_alignment/datasets/sample_dataset/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/mnn/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/scot/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/harmonic_alignment/nextflow.config" -includeConfig "$targetDir/modality_alignment/methods/sample_method/nextflow.config" -includeConfig "$targetDir/modality_alignment/metrics/knn_auc/nextflow.config" -includeConfig "$targetDir/modality_alignment/metrics/mse/nextflow.config" -includeConfig "$targetDir/common/extract_scores/nextflow.config" - -// other configs -docker { - runOptions = "-v \$(realpath --no-symlinks ${params.rootDir}):\$(realpath --no-symlinks ${params.rootDir})" -} - -process { - maxForks = 30 - cpus = 2 - errorStrategy='ignore' - container = 'nextflow/bash:latest' - - pod = [ [ nodeSelector: 'worker-group = m5s' ] ] - - withLabel: highmem { memory = 50.Gb } - withLabel: highcpu { cpus = 20 } - withLabel: highmem_highcpu { - cpus = 20 - memory = 128.Gb - } -} - - diff --git a/src/modality_alignment/workflows/main.nf b/src/modality_alignment/workflows/run/main.nf similarity index 67% rename from src/modality_alignment/workflows/main.nf rename to src/modality_alignment/workflows/run/main.nf index e91ca42662..657d0db829 100644 --- a/src/modality_alignment/workflows/main.nf +++ b/src/modality_alignment/workflows/run/main.nf @@ -22,12 +22,8 @@ include { knn_auc } from "$targetDir/modality_alignment/metrics/knn include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) // import helper functions -include { overrideOptionValue; overrideParams } from "$launchDir/src/common/workflows/utils.nf" include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) -// Helper function for redefining the ids of elements in a channel -// based on its files. -def renameID = { [ it[1].baseName, it[1], it[2] ] } /******************************************************* * Dataset processor workflows * @@ -41,14 +37,11 @@ def renameID = { [ it[1].baseName, it[1], it[2] ] } workflow get_scprep_csv_datasets { main: - output_ = Channel.fromPath(file("$launchDir/src/modality_alignment/datasets/datasets_scprep_csv.tsv")) \ - | splitCsv(header: true, sep: "\t") \ + output_ = Channel.fromPath("$launchDir/src/modality_alignment/datasets/datasets_scprep_csv.tsv") + | splitCsv(header: true, sep: "\t") | map { row -> - files = [ "input1": file(row.input1), "input2": file(row.input2) ] - newParams = overrideParams(params, row.processor, "id", row.id) - [ row.id, files, newParams, row ] - } \ - | map{ overrideOptionValue(it, "scprep_csv", "compression", it[3].compression)} \ + [ row.id, [ "input1": file(row.input1), "input2": file(row.input2), "id": row.id ]] + } | scprep_csv emit: output_ @@ -56,7 +49,7 @@ workflow get_scprep_csv_datasets { workflow get_sample_datasets { main: - output_ = Channel.fromList( [[ "sample_dataset", [], params]] ) \ + output_ = Channel.value( [ "sample_dataset", [:] ] ) | sample_dataset emit: output_ @@ -67,14 +60,16 @@ workflow get_sample_datasets { *******************************************************/ workflow { - (get_sample_datasets & get_scprep_csv_datasets) \ - | mix \ - | (sample_method & mnn & scot & harmonic_alignment) \ - | mix | map(renameID) \ - | (knn_auc & mse) \ - | mix | map(renameID) \ - | toSortedList \ - | map{ it -> [ "combined", it.collect{ a -> a[1] }, params ] } - | extract_scores + (get_sample_datasets & get_scprep_csv_datasets) + | mix + // | (sample_method & mnn & scot & harmonic_alignment) + // | mix + // | (knn_auc & mse) + // | mix + // | toSortedList + // | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + // | extract_scores.run( + // auto: [ publish: true ] + // ) } diff --git a/src/modality_alignment/workflows/run/nextflow.config b/src/modality_alignment/workflows/run/nextflow.config new file mode 100644 index 0000000000..91add22b77 --- /dev/null +++ b/src/modality_alignment/workflows/run/nextflow.config @@ -0,0 +1,16 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// set default container & default labels +process { + container = 'nextflow/bash:latest' + + withLabel: highmem { memory = 50.Gb } + withLabel: highcpu { cpus = 20 } +} diff --git a/src/modality_alignment/workflows/run_nextflow.sh b/src/modality_alignment/workflows/run/run_nextflow.sh similarity index 71% rename from src/modality_alignment/workflows/run_nextflow.sh rename to src/modality_alignment/workflows/run/run_nextflow.sh index 9c6e7d8b8c..415794f68a 100755 --- a/src/modality_alignment/workflows/run_nextflow.sh +++ b/src/modality_alignment/workflows/run/run_nextflow.sh @@ -10,12 +10,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" # choose a particular version of nextflow -export NXF_VER=21.04.1 +export NXF_VER=21.10.6 bin/nextflow \ run . \ - -main-script src/modality_alignment/workflows/main.nf \ - -c src/modality_alignment/workflows/nextflow.config \ + -main-script src/modality_alignment/workflows/run/main.nf \ --output output/modality_alignment \ - -resume + -resume \ + -with-docker diff --git a/src/modality_alignment/workflows/run_bash.sh b/src/modality_alignment/workflows/run_bash.sh deleted file mode 100755 index 4745e7c776..0000000000 --- a/src/modality_alignment/workflows/run_bash.sh +++ /dev/null @@ -1,60 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -TARGET=target/docker/modality_alignment -OUTPUT=output_bash/modality_alignment - -mkdir -p $OUTPUT/datasets -mkdir -p $OUTPUT/methods -mkdir -p $OUTPUT/metrics - -# generate datasets -if [ ! -f "$OUTPUT/datasets/citeseq_cbmc.h5ad" ]; then - tmp1=`tempfile` - tmp2=`tempfile` - wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz' -O "$tmp1" - wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz' -O "$tmp2" - "$TARGET/datasets/scprep_csv/scprep_csv" \ - --input1 "$tmp1" \ - --input2 "$tmp2" \ - --output "$OUTPUT/datasets/citeseq_cbmc.h5ad" - rm "$tmp1" "$tmp2" -fi - -# run all methods on all datasets -for meth in `ls "$TARGET/methods"`; do - for dat in `ls "$OUTPUT/datasets"`; do - dat_id="${dat%.*}" - input_h5ad="$OUTPUT/datasets/$dat_id.h5ad" - output_h5ad="$OUTPUT/methods/${dat_id}_$meth.h5ad" - if [ ! -f "$output_h5ad" ]; then - echo "> $TARGET/methods/$meth/$meth -i $input_h5ad -o $output_h5ad" - "$TARGET/methods/$meth/$meth" -i "$input_h5ad" -o "$output_h5ad" - fi - done -done - -# run all metrics on all outputs -for met in `ls "$TARGET/metrics"`; do - for outp in `ls "$OUTPUT/methods"`; do - out_id="${outp%.*}" - input_h5ad="$OUTPUT/methods/$out_id.h5ad" - output_h5ad="$OUTPUT/metrics/${out_id}_$met.h5ad" - if [ ! -f "$output_h5ad" ]; then - echo "> $TARGET/metrics/$met/$met" -i "$input_h5ad" -o "$output_h5ad" - "$TARGET/metrics/$met/$met" -i "$input_h5ad" -o "$output_h5ad" - fi - done -done - -# concatenate all scores into one tsv -INPUTS=$(ls -1 "$OUTPUT/metrics" | sed "s#.*#-i '$OUTPUT/metrics/&'#" | tr '\n' ' ') -eval "$TARGET/../common/extract_scores/extract_scores" $INPUTS -o "$OUTPUT/scores.tsv" diff --git a/src/modality_alignment/workflows/run_nextflow_from_repo.sh b/src/modality_alignment/workflows/run_nextflow_from_repo.sh deleted file mode 100755 index 7bf0016560..0000000000 --- a/src/modality_alignment/workflows/run_nextflow_from_repo.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -# choose a particular version of nextflow -export NXF_VER=21.04.1 - -bin/nextflow \ - run https://github.com/openproblems-bio/opsca-viash.git \ - -r main_build \ - -main-script src/modality_alignment/workflows/main.nf \ - -c src/modality_alignment/workflows/nextflow.config \ - --output output/modality_alignment \ - -resume - From 17c0533e7dc0bc416c37fd661866af414c617874 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 May 2022 17:56:59 +0200 Subject: [PATCH 0168/1233] run all methods Former-commit-id: 88e23d218b4f0220f1fa3df26e7a180b601c20b4 --- src/modality_alignment/workflows/run/main.nf | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/modality_alignment/workflows/run/main.nf b/src/modality_alignment/workflows/run/main.nf index 657d0db829..4c1cb68cf8 100644 --- a/src/modality_alignment/workflows/run/main.nf +++ b/src/modality_alignment/workflows/run/main.nf @@ -62,14 +62,14 @@ workflow get_sample_datasets { workflow { (get_sample_datasets & get_scprep_csv_datasets) | mix - // | (sample_method & mnn & scot & harmonic_alignment) - // | mix - // | (knn_auc & mse) - // | mix - // | toSortedList - // | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - // | extract_scores.run( - // auto: [ publish: true ] - // ) + | (sample_method & mnn & scot & harmonic_alignment) + | mix + | (knn_auc & mse) + | mix + | toSortedList + | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + | extract_scores.run( + auto: [ publish: true ] + ) } From a86a4e9649e318517d52a5e96f7578d87b234c49 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 May 2022 17:57:10 +0200 Subject: [PATCH 0169/1233] use viash 0.5.11 Former-commit-id: cdc07b042581f4a8b816867af18285471c6ced6d --- bin/init | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bin/init b/bin/init index 885f8e7ca6..5bb5901603 100755 --- a/bin/init +++ b/bin/init @@ -6,7 +6,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -curl -fsSL get.viash.io | bash -s -- --registry openpipeline --tag develop --log check_results/results.tsv +curl -fsSL get.viash.io | bash -s -- \ + --registry ghcr.io \ + --organisation openproblems-bio \ + --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ + --tag develop \ + --nextflow_variant vdsl3 cd bin From 97d2c9fed4b31e13a21e2dc1d2f3f0afc60857d5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 May 2022 17:57:22 +0200 Subject: [PATCH 0170/1233] add gitignore Former-commit-id: 716d5c33020198f901637f8d4198e465ae4d3e3f --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 724755c0c9..55fe3bd6d5 100644 --- a/.gitignore +++ b/.gitignore @@ -17,8 +17,9 @@ docker_output/ target/ check_results/ log.txt +.viash* # nextflow specific ignores .nextflow* work -output +output \ No newline at end of file From 6bd11ccbf3be6ddaa5e6902dcc9b644e2503d2b2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 May 2022 22:18:26 +0200 Subject: [PATCH 0171/1233] update to 0.5.12 Former-commit-id: 85a4ca230be15713bf5622bc9f8c9fed89fb810e --- bin/init | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/init b/bin/init index 5bb5901603..edfc0672b7 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag develop \ + --tag 0.5.12 \ --nextflow_variant vdsl3 cd bin From 8ff0bed0b26b4a1f706b0422c3baf71c67779d38 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 27 May 2022 17:39:40 +0200 Subject: [PATCH 0172/1233] update docker images Former-commit-id: 81c58379f326ec64cdf33128fa73ba87a974bdc3 --- src/common/base_images/scanpy-r-micromamba/Dockerfile | 2 +- src/common/base_images/scanpy-r-micromamba/README.md | 6 ++++++ src/common/base_images/scanpy-r-micromamba/env.yaml | 8 ++++---- src/common/base_images/scib-base/Dockerfile | 4 ++-- src/common/base_images/scib-base/README.md | 6 ++++++ src/common/base_images/scib-base/env.yaml | 11 ++++++----- 6 files changed, 25 insertions(+), 12 deletions(-) create mode 100644 src/common/base_images/scanpy-r-micromamba/README.md create mode 100644 src/common/base_images/scib-base/README.md diff --git a/src/common/base_images/scanpy-r-micromamba/Dockerfile b/src/common/base_images/scanpy-r-micromamba/Dockerfile index ad4f117162..aca04a3a35 100644 --- a/src/common/base_images/scanpy-r-micromamba/Dockerfile +++ b/src/common/base_images/scanpy-r-micromamba/Dockerfile @@ -1,4 +1,4 @@ -# version 0.1.2 +# version 1.9.1 FROM mambaorg/micromamba:0.14.0 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml && \ diff --git a/src/common/base_images/scanpy-r-micromamba/README.md b/src/common/base_images/scanpy-r-micromamba/README.md new file mode 100644 index 0000000000..160d3aa41d --- /dev/null +++ b/src/common/base_images/scanpy-r-micromamba/README.md @@ -0,0 +1,6 @@ +# Scanpy image with R in micromamba + +Build and tag: +```shell +docker build -t mumichae/scanpy-r-micromamba:1.9.1 . +``` diff --git a/src/common/base_images/scanpy-r-micromamba/env.yaml b/src/common/base_images/scanpy-r-micromamba/env.yaml index 9b8ac434b2..e1d17a36f1 100644 --- a/src/common/base_images/scanpy-r-micromamba/env.yaml +++ b/src/common/base_images/scanpy-r-micromamba/env.yaml @@ -3,11 +3,11 @@ channels: - conda-forge dependencies: - python=3.8 - - pip=21.1 - - rpy2=3.4.5 - - scanpy=1.8 + - pip=22.0 + - rpy2=3.4.2 + - scanpy=1.9.1 - r-base=4 - - anndata=0.7.6 + - anndata=0.8 - git - pip: - anndata2ri==1.0.6 diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile index 214d9a25bc..3f112f1ef2 100644 --- a/src/common/base_images/scib-base/Dockerfile +++ b/src/common/base_images/scib-base/Dockerfile @@ -1,5 +1,5 @@ -# version 1.0.0 -FROM mumichae/scanpy-r-micromamba:0.1.2 +# version 1.0.2 +FROM mumichae/scanpy-r-micromamba:1.9.1 COPY env.yaml /tmp/env.yaml RUN micromamba install -y -n base -f /tmp/env.yaml RUN Rscript -e "devtools::install_github('theislab/kBET')" diff --git a/src/common/base_images/scib-base/README.md b/src/common/base_images/scib-base/README.md new file mode 100644 index 0000000000..d3836105bd --- /dev/null +++ b/src/common/base_images/scib-base/README.md @@ -0,0 +1,6 @@ +# Image with scib based on scanpy-r-micromamba + +Build and tag: +```shell +docker build -t mumichae/scib-base:1.0.2 . +``` diff --git a/src/common/base_images/scib-base/env.yaml b/src/common/base_images/scib-base/env.yaml index a6f706feff..b6604c6b25 100644 --- a/src/common/base_images/scib-base/env.yaml +++ b/src/common/base_images/scib-base/env.yaml @@ -3,11 +3,12 @@ channels: - conda-forge dependencies: - python=3.8 - - pip=21.1 - - rpy2=3.4.5 - - scanpy=1.8 + - pip=22 + - rpy2=3.4.2 + - scanpy=1.9.1 - r-base=4 - - anndata=0.7.6 + - r-devtools + - anndata=0.8 - git - pip: - - scib==1.0.0 + - scib==1.0.2 From fb658790ed1b50ca125a3266cb68693690d56a89 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 27 May 2022 17:40:13 +0200 Subject: [PATCH 0173/1233] add example script for data loader Former-commit-id: 0ff175b1c67245f23300df0ec815a0cedd795afb --- src/common/data_loader/run_example.sh | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 src/common/data_loader/run_example.sh diff --git a/src/common/data_loader/run_example.sh b/src/common/data_loader/run_example.sh new file mode 100644 index 0000000000..b97738a331 --- /dev/null +++ b/src/common/data_loader/run_example.sh @@ -0,0 +1,4 @@ +bin/viash run src/common/data_loader/config.vsh.yaml -- \ + --output src/common/data_loader/resources/pancreas.h5ad \ + --url https://ndownloader.figshare.com/files/24539828 \ + --name pancreas --lognorm_available adata.X \ No newline at end of file From 4ac6dc282d22b33a36e38d244ee752bd8f0573a6 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Mon, 30 May 2022 12:05:56 +0200 Subject: [PATCH 0174/1233] move dataset resources to batch integration resources Former-commit-id: 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zet=oF&p%}v3h~Sv7fUX|)tWETDu|f9^N)lqoQ6GfhNO@VZVi)xTTXn9B(6o&$@U>c zH_xNQA3OuABd3fSb?eE8R@v*b8{L^_8 zKkX%v#lzC_eTz7$>9P8^t4V%HfKuGt+Yj_44!qPWnymF_k{KJ&WtGYFV$nCuFJPuY~8HH1} znFW_=L=Im)f*w3?h%5-_dQegR`JkXsK7IcgBq+rHf!sqF|AERQ|3VFQ85xu(%*X#@ z{0Hf2nj8HW59hxx{D1iWlmz5uB)|N#VV(cl^}kw#g5vmJ`t#qy_-5*8`Oo?vo%?6V z{|o-FXH*ode`);}K~$7~HSoXbqd#f(KWi#f)c Date: Mon, 30 May 2022 12:08:29 +0200 Subject: [PATCH 0175/1233] fix pancreas preprocessing on smaller dataset Former-commit-id: 8c1c9e17eb7e56fe44c1d6bad03745b81b2ed8c6 --- src/batch_integration/datasets/README.md | 8 ++++++++ .../datasets/pancreas/config.vsh.yaml | 4 ++-- .../datasets/pancreas/run_example.sh | 2 +- src/batch_integration/datasets/pancreas/script.py | 7 ++++++- src/batch_integration/datasets/pancreas/test.py | 13 +++++++------ 5 files changed, 24 insertions(+), 10 deletions(-) diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index 3cc1c9c160..7d5836489d 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -4,6 +4,14 @@ Viash component for preparing data **before** running data integration methods. ## API +### Requires + +* `adata.X`: raw counts +* batch label in `adata.obs` that is specified as a parameter to the script +* cell identity label in `adata.obs` that is specified as a parameter to the script + +### Returns + This module creates Anndata objects that contain: * `adata.uns['name']`: name of the dataset diff --git a/src/batch_integration/datasets/pancreas/config.vsh.yaml b/src/batch_integration/datasets/pancreas/config.vsh.yaml index 3869b12913..5c5a490b5b 100644 --- a/src/batch_integration/datasets/pancreas/config.vsh.yaml +++ b/src/batch_integration/datasets/pancreas/config.vsh.yaml @@ -43,9 +43,9 @@ functionality: tests: - type: python_script path: test.py - - path: '../resources/data_loader_pancreas.h5ad' + - path: '../../resources/data_loader_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 - type: native - type: nextflow diff --git a/src/batch_integration/datasets/pancreas/run_example.sh b/src/batch_integration/datasets/pancreas/run_example.sh index 1976744536..564fb73cda 100644 --- a/src/batch_integration/datasets/pancreas/run_example.sh +++ b/src/batch_integration/datasets/pancreas/run_example.sh @@ -4,7 +4,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/data_loader_pancreas.h5ad \ + --adata src/batch_integration/resources/data_loader_pancreas.h5ad \ --label celltype \ --batch tech \ --hvgs 100 \ diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index 84f6edc300..a4fa73eb25 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -35,7 +35,12 @@ # Rename columns adata.obs.rename(columns={label: 'label', batch: 'batch'}, inplace=True) -adata.layers['counts'] = adata.X +adata.layers['counts'] = adata.X.copy() + +print('Normalise and log-transform data') +sc.pp.normalize_total(adata) +sc.pp.log1p(adata) +adata.layers['logcounts'] = adata.X.copy() print(f'Select {hvgs} highly variable genes') hvg_list = hvg_batch(adata, 'batch', n_hvg=hvgs) diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/pancreas/test.py index c064440282..86878f929c 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/pancreas/test.py @@ -5,23 +5,24 @@ name = 'pancreas' anndata_in = 'data_loader_pancreas.h5ad' -anndata_out = 'data_loader_pancreas.h5ad' +anndata_out = 'datasets_pancreas.h5ad' print('>> Running script') +n_hvgs = 100 out = subprocess.check_output([ './pancreas', '--adata', anndata_in, '--label', 'celltype', '--batch', 'tech', - '--hvgs', '100', + '--hvgs', str(n_hvgs), '--output', anndata_out ]).decode('utf-8') print('>> Checking whether file exists') -assert path.exists(anndata_in) +assert path.exists(anndata_out) print('>> Check that output fits expected API') -adata = sc.read_h5ad(anndata_in) +adata = sc.read_h5ad(anndata_out) assert 'name' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns @@ -36,8 +37,8 @@ assert 'uni_connectivities' in adata.obsp assert adata.var['highly_variable'].dtype == 'bool' -assert adata.var['highly_variable'].sum() == 100 +assert adata.var['highly_variable'].sum() == n_hvgs assert -0.0000001 <= np.mean(adata.layers['logcounts_scaled']) <= 0.0000001 -assert 0.8 <= np.var(adata.layers['logcounts_scaled']) <= 1 +assert 0.75 <= np.var(adata.layers['logcounts_scaled']) <= 1 print('>> All tests passed successfully') From f9a20cdcc6db213cecae61e8679d7c5b0b66c47b Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 31 May 2022 17:54:40 +0200 Subject: [PATCH 0176/1233] add interactive run commands for docker images Former-commit-id: b3786d6a308683b0a69df9d2cd95d1296d061b54 --- src/common/base_images/scanpy-r-micromamba/README.md | 7 +++++++ src/common/base_images/scib-base/README.md | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/src/common/base_images/scanpy-r-micromamba/README.md b/src/common/base_images/scanpy-r-micromamba/README.md index 160d3aa41d..2630f72468 100644 --- a/src/common/base_images/scanpy-r-micromamba/README.md +++ b/src/common/base_images/scanpy-r-micromamba/README.md @@ -1,6 +1,13 @@ # Scanpy image with R in micromamba Build and tag: + ```shell docker build -t mumichae/scanpy-r-micromamba:1.9.1 . ``` + +Run the image interactively + +```shell +docker run -it mumichae/scanpy-r-micromamba:1.9.1 bash +``` \ No newline at end of file diff --git a/src/common/base_images/scib-base/README.md b/src/common/base_images/scib-base/README.md index d3836105bd..562ea17862 100644 --- a/src/common/base_images/scib-base/README.md +++ b/src/common/base_images/scib-base/README.md @@ -1,6 +1,13 @@ # Image with scib based on scanpy-r-micromamba Build and tag: + ```shell docker build -t mumichae/scib-base:1.0.2 . ``` + +Run the image interactively + +```shell +docker run -it mumichae/scib-base:1.0.2 bash +``` \ No newline at end of file From 6fbf9bcadaad66cebbfe58f1730f43d97089b2e1 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 1 Jun 2022 16:40:54 +0200 Subject: [PATCH 0177/1233] get bbknn running Former-commit-id: 3b8ddf8b7198daa80cfdd68ddbe60355cf40a712 --- src/batch_integration/graph/methods/bbknn/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/bbknn/test.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index 055564dc85..d281651192 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -39,10 +39,10 @@ functionality: path: test.py - type: python_script path: test_scaled_hvg.py - - path: '../../../datasets/resources/datasets_pancreas.h5ad' + - path: '../../../resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 setup: - type: python packages: diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index f5b4d27f5a..320b317f36 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -39,8 +39,8 @@ assert 'connectivities' in adata.obsp assert 'distances' in adata.obsp assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False +assert not adata.uns['hvg'] assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False +assert not adata.uns['scaled'] print(">> All tests passed successfully") From 52d0459e4fb68d39c550fa70d59b3c7efd286471 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 13 Jun 2022 12:32:15 +0200 Subject: [PATCH 0178/1233] update ci Former-commit-id: cb357daf3a312ea4bcfd35b61a400cad0cba7b1a --- .github/workflows/viash-build.yml | 92 ++++++++++++++++--------------- .github/workflows/viash-test.yml | 66 ++++++++++++---------- bin/init | 2 +- 3 files changed, 85 insertions(+), 75 deletions(-) diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml index c712c720b4..830e05eb5d 100644 --- a/.github/workflows/viash-build.yml +++ b/.github/workflows/viash-build.yml @@ -2,49 +2,32 @@ name: viash build CI on: push: - branches: [ main ] + branches: [ 'main' ] jobs: - viash-build: - runs-on: ${{ matrix.config.os }} + # phase 1 + list_components: + runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, 'ci skip')" - strategy: - fail-fast: true - matrix: - config: - - {name: 'main', os: ubuntu-latest } - steps: - uses: actions/checkout@v2 - - name: Cache executables - uses: actions/cache@v2 - with: - path: bin - key: executable-caching-${{ github.workflow }}-${{ matrix.config.name }} - - name: Fetch viash run: | bin/init bin/viash -h - - name: Build components + - name: Build target dir run: | # allow publishing the target folder - sed -i '/^target\/$/d' .gitignore - - # only build nextflow targets - bin/viash_build -m release -t main_build - - - name: Run tests - run: | - # create check_results folder - sed -i '/^check_results\/$/d' .gitignore - mkdir check_results + sed -i '/^target.*/d' .gitignore - # run tests - bin/viash_test -m release -t main_build --append=false --log=check_results/results.tsv + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t main_build - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -52,25 +35,46 @@ jobs: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . publish_branch: main_build + + - id: set_matrix + run: | + echo "::set-output name=matrix::$( bin/viash ns list -p docker --format json | jq -c '[ .[] | .info.config ]' )" + + outputs: + matrix: ${{ steps.set_matrix.outputs.matrix }} + + # phase 2 + build_containers: + needs: list_components + + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + component_path: ${{ fromJson(needs.list_components.outputs.matrix) }} + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + - name: Build container + run: | + SRC_DIR=`dirname ${{ matrix.component_path }}` + bin/viash_build -m release -t main_build -s "$SRC_DIR" - - name: Login to Docker Hub - if: false + - name: Login to container registry uses: docker/login-action@v1 with: - username: ${{ secrets.DOCKER_USERNAME }} - password: ${{ secrets.DOCKER_PASSWORD }} + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GTHB_PAT }} - name: Push containers - if: false run: | - bin/viash_push -m release -t main_build - - - name: Upload check results - uses: actions/upload-artifact@master - with: - name: ${{ matrix.config.name }}_results - path: check_results - - -# todo: add build for tag -# https://github.com/peaceiris/actions-gh-pages#%EF%B8%8F-create-git-tag + bin/viash_push -m release -t main_build --force diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index d811ac78db..77ca158552 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -1,50 +1,56 @@ name: viash test CI -on: [ push, pull_request ] +on: + push: + branches: [ '*' ] + pull_request: + branches: [ '*' ] + +# Skip older CI runs for pull requests (head_ref exists), otherwise allways build +# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-a-fallback-value +concurrency: + group: ${{ github.head_ref || github.run_id }} + cancel-in-progress: true jobs: - viash-test: - runs-on: ${{ matrix.config.os }} + # phase 1 + list_components: + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + + steps: + - uses: actions/checkout@v2 + - name: Fetch viash + run: | + bin/init + bin/viash -h + - id: set_matrix + run: | + echo "::set-output name=matrix::$( bin/viash ns list -p docker --format json | jq -c '[ .[] | .info.config ]' )" + outputs: + matrix: ${{ steps.set_matrix.outputs.matrix }} + + # phase 2 + viash_test: + needs: list_components + + runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, 'ci skip')" strategy: fail-fast: false matrix: - config: - - {name: 'main_only_common', os: ubuntu-latest, query: 'common' } - - {name: 'main_only_MA', os: ubuntu-latest, query: 'modality_alignment' } - - {name: 'main_only_TI', os: ubuntu-latest, query: 'trajectory_inference' } + component_path: ${{ fromJson(needs.list_components.outputs.matrix) }} steps: - uses: actions/checkout@v2 - - name: Cache executables - uses: actions/cache@v2 - with: - path: bin - key: executable-caching-${{ github.workflow }}-${{ matrix.config.name }} - - name: Fetch viash run: | bin/init bin/viash -h - - name: Run build - run: | - bin/viash_build -q '${{ matrix.config.query }}' - - - name: Run tests + - name: Run test run: | - # create check_results folder - sed -i '/^check_results\/$/d' .gitignore - mkdir check_results - - # run tests - bin/viash_test -q '${{ matrix.config.query }}' --append=false --log=check_results/results.tsv - - - name: Upload check results - uses: actions/upload-artifact@master - with: - name: ${{ matrix.config.name }}_results - path: check_results + bin/viash test -p docker ${{ matrix.component_path }} diff --git a/bin/init b/bin/init index edfc0672b7..5a2142094d 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.5.12 \ + --tag 0.5.13 \ --nextflow_variant vdsl3 cd bin From a4e4a734872af9c4bf3755cb856e4a9cbe97264d Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Fri, 13 May 2022 14:02:37 -0300 Subject: [PATCH 0179/1233] feat: pancreas load data Former-commit-id: 4438d14557e679edf3d5e3aaa2f39db4fd222743 --- src/common/data/pancreas/load/config.vsh.yaml | 40 ++++++++++++++++++ src/common/data/pancreas/load/fake_anndata.py | 14 +++++++ src/common/data/pancreas/load/load_save.py | 37 ++++++++++++++++ .../data/pancreas/load/load_save_test.py | 32 ++++++++++++++ .../datasets/pancreas/config.vsh.yaml | 42 +++++++++++++++++++ .../datasets/pancreas/pancreas.py | 0 6 files changed, 165 insertions(+) create mode 100644 src/common/data/pancreas/load/config.vsh.yaml create mode 100644 src/common/data/pancreas/load/fake_anndata.py create mode 100644 src/common/data/pancreas/load/load_save.py create mode 100644 src/common/data/pancreas/load/load_save_test.py create mode 100644 src/label_projection/datasets/pancreas/config.vsh.yaml create mode 100644 src/label_projection/datasets/pancreas/pancreas.py diff --git a/src/common/data/pancreas/load/config.vsh.yaml b/src/common/data/pancreas/load/config.vsh.yaml new file mode 100644 index 0000000000..6f9ca2c134 --- /dev/null +++ b/src/common/data/pancreas/load/config.vsh.yaml @@ -0,0 +1,40 @@ +functionality: + name: "load_pancreas" + namespace: "common/data/pancreas/load" + version: "dev" + description: "Common component to load pancreas data" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + arguments: + - name: "--url" + description: "Url where data should be download" + type: "string" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file donwloaded from 'url' input" + required: true + resources: + - type: python_script + path: load_save.py + tests: + - type: python_script + path: load_save_test.py + - path: load_save.py + - path: fake_anndata.py +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - scanpy + - openpyxl # to tests + - type: nextflow diff --git a/src/common/data/pancreas/load/fake_anndata.py b/src/common/data/pancreas/load/fake_anndata.py new file mode 100644 index 0000000000..ecbf5d1f48 --- /dev/null +++ b/src/common/data/pancreas/load/fake_anndata.py @@ -0,0 +1,14 @@ +import anndata +import pandas as pd +import numpy as np + + +def generate_fake_anndata(): + X = np.zeros((3, 3)) + obs = pd.DataFrame([['celseq', 'gamma', 0.02], ['celseq', 'gamma', 0.07], ['celseq', 'gamma', 0.03]], + columns=['tech', 'celltype', 'size_factors'], + index=['A1BG', 'A1CF', 'A2M']) + var = pd.DataFrame(index=['A1BG', 'A1CF', 'A2M']) + adata = anndata.AnnData(X=X, obs=obs, var=var) + adata.layers['counts'] = X + return adata diff --git a/src/common/data/pancreas/load/load_save.py b/src/common/data/pancreas/load/load_save.py new file mode 100644 index 0000000000..3254f11ea6 --- /dev/null +++ b/src/common/data/pancreas/load/load_save.py @@ -0,0 +1,37 @@ +## VIASH START +par = { + "url": "https://ndownloader.figshare.com/files/24539828", + "output": "/tmp/output.h5ad" +} +## VIASH END +import os +from os.path import exists +import scanpy as sc +import scprep +import tempfile + + +def load_data(url): + """Download pancreas data from url.""" + with tempfile.TemporaryDirectory() as tempdir: + filepath = os.path.join(tempdir, "pancreas.h5ad") + scprep.io.download.download_url(url, filepath) + adata = sc.read(filepath) + adata.X = adata.layers["counts"] + del adata.layers["counts"] + return adata + + +def save_data(adata, output): + adata.write(output) + return None + + +def run_script(par): + adata = load_data(par['url']) + save_data(adata, par['output']) + return None + + +if ("par" in locals()): + run_script(par) diff --git a/src/common/data/pancreas/load/load_save_test.py b/src/common/data/pancreas/load/load_save_test.py new file mode 100644 index 0000000000..5d5330c5a2 --- /dev/null +++ b/src/common/data/pancreas/load/load_save_test.py @@ -0,0 +1,32 @@ +import sys +sys.path.append("./") +import load_save +import fake_anndata +from os.path import exists +import unittest +import scanpy as sc +from unittest.mock import patch + + +URL = "https://fake.url" +OUTPUT = "/tmp/output.h5ad" + + +class LoadDataTest(unittest.TestCase): + @patch('scprep.io.download.download_url') + @patch('scanpy.read') + def test_load_data(self, read_method, download_url_method): + download_url_method.return_value = None + read_method.return_value = fake_anndata.generate_fake_anndata() + response = load_save.load_data(URL) + self.assertEqual((3, 3), response.X.shape) + + +class SaveDataTest(unittest.TestCase): + def test_save_data(self): + load_save.save_data(fake_anndata.generate_fake_anndata(), "./output.h5ad") + self.assertTrue(exists("./output.h5ad"), "File should exists") + + +if __name__ == "__main__": + unittest.main() diff --git a/src/label_projection/datasets/pancreas/config.vsh.yaml b/src/label_projection/datasets/pancreas/config.vsh.yaml new file mode 100644 index 0000000000..01fddb3eef --- /dev/null +++ b/src/label_projection/datasets/pancreas/config.vsh.yaml @@ -0,0 +1,42 @@ +functionality: + name: "pancreas_dataset" + namespace: "label_projections/datasets" + version: "dev" + description: "Pancreas datasets for label_projection tasks" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + arguments: + - name: "--dataset-type" + alternatives: ["-dt"] + type: "string" + description: "The dataset type that should used to get data" + required: true + # - name: "--output" + # alternatives: ["-o"] + # type: "file" + # direction: "output" + # default: "output.h5ad" + # description: "Output h5ad file containing both input matrices data" + # required: true + resources: + - type: python_script + path: pancreas.py + # - path: "../../utils/utils.py" + # tests: + # - type: python_script + # path: test.py +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - anndata # needed by utils.py + - pandas # needed by utils.py + - scanpy # needed by utils.py + - numpy # needed by utils.py + - type: nextflow diff --git a/src/label_projection/datasets/pancreas/pancreas.py b/src/label_projection/datasets/pancreas/pancreas.py new file mode 100644 index 0000000000..e69de29bb2 From 1b16b916b677599a097442ae02980d423a712985 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Thu, 19 May 2022 12:56:02 -0300 Subject: [PATCH 0180/1233] wip: preprocess Former-commit-id: e108d2e4ddbfee7f32529ff9cb7dea053660116d --- .../data/pancreas/preprocess/config.vsh.yaml | 51 +++++++++++ src/common/data/pancreas/preprocess/noise.py | 46 ++++++++++ .../data/pancreas/preprocess/preprocess.py | 88 +++++++++++++++++++ src/common/data/utils/preprocess.py | 7 ++ 4 files changed, 192 insertions(+) create mode 100644 src/common/data/pancreas/preprocess/config.vsh.yaml create mode 100644 src/common/data/pancreas/preprocess/noise.py create mode 100644 src/common/data/pancreas/preprocess/preprocess.py create mode 100644 src/common/data/utils/preprocess.py diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/data/pancreas/preprocess/config.vsh.yaml new file mode 100644 index 0000000000..2495b24441 --- /dev/null +++ b/src/common/data/pancreas/preprocess/config.vsh.yaml @@ -0,0 +1,51 @@ +functionality: + name: "load_pancreas" + namespace: "common/data/pancreas/preprocess" + version: "dev" + description: "Common component to preprocess pancreas data" + authors: + - name: "Scott Gigante" + roles: [ maintainer, author ] + props: { github: scottgigante } + arguments: + - name: "--input" + type: "file" + description: "Input data to be preprocessed" + required: true + - name: "--test" + description: "Indicates if should be returned a test preprocessed data" + type: "boolean" + required: true + - name: "--method" + description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" + type: "string" + required: true + default: "batch" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file donwloaded from 'url' input" + required: true + resources: + - type: python_script + path: preprocess.py + - path: noise.py + - path: "../../utils/" + tests: + - type: python_script + path: load_save_test.py + - path: load_save.py + - path: fake_anndata.py +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - scanpy + - openpyxl # to tests + - type: nextflow diff --git a/src/common/data/pancreas/preprocess/noise.py b/src/common/data/pancreas/preprocess/noise.py new file mode 100644 index 0000000000..36872f0269 --- /dev/null +++ b/src/common/data/pancreas/preprocess/noise.py @@ -0,0 +1,46 @@ +import numpy as np + + +def add_label_noise(adata, noise_prob): + """Inject random label noise in the dataset . + + This is done by permuting a fraction of the labels in the training set. + + By adding different levels of label noise metrics can be evaluated to show + generalization trends from training data even if ground truth is uncertain. + + Parameters + ------- + adata : AnnData + A dataset with the required fields for the label_projection task. + + noise_prob : Float + The probability of label noise in the training data. + + Returns + ------- + new_adata : AnnData + Dataset where training labels have been permuted by specified probability. + """ + + old_labels = adata.obs["labels"].pipe(np.array) + old_labels_train = old_labels[adata.obs["is_train"]].copy() + new_labels_train = old_labels_train.copy() + + label_names = np.unique(new_labels_train) + + n_labels = label_names.shape[0] + + reassign_probs = (noise_prob / (n_labels - 1)) * np.ones((n_labels, n_labels)) + + np.fill_diagonal(reassign_probs, 1 - noise_prob) + + for k, label in enumerate(label_names): + label_indices = np.where(old_labels_train == label)[0] + new_labels_train[label_indices] = np.random.choice( + label_names, label_indices.shape[0], p=reassign_probs[:, k] + ) + + adata.obs.loc[adata.obs["is_train"], "labels"] = new_labels_train + + return adata diff --git a/src/common/data/pancreas/preprocess/preprocess.py b/src/common/data/pancreas/preprocess/preprocess.py new file mode 100644 index 0000000000..5c907d17a6 --- /dev/null +++ b/src/common/data/pancreas/preprocess/preprocess.py @@ -0,0 +1,88 @@ +## VIASH START +par = { + "input": "data.h5ad", + "test": False, + "method": 'batch', + "output": "/tmp/output.h5ad" +} +resources_dir = '../../utils/' +## VIASH END +import sys +sys.path.append(resources_dir) +sys.path.append("./") +import noise +import preprocess +import numpy as np +import scanpy as sc + + +def batch(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] + adata.obs["is_train"] = [ + False if adata.obs["batch"][idx] in test_batches else True + for idx in adata.obs_names + ] + return + + +def random(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + return adata + + +def random_with_noise(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign trainin/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + # Inject label noise + adata = noise.add_label_noise(adata, noise_prob=0.2) + + +func_map = {'batch': batch, + 'random': random, + 'random_with_noise': random_with_noise} + + +def run_script(par): + method_func = func_map[par['method']] + adata = sc.read(par['input']) + if par['test']: + adata = adata[:, :500].copy() + preprocess.filter_genes_cells(adata) + + keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] + keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] + keep_tech_idx = adata.obs["tech"].isin(keep_techs) + keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) + adata = adata[keep_tech_idx & keep_celltype_idx].copy() + + sc.pp.subsample(adata, n_obs=500) + # Note: could also use 200-500 HVGs rather than 200 random genes + + # Ensure there are no cells or genes with 0 counts + preprocess.filter_genes_cells(adata) + else: + adata = preprocess.filter_genes_cells(adata) + preprocessed_adata = method_func(adata) + preprocessed_adata.write(par['output']) + return None + + +if ("par" in locals()): + run_script(par) diff --git a/src/common/data/utils/preprocess.py b/src/common/data/utils/preprocess.py new file mode 100644 index 0000000000..8189c467c1 --- /dev/null +++ b/src/common/data/utils/preprocess.py @@ -0,0 +1,7 @@ +import scanpy as sc + + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) From 2efb5e8e5a08da03ad0aa69a6a118a3ddb4ad062 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Fri, 20 May 2022 15:08:24 -0300 Subject: [PATCH 0181/1233] chore: Robrecht comments for load component Former-commit-id: 9f0e929af0d2a8f9ed06d5baf89ba0db4cfe9b16 --- src/common/data/pancreas/load/config.vsh.yaml | 6 +-- src/common/data/pancreas/load/fake_anndata.py | 14 ------- src/common/data/pancreas/load/load_save.py | 37 ------------------- .../data/pancreas/load/load_save_test.py | 32 ---------------- src/common/data/pancreas/load/script.py | 23 ++++++++++++ src/common/data/pancreas/load/test_script.py | 23 ++++++++++++ 6 files changed, 48 insertions(+), 87 deletions(-) delete mode 100644 src/common/data/pancreas/load/fake_anndata.py delete mode 100644 src/common/data/pancreas/load/load_save.py delete mode 100644 src/common/data/pancreas/load/load_save_test.py create mode 100644 src/common/data/pancreas/load/script.py create mode 100644 src/common/data/pancreas/load/test_script.py diff --git a/src/common/data/pancreas/load/config.vsh.yaml b/src/common/data/pancreas/load/config.vsh.yaml index 6f9ca2c134..7fe5792f7e 100644 --- a/src/common/data/pancreas/load/config.vsh.yaml +++ b/src/common/data/pancreas/load/config.vsh.yaml @@ -21,12 +21,10 @@ functionality: required: true resources: - type: python_script - path: load_save.py + path: script.py tests: - type: python_script - path: load_save_test.py - - path: load_save.py - - path: fake_anndata.py + path: test_script.py platforms: - type: native - type: docker diff --git a/src/common/data/pancreas/load/fake_anndata.py b/src/common/data/pancreas/load/fake_anndata.py deleted file mode 100644 index ecbf5d1f48..0000000000 --- a/src/common/data/pancreas/load/fake_anndata.py +++ /dev/null @@ -1,14 +0,0 @@ -import anndata -import pandas as pd -import numpy as np - - -def generate_fake_anndata(): - X = np.zeros((3, 3)) - obs = pd.DataFrame([['celseq', 'gamma', 0.02], ['celseq', 'gamma', 0.07], ['celseq', 'gamma', 0.03]], - columns=['tech', 'celltype', 'size_factors'], - index=['A1BG', 'A1CF', 'A2M']) - var = pd.DataFrame(index=['A1BG', 'A1CF', 'A2M']) - adata = anndata.AnnData(X=X, obs=obs, var=var) - adata.layers['counts'] = X - return adata diff --git a/src/common/data/pancreas/load/load_save.py b/src/common/data/pancreas/load/load_save.py deleted file mode 100644 index 3254f11ea6..0000000000 --- a/src/common/data/pancreas/load/load_save.py +++ /dev/null @@ -1,37 +0,0 @@ -## VIASH START -par = { - "url": "https://ndownloader.figshare.com/files/24539828", - "output": "/tmp/output.h5ad" -} -## VIASH END -import os -from os.path import exists -import scanpy as sc -import scprep -import tempfile - - -def load_data(url): - """Download pancreas data from url.""" - with tempfile.TemporaryDirectory() as tempdir: - filepath = os.path.join(tempdir, "pancreas.h5ad") - scprep.io.download.download_url(url, filepath) - adata = sc.read(filepath) - adata.X = adata.layers["counts"] - del adata.layers["counts"] - return adata - - -def save_data(adata, output): - adata.write(output) - return None - - -def run_script(par): - adata = load_data(par['url']) - save_data(adata, par['output']) - return None - - -if ("par" in locals()): - run_script(par) diff --git a/src/common/data/pancreas/load/load_save_test.py b/src/common/data/pancreas/load/load_save_test.py deleted file mode 100644 index 5d5330c5a2..0000000000 --- a/src/common/data/pancreas/load/load_save_test.py +++ /dev/null @@ -1,32 +0,0 @@ -import sys -sys.path.append("./") -import load_save -import fake_anndata -from os.path import exists -import unittest -import scanpy as sc -from unittest.mock import patch - - -URL = "https://fake.url" -OUTPUT = "/tmp/output.h5ad" - - -class LoadDataTest(unittest.TestCase): - @patch('scprep.io.download.download_url') - @patch('scanpy.read') - def test_load_data(self, read_method, download_url_method): - download_url_method.return_value = None - read_method.return_value = fake_anndata.generate_fake_anndata() - response = load_save.load_data(URL) - self.assertEqual((3, 3), response.X.shape) - - -class SaveDataTest(unittest.TestCase): - def test_save_data(self): - load_save.save_data(fake_anndata.generate_fake_anndata(), "./output.h5ad") - self.assertTrue(exists("./output.h5ad"), "File should exists") - - -if __name__ == "__main__": - unittest.main() diff --git a/src/common/data/pancreas/load/script.py b/src/common/data/pancreas/load/script.py new file mode 100644 index 0000000000..da42981c8b --- /dev/null +++ b/src/common/data/pancreas/load/script.py @@ -0,0 +1,23 @@ +## VIASH START +par = { + "url": "https://ndownloader.figshare.com/files/24539828", + "output": "/tmp/output.h5ad" +} +## VIASH END +print("Import libraries") +import os +import scanpy as sc +import scprep +import tempfile + + +with tempfile.TemporaryDirectory() as tempdir: + filepath = os.path.join(tempdir, "pancreas.h5ad") + print("Download data from '--url'") + scprep.io.download.download_url(par['url'], filepath) + adata = sc.read(filepath) + adata.X = adata.layers["counts"] + del adata.layers["counts"] + +print("Writing data in {output}".format(output=par['output'])) +adata.write(par['output']) diff --git a/src/common/data/pancreas/load/test_script.py b/src/common/data/pancreas/load/test_script.py new file mode 100644 index 0000000000..702eec3e22 --- /dev/null +++ b/src/common/data/pancreas/load/test_script.py @@ -0,0 +1,23 @@ +import subprocess +import scanpy as sc +from os import path + +URL = "https://ndownloader.figshare.com/files/24539828" +OUTPUT = "output.h5ad" + +print(">> Running script") +out = subprocess.check_output([ + "./load_pancreas", + "--url", URL, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that output fits expected API") +adata = sc.read_h5ad(OUTPUT) +# TODO: complete with API checks +assert "counts" not in adata.layers + +print(">> All tests passed successfully") From d93c06aafbc6928e5b4e9903b0574ec606000ea3 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Fri, 20 May 2022 15:08:53 -0300 Subject: [PATCH 0182/1233] wip: preprocess simplified Former-commit-id: 431fe3a3fdb4ca75fa8fbb553ae050d9d9259dc3 --- .../data/pancreas/preprocess/config.vsh.yaml | 19 ++-- .../data/pancreas/preprocess/preprocess.py | 89 +------------------ src/common/data/pancreas/preprocess/script.py | 78 ++++++++++++++++ 3 files changed, 93 insertions(+), 93 deletions(-) create mode 100644 src/common/data/pancreas/preprocess/script.py diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/data/pancreas/preprocess/config.vsh.yaml index 2495b24441..433f7ea846 100644 --- a/src/common/data/pancreas/preprocess/config.vsh.yaml +++ b/src/common/data/pancreas/preprocess/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "load_pancreas" + name: "preprocess_pancreas" namespace: "common/data/pancreas/preprocess" version: "dev" description: "Common component to preprocess pancreas data" @@ -19,6 +19,7 @@ functionality: - name: "--method" description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" type: "string" + values: ['batch', 'random', 'random_with_noise'] required: true default: "batch" - name: "--output" @@ -30,14 +31,16 @@ functionality: required: true resources: - type: python_script - path: preprocess.py - - path: noise.py - - path: "../../utils/" - tests: + path: script.py - type: python_script - path: load_save_test.py - - path: load_save.py - - path: fake_anndata.py + path: noise.py + - type: python_script + path: "../../utils/preprocess.py" + # tests: + # - type: python_script + # path: load_save_test.py + # - path: load_save.py + # - path: fake_anndata.py platforms: - type: native - type: docker diff --git a/src/common/data/pancreas/preprocess/preprocess.py b/src/common/data/pancreas/preprocess/preprocess.py index 5c907d17a6..8189c467c1 100644 --- a/src/common/data/pancreas/preprocess/preprocess.py +++ b/src/common/data/pancreas/preprocess/preprocess.py @@ -1,88 +1,7 @@ -## VIASH START -par = { - "input": "data.h5ad", - "test": False, - "method": 'batch', - "output": "/tmp/output.h5ad" -} -resources_dir = '../../utils/' -## VIASH END -import sys -sys.path.append(resources_dir) -sys.path.append("./") -import noise -import preprocess -import numpy as np import scanpy as sc -def batch(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] - adata.obs["is_train"] = [ - False if adata.obs["batch"][idx] in test_batches else True - for idx in adata.obs_names - ] - return - - -def random(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - return adata - - -def random_with_noise(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign trainin/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - # Inject label noise - adata = noise.add_label_noise(adata, noise_prob=0.2) - - -func_map = {'batch': batch, - 'random': random, - 'random_with_noise': random_with_noise} - - -def run_script(par): - method_func = func_map[par['method']] - adata = sc.read(par['input']) - if par['test']: - adata = adata[:, :500].copy() - preprocess.filter_genes_cells(adata) - - keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] - keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] - keep_tech_idx = adata.obs["tech"].isin(keep_techs) - keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) - adata = adata[keep_tech_idx & keep_celltype_idx].copy() - - sc.pp.subsample(adata, n_obs=500) - # Note: could also use 200-500 HVGs rather than 200 random genes - - # Ensure there are no cells or genes with 0 counts - preprocess.filter_genes_cells(adata) - else: - adata = preprocess.filter_genes_cells(adata) - preprocessed_adata = method_func(adata) - preprocessed_adata.write(par['output']) - return None - - -if ("par" in locals()): - run_script(par) +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) diff --git a/src/common/data/pancreas/preprocess/script.py b/src/common/data/pancreas/preprocess/script.py new file mode 100644 index 0000000000..9b3166ea56 --- /dev/null +++ b/src/common/data/pancreas/preprocess/script.py @@ -0,0 +1,78 @@ +## VIASH START +par = { + "input": "data.h5ad", + "test": False, + "method": 'batch', + "output": "/tmp/output.h5ad" +} +resources_dir = '../../utils/' +## VIASH END +# import sys +# sys.path.append(resources_dir, "./") +import noise +import preprocess +import numpy as np +import scanpy as sc + + +def batch(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] + adata.obs["is_train"] = [ + False if adata.obs["batch"][idx] in test_batches else True + for idx in adata.obs_names + ] + return + + +def random(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + return adata + + +def random_with_noise(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign trainin/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + # Inject label noise + adata = noise.add_label_noise(adata, noise_prob=0.2) + + +func_map = {'batch': batch, + 'random': random, + 'random_with_noise': random_with_noise} + +method_func = func_map[par['method']] +adata = sc.read(par['input']) + +if par['test']: + adata = adata[:, :500].copy() + preprocess.filter_genes_cells(adata) + keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] + keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] + keep_tech_idx = adata.obs["tech"].isin(keep_techs) + keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) + adata = adata[keep_tech_idx & keep_celltype_idx].copy() + sc.pp.subsample(adata, n_obs=500) + # Note: could also use 200-500 HVGs rather than 200 random genes + # Ensure there are no cells or genes with 0 counts + preprocess.filter_genes_cells(adata) +else: + adata = preprocess.filter_genes_cells(adata) + preprocessed_adata = method_func(adata) + preprocessed_adata.write(par['output']) From eb1cd0b6dc5e721acd7b4af196f50f7945e5cb88 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 23 May 2022 13:17:40 +0200 Subject: [PATCH 0183/1233] minor fixes to component Former-commit-id: e6eea77a41ef0a5c29b1daa220fba7ffa50bf62b --- src/common/data/pancreas/preprocess/config.vsh.yaml | 11 +++++------ src/common/data/pancreas/preprocess/script.py | 5 +++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/data/pancreas/preprocess/config.vsh.yaml index 433f7ea846..b55a1298ea 100644 --- a/src/common/data/pancreas/preprocess/config.vsh.yaml +++ b/src/common/data/pancreas/preprocess/config.vsh.yaml @@ -15,12 +15,13 @@ functionality: - name: "--test" description: "Indicates if should be returned a test preprocessed data" type: "boolean" - required: true + required: false + default: false - name: "--method" description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" type: "string" values: ['batch', 'random', 'random_with_noise'] - required: true + required: false default: "batch" - name: "--output" alternatives: ["-o"] @@ -32,10 +33,8 @@ functionality: resources: - type: python_script path: script.py - - type: python_script - path: noise.py - - type: python_script - path: "../../utils/preprocess.py" + - path: noise.py + - path: "../../utils/preprocess.py" # tests: # - type: python_script # path: load_save_test.py diff --git a/src/common/data/pancreas/preprocess/script.py b/src/common/data/pancreas/preprocess/script.py index 9b3166ea56..4738562cd3 100644 --- a/src/common/data/pancreas/preprocess/script.py +++ b/src/common/data/pancreas/preprocess/script.py @@ -7,8 +7,9 @@ } resources_dir = '../../utils/' ## VIASH END -# import sys -# sys.path.append(resources_dir, "./") + +import sys +sys.path.append(resources_dir) import noise import preprocess import numpy as np From 3461978fdc9c1fced4a33b64f0b761534ec37c1f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 23 May 2022 13:30:38 +0200 Subject: [PATCH 0184/1233] add example Former-commit-id: 12d27937d2fee87888df37775de90ac54229585d --- src/common/data/pancreas/load/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/data/pancreas/load/config.vsh.yaml b/src/common/data/pancreas/load/config.vsh.yaml index 7fe5792f7e..9027a99201 100644 --- a/src/common/data/pancreas/load/config.vsh.yaml +++ b/src/common/data/pancreas/load/config.vsh.yaml @@ -12,6 +12,7 @@ functionality: description: "Url where data should be download" type: "string" required: true + example: https://ndownloader.figshare.com/files/24539828 - name: "--output" alternatives: ["-o"] type: "file" @@ -26,7 +27,6 @@ functionality: - type: python_script path: test_script.py platforms: - - type: native - type: docker image: "python:3.8" setup: @@ -34,5 +34,5 @@ platforms: packages: - scprep - scanpy - - openpyxl # to tests + - type: native - type: nextflow From 03962c03944cf3956cbd1fb375ddd9dde4105d28 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 23 May 2022 11:59:49 -0300 Subject: [PATCH 0185/1233] feat: preprocess component for pancreas data Former-commit-id: 824cf748836c0284b58cb45e3e8957faad3cddac --- src/common/data/pancreas/load/config.vsh.yaml | 5 ++- .../data/pancreas/preprocess/config.vsh.yaml | 15 +++++--- .../data/pancreas/preprocess/preprocess.py | 7 ---- src/common/data/pancreas/preprocess/script.py | 16 +++++--- .../data/pancreas/preprocess/test_script.py | 37 +++++++++++++++++++ src/common/data/utils/preprocess.py | 2 + 6 files changed, 62 insertions(+), 20 deletions(-) delete mode 100644 src/common/data/pancreas/preprocess/preprocess.py create mode 100644 src/common/data/pancreas/preprocess/test_script.py diff --git a/src/common/data/pancreas/load/config.vsh.yaml b/src/common/data/pancreas/load/config.vsh.yaml index 9027a99201..8104562690 100644 --- a/src/common/data/pancreas/load/config.vsh.yaml +++ b/src/common/data/pancreas/load/config.vsh.yaml @@ -5,8 +5,11 @@ functionality: description: "Common component to load pancreas data" authors: - name: "Scott Gigante" - roles: [ maintainer, author ] + roles: [ author ] props: { github: scottgigante } + - name: "Vinicius Saraiva Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } arguments: - name: "--url" description: "Url where data should be download" diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/data/pancreas/preprocess/config.vsh.yaml index b55a1298ea..d18ba5daa2 100644 --- a/src/common/data/pancreas/preprocess/config.vsh.yaml +++ b/src/common/data/pancreas/preprocess/config.vsh.yaml @@ -5,8 +5,11 @@ functionality: description: "Common component to preprocess pancreas data" authors: - name: "Scott Gigante" - roles: [ maintainer, author ] + roles: [ author ] props: { github: scottgigante } + - name: "Vinicius Saraiva Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } arguments: - name: "--input" type: "file" @@ -35,11 +38,11 @@ functionality: path: script.py - path: noise.py - path: "../../utils/preprocess.py" - # tests: - # - type: python_script - # path: load_save_test.py - # - path: load_save.py - # - path: fake_anndata.py + tests: + - type: python_script + path: test_script.py + - type: file + path: test_data.h5ad platforms: - type: native - type: docker diff --git a/src/common/data/pancreas/preprocess/preprocess.py b/src/common/data/pancreas/preprocess/preprocess.py deleted file mode 100644 index 8189c467c1..0000000000 --- a/src/common/data/pancreas/preprocess/preprocess.py +++ /dev/null @@ -1,7 +0,0 @@ -import scanpy as sc - - -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) diff --git a/src/common/data/pancreas/preprocess/script.py b/src/common/data/pancreas/preprocess/script.py index 4738562cd3..f71de9a070 100644 --- a/src/common/data/pancreas/preprocess/script.py +++ b/src/common/data/pancreas/preprocess/script.py @@ -1,9 +1,9 @@ ## VIASH START par = { - "input": "data.h5ad", + "input": "./test/data.h5ad", "test": False, "method": 'batch', - "output": "/tmp/output.h5ad" + "output": "./test/preprocess.h5ad" } resources_dir = '../../utils/' ## VIASH END @@ -26,7 +26,7 @@ def batch(adata): False if adata.obs["batch"][idx] in test_batches else True for idx in adata.obs_names ] - return + return adata def random(adata): @@ -53,6 +53,8 @@ def random_with_noise(adata): # Inject label noise adata = noise.add_label_noise(adata, noise_prob=0.2) + return adata + func_map = {'batch': batch, 'random': random, @@ -74,6 +76,8 @@ def random_with_noise(adata): # Ensure there are no cells or genes with 0 counts preprocess.filter_genes_cells(adata) else: - adata = preprocess.filter_genes_cells(adata) - preprocessed_adata = method_func(adata) - preprocessed_adata.write(par['output']) + preprocess.filter_genes_cells(adata) + + +preprocessed_adata = method_func(adata) +preprocessed_adata.write(par['output']) diff --git a/src/common/data/pancreas/preprocess/test_script.py b/src/common/data/pancreas/preprocess/test_script.py new file mode 100644 index 0000000000..cc265d4e73 --- /dev/null +++ b/src/common/data/pancreas/preprocess/test_script.py @@ -0,0 +1,37 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data.h5ad" +OUTPUT = "preprocessed.h5ad" +METHODS = ["batch", "random", "random_with_noise"] + +print(">> Runing script as test") +out = subprocess.check_output([ + "./preprocess_pancreas", + "--input", INPUT, + "--test", "True", + "--output", OUTPUT +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that test output fits expected API") +adata = sc.read_h5ad(OUTPUT) +assert (500, 441) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + +for method in METHODS: + print(">> Running script for {} method".format(method)) + out = subprocess.check_output([ + "./preprocess_pancreas", + "--input", INPUT, + "--method", method, + "--output", OUTPUT + ]).decode("utf-8") + print(">> Checking whether file exists") + assert path.exists(OUTPUT) + print(">> Check that test output fits expected API") + adata = sc.read_h5ad(OUTPUT) + assert (16382, 18771) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + assert "batch" in adata.obs + assert "is_train" in adata.obs diff --git a/src/common/data/utils/preprocess.py b/src/common/data/utils/preprocess.py index 8189c467c1..01785bb0c2 100644 --- a/src/common/data/utils/preprocess.py +++ b/src/common/data/utils/preprocess.py @@ -5,3 +5,5 @@ def filter_genes_cells(adata): """Remove empty cells and genes.""" sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) + + return adata From 2ba5c6430a13459a968c63a03d4b0175a18f1f2d Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 23 May 2022 12:14:14 -0300 Subject: [PATCH 0186/1233] self-review Former-commit-id: 49187b2a1d7dec77b031716693513c9e7731249f --- .../data/pancreas/preprocess/config.vsh.yaml | 3 +- .../datasets/pancreas/config.vsh.yaml | 42 ------------------- .../datasets/pancreas/pancreas.py | 0 3 files changed, 1 insertion(+), 44 deletions(-) delete mode 100644 src/label_projection/datasets/pancreas/config.vsh.yaml delete mode 100644 src/label_projection/datasets/pancreas/pancreas.py diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/data/pancreas/preprocess/config.vsh.yaml index d18ba5daa2..468b39027c 100644 --- a/src/common/data/pancreas/preprocess/config.vsh.yaml +++ b/src/common/data/pancreas/preprocess/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: type: "file" direction: "output" default: "output.h5ad" - description: "Output h5ad file donwloaded from 'url' input" + description: "Output h5ad file preprocessed" required: true resources: - type: python_script @@ -52,5 +52,4 @@ platforms: packages: - scprep - scanpy - - openpyxl # to tests - type: nextflow diff --git a/src/label_projection/datasets/pancreas/config.vsh.yaml b/src/label_projection/datasets/pancreas/config.vsh.yaml deleted file mode 100644 index 01fddb3eef..0000000000 --- a/src/label_projection/datasets/pancreas/config.vsh.yaml +++ /dev/null @@ -1,42 +0,0 @@ -functionality: - name: "pancreas_dataset" - namespace: "label_projections/datasets" - version: "dev" - description: "Pancreas datasets for label_projection tasks" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } - arguments: - - name: "--dataset-type" - alternatives: ["-dt"] - type: "string" - description: "The dataset type that should used to get data" - required: true - # - name: "--output" - # alternatives: ["-o"] - # type: "file" - # direction: "output" - # default: "output.h5ad" - # description: "Output h5ad file containing both input matrices data" - # required: true - resources: - - type: python_script - path: pancreas.py - # - path: "../../utils/utils.py" - # tests: - # - type: python_script - # path: test.py -platforms: - - type: native - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - anndata # needed by utils.py - - pandas # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - type: nextflow diff --git a/src/label_projection/datasets/pancreas/pancreas.py b/src/label_projection/datasets/pancreas/pancreas.py deleted file mode 100644 index e69de29bb2..0000000000 From 1c0eba6022ca8d71e738946a8667a390b9e4786f Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Thu, 26 May 2022 15:34:55 -0300 Subject: [PATCH 0187/1233] wip: add preprocess to commons and add label_projection workflow Former-commit-id: 50eb71c362789716a97984ed5d4a267482cb8969 --- src/common/data/pancreas/load/config.vsh.yaml | 41 -- src/common/data/pancreas/load/script.py | 23 - src/common/data/pancreas/load/test_script.py | 23 - src/common/data_loader/config.vsh.yaml | 2 + .../pancreas => }/preprocess/config.vsh.yaml | 8 +- .../{data/pancreas => }/preprocess/noise.py | 5 - src/common/preprocess/preprocess | 418 ++++++++++++++++++ .../{data/utils => preprocess}/preprocess.py | 0 .../{data/pancreas => }/preprocess/script.py | 4 +- .../pancreas => }/preprocess/test_script.py | 4 +- src/label_projection/workflows/run/main.nf | 55 +++ .../workflows/run/nextflow.config | 16 + .../workflows/run/run_nextflow.sh | 22 + 13 files changed, 520 insertions(+), 101 deletions(-) delete mode 100644 src/common/data/pancreas/load/config.vsh.yaml delete mode 100644 src/common/data/pancreas/load/script.py delete mode 100644 src/common/data/pancreas/load/test_script.py rename src/common/{data/pancreas => }/preprocess/config.vsh.yaml (88%) rename src/common/{data/pancreas => }/preprocess/noise.py (99%) create mode 100755 src/common/preprocess/preprocess rename src/common/{data/utils => preprocess}/preprocess.py (100%) rename src/common/{data/pancreas => }/preprocess/script.py (97%) rename src/common/{data/pancreas => }/preprocess/test_script.py (94%) create mode 100644 src/label_projection/workflows/run/main.nf create mode 100644 src/label_projection/workflows/run/nextflow.config create mode 100644 src/label_projection/workflows/run/run_nextflow.sh diff --git a/src/common/data/pancreas/load/config.vsh.yaml b/src/common/data/pancreas/load/config.vsh.yaml deleted file mode 100644 index 8104562690..0000000000 --- a/src/common/data/pancreas/load/config.vsh.yaml +++ /dev/null @@ -1,41 +0,0 @@ -functionality: - name: "load_pancreas" - namespace: "common/data/pancreas/load" - version: "dev" - description: "Common component to load pancreas data" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Saraiva Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--url" - description: "Url where data should be download" - type: "string" - required: true - example: https://ndownloader.figshare.com/files/24539828 - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file donwloaded from 'url' input" - required: true - resources: - - type: python_script - path: script.py - tests: - - type: python_script - path: test_script.py -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - scanpy - - type: native - - type: nextflow diff --git a/src/common/data/pancreas/load/script.py b/src/common/data/pancreas/load/script.py deleted file mode 100644 index da42981c8b..0000000000 --- a/src/common/data/pancreas/load/script.py +++ /dev/null @@ -1,23 +0,0 @@ -## VIASH START -par = { - "url": "https://ndownloader.figshare.com/files/24539828", - "output": "/tmp/output.h5ad" -} -## VIASH END -print("Import libraries") -import os -import scanpy as sc -import scprep -import tempfile - - -with tempfile.TemporaryDirectory() as tempdir: - filepath = os.path.join(tempdir, "pancreas.h5ad") - print("Download data from '--url'") - scprep.io.download.download_url(par['url'], filepath) - adata = sc.read(filepath) - adata.X = adata.layers["counts"] - del adata.layers["counts"] - -print("Writing data in {output}".format(output=par['output'])) -adata.write(par['output']) diff --git a/src/common/data/pancreas/load/test_script.py b/src/common/data/pancreas/load/test_script.py deleted file mode 100644 index 702eec3e22..0000000000 --- a/src/common/data/pancreas/load/test_script.py +++ /dev/null @@ -1,23 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -URL = "https://ndownloader.figshare.com/files/24539828" -OUTPUT = "output.h5ad" - -print(">> Running script") -out = subprocess.check_output([ - "./load_pancreas", - "--url", URL, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(OUTPUT) - -print(">> Check that output fits expected API") -adata = sc.read_h5ad(OUTPUT) -# TODO: complete with API checks -assert "counts" not in adata.layers - -print(">> All tests passed successfully") diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml index c12a4f11c5..8e0bb8ce12 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -12,6 +12,7 @@ functionality: alternatives: ["-o"] type: "file" direction: "output" + deafult: "output.h5ad" description: "Output h5ad file of the cleaned dataset" required: true - name: "--url" @@ -20,6 +21,7 @@ functionality: required: true - name: "--name" type: "string" + default: "pbmc" description: "Name of dataset" required: true resources: diff --git a/src/common/data/pancreas/preprocess/config.vsh.yaml b/src/common/preprocess/config.vsh.yaml similarity index 88% rename from src/common/data/pancreas/preprocess/config.vsh.yaml rename to src/common/preprocess/config.vsh.yaml index 468b39027c..cfdefc4463 100644 --- a/src/common/data/pancreas/preprocess/config.vsh.yaml +++ b/src/common/preprocess/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: - name: "preprocess_pancreas" - namespace: "common/data/pancreas/preprocess" + name: "preprocess" + namespace: "common/preprocess" version: "dev" description: "Common component to preprocess pancreas data" authors: @@ -23,7 +23,7 @@ functionality: - name: "--method" description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" type: "string" - values: ['batch', 'random', 'random_with_noise'] + choices: ['batch', 'random', 'random_with_noise'] required: false default: "batch" - name: "--output" @@ -37,7 +37,7 @@ functionality: - type: python_script path: script.py - path: noise.py - - path: "../../utils/preprocess.py" + - path: preprocess.py tests: - type: python_script path: test_script.py diff --git a/src/common/data/pancreas/preprocess/noise.py b/src/common/preprocess/noise.py similarity index 99% rename from src/common/data/pancreas/preprocess/noise.py rename to src/common/preprocess/noise.py index 36872f0269..9cf639d743 100644 --- a/src/common/data/pancreas/preprocess/noise.py +++ b/src/common/preprocess/noise.py @@ -3,20 +3,15 @@ def add_label_noise(adata, noise_prob): """Inject random label noise in the dataset . - This is done by permuting a fraction of the labels in the training set. - By adding different levels of label noise metrics can be evaluated to show generalization trends from training data even if ground truth is uncertain. - Parameters ------- adata : AnnData A dataset with the required fields for the label_projection task. - noise_prob : Float The probability of label noise in the training data. - Returns ------- new_adata : AnnData diff --git a/src/common/preprocess/preprocess b/src/common/preprocess/preprocess new file mode 100755 index 0000000000..eea11f6282 --- /dev/null +++ b/src/common/preprocess/preprocess @@ -0,0 +1,418 @@ +#!/usr/bin/env bash + +# preprocess dev +# +# This wrapper script is auto-generated by viash 0.5.12 and is thus a derivative +# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data +# Intuitive. +# +# The component may contain files which fall under a different license. The +# authors of this component should specify the license in the header of such +# files, or include a separate license file detailing the licenses of all included +# files. +# +# Component authors: +# * Scott Gigante (author) {github: scottgigante} +# * Vinicius Saraiva Chagas (maintainer) {github: chagasVinicius} + +set -e + +if [ -z "$VIASH_TEMP" ]; then + VIASH_TEMP=/tmp +fi + +# define helper functions +# ViashQuote: put quotes around non flag values +# $1 : unquoted string +# return : possibly quoted string +# examples: +# ViashQuote --foo # returns --foo +# ViashQuote bar # returns 'bar' +# Viashquote --foo=bar # returns --foo='bar' +function ViashQuote { + if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then + echo "$1" | sed "s#=\(.*\)#='\1'#" + elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then + echo "$1" + else + echo "'$1'" + fi +} +# ViashRemoveFlags: Remove leading flag +# $1 : string with a possible leading flag +# return : string without possible leading flag +# examples: +# ViashRemoveFlags --foo=bar # returns bar +function ViashRemoveFlags { + echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' +} +# ViashSourceDir: return the path of a bash file, following symlinks +# usage : ViashSourceDir ${BASH_SOURCE[0]} +# $1 : Should always be set to ${BASH_SOURCE[0]} +# returns : The absolute path of the bash file +function ViashSourceDir { + SOURCE="$1" + while [ -h "$SOURCE" ]; do + DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" + done + cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd +} +# see https://en.wikipedia.org/wiki/Syslog#Severity_level +VIASH_LOGCODE_EMERGENCY=0 +VIASH_LOGCODE_ALERT=1 +VIASH_LOGCODE_CRITICAL=2 +VIASH_LOGCODE_ERROR=3 +VIASH_LOGCODE_WARNING=4 +VIASH_LOGCODE_NOTICE=5 +VIASH_LOGCODE_INFO=6 +VIASH_LOGCODE_DEBUG=7 +VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE + +# ViashLog: Log events depending on the verbosity level +# usage: ViashLog 1 alert Oh no something went wrong! +# $1: required verbosity level +# $2: display tag +# $3+: messages to display +# stdout: Your input, prepended by '[$2] '. +function ViashLog { + local required_level="$1" + local display_tag="$2" + shift 2 + if [ $VIASH_VERBOSITY -ge $required_level ]; then + echo "[$display_tag]" "$@" + fi +} + +# ViashEmergency: log events when the system is unstable +# usage: ViashEmergency Oh no something went wrong. +# stdout: Your input, prepended by '[emergency] '. +function ViashEmergency { + ViashLog $VIASH_LOGCODE_EMERGENCY emergency $@ +} + +# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) +# usage: ViashAlert Oh no something went wrong. +# stdout: Your input, prepended by '[alert] '. +function ViashAlert { + ViashLog $VIASH_LOGCODE_ALERT alert $@ +} + +# ViashCritical: log events when a critical condition occurs +# usage: ViashCritical Oh no something went wrong. +# stdout: Your input, prepended by '[critical] '. +function ViashCritical { + ViashLog $VIASH_LOGCODE_CRITICAL critical $@ +} + +# ViashError: log events when an error condition occurs +# usage: ViashError Oh no something went wrong. +# stdout: Your input, prepended by '[error] '. +function ViashError { + ViashLog $VIASH_LOGCODE_ERROR error $@ +} + +# ViashWarning: log potentially abnormal events +# usage: ViashWarning Something may have gone wrong. +# stdout: Your input, prepended by '[warning] '. +function ViashWarning { + ViashLog $VIASH_LOGCODE_WARNING warning $@ +} + +# ViashNotice: log significant but normal events +# usage: ViashNotice This just happened. +# stdout: Your input, prepended by '[notice] '. +function ViashNotice { + ViashLog $VIASH_LOGCODE_NOTICE notice $@ +} + +# ViashInfo: log normal events +# usage: ViashInfo This just happened. +# stdout: Your input, prepended by '[info] '. +function ViashInfo { + ViashLog $VIASH_LOGCODE_INFO info $@ +} + +# ViashDebug: log all events, for debugging purposes +# usage: ViashDebug This just happened. +# stdout: Your input, prepended by '[debug] '. +function ViashDebug { + ViashLog $VIASH_LOGCODE_DEBUG debug $@ +} + +# find source folder of this component +VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` + +# backwards compatibility +VIASH_RESOURCES_DIR="$VIASH_META_RESOURCES_DIR" + +# define meta fields +VIASH_META_FUNCTIONALITY_NAME="preprocess" + + +# ViashHelp: Display helpful explanation about this executable +function ViashHelp { + echo "preprocess dev" + echo "" + echo "Common component to preprocess pancreas data" + echo "" + echo "Options:" + echo " --input" + echo " type: file, required parameter" + echo " Input data to be preprocessed" + echo "" + echo " --test" + echo " type: boolean" + echo " default: false" + echo " Indicates if should be returned a test preprocessed data" + echo "" + echo " --method" + echo " type: string" + echo " default: batch" + echo " choices:" + echo " - batch" + echo " - random" + echo " - random_with_noise" + echo " The preprocess method to be used. Options: ['batch', 'random'," + echo "'random_with_noise']" + echo "" + echo " -o, --output" + echo " type: file, required parameter, output" + echo " default: output.h5ad" + echo " Output h5ad file preprocessed" +} + +# initialise array +VIASH_POSITIONAL_ARGS='' +VIASH_MODE='run' + +while [[ $# -gt 0 ]]; do + case "$1" in + -h|--help) + ViashHelp + exit + ;; + ---v|---verbose) + let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" + shift 1 + ;; + ---verbosity) + VIASH_VERBOSITY="$2" + shift 2 + ;; + ---verbosity=*) + VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" + shift 1 + ;; + --version) + echo "preprocess dev" + exit + ;; + --input) + VIASH_PAR_INPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input=*) + VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + --test) + VIASH_PAR_TEST="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --test. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --test=*) + VIASH_PAR_TEST=$(ViashRemoveFlags "$1") + shift 1 + ;; + --method) + VIASH_PAR_METHOD="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --method. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --method=*) + VIASH_PAR_METHOD=$(ViashRemoveFlags "$1") + shift 1 + ;; + --output) + VIASH_PAR_OUTPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output=*) + VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; + -o) + VIASH_PAR_OUTPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + *) # positional arg or unknown option + # since the positional args will be eval'd, can we always quote, instead of using ViashQuote + VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" + shift # past argument + ;; + esac +done + +# parse positional parameters +eval set -- $VIASH_POSITIONAL_ARGS + + + + +# check whether required parameters exist +if [ -z "$VIASH_PAR_INPUT" ]; then + ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_OUTPUT" ]; then + ViashError '--output' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi +if [ -z "$VIASH_PAR_TEST" ]; then + VIASH_PAR_TEST="false" +fi +if [ -z "$VIASH_PAR_METHOD" ]; then + VIASH_PAR_METHOD="batch" +fi + + +# check whether parameters values are of the right type + +if [[ -n "$VIASH_PAR_TEST" ]]; then + if ! [[ "$VIASH_PAR_TEST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then + ViashError '--test' has to be a boolean. Use "--help" to get more information on the parameters. + exit 1 + fi +fi + + + + +# check whether parameters values are of the right type + + +if [ ! -z "$VIASH_PAR_METHOD" ]; then + VIASH_PAR_METHOD_CHOICES=("batch:random:random_with_noise") + IFS=: + set -f + if ! [[ ":${VIASH_PAR_METHOD_CHOICES[*]}:" =~ ":$VIASH_PAR_METHOD:" ]]; then + ViashError '--method' specified value of \'$VIASH_PAR_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters. + exit 1 + fi + set +f + unset IFS +fi + + + +cat << VIASHEOF | bash +set -e +tempscript=\$(mktemp "$VIASH_TEMP/viash-run-preprocess-XXXXXX") +function clean_up { + rm "\$tempscript" +} +function interrupt { + echo -e "\nCTRL-C Pressed..." + exit 1 +} +trap clean_up EXIT +trap interrupt INT SIGINT +cat > "\$tempscript" << 'VIASHMAIN' +## VIASH START +# The following code has been auto-generated by Viash. +par = { + 'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "'${VIASH_PAR_INPUT//\'/\\\'}'"; else echo None; fi ), + 'test': $( if [ ! -z ${VIASH_PAR_TEST+x} ]; then echo "'${VIASH_PAR_TEST//\'/\\\'}'.lower() == 'true'"; else echo None; fi ), + 'method': $( if [ ! -z ${VIASH_PAR_METHOD+x} ]; then echo "'${VIASH_PAR_METHOD//\'/\\\'}'"; else echo None; fi ), + 'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "'${VIASH_PAR_OUTPUT//\'/\\\'}'"; else echo None; fi ) +} +meta = { + 'functionality_name': '$VIASH_META_FUNCTIONALITY_NAME', + 'resources_dir': '$VIASH_META_RESOURCES_DIR', + 'temp_dir': '$VIASH_TEMP' +} + +resources_dir = '$VIASH_META_RESOURCES_DIR' + +## VIASH END +import noise +import preprocess +import numpy as np +import scanpy as sc + + +def batch(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] + adata.obs["is_train"] = [ + False if adata.obs["batch"][idx] in test_batches else True + for idx in adata.obs_names + ] + return adata + + +def random(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + return adata + + +def random_with_noise(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign trainin/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + # Inject label noise + adata = noise.add_label_noise(adata, noise_prob=0.2) + + return adata + + +func_map = {'batch': batch, + 'random': random, + 'random_with_noise': random_with_noise} + +method_func = func_map[par['method']] +adata = sc.read(par['input']) + +if par['test']: + adata = adata[:, :500].copy() + preprocess.filter_genes_cells(adata) + keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] + keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] + keep_tech_idx = adata.obs["tech"].isin(keep_techs) + keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) + adata = adata[keep_tech_idx & keep_celltype_idx].copy() + sc.pp.subsample(adata, n_obs=500) + # Note: could also use 200-500 HVGs rather than 200 random genes + # Ensure there are no cells or genes with 0 counts + preprocess.filter_genes_cells(adata) +else: + preprocess.filter_genes_cells(adata) + + +preprocessed_adata = method_func(adata) +preprocessed_adata.write(par['output']) +VIASHMAIN +python "\$tempscript" & +wait "\$!" + +VIASHEOF diff --git a/src/common/data/utils/preprocess.py b/src/common/preprocess/preprocess.py similarity index 100% rename from src/common/data/utils/preprocess.py rename to src/common/preprocess/preprocess.py diff --git a/src/common/data/pancreas/preprocess/script.py b/src/common/preprocess/script.py similarity index 97% rename from src/common/data/pancreas/preprocess/script.py rename to src/common/preprocess/script.py index f71de9a070..1b110f34ee 100644 --- a/src/common/data/pancreas/preprocess/script.py +++ b/src/common/preprocess/script.py @@ -5,11 +5,9 @@ "method": 'batch', "output": "./test/preprocess.h5ad" } -resources_dir = '../../utils/' ## VIASH END - import sys -sys.path.append(resources_dir) +sys.path.append("./") import noise import preprocess import numpy as np diff --git a/src/common/data/pancreas/preprocess/test_script.py b/src/common/preprocess/test_script.py similarity index 94% rename from src/common/data/pancreas/preprocess/test_script.py rename to src/common/preprocess/test_script.py index cc265d4e73..97a37a5709 100644 --- a/src/common/data/pancreas/preprocess/test_script.py +++ b/src/common/preprocess/test_script.py @@ -8,7 +8,7 @@ print(">> Runing script as test") out = subprocess.check_output([ - "./preprocess_pancreas", + "./preprocess", "--input", INPUT, "--test", "True", "--output", OUTPUT @@ -23,7 +23,7 @@ for method in METHODS: print(">> Running script for {} method".format(method)) out = subprocess.check_output([ - "./preprocess_pancreas", + "./preprocess", "--input", INPUT, "--method", method, "--output", OUTPUT diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf new file mode 100644 index 0000000000..053e0db639 --- /dev/null +++ b/src/label_projection/workflows/run/main.nf @@ -0,0 +1,55 @@ +nextflow.enable.dsl=2 + +/* For now, you need to manually specify the + * root directory of this repository as follows. + * (it's a nextflow limitation I'm trying to figure out + * how to resolve.) */ + +targetDir = "${params.rootDir}/target/nextflow" + +// import dataset loaders +include { data_loader } from "$targetDir/common/data_loader/main.nf" params(params) +// include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) + +// import methods +// include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) +// include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) +// include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) +// include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) + +// import metrics +// include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) +// include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) + +// import helper functions +// include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) + + +/******************************************************* +* Dataset processor workflows * +*******************************************************/ +// This workflow reads in a tsv containing some metadata about each dataset. +// For each entry in the metadata, a dataset is generated, usually by downloading +// and processing some files. The end result of each of these workflows +// should be simply a channel of [id, h5adfile, params] triplets. +// +// If the need arises, these workflows could be split off into a separate file. + +workflow load_data { + main: + output_ = Channel.value(params) + | map { params -> ["new-id", ["url": params.url, "name": params.name]] } + | data_loader + emit: + output_ +} + +/******************************************************* +* Main workflow * +*******************************************************/ + +workflow { + load_data + | view() + +} diff --git a/src/label_projection/workflows/run/nextflow.config b/src/label_projection/workflows/run/nextflow.config new file mode 100644 index 0000000000..4e1452b19d --- /dev/null +++ b/src/label_projection/workflows/run/nextflow.config @@ -0,0 +1,16 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// set default container & default labels +process { + container = 'nextflow/bash:latest' + + withLabel: highmem { memory = 50.Gb } + withLabel: highcpu { cpus = 20 } +} diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_nextflow.sh new file mode 100644 index 0000000000..da8aad7273 --- /dev/null +++ b/src/label_projection/workflows/run/run_nextflow.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +# choose a particular version of nextflow +export NXF_VER=21.10.6 + +bin/nextflow \ + run . \ + -main-script src/label_projection/workflows/run/main.nf \ + --url "https://ndownloader.figshare.com/files/24539828" \ + --name "pbmc" \ + --output output/label_projection \ + -resume \ + -with-docker From c4574c939fac16c9f5ba2b618514ebac8ed54360 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 30 May 2022 10:53:17 -0300 Subject: [PATCH 0188/1233] feat: label_projection load_data + preprocess workflow Former-commit-id: e333eb67795d04d933a330d6d0d9167136fc01dc --- src/common/data_loader/config.vsh.yaml | 5 +- src/common/preprocess/config.vsh.yaml | 55 --- src/common/preprocess/noise.py | 41 -- src/common/preprocess/preprocess | 418 ------------------ src/common/preprocess/preprocess.py | 9 - src/common/preprocess/script.py | 81 ---- src/common/preprocess/test_script.py | 37 -- src/label_projection/workflows/run/main.nf | 29 +- .../workflows/run/run_nextflow.sh | 4 +- 9 files changed, 17 insertions(+), 662 deletions(-) delete mode 100644 src/common/preprocess/config.vsh.yaml delete mode 100644 src/common/preprocess/noise.py delete mode 100755 src/common/preprocess/preprocess delete mode 100644 src/common/preprocess/preprocess.py delete mode 100644 src/common/preprocess/script.py delete mode 100644 src/common/preprocess/test_script.py diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml index 8e0bb8ce12..77920515b4 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -12,16 +12,15 @@ functionality: alternatives: ["-o"] type: "file" direction: "output" - deafult: "output.h5ad" + example: "output.h5ad" description: "Output h5ad file of the cleaned dataset" - required: true - name: "--url" type: "string" description: "URL of dataset" required: true - name: "--name" type: "string" - default: "pbmc" + example: "pbmc" description: "Name of dataset" required: true resources: diff --git a/src/common/preprocess/config.vsh.yaml b/src/common/preprocess/config.vsh.yaml deleted file mode 100644 index cfdefc4463..0000000000 --- a/src/common/preprocess/config.vsh.yaml +++ /dev/null @@ -1,55 +0,0 @@ -functionality: - name: "preprocess" - namespace: "common/preprocess" - version: "dev" - description: "Common component to preprocess pancreas data" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Saraiva Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - type: "file" - description: "Input data to be preprocessed" - required: true - - name: "--test" - description: "Indicates if should be returned a test preprocessed data" - type: "boolean" - required: false - default: false - - name: "--method" - description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" - type: "string" - choices: ['batch', 'random', 'random_with_noise'] - required: false - default: "batch" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file preprocessed" - required: true - resources: - - type: python_script - path: script.py - - path: noise.py - - path: preprocess.py - tests: - - type: python_script - path: test_script.py - - type: file - path: test_data.h5ad -platforms: - - type: native - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - scanpy - - type: nextflow diff --git a/src/common/preprocess/noise.py b/src/common/preprocess/noise.py deleted file mode 100644 index 9cf639d743..0000000000 --- a/src/common/preprocess/noise.py +++ /dev/null @@ -1,41 +0,0 @@ -import numpy as np - - -def add_label_noise(adata, noise_prob): - """Inject random label noise in the dataset . - This is done by permuting a fraction of the labels in the training set. - By adding different levels of label noise metrics can be evaluated to show - generalization trends from training data even if ground truth is uncertain. - Parameters - ------- - adata : AnnData - A dataset with the required fields for the label_projection task. - noise_prob : Float - The probability of label noise in the training data. - Returns - ------- - new_adata : AnnData - Dataset where training labels have been permuted by specified probability. - """ - - old_labels = adata.obs["labels"].pipe(np.array) - old_labels_train = old_labels[adata.obs["is_train"]].copy() - new_labels_train = old_labels_train.copy() - - label_names = np.unique(new_labels_train) - - n_labels = label_names.shape[0] - - reassign_probs = (noise_prob / (n_labels - 1)) * np.ones((n_labels, n_labels)) - - np.fill_diagonal(reassign_probs, 1 - noise_prob) - - for k, label in enumerate(label_names): - label_indices = np.where(old_labels_train == label)[0] - new_labels_train[label_indices] = np.random.choice( - label_names, label_indices.shape[0], p=reassign_probs[:, k] - ) - - adata.obs.loc[adata.obs["is_train"], "labels"] = new_labels_train - - return adata diff --git a/src/common/preprocess/preprocess b/src/common/preprocess/preprocess deleted file mode 100755 index eea11f6282..0000000000 --- a/src/common/preprocess/preprocess +++ /dev/null @@ -1,418 +0,0 @@ -#!/usr/bin/env bash - -# preprocess dev -# -# This wrapper script is auto-generated by viash 0.5.12 and is thus a derivative -# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data -# Intuitive. -# -# The component may contain files which fall under a different license. The -# authors of this component should specify the license in the header of such -# files, or include a separate license file detailing the licenses of all included -# files. -# -# Component authors: -# * Scott Gigante (author) {github: scottgigante} -# * Vinicius Saraiva Chagas (maintainer) {github: chagasVinicius} - -set -e - -if [ -z "$VIASH_TEMP" ]; then - VIASH_TEMP=/tmp -fi - -# define helper functions -# ViashQuote: put quotes around non flag values -# $1 : unquoted string -# return : possibly quoted string -# examples: -# ViashQuote --foo # returns --foo -# ViashQuote bar # returns 'bar' -# Viashquote --foo=bar # returns --foo='bar' -function ViashQuote { - if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then - echo "$1" | sed "s#=\(.*\)#='\1'#" - elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then - echo "$1" - else - echo "'$1'" - fi -} -# ViashRemoveFlags: Remove leading flag -# $1 : string with a possible leading flag -# return : string without possible leading flag -# examples: -# ViashRemoveFlags --foo=bar # returns bar -function ViashRemoveFlags { - echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//' -} -# ViashSourceDir: return the path of a bash file, following symlinks -# usage : ViashSourceDir ${BASH_SOURCE[0]} -# $1 : Should always be set to ${BASH_SOURCE[0]} -# returns : The absolute path of the bash file -function ViashSourceDir { - SOURCE="$1" - while [ -h "$SOURCE" ]; do - DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" - SOURCE="$(readlink "$SOURCE")" - [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" - done - cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd -} -# see https://en.wikipedia.org/wiki/Syslog#Severity_level -VIASH_LOGCODE_EMERGENCY=0 -VIASH_LOGCODE_ALERT=1 -VIASH_LOGCODE_CRITICAL=2 -VIASH_LOGCODE_ERROR=3 -VIASH_LOGCODE_WARNING=4 -VIASH_LOGCODE_NOTICE=5 -VIASH_LOGCODE_INFO=6 -VIASH_LOGCODE_DEBUG=7 -VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE - -# ViashLog: Log events depending on the verbosity level -# usage: ViashLog 1 alert Oh no something went wrong! -# $1: required verbosity level -# $2: display tag -# $3+: messages to display -# stdout: Your input, prepended by '[$2] '. -function ViashLog { - local required_level="$1" - local display_tag="$2" - shift 2 - if [ $VIASH_VERBOSITY -ge $required_level ]; then - echo "[$display_tag]" "$@" - fi -} - -# ViashEmergency: log events when the system is unstable -# usage: ViashEmergency Oh no something went wrong. -# stdout: Your input, prepended by '[emergency] '. -function ViashEmergency { - ViashLog $VIASH_LOGCODE_EMERGENCY emergency $@ -} - -# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database) -# usage: ViashAlert Oh no something went wrong. -# stdout: Your input, prepended by '[alert] '. -function ViashAlert { - ViashLog $VIASH_LOGCODE_ALERT alert $@ -} - -# ViashCritical: log events when a critical condition occurs -# usage: ViashCritical Oh no something went wrong. -# stdout: Your input, prepended by '[critical] '. -function ViashCritical { - ViashLog $VIASH_LOGCODE_CRITICAL critical $@ -} - -# ViashError: log events when an error condition occurs -# usage: ViashError Oh no something went wrong. -# stdout: Your input, prepended by '[error] '. -function ViashError { - ViashLog $VIASH_LOGCODE_ERROR error $@ -} - -# ViashWarning: log potentially abnormal events -# usage: ViashWarning Something may have gone wrong. -# stdout: Your input, prepended by '[warning] '. -function ViashWarning { - ViashLog $VIASH_LOGCODE_WARNING warning $@ -} - -# ViashNotice: log significant but normal events -# usage: ViashNotice This just happened. -# stdout: Your input, prepended by '[notice] '. -function ViashNotice { - ViashLog $VIASH_LOGCODE_NOTICE notice $@ -} - -# ViashInfo: log normal events -# usage: ViashInfo This just happened. -# stdout: Your input, prepended by '[info] '. -function ViashInfo { - ViashLog $VIASH_LOGCODE_INFO info $@ -} - -# ViashDebug: log all events, for debugging purposes -# usage: ViashDebug This just happened. -# stdout: Your input, prepended by '[debug] '. -function ViashDebug { - ViashLog $VIASH_LOGCODE_DEBUG debug $@ -} - -# find source folder of this component -VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}` - -# backwards compatibility -VIASH_RESOURCES_DIR="$VIASH_META_RESOURCES_DIR" - -# define meta fields -VIASH_META_FUNCTIONALITY_NAME="preprocess" - - -# ViashHelp: Display helpful explanation about this executable -function ViashHelp { - echo "preprocess dev" - echo "" - echo "Common component to preprocess pancreas data" - echo "" - echo "Options:" - echo " --input" - echo " type: file, required parameter" - echo " Input data to be preprocessed" - echo "" - echo " --test" - echo " type: boolean" - echo " default: false" - echo " Indicates if should be returned a test preprocessed data" - echo "" - echo " --method" - echo " type: string" - echo " default: batch" - echo " choices:" - echo " - batch" - echo " - random" - echo " - random_with_noise" - echo " The preprocess method to be used. Options: ['batch', 'random'," - echo "'random_with_noise']" - echo "" - echo " -o, --output" - echo " type: file, required parameter, output" - echo " default: output.h5ad" - echo " Output h5ad file preprocessed" -} - -# initialise array -VIASH_POSITIONAL_ARGS='' -VIASH_MODE='run' - -while [[ $# -gt 0 ]]; do - case "$1" in - -h|--help) - ViashHelp - exit - ;; - ---v|---verbose) - let "VIASH_VERBOSITY=VIASH_VERBOSITY+1" - shift 1 - ;; - ---verbosity) - VIASH_VERBOSITY="$2" - shift 2 - ;; - ---verbosity=*) - VIASH_VERBOSITY="$(ViashRemoveFlags "$1")" - shift 1 - ;; - --version) - echo "preprocess dev" - exit - ;; - --input) - VIASH_PAR_INPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --input=*) - VIASH_PAR_INPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - --test) - VIASH_PAR_TEST="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --test. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --test=*) - VIASH_PAR_TEST=$(ViashRemoveFlags "$1") - shift 1 - ;; - --method) - VIASH_PAR_METHOD="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --method. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --method=*) - VIASH_PAR_METHOD=$(ViashRemoveFlags "$1") - shift 1 - ;; - --output) - VIASH_PAR_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - --output=*) - VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1") - shift 1 - ;; - -o) - VIASH_PAR_OUTPUT="$2" - [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1 - shift 2 - ;; - *) # positional arg or unknown option - # since the positional args will be eval'd, can we always quote, instead of using ViashQuote - VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'" - shift # past argument - ;; - esac -done - -# parse positional parameters -eval set -- $VIASH_POSITIONAL_ARGS - - - - -# check whether required parameters exist -if [ -z "$VIASH_PAR_INPUT" ]; then - ViashError '--input' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_OUTPUT" ]; then - ViashError '--output' is a required argument. Use "--help" to get more information on the parameters. - exit 1 -fi -if [ -z "$VIASH_PAR_TEST" ]; then - VIASH_PAR_TEST="false" -fi -if [ -z "$VIASH_PAR_METHOD" ]; then - VIASH_PAR_METHOD="batch" -fi - - -# check whether parameters values are of the right type - -if [[ -n "$VIASH_PAR_TEST" ]]; then - if ! [[ "$VIASH_PAR_TEST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then - ViashError '--test' has to be a boolean. Use "--help" to get more information on the parameters. - exit 1 - fi -fi - - - - -# check whether parameters values are of the right type - - -if [ ! -z "$VIASH_PAR_METHOD" ]; then - VIASH_PAR_METHOD_CHOICES=("batch:random:random_with_noise") - IFS=: - set -f - if ! [[ ":${VIASH_PAR_METHOD_CHOICES[*]}:" =~ ":$VIASH_PAR_METHOD:" ]]; then - ViashError '--method' specified value of \'$VIASH_PAR_METHOD\' is not in the list of allowed values. Use "--help" to get more information on the parameters. - exit 1 - fi - set +f - unset IFS -fi - - - -cat << VIASHEOF | bash -set -e -tempscript=\$(mktemp "$VIASH_TEMP/viash-run-preprocess-XXXXXX") -function clean_up { - rm "\$tempscript" -} -function interrupt { - echo -e "\nCTRL-C Pressed..." - exit 1 -} -trap clean_up EXIT -trap interrupt INT SIGINT -cat > "\$tempscript" << 'VIASHMAIN' -## VIASH START -# The following code has been auto-generated by Viash. -par = { - 'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "'${VIASH_PAR_INPUT//\'/\\\'}'"; else echo None; fi ), - 'test': $( if [ ! -z ${VIASH_PAR_TEST+x} ]; then echo "'${VIASH_PAR_TEST//\'/\\\'}'.lower() == 'true'"; else echo None; fi ), - 'method': $( if [ ! -z ${VIASH_PAR_METHOD+x} ]; then echo "'${VIASH_PAR_METHOD//\'/\\\'}'"; else echo None; fi ), - 'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "'${VIASH_PAR_OUTPUT//\'/\\\'}'"; else echo None; fi ) -} -meta = { - 'functionality_name': '$VIASH_META_FUNCTIONALITY_NAME', - 'resources_dir': '$VIASH_META_RESOURCES_DIR', - 'temp_dir': '$VIASH_TEMP' -} - -resources_dir = '$VIASH_META_RESOURCES_DIR' - -## VIASH END -import noise -import preprocess -import numpy as np -import scanpy as sc - - -def batch(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] - adata.obs["is_train"] = [ - False if adata.obs["batch"][idx] in test_batches else True - for idx in adata.obs_names - ] - return adata - - -def random(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - return adata - - -def random_with_noise(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign trainin/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - # Inject label noise - adata = noise.add_label_noise(adata, noise_prob=0.2) - - return adata - - -func_map = {'batch': batch, - 'random': random, - 'random_with_noise': random_with_noise} - -method_func = func_map[par['method']] -adata = sc.read(par['input']) - -if par['test']: - adata = adata[:, :500].copy() - preprocess.filter_genes_cells(adata) - keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] - keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] - keep_tech_idx = adata.obs["tech"].isin(keep_techs) - keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) - adata = adata[keep_tech_idx & keep_celltype_idx].copy() - sc.pp.subsample(adata, n_obs=500) - # Note: could also use 200-500 HVGs rather than 200 random genes - # Ensure there are no cells or genes with 0 counts - preprocess.filter_genes_cells(adata) -else: - preprocess.filter_genes_cells(adata) - - -preprocessed_adata = method_func(adata) -preprocessed_adata.write(par['output']) -VIASHMAIN -python "\$tempscript" & -wait "\$!" - -VIASHEOF diff --git a/src/common/preprocess/preprocess.py b/src/common/preprocess/preprocess.py deleted file mode 100644 index 01785bb0c2..0000000000 --- a/src/common/preprocess/preprocess.py +++ /dev/null @@ -1,9 +0,0 @@ -import scanpy as sc - - -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - - return adata diff --git a/src/common/preprocess/script.py b/src/common/preprocess/script.py deleted file mode 100644 index 1b110f34ee..0000000000 --- a/src/common/preprocess/script.py +++ /dev/null @@ -1,81 +0,0 @@ -## VIASH START -par = { - "input": "./test/data.h5ad", - "test": False, - "method": 'batch', - "output": "./test/preprocess.h5ad" -} -## VIASH END -import sys -sys.path.append("./") -import noise -import preprocess -import numpy as np -import scanpy as sc - - -def batch(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] - adata.obs["is_train"] = [ - False if adata.obs["batch"][idx] in test_batches else True - for idx in adata.obs_names - ] - return adata - - -def random(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - return adata - - -def random_with_noise(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign trainin/test - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - - # Inject label noise - adata = noise.add_label_noise(adata, noise_prob=0.2) - - return adata - - -func_map = {'batch': batch, - 'random': random, - 'random_with_noise': random_with_noise} - -method_func = func_map[par['method']] -adata = sc.read(par['input']) - -if par['test']: - adata = adata[:, :500].copy() - preprocess.filter_genes_cells(adata) - keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] - keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] - keep_tech_idx = adata.obs["tech"].isin(keep_techs) - keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) - adata = adata[keep_tech_idx & keep_celltype_idx].copy() - sc.pp.subsample(adata, n_obs=500) - # Note: could also use 200-500 HVGs rather than 200 random genes - # Ensure there are no cells or genes with 0 counts - preprocess.filter_genes_cells(adata) -else: - preprocess.filter_genes_cells(adata) - - -preprocessed_adata = method_func(adata) -preprocessed_adata.write(par['output']) diff --git a/src/common/preprocess/test_script.py b/src/common/preprocess/test_script.py deleted file mode 100644 index 97a37a5709..0000000000 --- a/src/common/preprocess/test_script.py +++ /dev/null @@ -1,37 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "test_data.h5ad" -OUTPUT = "preprocessed.h5ad" -METHODS = ["batch", "random", "random_with_noise"] - -print(">> Runing script as test") -out = subprocess.check_output([ - "./preprocess", - "--input", INPUT, - "--test", "True", - "--output", OUTPUT -]).decode("utf-8") -print(">> Checking whether file exists") -assert path.exists(OUTPUT) - -print(">> Check that test output fits expected API") -adata = sc.read_h5ad(OUTPUT) -assert (500, 441) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) - -for method in METHODS: - print(">> Running script for {} method".format(method)) - out = subprocess.check_output([ - "./preprocess", - "--input", INPUT, - "--method", method, - "--output", OUTPUT - ]).decode("utf-8") - print(">> Checking whether file exists") - assert path.exists(OUTPUT) - print(">> Check that test output fits expected API") - adata = sc.read_h5ad(OUTPUT) - assert (16382, 18771) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) - assert "batch" in adata.obs - assert "is_train" in adata.obs diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 053e0db639..d66862b46c 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -9,20 +9,14 @@ targetDir = "${params.rootDir}/target/nextflow" // import dataset loaders include { data_loader } from "$targetDir/common/data_loader/main.nf" params(params) -// include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) -// import methods -// include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) -// include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) -// include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) -// include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) +// import preprocess +include { preprocess } from "$targetDir/label_projection/data/preprocess/main.nf" params(params) +// import methods +// TODO // import metrics -// include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) -// include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) - -// import helper functions -// include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) +// TODO /******************************************************* @@ -35,11 +29,17 @@ include { data_loader } from "$targetDir/common/data_loader/main.nf" p // // If the need arises, these workflows could be split off into a separate file. +params.tsv = "$launchDir/src/label_projection/data/fake_anndata_loader.tsv" + workflow load_data { main: - output_ = Channel.value(params) - | map { params -> ["new-id", ["url": params.url, "name": params.name]] } - | data_loader + output_ = Channel.fromPath(params.tsv) + | splitCsv(header: true, sep: "\t") + | map { row -> + [ row.name, [ "url": row.url, "name": row.name ]] + } + | data_loader + | preprocess emit: output_ } @@ -51,5 +51,4 @@ workflow load_data { workflow { load_data | view() - } diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_nextflow.sh index da8aad7273..c7ac0a3a2a 100644 --- a/src/label_projection/workflows/run/run_nextflow.sh +++ b/src/label_projection/workflows/run/run_nextflow.sh @@ -15,8 +15,6 @@ export NXF_VER=21.10.6 bin/nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ - --url "https://ndownloader.figshare.com/files/24539828" \ - --name "pbmc" \ - --output output/label_projection \ + --publishDir output/label_projection \ -resume \ -with-docker From 479434f1fc853f699852a2faf3d66adb1be351a8 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 30 May 2022 10:56:40 -0300 Subject: [PATCH 0189/1233] feat: add preprocess for label_projection Former-commit-id: 598fbe387b77453b986516b3a7fbcee50a26241e --- .../data/preprocess/config.vsh.yaml | 56 +++++++++++++ src/label_projection/data/preprocess/noise.py | 41 ++++++++++ .../data/preprocess/preprocess.py | 9 +++ .../data/preprocess/script.py | 81 +++++++++++++++++++ .../data/preprocess/test_script.py | 37 +++++++++ 5 files changed, 224 insertions(+) create mode 100644 src/label_projection/data/preprocess/config.vsh.yaml create mode 100644 src/label_projection/data/preprocess/noise.py create mode 100644 src/label_projection/data/preprocess/preprocess.py create mode 100644 src/label_projection/data/preprocess/script.py create mode 100644 src/label_projection/data/preprocess/test_script.py diff --git a/src/label_projection/data/preprocess/config.vsh.yaml b/src/label_projection/data/preprocess/config.vsh.yaml new file mode 100644 index 0000000000..df309f07d1 --- /dev/null +++ b/src/label_projection/data/preprocess/config.vsh.yaml @@ -0,0 +1,56 @@ +functionality: + name: "preprocess" + namespace: "label_projection/data" + version: "dev" + description: "Common component to preprocess pancreas data" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Saraiva Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to be preprocessed" + required: true + - name: "--test" + description: "Indicates if should be returned a test preprocessed data" + type: "boolean" + required: false + default: false + - name: "--method" + description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" + type: "string" + choices: ['batch', 'random', 'random_with_noise'] + required: false + default: "batch" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "output.h5ad" + description: "Output h5ad file preprocessed" + required: true + resources: + - type: python_script + path: script.py + - path: noise.py + - path: preprocess.py + tests: + - type: python_script + path: test_script.py + - type: file + path: test_data.h5ad +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/data/preprocess/noise.py b/src/label_projection/data/preprocess/noise.py new file mode 100644 index 0000000000..9cf639d743 --- /dev/null +++ b/src/label_projection/data/preprocess/noise.py @@ -0,0 +1,41 @@ +import numpy as np + + +def add_label_noise(adata, noise_prob): + """Inject random label noise in the dataset . + This is done by permuting a fraction of the labels in the training set. + By adding different levels of label noise metrics can be evaluated to show + generalization trends from training data even if ground truth is uncertain. + Parameters + ------- + adata : AnnData + A dataset with the required fields for the label_projection task. + noise_prob : Float + The probability of label noise in the training data. + Returns + ------- + new_adata : AnnData + Dataset where training labels have been permuted by specified probability. + """ + + old_labels = adata.obs["labels"].pipe(np.array) + old_labels_train = old_labels[adata.obs["is_train"]].copy() + new_labels_train = old_labels_train.copy() + + label_names = np.unique(new_labels_train) + + n_labels = label_names.shape[0] + + reassign_probs = (noise_prob / (n_labels - 1)) * np.ones((n_labels, n_labels)) + + np.fill_diagonal(reassign_probs, 1 - noise_prob) + + for k, label in enumerate(label_names): + label_indices = np.where(old_labels_train == label)[0] + new_labels_train[label_indices] = np.random.choice( + label_names, label_indices.shape[0], p=reassign_probs[:, k] + ) + + adata.obs.loc[adata.obs["is_train"], "labels"] = new_labels_train + + return adata diff --git a/src/label_projection/data/preprocess/preprocess.py b/src/label_projection/data/preprocess/preprocess.py new file mode 100644 index 0000000000..01785bb0c2 --- /dev/null +++ b/src/label_projection/data/preprocess/preprocess.py @@ -0,0 +1,9 @@ +import scanpy as sc + + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) + + return adata diff --git a/src/label_projection/data/preprocess/script.py b/src/label_projection/data/preprocess/script.py new file mode 100644 index 0000000000..ac8747d05e --- /dev/null +++ b/src/label_projection/data/preprocess/script.py @@ -0,0 +1,81 @@ +## VIASH START +par = { + "input": "./test/data.h5ad", + "test": False, + "method": 'batch', + "output": "./test/preprocess.h5ad" +} +## VIASH END +import sys +sys.path.append(meta["resources_dir"]) +import noise +import preprocess +import numpy as np +import scanpy as sc + + +def batch(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] + adata.obs["is_train"] = [ + False if adata.obs["batch"][idx] in test_batches else True + for idx in adata.obs_names + ] + return adata + + +def random(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign training/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + return adata + + +def random_with_noise(adata): + adata.obs["labels"] = adata.obs["celltype"] + adata.obs["batch"] = adata.obs["tech"] + + # Assign trainin/test + adata.obs["is_train"] = np.random.choice( + [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + + # Inject label noise + adata = noise.add_label_noise(adata, noise_prob=0.2) + + return adata + + +func_map = {'batch': batch, + 'random': random, + 'random_with_noise': random_with_noise} + +method_func = func_map[par['method']] +adata = sc.read(par['input']) + +if par['test']: + adata = adata[:, :500].copy() + preprocess.filter_genes_cells(adata) + keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] + keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] + keep_tech_idx = adata.obs["tech"].isin(keep_techs) + keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) + adata = adata[keep_tech_idx & keep_celltype_idx].copy() + sc.pp.subsample(adata, n_obs=500) + # Note: could also use 200-500 HVGs rather than 200 random genes + # Ensure there are no cells or genes with 0 counts + preprocess.filter_genes_cells(adata) +else: + preprocess.filter_genes_cells(adata) + + +preprocessed_adata = method_func(adata) +preprocessed_adata.write(par['output']) diff --git a/src/label_projection/data/preprocess/test_script.py b/src/label_projection/data/preprocess/test_script.py new file mode 100644 index 0000000000..97a37a5709 --- /dev/null +++ b/src/label_projection/data/preprocess/test_script.py @@ -0,0 +1,37 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data.h5ad" +OUTPUT = "preprocessed.h5ad" +METHODS = ["batch", "random", "random_with_noise"] + +print(">> Runing script as test") +out = subprocess.check_output([ + "./preprocess", + "--input", INPUT, + "--test", "True", + "--output", OUTPUT +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that test output fits expected API") +adata = sc.read_h5ad(OUTPUT) +assert (500, 441) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + +for method in METHODS: + print(">> Running script for {} method".format(method)) + out = subprocess.check_output([ + "./preprocess", + "--input", INPUT, + "--method", method, + "--output", OUTPUT + ]).decode("utf-8") + print(">> Checking whether file exists") + assert path.exists(OUTPUT) + print(">> Check that test output fits expected API") + adata = sc.read_h5ad(OUTPUT) + assert (16382, 18771) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + assert "batch" in adata.obs + assert "is_train" in adata.obs From 436465a51b497ee0398ac51cca9b29a97c195188 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 30 May 2022 11:01:08 -0300 Subject: [PATCH 0190/1233] self-review Former-commit-id: 431d46b273db85e5c627f51c04006145a8f48e71 --- src/label_projection/data/preprocess/script.py | 2 +- src/label_projection/workflows/run/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/label_projection/data/preprocess/script.py b/src/label_projection/data/preprocess/script.py index ac8747d05e..453f89dccf 100644 --- a/src/label_projection/data/preprocess/script.py +++ b/src/label_projection/data/preprocess/script.py @@ -13,7 +13,7 @@ import numpy as np import scanpy as sc - +# TODO split the functions in different viash components def batch(adata): adata.obs["labels"] = adata.obs["celltype"] adata.obs["batch"] = adata.obs["tech"] diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d66862b46c..2f8ece797c 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -29,7 +29,7 @@ include { preprocess } from "$targetDir/label_projection/data/preprocess/ // // If the need arises, these workflows could be split off into a separate file. -params.tsv = "$launchDir/src/label_projection/data/fake_anndata_loader.tsv" +params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" workflow load_data { main: From a319064792b199355cc493a1863542536ead2f8c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 13 Jun 2022 12:40:34 +0200 Subject: [PATCH 0191/1233] set output as required Former-commit-id: e1c3933f39aa1650fde38414da2bd805b503dda6 --- src/common/data_loader/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml index 77920515b4..9d1d3fc2bb 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -14,6 +14,7 @@ functionality: direction: "output" example: "output.h5ad" description: "Output h5ad file of the cleaned dataset" + required: true - name: "--url" type: "string" description: "URL of dataset" From af5f6ce4fc6fbd14bf697a958cb4d18503ada9f6 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 14 Jun 2022 20:05:51 -0300 Subject: [PATCH 0192/1233] feat: create toy component and bash scripts to test Former-commit-id: 21da7eab3caad5091451daa5ed1ce5397dac7de9 --- src/common/data_loader/config.vsh.yaml | 1 + .../data/preprocess/config.vsh.yaml | 13 ++--- .../data/preprocess/preprocess.py | 9 ---- .../data/preprocess/script.py | 34 ++++++------ .../data/preprocess/test_script.py | 18 +------ src/label_projection/data/toy/config.vsh.yaml | 53 +++++++++++++++++++ src/label_projection/data/toy/script.py | 44 +++++++++++++++ src/label_projection/data/toy/test_script.py | 21 ++++++++ .../data/{preprocess => utils}/noise.py | 0 .../workflows/run/run_nextflow.sh | 2 +- .../workflows/test/load_raw_data.sh | 15 ++++++ .../test/toy_preprocessed_test_data.sh | 15 ++++++ .../workflows/test/toy_test_data.sh | 17 ++++++ 13 files changed, 187 insertions(+), 55 deletions(-) delete mode 100644 src/label_projection/data/preprocess/preprocess.py create mode 100644 src/label_projection/data/toy/config.vsh.yaml create mode 100644 src/label_projection/data/toy/script.py create mode 100644 src/label_projection/data/toy/test_script.py rename src/label_projection/data/{preprocess => utils}/noise.py (100%) create mode 100644 src/label_projection/workflows/test/load_raw_data.sh create mode 100644 src/label_projection/workflows/test/toy_preprocessed_test_data.sh create mode 100644 src/label_projection/workflows/test/toy_test_data.sh diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/data_loader/config.vsh.yaml index 9d1d3fc2bb..0ac7afb7c6 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/data_loader/config.vsh.yaml @@ -38,5 +38,6 @@ platforms: packages: - scanpy - scprep + - "anndata<0.8" - type: native - type: nextflow diff --git a/src/label_projection/data/preprocess/config.vsh.yaml b/src/label_projection/data/preprocess/config.vsh.yaml index df309f07d1..d5b7586886 100644 --- a/src/label_projection/data/preprocess/config.vsh.yaml +++ b/src/label_projection/data/preprocess/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "preprocess" namespace: "label_projection/data" version: "dev" - description: "Common component to preprocess pancreas data" + description: "Common component to preprocess data" authors: - name: "Scott Gigante" roles: [ author ] @@ -15,11 +15,6 @@ functionality: type: "file" description: "Input data to be preprocessed" required: true - - name: "--test" - description: "Indicates if should be returned a test preprocessed data" - type: "boolean" - required: false - default: false - name: "--method" description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" type: "string" @@ -36,15 +31,13 @@ functionality: resources: - type: python_script path: script.py - - path: noise.py - - path: preprocess.py + - path: "../utils/noise.py" tests: - type: python_script path: test_script.py - type: file - path: test_data.h5ad + path: "../../resources/toy_preprocessed_data.h5ad" platforms: - - type: native - type: docker image: "python:3.8" setup: diff --git a/src/label_projection/data/preprocess/preprocess.py b/src/label_projection/data/preprocess/preprocess.py deleted file mode 100644 index 01785bb0c2..0000000000 --- a/src/label_projection/data/preprocess/preprocess.py +++ /dev/null @@ -1,9 +0,0 @@ -import scanpy as sc - - -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - - return adata diff --git a/src/label_projection/data/preprocess/script.py b/src/label_projection/data/preprocess/script.py index 453f89dccf..9a66ef4f12 100644 --- a/src/label_projection/data/preprocess/script.py +++ b/src/label_projection/data/preprocess/script.py @@ -1,7 +1,6 @@ ## VIASH START par = { "input": "./test/data.h5ad", - "test": False, "method": 'batch', "output": "./test/preprocess.h5ad" } @@ -9,10 +8,18 @@ import sys sys.path.append(meta["resources_dir"]) import noise -import preprocess import numpy as np import scanpy as sc + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) + + return adata + + # TODO split the functions in different viash components def batch(adata): adata.obs["labels"] = adata.obs["celltype"] @@ -58,24 +65,13 @@ def random_with_noise(adata): 'random': random, 'random_with_noise': random_with_noise} -method_func = func_map[par['method']] +print(">> Load data") adata = sc.read(par['input']) -if par['test']: - adata = adata[:, :500].copy() - preprocess.filter_genes_cells(adata) - keep_celltypes = adata.obs["celltype"].dtype.categories[[0, 3]] - keep_techs = adata.obs["tech"].dtype.categories[[0, -3, -2]] - keep_tech_idx = adata.obs["tech"].isin(keep_techs) - keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) - adata = adata[keep_tech_idx & keep_celltype_idx].copy() - sc.pp.subsample(adata, n_obs=500) - # Note: could also use 200-500 HVGs rather than 200 random genes - # Ensure there are no cells or genes with 0 counts - preprocess.filter_genes_cells(adata) -else: - preprocess.filter_genes_cells(adata) - - +print(">> Process data using {} method".format(par['method'])) +filter_genes_cells(adata) +method_func = func_map[par['method']] preprocessed_adata = method_func(adata) + +print(">> Writing data") preprocessed_adata.write(par['output']) diff --git a/src/label_projection/data/preprocess/test_script.py b/src/label_projection/data/preprocess/test_script.py index 97a37a5709..bf268fe41d 100644 --- a/src/label_projection/data/preprocess/test_script.py +++ b/src/label_projection/data/preprocess/test_script.py @@ -2,24 +2,10 @@ import scanpy as sc from os import path -INPUT = "test_data.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "preprocessed.h5ad" METHODS = ["batch", "random", "random_with_noise"] -print(">> Runing script as test") -out = subprocess.check_output([ - "./preprocess", - "--input", INPUT, - "--test", "True", - "--output", OUTPUT -]).decode("utf-8") -print(">> Checking whether file exists") -assert path.exists(OUTPUT) - -print(">> Check that test output fits expected API") -adata = sc.read_h5ad(OUTPUT) -assert (500, 441) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) - for method in METHODS: print(">> Running script for {} method".format(method)) out = subprocess.check_output([ @@ -32,6 +18,6 @@ assert path.exists(OUTPUT) print(">> Check that test output fits expected API") adata = sc.read_h5ad(OUTPUT) - assert (16382, 18771) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + assert (500, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) assert "batch" in adata.obs assert "is_train" in adata.obs diff --git a/src/label_projection/data/toy/config.vsh.yaml b/src/label_projection/data/toy/config.vsh.yaml new file mode 100644 index 0000000000..dd70bc48e0 --- /dev/null +++ b/src/label_projection/data/toy/config.vsh.yaml @@ -0,0 +1,53 @@ +functionality: + name: "toy" + namespace: "label_projection/data" + version: "dev" + description: "Component to generate a toy data for tests finality" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Saraiva Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to be resized" + required: true + - name: "--celltype_categories" + type: "integer" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--tech_categories" + type: "integer" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + default: "toy_data.h5ad" + description: "Output h5ad file resized" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../resources/raw_data.h5ad" +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scprep + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/data/toy/script.py b/src/label_projection/data/toy/script.py new file mode 100644 index 0000000000..c8c897fdb0 --- /dev/null +++ b/src/label_projection/data/toy/script.py @@ -0,0 +1,44 @@ +## VIASH START +par = { + "input": "../test_data.h5ad", + "celltype_categories": [0, 3], + "tech_categories": [0, -3, -2], + "ouput": "./toy_data.h5ad" +} +## VIASH END + + +import scanpy as sc + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) + + return adata + + +print(">> Load data") +adata = sc.read(par['input']) +adata = adata[:, :500].copy() +filter_genes_cells(adata) + +print(">> Select indexes") +print(">> Selecting celltype_categories indexes {idx}".format(idx=par.get('celltype_categories'))) +keep_celltypes = par.get('celltype_categories') and adata.obs["celltype"].dtype.categories[par['celltype_categories']] +print(">> Selected celltype_categories {}".format(keep_celltypes)) +keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) + +print(">> Selecting tech_categories indexes {idx}".format(idx=par.get('tech_categories'))) +keep_techs = par.get('tech_categories') and adata.obs["tech"].dtype.categories[par['tech_categories']] +print(">> Selected tech_categories {}".format(keep_techs)) +keep_tech_idx = adata.obs["tech"].isin(keep_techs) + +adata = adata[keep_tech_idx & keep_celltype_idx].copy() +sc.pp.subsample(adata, n_obs=500) +# Note: could also use 200-500 HVGs rather than 200 random genes +# Ensure there are no cells or genes with 0 counts +filter_genes_cells(adata) + +print(">> Writing data") +adata.write(par['output']) diff --git a/src/label_projection/data/toy/test_script.py b/src/label_projection/data/toy/test_script.py new file mode 100644 index 0000000000..6d639ade11 --- /dev/null +++ b/src/label_projection/data/toy/test_script.py @@ -0,0 +1,21 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "raw_data.h5ad" +OUTPUT = "toy_data.h5ad" + +print(">> Runing script as test") +out = subprocess.check_output([ + "./toy", + "--input", INPUT, + "--celltype_categories", "0:3", + "--tech_categories", "0:-3:-2", + "--output", OUTPUT +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that test output fits expected API") +adata = sc.read_h5ad(OUTPUT) +assert (500, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) diff --git a/src/label_projection/data/preprocess/noise.py b/src/label_projection/data/utils/noise.py similarity index 100% rename from src/label_projection/data/preprocess/noise.py rename to src/label_projection/data/utils/noise.py diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_nextflow.sh index c7ac0a3a2a..2c244104d1 100644 --- a/src/label_projection/workflows/run/run_nextflow.sh +++ b/src/label_projection/workflows/run/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|utils' +# bin/viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) diff --git a/src/label_projection/workflows/test/load_raw_data.sh b/src/label_projection/workflows/test/load_raw_data.sh new file mode 100644 index 0000000000..45e79c79ec --- /dev/null +++ b/src/label_projection/workflows/test/load_raw_data.sh @@ -0,0 +1,15 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +target/docker/common/data_loader/data_loader\ + --url "https://ndownloader.figshare.com/files/24539828"\ + --name "pancreas"\ + --output src/label_projection/resources/raw_data.h5ad diff --git a/src/label_projection/workflows/test/toy_preprocessed_test_data.sh b/src/label_projection/workflows/test/toy_preprocessed_test_data.sh new file mode 100644 index 0000000000..e3197ea489 --- /dev/null +++ b/src/label_projection/workflows/test/toy_preprocessed_test_data.sh @@ -0,0 +1,15 @@ +#!/bin/bash +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +sh src/label_projection/workflows/test/toy_test_data.sh + +target/docker/label_projection/data/preprocess/preprocess\ + --input src/label_projection/resources/toy_data.h5ad\ + --output src/label_projection/resources/toy_preprocessed_data.h5ad diff --git a/src/label_projection/workflows/test/toy_test_data.sh b/src/label_projection/workflows/test/toy_test_data.sh new file mode 100644 index 0000000000..db856fc5c4 --- /dev/null +++ b/src/label_projection/workflows/test/toy_test_data.sh @@ -0,0 +1,17 @@ +#!/bin/bash +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +sh src/label_projection/workflows/test/load_raw_data.sh + +target/docker/label_projection/data/toy/toy\ + --input src/label_projection/resources/raw_data.h5ad\ + --celltype_categories "0:3"\ + --tech_categories "0:-3:-2"\ + --output src/label_projection/resources/toy_data.h5ad From b362d6046fb32a5b86314a23f84f47840114b9bf Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 15 Jun 2022 07:50:32 -0300 Subject: [PATCH 0193/1233] self-review Former-commit-id: 22bc415fe234bfe25ccc422f31ff73110dc9fe26 --- .../data/preprocess/{ => pancreas}/config.vsh.yaml | 14 +++++++------- .../data/preprocess/{ => pancreas}/script.py | 2 +- .../data/preprocess/{ => pancreas}/test_script.py | 2 +- src/label_projection/workflows/run/main.nf | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-) rename src/label_projection/data/preprocess/{ => pancreas}/config.vsh.yaml (70%) rename src/label_projection/data/preprocess/{ => pancreas}/script.py (97%) rename src/label_projection/data/preprocess/{ => pancreas}/test_script.py (95%) diff --git a/src/label_projection/data/preprocess/config.vsh.yaml b/src/label_projection/data/preprocess/pancreas/config.vsh.yaml similarity index 70% rename from src/label_projection/data/preprocess/config.vsh.yaml rename to src/label_projection/data/preprocess/pancreas/config.vsh.yaml index d5b7586886..ed06f42937 100644 --- a/src/label_projection/data/preprocess/config.vsh.yaml +++ b/src/label_projection/data/preprocess/pancreas/config.vsh.yaml @@ -1,8 +1,8 @@ functionality: - name: "preprocess" - namespace: "label_projection/data" + name: "pancreas_preprocess" + namespace: "label_projection/data/preprocess" version: "dev" - description: "Common component to preprocess data" + description: "Label_projection component to preprocess pancreas data" authors: - name: "Scott Gigante" roles: [ author ] @@ -13,10 +13,10 @@ functionality: arguments: - name: "--input" type: "file" - description: "Input data to be preprocessed" + description: "Input data to be processed" required: true - name: "--method" - description: "The preprocess method to be used. Options: ['batch', 'random', 'random_with_noise']" + description: "The process method to assign train/test. Options: ['batch', 'random', 'random_with_noise']" type: "string" choices: ['batch', 'random', 'random_with_noise'] required: false @@ -31,12 +31,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../utils/noise.py" + - path: "../../utils/noise.py" tests: - type: python_script path: test_script.py - type: file - path: "../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data/preprocess/script.py b/src/label_projection/data/preprocess/pancreas/script.py similarity index 97% rename from src/label_projection/data/preprocess/script.py rename to src/label_projection/data/preprocess/pancreas/script.py index 9a66ef4f12..a4cafcc2ea 100644 --- a/src/label_projection/data/preprocess/script.py +++ b/src/label_projection/data/preprocess/pancreas/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - "input": "./test/data.h5ad", + "input": "../../../raw_data.h5ad", "method": 'batch', "output": "./test/preprocess.h5ad" } diff --git a/src/label_projection/data/preprocess/test_script.py b/src/label_projection/data/preprocess/pancreas/test_script.py similarity index 95% rename from src/label_projection/data/preprocess/test_script.py rename to src/label_projection/data/preprocess/pancreas/test_script.py index bf268fe41d..0533037f3b 100644 --- a/src/label_projection/data/preprocess/test_script.py +++ b/src/label_projection/data/preprocess/pancreas/test_script.py @@ -9,7 +9,7 @@ for method in METHODS: print(">> Running script for {} method".format(method)) out = subprocess.check_output([ - "./preprocess", + "./pancreas_preprocess", "--input", INPUT, "--method", method, "--output", OUTPUT diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 2f8ece797c..d7b6d891ea 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -11,7 +11,7 @@ targetDir = "${params.rootDir}/target/nextflow" include { data_loader } from "$targetDir/common/data_loader/main.nf" params(params) // import preprocess -include { preprocess } from "$targetDir/label_projection/data/preprocess/main.nf" params(params) +include { pancreas_preprocess } from "$targetDir/label_projection/data/preprocess/pancreas_preprocess/main.nf" params(params) // import methods // TODO @@ -39,7 +39,7 @@ workflow load_data { [ row.name, [ "url": row.url, "name": row.name ]] } | data_loader - | preprocess + | pancreas_preprocess emit: output_ } From 407c9ab1039678c1e28c6759ff05a52d292dbd5a Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 31 May 2022 15:08:08 -0300 Subject: [PATCH 0194/1233] feat: majority_vote method and accuracy metric added Former-commit-id: 89d3ebfa63b29980d9399e7d16e23ce140aabeed --- .../baseline/majority_vote/config.vsh.yaml | 42 ++++++++++++++++++ .../methods/baseline/majority_vote/script.py | 22 ++++++++++ .../baseline/majority_vote/test_script.py | 22 ++++++++++ .../metrics/accuracy/config.vsh.yaml | 43 +++++++++++++++++++ .../metrics/accuracy/script.py | 29 +++++++++++++ .../metrics/accuracy/test_script.py | 27 ++++++++++++ src/label_projection/workflows/run/main.nf | 9 ++-- 7 files changed, 191 insertions(+), 3 deletions(-) create mode 100644 src/label_projection/methods/baseline/majority_vote/config.vsh.yaml create mode 100644 src/label_projection/methods/baseline/majority_vote/script.py create mode 100644 src/label_projection/methods/baseline/majority_vote/test_script.py create mode 100644 src/label_projection/metrics/accuracy/config.vsh.yaml create mode 100644 src/label_projection/metrics/accuracy/script.py create mode 100644 src/label_projection/metrics/accuracy/test_script.py diff --git a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml new file mode 100644 index 0000000000..510524d123 --- /dev/null +++ b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml @@ -0,0 +1,42 @@ +functionality: + name: "majority_vote" + namespace: "label_projection/methods/baseline" + version: "dev" + description: "Majority vote dummy" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to add prediction" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + description: "Ouput data labeled" + direction: "output" + example: "output.mv.h5ad" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: test_data.h5ad +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/methods/baseline/majority_vote/script.py b/src/label_projection/methods/baseline/majority_vote/script.py new file mode 100644 index 0000000000..2a8869991c --- /dev/null +++ b/src/label_projection/methods/baseline/majority_vote/script.py @@ -0,0 +1,22 @@ +## VIASH START +par = { + 'input': 'ouput.h5ad', + 'output': 'output.mv.h5ad' +} +## VIASH END +import numpy as np +import scanpy as sc + + +print("Load data") +adata = sc.read(par['input']) + +print("Add label prediction") +majority = adata.obs.labels[adata.obs.is_train].value_counts().index[0] +adata.obs["labels_pred"] = np.nan +adata.obs.loc[~adata.obs.is_train, "labels_pred"] = majority + + +print("Write output to file") +adata.uns["method_id"] = "majority_vote" +adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/methods/baseline/majority_vote/test_script.py b/src/label_projection/methods/baseline/majority_vote/test_script.py new file mode 100644 index 0000000000..5e5f3846bd --- /dev/null +++ b/src/label_projection/methods/baseline/majority_vote/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + + +INPUT = "test_data.h5ad" +OUTPUT = "output.mv.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./majority_vote", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "majority_vote" == adata.uns["method_id"] diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml new file mode 100644 index 0000000000..fd0dc4407f --- /dev/null +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -0,0 +1,43 @@ +functionality: + name: "accuracy" + namespace: "label_projection/metrics" + version: "dev" + description: "Accuracy of predictions" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to get accuracy" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + description: "Ouput data with metric value" + direction: "output" + example: "output.mv.h5ad" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: test_data.h5ad +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - sklearn + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py new file mode 100644 index 0000000000..d9e0523e44 --- /dev/null +++ b/src/label_projection/metrics/accuracy/script.py @@ -0,0 +1,29 @@ +## VIASH START +par = { + 'input': 'ouput.h5ad', + 'output': 'output.mv.h5ad' +} +## VIASH END +import numpy as np +import sklearn.preprocessing +import scanpy as sc + + +print("Load data") +adata = sc.read(par['input']) + +print("Get prediction accuracy") +encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["labels"]) +test_data = adata[~adata.obs["is_train"]] + +test_data.obs["labels"] = encoder.transform(test_data.obs["labels"]) +test_data.obs["labels_pred"] = encoder.transform(test_data.obs["labels_pred"]) + +accuracy = np.mean(test_data.obs["labels"] == test_data.obs["labels_pred"]) + +print("Store metric value") +adata.uns["metric_id"] = "accuracy" +adata.uns["metric_value"] = accuracy + +print("Writing adata to file") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/accuracy/test_script.py b/src/label_projection/metrics/accuracy/test_script.py new file mode 100644 index 0000000000..883711e04e --- /dev/null +++ b/src/label_projection/metrics/accuracy/test_script.py @@ -0,0 +1,27 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import numpy as np + +print(">> Running knn_auc") +out = subprocess.check_output([ + "./accuracy", + "--input", "test_data.h5ad", + "--output", "output.accuracy.h5ad" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists("output.accuracy.h5ad") + +print(">> Check that dataset fits expected API") +adata = sc.read_h5ad("output.accuracy.h5ad") + +# check id +assert "metric_id" in adata.uns +assert adata.uns["metric_id"] == "accuracy" +assert "metric_value" in adata.uns +assert type(adata.uns["metric_value"]) is np.float64 + +print(">> All tests passed successfully") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d7b6d891ea..aba124ac40 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -14,9 +14,9 @@ include { data_loader } from "$targetDir/common/data_loader/main.nf" p include { pancreas_preprocess } from "$targetDir/label_projection/data/preprocess/pancreas_preprocess/main.nf" params(params) // import methods -// TODO +include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" params(params) // import metrics -// TODO +include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" params(params) /******************************************************* @@ -29,7 +29,8 @@ include { pancreas_preprocess } from "$targetDir/label_projection/data/pr // // If the need arises, these workflows could be split off into a separate file. -params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" +// params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" +params.tsv = "$launchDir/src/label_projection/data/fake_anndata_loader.tsv" workflow load_data { main: @@ -50,5 +51,7 @@ workflow load_data { workflow { load_data + | majority_vote + | accuracy.run(auto: [ publish: true ]) | view() } From 64288936f6d826510390dd3bec37bfd4cd844b19 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 6 Jun 2022 16:33:23 -0300 Subject: [PATCH 0195/1233] feat: add knn_methods Former-commit-id: b6f640d2580b656c0ace38b8e91bea41c8b2e3c7 --- src/common/tools/normalize.py | 42 +++++++++++++++ .../knn_classifier/log_cpm/config.vsh.yaml | 47 +++++++++++++++++ .../methods/knn_classifier/log_cpm/script.py | 28 ++++++++++ .../knn_classifier/log_cpm/test_script.py | 21 ++++++++ .../knn_classifier/scran/config.vsh.yaml | 51 +++++++++++++++++++ .../methods/knn_classifier/scran/script.py | 28 ++++++++++ .../knn_classifier/scran/test_script.py | 21 ++++++++ src/label_projection/utils.py | 48 +++++++++++++++++ src/label_projection/workflows/run/main.nf | 15 ++++-- 9 files changed, 296 insertions(+), 5 deletions(-) create mode 100644 src/common/tools/normalize.py create mode 100644 src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml create mode 100644 src/label_projection/methods/knn_classifier/log_cpm/script.py create mode 100644 src/label_projection/methods/knn_classifier/log_cpm/test_script.py create mode 100644 src/label_projection/methods/knn_classifier/scran/config.vsh.yaml create mode 100644 src/label_projection/methods/knn_classifier/scran/script.py create mode 100644 src/label_projection/methods/knn_classifier/scran/test_script.py create mode 100644 src/label_projection/utils.py diff --git a/src/common/tools/normalize.py b/src/common/tools/normalize.py new file mode 100644 index 0000000000..873f454634 --- /dev/null +++ b/src/common/tools/normalize.py @@ -0,0 +1,42 @@ +import anndata as ad +import scanpy as sc +import scprep + + +_scran = scprep.run.RFunction( + setup=""" + library('scran') + library('BiocParallel') + """, + args="sce, min.mean=0.1", + body=""" + sce <- computeSumFactors( + sce, min.mean=min.mean, + assay.type="X", + BPPARAM=BiocParallel::MulticoreParam() + ) + sizeFactors(sce) + """ +) + + +def log_scran_pooling(adata: ad.AnnData) -> ad.AnnData: + """Normalize data with scran via rpy2.""" + adata.obs["size_factors"] = _scran(adata) + adata.X = scprep.utils.matrix_vector_elementwise_multiply( + adata.X, adata.obs["size_factors"], axis=0 + ) + sc.pp.log1p(adata) + return adata + + +def _cpm(adata: ad.AnnData): + adata.layers["counts"] = adata.X.copy() + sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") + + +def log_cpm(adata: ad.AnnData) -> ad.AnnData: + """Normalize data to log counts per million.""" + _cpm(adata) + sc.pp.log1p(adata) + return adata diff --git a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..1b0f69c9d2 --- /dev/null +++ b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml @@ -0,0 +1,47 @@ +functionality: + name: "knn_classifier_log_cpm" + namespace: "label_projection/methods/knn_classifier" + version: "dev" + description: "Run Harmonic Alignment" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/log_cpm/script.py b/src/label_projection/methods/knn_classifier/log_cpm/script.py new file mode 100644 index 0000000000..5c60a6095e --- /dev/null +++ b/src/label_projection/methods/knn_classifier/log_cpm/script.py @@ -0,0 +1,28 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.knnscran.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_cpm +from utils import classifier +import sklearn.neighbors + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +adata = log_cpm(adata) +adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) +adata.uns["method_id"] = "knn_classifier_log_cpm" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/knn_classifier/log_cpm/test_script.py b/src/label_projection/methods/knn_classifier/log_cpm/test_script.py new file mode 100644 index 0000000000..0b67ede891 --- /dev/null +++ b/src/label_projection/methods/knn_classifier/log_cpm/test_script.py @@ -0,0 +1,21 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.knnlogcpm.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./knn_classifier_log_cpm", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "knn_classifier_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml new file mode 100644 index 0000000000..b153921952 --- /dev/null +++ b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml @@ -0,0 +1,51 @@ +functionality: + name: "knn_classifier_scran" + namespace: "label_projection/methods/knn_classifier" + version: "dev" + description: "" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "singlecellopenproblems/openproblems-r-base:latest" + setup: + - type: r + bioc: + - scran + - BiocParallel + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/scran/script.py b/src/label_projection/methods/knn_classifier/scran/script.py new file mode 100644 index 0000000000..40930a9637 --- /dev/null +++ b/src/label_projection/methods/knn_classifier/scran/script.py @@ -0,0 +1,28 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.knnscran.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_scran_pooling +from utils import classifier +import sklearn.neighbors + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +adata = log_scran_pooling(adata) +adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) +adata.uns["method_id"] = "knn_classifier_scran" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/knn_classifier/scran/test_script.py b/src/label_projection/methods/knn_classifier/scran/test_script.py new file mode 100644 index 0000000000..c00328f2ae --- /dev/null +++ b/src/label_projection/methods/knn_classifier/scran/test_script.py @@ -0,0 +1,21 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.knnscran.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./knn_classifier_scran", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "knn_classifier_scran" == adata.uns["method_id"] diff --git a/src/label_projection/utils.py b/src/label_projection/utils.py new file mode 100644 index 0000000000..7370afefe1 --- /dev/null +++ b/src/label_projection/utils.py @@ -0,0 +1,48 @@ +import numpy as np +import sklearn.pipeline +import sklearn.preprocessing +import scipy.sparse +import sklearn.decomposition + + +def pca_op(adata_train, adata_test, n_components=100): + + is_sparse = scipy.sparse.issparse(adata_train.X) + + min_components = min( + [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + ) + if is_sparse: + min_components -= 1 + n_components = min([n_components, min_components]) + if is_sparse: + pca_op = sklearn.decomposition.TruncatedSVD + else: + pca_op = sklearn.decomposition.PCA + return pca_op(n_components=n_components) + + +def classifier(adata, estimator, n_pca=100, **kwargs): + """Run a generic scikit-learn classifier.""" + adata_train = adata[adata.obs["is_train"]] + adata_test = adata[~adata.obs["is_train"]].copy() + + classifier = sklearn.pipeline.Pipeline( + [ + ("pca", pca_op(adata_train, adata_test, n_components=n_pca)), + ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), + ("regression", estimator(**kwargs)), + ] + ) + + # Fit to train data + classifier.fit(adata_train.X, adata_train.obs["labels"].astype(str)) + + # Predict on test data + adata_test.obs["labels_pred"] = classifier.predict(adata_test.X) + + adata.obs["labels_pred"] = [ + adata_test.obs["labels_pred"][idx] if idx in adata_test.obs_names else np.nan + for idx in adata.obs_names + ] + return adata diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index aba124ac40..d0d3258e01 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -13,9 +13,13 @@ include { data_loader } from "$targetDir/common/data_loader/main.nf" p // import preprocess include { pancreas_preprocess } from "$targetDir/label_projection/data/preprocess/pancreas_preprocess/main.nf" params(params) -// import methods +// import methods TODO[baseline/random_labels, +// knn_classifier/scran, mlp/log_cpm, mlp/scran, sklearn/classifier, +// scvi, logistic_regression/log_cpm, logistic_regression/scran] include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" params(params) -// import metrics +include { knn_classifier_log_cpm } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_log_cpm/main.nf" params(params) + +// import metrics TODO [f1] include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" params(params) @@ -51,7 +55,8 @@ workflow load_data { workflow { load_data - | majority_vote - | accuracy.run(auto: [ publish: true ]) - | view() + | view + | (majority_vote & knn_classifier_log_cpm) + | mix + | view } From 295c6959326b97171d8f1bc6aff685114293e3c9 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 7 Jun 2022 09:18:50 -0300 Subject: [PATCH 0196/1233] feat: mlp_methods Former-commit-id: 4cf065663167b19636139cc7906cb79a8b9b2533 --- .../methods/mlp/log_cpm/config.vsh.yaml | 58 ++++++++++++++++++ .../methods/mlp/log_cpm/script.py | 32 ++++++++++ .../methods/mlp/log_cpm/test_script.py | 23 ++++++++ .../methods/mlp/scran/config.vsh.yaml | 59 +++++++++++++++++++ .../methods/mlp/scran/script.py | 30 ++++++++++ .../methods/mlp/scran/test_script.py | 23 ++++++++ src/label_projection/workflows/run/main.nf | 10 +++- 7 files changed, 232 insertions(+), 3 deletions(-) create mode 100644 src/label_projection/methods/mlp/log_cpm/config.vsh.yaml create mode 100644 src/label_projection/methods/mlp/log_cpm/script.py create mode 100644 src/label_projection/methods/mlp/log_cpm/test_script.py create mode 100644 src/label_projection/methods/mlp/scran/config.vsh.yaml create mode 100644 src/label_projection/methods/mlp/scran/script.py create mode 100644 src/label_projection/methods/mlp/scran/test_script.py diff --git a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..db0c9b9342 --- /dev/null +++ b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml @@ -0,0 +1,58 @@ +functionality: + name: "mlp_log_cpm" + namespace: "label_projection/methods/mlp" + version: "dev" + description: "Run Harmonic Alignment" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--hidden_layer_sizes" + type: "integer" + multiple: true + description: "The ith element represents the number of neurons in the ith hidden layer." + required: true + - name: "--max_iter" + type: "integer" + example: "100" + description: "Maximum number of iterations" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: native + - type: nextflow diff --git a/src/label_projection/methods/mlp/log_cpm/script.py b/src/label_projection/methods/mlp/log_cpm/script.py new file mode 100644 index 0000000000..ca23bb7572 --- /dev/null +++ b/src/label_projection/methods/mlp/log_cpm/script.py @@ -0,0 +1,32 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.mlplogcpm.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_cpm +from utils import classifier +import sklearn.neural_network + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +hidden_layer_sizes = tuple(par['hidden_layer_sizes']) +print(hidden_layer_sizes, "A") +max_iter = par['max_iter'] +print(max_iter, "B") +adata = log_cpm(adata) +adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) +adata.uns["method_id"] = "mlp_log_cpm" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/mlp/log_cpm/test_script.py b/src/label_projection/methods/mlp/log_cpm/test_script.py new file mode 100644 index 0000000000..9984803131 --- /dev/null +++ b/src/label_projection/methods/mlp/log_cpm/test_script.py @@ -0,0 +1,23 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.mlplogcpm.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./mlp_log_cpm", + "--input", INPUT, + "--hidden_layer_sizes", "20", + "--max_iter", "100", + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "mlp_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/scran/config.vsh.yaml b/src/label_projection/methods/mlp/scran/config.vsh.yaml new file mode 100644 index 0000000000..703f766df0 --- /dev/null +++ b/src/label_projection/methods/mlp/scran/config.vsh.yaml @@ -0,0 +1,59 @@ +functionality: + name: "mlp_scran" + namespace: "label_projection/methods/mlp" + version: "dev" + description: "" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--hidden_layer_sizes" + type: "integer" + multiple: true + description: "The ith element represents the number of neurons in the ith hidden layer." + - name: "--max_iter" + type: "integer" + example: "100" + description: "Maximum number of iterations" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "singlecellopenproblems/openproblems-r-base:latest" + setup: + - type: r + bioc: + - scran + - BiocParallel + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/methods/mlp/scran/script.py b/src/label_projection/methods/mlp/scran/script.py new file mode 100644 index 0000000000..5adde85929 --- /dev/null +++ b/src/label_projection/methods/mlp/scran/script.py @@ -0,0 +1,30 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.mlpscran.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_scran_pooling +from utils import classifier +import sklearn.neural_network + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +hidden_layer_sizes = tuple(par['hidden_layer_sizes']) +max_iter = par['max_iter'] +adata = log_scran_pooling(adata) +adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) +adata.uns["method_id"] = "mlp_scran" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/mlp/scran/test_script.py b/src/label_projection/methods/mlp/scran/test_script.py new file mode 100644 index 0000000000..f31915d3cb --- /dev/null +++ b/src/label_projection/methods/mlp/scran/test_script.py @@ -0,0 +1,23 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.mlpscran.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./mlp_scran", + "--input", INPUT, + "--hidden_layer_sizes", "20", + "--max_iter", "100", + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "mlp_scran" == adata.uns["method_id"] diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d0d3258e01..64bc12e9f1 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -16,8 +16,11 @@ include { pancreas_preprocess } from "$targetDir/label_projection/data/pr // import methods TODO[baseline/random_labels, // knn_classifier/scran, mlp/log_cpm, mlp/scran, sklearn/classifier, // scvi, logistic_regression/log_cpm, logistic_regression/scran] -include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" params(params) -include { knn_classifier_log_cpm } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_log_cpm/main.nf" params(params) +include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" params(params) +include { knn_classifier_log_cpm } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_log_cpm/main.nf" params(params) +include { knn_classifier_scran } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_scran/main.nf" params(params)//LOCALY OUT OF MEMORY +include { mlp_log_cpm } from "$targetDir/label_projection/methods/mlp/mlp_log_cpm/main.nf" params(params) //LOCALY OUT OF MEMORY +include { mlp_scran } from "$targetDir/label_projection/methods/mlp/mlp_scran/main.nf" params(params) //LOCALY OUT OF MEMORY // import metrics TODO [f1] include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" params(params) @@ -56,7 +59,8 @@ workflow load_data { workflow { load_data | view - | (majority_vote & knn_classifier_log_cpm) + | (majority_vote & knn_classifier_log_cpm & knn_classifier_scran & mlp_log_cpm & mlp_scran) | mix + | accuracy | view } From 4c057e481966dba28158a92bbf0794c76987161a Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 8 Jun 2022 09:17:08 -0300 Subject: [PATCH 0197/1233] feat: logistic_regression Former-commit-id: 979d40e6ae60cfcbd22fad4f8e728a4cf71546d9 --- .../data/fake_anndata_loader.tsv | 2 + .../log_cpm/config.vsh.yaml | 53 ++++++++++++++++++ .../logistic_regression/log_cpm/script.py | 29 ++++++++++ .../log_cpm/test_script.py | 22 ++++++++ .../logistic_regression/scran/config.vsh.yaml | 55 +++++++++++++++++++ .../logistic_regression/scran/script.py | 29 ++++++++++ .../logistic_regression/scran/test_script.py | 22 ++++++++ .../methods/mlp/log_cpm/script.py | 2 - 8 files changed, 212 insertions(+), 2 deletions(-) create mode 100644 src/label_projection/data/fake_anndata_loader.tsv create mode 100644 src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml create mode 100644 src/label_projection/methods/logistic_regression/log_cpm/script.py create mode 100644 src/label_projection/methods/logistic_regression/log_cpm/test_script.py create mode 100644 src/label_projection/methods/logistic_regression/scran/config.vsh.yaml create mode 100644 src/label_projection/methods/logistic_regression/scran/script.py create mode 100644 src/label_projection/methods/logistic_regression/scran/test_script.py diff --git a/src/label_projection/data/fake_anndata_loader.tsv b/src/label_projection/data/fake_anndata_loader.tsv new file mode 100644 index 0000000000..2b84d064f9 --- /dev/null +++ b/src/label_projection/data/fake_anndata_loader.tsv @@ -0,0 +1,2 @@ +processor name url +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 diff --git a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..df603eb58c --- /dev/null +++ b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml @@ -0,0 +1,53 @@ +functionality: + name: "logistic_regression_log_cpm" + namespace: "label_projection/methods/logistic_regression" + version: "dev" + description: "Run Harmonic Alignment" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--max_iter" + type: "integer" + example: "100" + description: "Maximum number of iterations" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: native + - type: nextflow diff --git a/src/label_projection/methods/logistic_regression/log_cpm/script.py b/src/label_projection/methods/logistic_regression/log_cpm/script.py new file mode 100644 index 0000000000..bb6ba9e791 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/log_cpm/script.py @@ -0,0 +1,29 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.knnscran.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_cpm +from utils import classifier +import sklearn.linear_model + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +adata = log_cpm(adata) +max_iter = par['max_iter'] +adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) +adata.uns["method_id"] = "logistic_regression_log_cpm" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/log_cpm/test_script.py b/src/label_projection/methods/logistic_regression/log_cpm/test_script.py new file mode 100644 index 0000000000..b5d47af7e5 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/log_cpm/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.lrlogcpm.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./logistic_regression_log_cpm", + "--input", INPUT, + "--max_iter", "100", + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "logistic_regression_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml new file mode 100644 index 0000000000..8bd43d61c4 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml @@ -0,0 +1,55 @@ +functionality: + name: "logistic_regression_scran" + namespace: "label_projection/methods/logistic_regression" + version: "dev" + description: "" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--max_iter" + type: "integer" + example: "100" + description: "Maximum number of iterations" + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../../../common/tools/normalize.py" + - path: "../../../utils.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "singlecellopenproblems/openproblems-r-base:latest" + setup: + - type: r + bioc: + - scran + - BiocParallel + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/methods/logistic_regression/scran/script.py b/src/label_projection/methods/logistic_regression/scran/script.py new file mode 100644 index 0000000000..e926954760 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/scran/script.py @@ -0,0 +1,29 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.mlpscran.h5ad' +} +## VIASH END +resources_dir = "../../../../common/tools/" +utils_dir = "../../../" + +import sys +sys.path.append(resources_dir) +sys.path.append(utils_dir) +sys.path.append(meta['resources_dir']) +import scanpy as sc +from normalize import log_scran_pooling +from utils import classifier +import sklearn.linear_model + +print("Load input data") +adata = sc.read(par['input']) + +print("Run classifier") +max_iter = par['max_iter'] +adata = log_scran_pooling(adata) +adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) +adata.uns["method_id"] = "logistic_regression_scran" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/scran/test_script.py b/src/label_projection/methods/logistic_regression/scran/test_script.py new file mode 100644 index 0000000000..194e5abb71 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/scran/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "test_data_preprocessed.h5ad" +OUTPUT = "output.lrscran.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./logistic_regression_scran", + "--input", INPUT, + "--max_iter", "100", + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "logistic_regression_scran" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/log_cpm/script.py b/src/label_projection/methods/mlp/log_cpm/script.py index ca23bb7572..bfc7c4c83c 100644 --- a/src/label_projection/methods/mlp/log_cpm/script.py +++ b/src/label_projection/methods/mlp/log_cpm/script.py @@ -21,9 +21,7 @@ print("Run classifier") hidden_layer_sizes = tuple(par['hidden_layer_sizes']) -print(hidden_layer_sizes, "A") max_iter = par['max_iter'] -print(max_iter, "B") adata = log_cpm(adata) adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) adata.uns["method_id"] = "mlp_log_cpm" From 182515c1c6a6d0c6b84d895ec76c327ada36b72b Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Thu, 9 Jun 2022 09:27:15 -0300 Subject: [PATCH 0198/1233] chore: scvi_tools Former-commit-id: 841bdb1dcbb4564d608ad9e056638774f495c4f9 --- .../scvi/scanvi_all_genes/config.vsh.yaml | 49 +++++++++++++++++++ .../methods/scvi/scanvi_all_genes/script.py | 33 +++++++++++++ src/label_projection/methods/scvi/tools.py | 42 ++++++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml create mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/script.py create mode 100644 src/label_projection/methods/scvi/tools.py diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml new file mode 100644 index 0000000000..90958f9151 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -0,0 +1,49 @@ +functionality: + name: "scanvi_all_genes" + namespace: "label_projection/methods/scvi" + version: "dev" + description: "Probabilistic harmonization and annotation of single-cell" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../../tools.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../data/test_data_preprocessed.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - "scvi==0.6.8" + - "scvi-tools==0.13.0" + - type: native + - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py new file mode 100644 index 0000000000..13e335e827 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_all_genes/script.py @@ -0,0 +1,33 @@ +## VIASH START +par = { + 'input': '../../../data/test_data_preprocessed.h5ad', + 'output': 'output.mlplogcpm.h5ad' +} +## VIASH END +resources_dir="../" + +import sys +sys.path.append(resources_dir) +sys.path.append(meta['resources_dir']) +import scvi +import scanpy as sc +from tools import scanvi + +###TODO add these as input +### n_hidden, n_latent, n_layers +n_latent, n_layers, n_hidden = (10, 1, 32) + +print("Load input data") +adata = sc.read(par['input']) + +train_kwargs = { + "train_size": 0.9, + "early_stopping": True, +} + +# check parameters for test exists +par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) +par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) +par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) + +adata.obs["labels_pred"] = scanvi(adata, n_hidden, n_latent, n_layers, **train_kwargs) diff --git a/src/label_projection/methods/scvi/tools.py b/src/label_projection/methods/scvi/tools.py new file mode 100644 index 0000000000..6cfc4daff8 --- /dev/null +++ b/src/label_projection/methods/scvi/tools.py @@ -0,0 +1,42 @@ +import scanpy as sc +import scvi + +def hvg_kwargs(n_top_genes=2000): + return { + "flavor": "seurat_v3", + "inplace": False, + "n_top_genes": n_top_genes, + "batch_key": "batch", + } + +def hvg (adata, hvg_kwargs): + try: + return sc.pp.highly_variable_genes(adata[adata.obs["is_train"]], **hvg_kwargs) + except ValueError: # loess estimation can fail on small data with seurat_v3 flavor + # in this case we try seurat flavor + # and copy the data because it needs normalized counts + # but later we need raw counts + hvg_kwargs["flavor"] = "seurat" + normdata = adata.copy() + sc.pp.normalize_total(normdata, target_sum=1e4) + sc.pp.log1p(normdata) + return sc.pp.highly_variable_genes( + normdata[normdata.obs["is_train"]], **hvg_kwargs + ) + +def scanvi(adata, n_hidden=None, n_latent=None, n_layers=None, **train_kwargs): + scanvi_labels = adata.obs["labels"].to_numpy() + # test set labels masked + scanvi_labels[~adata.obs["is_train"].to_numpy()] = "Unknown" + adata.obs["scanvi_labels"] = scanvi_labels + scvi.model.SCVI.setup_anndata(adata, batch_key="batch", labels_key="scanvi_labels") + scvi_model = scvi.model.SCVI( + adata, n_hidden=n_hidden, n_latent=n_latent, n_layers=n_layers + ) + scvi_model.train(**train_kwargs) + model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") + model.train(**train_kwargs) + preds = model.predict(adata) + del adata.obs["scanvi_labels"] + # predictions for train and test + return preds From dd144f673691fe10c51f3785d2bb05e9d760b4e7 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 14 Jun 2022 20:15:05 -0300 Subject: [PATCH 0199/1233] fix: using test scripts results in methods tests Former-commit-id: 19180b0523ffcb55077ac6a1e1dc100bbbde6cde --- .../methods/baseline/majority_vote/config.vsh.yaml | 2 +- .../methods/baseline/majority_vote/test_script.py | 2 +- .../methods/knn_classifier/log_cpm/config.vsh.yaml | 2 +- .../methods/knn_classifier/log_cpm/test_script.py | 2 +- .../methods/knn_classifier/scran/config.vsh.yaml | 2 +- .../methods/knn_classifier/scran/test_script.py | 2 +- .../methods/logistic_regression/log_cpm/config.vsh.yaml | 2 +- .../methods/logistic_regression/log_cpm/test_script.py | 2 +- .../methods/logistic_regression/scran/config.vsh.yaml | 2 +- .../methods/logistic_regression/scran/test_script.py | 2 +- src/label_projection/methods/mlp/log_cpm/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/log_cpm/test_script.py | 2 +- src/label_projection/methods/mlp/scran/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/scran/test_script.py | 2 +- 14 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml index 510524d123..13ddaf6cbf 100644 --- a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml +++ b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: test_data.h5ad + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/methods/baseline/majority_vote/test_script.py b/src/label_projection/methods/baseline/majority_vote/test_script.py index 5e5f3846bd..6c4b3b087f 100644 --- a/src/label_projection/methods/baseline/majority_vote/test_script.py +++ b/src/label_projection/methods/baseline/majority_vote/test_script.py @@ -3,7 +3,7 @@ from os import path -INPUT = "test_data.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.mv.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml index 1b0f69c9d2..c408a08fc3 100644 --- a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/knn_classifier/log_cpm/test_script.py b/src/label_projection/methods/knn_classifier/log_cpm/test_script.py index 0b67ede891..79fa1362ce 100644 --- a/src/label_projection/methods/knn_classifier/log_cpm/test_script.py +++ b/src/label_projection/methods/knn_classifier/log_cpm/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.knnlogcpm.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml index b153921952..e92512cb6b 100644 --- a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" diff --git a/src/label_projection/methods/knn_classifier/scran/test_script.py b/src/label_projection/methods/knn_classifier/scran/test_script.py index c00328f2ae..6452088740 100644 --- a/src/label_projection/methods/knn_classifier/scran/test_script.py +++ b/src/label_projection/methods/knn_classifier/scran/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.knnscran.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml index df603eb58c..55f116f46a 100644 --- a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/logistic_regression/log_cpm/test_script.py b/src/label_projection/methods/logistic_regression/log_cpm/test_script.py index b5d47af7e5..26c5853193 100644 --- a/src/label_projection/methods/logistic_regression/log_cpm/test_script.py +++ b/src/label_projection/methods/logistic_regression/log_cpm/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.lrlogcpm.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml index 8bd43d61c4..454eb052f3 100644 --- a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" diff --git a/src/label_projection/methods/logistic_regression/scran/test_script.py b/src/label_projection/methods/logistic_regression/scran/test_script.py index 194e5abb71..c64ad9b6cc 100644 --- a/src/label_projection/methods/logistic_regression/scran/test_script.py +++ b/src/label_projection/methods/logistic_regression/scran/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.lrscran.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml index db0c9b9342..ae58f4242c 100644 --- a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/mlp/log_cpm/test_script.py b/src/label_projection/methods/mlp/log_cpm/test_script.py index 9984803131..13722e7af3 100644 --- a/src/label_projection/methods/mlp/log_cpm/test_script.py +++ b/src/label_projection/methods/mlp/log_cpm/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.mlplogcpm.h5ad" print(">> Running script as test") diff --git a/src/label_projection/methods/mlp/scran/config.vsh.yaml b/src/label_projection/methods/mlp/scran/config.vsh.yaml index 703f766df0..1312a4831e 100644 --- a/src/label_projection/methods/mlp/scran/config.vsh.yaml +++ b/src/label_projection/methods/mlp/scran/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" diff --git a/src/label_projection/methods/mlp/scran/test_script.py b/src/label_projection/methods/mlp/scran/test_script.py index f31915d3cb..1b66023ece 100644 --- a/src/label_projection/methods/mlp/scran/test_script.py +++ b/src/label_projection/methods/mlp/scran/test_script.py @@ -2,7 +2,7 @@ import scanpy as sc from os import path -INPUT = "test_data_preprocessed.h5ad" +INPUT = "toy_preprocessed_data.h5ad" OUTPUT = "output.mlpscran.h5ad" print(">> Running script as test") From bb542f53d4df3f7f208ae3f8b98839120dee6f3f Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 19 Jun 2022 15:43:16 -0300 Subject: [PATCH 0200/1233] feat: scvi_methods - scanvi_all_genes Former-commit-id: c5e9796442ce41e4b3fae8b5f4769198bcecf77d --- .../scvi/scanvi_all_genes/config.vsh.yaml | 30 +++++++++-- .../methods/scvi/scanvi_all_genes/script.py | 22 +++++--- .../scvi/scanvi_all_genes/test_script.py | 27 ++++++++++ src/label_projection/methods/scvi/tools.py | 50 +++++++++++++++---- 4 files changed, 106 insertions(+), 23 deletions(-) create mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/test_script.py diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 90958f9151..6bbdf241c2 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "scanvi_all_genes" namespace: "label_projection/methods/scvi" version: "dev" - description: "Probabilistic harmonization and annotation of single-cell" + description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." authors: - name: "Scott Gigante" roles: [ author ] @@ -17,6 +17,27 @@ functionality: example: "input.h5ad" description: "Input file that will be used to generate predictions" required: true + - name: "--n_hidden" + type: "integer" + required: true + default: "10" + - name: "--n_layers" + type: "integer" + required: true + default: "1" + - name: "--n_latent" + type: "integer" + required: true + default: "10" + - name: "--max_epochs" + type: "integer" + required: false + - name: "--limit_brain_batches" + type: "integer" + required: false + - name: "--limit_val_batches" + type: "integer" + required: false - name: "--output" alternatives: ["-o"] type: "file" @@ -27,12 +48,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../tools.py" + - path: "../tools.py" tests: - type: python_script path: test_script.py - type: file - path: "../../../data/test_data_preprocessed.h5ad" + path: "../../../resources/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" @@ -43,7 +64,6 @@ platforms: - scprep - sklearn - "anndata<0.8" - - "scvi==0.6.8" - - "scvi-tools==0.13.0" + - scvi-tools - type: native - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py index 13e335e827..ab84c0c4fb 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scanvi_all_genes/script.py @@ -1,7 +1,13 @@ ## VIASH START par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.mlplogcpm.h5ad' + 'input': '../../../resources/toy_preprocessed_data.h5ad', + 'n_latent': 10, + 'n_layers': 1, + 'n_hidden': 32, + 'max_epochs': 1, + 'limit_train_batches': 10, + 'limit_val_batches': 10, + 'output': 'output.scviallgenes.h5ad' } ## VIASH END resources_dir="../" @@ -13,10 +19,6 @@ import scanpy as sc from tools import scanvi -###TODO add these as input -### n_hidden, n_latent, n_layers -n_latent, n_layers, n_hidden = (10, 1, 32) - print("Load input data") adata = sc.read(par['input']) @@ -25,9 +27,13 @@ "early_stopping": True, } -# check parameters for test exists +# check if parameters for test exists par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) -adata.obs["labels_pred"] = scanvi(adata, n_hidden, n_latent, n_layers, **train_kwargs) +adata.obs["labels_pred"] = scanvi(adata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) +adata.uns["method_id"] = "scanvi_all_genes" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py new file mode 100644 index 0000000000..d3677dfa14 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py @@ -0,0 +1,27 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.scanviallgenes.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./scanvi_all_genes", + '--n_hidden', "32", + '--n_layers', "1", + '--n_latent', "10", + '--max_epochs', "1", + '--limit_train_batches', "10", + '--limit_val_batches', "10", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "scanvi_all_genes" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/tools.py b/src/label_projection/methods/scvi/tools.py index 6cfc4daff8..bb59369060 100644 --- a/src/label_projection/methods/scvi/tools.py +++ b/src/label_projection/methods/scvi/tools.py @@ -1,15 +1,8 @@ import scanpy as sc import scvi -def hvg_kwargs(n_top_genes=2000): - return { - "flavor": "seurat_v3", - "inplace": False, - "n_top_genes": n_top_genes, - "batch_key": "batch", - } - -def hvg (adata, hvg_kwargs): + +def hvg (adata, **hvg_kwargs): try: return sc.pp.highly_variable_genes(adata[adata.obs["is_train"]], **hvg_kwargs) except ValueError: # loess estimation can fail on small data with seurat_v3 flavor @@ -36,7 +29,44 @@ def scanvi(adata, n_hidden=None, n_latent=None, n_layers=None, **train_kwargs): scvi_model.train(**train_kwargs) model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") model.train(**train_kwargs) - preds = model.predict(adata) + del adata.obs["scanvi_labels"] + # predictions for train and test + return model.predict(adata) + +def scanvi_scarches(adata, n_hidden=None, n_latent=None, n_layers=None, train_kwargs={}): + model_train_kwargs = train_kwargs['model_train_kwargs'] + query_model_train_kwargs = train_kwargs['query_model_train_kwargs'] + # new obs labels to mask test set + adata_train = adata[adata.obs["is_train"]].copy() + adata_train.obs["scanvi_labels"] = adata_train.obs["labels"].copy() + adata_test = adata[~adata.obs["is_train"]].copy() + adata_test.obs["scanvi_labels"] = "Unknown" + scvi.model.SCVI.setup_anndata( + adata_train, batch_key="batch", labels_key="scanvi_labels" + ) + + # specific scArches parameters + arches_params = dict( + use_layer_norm="both", + use_batch_norm="none", + encode_covariates=True, + dropout_rate=0.2, + n_hidden=n_hidden, + n_layers=n_layers, + n_latent=n_latent, + ) + scvi_model = scvi.model.SCVI(adata_train, **arches_params) + + scvi_model.train(**model_train_kwargs) + model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") + model.train(**model_train_kwargs) + + query_model = scvi.model.SCANVI.load_query_data(adata_test, model) + query_model.train(plan_kwargs=dict(weight_decay=0.0), **query_model_train_kwargs) + + # this is temporary and won't be used + adata.obs["scanvi_labels"] = "Unknown" + preds = query_model.predict(adata) del adata.obs["scanvi_labels"] # predictions for train and test return preds From a2dd2eb1927b16776b439b884f6e58b37da85b1a Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 19 Jun 2022 15:47:56 -0300 Subject: [PATCH 0201/1233] feat: scvi_methods - scanvi_hvg Former-commit-id: b8e405eb207f53781b1576b73ade56605c3d1aa1 --- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 77 +++++++++++++++++++ .../methods/scvi/scanvi_hvg/script.py | 51 ++++++++++++ .../methods/scvi/scanvi_hvg/test_script.py | 29 +++++++ 3 files changed, 157 insertions(+) create mode 100644 src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml create mode 100644 src/label_projection/methods/scvi/scanvi_hvg/script.py create mode 100644 src/label_projection/methods/scvi/scanvi_hvg/test_script.py diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml new file mode 100644 index 0000000000..fa2bd5df37 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -0,0 +1,77 @@ +functionality: + name: "scanvi_hvg" + namespace: "label_projection/methods/scvi" + version: "dev" + description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--n_hidden" + type: "integer" + required: true + default: "10" + - name: "--n_layers" + type: "integer" + required: true + default: "1" + - name: "--n_latent" + type: "integer" + required: true + default: "10" + - name: "--n_top_genes" + type: "integer" + required: true + default: "2000" + - name: "--span" + type: "double" + required: false + - name: "--max_epochs" + type: "integer" + required: false + - name: "--limit_brain_batches" + type: "integer" + required: false + - name: "--limit_val_batches" + type: "integer" + required: false + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../tools.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../resources/toy_preprocessed_data.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - scvi-tools + - scikit-misc + - type: native + - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_hvg/script.py b/src/label_projection/methods/scvi/scanvi_hvg/script.py new file mode 100644 index 0000000000..28c5ef2770 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_hvg/script.py @@ -0,0 +1,51 @@ +## VIASH START +par = { + 'input': '../../../resources/toy_preprocessed_data.h5ad', + 'n_top_genes': 2000, + 'max_epochs': 1, + 'limit_train_batches': 10, + 'span': 0.8, + 'limit_val_batches': 10, + 'output': 'output.scviallgenes.h5ad' +} +## VIASH END +resources_dir="../" + +import sys +sys.path.append(resources_dir) +sys.path.append(meta['resources_dir']) +import scvi +import scanpy as sc +from tools import scanvi, hvg + +print("Load input data") +adata = sc.read(par['input']) + +hvg_kwargs = { + "flavor": "seurat_v3", + "inplace": False, + "n_top_genes": par['n_top_genes'], + "batch_key": "batch", + +} + +# check parameters for test exists +par.get("span") and hvg_kwargs.update({"span": par['span']}) + +train_kwargs = { + "train_size": 0.9, + "early_stopping": True, +} + +# check parameters for test exists +par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) +par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) +par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) + +hvg_df = hvg(adata, **hvg_kwargs) +bdata = adata[:, hvg_df.highly_variable].copy() +adata.obs["labels_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) +adata.uns["method_id"] = "scanvi_hvg" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scanvi_hvg/test_script.py new file mode 100644 index 0000000000..26bdfe08b2 --- /dev/null +++ b/src/label_projection/methods/scvi/scanvi_hvg/test_script.py @@ -0,0 +1,29 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.scanviallgenes.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./scanvi_hvg", + '--n_hidden', "32", + '--n_layers', "1", + '--n_latent', "10", + '--n_top_genes', "2000", + '--spane', "0.8", + '--max_epochs', "1", + '--limit_train_batches', "10", + '--limit_val_batches', "10", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "scanvi_hvg" == adata.uns["method_id"] From 2a8285b72e731ac457b1f02a5a34639db23d80cb Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 19 Jun 2022 15:50:28 -0300 Subject: [PATCH 0202/1233] feat: scvi_methods - scarches_scanvi_all_genes Former-commit-id: 8ebb7499746eef8c305ec48d62aa70879b943862 --- .../scarches_scanvi_all_genes/config.vsh.yaml | 69 +++++++++++++++++++ .../scvi/scarches_scanvi_all_genes/script.py | 42 +++++++++++ .../scarches_scanvi_all_genes/test_script.py | 27 ++++++++ 3 files changed, 138 insertions(+) create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml new file mode 100644 index 0000000000..4fa524324d --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -0,0 +1,69 @@ +functionality: + name: "scarches_scanvi_all_genes" + namespace: "label_projection/methods/scvi" + version: "dev" + description: "Probabilistic harmonization and annotation of single-cell" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--n_hidden" + type: "integer" + required: true + default: "10" + - name: "--n_layers" + type: "integer" + required: true + default: "1" + - name: "--n_latent" + type: "integer" + required: true + default: "10" + - name: "--max_epochs" + type: "integer" + required: false + - name: "--limit_brain_batches" + type: "integer" + required: false + - name: "--limit_val_batches" + type: "integer" + required: false + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../tools.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../resources/toy_preprocessed_data.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - scvi-tools + - type: native + - type: nextflow diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py new file mode 100644 index 0000000000..7ecdac0ad3 --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py @@ -0,0 +1,42 @@ +## VIASH START +par = { + 'input': '../../../resources/toy_preprocessed_data.h5ad', + 'max_epochs': 1, + 'limit_train_batches': 10, + 'limit_val_batches': 10, + 'output': 'output.scviallgenes.h5ad' +} +## VIASH END +resources_dir="../" + +import sys +sys.path.append(resources_dir) +sys.path.append(meta['resources_dir']) +import scvi +import scanpy as sc +from tools import scanvi_scarches + +print("Load input data") +adata = sc.read(par['input']) + +model_train_kwargs = { + "train_size": 0.9, + "early_stopping": True, +} + +query_model_train_kwargs = { + "max_epochs": 200, + "early_stopping": True, +} + +# check parameters for test exists +par.get("max_epochs") and model_train_kwargs.update({"max_epochs": par['max_epochs']}) and query_model_train_kwargs.update({"max_epochs": par['max_epochs']}) +par.get("limit_train_batches") and model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) and query_model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) +par.get("limit_val_batches") and model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) and query_model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) + +adata.obs["labels_pred"] = scanvi_scarches(adata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, + 'query_model_train_kwargs': query_model_train_kwargs}) +adata.uns["method_id"] = "scarches_scanvi_all_genes" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py new file mode 100644 index 0000000000..7316a719b8 --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py @@ -0,0 +1,27 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.scarchesallgenes.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./scarches_scanvi_all_genes", + '--n_hidden', "32", + '--n_layers', "1", + '--n_latent', "10", + '--max_epochs', "1", + '--limit_train_batches', "10", + '--limit_val_batches', "10", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "scarches_scanvi_all_genes" == adata.uns["method_id"] From 328a85fbf80a318e5cb14c4336fd43d85fac1c34 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 19 Jun 2022 15:52:41 -0300 Subject: [PATCH 0203/1233] feat: scvi_methods - scarches_scanvi_hvg Former-commit-id: 5be853764979da380a027a4cdb56b47b88b1a116 --- .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 77 +++++++++++++++++++ .../scvi/scarches_scanvi_hvg/script.py | 57 ++++++++++++++ .../scvi/scarches_scanvi_hvg/test_script.py | 29 +++++++ 3 files changed, 163 insertions(+) create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py create mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml new file mode 100644 index 0000000000..51cc457072 --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -0,0 +1,77 @@ +functionality: + name: "scarches_scanvi_hvg" + namespace: "label_projection/methods/scvi" + version: "dev" + description: "Probabilistic harmonization and annotation of single-cell" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--n_hidden" + type: "integer" + required: true + default: "10" + - name: "--n_layers" + type: "integer" + required: true + default: "1" + - name: "--n_latent" + type: "integer" + required: true + default: "10" + - name: "--max_epochs" + type: "integer" + required: false + - name: "--limit_brain_batches" + type: "integer" + required: false + - name: "--limit_val_batches" + type: "integer" + required: false + - name: "--n_top_genes" + type: "integer" + required: true + default: "2000" + - name: "--span" + type: "double" + required: false + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + - path: "../tools.py" + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../resources/toy_preprocessed_data.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - scprep + - sklearn + - "anndata<0.8" + - scvi-tools + - scikit-misc + - type: native + - type: nextflow diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py new file mode 100644 index 0000000000..2c5c0b0b77 --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py @@ -0,0 +1,57 @@ +## VIASH START +par = { + 'input': '../../../resources/toy_preprocessed_data.h5ad', + 'span': 0.8, + 'n_top_genes': 2000, + 'max_epochs': 1, + 'limit_train_batches': 10, + 'limit_val_batches': 10, + 'output': 'output.scviallgenes.h5ad' +} +## VIASH END +resources_dir="../" + +import sys +sys.path.append(resources_dir) +sys.path.append(meta['resources_dir']) +import scvi +import scanpy as sc +from tools import scanvi_scarches, hvg + +print("Load input data") +adata = sc.read(par['input']) + +hvg_kwargs = { + "flavor": "seurat_v3", + "inplace": False, + "n_top_genes": par['n_top_genes'], + "batch_key": "batch", + +} + +# check parameters for test exists +par.get("span") and hvg_kwargs.update({"span": par['span']}) + +model_train_kwargs = { + "train_size": 0.9, + "early_stopping": True, +} + +query_model_train_kwargs = { + "max_epochs": 200, + "early_stopping": True, +} + +# check parameters for test exists +par.get("max_epochs") and model_train_kwargs.update({"max_epochs": par['max_epochs']}) and query_model_train_kwargs.update({"max_epochs": par['max_epochs']}) +par.get("limit_train_batches") and model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) and query_model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) +par.get("limit_val_batches") and model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) and query_model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) + +hvg_df = hvg(adata, **hvg_kwargs) +bdata = adata[:, hvg_df.highly_variable].copy() +adata.obs["labels_pred"] = scanvi_scarches(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, + 'query_model_train_kwargs': query_model_train_kwargs}) +adata.uns["method_id"] = "scarches_scanvi_hvg" + +print("Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py new file mode 100644 index 0000000000..fae6c3e6d0 --- /dev/null +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py @@ -0,0 +1,29 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.scarchesallgenes.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./scarches_scanvi_hvg", + '--n_hidden', "32", + '--n_layers', "1", + '--n_latent', "10", + '--span', "0.8", + '--n_top_genes', "2000", + '--max_epochs', "1", + '--limit_train_batches', "10", + '--limit_val_batches', "10", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "labels_pred" in adata.obs +assert "scarches_scanvi_hvg" == adata.uns["method_id"] From 4a74851663eebf00b6f1628218ea39d1122e105d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 20 Jun 2022 13:28:04 +0200 Subject: [PATCH 0204/1233] rename components and namespaces Former-commit-id: 7f5415b03a72517be9cafbaf882023bb6c77f9dd --- .../pancreas => data_processing/randomize}/config.vsh.yaml | 4 ++-- .../pancreas => data_processing/randomize}/script.py | 0 .../pancreas => data_processing/randomize}/test_script.py | 2 +- .../{data/toy => data_processing/subsample}/config.vsh.yaml | 2 +- .../{data/toy => data_processing/subsample}/script.py | 0 .../{data/toy => data_processing/subsample}/test_script.py | 2 +- src/label_projection/{data => data_processing}/utils/noise.py | 0 7 files changed, 5 insertions(+), 5 deletions(-) rename src/label_projection/{data/preprocess/pancreas => data_processing/randomize}/config.vsh.yaml (94%) rename src/label_projection/{data/preprocess/pancreas => data_processing/randomize}/script.py (100%) rename src/label_projection/{data/preprocess/pancreas => data_processing/randomize}/test_script.py (94%) rename src/label_projection/{data/toy => data_processing/subsample}/config.vsh.yaml (98%) rename src/label_projection/{data/toy => data_processing/subsample}/script.py (100%) rename src/label_projection/{data/toy => data_processing/subsample}/test_script.py (93%) rename src/label_projection/{data => data_processing}/utils/noise.py (100%) diff --git a/src/label_projection/data/preprocess/pancreas/config.vsh.yaml b/src/label_projection/data_processing/randomize/config.vsh.yaml similarity index 94% rename from src/label_projection/data/preprocess/pancreas/config.vsh.yaml rename to src/label_projection/data_processing/randomize/config.vsh.yaml index ed06f42937..d7f8eff910 100644 --- a/src/label_projection/data/preprocess/pancreas/config.vsh.yaml +++ b/src/label_projection/data_processing/randomize/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: - name: "pancreas_preprocess" - namespace: "label_projection/data/preprocess" + name: "randomize" + namespace: "label_projection/data_processing" version: "dev" description: "Label_projection component to preprocess pancreas data" authors: diff --git a/src/label_projection/data/preprocess/pancreas/script.py b/src/label_projection/data_processing/randomize/script.py similarity index 100% rename from src/label_projection/data/preprocess/pancreas/script.py rename to src/label_projection/data_processing/randomize/script.py diff --git a/src/label_projection/data/preprocess/pancreas/test_script.py b/src/label_projection/data_processing/randomize/test_script.py similarity index 94% rename from src/label_projection/data/preprocess/pancreas/test_script.py rename to src/label_projection/data_processing/randomize/test_script.py index 0533037f3b..c5d27ccc1c 100644 --- a/src/label_projection/data/preprocess/pancreas/test_script.py +++ b/src/label_projection/data_processing/randomize/test_script.py @@ -9,7 +9,7 @@ for method in METHODS: print(">> Running script for {} method".format(method)) out = subprocess.check_output([ - "./pancreas_preprocess", + "./" + meta["functionality_name"], "--input", INPUT, "--method", method, "--output", OUTPUT diff --git a/src/label_projection/data/toy/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml similarity index 98% rename from src/label_projection/data/toy/config.vsh.yaml rename to src/label_projection/data_processing/subsample/config.vsh.yaml index dd70bc48e0..a20fc4de54 100644 --- a/src/label_projection/data/toy/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "toy" + name: "subsample" namespace: "label_projection/data" version: "dev" description: "Component to generate a toy data for tests finality" diff --git a/src/label_projection/data/toy/script.py b/src/label_projection/data_processing/subsample/script.py similarity index 100% rename from src/label_projection/data/toy/script.py rename to src/label_projection/data_processing/subsample/script.py diff --git a/src/label_projection/data/toy/test_script.py b/src/label_projection/data_processing/subsample/test_script.py similarity index 93% rename from src/label_projection/data/toy/test_script.py rename to src/label_projection/data_processing/subsample/test_script.py index 6d639ade11..4eb07c03ff 100644 --- a/src/label_projection/data/toy/test_script.py +++ b/src/label_projection/data_processing/subsample/test_script.py @@ -7,7 +7,7 @@ print(">> Runing script as test") out = subprocess.check_output([ - "./toy", + "./" + meta["functionality_name"], "--input", INPUT, "--celltype_categories", "0:3", "--tech_categories", "0:-3:-2", diff --git a/src/label_projection/data/utils/noise.py b/src/label_projection/data_processing/utils/noise.py similarity index 100% rename from src/label_projection/data/utils/noise.py rename to src/label_projection/data_processing/utils/noise.py From 14e0f177a6bc1f7ab2e98174c32af51186a47581 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 20 Jun 2022 13:28:25 +0200 Subject: [PATCH 0205/1233] simplify script Former-commit-id: 3c61ee4cbab0cd88f432f7ca6001572732b37d29 --- .../data_processing/randomize/script.py | 60 ++++--------------- 1 file changed, 13 insertions(+), 47 deletions(-) diff --git a/src/label_projection/data_processing/randomize/script.py b/src/label_projection/data_processing/randomize/script.py index a4cafcc2ea..7feef496f9 100644 --- a/src/label_projection/data_processing/randomize/script.py +++ b/src/label_projection/data_processing/randomize/script.py @@ -11,67 +11,33 @@ import numpy as np import scanpy as sc +print(">> Load data") +adata = sc.read(par['input']) -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - - return adata - +print(">> Process data using {} method".format(par['method'])) +# Remove empty cells and genes. +sc.pp.filter_genes(adata, min_cells=1) +sc.pp.filter_cells(adata, min_counts=2) -# TODO split the functions in different viash components -def batch(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] +# Assign training/test +adata.obs["labels"] = adata.obs["celltype"] +adata.obs["batch"] = adata.obs["tech"] - # Assign training/test +if par["method"] == "batch": test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] adata.obs["is_train"] = [ False if adata.obs["batch"][idx] in test_batches else True for idx in adata.obs_names ] - return adata - - -def random(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign training/test +elif par["method"] == "random": adata.obs["is_train"] = np.random.choice( [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] ) - - return adata - - -def random_with_noise(adata): - adata.obs["labels"] = adata.obs["celltype"] - adata.obs["batch"] = adata.obs["tech"] - - # Assign trainin/test +elif par["method"] == "random_with_noise": adata.obs["is_train"] = np.random.choice( [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] ) - - # Inject label noise adata = noise.add_label_noise(adata, noise_prob=0.2) - return adata - - -func_map = {'batch': batch, - 'random': random, - 'random_with_noise': random_with_noise} - -print(">> Load data") -adata = sc.read(par['input']) - -print(">> Process data using {} method".format(par['method'])) -filter_genes_cells(adata) -method_func = func_map[par['method']] -preprocessed_adata = method_func(adata) - print(">> Writing data") -preprocessed_adata.write(par['output']) +adata.write(par['output']) From dcc72d0245abf9f3dc023cc842ebb96569836950 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 20 Jun 2022 13:55:42 +0200 Subject: [PATCH 0206/1233] move resource data Former-commit-id: 4e0e591b32652cae2944ce75b32e6f7903e57f05 --- .../data_processing/randomize/config.vsh.yaml | 4 +-- .../data_processing/randomize/test_script.py | 7 ++++- .../data_processing/subsample/config.vsh.yaml | 4 +-- .../data_processing/subsample/test_script.py | 5 +++- .../generate_test_resources/pancreas.sh | 29 +++++++++++++++++++ .../workflows/test/load_raw_data.sh | 15 ---------- .../test/toy_preprocessed_test_data.sh | 15 ---------- .../workflows/test/toy_test_data.sh | 17 ----------- 8 files changed, 43 insertions(+), 53 deletions(-) create mode 100755 src/label_projection/workflows/generate_test_resources/pancreas.sh delete mode 100644 src/label_projection/workflows/test/load_raw_data.sh delete mode 100644 src/label_projection/workflows/test/toy_preprocessed_test_data.sh delete mode 100644 src/label_projection/workflows/test/toy_test_data.sh diff --git a/src/label_projection/data_processing/randomize/config.vsh.yaml b/src/label_projection/data_processing/randomize/config.vsh.yaml index d7f8eff910..04d2d758da 100644 --- a/src/label_projection/data_processing/randomize/config.vsh.yaml +++ b/src/label_projection/data_processing/randomize/config.vsh.yaml @@ -31,12 +31,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../utils/noise.py" + - path: "../utils/noise.py" tests: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../resources/pancreas" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data_processing/randomize/test_script.py b/src/label_projection/data_processing/randomize/test_script.py index c5d27ccc1c..53f64038dc 100644 --- a/src/label_projection/data_processing/randomize/test_script.py +++ b/src/label_projection/data_processing/randomize/test_script.py @@ -2,7 +2,10 @@ import scanpy as sc from os import path -INPUT = "toy_preprocessed_data.h5ad" +## VIASH START +## VIASH END + +INPUT = f"{meta['resources_dir']}/pancreas/toy_preprocessed_data.h5ad" OUTPUT = "preprocessed.h5ad" METHODS = ["batch", "random", "random_with_noise"] @@ -14,8 +17,10 @@ "--method", method, "--output", OUTPUT ]).decode("utf-8") + print(">> Checking whether file exists") assert path.exists(OUTPUT) + print(">> Check that test output fits expected API") adata = sc.read_h5ad(OUTPUT) assert (500, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index a20fc4de54..3d35db3dd7 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "subsample" - namespace: "label_projection/data" + namespace: "label_projection/data_processing" version: "dev" description: "Component to generate a toy data for tests finality" authors: @@ -39,7 +39,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/raw_data.h5ad" + path: "../../resources/pancreas" platforms: - type: native - type: docker diff --git a/src/label_projection/data_processing/subsample/test_script.py b/src/label_projection/data_processing/subsample/test_script.py index 4eb07c03ff..3dfe6c2608 100644 --- a/src/label_projection/data_processing/subsample/test_script.py +++ b/src/label_projection/data_processing/subsample/test_script.py @@ -2,7 +2,10 @@ import scanpy as sc from os import path -INPUT = "raw_data.h5ad" +## VIASH START +## VIASH END + +INPUT = f"{meta['resources_dir']}/pancreas/raw_data.h5ad" OUTPUT = "toy_data.h5ad" print(">> Runing script as test") diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/label_projection/workflows/generate_test_resources/pancreas.sh new file mode 100755 index 0000000000..c8036fd7cb --- /dev/null +++ b/src/label_projection/workflows/generate_test_resources/pancreas.sh @@ -0,0 +1,29 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=src/label_projection/resources/pancreas + +mkdir -p $DATASET_DIR + +target/docker/common/data_loader/data_loader\ + --url "https://ndownloader.figshare.com/files/24539828"\ + --name "pancreas"\ + --output $DATASET_DIR/raw_data.h5ad + +target/docker/label_projection/data_processing/subsample/subsample\ + --input $DATASET_DIR/raw_data.h5ad\ + --celltype_categories "0:3"\ + --tech_categories "0:-3:-2"\ + --output $DATASET_DIR/toy_data.h5ad + +target/docker/label_projection/data_processing/randomize/randomize\ + --input $DATASET_DIR/toy_data.h5ad\ + --output $DATASET_DIR/toy_preprocessed_data.h5ad diff --git a/src/label_projection/workflows/test/load_raw_data.sh b/src/label_projection/workflows/test/load_raw_data.sh deleted file mode 100644 index 45e79c79ec..0000000000 --- a/src/label_projection/workflows/test/load_raw_data.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -target/docker/common/data_loader/data_loader\ - --url "https://ndownloader.figshare.com/files/24539828"\ - --name "pancreas"\ - --output src/label_projection/resources/raw_data.h5ad diff --git a/src/label_projection/workflows/test/toy_preprocessed_test_data.sh b/src/label_projection/workflows/test/toy_preprocessed_test_data.sh deleted file mode 100644 index e3197ea489..0000000000 --- a/src/label_projection/workflows/test/toy_preprocessed_test_data.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -#make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -sh src/label_projection/workflows/test/toy_test_data.sh - -target/docker/label_projection/data/preprocess/preprocess\ - --input src/label_projection/resources/toy_data.h5ad\ - --output src/label_projection/resources/toy_preprocessed_data.h5ad diff --git a/src/label_projection/workflows/test/toy_test_data.sh b/src/label_projection/workflows/test/toy_test_data.sh deleted file mode 100644 index db856fc5c4..0000000000 --- a/src/label_projection/workflows/test/toy_test_data.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash -#make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -sh src/label_projection/workflows/test/load_raw_data.sh - -target/docker/label_projection/data/toy/toy\ - --input src/label_projection/resources/raw_data.h5ad\ - --celltype_categories "0:3"\ - --tech_categories "0:-3:-2"\ - --output src/label_projection/resources/toy_data.h5ad From 0cb9dbd1682e2cdb78919f19cb25623adf5da3ef Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 21 Jun 2022 07:11:23 -0300 Subject: [PATCH 0207/1233] fix: using new resources directory Former-commit-id: 4875e67fbc055e98f1a289fede34e49fec050615 --- .../methods/baseline/majority_vote/config.vsh.yaml | 2 +- .../methods/knn_classifier/log_cpm/config.vsh.yaml | 2 +- .../methods/knn_classifier/scran/config.vsh.yaml | 2 +- .../methods/logistic_regression/log_cpm/config.vsh.yaml | 2 +- .../methods/logistic_regression/scran/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/log_cpm/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/scran/config.vsh.yaml | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml index 13ddaf6cbf..6530cc99f5 100644 --- a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml +++ b/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml index c408a08fc3..587fd963eb 100644 --- a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml index e92512cb6b..fdf18ba887 100644 --- a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" diff --git a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml index 55f116f46a..2101c1fd16 100644 --- a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml index 454eb052f3..28fc8fe973 100644 --- a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" diff --git a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml index ae58f4242c..73056fb61b 100644 --- a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/mlp/scran/config.vsh.yaml b/src/label_projection/methods/mlp/scran/config.vsh.yaml index 1312a4831e..ace6715966 100644 --- a/src/label_projection/methods/mlp/scran/config.vsh.yaml +++ b/src/label_projection/methods/mlp/scran/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "singlecellopenproblems/openproblems-r-base:latest" From a8580193b1cfe0e5b7b0c2b3e01b467a7b78e087 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 21 Jun 2022 07:26:50 -0300 Subject: [PATCH 0208/1233] fix: nextflow script Former-commit-id: 67c75d6e815167282143f7f391b313d7568da069 --- .../resources/data_loader/fake_anndata_loader.tsv | 2 ++ src/label_projection/workflows/run/main.nf | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 src/label_projection/resources/data_loader/fake_anndata_loader.tsv diff --git a/src/label_projection/resources/data_loader/fake_anndata_loader.tsv b/src/label_projection/resources/data_loader/fake_anndata_loader.tsv new file mode 100644 index 0000000000..2b84d064f9 --- /dev/null +++ b/src/label_projection/resources/data_loader/fake_anndata_loader.tsv @@ -0,0 +1,2 @@ +processor name url +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 64bc12e9f1..7ba0538d7e 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -37,7 +37,7 @@ include { accuracy } from "$targetDir/label_projection/metrics/accuracy // If the need arises, these workflows could be split off into a separate file. // params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" -params.tsv = "$launchDir/src/label_projection/data/fake_anndata_loader.tsv" +params.tsv = "$launchDir/src/label_projection/resources/data_loader/fake_anndata_loader.tsv" workflow load_data { main: @@ -59,7 +59,7 @@ workflow load_data { workflow { load_data | view - | (majority_vote & knn_classifier_log_cpm & knn_classifier_scran & mlp_log_cpm & mlp_scran) + | (majority_vote & knn_classifier_log_cpm & mlp_log_cpm) | mix | accuracy | view From a28f8363a84d5cee9358137efa876f5225ae11e7 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 21 Jun 2022 08:33:44 -0300 Subject: [PATCH 0209/1233] fix: nextflow pipeline Former-commit-id: 4d6da83f0c23f5125bc943705d41924af4685399 --- src/label_projection/workflows/run/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d7b6d891ea..d61f112804 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -11,7 +11,7 @@ targetDir = "${params.rootDir}/target/nextflow" include { data_loader } from "$targetDir/common/data_loader/main.nf" params(params) // import preprocess -include { pancreas_preprocess } from "$targetDir/label_projection/data/preprocess/pancreas_preprocess/main.nf" params(params) +include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" params(params) // import methods // TODO @@ -39,7 +39,7 @@ workflow load_data { [ row.name, [ "url": row.url, "name": row.name ]] } | data_loader - | pancreas_preprocess + | randomize emit: output_ } From 7452e74e91b5e2b8e0255da282b0ccde69a120e6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 21 Jun 2022 13:53:47 +0200 Subject: [PATCH 0210/1233] use r2u containers Former-commit-id: 7208e786e9ed8e55408e98f0ecb39be43e7e738d --- .../methods/mlp/scran/config.vsh.yaml | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/src/label_projection/methods/mlp/scran/config.vsh.yaml b/src/label_projection/methods/mlp/scran/config.vsh.yaml index ace6715966..678ad75ca4 100644 --- a/src/label_projection/methods/mlp/scran/config.vsh.yaml +++ b/src/label_projection/methods/mlp/scran/config.vsh.yaml @@ -44,16 +44,12 @@ functionality: path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker - image: "singlecellopenproblems/openproblems-r-base:latest" + image: eddelbuettel/r2u:22.04 setup: - type: r - bioc: - - scran - - BiocParallel + cran: [ scran, BiocParallel, rlang ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - packages: - - scanpy - - scprep - - sklearn - - "anndata<0.8" + pip: [ scanpy, anndata<0.8, scprep, sklearn, rpy2 ] - type: nextflow From 980545468b8f8f2c159a27069ef8620bf33783d9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 21 Jun 2022 14:31:20 +0200 Subject: [PATCH 0211/1233] rework anndata loader Former-commit-id: 4ce12be48d54cf3b2f8fe400e925613f0625755e --- CHANGELOG.md | 11 ++++ src/common/data_loader/script.py | 39 ------------ src/common/data_loader/test.py | 25 -------- .../download}/anndata_loader.tsv | 10 +-- .../download}/config.vsh.yaml | 13 ++-- src/common/dataset_loader/download/script.py | 61 +++++++++++++++++++ src/common/dataset_loader/download/test.py | 35 +++++++++++ 7 files changed, 121 insertions(+), 73 deletions(-) create mode 100644 CHANGELOG.md delete mode 100644 src/common/data_loader/script.py delete mode 100644 src/common/data_loader/test.py rename src/common/{data_loader => dataset_loader/download}/anndata_loader.tsv (69%) rename src/common/{data_loader => dataset_loader/download}/config.vsh.yaml (72%) create mode 100644 src/common/dataset_loader/download/script.py create mode 100644 src/common/dataset_loader/download/test.py diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000000..94161d41ad --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,11 @@ +# openproblems-v2 0.1.0 + +## common + +### NEW FUNCTIONALITY + +* `dataset_loader/download`: Download an AnnData dataset from a URL. + +* `extract_scores`: Summarise a metrics output tsv. + +## \ No newline at end of file diff --git a/src/common/data_loader/script.py b/src/common/data_loader/script.py deleted file mode 100644 index dcd1c95848..0000000000 --- a/src/common/data_loader/script.py +++ /dev/null @@ -1,39 +0,0 @@ -## VIASH START -par = { - "url": "https://ndownloader.figshare.com/files/24974582", # PBMC data - "name": "pbmc", - "output": "test_data.h5ad" -} -## VIASH END - -print("Importing libraries") -import sys -import scanpy as sc -import tempfile -import os -import scprep - - -with tempfile.TemporaryDirectory() as tempdir: - URL = par['url'] - print("Downloading", URL) - sys.stdout.flush() - filepath = os.path.join(tempdir, "pancreas.h5ad") - scprep.io.download.download_url(URL, filepath) - - print("Read file") - adata = sc.read(filepath) - adata.uns["name"] = par["name"] - - # Remove preprocessing - if "counts" in adata.layers: - adata.X = adata.layers["counts"] - del adata.layers["counts"] - - # Ensure there are no cells or genes with 0 counts - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - - -print("Writing adata to file") -adata.write(par["output"], compression="gzip") diff --git a/src/common/data_loader/test.py b/src/common/data_loader/test.py deleted file mode 100644 index 7e36071407..0000000000 --- a/src/common/data_loader/test.py +++ /dev/null @@ -1,25 +0,0 @@ -from os import path -import subprocess -import scanpy as sc - -name = "pbmc" -anndata_file = "pcmc.h5ad" - -print(">> Running script") -out = subprocess.check_output([ - "./data_loader", - "--url", "https://ndownloader.figshare.com/files/24974582", - "--name", name, - "--output", anndata_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(anndata_file) - -print(">> Check that output fits expected API") -adata = sc.read_h5ad(anndata_file) -# TODO: complete with API checks -assert "counts" not in adata.layers -assert adata.uns["name"] == name - -print(">> All tests passed successfully") diff --git a/src/common/data_loader/anndata_loader.tsv b/src/common/dataset_loader/download/anndata_loader.tsv similarity index 69% rename from src/common/data_loader/anndata_loader.tsv rename to src/common/dataset_loader/download/anndata_loader.tsv index bfa73d8704..45c044681e 100644 --- a/src/common/data_loader/anndata_loader.tsv +++ b/src/common/dataset_loader/download/anndata_loader.tsv @@ -1,5 +1,5 @@ -processor name url -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 -anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 -anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 +processor name url obs_celltype obs_batch +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech +anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 foo bar +anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA +anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA diff --git a/src/common/data_loader/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml similarity index 72% rename from src/common/data_loader/config.vsh.yaml rename to src/common/dataset_loader/download/config.vsh.yaml index 0ac7afb7c6..80ddde03bf 100644 --- a/src/common/data_loader/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -1,8 +1,8 @@ functionality: - name: "data_loader" - namespace: "common" + name: "download" + namespace: "common/dataset_loader" version: "dev" - description: "Load datasets" + description: "Download a dataset." authors: - name: "Michaela Mueller " roles: [ maintainer, author ] @@ -24,6 +24,12 @@ functionality: example: "pbmc" description: "Name of dataset" required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." resources: - type: python_script path: script.py @@ -37,7 +43,6 @@ platforms: - type: python packages: - scanpy - - scprep - "anndata<0.8" - type: native - type: nextflow diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py new file mode 100644 index 0000000000..e3616a9bdd --- /dev/null +++ b/src/common/dataset_loader/download/script.py @@ -0,0 +1,61 @@ +print("Importing libraries") +import scanpy as sc +import tempfile +import os +import urllib + +_FAKE_HEADERS = [("User-Agent", "Mozilla/5.0")] + +## VIASH START +par = { + "url": "https://ndownloader.figshare.com/files/24539828", + "name": "pancreas", + "obs_celltype": "celltype", + "obs_batch": "tech", + "output": "test_data.h5ad" +} +## VIASH END + +with tempfile.TemporaryDirectory() as tempdir: + print("Downloading", par['url'], flush=True) + filepath = os.path.join(tempdir, "dataset.h5ad") + + with open(filepath, "wb") as filehandle: + opener = urllib.request.build_opener() + opener.addheaders = _FAKE_HEADERS + urllib.request.install_opener(opener) + with urllib.request.urlopen(par["url"]) as urlhandle: + filehandle.write(urlhandle.read()) + # scprep.io.download.download_url(par['url'], filepath) + + print("Reading file") + adata = sc.read_h5ad(filepath) + +print("Copying .layers['counts'] to .X") +if "counts" in adata.layers: + adata.X = adata.layers["counts"] + del adata.layers["counts"] + +print("Setting .uns['dataset_id']") +adata.uns["dataset_id"] = par["name"] + +print("Setting .obs['celltype']") +if par["obs_celltype"]: + if par["obs_celltype"] in adata.obs: + adata.obs["celltype"] = adata.obs[par["obs_celltype"]] + else: + print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.") + +print("Setting .obs['batch']") +if par["obs_batch"]: + if par["obs_batch"] in adata.obs: + adata.obs["batch"] = adata.obs[par["obs_batch"]] + else: + print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.") + +print("Remove cells or genes with 0 counts") +sc.pp.filter_genes(adata, min_cells=1) +sc.pp.filter_cells(adata, min_counts=2) + +print("Writing adata to file") +adata.write(par["output"], compression="gzip") diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py new file mode 100644 index 0000000000..328c6c19be --- /dev/null +++ b/src/common/dataset_loader/download/test.py @@ -0,0 +1,35 @@ +from os import path +import subprocess +import scanpy as sc + +name = "pancreas" +anndata_file = "dataset.h5ad" +url = "https://ndownloader.figshare.com/files/24974582" +obs_celltype = "celltype" +obs_batch = "tech" + +print(">> Running script") +out = subprocess.check_output([ + f"./{meta['functionality_name']}", + "--url", url, + "--name", name, + "--obs_celltype", obs_celltype, + "--obs_batch", obs_batch, + "--output", anndata_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(anndata_file) + +print(">> Read output anndata") +adata = sc.read_h5ad(anndata_file) + +print(">> Check that output fits expected API") +assert "counts" not in adata.layers +assert adata.uns["dataset_id"] == name +if obs_celltype: + assert "celltype" in adata.obs +if obs_batch: + assert "batch" in adata.obs + +print(">> All tests passed successfully") From d255d6a05acd79bea371d5a7092f721cd3967b26 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 21 Jun 2022 14:47:31 +0200 Subject: [PATCH 0212/1233] rework dataset loader component Former-commit-id: 95ffda8fbf69bad3e474bd4efde77b1b30d1c41c --- .../dataset_loader/download/config.vsh.yaml | 3 +++ .../{anndata_loader.tsv => datasets.tsv} | 10 ++++----- src/common/dataset_loader/download/script.py | 7 ++++++ .../data_processing/randomize/script.py | 4 ---- src/label_projection/workflows/run/main.nf | 22 +++++++------------ .../workflows/run/run_nextflow.sh | 0 6 files changed, 23 insertions(+), 23 deletions(-) rename src/common/dataset_loader/download/{anndata_loader.tsv => datasets.tsv} (62%) mode change 100644 => 100755 src/label_projection/workflows/run/run_nextflow.sh diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 80ddde03bf..f11782ef8a 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -30,6 +30,9 @@ functionality: - name: "--obs_batch" type: "string" description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." resources: - type: python_script path: script.py diff --git a/src/common/dataset_loader/download/anndata_loader.tsv b/src/common/dataset_loader/download/datasets.tsv similarity index 62% rename from src/common/dataset_loader/download/anndata_loader.tsv rename to src/common/dataset_loader/download/datasets.tsv index 45c044681e..a9a4934684 100644 --- a/src/common/dataset_loader/download/anndata_loader.tsv +++ b/src/common/dataset_loader/download/datasets.tsv @@ -1,5 +1,5 @@ -processor name url obs_celltype obs_batch -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 foo bar -anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA -anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA +processor name url obs_celltype obs_batch obs_tissue +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA +anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue +anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA +anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index e3616a9bdd..a5533fdbc0 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -53,6 +53,13 @@ else: print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.") +print("Setting .obs['tissue']") +if par["obs_tissue"]: + if par["obs_tissue"] in adata.obs: + adata.obs["tissue"] = adata.obs[par["obs_tissue"]] + else: + print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") + print("Remove cells or genes with 0 counts") sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) diff --git a/src/label_projection/data_processing/randomize/script.py b/src/label_projection/data_processing/randomize/script.py index 7feef496f9..13d3a108e0 100644 --- a/src/label_projection/data_processing/randomize/script.py +++ b/src/label_projection/data_processing/randomize/script.py @@ -19,10 +19,6 @@ sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) -# Assign training/test -adata.obs["labels"] = adata.obs["celltype"] -adata.obs["batch"] = adata.obs["tech"] - if par["method"] == "batch": test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] adata.obs["is_train"] = [ diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d61f112804..81258bbe9c 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -1,17 +1,12 @@ nextflow.enable.dsl=2 -/* For now, you need to manually specify the - * root directory of this repository as follows. - * (it's a nextflow limitation I'm trying to figure out - * how to resolve.) */ - targetDir = "${params.rootDir}/target/nextflow" // import dataset loaders -include { data_loader } from "$targetDir/common/data_loader/main.nf" params(params) +include { download } from "$targetDir/common/dataset_loader/download/main.nf" // import preprocess -include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" params(params) +include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" // import methods // TODO @@ -25,21 +20,19 @@ include { randomize } from "$targetDir/label_projection/data_processing/r // This workflow reads in a tsv containing some metadata about each dataset. // For each entry in the metadata, a dataset is generated, usually by downloading // and processing some files. The end result of each of these workflows -// should be simply a channel of [id, h5adfile, params] triplets. +// should be simply a channel of [id, h5adfile] triplets. // // If the need arises, these workflows could be split off into a separate file. -params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" +params.tsv = "$launchDir/src/common/dataset_loader/download/datasets.tsv" workflow load_data { main: output_ = Channel.fromPath(params.tsv) | splitCsv(header: true, sep: "\t") - | map { row -> - [ row.name, [ "url": row.url, "name": row.name ]] - } - | data_loader - | randomize + | filter{ it.obs_celltype != "NA" && it.obs_batch != "NA" } + | map{ [ it.name, it ] } + | download emit: output_ } @@ -50,5 +43,6 @@ workflow load_data { workflow { load_data + | randomize | view() } diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_nextflow.sh old mode 100644 new mode 100755 From ba907345d834ce61f1c835bfdeaa678aed8350a0 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 22 Jun 2022 10:08:51 -0300 Subject: [PATCH 0213/1233] feat: log_cpm component Former-commit-id: d5407b3acd6df911d6d4a278e40c64339a88dc0d --- .../normalize/log_cpm/config.vsh.yaml | 43 +++++++++++++++++++ .../normalize/log_cpm/script.py | 20 +++++++++ .../normalize/log_cpm/test_script.py | 20 +++++++++ 3 files changed, 83 insertions(+) create mode 100644 src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml create mode 100644 src/label_projection/data_processing/normalize/log_cpm/script.py create mode 100644 src/label_projection/data_processing/normalize/log_cpm/test_script.py diff --git a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..423e66498c --- /dev/null +++ b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml @@ -0,0 +1,43 @@ +functionality: + name: "log_cpm" + namespace: "label_projection/data_processing/normalize/log_cpm" + version: "dev" + description: "Normalize data" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be used to generate predictions" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/data_processing/normalize/log_cpm/script.py b/src/label_projection/data_processing/normalize/log_cpm/script.py new file mode 100644 index 0000000000..af9292b950 --- /dev/null +++ b/src/label_projection/data_processing/normalize/log_cpm/script.py @@ -0,0 +1,20 @@ +##VIASH START +par = { + 'input': "../../resources/pancreas/toy_preprocessed_data.h5ad", + 'output': "output.h5ad" +} +##VIASH END + +import scanpy as sc + +print(">> Load data") +adata = sc.read(par['input']) + +print(">> Normalize data") +adata.layers["counts"] = adata.X.copy() +sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") +sc.pp.log1p(adata) +adata.uns["normalization_method"] = "log_cpm" + +print(">> Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/data_processing/normalize/log_cpm/test_script.py b/src/label_projection/data_processing/normalize/log_cpm/test_script.py new file mode 100644 index 0000000000..8cae3c0f3a --- /dev/null +++ b/src/label_projection/data_processing/normalize/log_cpm/test_script.py @@ -0,0 +1,20 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.logcpm.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./log_cpm", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "log_cpm" == adata.uns["normalization_method"] From 718b0a580ce106af0eb7473021796fce6c9fda00 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 22 Jun 2022 10:09:19 -0300 Subject: [PATCH 0214/1233] chore: scran component Former-commit-id: 004a9ee21469944a01509c026ad2200c9b8430e3 --- .../data_processing/normalize/scran/script.R | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 src/label_projection/data_processing/normalize/scran/script.R diff --git a/src/label_projection/data_processing/normalize/scran/script.R b/src/label_projection/data_processing/normalize/scran/script.R new file mode 100644 index 0000000000..0ecb9a9c9b --- /dev/null +++ b/src/label_projection/data_processing/normalize/scran/script.R @@ -0,0 +1,17 @@ +## VIASH START +par <- list( + input = "src/label_projection/resources/pancreas/toy_preprocessed_data.h5ad", + output = "output.scran.h5ad" +) +## VIASH END + +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(scran, warn.conflicts = FALSE) +library(BiocParallel, warn.conflicts = FALSE) + +cat(">> Load data\n") +adata <- anndata::read_h5ad(par$input) +sce <- scran::calculateSumFactors(t(adata$X), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) +adata$obs[["size_factors"]] <- sce +adata$X <- log1p(t(t(adata$X) * sce)) From 8f2a34a97bde39b2472867ab5b7532a3297f08d2 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 26 Jun 2022 15:41:39 -0300 Subject: [PATCH 0215/1233] feat: log_scran_pooling component Former-commit-id: 1f431145b5e634c79206db8a227733992eead72f --- .../normalize/scran/config.vsh.yaml | 45 +++++++++++++++++++ .../data_processing/normalize/scran/script.R | 8 +++- .../normalize/scran/test_script.py | 20 +++++++++ .../generate_test_resources/pancreas.sh | 12 ++++- 4 files changed, 83 insertions(+), 2 deletions(-) create mode 100644 src/label_projection/data_processing/normalize/scran/config.vsh.yaml create mode 100644 src/label_projection/data_processing/normalize/scran/test_script.py diff --git a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml new file mode 100644 index 0000000000..1026843295 --- /dev/null +++ b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml @@ -0,0 +1,45 @@ +functionality: + name: "log_scran_pooling" + namespace: "label_projection/data_processing/normalize/scran" + version: "dev" + description: "Normalize data" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + alternatives: ["-i"] + type: "file" + example: "input.h5ad" + description: "Input file that will be normalized" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output data labeled" + required: true + resources: + - type: r_script + path: script.R + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ scran, BiocParallel, rlang, anndata] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [anndata<0.8, scanpy] + - type: nextflow diff --git a/src/label_projection/data_processing/normalize/scran/script.R b/src/label_projection/data_processing/normalize/scran/script.R index 0ecb9a9c9b..9145a9d17f 100644 --- a/src/label_projection/data_processing/normalize/scran/script.R +++ b/src/label_projection/data_processing/normalize/scran/script.R @@ -12,6 +12,12 @@ library(BiocParallel, warn.conflicts = FALSE) cat(">> Load data\n") adata <- anndata::read_h5ad(par$input) + +cat(">> Normalizing data") sce <- scran::calculateSumFactors(t(adata$X), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) adata$obs[["size_factors"]] <- sce -adata$X <- log1p(t(t(adata$X) * sce)) +adata$X <- log1p(sce * adata$X) + +cat("Writing to file\n") +adata$uns["normalization_method"] <- "log_scran_pooling" +zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/label_projection/data_processing/normalize/scran/test_script.py b/src/label_projection/data_processing/normalize/scran/test_script.py new file mode 100644 index 0000000000..7b75372d87 --- /dev/null +++ b/src/label_projection/data_processing/normalize/scran/test_script.py @@ -0,0 +1,20 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.scran.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./log_scran_pooling", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "log_scran_pooling" == adata.uns["normalization_method"] diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/label_projection/workflows/generate_test_resources/pancreas.sh index c8036fd7cb..4bc2d0aeee 100755 --- a/src/label_projection/workflows/generate_test_resources/pancreas.sh +++ b/src/label_projection/workflows/generate_test_resources/pancreas.sh @@ -13,8 +13,10 @@ DATASET_DIR=src/label_projection/resources/pancreas mkdir -p $DATASET_DIR -target/docker/common/data_loader/data_loader\ +target/docker/common/dataset_loader/download/download\ --url "https://ndownloader.figshare.com/files/24539828"\ + --obs_celltype "celltype"\ + --obs_batch "tech"\ --name "pancreas"\ --output $DATASET_DIR/raw_data.h5ad @@ -27,3 +29,11 @@ target/docker/label_projection/data_processing/subsample/subsample\ target/docker/label_projection/data_processing/randomize/randomize\ --input $DATASET_DIR/toy_data.h5ad\ --output $DATASET_DIR/toy_preprocessed_data.h5ad + +target/docker/label_projection/data_processing/normalize/log_cpm\ + --input $DATASET_DIR/toy_preprocessed_data.h5ad\ + --output $DATASET_DIR/toy_normalized_log_cpm_data.h5ad + +target/docker/label_projection/data_processing/normalize/log_scran_pooling\ + --input $DATASET_DIR/toy_preprocessed_data.h5ad\ + --output $DATASET_DIR/toy_normalized_log_scran_pooling_data.h5ad From d7727211b932a694ccdd5317363c4d1ab09a148e Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 26 Jun 2022 17:25:41 -0300 Subject: [PATCH 0216/1233] feat: use new normalization components to methods Former-commit-id: bb1808cf99d2a2d26dc14dbff29a5cab8c0f2cc9 --- src/common/dataset_loader/download/script.py | 1 - .../normalize/log_cpm/config.vsh.yaml | 2 +- .../data_processing/normalize/scran/script.R | 4 +- .../data_processing/randomize/script.py | 2 +- .../data_processing/utils/noise.py | 36 ++++++------ .../methods/baseline/majority_vote/script.py | 8 +-- .../baseline/majority_vote/test_script.py | 2 +- .../{log_cpm => }/config.vsh.yaml | 9 ++- .../knn_classifier/log_cpm/test_script.py | 21 ------- .../knn_classifier/scran/config.vsh.yaml | 51 ----------------- .../methods/knn_classifier/scran/script.py | 28 ---------- .../knn_classifier/scran/test_script.py | 21 ------- .../knn_classifier/{log_cpm => }/script.py | 4 +- .../methods/knn_classifier/test_script.py | 22 ++++++++ .../{log_cpm => }/config.vsh.yaml | 9 ++- .../log_cpm/test_script.py | 22 -------- .../logistic_regression/scran/config.vsh.yaml | 55 ------------------- .../logistic_regression/scran/script.py | 29 ---------- .../logistic_regression/scran/test_script.py | 22 -------- .../{log_cpm => }/script.py | 8 +-- .../logistic_regression/test_script.py | 23 ++++++++ .../methods/mlp/{log_cpm => }/config.vsh.yaml | 10 ++-- .../methods/mlp/log_cpm/test_script.py | 23 -------- .../methods/mlp/scran/config.vsh.yaml | 55 ------------------- .../methods/mlp/scran/script.py | 30 ---------- .../methods/mlp/scran/test_script.py | 23 -------- .../methods/mlp/{log_cpm => }/script.py | 13 +++-- .../methods/mlp/test_script.py | 24 ++++++++ .../scvi/scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- src/label_projection/methods/scvi/tools.py | 4 +- .../data_loader/fake_anndata_loader.tsv | 2 - src/label_projection/utils.py | 8 +-- .../generate_test_resources/pancreas.sh | 4 +- 36 files changed, 131 insertions(+), 452 deletions(-) rename src/label_projection/methods/knn_classifier/{log_cpm => }/config.vsh.yaml (83%) delete mode 100644 src/label_projection/methods/knn_classifier/log_cpm/test_script.py delete mode 100644 src/label_projection/methods/knn_classifier/scran/config.vsh.yaml delete mode 100644 src/label_projection/methods/knn_classifier/scran/script.py delete mode 100644 src/label_projection/methods/knn_classifier/scran/test_script.py rename src/label_projection/methods/knn_classifier/{log_cpm => }/script.py (85%) create mode 100644 src/label_projection/methods/knn_classifier/test_script.py rename src/label_projection/methods/logistic_regression/{log_cpm => }/config.vsh.yaml (85%) delete mode 100644 src/label_projection/methods/logistic_regression/log_cpm/test_script.py delete mode 100644 src/label_projection/methods/logistic_regression/scran/config.vsh.yaml delete mode 100644 src/label_projection/methods/logistic_regression/scran/script.py delete mode 100644 src/label_projection/methods/logistic_regression/scran/test_script.py rename src/label_projection/methods/logistic_regression/{log_cpm => }/script.py (73%) create mode 100644 src/label_projection/methods/logistic_regression/test_script.py rename src/label_projection/methods/mlp/{log_cpm => }/config.vsh.yaml (86%) delete mode 100644 src/label_projection/methods/mlp/log_cpm/test_script.py delete mode 100644 src/label_projection/methods/mlp/scran/config.vsh.yaml delete mode 100644 src/label_projection/methods/mlp/scran/script.py delete mode 100644 src/label_projection/methods/mlp/scran/test_script.py rename src/label_projection/methods/mlp/{log_cpm => }/script.py (74%) create mode 100644 src/label_projection/methods/mlp/test_script.py delete mode 100644 src/label_projection/resources/data_loader/fake_anndata_loader.tsv diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index a5533fdbc0..a95b85ffaf 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -26,7 +26,6 @@ urllib.request.install_opener(opener) with urllib.request.urlopen(par["url"]) as urlhandle: filehandle.write(urlhandle.read()) - # scprep.io.download.download_url(par['url'], filepath) print("Reading file") adata = sc.read_h5ad(filepath) diff --git a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml index 423e66498c..063d11e94f 100644 --- a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "log_cpm" - namespace: "label_projection/data_processing/normalize/log_cpm" + namespace: "label_projection/data_processing/normalize" version: "dev" description: "Normalize data" authors: diff --git a/src/label_projection/data_processing/normalize/scran/script.R b/src/label_projection/data_processing/normalize/scran/script.R index 9145a9d17f..fc724d90f5 100644 --- a/src/label_projection/data_processing/normalize/scran/script.R +++ b/src/label_projection/data_processing/normalize/scran/script.R @@ -13,11 +13,11 @@ library(BiocParallel, warn.conflicts = FALSE) cat(">> Load data\n") adata <- anndata::read_h5ad(par$input) -cat(">> Normalizing data") +cat(">> Normalizing data\n") sce <- scran::calculateSumFactors(t(adata$X), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) adata$obs[["size_factors"]] <- sce adata$X <- log1p(sce * adata$X) -cat("Writing to file\n") +cat(">> Writing to file\n") adata$uns["normalization_method"] <- "log_scran_pooling" zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/label_projection/data_processing/randomize/script.py b/src/label_projection/data_processing/randomize/script.py index 13d3a108e0..6538ef0c12 100644 --- a/src/label_projection/data_processing/randomize/script.py +++ b/src/label_projection/data_processing/randomize/script.py @@ -33,7 +33,7 @@ adata.obs["is_train"] = np.random.choice( [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] ) - adata = noise.add_label_noise(adata, noise_prob=0.2) + adata = noise.add_celltype_noise(adata, noise_prob=0.2) print(">> Writing data") adata.write(par['output']) diff --git a/src/label_projection/data_processing/utils/noise.py b/src/label_projection/data_processing/utils/noise.py index 9cf639d743..0673985c89 100644 --- a/src/label_projection/data_processing/utils/noise.py +++ b/src/label_projection/data_processing/utils/noise.py @@ -1,41 +1,41 @@ import numpy as np -def add_label_noise(adata, noise_prob): - """Inject random label noise in the dataset . - This is done by permuting a fraction of the labels in the training set. - By adding different levels of label noise metrics can be evaluated to show +def add_celltype_noise(adata, noise_prob): + """Inject random celltype noise in the dataset . + This is done by permuting a fraction of the celltypes in the training set. + By adding different levels of celltype noise metrics can be evaluated to show generalization trends from training data even if ground truth is uncertain. Parameters ------- adata : AnnData - A dataset with the required fields for the label_projection task. + A dataset with the required fields for the celltype_projection task. noise_prob : Float - The probability of label noise in the training data. + The probability of celltype noise in the training data. Returns ------- new_adata : AnnData - Dataset where training labels have been permuted by specified probability. + Dataset where training celltypes have been permuted by specified probability. """ - old_labels = adata.obs["labels"].pipe(np.array) - old_labels_train = old_labels[adata.obs["is_train"]].copy() - new_labels_train = old_labels_train.copy() + old_celltype = adata.obs["celltype"].pipe(np.array) + old_celltype_train = old_celltype[adata.obs["is_train"]].copy() + new_celltype_train = old_celltype_train.copy() - label_names = np.unique(new_labels_train) + celltype_names = np.unique(new_celltype_train) - n_labels = label_names.shape[0] + n_celltype = celltype_names.shape[0] - reassign_probs = (noise_prob / (n_labels - 1)) * np.ones((n_labels, n_labels)) + reassign_probs = (noise_prob / (n_celltype - 1)) * np.ones((n_celltype, n_celltype)) np.fill_diagonal(reassign_probs, 1 - noise_prob) - for k, label in enumerate(label_names): - label_indices = np.where(old_labels_train == label)[0] - new_labels_train[label_indices] = np.random.choice( - label_names, label_indices.shape[0], p=reassign_probs[:, k] + for k, celltype in enumerate(celltype_names): + celltype_indices = np.where(old_celltype_train == celltype)[0] + new_celltype_train[celltype_indices] = np.random.choice( + celltype_names, celltype_indices.shape[0], p=reassign_probs[:, k] ) - adata.obs.loc[adata.obs["is_train"], "labels"] = new_labels_train + adata.obs.loc[adata.obs["is_train"], "celltype"] = new_celltype_train return adata diff --git a/src/label_projection/methods/baseline/majority_vote/script.py b/src/label_projection/methods/baseline/majority_vote/script.py index 2a8869991c..6db158547f 100644 --- a/src/label_projection/methods/baseline/majority_vote/script.py +++ b/src/label_projection/methods/baseline/majority_vote/script.py @@ -11,10 +11,10 @@ print("Load data") adata = sc.read(par['input']) -print("Add label prediction") -majority = adata.obs.labels[adata.obs.is_train].value_counts().index[0] -adata.obs["labels_pred"] = np.nan -adata.obs.loc[~adata.obs.is_train, "labels_pred"] = majority +print("Add celltype prediction") +majority = adata.obs.celltype[adata.obs.is_train].value_counts().index[0] +adata.obs["celltype_pred"] = np.nan +adata.obs.loc[~adata.obs.is_train, "celltype_pred"] = majority print("Write output to file") diff --git a/src/label_projection/methods/baseline/majority_vote/test_script.py b/src/label_projection/methods/baseline/majority_vote/test_script.py index 6c4b3b087f..86a229beed 100644 --- a/src/label_projection/methods/baseline/majority_vote/test_script.py +++ b/src/label_projection/methods/baseline/majority_vote/test_script.py @@ -18,5 +18,5 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs +assert "celltype_pred" in adata.obs assert "majority_vote" == adata.uns["method_id"] diff --git a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml similarity index 83% rename from src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml rename to src/label_projection/methods/knn_classifier/config.vsh.yaml index 587fd963eb..4d62d700fe 100644 --- a/src/label_projection/methods/knn_classifier/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "knn_classifier_log_cpm" + name: "knn_classifier" namespace: "label_projection/methods/knn_classifier" version: "dev" description: "Run Harmonic Alignment" @@ -27,13 +27,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" + - path: "../../utils.py" tests: - type: python_script path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/knn_classifier/log_cpm/test_script.py b/src/label_projection/methods/knn_classifier/log_cpm/test_script.py deleted file mode 100644 index 79fa1362ce..0000000000 --- a/src/label_projection/methods/knn_classifier/log_cpm/test_script.py +++ /dev/null @@ -1,21 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.knnlogcpm.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./knn_classifier_log_cpm", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "knn_classifier_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml b/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml deleted file mode 100644 index fdf18ba887..0000000000 --- a/src/label_projection/methods/knn_classifier/scran/config.vsh.yaml +++ /dev/null @@ -1,51 +0,0 @@ -functionality: - name: "knn_classifier_scran" - namespace: "label_projection/methods/knn_classifier" - version: "dev" - description: "" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data labeled" - required: true - resources: - - type: python_script - path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" - tests: - - type: python_script - path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "singlecellopenproblems/openproblems-r-base:latest" - setup: - - type: r - bioc: - - scran - - BiocParallel - - type: python - packages: - - scanpy - - scprep - - sklearn - - "anndata<0.8" - - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/scran/script.py b/src/label_projection/methods/knn_classifier/scran/script.py deleted file mode 100644 index 40930a9637..0000000000 --- a/src/label_projection/methods/knn_classifier/scran/script.py +++ /dev/null @@ -1,28 +0,0 @@ -## VIASH START -par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.knnscran.h5ad' -} -## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../../" - -import sys -sys.path.append(resources_dir) -sys.path.append(utils_dir) -sys.path.append(meta['resources_dir']) -import scanpy as sc -from normalize import log_scran_pooling -from utils import classifier -import sklearn.neighbors - -print("Load input data") -adata = sc.read(par['input']) - -print("Run classifier") -adata = log_scran_pooling(adata) -adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) -adata.uns["method_id"] = "knn_classifier_scran" - -print("Write data") -adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/knn_classifier/scran/test_script.py b/src/label_projection/methods/knn_classifier/scran/test_script.py deleted file mode 100644 index 6452088740..0000000000 --- a/src/label_projection/methods/knn_classifier/scran/test_script.py +++ /dev/null @@ -1,21 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.knnscran.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./knn_classifier_scran", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "knn_classifier_scran" == adata.uns["method_id"] diff --git a/src/label_projection/methods/knn_classifier/log_cpm/script.py b/src/label_projection/methods/knn_classifier/script.py similarity index 85% rename from src/label_projection/methods/knn_classifier/log_cpm/script.py rename to src/label_projection/methods/knn_classifier/script.py index 5c60a6095e..c9f9b4c34a 100644 --- a/src/label_projection/methods/knn_classifier/log_cpm/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -12,7 +12,6 @@ sys.path.append(utils_dir) sys.path.append(meta['resources_dir']) import scanpy as sc -from normalize import log_cpm from utils import classifier import sklearn.neighbors @@ -20,9 +19,8 @@ adata = sc.read(par['input']) print("Run classifier") -adata = log_cpm(adata) adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) -adata.uns["method_id"] = "knn_classifier_log_cpm" +adata.uns["method_id"] = "knn_classifier" print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/knn_classifier/test_script.py b/src/label_projection/methods/knn_classifier/test_script.py new file mode 100644 index 0000000000..ec0f50db63 --- /dev/null +++ b/src/label_projection/methods/knn_classifier/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] +OUTPUT = ["output.knnlogcpm.h5ad", "output.knnscran.h5ad"] + +for input, output in zip(INPUT, OUTPUT): + print(">> Running script as test") + out = subprocess.check_output([ + "./knn_classifier", + "--input", input, + "--output", output + ]).decode("utf-8") + + print(">> Checking if output file exists") + assert path.exists(output) + + print(">> Checking if predictions were added") + adata = sc.read_h5ad(output) + assert "celltype_pred" in adata.obs + assert "knn_classifier" == adata.uns["method_id"] diff --git a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml similarity index 85% rename from src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml rename to src/label_projection/methods/logistic_regression/config.vsh.yaml index 2101c1fd16..395bcc5099 100644 --- a/src/label_projection/methods/logistic_regression/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "logistic_regression_log_cpm" + name: "logistic_regression" namespace: "label_projection/methods/logistic_regression" version: "dev" description: "Run Harmonic Alignment" @@ -32,13 +32,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" + - path: "../../utils.py" tests: - type: python_script path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/logistic_regression/log_cpm/test_script.py b/src/label_projection/methods/logistic_regression/log_cpm/test_script.py deleted file mode 100644 index 26c5853193..0000000000 --- a/src/label_projection/methods/logistic_regression/log_cpm/test_script.py +++ /dev/null @@ -1,22 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.lrlogcpm.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./logistic_regression_log_cpm", - "--input", INPUT, - "--max_iter", "100", - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "logistic_regression_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml b/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml deleted file mode 100644 index 28fc8fe973..0000000000 --- a/src/label_projection/methods/logistic_regression/scran/config.vsh.yaml +++ /dev/null @@ -1,55 +0,0 @@ -functionality: - name: "logistic_regression_scran" - namespace: "label_projection/methods/logistic_regression" - version: "dev" - description: "" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--max_iter" - type: "integer" - example: "100" - description: "Maximum number of iterations" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data labeled" - required: true - resources: - - type: python_script - path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" - tests: - - type: python_script - path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "singlecellopenproblems/openproblems-r-base:latest" - setup: - - type: r - bioc: - - scran - - BiocParallel - - type: python - packages: - - scanpy - - scprep - - sklearn - - "anndata<0.8" - - type: nextflow diff --git a/src/label_projection/methods/logistic_regression/scran/script.py b/src/label_projection/methods/logistic_regression/scran/script.py deleted file mode 100644 index e926954760..0000000000 --- a/src/label_projection/methods/logistic_regression/scran/script.py +++ /dev/null @@ -1,29 +0,0 @@ -## VIASH START -par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.mlpscran.h5ad' -} -## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../../" - -import sys -sys.path.append(resources_dir) -sys.path.append(utils_dir) -sys.path.append(meta['resources_dir']) -import scanpy as sc -from normalize import log_scran_pooling -from utils import classifier -import sklearn.linear_model - -print("Load input data") -adata = sc.read(par['input']) - -print("Run classifier") -max_iter = par['max_iter'] -adata = log_scran_pooling(adata) -adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) -adata.uns["method_id"] = "logistic_regression_scran" - -print("Write data") -adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/scran/test_script.py b/src/label_projection/methods/logistic_regression/scran/test_script.py deleted file mode 100644 index c64ad9b6cc..0000000000 --- a/src/label_projection/methods/logistic_regression/scran/test_script.py +++ /dev/null @@ -1,22 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.lrscran.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./logistic_regression_scran", - "--input", INPUT, - "--max_iter", "100", - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "logistic_regression_scran" == adata.uns["method_id"] diff --git a/src/label_projection/methods/logistic_regression/log_cpm/script.py b/src/label_projection/methods/logistic_regression/script.py similarity index 73% rename from src/label_projection/methods/logistic_regression/log_cpm/script.py rename to src/label_projection/methods/logistic_regression/script.py index bb6ba9e791..380f0691b8 100644 --- a/src/label_projection/methods/logistic_regression/log_cpm/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -4,15 +4,12 @@ 'output': 'output.knnscran.h5ad' } ## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../../" +utils_dir = "../../" import sys -sys.path.append(resources_dir) sys.path.append(utils_dir) sys.path.append(meta['resources_dir']) import scanpy as sc -from normalize import log_cpm from utils import classifier import sklearn.linear_model @@ -20,10 +17,9 @@ adata = sc.read(par['input']) print("Run classifier") -adata = log_cpm(adata) max_iter = par['max_iter'] adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) -adata.uns["method_id"] = "logistic_regression_log_cpm" +adata.uns["method_id"] = "logistic_regression" print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/test_script.py b/src/label_projection/methods/logistic_regression/test_script.py new file mode 100644 index 0000000000..2683be0ba7 --- /dev/null +++ b/src/label_projection/methods/logistic_regression/test_script.py @@ -0,0 +1,23 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] +OUTPUT = ["output.lrlogcpm.h5ad", "output.lrscran.h5ad"] + +for input, output in zip(INPUT, OUTPUT): + print(">> Running script as test") + out = subprocess.check_output([ + "./logistic_regression", + "--input", input, + "--max_iter", "100", + "--output", output + ]).decode("utf-8") + + print(">> Checking if output file exists") + assert path.exists(output) + + print(">> Checking if predictions were added") + adata = sc.read_h5ad(output) + assert "celltype_pred" in adata.obs + assert "logistic_regression" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml similarity index 86% rename from src/label_projection/methods/mlp/log_cpm/config.vsh.yaml rename to src/label_projection/methods/mlp/config.vsh.yaml index 73056fb61b..f07150e973 100644 --- a/src/label_projection/methods/mlp/log_cpm/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "mlp_log_cpm" + name: "mlp" namespace: "label_projection/methods/mlp" version: "dev" description: "Run Harmonic Alignment" @@ -37,13 +37,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" + - path: "../../utils.py" tests: - type: python_script path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" @@ -51,7 +50,6 @@ platforms: - type: python packages: - scanpy - - scprep - sklearn - "anndata<0.8" - type: native diff --git a/src/label_projection/methods/mlp/log_cpm/test_script.py b/src/label_projection/methods/mlp/log_cpm/test_script.py deleted file mode 100644 index 13722e7af3..0000000000 --- a/src/label_projection/methods/mlp/log_cpm/test_script.py +++ /dev/null @@ -1,23 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.mlplogcpm.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./mlp_log_cpm", - "--input", INPUT, - "--hidden_layer_sizes", "20", - "--max_iter", "100", - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "mlp_log_cpm" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/scran/config.vsh.yaml b/src/label_projection/methods/mlp/scran/config.vsh.yaml deleted file mode 100644 index 678ad75ca4..0000000000 --- a/src/label_projection/methods/mlp/scran/config.vsh.yaml +++ /dev/null @@ -1,55 +0,0 @@ -functionality: - name: "mlp_scran" - namespace: "label_projection/methods/mlp" - version: "dev" - description: "" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--hidden_layer_sizes" - type: "integer" - multiple: true - description: "The ith element represents the number of neurons in the ith hidden layer." - - name: "--max_iter" - type: "integer" - example: "100" - description: "Maximum number of iterations" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data labeled" - required: true - resources: - - type: python_script - path: script.py - - path: "../../../../common/tools/normalize.py" - - path: "../../../utils.py" - tests: - - type: python_script - path: test_script.py - - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: eddelbuettel/r2u:22.04 - setup: - - type: r - cran: [ scran, BiocParallel, rlang ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ scanpy, anndata<0.8, scprep, sklearn, rpy2 ] - - type: nextflow diff --git a/src/label_projection/methods/mlp/scran/script.py b/src/label_projection/methods/mlp/scran/script.py deleted file mode 100644 index 5adde85929..0000000000 --- a/src/label_projection/methods/mlp/scran/script.py +++ /dev/null @@ -1,30 +0,0 @@ -## VIASH START -par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.mlpscran.h5ad' -} -## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../../" - -import sys -sys.path.append(resources_dir) -sys.path.append(utils_dir) -sys.path.append(meta['resources_dir']) -import scanpy as sc -from normalize import log_scran_pooling -from utils import classifier -import sklearn.neural_network - -print("Load input data") -adata = sc.read(par['input']) - -print("Run classifier") -hidden_layer_sizes = tuple(par['hidden_layer_sizes']) -max_iter = par['max_iter'] -adata = log_scran_pooling(adata) -adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) -adata.uns["method_id"] = "mlp_scran" - -print("Write data") -adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/mlp/scran/test_script.py b/src/label_projection/methods/mlp/scran/test_script.py deleted file mode 100644 index 1b66023ece..0000000000 --- a/src/label_projection/methods/mlp/scran/test_script.py +++ /dev/null @@ -1,23 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.mlpscran.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./mlp_scran", - "--input", INPUT, - "--hidden_layer_sizes", "20", - "--max_iter", "100", - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs -assert "mlp_scran" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/log_cpm/script.py b/src/label_projection/methods/mlp/script.py similarity index 74% rename from src/label_projection/methods/mlp/log_cpm/script.py rename to src/label_projection/methods/mlp/script.py index bfc7c4c83c..777763f246 100644 --- a/src/label_projection/methods/mlp/log_cpm/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -1,30 +1,33 @@ ## VIASH START par = { - 'input': '../../../data/test_data_preprocessed.h5ad', + 'input': '../../resources/pancreas/toy_preprocessed_data.h5ad', 'output': 'output.mlplogcpm.h5ad' } ## VIASH END resources_dir = "../../../../common/tools/" -utils_dir = "../../../" +utils_dir = "../../" import sys sys.path.append(resources_dir) sys.path.append(utils_dir) sys.path.append(meta['resources_dir']) import scanpy as sc -from normalize import log_cpm from utils import classifier import sklearn.neural_network + print("Load input data") adata = sc.read(par['input']) +if "normalization_method" not in adata.uns: + print("Warning: trying to predict for a not normalized data") + + print("Run classifier") hidden_layer_sizes = tuple(par['hidden_layer_sizes']) max_iter = par['max_iter'] -adata = log_cpm(adata) adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) -adata.uns["method_id"] = "mlp_log_cpm" +adata.uns["method_id"] = "mlp" print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/mlp/test_script.py b/src/label_projection/methods/mlp/test_script.py new file mode 100644 index 0000000000..ea94e9e7c4 --- /dev/null +++ b/src/label_projection/methods/mlp/test_script.py @@ -0,0 +1,24 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] +OUTPUT = ["output.mlplogcpm.h5ad", "output.mlpscran.h5ad"] + +for input, output in zip(INPUT, OUTPUT): + print(">> Running script as test") + out = subprocess.check_output([ + "./mlp", + "--input", input, + "--hidden_layer_sizes", "20", + "--max_iter", "100", + "--output", output + ]).decode("utf-8") + + print(">> Checking if output file exists") + assert path.exists(output) + + print(">> Checking if predictions were added") + adata = sc.read_h5ad(output) + assert "celltype_pred" in adata.obs + assert "mlp" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 6bbdf241c2..500d19090b 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -53,7 +53,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index fa2bd5df37..44b76194e2 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 4fa524324d..3ff2b5b6bd 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -53,7 +53,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index 51cc457072..e1b224b8f1 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/toy_preprocessed_data.h5ad" + path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/tools.py b/src/label_projection/methods/scvi/tools.py index bb59369060..79674c5201 100644 --- a/src/label_projection/methods/scvi/tools.py +++ b/src/label_projection/methods/scvi/tools.py @@ -18,7 +18,7 @@ def hvg (adata, **hvg_kwargs): ) def scanvi(adata, n_hidden=None, n_latent=None, n_layers=None, **train_kwargs): - scanvi_labels = adata.obs["labels"].to_numpy() + scanvi_labels = adata.obs["celltype"].to_numpy() # test set labels masked scanvi_labels[~adata.obs["is_train"].to_numpy()] = "Unknown" adata.obs["scanvi_labels"] = scanvi_labels @@ -38,7 +38,7 @@ def scanvi_scarches(adata, n_hidden=None, n_latent=None, n_layers=None, train_kw query_model_train_kwargs = train_kwargs['query_model_train_kwargs'] # new obs labels to mask test set adata_train = adata[adata.obs["is_train"]].copy() - adata_train.obs["scanvi_labels"] = adata_train.obs["labels"].copy() + adata_train.obs["scanvi_labels"] = adata_train.obs["celltype"].copy() adata_test = adata[~adata.obs["is_train"]].copy() adata_test.obs["scanvi_labels"] = "Unknown" scvi.model.SCVI.setup_anndata( diff --git a/src/label_projection/resources/data_loader/fake_anndata_loader.tsv b/src/label_projection/resources/data_loader/fake_anndata_loader.tsv deleted file mode 100644 index 2b84d064f9..0000000000 --- a/src/label_projection/resources/data_loader/fake_anndata_loader.tsv +++ /dev/null @@ -1,2 +0,0 @@ -processor name url -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 diff --git a/src/label_projection/utils.py b/src/label_projection/utils.py index 7370afefe1..30c6851742 100644 --- a/src/label_projection/utils.py +++ b/src/label_projection/utils.py @@ -36,13 +36,13 @@ def classifier(adata, estimator, n_pca=100, **kwargs): ) # Fit to train data - classifier.fit(adata_train.X, adata_train.obs["labels"].astype(str)) + classifier.fit(adata_train.X, adata_train.obs["celltype"].astype(str)) # Predict on test data - adata_test.obs["labels_pred"] = classifier.predict(adata_test.X) + adata_test.obs["celltype_pred"] = classifier.predict(adata_test.X) - adata.obs["labels_pred"] = [ - adata_test.obs["labels_pred"][idx] if idx in adata_test.obs_names else np.nan + adata.obs["celltype_pred"] = [ + adata_test.obs["celltype_pred"][idx] if idx in adata_test.obs_names else np.nan for idx in adata.obs_names ] return adata diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/label_projection/workflows/generate_test_resources/pancreas.sh index 4bc2d0aeee..cb6d9296eb 100755 --- a/src/label_projection/workflows/generate_test_resources/pancreas.sh +++ b/src/label_projection/workflows/generate_test_resources/pancreas.sh @@ -30,10 +30,10 @@ target/docker/label_projection/data_processing/randomize/randomize\ --input $DATASET_DIR/toy_data.h5ad\ --output $DATASET_DIR/toy_preprocessed_data.h5ad -target/docker/label_projection/data_processing/normalize/log_cpm\ +target/docker/label_projection/data_processing/normalize/log_cpm/log_cpm\ --input $DATASET_DIR/toy_preprocessed_data.h5ad\ --output $DATASET_DIR/toy_normalized_log_cpm_data.h5ad -target/docker/label_projection/data_processing/normalize/log_scran_pooling\ +target/docker/label_projection/data_processing/normalize/scran/log_scran_pooling/log_scran_pooling\ --input $DATASET_DIR/toy_preprocessed_data.h5ad\ --output $DATASET_DIR/toy_normalized_log_scran_pooling_data.h5ad From 93b1c19ddb62b651af0812c751b262beee00dee2 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 27 Jun 2022 07:43:19 -0300 Subject: [PATCH 0217/1233] self-review Former-commit-id: 9cf8d6e8435b9c294b378e1b4920a4cb57d3eb8c --- src/common/tools/normalize.py | 42 ----------------------------------- 1 file changed, 42 deletions(-) delete mode 100644 src/common/tools/normalize.py diff --git a/src/common/tools/normalize.py b/src/common/tools/normalize.py deleted file mode 100644 index 873f454634..0000000000 --- a/src/common/tools/normalize.py +++ /dev/null @@ -1,42 +0,0 @@ -import anndata as ad -import scanpy as sc -import scprep - - -_scran = scprep.run.RFunction( - setup=""" - library('scran') - library('BiocParallel') - """, - args="sce, min.mean=0.1", - body=""" - sce <- computeSumFactors( - sce, min.mean=min.mean, - assay.type="X", - BPPARAM=BiocParallel::MulticoreParam() - ) - sizeFactors(sce) - """ -) - - -def log_scran_pooling(adata: ad.AnnData) -> ad.AnnData: - """Normalize data with scran via rpy2.""" - adata.obs["size_factors"] = _scran(adata) - adata.X = scprep.utils.matrix_vector_elementwise_multiply( - adata.X, adata.obs["size_factors"], axis=0 - ) - sc.pp.log1p(adata) - return adata - - -def _cpm(adata: ad.AnnData): - adata.layers["counts"] = adata.X.copy() - sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") - - -def log_cpm(adata: ad.AnnData) -> ad.AnnData: - """Normalize data to log counts per million.""" - _cpm(adata) - sc.pp.log1p(adata) - return adata From 199778b040469117d23e714db885c51f640cd093 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 27 Jun 2022 08:52:00 -0300 Subject: [PATCH 0218/1233] chore: nextflow workflow Former-commit-id: bae117aadba722cb1cf63a100956d4db940addce --- .../data_processing/fake_anndata_loader.tsv | 4 +- .../methods/knn_classifier/config.vsh.yaml | 2 +- .../logistic_regression/config.vsh.yaml | 2 +- .../methods/mlp/config.vsh.yaml | 2 +- src/label_projection/workflows/run/main.nf | 41 +++++++++++++------ 5 files changed, 33 insertions(+), 18 deletions(-) diff --git a/src/label_projection/data_processing/fake_anndata_loader.tsv b/src/label_projection/data_processing/fake_anndata_loader.tsv index 2b84d064f9..51c45f1a1c 100644 --- a/src/label_projection/data_processing/fake_anndata_loader.tsv +++ b/src/label_projection/data_processing/fake_anndata_loader.tsv @@ -1,2 +1,2 @@ -processor name url -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 +processor name url obs_celltype obs_batch obs_tissue +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 4d62d700fe..3729e34297 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "knn_classifier" - namespace: "label_projection/methods/knn_classifier" + namespace: "label_projection/methods" version: "dev" description: "Run Harmonic Alignment" authors: diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 395bcc5099..2e5aaed388 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "logistic_regression" - namespace: "label_projection/methods/logistic_regression" + namespace: "label_projection/methods" version: "dev" description: "Run Harmonic Alignment" authors: diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index f07150e973..17bb6ca8b4 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "mlp" - namespace: "label_projection/methods/mlp" + namespace: "label_projection/methods" version: "dev" description: "Run Harmonic Alignment" authors: diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 6aaf60ae5e..d89b48fcdd 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -7,18 +7,25 @@ include { download } from "$targetDir/common/dataset_loader/download/main.nf" // import preprocess include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" +// for test finallity +include { subsample } from "$targetDir/label_projection/data_processing/subsample/main.nf" -// import methods TODO[baseline/random_labels, -// knn_classifier/scran, mlp/log_cpm, mlp/scran, sklearn/classifier, -// scvi, logistic_regression/log_cpm, logistic_regression/scran] -include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" params(params) -include { knn_classifier_log_cpm } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_log_cpm/main.nf" params(params) -include { knn_classifier_scran } from "$targetDir/label_projection/methods/knn_classifier/knn_classifier_scran/main.nf" params(params)//LOCALY OUT OF MEMORY -include { mlp_log_cpm } from "$targetDir/label_projection/methods/mlp/mlp_log_cpm/main.nf" params(params) //LOCALY OUT OF MEMORY -include { mlp_scran } from "$targetDir/label_projection/methods/mlp/mlp_scran/main.nf" params(params) //LOCALY OUT OF MEMORY +// import normalization +include { log_scran_pooling } from "$targetDir/label_projection/data_processing/normalize/scran/log_scran_pooling/main.nf" +include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" + +// import methods TODO[baseline/random_labels] +include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" +include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" +include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" +include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" +include { scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scanvi_hvg/main.nf" +include { scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scanvi_all_genes/main.nf" +include { scarches_scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_all_genes/main.nf" +include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_hvg/main.nf" // import metrics TODO [f1] -include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" params(params) +include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" /******************************************************* @@ -32,7 +39,7 @@ include { accuracy } from "$targetDir/label_projection/metrics/accuracy // If the need arises, these workflows could be split off into a separate file. // params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" -params.tsv = "$launchDir/src/label_projection/resources/data_loader/fake_anndata_loader.tsv" +params.tsv = "$launchDir/src/label_projection/data_processing/fake_anndata_loader.tsv" //tests finallity workflow load_data { main: @@ -52,8 +59,16 @@ workflow load_data { workflow { load_data | randomize - | (majority_vote & knn_classifier_log_cpm & mlp_log_cpm) - | mix - | accuracy + | subsample.run( + map: { [it[0], [input: it[1], + celltype_categories: "0:3", + tech_categories: "0:-3:-2"]] } + ) + | (log_cpm & log_scran_pooling) + | majority_vote | view + // | (majority_vote & knn_classifier & mlp & logistic_regression & scanvi_hvg & scanvi_all_genes & scarches_scanvi_all_genes & scarches_scanvi_hvg) + // | mix + // | accuracy + // | view } From c9dfa806d8ea964b4ce8626fae002e25043e0948 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 28 Jun 2022 07:56:56 -0300 Subject: [PATCH 0219/1233] fix: accuracy component Former-commit-id: c9874df16c1b9f20f3163cb5d8b06bc2cd2499ec --- .../metrics/accuracy/config.vsh.yaml | 3 +-- .../metrics/accuracy/script.py | 8 +++--- .../metrics/accuracy/test_script.py | 11 +++++--- .../generate_test_resources/pancreas.sh | 4 +++ src/label_projection/workflows/run/main.nf | 25 +++++++++++++------ 5 files changed, 33 insertions(+), 18 deletions(-) diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index fd0dc4407f..9bf0bd7917 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -28,8 +28,7 @@ functionality: tests: - type: python_script path: test_script.py - - type: file - path: test_data.h5ad + - path: "../../resources/pancreas/toy_baseline_pred_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index d9e0523e44..58d9e572a3 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -13,13 +13,13 @@ adata = sc.read(par['input']) print("Get prediction accuracy") -encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["labels"]) +encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["celltype"]) test_data = adata[~adata.obs["is_train"]] -test_data.obs["labels"] = encoder.transform(test_data.obs["labels"]) -test_data.obs["labels_pred"] = encoder.transform(test_data.obs["labels_pred"]) +test_data.obs["celltype"] = encoder.transform(test_data.obs["celltype"]) +test_data.obs["celltype_pred"] = encoder.transform(test_data.obs["celltype_pred"]) -accuracy = np.mean(test_data.obs["labels"] == test_data.obs["labels_pred"]) +accuracy = np.mean(test_data.obs["celltype"] == test_data.obs["celltype_pred"]) print("Store metric value") adata.uns["metric_id"] = "accuracy" diff --git a/src/label_projection/metrics/accuracy/test_script.py b/src/label_projection/metrics/accuracy/test_script.py index 883711e04e..feb326a997 100644 --- a/src/label_projection/metrics/accuracy/test_script.py +++ b/src/label_projection/metrics/accuracy/test_script.py @@ -5,18 +5,21 @@ import scanpy as sc import numpy as np +INPUT = "toy_baseline_pred_data.h5ad" +OUTPUT = "output.accuracy.h5ad" + print(">> Running knn_auc") out = subprocess.check_output([ "./accuracy", - "--input", "test_data.h5ad", - "--output", "output.accuracy.h5ad" + "--input", INPUT, + "--output", OUTPUT ]).decode("utf-8") print(">> Checking whether file exists") -assert path.exists("output.accuracy.h5ad") +assert path.exists(OUTPUT) print(">> Check that dataset fits expected API") -adata = sc.read_h5ad("output.accuracy.h5ad") +adata = sc.read_h5ad(OUTPUT) # check id assert "metric_id" in adata.uns diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/label_projection/workflows/generate_test_resources/pancreas.sh index cb6d9296eb..b9afd9b6f4 100755 --- a/src/label_projection/workflows/generate_test_resources/pancreas.sh +++ b/src/label_projection/workflows/generate_test_resources/pancreas.sh @@ -37,3 +37,7 @@ target/docker/label_projection/data_processing/normalize/log_cpm/log_cpm\ target/docker/label_projection/data_processing/normalize/scran/log_scran_pooling/log_scran_pooling\ --input $DATASET_DIR/toy_preprocessed_data.h5ad\ --output $DATASET_DIR/toy_normalized_log_scran_pooling_data.h5ad + +target/docker/label_projection/methods/baseline/majority_vote/majority_vote\ + --input $DATASET_DIR/toy_normalized_log_cpm_data.h5ad\ + --output $DATASET_DIR/toy_baseline_pred_data.h5ad diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d89b48fcdd..63cab03239 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -7,7 +7,7 @@ include { download } from "$targetDir/common/dataset_loader/download/main.nf" // import preprocess include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" -// for test finallity +// for tests include { subsample } from "$targetDir/label_projection/data_processing/subsample/main.nf" // import normalization @@ -39,7 +39,7 @@ include { accuracy } from "$targetDir/label_projection/metrics/accuracy // If the need arises, these workflows could be split off into a separate file. // params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" -params.tsv = "$launchDir/src/label_projection/data_processing/fake_anndata_loader.tsv" //tests finallity +params.tsv = "$launchDir/src/label_projection/data_processing/fake_anndata_loader.tsv" //for tests workflow load_data { main: @@ -52,6 +52,14 @@ workflow load_data { output_ } +def mlp0 = mlp.run( + map: { [it[0], [input: it[1], max_iter: 100, hidden_layer_sizes: 20]] } +) + +def lr0 = logistic_regression.run( + map: { [it[0], [input: it[1], max_iter: 100]] } +) + /******************************************************* * Main workflow * *******************************************************/ @@ -64,11 +72,12 @@ workflow { celltype_categories: "0:3", tech_categories: "0:-3:-2"]] } ) - | (log_cpm & log_scran_pooling) - | majority_vote | view - // | (majority_vote & knn_classifier & mlp & logistic_regression & scanvi_hvg & scanvi_all_genes & scarches_scanvi_all_genes & scarches_scanvi_hvg) - // | mix - // | accuracy - // | view + | log_cpm + | view + | (majority_vote & knn_classifier & mlp0 & lr0) + | mix + | view + | accuracy + | view } From 4b83b9f69fe6a935113b3e76be4e30249b7a7369 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 28 Jun 2022 09:51:28 -0300 Subject: [PATCH 0220/1233] fix: scvi methods Former-commit-id: 4f7bfb707dc3f953eea9e201b8bcebe0a0db36f5 --- src/label_projection/methods/scvi/scanvi_all_genes/script.py | 2 +- .../methods/scvi/scanvi_all_genes/test_script.py | 2 +- src/label_projection/methods/scvi/scanvi_hvg/script.py | 2 +- src/label_projection/methods/scvi/scanvi_hvg/test_script.py | 2 +- .../methods/scvi/scarches_scanvi_all_genes/script.py | 2 +- .../methods/scvi/scarches_scanvi_all_genes/test_script.py | 2 +- src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py | 2 +- .../methods/scvi/scarches_scanvi_hvg/test_script.py | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py index ab84c0c4fb..b0fed618bc 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scanvi_all_genes/script.py @@ -32,7 +32,7 @@ par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) -adata.obs["labels_pred"] = scanvi(adata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) +adata.obs["celltype_pred"] = scanvi(adata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) adata.uns["method_id"] = "scanvi_all_genes" print("Write data") diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py index d3677dfa14..27187a2549 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py +++ b/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py @@ -23,5 +23,5 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs +assert "celltype_pred" in adata.obs assert "scanvi_all_genes" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scanvi_hvg/script.py b/src/label_projection/methods/scvi/scanvi_hvg/script.py index 28c5ef2770..ef8b1be384 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scanvi_hvg/script.py @@ -44,7 +44,7 @@ hvg_df = hvg(adata, **hvg_kwargs) bdata = adata[:, hvg_df.highly_variable].copy() -adata.obs["labels_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) +adata.obs["celltype_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) adata.uns["method_id"] = "scanvi_hvg" print("Write data") diff --git a/src/label_projection/methods/scvi/scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scanvi_hvg/test_script.py index 26bdfe08b2..2025a5d6da 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/test_script.py +++ b/src/label_projection/methods/scvi/scanvi_hvg/test_script.py @@ -25,5 +25,5 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs +assert "celltype_pred" in adata.obs assert "scanvi_hvg" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py index 7ecdac0ad3..266247bdd2 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py @@ -34,7 +34,7 @@ par.get("limit_train_batches") and model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) and query_model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) par.get("limit_val_batches") and model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) and query_model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) -adata.obs["labels_pred"] = scanvi_scarches(adata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, +adata.obs["celltype_pred"] = scanvi_scarches(adata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, 'query_model_train_kwargs': query_model_train_kwargs}) adata.uns["method_id"] = "scarches_scanvi_all_genes" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py index 7316a719b8..69bec5f02f 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py @@ -23,5 +23,5 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs +assert "celltype_pred" in adata.obs assert "scarches_scanvi_all_genes" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py index 2c5c0b0b77..12a72a4854 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py @@ -49,7 +49,7 @@ hvg_df = hvg(adata, **hvg_kwargs) bdata = adata[:, hvg_df.highly_variable].copy() -adata.obs["labels_pred"] = scanvi_scarches(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, +adata.obs["celltype_pred"] = scanvi_scarches(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, 'query_model_train_kwargs': query_model_train_kwargs}) adata.uns["method_id"] = "scarches_scanvi_hvg" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py index fae6c3e6d0..eb6e79bc07 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py @@ -25,5 +25,5 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) -assert "labels_pred" in adata.obs +assert "celltype_pred" in adata.obs assert "scarches_scanvi_hvg" == adata.uns["method_id"] From 33208d85b7a5ca65867275db6a725819eedeb2d7 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Sun, 3 Jul 2022 17:43:29 -0300 Subject: [PATCH 0221/1233] feat: extract_scores Former-commit-id: 0a44db0e099ae3826eadfd389fa91c56e27a1b8e --- src/common/extract_scores/script.R | 10 ++++- src/label_projection/workflows/run/main.nf | 47 +++++++++++++++++++--- 2 files changed, 49 insertions(+), 8 deletions(-) diff --git a/src/common/extract_scores/script.R b/src/common/extract_scores/script.R index dbfcdc7f99..337c34167f 100644 --- a/src/common/extract_scores/script.R +++ b/src/common/extract_scores/script.R @@ -17,14 +17,20 @@ scores <- map_df(par$input, function(inp) { cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) - for (uns_name in c("dataset_id", "method_id", "metric_id", "metric_value")) { + if ("normalization_method" %in% names(ad$uns)) { + uns_names <- c("dataset_id", "normalization_method", "method_id", "metric_id", "metric_value") + } else { + uns_names <- c("dataset_id", "method_id", "metric_id", "metric_value") + } + + for (uns_name in uns_names) { assert_that( uns_name %in% names(ad$uns), msg = paste0("File ", inp, " must contain `uns['", uns_name, "']`") ) } - as_tibble(ad$uns[c("dataset_id", "method_id", "metric_id", "metric_value")]) + as_tibble(ad$uns[uns_names]) }) write_tsv(scores, par$output) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 63cab03239..5ebc3f7fc1 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -27,6 +27,9 @@ include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/s // import metrics TODO [f1] include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" +// import helper functions +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" + /******************************************************* * Dataset processor workflows * @@ -53,13 +56,38 @@ workflow load_data { } def mlp0 = mlp.run( - map: { [it[0], [input: it[1], max_iter: 100, hidden_layer_sizes: 20]] } + args: [max_iter: 100, hidden_layer_sizes: 20] ) def lr0 = logistic_regression.run( - map: { [it[0], [input: it[1], max_iter: 100]] } + args: [max_iter: 100] +) + +def scvi_hvg0 = scanvi_hvg.run( + args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, + span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] +) + +def scvi_allgns0 = scanvi_all_genes.run( + args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, + span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] +) + +def scarches_hvg0 = scarches_scanvi_hvg.run( + args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, + span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] +) + +def scarches_allgns0 = scarches_scanvi_all_genes.run( + args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, + span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] ) +def unique_file_name(params){ + output = "${params[1].parent[-1]}_${params[1].baseName}" + return [params[0], [input: params[1], output: output]] +} + /******************************************************* * Main workflow * *******************************************************/ @@ -72,12 +100,19 @@ workflow { celltype_categories: "0:3", tech_categories: "0:-3:-2"]] } ) - | view - | log_cpm - | view + | map { [it[0], [input: it[1]]] } + | (log_cpm & log_scran_pooling) + | mix + | map { [it[0], [input: it[1]]] } | (majority_vote & knn_classifier & mlp0 & lr0) | mix - | view + // | map { [it[0], [input: it[1]]] } + | map { unique_file_name(it) } | accuracy + | toSortedList + | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } | view + | extract_scores.run( + auto: [ publish: true ] + ) } From 6c8b5fa4dc43e88ddb57f6c5f1a7dfe251c1a337 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 4 Jul 2022 13:30:51 +0200 Subject: [PATCH 0222/1233] rework unique_file_name Former-commit-id: 7c24d61b7c0bf08ee8619bedcf48aeb9c8fc207b --- src/label_projection/workflows/run/main.nf | 45 ++++++++++------------ 1 file changed, 21 insertions(+), 24 deletions(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 5ebc3f7fc1..de5a723cce 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -83,9 +83,8 @@ def scarches_allgns0 = scarches_scanvi_all_genes.run( span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] ) -def unique_file_name(params){ - output = "${params[1].parent[-1]}_${params[1].baseName}" - return [params[0], [input: params[1], output: output]] +def unique_file_name(tuple) { + return [tuple[1].baseName.replaceAll('\\.output$', ''), tuple[1]] } /******************************************************* @@ -94,25 +93,23 @@ def unique_file_name(params){ workflow { load_data - | randomize - | subsample.run( - map: { [it[0], [input: it[1], - celltype_categories: "0:3", - tech_categories: "0:-3:-2"]] } - ) - | map { [it[0], [input: it[1]]] } - | (log_cpm & log_scran_pooling) - | mix - | map { [it[0], [input: it[1]]] } - | (majority_vote & knn_classifier & mlp0 & lr0) - | mix - // | map { [it[0], [input: it[1]]] } - | map { unique_file_name(it) } - | accuracy - | toSortedList - | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - | view - | extract_scores.run( - auto: [ publish: true ] - ) + | randomize + | subsample.run( + map: { [it[0], [input: it[1], + celltype_categories: "0:3", + tech_categories: "0:-3:-2"]] } + ) + | (log_cpm & log_scran_pooling) + | mix + | map { unique_file_name(it) } + | (majority_vote & knn_classifier & mlp0 & lr0) + | mix + | map { unique_file_name(it) } + | accuracy + | toSortedList + | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + | view + | extract_scores.run( + auto: [ publish: true ] + ) } From 828a33ffc9fa91f0ba10e7f5eb689a28066b11ff Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 4 Jul 2022 13:31:10 +0200 Subject: [PATCH 0223/1233] switch to develop for now Former-commit-id: 0db8fad944300788a05a22ecf6365f8fbf146e37 --- bin/init | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/init b/bin/init index 5a2142094d..5bb5901603 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.5.13 \ + --tag develop \ --nextflow_variant vdsl3 cd bin From e3f0b99162ebda97a487f7b3207178ab89b99bf2 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 4 Jul 2022 20:47:00 -0300 Subject: [PATCH 0224/1233] fix: subsample dataset_id Former-commit-id: 537684a18ab52465dfa5bac304b1d5a2ec5014ed --- src/label_projection/data_processing/subsample/script.py | 1 + src/label_projection/workflows/run/main.nf | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/data_processing/subsample/script.py b/src/label_projection/data_processing/subsample/script.py index c8c897fdb0..da046a4d5c 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/label_projection/data_processing/subsample/script.py @@ -39,6 +39,7 @@ def filter_genes_cells(adata): # Note: could also use 200-500 HVGs rather than 200 random genes # Ensure there are no cells or genes with 0 counts filter_genes_cells(adata) +adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" print(">> Writing data") adata.write(par['output']) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index de5a723cce..1cb09cc3fc 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -108,7 +108,6 @@ workflow { | accuracy | toSortedList | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - | view | extract_scores.run( auto: [ publish: true ] ) From 3951ea31179666321ae5cdd352c3c3464c4496b2 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 4 Jul 2022 22:46:53 -0300 Subject: [PATCH 0225/1233] feat: add last components Former-commit-id: 94ae5393c95f3366c6ec394c40ca2d8a1ee5069a --- src/common/dataset_loader/download/test.py | 6 +-- .../baseline_majority_vote}/config.vsh.yaml | 6 +-- .../baseline_majority_vote}/script.py | 0 .../baseline_majority_vote}/test_script.py | 0 .../baseline_random_celltype/config.vsh.yaml | 42 +++++++++++++++++ .../baseline_random_celltype/script.py | 28 +++++++++++ .../baseline_random_celltype/test_script.py | 22 +++++++++ .../metrics/accuracy/test_script.py | 2 +- .../metrics/f1/config.vsh.yaml | 46 +++++++++++++++++++ src/label_projection/metrics/f1/script.py | 32 +++++++++++++ .../metrics/f1/test_script.py | 32 +++++++++++++ src/label_projection/workflows/run/main.nf | 17 +++++-- 12 files changed, 221 insertions(+), 12 deletions(-) rename src/label_projection/{methods/baseline/majority_vote => control_methods/baseline_majority_vote}/config.vsh.yaml (86%) rename src/label_projection/{methods/baseline/majority_vote => control_methods/baseline_majority_vote}/script.py (100%) rename src/label_projection/{methods/baseline/majority_vote => control_methods/baseline_majority_vote}/test_script.py (100%) create mode 100644 src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml create mode 100644 src/label_projection/control_methods/baseline_random_celltype/script.py create mode 100644 src/label_projection/control_methods/baseline_random_celltype/test_script.py create mode 100644 src/label_projection/metrics/f1/config.vsh.yaml create mode 100644 src/label_projection/metrics/f1/script.py create mode 100644 src/label_projection/metrics/f1/test_script.py diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py index 328c6c19be..427acbac5c 100644 --- a/src/common/dataset_loader/download/test.py +++ b/src/common/dataset_loader/download/test.py @@ -4,7 +4,7 @@ name = "pancreas" anndata_file = "dataset.h5ad" -url = "https://ndownloader.figshare.com/files/24974582" +url = "https://ndownloader.figshare.com/files/24539828" obs_celltype = "celltype" obs_batch = "tech" @@ -28,8 +28,8 @@ assert "counts" not in adata.layers assert adata.uns["dataset_id"] == name if obs_celltype: - assert "celltype" in adata.obs + assert "celltype" in adata.obs.columns if obs_batch: - assert "batch" in adata.obs + assert "batch" in adata.obs.columns print(">> All tests passed successfully") diff --git a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml similarity index 86% rename from src/label_projection/methods/baseline/majority_vote/config.vsh.yaml rename to src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml index 6530cc99f5..c0c16984ff 100644 --- a/src/label_projection/methods/baseline/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: - name: "majority_vote" - namespace: "label_projection/methods/baseline" + name: "baseline_majority_vote" + namespace: "label_projection/control_methods" version: "dev" description: "Majority vote dummy" authors: @@ -29,7 +29,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/methods/baseline/majority_vote/script.py b/src/label_projection/control_methods/baseline_majority_vote/script.py similarity index 100% rename from src/label_projection/methods/baseline/majority_vote/script.py rename to src/label_projection/control_methods/baseline_majority_vote/script.py diff --git a/src/label_projection/methods/baseline/majority_vote/test_script.py b/src/label_projection/control_methods/baseline_majority_vote/test_script.py similarity index 100% rename from src/label_projection/methods/baseline/majority_vote/test_script.py rename to src/label_projection/control_methods/baseline_majority_vote/test_script.py diff --git a/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml b/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml new file mode 100644 index 0000000000..32c5b8eb07 --- /dev/null +++ b/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml @@ -0,0 +1,42 @@ +functionality: + name: "baseline_random_celltype" + namespace: "label_projection/control_methods" + version: "dev" + description: "Majority vote dummy" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to add prediction" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + description: "Ouput data labeled" + direction: "output" + example: "output.mv.h5ad" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../resources/pancreas/toy_preprocessed_data.h5ad" +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/control_methods/baseline_random_celltype/script.py b/src/label_projection/control_methods/baseline_random_celltype/script.py new file mode 100644 index 0000000000..81cb35b5ce --- /dev/null +++ b/src/label_projection/control_methods/baseline_random_celltype/script.py @@ -0,0 +1,28 @@ +## VIASH START +par = { + 'input': 'ouput.h5ad', + 'output': 'output.mv.h5ad' +} +## VIASH END +import numpy as np +import scanpy as sc + + +print("Load data") +adata = sc.read(par['input']) + +print("Add celltype prediction") +celltype_distribution = adata.obs.celltype[adata.obs.is_train].value_counts() +celltype_distribution = celltype_distribution / celltype_distribution.sum() +adata.obs["celltype_pred"] = np.nan +adata.obs.loc[~adata.obs.is_train, "celltype_pred"] = np.random.choice( + celltype_distribution.index, + size=(~adata.obs.is_train).sum(), + replace=True, + p=celltype_distribution +) + + +print("Write output to file") +adata.uns["method_id"] = "random_celltype" +adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/baseline_random_celltype/test_script.py b/src/label_projection/control_methods/baseline_random_celltype/test_script.py new file mode 100644 index 0000000000..7e5026e2de --- /dev/null +++ b/src/label_projection/control_methods/baseline_random_celltype/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.mv.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./random_celltype", + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "celltype_pred" in adata.obs +assert "random_celltype" == adata.uns["method_id"] diff --git a/src/label_projection/metrics/accuracy/test_script.py b/src/label_projection/metrics/accuracy/test_script.py index feb326a997..f437cc715f 100644 --- a/src/label_projection/metrics/accuracy/test_script.py +++ b/src/label_projection/metrics/accuracy/test_script.py @@ -8,7 +8,7 @@ INPUT = "toy_baseline_pred_data.h5ad" OUTPUT = "output.accuracy.h5ad" -print(">> Running knn_auc") +print(">> Running accuracy component") out = subprocess.check_output([ "./accuracy", "--input", INPUT, diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml new file mode 100644 index 0000000000..7a2ffc6d91 --- /dev/null +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -0,0 +1,46 @@ +functionality: + name: "f1" + namespace: "label_projection/metrics" + version: "dev" + description: "Accuracy of predictions" + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to get accuracy" + required: true + - name: "--average" + type: "string" + example: "weighted" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + description: "Ouput data with metric value" + direction: "output" + example: "output.mv.h5ad" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - path: "../../resources/pancreas/toy_baseline_pred_data.h5ad" +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - sklearn + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py new file mode 100644 index 0000000000..71f8893bc0 --- /dev/null +++ b/src/label_projection/metrics/f1/script.py @@ -0,0 +1,32 @@ +## VIASH START +par = { + 'input': 'ouput.h5ad', + 'average': 'weighted', + 'output': 'output.mv.h5ad' +} +## VIASH END +import sklearn.metrics +import sklearn.preprocessing +import scanpy as sc + + +print("Load data") +adata = sc.read(par['input']) + +print("Get prediction accuracy") +encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["celltype"]) +test_data = adata[~adata.obs["is_train"]] + +test_data.obs["celltype"] = encoder.transform(test_data.obs["celltype"]) +test_data.obs["celltype_pred"] = encoder.transform(test_data.obs["celltype_pred"]) + +metrics = sklearn.metrics.f1_score( + test_data.obs["celltype"], test_data.obs["celltype_pred"], average=par["average"] +) + +print("Store metric value") +adata.uns["metric_id"] = "f1" +adata.uns["metric_value"] = metrics + +print("Writing adata to file") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/f1/test_script.py b/src/label_projection/metrics/f1/test_script.py new file mode 100644 index 0000000000..1b291939b3 --- /dev/null +++ b/src/label_projection/metrics/f1/test_script.py @@ -0,0 +1,32 @@ +import os +from os import path +import subprocess + +import scanpy as sc +import numpy as np + +INPUT = "toy_baseline_pred_data.h5ad" +OUTPUT = "output.accuracy.h5ad" +AVG = "weighted" + +print(">> Running f1 component") +out = subprocess.check_output([ + "./f1", + "--input", INPUT, + "--average", AVG, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that dataset fits expected API") +adata = sc.read_h5ad(OUTPUT) + +# check id +assert "metric_id" in adata.uns +assert adata.uns["metric_id"] == "f1" +assert "metric_value" in adata.uns +assert type(adata.uns["metric_value"]) is np.float64 + +print(">> All tests passed successfully") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 1cb09cc3fc..38ad0168e5 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -14,8 +14,9 @@ include { subsample } from "$targetDir/label_projection/data_processing/subsampl include { log_scran_pooling } from "$targetDir/label_projection/data_processing/normalize/scran/log_scran_pooling/main.nf" include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" -// import methods TODO[baseline/random_labels] -include { majority_vote } from "$targetDir/label_projection/methods/baseline/majority_vote/main.nf" +// import methods +include { baseline_majority_vote } from "$targetDir/label_projection/control_methods/baseline_majority_vote/main.nf" +include { baseline_random_celltype } from "$targetDir/label_projection/control_methods/baseline_random_celltype/main.nf" include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" @@ -24,8 +25,9 @@ include { scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scan include { scarches_scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_all_genes/main.nf" include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_hvg/main.nf" -// import metrics TODO [f1] +// import metrics include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" +include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" // import helper functions include { extract_scores } from "$targetDir/common/extract_scores/main.nf" @@ -83,6 +85,10 @@ def scarches_allgns0 = scarches_scanvi_all_genes.run( span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] ) +def f1a = f1.run( + args: [average: "weighted"] +) + def unique_file_name(tuple) { return [tuple[1].baseName.replaceAll('\\.output$', ''), tuple[1]] } @@ -102,10 +108,11 @@ workflow { | (log_cpm & log_scran_pooling) | mix | map { unique_file_name(it) } - | (majority_vote & knn_classifier & mlp0 & lr0) + | (knn_classifier & mlp0 & lr0 & baseline_random_celltype & baseline_majority_vote) | mix | map { unique_file_name(it) } - | accuracy + | (accuracy & f1a) + | mix | toSortedList | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } | extract_scores.run( From 461340e4869cbf6dd15dd9dd107b99ff22d5441f Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 5 Jul 2022 09:50:55 -0300 Subject: [PATCH 0226/1233] feat: add new datasets and concatenate component Former-commit-id: b58815eb30d4c51d70b0d7307955761f05b611da --- .../dataset_loader/download/datasets.tsv | 2 +- .../baseline_majority_vote/test_script.py | 2 +- .../baseline_random_celltype/test_script.py | 2 +- .../data_processing/anndata_loader.tsv | 4 ++ .../dataset_concatenate/config.vsh.yaml | 41 +++++++++++++++++++ .../dataset_concatenate/script.py | 21 ++++++++++ .../dataset_concatenate/test_script.py | 22 ++++++++++ .../data_processing/fake_anndata_loader.tsv | 2 - 8 files changed, 91 insertions(+), 5 deletions(-) create mode 100644 src/label_projection/data_processing/anndata_loader.tsv create mode 100644 src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml create mode 100644 src/label_projection/data_processing/dataset_concatenate/script.py create mode 100644 src/label_projection/data_processing/dataset_concatenate/test_script.py delete mode 100644 src/label_projection/data_processing/fake_anndata_loader.tsv diff --git a/src/common/dataset_loader/download/datasets.tsv b/src/common/dataset_loader/download/datasets.tsv index a9a4934684..ad3d13e354 100644 --- a/src/common/dataset_loader/download/datasets.tsv +++ b/src/common/dataset_loader/download/datasets.tsv @@ -1,5 +1,5 @@ processor name url obs_celltype obs_batch obs_tissue anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue +anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 afinal_annotation batch tissue anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA diff --git a/src/label_projection/control_methods/baseline_majority_vote/test_script.py b/src/label_projection/control_methods/baseline_majority_vote/test_script.py index 86a229beed..1d23997b19 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/test_script.py +++ b/src/label_projection/control_methods/baseline_majority_vote/test_script.py @@ -8,7 +8,7 @@ print(">> Running script as test") out = subprocess.check_output([ - "./majority_vote", + "./" + meta["functionality_name"], "--input", INPUT, "--output", OUTPUT ]).decode("utf-8") diff --git a/src/label_projection/control_methods/baseline_random_celltype/test_script.py b/src/label_projection/control_methods/baseline_random_celltype/test_script.py index 7e5026e2de..3cb9827880 100644 --- a/src/label_projection/control_methods/baseline_random_celltype/test_script.py +++ b/src/label_projection/control_methods/baseline_random_celltype/test_script.py @@ -8,7 +8,7 @@ print(">> Running script as test") out = subprocess.check_output([ - "./random_celltype", + "./" + meta["functionality_name"], "--input", INPUT, "--output", OUTPUT ]).decode("utf-8") diff --git a/src/label_projection/data_processing/anndata_loader.tsv b/src/label_projection/data_processing/anndata_loader.tsv new file mode 100644 index 0000000000..85351d930d --- /dev/null +++ b/src/label_projection/data_processing/anndata_loader.tsv @@ -0,0 +1,4 @@ +processor name url obs_celltype obs_batch obs_tissue +anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA +anndata_loader cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue +anndata_loader zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA diff --git a/src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml b/src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml new file mode 100644 index 0000000000..7b8e05a3d2 --- /dev/null +++ b/src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml @@ -0,0 +1,41 @@ +functionality: + name: "dataset_concatenate" + namespace: "label_projection/data_processing" + version: "dev" + description: "Concatenate datasets." + authors: + - name: "Michaela Mueller " + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: "--inputs" + alternatives: ["-i"] + type: "file" + multiple: true + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output h5ad file of the cleaned dataset" + required: true + + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../resources/pancreas" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: native + - type: nextflow diff --git a/src/label_projection/data_processing/dataset_concatenate/script.py b/src/label_projection/data_processing/dataset_concatenate/script.py new file mode 100644 index 0000000000..2d4e375f65 --- /dev/null +++ b/src/label_projection/data_processing/dataset_concatenate/script.py @@ -0,0 +1,21 @@ +import scanpy as sc + +###VIASH START +par = { + "inputs": ["../resources/pancreas/toy_data.h5ad", "../resources/pancreas/toy_data.h5ad"], + "output": "output.h5ad" +} +###VIASH END + +adata_list = [] +for i in par["inputs"]: + print("Loading {}".format(i)) + adata_list.append( + sc.read_h5ad(i) + ) + +print("Concatenate anndatas") +adata = adata_list[0].concatenate(adata_list[1:]) + +print("Writing result file") +adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/data_processing/dataset_concatenate/test_script.py b/src/label_projection/data_processing/dataset_concatenate/test_script.py new file mode 100644 index 0000000000..a4257c9753 --- /dev/null +++ b/src/label_projection/data_processing/dataset_concatenate/test_script.py @@ -0,0 +1,22 @@ +import subprocess +import scanpy as sc +from os import path + +## VIASH START +## VIASH END +INPUT = f"{meta['resources_dir']}/pancreas/toy_data.h5ad" +INPUTS = f"{INPUT}:{INPUT}" +OUTPUT = "toy_data_concatenated.h5ad" + +print(">> Runing script as test") +out = subprocess.check_output([ + "./" + meta["functionality_name"], + "--inputs", INPUTS, + "--output", OUTPUT +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that test output fits expected API") +adata = sc.read_h5ad(OUTPUT) +assert (1000, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) diff --git a/src/label_projection/data_processing/fake_anndata_loader.tsv b/src/label_projection/data_processing/fake_anndata_loader.tsv deleted file mode 100644 index 51c45f1a1c..0000000000 --- a/src/label_projection/data_processing/fake_anndata_loader.tsv +++ /dev/null @@ -1,2 +0,0 @@ -processor name url obs_celltype obs_batch obs_tissue -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA From cb13cc4adbab90d841c078b6db0334a270fa9862 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Thu, 7 Jul 2022 15:42:02 -0300 Subject: [PATCH 0227/1233] feat: all data added Former-commit-id: 5e8d92bafc9c781221710250e4abebce6e0635e7 --- .../data_processing/anndata_loader.tsv | 2 + .../data_processing/subsample/config.vsh.yaml | 10 ++-- .../data_processing/subsample/script.py | 54 +++++++++++-------- .../data_processing/subsample/test_script.py | 25 ++++++--- .../generate_test_resources/pancreas.sh | 4 +- src/label_projection/workflows/run/main.nf | 9 ++-- 6 files changed, 65 insertions(+), 39 deletions(-) diff --git a/src/label_projection/data_processing/anndata_loader.tsv b/src/label_projection/data_processing/anndata_loader.tsv index 85351d930d..92b362c170 100644 --- a/src/label_projection/data_processing/anndata_loader.tsv +++ b/src/label_projection/data_processing/anndata_loader.tsv @@ -2,3 +2,5 @@ processor name url obs_celltype obs_batch obs_tissue anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA anndata_loader cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue anndata_loader zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA +anndata_loader tabula_muris_senis_facs_lung https://ndownloader.figshare.com/files/23872619 free_annotation mouse.id NA +anndata_loader tabula_muris_senis_droplet_lung https://ndownloader.figshare.com/files/23873012 free_annotation mouse.id NA diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index 3d35db3dd7..88d79ddb47 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -15,16 +15,18 @@ functionality: type: "file" description: "Input data to be resized" required: true - - name: "--celltype_categories" - type: "integer" + - name: "--keep_celltype_categories" + type: "string" multiple: true description: "Categories indexes to be selected" required: false - - name: "--tech_categories" - type: "integer" + - name: "--keep_batch_categories" + type: "string" multiple: true description: "Categories indexes to be selected" required: false + - name: "--even" + type: "boolean_true" - name: "--output" alternatives: ["-o"] type: "file" diff --git a/src/label_projection/data_processing/subsample/script.py b/src/label_projection/data_processing/subsample/script.py index da046a4d5c..51c3de1052 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/label_projection/data_processing/subsample/script.py @@ -1,14 +1,13 @@ -## VIASH START +import scanpy as sc +### VIASH START par = { - "input": "../test_data.h5ad", - "celltype_categories": [0, 3], - "tech_categories": [0, -3, -2], + "input": "../../resources/pancreas/raw_data.h5ad", + # "keep_celltype_categories": ["acinar", "beta"], + # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], + "even": True, "ouput": "./toy_data.h5ad" } -## VIASH END - - -import scanpy as sc +### VIASH END def filter_genes_cells(adata): """Remove empty cells and genes.""" @@ -20,24 +19,37 @@ def filter_genes_cells(adata): print(">> Load data") adata = sc.read(par['input']) -adata = adata[:, :500].copy() -filter_genes_cells(adata) +if par.get('even'): + keep_batch_categories = adata.obs["batch"].unique() + adata_out = None + n_batch_obs_per_value = 500 // len(keep_batch_categories) + for t in keep_batch_categories: + batch_idx = adata.obs["batch"] == t + adata_subset = adata[batch_idx].copy() + sc.pp.subsample(adata_subset, n_obs=min(n_batch_obs_per_value, adata_subset.shape[0])) + if adata_out is None: + adata_out = adata_subset + else: + adata_out = adata_out.concatenate(adata_subset, batch_key="_obs_batch") + adata_out.uns = adata.uns + adata_out.varm = adata.varm + adata_out.varp = adata.varp + adata = adata_out[:, :500].copy() +else: + adata = adata[:, :500].copy() -print(">> Select indexes") -print(">> Selecting celltype_categories indexes {idx}".format(idx=par.get('celltype_categories'))) -keep_celltypes = par.get('celltype_categories') and adata.obs["celltype"].dtype.categories[par['celltype_categories']] -print(">> Selected celltype_categories {}".format(keep_celltypes)) -keep_celltype_idx = adata.obs["celltype"].isin(keep_celltypes) +filter_genes_cells(adata) -print(">> Selecting tech_categories indexes {idx}".format(idx=par.get('tech_categories'))) -keep_techs = par.get('tech_categories') and adata.obs["tech"].dtype.categories[par['tech_categories']] -print(">> Selected tech_categories {}".format(keep_techs)) -keep_tech_idx = adata.obs["tech"].isin(keep_techs) +if par.get('keep_celltype_categories') and par.get('keep_batch_categories'): + print(">> Selecting celltype_categories {categories}".format(categories=par.get('keep_celltype_categories'))) + print(">> Selecting batch_categories {categories}".format(categories=par.get('keep_batch_categories'))) + keep_batch_idx = adata.obs["batch"].isin(par['keep_batch_categories']) + keep_celltype_idx = adata.obs["celltype"].isin(par['keep_celltype_categories']) + adata = adata[keep_celltype_idx & keep_batch_idx].copy() -adata = adata[keep_tech_idx & keep_celltype_idx].copy() -sc.pp.subsample(adata, n_obs=500) # Note: could also use 200-500 HVGs rather than 200 random genes # Ensure there are no cells or genes with 0 counts +sc.pp.subsample(adata, n_obs=min(500, adata.shape[0])) filter_genes_cells(adata) adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" diff --git a/src/label_projection/data_processing/subsample/test_script.py b/src/label_projection/data_processing/subsample/test_script.py index 3dfe6c2608..4677a71539 100644 --- a/src/label_projection/data_processing/subsample/test_script.py +++ b/src/label_projection/data_processing/subsample/test_script.py @@ -2,18 +2,31 @@ import scanpy as sc from os import path -## VIASH START -## VIASH END - +### VIASH START +### VIASH END INPUT = f"{meta['resources_dir']}/pancreas/raw_data.h5ad" OUTPUT = "toy_data.h5ad" -print(">> Runing script as test") +print(">> Runing script as test for even") +out = subprocess.check_output([ + "./" + meta["functionality_name"], + "--input", INPUT, + "--output", OUTPUT, + "--even" +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(OUTPUT) + +print(">> Check that test output fits expected API") +adata = sc.read_h5ad(OUTPUT) +assert (495, 467) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + +print(">> Runing script as test for specific batch and celltype categories") out = subprocess.check_output([ "./" + meta["functionality_name"], "--input", INPUT, - "--celltype_categories", "0:3", - "--tech_categories", "0:-3:-2", + "--keep_celltype_categories", "acinar:beta", + "--keep_batch_categories", "celseq:inDrop4:smarter", "--output", OUTPUT ]).decode("utf-8") print(">> Checking whether file exists") diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/label_projection/workflows/generate_test_resources/pancreas.sh index b9afd9b6f4..548d67554d 100755 --- a/src/label_projection/workflows/generate_test_resources/pancreas.sh +++ b/src/label_projection/workflows/generate_test_resources/pancreas.sh @@ -22,8 +22,8 @@ target/docker/common/dataset_loader/download/download\ target/docker/label_projection/data_processing/subsample/subsample\ --input $DATASET_DIR/raw_data.h5ad\ - --celltype_categories "0:3"\ - --tech_categories "0:-3:-2"\ + --celltype_categories "acinar:beta"\ + --tech_categories "celseq:inDrop4:smarter"\ --output $DATASET_DIR/toy_data.h5ad target/docker/label_projection/data_processing/randomize/randomize\ diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 38ad0168e5..e5b75d98d3 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -43,14 +43,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // // If the need arises, these workflows could be split off into a separate file. -// params.tsv = "$launchDir/src/common/data_loader/anndata_loader.tsv" -params.tsv = "$launchDir/src/label_projection/data_processing/fake_anndata_loader.tsv" //for tests +params.tsv = "$launchDir/src/label_projection/data_processing/anndata_loader.tsv" workflow load_data { main: output_ = Channel.fromPath(params.tsv) | splitCsv(header: true, sep: "\t") - | filter{ it.obs_celltype != "NA" && it.obs_batch != "NA" } + | filter{ it.name != "tabula_muris_senis_facs_lung" || it.name != "tabula_muris_senis_droplet_lung" } //TODO | map{ [ it.name, it ] } | download emit: @@ -101,9 +100,7 @@ workflow { load_data | randomize | subsample.run( - map: { [it[0], [input: it[1], - celltype_categories: "0:3", - tech_categories: "0:-3:-2"]] } + map: { [it[0], [input: it[1], even: true]] } ) | (log_cpm & log_scran_pooling) | mix From b7fc278f6f4ad62499322504e5cf26693afe7570 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Thu, 7 Jul 2022 15:52:36 -0300 Subject: [PATCH 0228/1233] chore: self-review Former-commit-id: b2fff87e649ffdfa221b23996372bcad44edc682 --- src/common/dataset_loader/download/datasets.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/dataset_loader/download/datasets.tsv b/src/common/dataset_loader/download/datasets.tsv index ad3d13e354..a9a4934684 100644 --- a/src/common/dataset_loader/download/datasets.tsv +++ b/src/common/dataset_loader/download/datasets.tsv @@ -1,5 +1,5 @@ processor name url obs_celltype obs_batch obs_tissue anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 afinal_annotation batch tissue +anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA From c28c62d282e3593a253152c25c97494c5e14c122 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 8 Jul 2022 09:44:37 +0200 Subject: [PATCH 0229/1233] fix nxf scripts Former-commit-id: db2a6f896e1ab44c3d0dd79672c0071ab3360356 --- src/modality_alignment/workflows/run/run_nextflow.sh | 2 +- src/trajectory_inference/workflows/run_nextflow.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/modality_alignment/workflows/run/run_nextflow.sh b/src/modality_alignment/workflows/run/run_nextflow.sh index 415794f68a..e0b946aa54 100755 --- a/src/modality_alignment/workflows/run/run_nextflow.sh +++ b/src/modality_alignment/workflows/run/run_nextflow.sh @@ -15,7 +15,7 @@ export NXF_VER=21.10.6 bin/nextflow \ run . \ -main-script src/modality_alignment/workflows/run/main.nf \ - --output output/modality_alignment \ + --publish_dir output/modality_alignment \ -resume \ -with-docker diff --git a/src/trajectory_inference/workflows/run_nextflow.sh b/src/trajectory_inference/workflows/run_nextflow.sh index 9e2da87cce..133c32343d 100755 --- a/src/trajectory_inference/workflows/run_nextflow.sh +++ b/src/trajectory_inference/workflows/run_nextflow.sh @@ -11,5 +11,5 @@ cd "$REPO_ROOT" NXF_VER=20.10.0 bin/nextflow run src/trajectory_inference/workflows/main.nf \ -resume \ - --output output/trajectory_inference + --publish_dir output/trajectory_inference From 4475dfc9c14a5eab0f0375557767b6710b6931cc Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 11 Jul 2022 07:55:28 -0300 Subject: [PATCH 0230/1233] chore: self-review Former-commit-id: b221602f21c936c95cf265b1b28426eb9f751c76 --- .../control_methods/baseline_majority_vote/config.vsh.yaml | 4 ++-- .../control_methods/baseline_majority_vote/script.py | 2 +- .../baseline_random_celltype/config.vsh.yaml | 6 +++--- src/label_projection/methods/knn_classifier/config.vsh.yaml | 4 ++-- .../methods/logistic_regression/config.vsh.yaml | 4 ++-- src/label_projection/methods/mlp/config.vsh.yaml | 4 ++-- .../methods/scvi/scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 4 ++-- 11 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml b/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml index c0c16984ff..97812b7ab9 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml @@ -13,12 +13,12 @@ functionality: arguments: - name: "--input" type: "file" - description: "Input data to add prediction" + description: "Input data to predict" required: true - name: "--output" alternatives: ["-o"] type: "file" - description: "Ouput data labeled" + description: "Ouput data containing predictions" direction: "output" example: "output.mv.h5ad" required: true diff --git a/src/label_projection/control_methods/baseline_majority_vote/script.py b/src/label_projection/control_methods/baseline_majority_vote/script.py index 6db158547f..40ed1afa84 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/script.py +++ b/src/label_projection/control_methods/baseline_majority_vote/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'input': 'ouput.h5ad', + 'input': '../../resources/pancreas/toy_normalized_log_cpm.h5ad', 'output': 'output.mv.h5ad' } ## VIASH END diff --git a/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml b/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml index 32c5b8eb07..034cde60c0 100644 --- a/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "baseline_random_celltype" namespace: "label_projection/control_methods" version: "dev" - description: "Majority vote dummy" + description: "Random Labels dummy" authors: - name: "Scott Gigante" roles: [ author ] @@ -13,12 +13,12 @@ functionality: arguments: - name: "--input" type: "file" - description: "Input data to add prediction" + description: "Input data to predict" required: true - name: "--output" alternatives: ["-o"] type: "file" - description: "Ouput data labeled" + description: "Ouput data containing predictions" direction: "output" example: "output.mv.h5ad" required: true diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 3729e34297..07eb22c674 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "knn_classifier" namespace: "label_projection/methods" version: "dev" - description: "Run Harmonic Alignment" + description: "Nearest neighbor pattern classification" authors: - name: "Scott Gigante" roles: [ author ] @@ -22,7 +22,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 2e5aaed388..a20a525cba 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "logistic_regression" namespace: "label_projection/methods" version: "dev" - description: "Run Harmonic Alignment" + description: "Applied Logistic Regression" authors: - name: "Scott Gigante" roles: [ author ] @@ -27,7 +27,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 17bb6ca8b4..0440dba95e 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "mlp" namespace: "label_projection/methods" version: "dev" - description: "Run Harmonic Alignment" + description: "Multilayer perceptron" authors: - name: "Scott Gigante" roles: [ author ] @@ -32,7 +32,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data contatining predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 500d19090b..78638f1532 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index 44b76194e2..ef0d5e30c2 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -50,7 +50,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 3ff2b5b6bd..4b011f4831 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index e1b224b8f1..df1992b3ff 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -50,7 +50,7 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output data labeled" + description: "Output data containing predictions" required: true resources: - type: python_script diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 7a2ffc6d91..fd6408f85e 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -2,7 +2,7 @@ functionality: name: "f1" namespace: "label_projection/metrics" version: "dev" - description: "Accuracy of predictions" + description: "balanced F-score or F-measure" authors: - name: "Scott Gigante" roles: [ author ] @@ -13,7 +13,7 @@ functionality: arguments: - name: "--input" type: "file" - description: "Input data to get accuracy" + description: "Input data with predictions to get f1-score" required: true - name: "--average" type: "string" From 4c36db75f4e6d7c59966ff5e8d25c4e99e3c39b2 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 13 Jul 2022 08:18:45 -0300 Subject: [PATCH 0231/1233] fix: requested changes Former-commit-id: ef997a923672d989e1bfefc932f670723cc2805b --- CHANGELOG.md | 6 ++- .../dataset_concatenate/config.vsh.yaml | 2 +- .../dataset_concatenate/script.py | 0 .../dataset_concatenate/test_script.py | 2 +- src/common/extract_scores/config.vsh.yaml | 5 +++ src/common/extract_scores/script.R | 8 +--- .../config.vsh.yaml | 5 ++- .../script.py | 2 +- .../test_script.py | 2 +- .../config.vsh.yaml | 5 ++- .../script.py | 2 +- .../test_script.py | 2 +- .../data_processing/randomize/test_script.py | 2 +- .../methods/knn_classifier/config.vsh.yaml | 5 ++- .../methods/knn_classifier/script.py | 2 +- .../methods/knn_classifier/test_script.py | 22 ---------- .../logistic_regression/config.vsh.yaml | 5 ++- .../methods/logistic_regression/script.py | 2 +- .../logistic_regression/test_script.py | 23 ---------- .../methods/mlp/config.vsh.yaml | 5 ++- src/label_projection/methods/mlp/script.py | 2 +- .../methods/mlp/test_script.py | 24 ----------- .../scvi/scanvi_all_genes/config.vsh.yaml | 5 ++- .../methods/scvi/scanvi_all_genes/script.py | 2 +- .../scvi/scanvi_all_genes/test_script.py | 27 ------------ .../methods/scvi/scanvi_hvg/config.vsh.yaml | 5 ++- .../methods/scvi/scanvi_hvg/script.py | 2 +- .../methods/scvi/scanvi_hvg/test_script.py | 29 ------------- .../scarches_scanvi_all_genes/config.vsh.yaml | 5 ++- .../scvi/scarches_scanvi_all_genes/script.py | 2 +- .../scarches_scanvi_all_genes/test_script.py | 27 ------------ .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 5 ++- .../scvi/scarches_scanvi_hvg/script.py | 2 +- .../scvi/scarches_scanvi_hvg/test_script.py | 29 ------------- .../methods/scvi/unit_tests/test_method.py | 42 +++++++++++++++++++ .../methods/unit_tests/test_method.py | 29 +++++++++++++ .../metrics/accuracy/script.py | 2 +- src/label_projection/metrics/f1/script.py | 2 +- src/label_projection/workflows/run/main.nf | 1 + 39 files changed, 135 insertions(+), 214 deletions(-) rename src/{label_projection/data_processing => common}/dataset_concatenate/config.vsh.yaml (94%) rename src/{label_projection/data_processing => common}/dataset_concatenate/script.py (100%) rename src/{label_projection/data_processing => common}/dataset_concatenate/test_script.py (89%) rename src/label_projection/control_methods/{baseline_majority_vote => nayve_majority_vote}/config.vsh.yaml (91%) rename src/label_projection/control_methods/{baseline_majority_vote => nayve_majority_vote}/script.py (90%) rename src/label_projection/control_methods/{baseline_majority_vote => nayve_majority_vote}/test_script.py (88%) rename src/label_projection/control_methods/{baseline_random_celltype => nayve_random_celltype}/config.vsh.yaml (91%) rename src/label_projection/control_methods/{baseline_random_celltype => nayve_random_celltype}/script.py (92%) rename src/label_projection/control_methods/{baseline_random_celltype => nayve_random_celltype}/test_script.py (88%) delete mode 100644 src/label_projection/methods/knn_classifier/test_script.py delete mode 100644 src/label_projection/methods/logistic_regression/test_script.py delete mode 100644 src/label_projection/methods/mlp/test_script.py delete mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/test_script.py delete mode 100644 src/label_projection/methods/scvi/scanvi_hvg/test_script.py delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py create mode 100644 src/label_projection/methods/scvi/unit_tests/test_method.py create mode 100644 src/label_projection/methods/unit_tests/test_method.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 94161d41ad..a4bc7e0b8e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,4 +8,8 @@ * `extract_scores`: Summarise a metrics output tsv. -## \ No newline at end of file +* `dataset_concatenate`: concatenate N AnnData datasets + +* `label_projection`: all components for **label_projection** task + +## diff --git a/src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml similarity index 94% rename from src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml rename to src/common/dataset_concatenate/config.vsh.yaml index 7b8e05a3d2..3e590b5622 100644 --- a/src/label_projection/data_processing/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/pancreas" + path: "../../label_projection/resources/pancreas" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data_processing/dataset_concatenate/script.py b/src/common/dataset_concatenate/script.py similarity index 100% rename from src/label_projection/data_processing/dataset_concatenate/script.py rename to src/common/dataset_concatenate/script.py diff --git a/src/label_projection/data_processing/dataset_concatenate/test_script.py b/src/common/dataset_concatenate/test_script.py similarity index 89% rename from src/label_projection/data_processing/dataset_concatenate/test_script.py rename to src/common/dataset_concatenate/test_script.py index a4257c9753..f97356527a 100644 --- a/src/label_projection/data_processing/dataset_concatenate/test_script.py +++ b/src/common/dataset_concatenate/test_script.py @@ -19,4 +19,4 @@ print(">> Check that test output fits expected API") adata = sc.read_h5ad(OUTPUT) -assert (1000, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) +assert (1000, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 5dd81f7ae3..e8225bc863 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -10,6 +10,11 @@ functionality: multiple: true default: "input.h5ad" description: "Input h5ad files containing metadata and metrics in adata.uns" + - name: "--column_names" + type: "string" + multiple: true + default: [ "dataset_id", "method_id", "metric_id", "metric_value" ] + description: "Which fields from adata.uns to extract and store as a data frame." - name: "--output" alternatives: ["-o"] type: "file" diff --git a/src/common/extract_scores/script.R b/src/common/extract_scores/script.R index 337c34167f..c3ea344236 100644 --- a/src/common/extract_scores/script.R +++ b/src/common/extract_scores/script.R @@ -17,13 +17,7 @@ scores <- map_df(par$input, function(inp) { cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) - if ("normalization_method" %in% names(ad$uns)) { - uns_names <- c("dataset_id", "normalization_method", "method_id", "metric_id", "metric_value") - } else { - uns_names <- c("dataset_id", "method_id", "metric_id", "metric_value") - } - - for (uns_name in uns_names) { + for (uns_name in par$column_names) { assert_that( uns_name %in% names(ad$uns), msg = paste0("File ", inp, " must contain `uns['", uns_name, "']`") diff --git a/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml b/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml similarity index 91% rename from src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml rename to src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml index 97812b7ab9..0a05d330a3 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml @@ -1,8 +1,11 @@ functionality: - name: "baseline_majority_vote" + name: "nayve_majority_vote" namespace: "label_projection/control_methods" version: "dev" description: "Majority vote dummy" + info: + type: nayve_control + label: Random prediction authors: - name: "Scott Gigante" roles: [ author ] diff --git a/src/label_projection/control_methods/baseline_majority_vote/script.py b/src/label_projection/control_methods/nayve_majority_vote/script.py similarity index 90% rename from src/label_projection/control_methods/baseline_majority_vote/script.py rename to src/label_projection/control_methods/nayve_majority_vote/script.py index 40ed1afa84..02cdb01fe7 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/script.py +++ b/src/label_projection/control_methods/nayve_majority_vote/script.py @@ -18,5 +18,5 @@ print("Write output to file") -adata.uns["method_id"] = "majority_vote" +adata.uns["method_id"] = meta["functionality_name"] adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/baseline_majority_vote/test_script.py b/src/label_projection/control_methods/nayve_majority_vote/test_script.py similarity index 88% rename from src/label_projection/control_methods/baseline_majority_vote/test_script.py rename to src/label_projection/control_methods/nayve_majority_vote/test_script.py index 1d23997b19..b961f3cce0 100644 --- a/src/label_projection/control_methods/baseline_majority_vote/test_script.py +++ b/src/label_projection/control_methods/nayve_majority_vote/test_script.py @@ -19,4 +19,4 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) assert "celltype_pred" in adata.obs -assert "majority_vote" == adata.uns["method_id"] +assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml b/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml similarity index 91% rename from src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml rename to src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml index 034cde60c0..5838843f77 100644 --- a/src/label_projection/control_methods/baseline_random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml @@ -1,8 +1,11 @@ functionality: - name: "baseline_random_celltype" + name: "nayve_random_celltype" namespace: "label_projection/control_methods" version: "dev" description: "Random Labels dummy" + info: + type: nayve_control + label: Random prediction authors: - name: "Scott Gigante" roles: [ author ] diff --git a/src/label_projection/control_methods/baseline_random_celltype/script.py b/src/label_projection/control_methods/nayve_random_celltype/script.py similarity index 92% rename from src/label_projection/control_methods/baseline_random_celltype/script.py rename to src/label_projection/control_methods/nayve_random_celltype/script.py index 81cb35b5ce..5b2dc04c79 100644 --- a/src/label_projection/control_methods/baseline_random_celltype/script.py +++ b/src/label_projection/control_methods/nayve_random_celltype/script.py @@ -24,5 +24,5 @@ print("Write output to file") -adata.uns["method_id"] = "random_celltype" +adata.uns["method_id"] = meta["functionality_name"] adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/baseline_random_celltype/test_script.py b/src/label_projection/control_methods/nayve_random_celltype/test_script.py similarity index 88% rename from src/label_projection/control_methods/baseline_random_celltype/test_script.py rename to src/label_projection/control_methods/nayve_random_celltype/test_script.py index 3cb9827880..b961f3cce0 100644 --- a/src/label_projection/control_methods/baseline_random_celltype/test_script.py +++ b/src/label_projection/control_methods/nayve_random_celltype/test_script.py @@ -19,4 +19,4 @@ print(">> Checking if predictions were added") adata = sc.read_h5ad(OUTPUT) assert "celltype_pred" in adata.obs -assert "random_celltype" == adata.uns["method_id"] +assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/data_processing/randomize/test_script.py b/src/label_projection/data_processing/randomize/test_script.py index 53f64038dc..838c00adee 100644 --- a/src/label_projection/data_processing/randomize/test_script.py +++ b/src/label_projection/data_processing/randomize/test_script.py @@ -23,6 +23,6 @@ print(">> Check that test output fits expected API") adata = sc.read_h5ad(OUTPUT) - assert (500, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + assert (500, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) assert "batch" in adata.obs assert "is_train" in adata.obs diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 07eb22c674..329651b08d 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods" version: "dev" description: "Nearest neighbor pattern classification" + info: + type: baseline + label: KNN authors: - name: "Scott Gigante" roles: [ author ] @@ -30,7 +33,7 @@ functionality: - path: "../../utils.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index c9f9b4c34a..e0dd20dd68 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -20,7 +20,7 @@ print("Run classifier") adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) -adata.uns["method_id"] = "knn_classifier" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/knn_classifier/test_script.py b/src/label_projection/methods/knn_classifier/test_script.py deleted file mode 100644 index ec0f50db63..0000000000 --- a/src/label_projection/methods/knn_classifier/test_script.py +++ /dev/null @@ -1,22 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] -OUTPUT = ["output.knnlogcpm.h5ad", "output.knnscran.h5ad"] - -for input, output in zip(INPUT, OUTPUT): - print(">> Running script as test") - out = subprocess.check_output([ - "./knn_classifier", - "--input", input, - "--output", output - ]).decode("utf-8") - - print(">> Checking if output file exists") - assert path.exists(output) - - print(">> Checking if predictions were added") - adata = sc.read_h5ad(output) - assert "celltype_pred" in adata.obs - assert "knn_classifier" == adata.uns["method_id"] diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index a20a525cba..ebfd8adac2 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods" version: "dev" description: "Applied Logistic Regression" + info: + type: baseline + label: Logistic Regression authors: - name: "Scott Gigante" roles: [ author ] @@ -35,7 +38,7 @@ functionality: - path: "../../utils.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 380f0691b8..0f44a543bd 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -19,7 +19,7 @@ print("Run classifier") max_iter = par['max_iter'] adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) -adata.uns["method_id"] = "logistic_regression" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/test_script.py b/src/label_projection/methods/logistic_regression/test_script.py deleted file mode 100644 index 2683be0ba7..0000000000 --- a/src/label_projection/methods/logistic_regression/test_script.py +++ /dev/null @@ -1,23 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] -OUTPUT = ["output.lrlogcpm.h5ad", "output.lrscran.h5ad"] - -for input, output in zip(INPUT, OUTPUT): - print(">> Running script as test") - out = subprocess.check_output([ - "./logistic_regression", - "--input", input, - "--max_iter", "100", - "--output", output - ]).decode("utf-8") - - print(">> Checking if output file exists") - assert path.exists(output) - - print(">> Checking if predictions were added") - adata = sc.read_h5ad(output) - assert "celltype_pred" in adata.obs - assert "logistic_regression" == adata.uns["method_id"] diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 0440dba95e..415f910bfe 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods" version: "dev" description: "Multilayer perceptron" + info: + type: baseline + label: Multilayer perceptron authors: - name: "Scott Gigante" roles: [ author ] @@ -40,7 +43,7 @@ functionality: - path: "../../utils.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad platforms: diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 777763f246..33438f1190 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -27,7 +27,7 @@ hidden_layer_sizes = tuple(par['hidden_layer_sizes']) max_iter = par['max_iter'] adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) -adata.uns["method_id"] = "mlp" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/mlp/test_script.py b/src/label_projection/methods/mlp/test_script.py deleted file mode 100644 index ea94e9e7c4..0000000000 --- a/src/label_projection/methods/mlp/test_script.py +++ /dev/null @@ -1,24 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] -OUTPUT = ["output.mlplogcpm.h5ad", "output.mlpscran.h5ad"] - -for input, output in zip(INPUT, OUTPUT): - print(">> Running script as test") - out = subprocess.check_output([ - "./mlp", - "--input", input, - "--hidden_layer_sizes", "20", - "--max_iter", "100", - "--output", output - ]).decode("utf-8") - - print(">> Checking if output file exists") - assert path.exists(output) - - print(">> Checking if predictions were added") - adata = sc.read_h5ad(output) - assert "celltype_pred" in adata.obs - assert "mlp" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 78638f1532..25f9026c9e 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods/scvi" version: "dev" description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." + info: + type: baseline + label: Scanvi_ALL_GENES authors: - name: "Scott Gigante" roles: [ author ] @@ -51,7 +54,7 @@ functionality: - path: "../tools.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - type: file path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py index b0fed618bc..cf3b26d4e4 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scanvi_all_genes/script.py @@ -33,7 +33,7 @@ par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) adata.obs["celltype_pred"] = scanvi(adata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) -adata.uns["method_id"] = "scanvi_all_genes" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py deleted file mode 100644 index 27187a2549..0000000000 --- a/src/label_projection/methods/scvi/scanvi_all_genes/test_script.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.scanviallgenes.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./scanvi_all_genes", - '--n_hidden', "32", - '--n_layers', "1", - '--n_latent', "10", - '--max_epochs', "1", - '--limit_train_batches', "10", - '--limit_val_batches', "10", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert "scanvi_all_genes" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index ef0d5e30c2..6ec5bda8d8 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods/scvi" version: "dev" description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." + info: + type: baseline + label: Scanvi_HVG authors: - name: "Scott Gigante" roles: [ author ] @@ -58,7 +61,7 @@ functionality: - path: "../tools.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - type: file path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: diff --git a/src/label_projection/methods/scvi/scanvi_hvg/script.py b/src/label_projection/methods/scvi/scanvi_hvg/script.py index ef8b1be384..cdc4a6f4f1 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scanvi_hvg/script.py @@ -45,7 +45,7 @@ hvg_df = hvg(adata, **hvg_kwargs) bdata = adata[:, hvg_df.highly_variable].copy() adata.obs["celltype_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) -adata.uns["method_id"] = "scanvi_hvg" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scanvi_hvg/test_script.py deleted file mode 100644 index 2025a5d6da..0000000000 --- a/src/label_projection/methods/scvi/scanvi_hvg/test_script.py +++ /dev/null @@ -1,29 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.scanviallgenes.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./scanvi_hvg", - '--n_hidden', "32", - '--n_layers', "1", - '--n_latent', "10", - '--n_top_genes', "2000", - '--spane', "0.8", - '--max_epochs', "1", - '--limit_train_batches', "10", - '--limit_val_batches', "10", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert "scanvi_hvg" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 4b011f4831..18e3bffd25 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods/scvi" version: "dev" description: "Probabilistic harmonization and annotation of single-cell" + info: + type: baseline + label: Scarches_scanvi_ALL_GENES authors: - name: "Scott Gigante" roles: [ author ] @@ -51,7 +54,7 @@ functionality: - path: "../tools.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - type: file path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py index 266247bdd2..d51a6d6a3f 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py @@ -36,7 +36,7 @@ adata.obs["celltype_pred"] = scanvi_scarches(adata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, 'query_model_train_kwargs': query_model_train_kwargs}) -adata.uns["method_id"] = "scarches_scanvi_all_genes" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py deleted file mode 100644 index 69bec5f02f..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/test_script.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.scarchesallgenes.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./scarches_scanvi_all_genes", - '--n_hidden', "32", - '--n_layers', "1", - '--n_latent', "10", - '--max_epochs', "1", - '--limit_train_batches', "10", - '--limit_val_batches', "10", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert "scarches_scanvi_all_genes" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index df1992b3ff..43a5800f95 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -3,6 +3,9 @@ functionality: namespace: "label_projection/methods/scvi" version: "dev" description: "Probabilistic harmonization and annotation of single-cell" + info: + type: baseline + label: Scarches_scanvi_HVG authors: - name: "Scott Gigante" roles: [ author ] @@ -58,7 +61,7 @@ functionality: - path: "../tools.py" tests: - type: python_script - path: test_script.py + path: ../unit_tests/test_method.py - type: file path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" platforms: diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py index 12a72a4854..6342978248 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py @@ -51,7 +51,7 @@ bdata = adata[:, hvg_df.highly_variable].copy() adata.obs["celltype_pred"] = scanvi_scarches(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, 'query_model_train_kwargs': query_model_train_kwargs}) -adata.uns["method_id"] = "scarches_scanvi_hvg" +adata.uns["method_id"] = meta["functionality_name"] print("Write data") adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py deleted file mode 100644 index eb6e79bc07..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/test_script.py +++ /dev/null @@ -1,29 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.scarchesallgenes.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./scarches_scanvi_hvg", - '--n_hidden', "32", - '--n_layers', "1", - '--n_latent', "10", - '--span', "0.8", - '--n_top_genes', "2000", - '--max_epochs', "1", - '--limit_train_batches', "10", - '--limit_val_batches', "10", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert "scarches_scanvi_hvg" == adata.uns["method_id"] diff --git a/src/label_projection/methods/scvi/unit_tests/test_method.py b/src/label_projection/methods/scvi/unit_tests/test_method.py new file mode 100644 index 0000000000..438d67b70b --- /dev/null +++ b/src/label_projection/methods/scvi/unit_tests/test_method.py @@ -0,0 +1,42 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "result.scvimethod.h5ad" + +methods_params = { + "./scarches_scanvi_all_genes": ['--n_hidden', "32", '--n_layers', "1", + '--n_latent', "10", '--max_epochs', "1", + '--limit_train_batches', "10", + '--limit_val_batches', "10"], + "./scarches_scanvi_hvg": ['--n_hidden', "32", '--n_layers', "1", + '--n_latent', "10", '--span', "0.8", + '--n_top_genes', "2000", '--max_epochs', "1", + '--limit_train_batches', "10", '--limit_val_batches', "10"], + "./scanvi_hvg": ['--n_hidden', "32", '--n_layers', "1", + '--n_latent', "10", '--span', "0.8", + '--n_top_genes', "2000", '--max_epochs', "1", + '--limit_train_batches', "10", '--limit_val_batches', "10"], + "./scanvi_all_genes": ['--n_hidden', "32", '--n_layers', "1", + '--n_latent', "10", '--max_epochs', "1", + '--limit_train_batches', "10", '--limit_val_batches', "10"] + } + + +_command = "./" + meta['functionality_name'] +method_param = methods_params[_command] + +default_params = ["--input", INPUT, "--output", OUTPUT] +params = [_command] + default_params + method_param + +print(">> Running script as test") +out = subprocess.check_output(params).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "celltype_pred" in adata.obs +assert meta['functionality_name'] == adata.uns["method_id"] diff --git a/src/label_projection/methods/unit_tests/test_method.py b/src/label_projection/methods/unit_tests/test_method.py new file mode 100644 index 0000000000..1fa355bf0d --- /dev/null +++ b/src/label_projection/methods/unit_tests/test_method.py @@ -0,0 +1,29 @@ +import subprocess +import scanpy as sc +from os import path + +INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] +OUTPUT = ["result.logcpm.h5ad", "result.lrscran.h5ad"] +methods_params = { + "./mlp": ["--hidden_layer_sizes", "20", "--max_iter", "100"], + "./logistic_regression": ["--max_iter", "100"], + "./knn_classifier": [] + } + + +_command = "./" + meta['functionality_name'] +method_param = methods_params[_command] + +for input, output in zip(INPUT, OUTPUT): + default_params = ["--input", input, "--output", output] + params = [_command] + default_params + method_param + print(">> Running script as test") + out = subprocess.check_output(params).decode("utf-8") + + print(">> Checking if output file exists") + assert path.exists(output) + + print(">> Checking if predictions were added") + adata = sc.read_h5ad(output) + assert "celltype_pred" in adata.obs + assert meta['functionality_name'] == adata.uns["method_id"] diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index 58d9e572a3..3798037c6c 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -22,7 +22,7 @@ accuracy = np.mean(test_data.obs["celltype"] == test_data.obs["celltype_pred"]) print("Store metric value") -adata.uns["metric_id"] = "accuracy" +adata.uns["metric_id"] = meta["functionality_name"] adata.uns["metric_value"] = accuracy print("Writing adata to file") diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 71f8893bc0..31f88d5e3f 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -25,7 +25,7 @@ ) print("Store metric value") -adata.uns["metric_id"] = "f1" +adata.uns["metric_id"] = meta["functionality_name"] adata.uns["metric_value"] = metrics print("Writing adata to file") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index e5b75d98d3..e281a16818 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -113,6 +113,7 @@ workflow { | toSortedList | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } | extract_scores.run( + args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"] auto: [ publish: true ] ) } From 3163e1de0e7817e81d745f1c378bc80c0d44db1f Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Wed, 13 Jul 2022 08:31:28 -0300 Subject: [PATCH 0232/1233] minor-changes Former-commit-id: 2da80f7f0943b398936d603c353de66441e52e3d --- src/common/dataset_concatenate/config.vsh.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index 3e590b5622..4bf4ad6e31 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -4,9 +4,12 @@ functionality: version: "dev" description: "Concatenate datasets." authors: - - name: "Michaela Mueller " - roles: [ maintainer, author ] - props: { github: mumichae } + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas " + roles: [ maintainer ] + props: { github: chagasVinicius } arguments: - name: "--inputs" alternatives: ["-i"] From d847dfd0ec3231bddbed615a9168e585370d806c Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Fri, 15 Jul 2022 09:12:22 -0300 Subject: [PATCH 0233/1233] fix: scran Former-commit-id: 43af76e92649640d74ba85b1cffc5694cd4fb39f --- src/common/extract_scores/script.R | 2 +- .../data_processing/normalize/scran/config.vsh.yaml | 2 +- .../data_processing/normalize/scran/script.R | 2 +- src/label_projection/workflows/run/main.nf | 8 ++++---- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/common/extract_scores/script.R b/src/common/extract_scores/script.R index c3ea344236..670ccf2aea 100644 --- a/src/common/extract_scores/script.R +++ b/src/common/extract_scores/script.R @@ -24,7 +24,7 @@ scores <- map_df(par$input, function(inp) { ) } - as_tibble(ad$uns[uns_names]) + as_tibble(ad$uns[par$column_names]) }) write_tsv(scores, par$output) diff --git a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml index 1026843295..97f8d59e8b 100644 --- a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml @@ -37,7 +37,7 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ scran, BiocParallel, rlang, anndata] + cran: [ Matrix, scran, BiocParallel, rlang, anndata] - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python diff --git a/src/label_projection/data_processing/normalize/scran/script.R b/src/label_projection/data_processing/normalize/scran/script.R index fc724d90f5..4e1b514dd8 100644 --- a/src/label_projection/data_processing/normalize/scran/script.R +++ b/src/label_projection/data_processing/normalize/scran/script.R @@ -14,7 +14,7 @@ cat(">> Load data\n") adata <- anndata::read_h5ad(par$input) cat(">> Normalizing data\n") -sce <- scran::calculateSumFactors(t(adata$X), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) +sce <- scran::calculateSumFactors(as.matrix(t(adata$X)), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) adata$obs[["size_factors"]] <- sce adata$X <- log1p(sce * adata$X) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index e281a16818..f251bfe106 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -15,8 +15,8 @@ include { log_scran_pooling } from "$targetDir/label_projection/data_processing/ include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" // import methods -include { baseline_majority_vote } from "$targetDir/label_projection/control_methods/baseline_majority_vote/main.nf" -include { baseline_random_celltype } from "$targetDir/label_projection/control_methods/baseline_random_celltype/main.nf" +include { nayve_majority_vote } from "$targetDir/label_projection/control_methods/nayve_majority_vote/main.nf" +include { nayve_random_celltype } from "$targetDir/label_projection/control_methods/nayve_random_celltype/main.nf" include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" @@ -105,7 +105,7 @@ workflow { | (log_cpm & log_scran_pooling) | mix | map { unique_file_name(it) } - | (knn_classifier & mlp0 & lr0 & baseline_random_celltype & baseline_majority_vote) + | (knn_classifier & mlp0 & lr0 & nayve_random_celltype & nayve_majority_vote) | mix | map { unique_file_name(it) } | (accuracy & f1a) @@ -113,7 +113,7 @@ workflow { | toSortedList | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } | extract_scores.run( - args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"] + args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"], auto: [ publish: true ] ) } From 99bcd02f9f9f9c3f7c8efa758a9fcbf09ee4f63a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:31:58 +0200 Subject: [PATCH 0234/1233] add sync folder component Former-commit-id: cb680ea41d63a536267c9a5013f50be86f218ee1 --- .gitignore | 1 + .../sync_test_resources/config.vsh.yaml | 50 +++++++++++++++++++ src/common/sync_test_resources/run_test.sh | 15 ++++++ src/common/sync_test_resources/script.sh | 34 +++++++++++++ 4 files changed, 100 insertions(+) create mode 100644 src/common/sync_test_resources/config.vsh.yaml create mode 100755 src/common/sync_test_resources/run_test.sh create mode 100644 src/common/sync_test_resources/script.sh diff --git a/.gitignore b/.gitignore index 55fe3bd6d5..d4e373c1e6 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ target/ check_results/ log.txt .viash* +resources_test/ # nextflow specific ignores .nextflow* diff --git a/src/common/sync_test_resources/config.vsh.yaml b/src/common/sync_test_resources/config.vsh.yaml new file mode 100644 index 0000000000..d5c587f0f4 --- /dev/null +++ b/src/common/sync_test_resources/config.vsh.yaml @@ -0,0 +1,50 @@ +functionality: + name: "sync_test_resources" + namespace: "common" + version: "dev" + description: Synchronise the test resources from s3 to resources_test + usage: | + sync_test_resources + sync_test_resources --input s3://openproblems-data --output resources_test + authors: + - name: Robrecht Cannoodt + email: rcannood@gmail.com + roles: [ maintainer ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + arguments: + - name: "--input" + alternatives: ["-i"] + type: string + description: "Path to the S3 bucket to sync from." + default: "s3://openproblems-data" + - name: "--output" + alternatives: ["-o"] + type: file + default: resources_test + direction: output + description: "Path to the test resource directory." + - name: "--quiet" + type: boolean_true + description: "Displays the operations that would be performed using the specified command without actually running them." + - name: "--dryrun" + type: boolean_true + description: "Does not display the operations performed from the specified command." + - name: "--delete" + type: boolean_true + description: "Files that exist in the destination but not in the source are deleted during sync." + - name: "--exclude" + type: "string" + multiple: true + description: Exclude all files or objects from the command that matches the specified pattern. + resources: + - type: bash_script + path: script.sh + test_resources: + - type: bash_script + path: run_test.sh +platforms: + - type: docker + image: "amazon/aws-cli:2.7.12" + - type: native + - type: nextflow + variant: vdsl3 diff --git a/src/common/sync_test_resources/run_test.sh b/src/common/sync_test_resources/run_test.sh new file mode 100755 index 0000000000..ec2d137af6 --- /dev/null +++ b/src/common/sync_test_resources/run_test.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +echo ">> Run aws s3 sync" +./$meta_functionality_name \ + --input s3://openproblems-data/pancreas \ + --output foo \ + --quiet + +echo ">> Check whether the right files were copied" +[ ! -f foo/raw_data.h5ad ] && echo csv should have been copied && exit 1 + +echo ">> Test succeeded!" \ No newline at end of file diff --git a/src/common/sync_test_resources/script.sh b/src/common/sync_test_resources/script.sh new file mode 100644 index 0000000000..fe86a59c33 --- /dev/null +++ b/src/common/sync_test_resources/script.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +## VIASH START +par_input='s3://openproblems-data' +par_output='resources_test' +## VIASH END + +extra_params=( ) + +if [ "$par_quiet" == "true" ]; then + extra_params+=( "--quiet" ) +fi +if [ "$par_dryrun" == "true" ]; then + extra_params+=( "--dryrun" ) +fi +if [ "$par_delete" == "true" ]; then + extra_params+=( "--delete" ) +fi + +if [ ! -z ${par_exclude+x} ]; then + IFS=":" + for var in $par_exclude; do + unset IFS + extra_params+=( "--exclude" "$var" ) + done +fi + + +# Disable the use of the Amazon EC2 instance metadata service (IMDS). +# see https://florian.ec/blog/github-actions-awscli-errors/ +# or https://github.com/aws/aws-cli/issues/5234#issuecomment-705831465 +export AWS_EC2_METADATA_DISABLED=true + +aws s3 sync "$par_input" "$par_output" --no-sign-request "${extra_params[@]}" From 966222466895b71a821dd5a7a49bfb6af8aa0a90 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:35:09 +0200 Subject: [PATCH 0235/1233] update ci Former-commit-id: f0e41e4f3bbeddb0379f2616a4fbe1e18859a7e4 --- .github/workflows/integration-test.yml | 161 +++++++++++++++++++++++++ .github/workflows/main-build.yml | 112 +++++++++++++++++ .github/workflows/viash-build.yml | 80 ------------ .github/workflows/viash-test.yml | 68 +++++++++-- 4 files changed, 328 insertions(+), 93 deletions(-) create mode 100644 .github/workflows/integration-test.yml create mode 100644 .github/workflows/main-build.yml delete mode 100644 .github/workflows/viash-build.yml diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml new file mode 100644 index 0000000000..14afa846df --- /dev/null +++ b/.github/workflows/integration-test.yml @@ -0,0 +1,161 @@ +name: integration CI + +on: workflow_dispatch + # push: + # branches: [ '**' ] + + +jobs: + # phase 1 + list_components: + env: + s3_bucket: s3://openproblems-data/ + runs-on: ubuntu-latest + # if: "contains(github.event.head_commit.message, '#integration')" + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + # create cachehash key + - name: Create hash key + id: cachehash + run: | + AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt + echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + + # initialize cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ steps.cachehash.outputs.cachehash }} + restore-keys: resources_test_ + + # sync if need be + - name: Sync test resources + run: | + bin/viash run \ + -p native \ + src/common/sync_test_resources/config.vsh.yaml -- \ + --input $s3_bucket \ + --delete + tree resources_test/ -L 3 + + - name: Build target dir + run: | + # allow publishing the target folder + sed -i '/^target.*/d' .gitignore + + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t integration_build + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: integration_build + + # store component locations + - id: set_matrix + run: | + component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + echo "::set-output name=component_matrix::$component_json" + workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') + echo "::set-output name=workflow_matrix::$workflow_json" + outputs: + component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} + cachehash: ${{ steps.cachehash.outputs.cachehash }} + + # phase 2 + build_containers: + needs: list_components + + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + - name: Build container + run: | + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_build -m release -t integration_build -s "$SRC_DIR" + + - name: Login to container registry + uses: docker/login-action@v1 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GTHB_PAT }} + + - name: Push containers + run: | + bin/viash_push -m release -t integration_build --force + + ###################################3 + # phase 3 + integration_test: + needs: [ build_containers, list_components ] + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.workflow_matrix) }} + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + # build target dir + # use containers from integration_build branch, hopefully these are available + - name: Build target dir + run: | + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t integration_build + + # use cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ needs.list_components.outputs.cachehash }} + + - name: Run integration test + run: | + # todo: replace with viash test command + config_dir=`dirname ${{ matrix.component.config }}` + script="$config_dir/${{ matrix.component.test_script }}" + bin/nextflow run . \ + -main-script "$script" \ + -entry ${{ matrix.component.entry }} \ + -profile docker,mount_temp \ + -c workflows/utils/labels_ci.config diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml new file mode 100644 index 0000000000..4ac886e4ef --- /dev/null +++ b/.github/workflows/main-build.yml @@ -0,0 +1,112 @@ +name: main build + +on: + push: + branches: [ 'main' ] + +jobs: + # phase 1 + list_components: + env: + s3_bucket: s3://openproblems-data/ + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + # create cachehash key + - name: Create hash key + id: cachehash + run: | + AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt + echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + + # initialize cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ steps.cachehash.outputs.cachehash }} + restore-keys: resources_test_ + + # sync if need be + - name: Sync test resources + run: | + bin/viash run \ + -p native \ + src/common/sync_test_resources/config.vsh.yaml -- \ + --input $s3_bucket \ + --delete + tree resources_test/ -L 3 + + - name: Build target dir + run: | + # allow publishing the target folder + sed -i '/^target.*/d' .gitignore + + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t main_build + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: main_build + + # store component locations + - id: set_matrix + run: | + component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + echo "::set-output name=component_matrix::$component_json" + workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') + echo "::set-output name=workflow_matrix::$workflow_json" + outputs: + component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} + cachehash: ${{ steps.cachehash.outputs.cachehash }} + + # phase 2 + build_containers: + needs: list_components + + runs-on: ubuntu-latest + if: "!contains(github.event.head_commit.message, 'ci skip')" + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + + steps: + - uses: actions/checkout@v2 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + - name: Build container + run: | + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_build -m release -t main_build -s "$SRC_DIR" + + - name: Login to container registry + uses: docker/login-action@v1 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GTHB_PAT }} + + - name: Push containers + run: | + bin/viash_push -m release -t main_build --force \ No newline at end of file diff --git a/.github/workflows/viash-build.yml b/.github/workflows/viash-build.yml deleted file mode 100644 index 830e05eb5d..0000000000 --- a/.github/workflows/viash-build.yml +++ /dev/null @@ -1,80 +0,0 @@ -name: viash build CI - -on: - push: - branches: [ 'main' ] - -jobs: - # phase 1 - list_components: - runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" - - steps: - - uses: actions/checkout@v2 - - - name: Fetch viash - run: | - bin/init - bin/viash -h - - - name: Build target dir - run: | - # allow publishing the target folder - sed -i '/^target.*/d' .gitignore - - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - - # build target dir - bin/viash_build -m release -t main_build - - - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: . - publish_branch: main_build - - - id: set_matrix - run: | - echo "::set-output name=matrix::$( bin/viash ns list -p docker --format json | jq -c '[ .[] | .info.config ]' )" - - outputs: - matrix: ${{ steps.set_matrix.outputs.matrix }} - - # phase 2 - build_containers: - needs: list_components - - runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" - - strategy: - fail-fast: false - matrix: - component_path: ${{ fromJson(needs.list_components.outputs.matrix) }} - - steps: - - uses: actions/checkout@v2 - - - name: Fetch viash - run: | - bin/init - bin/viash -h - - - name: Build container - run: | - SRC_DIR=`dirname ${{ matrix.component_path }}` - bin/viash_build -m release -t main_build -s "$SRC_DIR" - - - name: Login to container registry - uses: docker/login-action@v1 - with: - registry: ghcr.io - username: ${{ github.actor }} - password: ${{ secrets.GTHB_PAT }} - - - name: Push containers - run: | - bin/viash_push -m release -t main_build --force diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 77ca158552..2cf6676ff1 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -2,33 +2,68 @@ name: viash test CI on: push: - branches: [ '*' ] - pull_request: - branches: [ '*' ] - -# Skip older CI runs for pull requests (head_ref exists), otherwise allways build -# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-a-fallback-value -concurrency: - group: ${{ github.head_ref || github.run_id }} - cancel-in-progress: true + branches: [ '**' ] jobs: + cancel: + name: 'Cancel Previous Runs' + runs-on: ubuntu-latest + timeout-minutes: 3 + if: github.ref != 'refs/heads/main' + steps: + - uses: styfle/cancel-workflow-action@0.10.0 + with: + all_but_latest: true + access_token: ${{ github.token }} + # phase 1 list_components: + env: + s3_bucket: s3://openproblems-data/ runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, 'ci skip')" steps: - uses: actions/checkout@v2 + - name: Fetch viash run: | bin/init bin/viash -h + + # create cachehash key + - name: Create hash key + id: cachehash + run: | + AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt + echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + + # initialize cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ steps.cachehash.outputs.cachehash }} + restore-keys: resources_test_ + + # sync if need be + - name: Sync test resources + run: | + bin/viash run \ + -p native \ + src/common/sync_test_resources/config.vsh.yaml -- \ + --input $s3_bucket \ + --delete + tree resources_test/ -L 3 + + # store component locations - id: set_matrix run: | - echo "::set-output name=matrix::$( bin/viash ns list -p docker --format json | jq -c '[ .[] | .info.config ]' )" + json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + echo "::set-output name=matrix::$json" outputs: - matrix: ${{ steps.set_matrix.outputs.matrix }} + matrix: ${{ steps.set_matrix.outputs.matrix }} + cachehash: ${{ steps.cachehash.outputs.cachehash }} # phase 2 viash_test: @@ -40,7 +75,7 @@ jobs: strategy: fail-fast: false matrix: - component_path: ${{ fromJson(needs.list_components.outputs.matrix) }} + component: ${{ fromJson(needs.list_components.outputs.matrix) }} steps: - uses: actions/checkout@v2 @@ -50,7 +85,14 @@ jobs: bin/init bin/viash -h + # use cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ needs.list_components.outputs.cachehash }} + - name: Run test run: | - bin/viash test -p docker ${{ matrix.component_path }} + bin/viash test -p docker ${{ matrix.component.config }} From 38280b5e5e8ea52a382f9bb8900ca473ab36819a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:36:58 +0200 Subject: [PATCH 0236/1233] switch to viash 0.5.15 Former-commit-id: 5c33071d427deb01c34313ab035d2ef3f729f863 --- bin/init | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/init b/bin/init index 5a2142094d..5cd42d8bcf 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.5.13 \ + --tag 0.5.15 \ --nextflow_variant vdsl3 cd bin From a1e5d023fe57fd0857ea22ce99079d697b15c8fe Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:46:32 +0200 Subject: [PATCH 0237/1233] move pancreas script Former-commit-id: 60587eea06e441cf1144a21d8afcc667671989b6 --- src/common/resources_test_scripts/aws_sync.sh | 6 ++++++ .../resources_test_scripts}/pancreas.sh | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 src/common/resources_test_scripts/aws_sync.sh rename src/{label_projection/workflows/generate_test_resources => common/resources_test_scripts}/pancreas.sh (96%) diff --git a/src/common/resources_test_scripts/aws_sync.sh b/src/common/resources_test_scripts/aws_sync.sh new file mode 100644 index 0000000000..f4de74a125 --- /dev/null +++ b/src/common/resources_test_scripts/aws_sync.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +echo "Run the command in this script manually" +exit 1 + +aws s3 sync "resources_test" "s3://openproblems-data" --exclude */temp_* --delete --dryrun \ No newline at end of file diff --git a/src/label_projection/workflows/generate_test_resources/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh similarity index 96% rename from src/label_projection/workflows/generate_test_resources/pancreas.sh rename to src/common/resources_test_scripts/pancreas.sh index 548d67554d..3f5a699413 100755 --- a/src/label_projection/workflows/generate_test_resources/pancreas.sh +++ b/src/common/resources_test_scripts/pancreas.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -DATASET_DIR=src/label_projection/resources/pancreas +DATASET_DIR=resources_test/label_projection/pancreas mkdir -p $DATASET_DIR From 08d41f4866ddbc456cf4e872f511f2b0721b9006 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:47:28 +0200 Subject: [PATCH 0238/1233] update resource paths in components Former-commit-id: 178aec62220b76b8e4208cd4854c0ebd2e0a1d6c --- .../control_methods/nayve_majority_vote/config.vsh.yaml | 2 +- .../control_methods/nayve_majority_vote/script.py | 2 +- .../control_methods/nayve_random_celltype/config.vsh.yaml | 2 +- .../data_processing/normalize/log_cpm/config.vsh.yaml | 2 +- .../data_processing/normalize/log_cpm/script.py | 2 +- .../data_processing/normalize/scran/config.vsh.yaml | 2 +- .../data_processing/randomize/config.vsh.yaml | 2 +- .../data_processing/subsample/config.vsh.yaml | 2 +- src/label_projection/data_processing/subsample/script.py | 2 +- src/label_projection/methods/knn_classifier/config.vsh.yaml | 4 ++-- .../methods/logistic_regression/config.vsh.yaml | 4 ++-- src/label_projection/methods/mlp/config.vsh.yaml | 4 ++-- src/label_projection/methods/mlp/script.py | 2 +- .../methods/scvi/scanvi_all_genes/config.vsh.yaml | 2 +- src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- src/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 2 +- 19 files changed, 22 insertions(+), 22 deletions(-) diff --git a/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml b/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml index 0a05d330a3..c32afe38dd 100644 --- a/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/control_methods/nayve_majority_vote/script.py b/src/label_projection/control_methods/nayve_majority_vote/script.py index 02cdb01fe7..05a8f40296 100644 --- a/src/label_projection/control_methods/nayve_majority_vote/script.py +++ b/src/label_projection/control_methods/nayve_majority_vote/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'input': '../../resources/pancreas/toy_normalized_log_cpm.h5ad', + 'input': '../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm.h5ad', 'output': 'output.mv.h5ad' } ## VIASH END diff --git a/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml b/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml index 5838843f77..6bff3bb08a 100644 --- a/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml index 063d11e94f..606c122850 100644 --- a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data_processing/normalize/log_cpm/script.py b/src/label_projection/data_processing/normalize/log_cpm/script.py index af9292b950..e272c4d027 100644 --- a/src/label_projection/data_processing/normalize/log_cpm/script.py +++ b/src/label_projection/data_processing/normalize/log_cpm/script.py @@ -1,6 +1,6 @@ ##VIASH START par = { - 'input': "../../resources/pancreas/toy_preprocessed_data.h5ad", + 'input': "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad", 'output': "output.h5ad" } ##VIASH END diff --git a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml index 97f8d59e8b..24b46e76e2 100644 --- a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: eddelbuettel/r2u:22.04 diff --git a/src/label_projection/data_processing/randomize/config.vsh.yaml b/src/label_projection/data_processing/randomize/config.vsh.yaml index 04d2d758da..8c2a6d78cc 100644 --- a/src/label_projection/data_processing/randomize/config.vsh.yaml +++ b/src/label_projection/data_processing/randomize/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/pancreas" + path: "../../../../resources_test/label_projection/pancreas" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index 88d79ddb47..23c595a9b1 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../resources/pancreas" + path: "../../../../resources_test/label_projection/pancreas" platforms: - type: native - type: docker diff --git a/src/label_projection/data_processing/subsample/script.py b/src/label_projection/data_processing/subsample/script.py index 51c3de1052..46e6c3327b 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/label_projection/data_processing/subsample/script.py @@ -1,7 +1,7 @@ import scanpy as sc ### VIASH START par = { - "input": "../../resources/pancreas/raw_data.h5ad", + "input": "../../../../resources_test/label_projection/pancreas/raw_data.h5ad", # "keep_celltype_categories": ["acinar", "beta"], # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], "even": True, diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 329651b08d..17dde8477f 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -34,8 +34,8 @@ functionality: tests: - type: python_script path: ../unit_tests/test_method.py - - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index ebfd8adac2..15eed6ef26 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -39,8 +39,8 @@ functionality: tests: - type: python_script path: ../unit_tests/test_method.py - - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 415f910bfe..50efa28613 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -44,8 +44,8 @@ functionality: tests: - type: python_script path: ../unit_tests/test_method.py - - path: ../../resources/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../resources/pancreas/toy_normalized_log_cpm_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad + - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 33438f1190..be3abe07a1 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'input': '../../resources/pancreas/toy_preprocessed_data.h5ad', + 'input': '../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad', 'output': 'output.mlplogcpm.h5ad' } ## VIASH END diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 25f9026c9e..b28b96ad05 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: - type: python_script path: ../unit_tests/test_method.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index 6ec5bda8d8..38e12510e1 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -63,7 +63,7 @@ functionality: - type: python_script path: ../unit_tests/test_method.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 18e3bffd25..2eef3d7d58 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: - type: python_script path: ../unit_tests/test_method.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index 43a5800f95..3ff61ab591 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -63,7 +63,7 @@ functionality: - type: python_script path: ../unit_tests/test_method.py - type: file - path: "../../../resources/pancreas/toy_preprocessed_data.h5ad" + path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 9bf0bd7917..151e55c940 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: tests: - type: python_script path: test_script.py - - path: "../../resources/pancreas/toy_baseline_pred_data.h5ad" + - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" platforms: - type: native - type: docker diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index fd6408f85e..920865c28e 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: tests: - type: python_script path: test_script.py - - path: "../../resources/pancreas/toy_baseline_pred_data.h5ad" + - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" platforms: - type: native - type: docker From 3e1ced2d45a778a8f32ff13257a15c2c4a9b6608 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Jul 2022 14:55:17 +0200 Subject: [PATCH 0239/1233] fix test Former-commit-id: 05172695e2912ab0a7a3dc879d194daf55a75a89 --- src/common/sync_test_resources/run_test.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/sync_test_resources/run_test.sh b/src/common/sync_test_resources/run_test.sh index ec2d137af6..1160a2c34e 100755 --- a/src/common/sync_test_resources/run_test.sh +++ b/src/common/sync_test_resources/run_test.sh @@ -5,7 +5,7 @@ echo ">> Run aws s3 sync" ./$meta_functionality_name \ - --input s3://openproblems-data/pancreas \ + --input s3://openproblems-data/label_projection/pancreas \ --output foo \ --quiet From daaa2bfdf0afac7c75b6bd91cd89656caecd472c Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 18 Jul 2022 08:07:27 -0300 Subject: [PATCH 0240/1233] fix: dataset_concatenate test Former-commit-id: a5b3ace2a0b6983c98e1d10e6555f6976ef3eb34 --- src/common/dataset_concatenate/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index 4bf4ad6e31..645d221cb4 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../label_projection/resources/pancreas" + path: "../../../resources_test/label_projection/resources/pancreas" platforms: - type: docker image: "python:3.8" From 8ba20d6903562530055fe1f3061a1a8faa08bf71 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 18 Jul 2022 08:39:56 -0300 Subject: [PATCH 0241/1233] fix: test Former-commit-id: af134ff6cd66b3c5220cc8d034dcde8388069db6 --- src/common/dataset_concatenate/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index 645d221cb4..d6dbd6a7a3 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources_test/label_projection/resources/pancreas" + path: "../../../resources_test/label_projection/pancreas" platforms: - type: docker image: "python:3.8" From 948716e55ed4aac2ef4460a8d8282725ecf7cf53 Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Mon, 8 Aug 2022 19:33:44 -0300 Subject: [PATCH 0242/1233] fix: correct control method labels Former-commit-id: efa83a3821b3f3fd6b7777635713481153e63c9c --- .../config.vsh.yaml | 4 +- .../control_methods/all_correct/script.py | 20 +++++++++ .../all_correct/test_script.py | 23 ++++++++++ .../majority_vote/config.vsh.yaml | 45 +++++++++++++++++++ .../script.py | 0 .../test_script.py | 0 .../config.vsh.yaml | 6 +-- .../script.py | 0 .../test_script.py | 0 .../methods/knn_classifier/config.vsh.yaml | 2 +- .../logistic_regression/config.vsh.yaml | 2 +- .../methods/mlp/config.vsh.yaml | 2 +- .../scvi/scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- src/label_projection/workflows/run/main.nf | 6 +-- 17 files changed, 103 insertions(+), 15 deletions(-) rename src/label_projection/control_methods/{nayve_majority_vote => all_correct}/config.vsh.yaml (95%) create mode 100644 src/label_projection/control_methods/all_correct/script.py create mode 100644 src/label_projection/control_methods/all_correct/test_script.py create mode 100644 src/label_projection/control_methods/majority_vote/config.vsh.yaml rename src/label_projection/control_methods/{nayve_majority_vote => majority_vote}/script.py (100%) rename src/label_projection/control_methods/{nayve_majority_vote => majority_vote}/test_script.py (100%) rename src/label_projection/control_methods/{nayve_random_celltype => random_celltype}/config.vsh.yaml (93%) rename src/label_projection/control_methods/{nayve_random_celltype => random_celltype}/script.py (100%) rename src/label_projection/control_methods/{nayve_random_celltype => random_celltype}/test_script.py (100%) diff --git a/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml b/src/label_projection/control_methods/all_correct/config.vsh.yaml similarity index 95% rename from src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml rename to src/label_projection/control_methods/all_correct/config.vsh.yaml index c32afe38dd..751b6ce77f 100644 --- a/src/label_projection/control_methods/nayve_majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/all_correct/config.vsh.yaml @@ -1,10 +1,10 @@ functionality: - name: "nayve_majority_vote" + name: "majority_vote" namespace: "label_projection/control_methods" version: "dev" description: "Majority vote dummy" info: - type: nayve_control + type: negative_control label: Random prediction authors: - name: "Scott Gigante" diff --git a/src/label_projection/control_methods/all_correct/script.py b/src/label_projection/control_methods/all_correct/script.py new file mode 100644 index 0000000000..ce2b1178e5 --- /dev/null +++ b/src/label_projection/control_methods/all_correct/script.py @@ -0,0 +1,20 @@ +## VIASH START +par = { + 'input': '../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad', + 'output': 'output.mv.h5ad' +} +## VIASH END +import numpy as np +import scanpy as sc + + +print("Load data") +adata = sc.read(par['input']) + +print("Add celltype prediction") +adata.obs["celltype_pred"] = adata.obs.celltype + + +print("Write output to file") +adata.uns["method_id"] = meta["functionality_name"] +adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/all_correct/test_script.py b/src/label_projection/control_methods/all_correct/test_script.py new file mode 100644 index 0000000000..ae82a8b75b --- /dev/null +++ b/src/label_projection/control_methods/all_correct/test_script.py @@ -0,0 +1,23 @@ +import subprocess +import scanpy as sc +from os import path + + +INPUT = "toy_preprocessed_data.h5ad" +OUTPUT = "output.mv.h5ad" + +print(">> Running script as test") +out = subprocess.check_output([ + "./" + meta["functionality_name"], + "--input", INPUT, + "--output", OUTPUT +]).decode("utf-8") + +print(">> Checking if output file exists") +assert path.exists(OUTPUT) + +print(">> Checking if predictions were added") +adata = sc.read_h5ad(OUTPUT) +assert "celltype_pred" in adata.obs +assert (adata.obs.celltype_pred == adata.obs.celltype).all() +assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml new file mode 100644 index 0000000000..751b6ce77f --- /dev/null +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -0,0 +1,45 @@ +functionality: + name: "majority_vote" + namespace: "label_projection/control_methods" + version: "dev" + description: "Majority vote dummy" + info: + type: negative_control + label: Random prediction + authors: + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: "Vinicius Chagas" + roles: [ maintainer ] + props: { github: chagasVinicius } + arguments: + - name: "--input" + type: "file" + description: "Input data to predict" + required: true + - name: "--output" + alternatives: ["-o"] + type: "file" + description: "Ouput data containing predictions" + direction: "output" + example: "output.mv.h5ad" + required: true + resources: + - type: python_script + path: script.py + tests: + - type: python_script + path: test_script.py + - type: file + path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" +platforms: + - type: native + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/control_methods/nayve_majority_vote/script.py b/src/label_projection/control_methods/majority_vote/script.py similarity index 100% rename from src/label_projection/control_methods/nayve_majority_vote/script.py rename to src/label_projection/control_methods/majority_vote/script.py diff --git a/src/label_projection/control_methods/nayve_majority_vote/test_script.py b/src/label_projection/control_methods/majority_vote/test_script.py similarity index 100% rename from src/label_projection/control_methods/nayve_majority_vote/test_script.py rename to src/label_projection/control_methods/majority_vote/test_script.py diff --git a/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml b/src/label_projection/control_methods/random_celltype/config.vsh.yaml similarity index 93% rename from src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml rename to src/label_projection/control_methods/random_celltype/config.vsh.yaml index 6bff3bb08a..3430fd5d2e 100644 --- a/src/label_projection/control_methods/nayve_random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/random_celltype/config.vsh.yaml @@ -1,10 +1,10 @@ functionality: - name: "nayve_random_celltype" + name: "random_celltype" namespace: "label_projection/control_methods" - version: "dev" + versionn: "dev" description: "Random Labels dummy" info: - type: nayve_control + type: negative_control label: Random prediction authors: - name: "Scott Gigante" diff --git a/src/label_projection/control_methods/nayve_random_celltype/script.py b/src/label_projection/control_methods/random_celltype/script.py similarity index 100% rename from src/label_projection/control_methods/nayve_random_celltype/script.py rename to src/label_projection/control_methods/random_celltype/script.py diff --git a/src/label_projection/control_methods/nayve_random_celltype/test_script.py b/src/label_projection/control_methods/random_celltype/test_script.py similarity index 100% rename from src/label_projection/control_methods/nayve_random_celltype/test_script.py rename to src/label_projection/control_methods/random_celltype/test_script.py diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 17dde8477f..9b22dc2bd2 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Nearest neighbor pattern classification" info: - type: baseline + type: method label: KNN authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 15eed6ef26..a32883ce50 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Applied Logistic Regression" info: - type: baseline + type: method label: Logistic Regression authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 50efa28613..0a2b56a0d0 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Multilayer perceptron" info: - type: baseline + type: method label: Multilayer perceptron authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index b28b96ad05..dbd568d0a4 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." info: - type: baseline + type: method label: Scanvi_ALL_GENES authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index 38e12510e1..5c8a618825 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." info: - type: baseline + type: method label: Scanvi_HVG authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 2eef3d7d58..e4259ffa53 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Probabilistic harmonization and annotation of single-cell" info: - type: baseline + type: method label: Scarches_scanvi_ALL_GENES authors: - name: "Scott Gigante" diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index 3ff61ab591..027a6e28a5 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: version: "dev" description: "Probabilistic harmonization and annotation of single-cell" info: - type: baseline + type: method label: Scarches_scanvi_HVG authors: - name: "Scott Gigante" diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index f251bfe106..cbaabc3896 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -15,8 +15,8 @@ include { log_scran_pooling } from "$targetDir/label_projection/data_processing/ include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" // import methods -include { nayve_majority_vote } from "$targetDir/label_projection/control_methods/nayve_majority_vote/main.nf" -include { nayve_random_celltype } from "$targetDir/label_projection/control_methods/nayve_random_celltype/main.nf" +include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" +include { random_celltype } from "$targetDir/label_projection/control_methods/random_celltype/main.nf" include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" @@ -105,7 +105,7 @@ workflow { | (log_cpm & log_scran_pooling) | mix | map { unique_file_name(it) } - | (knn_classifier & mlp0 & lr0 & nayve_random_celltype & nayve_majority_vote) + | (knn_classifier & mlp0 & lr0 & random_celltype & majority_vote) | mix | map { unique_file_name(it) } | (accuracy & f1a) From 2bba6065bf2a9bb249e126e7650692d88dc71820 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 9 Aug 2022 11:48:28 +0200 Subject: [PATCH 0243/1233] fix dataset_loader Former-commit-id: 112f8b84d33ddd806b1086fd320869526dcbd2b8 --- src/common/dataset_loader/download/config.vsh.yaml | 4 ---- src/common/dataset_loader/download/run_example.sh | 8 +++++--- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 5ab73be5ac..6d9e737d6c 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -23,10 +23,6 @@ functionality: type: "string" example: "pbmc" description: "Name of dataset" - - name: "--lognorm_available" - type: "string" - description: "Location of lognorm counts if exists, else empty" - required: true - name: "--obs_celltype" type: "string" description: "Location of where to find the observation cell types." diff --git a/src/common/dataset_loader/download/run_example.sh b/src/common/dataset_loader/download/run_example.sh index b97738a331..6130cb3925 100644 --- a/src/common/dataset_loader/download/run_example.sh +++ b/src/common/dataset_loader/download/run_example.sh @@ -1,4 +1,6 @@ -bin/viash run src/common/data_loader/config.vsh.yaml -- \ - --output src/common/data_loader/resources/pancreas.h5ad \ +bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ + --output src/common/dataset_loader/download/resources/pancreas.h5ad \ --url https://ndownloader.figshare.com/files/24539828 \ - --name pancreas --lognorm_available adata.X \ No newline at end of file + --name pancreas \ + --obs_cell_type celltype \ + --obs_batch tech From 7deb383285d26afd35dae9daa06f719c10db056c Mon Sep 17 00:00:00 2001 From: Vinicius Saraiva Date: Tue, 9 Aug 2022 09:37:03 -0300 Subject: [PATCH 0244/1233] fix: minor changes and add new control to nextflow workflow Former-commit-id: b911ae28b3c46522f1d940c6f4f78729da7426a3 --- .../control_methods/all_correct/config.vsh.yaml | 8 ++++---- .../control_methods/random_celltype/config.vsh.yaml | 2 +- src/label_projection/workflows/run/main.nf | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/src/label_projection/control_methods/all_correct/config.vsh.yaml b/src/label_projection/control_methods/all_correct/config.vsh.yaml index 751b6ce77f..c5cf7ecf0e 100644 --- a/src/label_projection/control_methods/all_correct/config.vsh.yaml +++ b/src/label_projection/control_methods/all_correct/config.vsh.yaml @@ -1,11 +1,11 @@ functionality: - name: "majority_vote" + name: "all_correct" namespace: "label_projection/control_methods" version: "dev" - description: "Majority vote dummy" + description: "Positive control method" info: - type: negative_control - label: Random prediction + type: positive_control + label: All predictions are correct authors: - name: "Scott Gigante" roles: [ author ] diff --git a/src/label_projection/control_methods/random_celltype/config.vsh.yaml b/src/label_projection/control_methods/random_celltype/config.vsh.yaml index 3430fd5d2e..cc5e44bcba 100644 --- a/src/label_projection/control_methods/random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/random_celltype/config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "random_celltype" namespace: "label_projection/control_methods" - versionn: "dev" + version: "dev" description: "Random Labels dummy" info: type: negative_control diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index cbaabc3896..c73d97b1ef 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -15,6 +15,7 @@ include { log_scran_pooling } from "$targetDir/label_projection/data_processing/ include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" // import methods +include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" include { random_celltype } from "$targetDir/label_projection/control_methods/random_celltype/main.nf" include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" @@ -105,7 +106,7 @@ workflow { | (log_cpm & log_scran_pooling) | mix | map { unique_file_name(it) } - | (knn_classifier & mlp0 & lr0 & random_celltype & majority_vote) + | (knn_classifier & mlp0 & lr0 & random_celltype & majority_vote & all_correct) | mix | map { unique_file_name(it) } | (accuracy & f1a) From eb9635ec6db7fa183a28478a73bfc2d4ed50a63d Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 9 Aug 2022 14:37:13 +0200 Subject: [PATCH 0245/1233] fix pancreas data processing Former-commit-id: da43aa758f06bd912f45b5762ee6e0756f6fa3c9 --- src/batch_integration/datasets/pancreas/run_example.sh | 2 +- src/batch_integration/datasets/pancreas/script.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/batch_integration/datasets/pancreas/run_example.sh b/src/batch_integration/datasets/pancreas/run_example.sh index 564fb73cda..d56acb3061 100644 --- a/src/batch_integration/datasets/pancreas/run_example.sh +++ b/src/batch_integration/datasets/pancreas/run_example.sh @@ -8,5 +8,5 @@ bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ --label celltype \ --batch tech \ --hvgs 100 \ - --output src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --output src/batch_integration/resources/datasets_pancreas.h5ad \ --debug true diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index a4fa73eb25..bc815eb6bb 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -34,7 +34,8 @@ adata = sc.read(adata_file) # Rename columns -adata.obs.rename(columns={label: 'label', batch: 'batch'}, inplace=True) +adata.obs['label'] = adata.obs[label] +adata.obs['batch'] = adata.obs[batch] adata.layers['counts'] = adata.X.copy() print('Normalise and log-transform data') From b4df618da879544f9f42ce363d3a91ed77437e88 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 9 Aug 2022 14:38:20 +0200 Subject: [PATCH 0246/1233] create module for test data subsetting Former-commit-id: fced66739a21eff39cbfb0658e65b7d2faf50f2e --- .../datasets/subsample/config.vsh.yaml | 47 +++++++++++++++++ .../datasets/subsample/run_example.sh | 11 ++++ .../datasets/subsample/script.py | 52 +++++++++++++++++++ .../resources/subset_data.py | 33 ------------ 4 files changed, 110 insertions(+), 33 deletions(-) create mode 100644 src/batch_integration/datasets/subsample/config.vsh.yaml create mode 100644 src/batch_integration/datasets/subsample/run_example.sh create mode 100644 src/batch_integration/datasets/subsample/script.py delete mode 100644 src/batch_integration/resources/subset_data.py diff --git a/src/batch_integration/datasets/subsample/config.vsh.yaml b/src/batch_integration/datasets/subsample/config.vsh.yaml new file mode 100644 index 0000000000..9f6c68229d --- /dev/null +++ b/src/batch_integration/datasets/subsample/config.vsh.yaml @@ -0,0 +1,47 @@ +functionality: + name: subsample + namespace: batch_integration/subsample + version: dev + description: Subset adata object for testing + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output h5ad file of the cleaned dataset + required: true + - name: --adata + type: file + description: Anndata HDF5 file + required: true + - name: --label + type: string + description: Cell annotation label in adata.obs + required: true + - name: --batch + type: string + description: Batch assignment in adata.obs + required: true + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false + resources: + - type: python_script + path: script.py + - path: "../../resources/g2m_genes_tirosh_hm.txt" + - path: "../../resources/s_genes_tirosh_hm.txt" + tests: + - type: python_script + path: test.py + - path: '../../../common/dataset_loader/download/resources/pancreas.h5ad' +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + - type: native + - type: nextflow diff --git a/src/batch_integration/datasets/subsample/run_example.sh b/src/batch_integration/datasets/subsample/run_example.sh new file mode 100644 index 0000000000..a2e9963121 --- /dev/null +++ b/src/batch_integration/datasets/subsample/run_example.sh @@ -0,0 +1,11 @@ +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --adata src/common/dataset_loader/download/resources/pancreas.h5ad \ + --label celltype \ + --batch tech \ + --output src/batch_integration/resources/data_loader_pancreas.h5ad \ + --debug true diff --git a/src/batch_integration/datasets/subsample/script.py b/src/batch_integration/datasets/subsample/script.py new file mode 100644 index 0000000000..8d2bb3550b --- /dev/null +++ b/src/batch_integration/datasets/subsample/script.py @@ -0,0 +1,52 @@ +""" +This script subsets a downloaded dataset for testing all the batch integration modules +""" +## VIASH START +par = { + 'adata': 'src/common/dataset_loader/download/resources/pancreas.h5ad', + 'label': 'celltype', + 'batch': 'tech', + 'output': 'src/batch_integration/resources/data_loader_pancreas.h5ad', + 'debug': True +} +resources_dir = './src/batch_integration/datasets' +## VIASH END + +print('Importing libraries') +import scanpy as sc +from pprint import pprint + +if par['debug']: + pprint(par) + +adata_file = par['adata'] +label = par['label'] +batch = par['batch'] +output = par['output'] +g2m_file = f'{resources_dir}g2m_genes_tirosh_hm.txt' +s_file = f'{resources_dir}s_genes_tirosh_hm.txt' + +print('Read adata') +adata = sc.read(adata_file) + +print('Get batch and label subsets') +head_batches = adata.obs[batch].unique().tolist()[0:3] +head_labels = adata.obs[label].unique().tolist()[0:2] + +print('Get features subsets') +g2m_genes = [x.strip() for x in open(g2m_file).readlines()] +s_genes = [x.strip() for x in open(s_file).readlines()] + +all_genes = adata.var.index.tolist() +cc_genes = [x for x in g2m_genes + s_genes if x in all_genes] +head_genes = list(set(cc_genes + all_genes[:100])) + +print('Subset adata') +adata = adata[adata.obs[batch].isin(head_batches)] +adata = adata[adata.obs[label].isin(head_labels)] +adata = adata[:, head_genes] +sc.pp.subsample(adata, 0.3, random_state=42) + +print(adata) + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/resources/subset_data.py b/src/batch_integration/resources/subset_data.py deleted file mode 100644 index aed18063d9..0000000000 --- a/src/batch_integration/resources/subset_data.py +++ /dev/null @@ -1,33 +0,0 @@ -import scanpy as sc - -adata_file = 'src/common/data_loader/resources/pancreas.h5ad' -adata_out_file = 'src/batch_integration/resources/data_loader_pancreas.h5ad' -batch = 'tech' -label = 'celltype' - -adata = sc.read(adata_file) -print(adata) - -# observation subset -head_batches = adata.obs[batch].unique().tolist()[0:3] -head_labels = adata.obs[label].unique().tolist()[0:2] - -# feature subset -g2m_file = 'src/batch_integration/resources/g2m_genes_tirosh_hm.txt' -s_file = 'src/batch_integration/resources/s_genes_tirosh_hm.txt' -g2m_genes = [x.strip() for x in open(g2m_file).readlines()] -s_genes = [x.strip() for x in open(s_file).readlines()] - -all_genes = adata.var.index.tolist() -cc_genes = [x for x in g2m_genes + s_genes if x in all_genes] -head_genes = list(set(cc_genes + all_genes[:100])) - -# subset adata -adata = adata[adata.obs[batch].isin(head_batches)] -adata = adata[adata.obs[label].isin(head_labels)] -adata = adata[:, head_genes] -sc.pp.subsample(adata, 0.3, random_state=42) - -print(adata) - -adata.write(adata_out_file, compression='gzip') From b614864489f0f6c52ca231d7e77a0edee9846c70 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 22 Aug 2022 05:04:30 +0200 Subject: [PATCH 0247/1233] change license to MIT Former-commit-id: 2770b1bfb69869660836b0a69bee7723b48c676e --- LICENSE | 695 ++------------------------------------------------------ 1 file changed, 21 insertions(+), 674 deletions(-) diff --git a/LICENSE b/LICENSE index 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From 1664241f58934131de72190e86d619de94117ac9 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Sep 2022 13:59:42 +0200 Subject: [PATCH 0248/1233] add nexflow workflow for data subset Former-commit-id: 7a1f90474934b2466e4dfcb972e20d22b087d956 --- src/batch_integration/workflows/test/main.nf | 102 ++++++++++++++++++ .../workflows/test/nextflow.config | 16 +++ .../workflows/test/run_nextflow.sh | 21 ++++ 3 files changed, 139 insertions(+) create mode 100644 src/batch_integration/workflows/test/main.nf create mode 100644 src/batch_integration/workflows/test/nextflow.config create mode 100755 src/batch_integration/workflows/test/run_nextflow.sh diff --git a/src/batch_integration/workflows/test/main.nf b/src/batch_integration/workflows/test/main.nf new file mode 100644 index 0000000000..636218ebb7 --- /dev/null +++ b/src/batch_integration/workflows/test/main.nf @@ -0,0 +1,102 @@ +nextflow.enable.dsl=2 + +targetDir = "${params.rootDir}/target/nextflow" +params.tsv = "$launchDir/src/batch_integration/datasets/params.tsv" + +// import dataset loaders +include { download } from "$targetDir/common/dataset_loader/download/main.nf" params(params) +include { subsample } from "$targetDir/batch_integration/datasets/subsample/main.nf" params(params) +include { preprocessing } from "$targetDir/batch_integration/datasets/preprocessing/main.nf" params(params) + +// import methods +include { bbknn } from "$targetDir/batch_integration/graph/methods/bbknn/main.nf" params(params) +include { combat } from "$targetDir/batch_integration/graph/methods/combat/main.nf" params(params) +include { scanorama_embed } from "$targetDir/batch_integration/graph/methods/scanorama_embed/main.nf" params(params) +include { scanorama_feature } from "$targetDir/batch_integration/graph/methods/scanorama_feature/main.nf" params(params) +include { scvi } from "$targetDir/batch_integration/graph/methods/scvi/main.nf" params(params) + +// import metrics +include { ari } from "$targetDir/batch_integration/graph/metrics/ari/main.nf" params(params) +include { nmi } from "$targetDir/batch_integration/graph/metrics/nmi/main.nf" params(params) + +/******************************************************* +* Dataset processor workflows * +*******************************************************/ +// This workflow reads in a tsv containing some metadata about each dataset. +// For each entry in the metadata, a dataset is generated, usually by downloading +// and processing some files. The end result of each of these workflows +// should be simply a channel of [id, h5adfile, params] triplets. +// +// If the need arises, these workflows could be split off into a separate file. + + +workflow load_data { + main: + output_ = Channel.fromPath(params.tsv) + | splitCsv(header: true, sep: "\t") + | map { row -> + [ + row.name, + [ + "url": row.url, + "name": row.name, + "obs_cell_type": row.label, + "obs_batch": row.batch, + ] + ] + } + | download + emit: + output_ +} + +workflow process_data { + +take: + channel_in + main: + additional_params = Channel.fromPath(params.tsv) + | splitCsv(header: true, sep: "\t") + | map { [ it.name, it ] } + + subset = channel_in.join(additional_params) + | map { id, data, additional -> + [ id, [ input: data ] + additional ] + } + | subsample + + output_ = subset.join(additional_params) + | map { id, data, additional -> + [ id, [ input: data ] + additional ] + } + | preprocessing + | join(additional_params) + | map { id, data, additional -> + [ id, [ input: data ] + additional + [hvg: additional.hvgs.toInteger() > 0] ] + } + + emit: + output_ +} + +/******************************************************* +* Main workflow * +*******************************************************/ + +workflow { + load_data + | process_data + | view{ "process_data: $it" } +/** +| (bbknn & combat & scvi & scanorama_embed & scanorama_feature) +| mix +| toSortedList + | view + | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + | (ari & nmi) + | extract_scores.run( + auto: [ publish: true ] + ) +*/ + +} diff --git a/src/batch_integration/workflows/test/nextflow.config b/src/batch_integration/workflows/test/nextflow.config new file mode 100644 index 0000000000..3df04f176a --- /dev/null +++ b/src/batch_integration/workflows/test/nextflow.config @@ -0,0 +1,16 @@ +manifest { + nextflowVersion = '!>=20.12.1-edge' +} + +// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// set default container & default labels +process { + container = 'nextflow/bash:latest' + + withLabel: highmem { memory = 10.Gb } + withLabel: highcpu { cpus = 5 } +} diff --git a/src/batch_integration/workflows/test/run_nextflow.sh b/src/batch_integration/workflows/test/run_nextflow.sh new file mode 100755 index 0000000000..04c18910e1 --- /dev/null +++ b/src/batch_integration/workflows/test/run_nextflow.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'modality_alignment|utils' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +# choose a particular version of nextflow +export NXF_VER=21.10.6 + +bin/nextflow \ + run . \ + -main-script src/batch_integration/workflows/run/main.nf \ + --publishDir output/batch_integration \ + -resume \ + -with-docker + From 33c04d005cb1121741704da4c63e5fbc45fbec88 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Thu, 15 Sep 2022 14:02:44 +0200 Subject: [PATCH 0249/1233] fix data processing for pipeline Former-commit-id: da863b2c6678477dda5e451097fdee88bd09c661 --- src/batch_integration/datasets/params.tsv | 5 ++-- .../config.vsh.yaml | 6 ++--- .../run_example.sh | 2 +- .../{pancreas => preprocessing}/script.py | 7 ++--- .../{pancreas => preprocessing}/test.py | 8 +++--- .../datasets/subsample/config.vsh.yaml | 6 ++--- .../datasets/subsample/script.py | 13 ++++++--- .../datasets/subsample/test.py | 27 +++++++++++++++++++ .../dataset_loader/download/config.vsh.yaml | 2 +- 9 files changed, 54 insertions(+), 22 deletions(-) rename src/batch_integration/datasets/{pancreas => preprocessing}/config.vsh.yaml (95%) rename src/batch_integration/datasets/{pancreas => preprocessing}/run_example.sh (80%) rename src/batch_integration/datasets/{pancreas => preprocessing}/script.py (90%) rename src/batch_integration/datasets/{pancreas => preprocessing}/test.py (91%) create mode 100644 src/batch_integration/datasets/subsample/test.py diff --git a/src/batch_integration/datasets/params.tsv b/src/batch_integration/datasets/params.tsv index 37251ea0bf..a2b0b41997 100644 --- a/src/batch_integration/datasets/params.tsv +++ b/src/batch_integration/datasets/params.tsv @@ -1,3 +1,2 @@ -name label batch hvgs -pancreas celltype tech 2000 -immune_cells final_annotation batch 2000 +name label batch hvgs url +pancreas celltype tech 2000 https://ndownloader.figshare.com/files/24539828 diff --git a/src/batch_integration/datasets/pancreas/config.vsh.yaml b/src/batch_integration/datasets/preprocessing/config.vsh.yaml similarity index 95% rename from src/batch_integration/datasets/pancreas/config.vsh.yaml rename to src/batch_integration/datasets/preprocessing/config.vsh.yaml index 5c5a490b5b..1b0075a36f 100644 --- a/src/batch_integration/datasets/pancreas/config.vsh.yaml +++ b/src/batch_integration/datasets/preprocessing/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: pancreas + name: preprocessing namespace: batch_integration/datasets version: dev description: Preprocess adata object for data integration @@ -14,7 +14,7 @@ functionality: direction: output description: Output h5ad file of the cleaned dataset required: true - - name: --adata + - name: --input type: file description: Anndata HDF5 file required: true @@ -40,7 +40,7 @@ functionality: - type: python_script path: script.py - path: "../utils/_hvg_batch.py" - tests: + test_resources: - type: python_script path: test.py - path: '../../resources/data_loader_pancreas.h5ad' diff --git a/src/batch_integration/datasets/pancreas/run_example.sh b/src/batch_integration/datasets/preprocessing/run_example.sh similarity index 80% rename from src/batch_integration/datasets/pancreas/run_example.sh rename to src/batch_integration/datasets/preprocessing/run_example.sh index d56acb3061..bd12c9796c 100644 --- a/src/batch_integration/datasets/pancreas/run_example.sh +++ b/src/batch_integration/datasets/preprocessing/run_example.sh @@ -4,7 +4,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/resources/data_loader_pancreas.h5ad \ + --input src/batch_integration/resources/data_loader_pancreas.h5ad \ --label celltype \ --batch tech \ --hvgs 100 \ diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/preprocessing/script.py similarity index 90% rename from src/batch_integration/datasets/pancreas/script.py rename to src/batch_integration/datasets/preprocessing/script.py index bc815eb6bb..cf9449907e 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/preprocessing/script.py @@ -3,7 +3,7 @@ print(os.getcwd()) par = { - 'adata': './src/batch_integration/datasets/resources/data_loader_pancreas.h5ad', + 'input': './src/batch_integration/datasets/resources/data_loader_pancreas.h5ad', 'label': 'celltype', 'batch': 'tech', 'hvgs': 2000, @@ -24,16 +24,17 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] label = par['label'] batch = par['batch'] hvgs = par['hvgs'] output = par['output'] print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) # Rename columns +print('Rename columns') adata.obs['label'] = adata.obs[label] adata.obs['batch'] = adata.obs[batch] adata.layers['counts'] = adata.X.copy() diff --git a/src/batch_integration/datasets/pancreas/test.py b/src/batch_integration/datasets/preprocessing/test.py similarity index 91% rename from src/batch_integration/datasets/pancreas/test.py rename to src/batch_integration/datasets/preprocessing/test.py index 86878f929c..2e44618005 100644 --- a/src/batch_integration/datasets/pancreas/test.py +++ b/src/batch_integration/datasets/preprocessing/test.py @@ -3,15 +3,15 @@ import scanpy as sc import numpy as np -name = 'pancreas' +name = 'preprocessing' anndata_in = 'data_loader_pancreas.h5ad' anndata_out = 'datasets_pancreas.h5ad' print('>> Running script') n_hvgs = 100 out = subprocess.check_output([ - './pancreas', - '--adata', anndata_in, + './preprocessing', + '--input', anndata_in, '--label', 'celltype', '--batch', 'tech', '--hvgs', str(n_hvgs), @@ -23,7 +23,7 @@ print('>> Check that output fits expected API') adata = sc.read_h5ad(anndata_out) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/datasets/subsample/config.vsh.yaml b/src/batch_integration/datasets/subsample/config.vsh.yaml index 9f6c68229d..c4be1a57b8 100644 --- a/src/batch_integration/datasets/subsample/config.vsh.yaml +++ b/src/batch_integration/datasets/subsample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: subsample - namespace: batch_integration/subsample + namespace: batch_integration/datasets version: dev description: Subset adata object for testing authors: @@ -14,7 +14,7 @@ functionality: direction: output description: Output h5ad file of the cleaned dataset required: true - - name: --adata + - name: --input type: file description: Anndata HDF5 file required: true @@ -36,7 +36,7 @@ functionality: path: script.py - path: "../../resources/g2m_genes_tirosh_hm.txt" - path: "../../resources/s_genes_tirosh_hm.txt" - tests: + test_resources: - type: python_script path: test.py - path: '../../../common/dataset_loader/download/resources/pancreas.h5ad' diff --git a/src/batch_integration/datasets/subsample/script.py b/src/batch_integration/datasets/subsample/script.py index 8d2bb3550b..a12c3513d1 100644 --- a/src/batch_integration/datasets/subsample/script.py +++ b/src/batch_integration/datasets/subsample/script.py @@ -19,15 +19,20 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] label = par['label'] batch = par['batch'] output = par['output'] -g2m_file = f'{resources_dir}g2m_genes_tirosh_hm.txt' -s_file = f'{resources_dir}s_genes_tirosh_hm.txt' +g2m_file = f'{resources_dir}/g2m_genes_tirosh_hm.txt' +s_file = f'{resources_dir}/s_genes_tirosh_hm.txt' + +print(g2m_file) +import os +print(os.getcwd()) +print(os.listdir()) print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) print('Get batch and label subsets') head_batches = adata.obs[batch].unique().tolist()[0:3] diff --git a/src/batch_integration/datasets/subsample/test.py b/src/batch_integration/datasets/subsample/test.py new file mode 100644 index 0000000000..a61093382c --- /dev/null +++ b/src/batch_integration/datasets/subsample/test.py @@ -0,0 +1,27 @@ +from os import path +import subprocess +import scanpy as sc +import numpy as np + +name = 'subsample' +anndata_in = 'pancreas.h5ad' +anndata_out = 'pancreas_sub.h5ad' + +print('>> Running script') +n_hvgs = 100 +out = subprocess.check_output([ + './subsample', + '--input', anndata_in, + '--label', 'celltype', + '--batch', 'tech', + '--output', anndata_out +]).decode('utf-8') + +print('>> Checking whether file exists') +assert path.exists(anndata_out) + +print('>> Check that output fits expected API') +adata = sc.read_h5ad(anndata_out) +assert 'dataset_id' in adata.uns + +print('>> All tests passed successfully') diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 6d9e737d6c..a0f9410c8e 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py platforms: From cdacc44b07ee5e04e3b5a6153072cb99055c3d50 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 17 Oct 2022 16:39:38 +0200 Subject: [PATCH 0250/1233] port readme, use qmd to generate the readme Former-commit-id: 710ec7f9c2d30a8f9edd6342399bc6d405253f87 --- src/label_projection/README.md | 63 +++++++++++++++++++++++++++++++++ src/label_projection/README.qmd | 39 ++++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 src/label_projection/README.md create mode 100644 src/label_projection/README.qmd diff --git a/src/label_projection/README.md b/src/label_projection/README.md new file mode 100644 index 0000000000..f04c5fb0ac --- /dev/null +++ b/src/label_projection/README.md @@ -0,0 +1,63 @@ + +# Label Projection + +## The task + +A major challenge for integrating single cell datasets is creating +matching cell type annotations for each cell. One of the most common +strategies for annotating cell types is referred to as +[“cluster-then-annotate”](https://www.nature.com/articles/s41576-018-0088-9) +whereby cells are aggregated into clusters based on feature similarity +and then manually characterized based on differential gene expression or +previously identified marker genes. Recently, methods have emerged to +build on this strategy and annotate cells using [known marker +genes](https://www.nature.com/articles/s41592-019-0535-3). However, +these strategies pose a difficulty for integrating atlas-scale datasets +as the particular annotations may not match. + +To ensure that the cell type labels in newly generated datasets match +existing reference datasets, some methods align cells to a previously +annotated [reference +dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) +and then *project* labels from the reference to the new dataset. + +Here, we compare methods for annotation based on a reference dataset. +The datasets consist of two or more samples of single cell profiles that +have been manually annotated with matching labels. These datasets are +then split into training and test batches, and the task of each method +is to train a cell type classifer on the training set and project those +labels onto the test set. + +## The metrics + +Metrics for label projection aim to characterize how well each classifer +correctly assigns cell type labels to cells in the test set. + +- **Accuracy**: Average number of correctly applied labels. +- **F1 score**: The [F1 + score](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html) + is a weighted average of the precision and recall over all class + labels, where an F1 score reaches its best value at 1 and worst score + at 0, where each class contributes to the score relative to its + frequency in the dataset. +- **Macro F1 score**: The macro F1 score is an unweighted F1 score, + where each class contributes equally, regardless of its frequency. + +## API + +Datasets should contain the following attributes: + +- `adata.obs["labels"]` with ground truth celltype labels, +- `adata.obs["batch"]` with information of batches in the data, and +- `adata.obs["is_train"]` with a train vs. test split + +It should be noted that datasets may only contain a single batch, or not +contain discriminative batch information. + +Methods should assign output celltype labels to +`adata.obs['labels_pred']` using only the labels from the training data. + +Note that the true labels are contained in `adata['labels']`. + +Metrics can compare `adata['labels']` to `adata.obs['labels_pred']` +using only the labels from the test data. diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd new file mode 100644 index 0000000000..3e536bc7c1 --- /dev/null +++ b/src/label_projection/README.qmd @@ -0,0 +1,39 @@ +--- +format: gfm +info: + migration_date: "2022-10-17 12:49:00 GMT" +--- + +# Label Projection + +## The task + +A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) whereby cells are aggregated into clusters based on feature similarity and then manually characterized based on differential gene expression or previously identified marker genes. Recently, methods have emerged to build on this strategy and annotate cells using [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. + +To ensure that the cell type labels in newly generated datasets match existing reference datasets, some methods align cells to a previously annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) and then _project_ labels from the reference to the new dataset. + +Here, we compare methods for annotation based on a reference dataset. The datasets consist of two or more samples of single cell profiles that have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. + +## The metrics + +Metrics for label projection aim to characterize how well each classifer correctly assigns cell type labels to cells in the test set. + +* **Accuracy**: Average number of correctly applied labels. +* **F1 score**: The [F1 score](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html) is a weighted average of the precision and recall over all class labels, where an F1 score reaches its best value at 1 and worst score at 0, where each class contributes to the score relative to its frequency in the dataset. +* **Macro F1 score**: The macro F1 score is an unweighted F1 score, where each class contributes equally, regardless of its frequency. + +## API + +Datasets should contain the following attributes: + +* `adata.obs["labels"]` with ground truth celltype labels, +* `adata.obs["batch"]` with information of batches in the data, and +* `adata.obs["is_train"]` with a train vs. test split + +It should be noted that datasets may only contain a single batch, or not contain discriminative batch information. + +Methods should assign output celltype labels to `adata.obs['labels_pred']` using only the labels from the training data. + +Note that the true labels are contained in `adata['labels']`. + +Metrics can compare `adata['labels']` to `adata.obs['labels_pred']` using only the labels from the test data. From 091a58222f70ca77e0fad2c836b7439ace016819 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 17 Oct 2022 16:39:49 +0200 Subject: [PATCH 0251/1233] add api yml spec Former-commit-id: a0686838a81f100bda3aeb142ad6918321862e77 --- src/label_projection/api.yml | 89 ++++++++++++++++++++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 src/label_projection/api.yml diff --git a/src/label_projection/api.yml b/src/label_projection/api.yml new file mode 100644 index 0000000000..a9c98f791a --- /dev/null +++ b/src/label_projection/api.yml @@ -0,0 +1,89 @@ +dataset_preprocessing: + input: + type: h5ad + X: Raw counts + obs: + labels: Ground truth cell type labels + batch: Batch information + uns: + dataset_id: "A unique identifier for the dataset" + output: + type: h5ad + X: Raw counts + layers: + lognorm: Normalized, log-transformed counts + obs: + labels: Ground truth cell type labels + batch: Batch information + uns: + dataset_id: "A unique identifier for the dataset" + raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" + +dataset_censoring: + input: ${dataset_preprocessing.output} + output_train: + type: h5ad + X: Raw counts + layers: + lognorm: Normalised, log-transformed counts + obs: + labels: Ground truth cell type labels + batch: Batch information + output_test: + type: h5ad + X: Raw counts + layers: + lognorm: Normalised, log-transformed counts + obs: + batch: Batch information + uns: + dataset_id: "A unique identifier for the dataset" + raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" + output_solution: + type: h5ad + X: Raw counts + layers: + lognorm: Normalised, log-transformed counts + obs: + batch: Batch information + uns: + dataset_id: "A unique identifier for the dataset" + raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" + +method: + input_train: ${dataset_censoring.output_train} + input_test: ${dataset_censoring.output_test} + output: + type: h5ad + obs: + labels_pred: Predicted labels for the test cells. + uns: + dataset_id: "A unique identifier for the dataset" + raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" + method_id: "A unique identifier for the method" + config_info: + method_label: "Short descriptive label of the method, ideally 10 characters at most." + method_name: "The method name, ideally four words at most" + method_type: "Must be one of 'method', 'positive_control', 'negative_control', 'baseline'." + paper_name: + paper_doi: + paper_year: + code_url: + code_version: + +metric: + input_solution: ${dataset_censoring.output_solution} + input_prediction: ${method.output} + output: + type: h5ad + uns: + dataset_id: "A unique identifier for the dataset" + raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" + method_id: "A unique identifier for the method" + metric_ids: "A vector of unique metric identifiers" + metric_values: "The metric values obtained for the given prediction" + config_info: + metric_ids: "The unique identifiers of metrics contained in this component" + metric_mins: "The minimum value of each metric" + metric_maxs: "The maximum value of each metric" + metric_maximise: "Whether a higher value is better" \ No newline at end of file From 4e5d557bc7720ef3ae7e24101ed44ae5f8557f8f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Oct 2022 11:19:44 +0200 Subject: [PATCH 0252/1233] Split up API yamls Former-commit-id: 19af6117ad9c5be965f2aafc7c113f272b8d78be --- src/label_projection/api.yml | 89 ------------ .../api/dataset_censoring.yaml | 136 ++++++++++++++++++ .../api/dataset_preprocessing.yaml | 50 +++++++ src/label_projection/api/method.yaml | 104 ++++++++++++++ src/label_projection/api/metric.yaml | 102 +++++++++++++ 5 files changed, 392 insertions(+), 89 deletions(-) delete mode 100644 src/label_projection/api.yml create mode 100644 src/label_projection/api/dataset_censoring.yaml create mode 100644 src/label_projection/api/dataset_preprocessing.yaml create mode 100644 src/label_projection/api/method.yaml create mode 100644 src/label_projection/api/metric.yaml diff --git a/src/label_projection/api.yml b/src/label_projection/api.yml deleted file mode 100644 index a9c98f791a..0000000000 --- a/src/label_projection/api.yml +++ /dev/null @@ -1,89 +0,0 @@ -dataset_preprocessing: - input: - type: h5ad - X: Raw counts - obs: - labels: Ground truth cell type labels - batch: Batch information - uns: - dataset_id: "A unique identifier for the dataset" - output: - type: h5ad - X: Raw counts - layers: - lognorm: Normalized, log-transformed counts - obs: - labels: Ground truth cell type labels - batch: Batch information - uns: - dataset_id: "A unique identifier for the dataset" - raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" - -dataset_censoring: - input: ${dataset_preprocessing.output} - output_train: - type: h5ad - X: Raw counts - layers: - lognorm: Normalised, log-transformed counts - obs: - labels: Ground truth cell type labels - batch: Batch information - output_test: - type: h5ad - X: Raw counts - layers: - lognorm: Normalised, log-transformed counts - obs: - batch: Batch information - uns: - dataset_id: "A unique identifier for the dataset" - raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" - output_solution: - type: h5ad - X: Raw counts - layers: - lognorm: Normalised, log-transformed counts - obs: - batch: Batch information - uns: - dataset_id: "A unique identifier for the dataset" - raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" - -method: - input_train: ${dataset_censoring.output_train} - input_test: ${dataset_censoring.output_test} - output: - type: h5ad - obs: - labels_pred: Predicted labels for the test cells. - uns: - dataset_id: "A unique identifier for the dataset" - raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" - method_id: "A unique identifier for the method" - config_info: - method_label: "Short descriptive label of the method, ideally 10 characters at most." - method_name: "The method name, ideally four words at most" - method_type: "Must be one of 'method', 'positive_control', 'negative_control', 'baseline'." - paper_name: - paper_doi: - paper_year: - code_url: - code_version: - -metric: - input_solution: ${dataset_censoring.output_solution} - input_prediction: ${method.output} - output: - type: h5ad - uns: - dataset_id: "A unique identifier for the dataset" - raw_dataset_id: "A unique identifier for the original dataset (before preprocessing)" - method_id: "A unique identifier for the method" - metric_ids: "A vector of unique metric identifiers" - metric_values: "The metric values obtained for the given prediction" - config_info: - metric_ids: "The unique identifiers of metrics contained in this component" - metric_mins: "The minimum value of each metric" - metric_maxs: "The maximum value of each metric" - metric_maximise: "Whether a higher value is better" \ No newline at end of file diff --git a/src/label_projection/api/dataset_censoring.yaml b/src/label_projection/api/dataset_censoring.yaml new file mode 100644 index 0000000000..e517ff3b93 --- /dev/null +++ b/src/label_projection/api/dataset_censoring.yaml @@ -0,0 +1,136 @@ +functionality: + name: dataset_censoring + arguments: + - name: "--input" + type: h5ad_file + description: "A preprocessed dataset" + example: "preprocessed.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + - name: "--output_train" + type: h5ad_file + description: "The training data" + example: "training.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + direction: output + - name: "--output_test" + type: h5ad_file + description: "The censored test data" + example: "test.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + direction: output + - name: "--output_solution" + type: h5ad_file + description: "The solution for the test data" + example: "solution.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + direction: output + resources: + # A custom python script with additional checks + - type: python_script + path: format_check.py + text: | + import anndata as ad + + input = ad.read_h5ad(par["input"]) + output_train = ad.read_h5ad(par["output_train"]) + output_test = ad.read_h5ad(par["output_test"]) + output_solution = ad.read_h5ad(par["output_solution"]) + + print("Checking dimensions") + assert input.n_obs == output_train.n_obs + output_test.n_obs + assert output_test.n_obs == output_solution.n_obs + assert input.n_vars == output_train.n_vars + assert input.n_vars == output_test.n_vars + + print("Checking whether data from input was copied properly to output") + assert input.uns["dataset_id"] == output_train.uns["dataset_id"] + assert input.uns["raw_dataset_id"] == output_train.uns["raw_dataset_id"] + assert input.uns["dataset_id"] == output_test.uns["dataset_id"] + assert input.uns["raw_dataset_id"] == output_test.uns["raw_dataset_id"] + assert input.uns["dataset_id"] == output_solution.uns["dataset_id"] + assert input.uns["raw_dataset_id"] == output_solution.uns["raw_dataset_id"] + + # todo: check .obs and .layers + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/label_projection/api/dataset_preprocessing.yaml b/src/label_projection/api/dataset_preprocessing.yaml new file mode 100644 index 0000000000..37ee8e8b31 --- /dev/null +++ b/src/label_projection/api/dataset_preprocessing.yaml @@ -0,0 +1,50 @@ +functionality: + name: dataset_preprocessing + arguments: + - name: "--input" + type: h5ad_file + description: "An unprocessed dataset." + example: "unprocessed.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - name: "--output" + type: h5ad_file + description: "A preprocessed dataset" + example: "preprocessed.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + direction: output \ No newline at end of file diff --git a/src/label_projection/api/method.yaml b/src/label_projection/api/method.yaml new file mode 100644 index 0000000000..1fd9688968 --- /dev/null +++ b/src/label_projection/api/method.yaml @@ -0,0 +1,104 @@ +functionality: + name: method + meta: + # Short descriptive label of the method, ideally 10 characters at most. + method_label: "foo_bar" + + # The method name, ideally four words at most + method_name: "Method foo param bar" + + # The type of method. Must be one of: method, positive_control, negative_control, baseline + method_type: method + + # The doi of an associated paper (optional). + # paper_doi: "10.1234/s56789-012-3456-7" + + # URL to the main codebase of this method (optional). + # code_url: "https://github.com/foo/bar" + arguments: + - name: "--input_train" + type: h5ad_file + description: "The training data" + example: "training.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + - name: "--input_test" + type: h5ad_file + description: "The censored test data" + example: "test.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + - name: "--output" + type: h5ad_file + description: "The prediction file" + example: "prediction.h5ad" + slots: + obs: + - type: double + name: labels_pred + description: Predicted labels for the test cells. + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: method_id + description: "A unique identifier for the method" + direction: output + resources: + # A custom python script with additional checks + - type: python_script + path: format_check.py + text: | + import anndata as ad + + # input_train = ad.read_h5ad(par["input_train"]) + input_test = ad.read_h5ad(par["input_test"]) + output = ad.read_h5ad(par["output"]) + + print("Checking whether data from input was copied properly to output") + assert input_test.n_obs == output.n_obs + assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + assert input_test.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/label_projection/api/metric.yaml b/src/label_projection/api/metric.yaml new file mode 100644 index 0000000000..870f5192d1 --- /dev/null +++ b/src/label_projection/api/metric.yaml @@ -0,0 +1,102 @@ +functionality: + name: metric + meta: + # The unique identifier(s) of metrics contained in this component + metric_ids: [ "my_metric" ] + + # The minimum value of each metric + metric_mins: [ 0 ] + + # The maximum value of each metric + metric_maxs: [ 1 ] + + # Whether a higher value is better + metric_maximise: [ true ] + + arguments: + - name: "--input_solution" + type: h5ad_file + description: "The solution for the test data" + example: "solution.h5ad" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: labels + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: dataset + description: "A unique identifier for the dataset" + - name: "--input_prediction" + type: h5ad_file + description: "The prediction file" + example: "prediction.h5ad" + slots: + obs: + - type: double + name: labels_pred + description: Predicted labels for the test cells. + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: method_id + description: "A unique identifier for the method" + - name: "--output" + description: "Metric score file" + example: "output.h5ad" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: method_id + description: "A unique identifier for the method" + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true + resources: + # A custom python script with additional checks + - type: python_script + path: format_check.py + text: | + import anndata as ad + + input_solution = ad.read_h5ad(par["input_solution"]) + input_prediction = ad.read_h5ad(par["input_prediction"]) + output = ad.read_h5ad(par["output"]) + + print("Checking whether data from input was copied properly to output") + assert input_solution.uns["dataset_id"] == input_prediction.uns["dataset_id"] + assert input_solution.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] + assert input_prediction.uns["dataset_id"] == output.uns["dataset_id"] + assert input_prediction.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] + assert input_prediction.uns["method_id"] == output.uns["method_id"] + + print("All checks succeeded!") \ No newline at end of file From 11c3ba97629adecb1a53e933ec99f65faaf8b35d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Oct 2022 16:07:34 +0200 Subject: [PATCH 0253/1233] render readme from api yaml Former-commit-id: 9708e565a72a9e153466492b90e374255368de12 --- src/label_projection/README.md | 176 +++++++++++++++++- src/label_projection/README.qmd | 125 +++++++++++++ .../api/dataset_censoring.yaml | 12 +- .../api/dataset_preprocessing.yaml | 8 +- src/label_projection/api/method.yaml | 18 +- src/label_projection/api/metric.yaml | 12 +- 6 files changed, 333 insertions(+), 18 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index f04c5fb0ac..fdbeecda52 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -45,19 +45,177 @@ correctly assigns cell type labels to cells in the test set. ## API +``` mermaid +flowchart LR + dataset_censoring__output_train(Training data) +dataset_censoring__output_test(Test data) +dataset_censoring__output_solution(Solution) +dataset_preprocessing__input(Raw dataset) +dataset_preprocessing__output(Pre-processed dataset) +method__output(Prediction) +metric__output(Scores) +dataset_censoring[/Dataset censoring/] +dataset_preprocessing[/Dataset preprocessing/] +method[/Method/] +metric[/Metric/] + dataset_preprocessing__output---dataset_censoring +dataset_preprocessing__input---dataset_preprocessing +dataset_censoring__output_train---method +dataset_censoring__output_test---method +dataset_censoring__output_solution---metric +method__output---metric +dataset_censoring-->dataset_censoring__output_train +dataset_censoring-->dataset_censoring__output_test +dataset_censoring-->dataset_censoring__output_solution +dataset_preprocessing-->dataset_preprocessing__output +method-->method__output +metric-->metric__output +``` + +### Training data + +The training data + +Used in: + +- dataset_censoring: output_train (as output) +- method: input_train (as input) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | labels | double | Ground truth cell type labels | +| obs | batch | double | Batch information | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | dataset | string | A unique identifier for the dataset | + +### Test data + +The censored test data + +Used in: + +- dataset_censoring: output_test (as output) +- method: input_test (as input) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | batch | double | Batch information | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | dataset | string | A unique identifier for the dataset | + +### Solution + +The solution for the test data + +Used in: + +- dataset_censoring: output_solution (as output) +- metric: input_solution (as input) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | labels | double | Ground truth cell type labels | +| obs | batch | double | Batch information | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | dataset | string | A unique identifier for the dataset | + +### Raw dataset + +An unprocessed dataset. + +Used in: + +- dataset_preprocessing: input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| obs | labels | double | Ground truth cell type labels | +| obs | batch | double | Batch information | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | + +### Pre-processed dataset + +A preprocessed dataset + +Used in: + +- dataset_censoring: input (as input) +- dataset_preprocessing: output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | labels | double | Ground truth cell type labels | +| obs | batch | double | Batch information | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | dataset | string | A unique identifier for the dataset | + +### Prediction + +The prediction file + +Used in: + +- method: output (as output) +- metric: input_prediction (as input) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:-------|:--------------------------------------------------------------------| +| obs | labels_pred | double | Predicted labels for the test cells. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | method_id | string | A unique identifier for the method | + +### Scores + +Metric score file + +Used in: + +- metric: output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:---------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + + diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 3e536bc7c1..c333567f31 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -4,6 +4,18 @@ info: migration_date: "2022-10-17 12:49:00 GMT" --- +```{r setup, include=FALSE} +library(tidyverse) +library(rlang) + +strip_margin <- function(text, symbol = "\\|") { + str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") +} + +dir <- "src/label_projection" +dir <- "." +``` + # Label Projection ## The task @@ -24,6 +36,118 @@ Metrics for label projection aim to characterize how well each classifer correct ## API +```{r data, include=FALSE} +yaml_files <- list.files(paste0(dir, "/api"), full.names = TRUE) + +file_arg_info <- map_df(yaml_files, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + tibble( + comp = conf$functionality$name, + arg_name = str_replace_all(arg$name, "^-*", ""), + id = paste0(comp, "__", arg_name), + short_description = arg$meta$short_description, + description = arg$description, + direction = arg$direction %||% "input", + from = arg$meta$from + ) + }) +}) + +comp_info <- map_df(yaml_files, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + tibble( + name = conf$functionality$name, + label = conf$functionality$meta$label %||% str_replace_all(name, "_", " ") + ) +}) + +slot_info <- map_df(yaml_files, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + out <- map2_df(names(arg$slots), arg$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + as_tibble(df) + }) + out$component <- conf$functionality$name + out$argument <- str_replace_all(arg$name, "^-*", "") + out$direction <- arg$direction %||% "input" + out + }) +}) %>% + select(component, argument, struct, name, everything()) %>% + mutate(multiple = multiple %|% FALSE, id = paste0(component, "__", argument)) +``` + +```{r flow, echo=FALSE,warning=FALSE,error=FALSE} +nodes <- bind_rows( + file_arg_info %>% + filter(!is.na(short_description)) %>% + transmute(id, label = short_description, is_comp = FALSE), + comp_info %>% + transmute(id = name, label, is_comp = TRUE) +) %>% + mutate(str = paste0( + id, + ifelse(is_comp, "[/", "("), + label, + ifelse(is_comp, "/]", ")") + )) +edges <- bind_rows( + file_arg_info %>% + filter(direction == "input") %>% + transmute(from = ifelse(!is.na(from), from, id), to = comp, arrow = "---"), + file_arg_info %>% + filter(direction == "output") %>% + transmute(from = comp, to = id, arrow = "-->") +) %>% + mutate(str = paste0(from, arrow, to)) + +out_str <- strip_margin(glue::glue(" + §```{{mermaid}} + §%%| column: screen-inset-shaded + §flowchart LR + § {paste(nodes$str, collapse = '\n ')} + § {paste(edges$str, collapse = '\n ')} + §``` + §"), symbol = "§") +knitr::asis_output(out_str) +``` + +```{r api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +obj_ids <- file_arg_info %>% filter(!is.na(short_description)) %>% pull(id) +for (obj_id in obj_ids) { + arg_info <- file_arg_info %>% filter(id == obj_id) + sub_out <- slot_info %>% + filter(id == obj_id) %>% + select(struct, name, type, description) + used_in <- file_arg_info %>% + filter(id == obj_id | from == obj_id) %>% + mutate(str = paste0("* ", comp, ": ", arg_name, " (as ", direction, ")")) %>% + pull(str) + + out_str <- strip_margin(glue::glue(" + §### {arg_info$short_description} + § + §{arg_info$description} + § + §Used in: + § + §{paste(used_in, collapse = '\n')} + § + §Slots: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + §"), symbol = "§") + cat(out_str) +} +``` + + \ No newline at end of file diff --git a/src/label_projection/api/dataset_censoring.yaml b/src/label_projection/api/dataset_censoring.yaml index e517ff3b93..10e6e682b9 100644 --- a/src/label_projection/api/dataset_censoring.yaml +++ b/src/label_projection/api/dataset_censoring.yaml @@ -1,10 +1,14 @@ functionality: name: dataset_censoring + meta: + label: "Dataset censoring" arguments: - name: "--input" type: h5ad_file description: "A preprocessed dataset" example: "preprocessed.h5ad" + meta: + from: dataset_preprocessing__output slots: layers: - type: integer @@ -31,6 +35,8 @@ functionality: type: h5ad_file description: "The training data" example: "training.h5ad" + meta: + short_description: "Training data" slots: layers: - type: integer @@ -58,6 +64,8 @@ functionality: type: h5ad_file description: "The censored test data" example: "test.h5ad" + meta: + short_description: "Test data" slots: layers: - type: integer @@ -82,6 +90,8 @@ functionality: type: h5ad_file description: "The solution for the test data" example: "solution.h5ad" + meta: + short_description: "Solution" slots: layers: - type: integer @@ -133,4 +143,4 @@ functionality: # todo: check .obs and .layers - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!") diff --git a/src/label_projection/api/dataset_preprocessing.yaml b/src/label_projection/api/dataset_preprocessing.yaml index 37ee8e8b31..e2aaa6bf9a 100644 --- a/src/label_projection/api/dataset_preprocessing.yaml +++ b/src/label_projection/api/dataset_preprocessing.yaml @@ -1,10 +1,14 @@ functionality: name: dataset_preprocessing + meta: + label: "Dataset preprocessing" arguments: - name: "--input" type: h5ad_file description: "An unprocessed dataset." example: "unprocessed.h5ad" + meta: + short_description: "Raw dataset" slots: layers: - type: integer @@ -25,6 +29,8 @@ functionality: type: h5ad_file description: "A preprocessed dataset" example: "preprocessed.h5ad" + meta: + short_description: "Pre-processed dataset" slots: layers: - type: integer @@ -47,4 +53,4 @@ functionality: - type: string name: dataset description: "A unique identifier for the dataset" - direction: output \ No newline at end of file + direction: output diff --git a/src/label_projection/api/method.yaml b/src/label_projection/api/method.yaml index 1fd9688968..d4d8d0ea1e 100644 --- a/src/label_projection/api/method.yaml +++ b/src/label_projection/api/method.yaml @@ -1,14 +1,14 @@ functionality: name: method - meta: + meta: # Short descriptive label of the method, ideally 10 characters at most. - method_label: "foo_bar" + label: "Method" # The method name, ideally four words at most - method_name: "Method foo param bar" + name: "Method foo param bar" # The type of method. Must be one of: method, positive_control, negative_control, baseline - method_type: method + type: method # The doi of an associated paper (optional). # paper_doi: "10.1234/s56789-012-3456-7" @@ -20,6 +20,8 @@ functionality: type: h5ad_file description: "The training data" example: "training.h5ad" + meta: + from: dataset_censoring__output_train slots: layers: - type: integer @@ -40,12 +42,14 @@ functionality: name: raw_dataset_id description: "A unique identifier for the original dataset (before preprocessing)" - type: string - name: dataset + name: dataset_id description: "A unique identifier for the dataset" - name: "--input_test" type: h5ad_file description: "The censored test data" example: "test.h5ad" + meta: + from: dataset_censoring__output_test slots: layers: - type: integer @@ -69,6 +73,8 @@ functionality: type: h5ad_file description: "The prediction file" example: "prediction.h5ad" + meta: + short_description: "Prediction" slots: obs: - type: double @@ -101,4 +107,4 @@ functionality: assert input_test.uns["dataset_id"] == output.uns["dataset_id"] assert input_test.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!") diff --git a/src/label_projection/api/metric.yaml b/src/label_projection/api/metric.yaml index 870f5192d1..2141f967f1 100644 --- a/src/label_projection/api/metric.yaml +++ b/src/label_projection/api/metric.yaml @@ -1,6 +1,9 @@ functionality: name: metric meta: + # pretty version of the functionality.name + label: "Metric" + # The unique identifier(s) of metrics contained in this component metric_ids: [ "my_metric" ] @@ -18,6 +21,8 @@ functionality: type: h5ad_file description: "The solution for the test data" example: "solution.h5ad" + meta: + from: dataset_censoring__output_solution slots: layers: - type: integer @@ -44,6 +49,8 @@ functionality: type: h5ad_file description: "The prediction file" example: "prediction.h5ad" + meta: + from: method__output slots: obs: - type: double @@ -62,6 +69,8 @@ functionality: - name: "--output" description: "Metric score file" example: "output.h5ad" + meta: + short_description: "Scores" slots: uns: - type: string @@ -81,6 +90,7 @@ functionality: name: metric_values description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." multiple: true + direction: output resources: # A custom python script with additional checks - type: python_script @@ -99,4 +109,4 @@ functionality: assert input_prediction.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] assert input_prediction.uns["method_id"] == output.uns["method_id"] - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!") From b687a6d00b32bc6afc8f169788829eb7db47af0b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Oct 2022 16:08:23 +0200 Subject: [PATCH 0254/1233] undo escape Former-commit-id: d6179455f35ee69c3449f773d383b62212fc70af --- src/label_projection/README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index fdbeecda52..effcc26eca 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -64,12 +64,12 @@ dataset_censoring__output_train---method dataset_censoring__output_test---method dataset_censoring__output_solution---metric method__output---metric -dataset_censoring-->dataset_censoring__output_train -dataset_censoring-->dataset_censoring__output_test -dataset_censoring-->dataset_censoring__output_solution -dataset_preprocessing-->dataset_preprocessing__output -method-->method__output -metric-->metric__output +dataset_censoring-->dataset_censoring__output_train +dataset_censoring-->dataset_censoring__output_test +dataset_censoring-->dataset_censoring__output_solution +dataset_preprocessing-->dataset_preprocessing__output +method-->method__output +metric-->metric__output ``` ### Training data From 23031214474298ccda5c3a986531d53958f994a4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Oct 2022 16:32:05 +0200 Subject: [PATCH 0255/1233] update graph Former-commit-id: 2a97dc9a8d254f0f9e9ee94c4613c46b16de55c6 --- src/label_projection/README.md | 43 +++++++++++++++++---------------- src/label_projection/README.qmd | 10 +++++--- 2 files changed, 28 insertions(+), 25 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index effcc26eca..99717870df 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -46,30 +46,31 @@ correctly assigns cell type labels to cells in the test set. ## API ``` mermaid +%%| column: screen-inset-shaded flowchart LR dataset_censoring__output_train(Training data) -dataset_censoring__output_test(Test data) -dataset_censoring__output_solution(Solution) -dataset_preprocessing__input(Raw dataset) -dataset_preprocessing__output(Pre-processed dataset) -method__output(Prediction) -metric__output(Scores) -dataset_censoring[/Dataset censoring/] -dataset_preprocessing[/Dataset preprocessing/] -method[/Method/] -metric[/Metric/] + dataset_censoring__output_test(Test data) + dataset_censoring__output_solution(Solution) + dataset_preprocessing__input(Raw dataset) + dataset_preprocessing__output(Pre-processed dataset) + method__output(Prediction) + metric__output(Scores) + dataset_censoring[/Dataset censoring/] + dataset_preprocessing[/Dataset preprocessing/] + method[/Method/] + metric[/Metric/] dataset_preprocessing__output---dataset_censoring -dataset_preprocessing__input---dataset_preprocessing -dataset_censoring__output_train---method -dataset_censoring__output_test---method -dataset_censoring__output_solution---metric -method__output---metric -dataset_censoring-->dataset_censoring__output_train -dataset_censoring-->dataset_censoring__output_test -dataset_censoring-->dataset_censoring__output_solution -dataset_preprocessing-->dataset_preprocessing__output -method-->method__output -metric-->metric__output + dataset_preprocessing__input---dataset_preprocessing + dataset_censoring__output_train---method + dataset_censoring__output_test---method + dataset_censoring__output_solution---metric + method__output---metric + dataset_censoring-->dataset_censoring__output_train + dataset_censoring-->dataset_censoring__output_test + dataset_censoring-->dataset_censoring__output_solution + dataset_preprocessing-->dataset_preprocessing__output + method-->method__output + metric-->metric__output ``` ### Training data diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index c333567f31..e3b8eface7 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -92,6 +92,7 @@ nodes <- bind_rows( transmute(id = name, label, is_comp = TRUE) ) %>% mutate(str = paste0( + " ", id, ifelse(is_comp, "[/", "("), label, @@ -105,14 +106,15 @@ edges <- bind_rows( filter(direction == "output") %>% transmute(from = comp, to = id, arrow = "-->") ) %>% - mutate(str = paste0(from, arrow, to)) + mutate(str = paste0(" ", from, arrow, to)) +# note: use ```{mermaid} instead of ```mermaid when rendering to html out_str <- strip_margin(glue::glue(" - §```{{mermaid}} + §```mermaid §%%| column: screen-inset-shaded §flowchart LR - § {paste(nodes$str, collapse = '\n ')} - § {paste(edges$str, collapse = '\n ')} + §{paste(nodes$str, collapse = '\n')} + §{paste(edges$str, collapse = '\n')} §``` §"), symbol = "§") knitr::asis_output(out_str) From 9d0d1568723a5959fe1fd3a961b7e7ae7bef4209 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Oct 2022 06:49:24 +0200 Subject: [PATCH 0256/1233] update modality alignment readme Former-commit-id: e0f6de449a5090c1909058aa040b2900ebc4a730 --- src/modality_alignment/README.md | 54 ++++++++++++++++++++++++++++--- src/modality_alignment/README.qmd | 30 +++++++++++++++++ 2 files changed, 79 insertions(+), 5 deletions(-) create mode 100644 src/modality_alignment/README.qmd diff --git a/src/modality_alignment/README.md b/src/modality_alignment/README.md index 93c41615fe..1775873fec 100644 --- a/src/modality_alignment/README.md +++ b/src/modality_alignment/README.md @@ -1,11 +1,55 @@ -# Modality alignment -Modality alignment refers to the task of combining together two datasets of different modalities of measurements (e.g., single-cell RNA sequencing and single-cell ATAC sequencing) on different observations of the same biological system. Integrating such measurements allows us to analyze the interaction between the different modalities, without requiring an explicitly joint measurement like [sci-CAR](https://doi.org/10.1126/science.aau0730) or [CITE-seq](https://doi.org/10.1038/nmeth.4380). +# Multimodal data integration + +## The task + +Cellular function is regulated by the complex interplay of different +types of biological molecules (DNA, RNA, proteins, etc.), which +determine the state of a cell. Several recently described technologies +allow for simultaneous measurement of different aspects of cellular +state. For example, [sci-CAR](https://doi.org/10.1126/science.aau0730) +jointly profiles RNA expression and chromatin accessibility on the same +cell and [CITE-seq](https://doi.org/10.1038/nmeth.4380) measures surface +protein abundance and RNA expression from each cell. These technologies +enable us to better understand cellular function, however datasets are +still rare and there are tradeoffs that these measurements make for to +profile multiple modalities. + +Joint methods can be more expensive or lower throughput or more noisy +than measuring a single modality at a time. Therefore it is useful to +develop methods that are capable of integrating measurements of the same +biological system but obtained using different technologies on different +cells. + +Here the goal is to learn a latent space where cells profiled by +different technologies in different modalities are matched if they have +the same state. We use jointly profiled data as ground truth so that we +can evaluate when the observations from the same cell acquired using +different modalities are similar. A perfect result has each of the +paired observations sharing the same coordinates in the latent space. + +## The metrics + +Metrics for multimodal data integration aim to characterize how well the +aligned datasets correspond to the ground truth. + +- **kNN AUC**: Let $f(i) ∈ F$ be the scRNA-seq measurement of cell $i$, + and $g(i) ∈ G$ be the scATAC- seq measurement of cell $i$. kNN-AUC + calculates the average percentage overlap of neighborhoods of $f(i)$ + in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. +- **MSE**: Mean squared error (MSE) is the average distance between each + pair of matched observations of the same cell in the learned latent + space. Lower is better. ## API -Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. The dataset identifier should be stored in `adata.uns["dataset_id"]`. +Datasets should include matched measurements from two modalities, which +are contained in `adata` and `adata.obsm["mode2"]`. The task is to align +these two modalities as closely as possible, without using the known +bijection between the datasets. -Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. The method identifier should be stored in `adata.uns["method_id"]`. +Methods should create joint matrices `adata.obsm["aligned"]` and +`adata.obsm["mode2_aligned"]` which reside in a joint space. -Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. The metric identifier should be stored in `adata.uns["metric_id"]`. The metric value should be stored in `adata.uns["metric_value"]`. +Metrics should evaluate how well the cells which are known to be +equivalent are aligned in the joint space. diff --git a/src/modality_alignment/README.qmd b/src/modality_alignment/README.qmd new file mode 100644 index 0000000000..851b4469ee --- /dev/null +++ b/src/modality_alignment/README.qmd @@ -0,0 +1,30 @@ +--- +format: gfm +info: + migration_date: "2022-10-17 12:33:00 GMT" +--- + +# Multimodal data integration + +## The task + +Cellular function is regulated by the complex interplay of different types of biological molecules (DNA, RNA, proteins, etc.), which determine the state of a cell. Several recently described technologies allow for simultaneous measurement of different aspects of cellular state. For example, [sci-CAR](https://doi.org/10.1126/science.aau0730) jointly profiles RNA expression and chromatin accessibility on the same cell and [CITE-seq](https://doi.org/10.1038/nmeth.4380) measures surface protein abundance and RNA expression from each cell. These technologies enable us to better understand cellular function, however datasets are still rare and there are tradeoffs that these measurements make for to profile multiple modalities. + +Joint methods can be more expensive or lower throughput or more noisy than measuring a single modality at a time. Therefore it is useful to develop methods that are capable of integrating measurements of the same biological system but obtained using different technologies on different cells. + +Here the goal is to learn a latent space where cells profiled by different technologies in different modalities are matched if they have the same state. We use jointly profiled data as ground truth so that we can evaluate when the observations from the same cell acquired using different modalities are similar. A perfect result has each of the paired observations sharing the same coordinates in the latent space. + +## The metrics + +Metrics for multimodal data integration aim to characterize how well the aligned datasets correspond to the ground truth. + +* **kNN AUC**: Let $f(i) ∈ F$ be the scRNA-seq measurement of cell $i$, and $g(i) ∈ G$ be the scATAC- seq measurement of cell $i$. kNN-AUC calculates the average percentage overlap of neighborhoods of $f(i)$ in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. +* **MSE**: Mean squared error (MSE) is the average distance between each pair of matched observations of the same cell in the learned latent space. Lower is better. + +## API + +Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. + +Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. + +Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. From df42c0f05675140fed28ebe7d6df67bb8e0c4e52 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Oct 2022 06:49:43 +0200 Subject: [PATCH 0257/1233] clean up script Former-commit-id: 323e3a368ec300672237dcea1c6975e9de307eb2 --- .../methods/harmonic_alignment/config.vsh.yaml | 9 +++------ .../methods/harmonic_alignment/script.py | 10 +++++----- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml index 4cb6eadc62..1a61ae3bb7 100644 --- a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml +++ b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml @@ -13,15 +13,12 @@ functionality: paper_doi: "10.1137/1.9781611976236.36" paper_year: "2020" code_url: "https://github.com/KrishnaswamyLab/harmonic-alignment" - code_version: "0.0" arguments: - - name: "--input" - alternatives: ["-i"] + - name: "--input_mod1" type: "file" - default: "input.h5ad" + default: "dataset_mod1_censored.h5ad" description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - name: "--output" - alternatives: ["-o"] type: "file" direction: "output" default: "output.h5ad" @@ -40,7 +37,7 @@ functionality: description: "Number of eigenvectors of the normalized Laplacian on which to perform alignment." resources: - type: python_script - path: ./script.py + path: script.py - path: "../../utils/preprocessing.py" tests: - type: python_script diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/modality_alignment/methods/harmonic_alignment/script.py index cdf29c75e9..b9f2d20251 100644 --- a/src/modality_alignment/methods/harmonic_alignment/script.py +++ b/src/modality_alignment/methods/harmonic_alignment/script.py @@ -1,3 +1,8 @@ +print("Loading dependencies") +import scanpy as sc +import harmonicalignment +import sklearn.decomposition + ## VIASH START par = { input = "output.h5ad", @@ -9,11 +14,6 @@ resources_dir = "../../utils/" ## VIASH END -print("Loading dependencies") -import scanpy as sc -import harmonicalignment -import sklearn.decomposition - # importing helper functions from common preprocessing.py file in resources dir import sys sys.path.append(resources_dir) From c14713e12c7877dd1b6194cf7bfaba08c5ebbbb6 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 26 Oct 2022 13:59:49 +0200 Subject: [PATCH 0258/1233] update components Former-commit-id: d0a4ddeaf9e22c165752a1c03fb93f088da66d9a --- src/batch_integration/graph/methods/bbknn/config.vsh.yaml | 2 +- src/batch_integration/graph/methods/bbknn/run_example.sh | 2 +- src/batch_integration/graph/methods/bbknn/script.py | 4 ++-- src/batch_integration/graph/methods/bbknn/test.py | 2 +- src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py | 2 +- src/batch_integration/graph/methods/combat/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/combat/run_example.sh | 2 +- src/batch_integration/graph/methods/combat/script.py | 4 ++-- src/batch_integration/graph/methods/combat/test.py | 2 +- .../graph/methods/scanorama_embed/config.vsh.yaml | 2 +- .../graph/methods/scanorama_embed/run_example.sh | 2 +- src/batch_integration/graph/methods/scanorama_embed/script.py | 4 ++-- src/batch_integration/graph/methods/scanorama_embed/test.py | 2 +- .../graph/methods/scanorama_feature/config.vsh.yaml | 2 +- .../graph/methods/scanorama_feature/run_example.sh | 2 +- .../graph/methods/scanorama_feature/script.py | 4 ++-- src/batch_integration/graph/methods/scanorama_feature/test.py | 2 +- src/batch_integration/graph/methods/scvi/config.vsh.yaml | 2 +- src/batch_integration/graph/methods/scvi/run_example.sh | 2 +- src/batch_integration/graph/methods/scvi/script.py | 4 ++-- src/batch_integration/graph/methods/scvi/test.py | 2 +- 21 files changed, 27 insertions(+), 27 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index d281651192..6daa2204fe 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: direction: output description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] required: true - - name: --adata + - name: --input type: file description: Unintegrated anndata HDF5 file required: true diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh index b89da943c8..f5c341e495 100644 --- a/src/batch_integration/graph/methods/bbknn/run_example.sh +++ b/src/batch_integration/graph/methods/bbknn/run_example.sh @@ -5,7 +5,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_bbknn.h5ad \ diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 3d5cd08318..caf122afc9 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', 'hvg': True, 'scaling': True, @@ -16,7 +16,7 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index 320b317f36..f53a9c90be 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 87b4d91039..c47e3c6e4f 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'True', "--scaling", 'True', "--output", output_file diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml index 9c5615f98a..4469797fe3 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: combat - namespace: batch_integration/embedding/methods + namespace: batch_integration/graph/methods version: dev description: Run Combat authors: @@ -14,7 +14,7 @@ functionality: direction: output description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] required: true - - name: --adata + - name: --input type: file description: Unintegrated anndata HDF5 file required: true diff --git a/src/batch_integration/graph/methods/combat/run_example.sh b/src/batch_integration/graph/methods/combat/run_example.sh index 6db4a0f885..ce00a91fac 100644 --- a/src/batch_integration/graph/methods/combat/run_example.sh +++ b/src/batch_integration/graph/methods/combat/run_example.sh @@ -5,7 +5,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --label celltype \ --batch batch \ --hvg true \ diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index ae88261e71..3f69f6f2f9 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', 'hvg': True, 'scaling': True, @@ -16,7 +16,7 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] diff --git a/src/batch_integration/graph/methods/combat/test.py b/src/batch_integration/graph/methods/combat/test.py index 8347702971..3549f689e6 100644 --- a/src/batch_integration/graph/methods/combat/test.py +++ b/src/batch_integration/graph/methods/combat/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml index 77ced015b5..c6e68c9dc9 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: direction: output description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] required: true - - name: --adata + - name: --input type: file description: Unintegrated anndata HDF5 file required: true diff --git a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh index 1495b11ae8..6b9ec6c6eb 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh +++ b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh @@ -5,7 +5,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scanorama_embed.h5ad \ diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/graph/methods/scanorama_embed/script.py index 08b1017bba..32609ba5f9 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/script.py +++ b/src/batch_integration/graph/methods/scanorama_embed/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', 'hvg': True, 'scaling': True, @@ -16,7 +16,7 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] diff --git a/src/batch_integration/graph/methods/scanorama_embed/test.py b/src/batch_integration/graph/methods/scanorama_embed/test.py index 488bdfde11..682c1adaad 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/test.py +++ b/src/batch_integration/graph/methods/scanorama_embed/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index 980a9510c2..cf7b4acb28 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: direction: output description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] required: true - - name: --adata + - name: --input type: file description: Unintegrated anndata HDF5 file required: true diff --git a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh index afac7b5393..0494839c05 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh +++ b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh @@ -5,7 +5,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scanorama_feature.h5ad \ diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index c730684f01..ac6dcc0ef6 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', 'hvg': True, 'scaling': True, @@ -16,7 +16,7 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] diff --git a/src/batch_integration/graph/methods/scanorama_feature/test.py b/src/batch_integration/graph/methods/scanorama_feature/test.py index cb6676df11..404231915f 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/test.py +++ b/src/batch_integration/graph/methods/scanorama_feature/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml index 3dfd7e5cbf..174ec9344e 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: direction: output description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] required: true - - name: --adata + - name: --input type: file description: Unintegrated anndata HDF5 file required: true diff --git a/src/batch_integration/graph/methods/scvi/run_example.sh b/src/batch_integration/graph/methods/scvi/run_example.sh index 6e86cf3aaa..cf93de8974 100644 --- a/src/batch_integration/graph/methods/scvi/run_example.sh +++ b/src/batch_integration/graph/methods/scvi/run_example.sh @@ -5,7 +5,7 @@ SCRIPTPATH="$( )" bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ --hvg true \ --scaling true \ --output src/batch_integration/resources/graph_pancreas_scvi.h5ad \ diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/graph/methods/scvi/script.py index b202ca9daa..2cd2520578 100644 --- a/src/batch_integration/graph/methods/scvi/script.py +++ b/src/batch_integration/graph/methods/scvi/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', 'hvg': True, 'scaling': True, @@ -16,7 +16,7 @@ if par['debug']: pprint(par) -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] diff --git a/src/batch_integration/graph/methods/scvi/test.py b/src/batch_integration/graph/methods/scvi/test.py index 1ae0c44ed7..700684b6fb 100644 --- a/src/batch_integration/graph/methods/scvi/test.py +++ b/src/batch_integration/graph/methods/scvi/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--adata", 'datasets_pancreas.h5ad', + "--input", 'datasets_pancreas.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file From f1ba22a9930ec534223769416f3c91ff36a68149 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 26 Oct 2022 14:04:22 +0200 Subject: [PATCH 0259/1233] update parameter passing for test pipeline Former-commit-id: f5767afb36c66684e9ec37c1d0f0d8e1db70b1ff --- src/batch_integration/datasets/params.tsv | 2 -- src/batch_integration/workflows/download.tsv | 2 ++ src/batch_integration/workflows/test/main.nf | 26 +++++++------------ .../workflows/test/preprocessing.tsv | 6 +++++ .../workflows/test/run_nextflow.sh | 2 +- 5 files changed, 18 insertions(+), 20 deletions(-) delete mode 100644 src/batch_integration/datasets/params.tsv create mode 100644 src/batch_integration/workflows/download.tsv create mode 100644 src/batch_integration/workflows/test/preprocessing.tsv diff --git a/src/batch_integration/datasets/params.tsv b/src/batch_integration/datasets/params.tsv deleted file mode 100644 index a2b0b41997..0000000000 --- a/src/batch_integration/datasets/params.tsv +++ /dev/null @@ -1,2 +0,0 @@ -name label batch hvgs url -pancreas celltype tech 2000 https://ndownloader.figshare.com/files/24539828 diff --git a/src/batch_integration/workflows/download.tsv b/src/batch_integration/workflows/download.tsv new file mode 100644 index 0000000000..1d07a3165a --- /dev/null +++ b/src/batch_integration/workflows/download.tsv @@ -0,0 +1,2 @@ +name obs_cell_type obs_batch url +pancreas celltype tech https://ndownloader.figshare.com/files/24539828 diff --git a/src/batch_integration/workflows/test/main.nf b/src/batch_integration/workflows/test/main.nf index 636218ebb7..01b1af476f 100644 --- a/src/batch_integration/workflows/test/main.nf +++ b/src/batch_integration/workflows/test/main.nf @@ -1,7 +1,8 @@ nextflow.enable.dsl=2 targetDir = "${params.rootDir}/target/nextflow" -params.tsv = "$launchDir/src/batch_integration/datasets/params.tsv" +params.download = "$launchDir/src/batch_integration/workflows/download.tsv" +params.preprocessing = "$launchDir/src/batch_integration/workflows/test/preprocessing.tsv" // import dataset loaders include { download } from "$targetDir/common/dataset_loader/download/main.nf" params(params) @@ -32,32 +33,22 @@ include { nmi } from "$targetDir/batch_integration/graph/metrics/nmi/main. workflow load_data { main: - output_ = Channel.fromPath(params.tsv) + output_ = Channel.fromPath(params.download) | splitCsv(header: true, sep: "\t") - | map { row -> - [ - row.name, - [ - "url": row.url, - "name": row.name, - "obs_cell_type": row.label, - "obs_batch": row.batch, - ] - ] - } + | map { [ it.name, it ] } | download emit: output_ } workflow process_data { - -take: + take: channel_in main: - additional_params = Channel.fromPath(params.tsv) + additional_params = Channel.fromPath(params.preprocessing) | splitCsv(header: true, sep: "\t") | map { [ it.name, it ] } + | view { "additional_params $it" } subset = channel_in.join(additional_params) | map { id, data, additional -> @@ -69,10 +60,11 @@ take: | map { id, data, additional -> [ id, [ input: data ] + additional ] } + | view { "preprocessing $it" } | preprocessing | join(additional_params) | map { id, data, additional -> - [ id, [ input: data ] + additional + [hvg: additional.hvgs.toInteger() > 0] ] + [ id, [ input: data ] + additional ] } emit: diff --git a/src/batch_integration/workflows/test/preprocessing.tsv b/src/batch_integration/workflows/test/preprocessing.tsv new file mode 100644 index 0000000000..422356511b --- /dev/null +++ b/src/batch_integration/workflows/test/preprocessing.tsv @@ -0,0 +1,6 @@ +name label batch hvgs scaling +pancreas celltype tech 0 false +pancreas celltype tech 0 true +pancreas celltype tech 2000 false +pancreas celltype tech 2000 true +pancreas celltype tech 2000 true \ No newline at end of file diff --git a/src/batch_integration/workflows/test/run_nextflow.sh b/src/batch_integration/workflows/test/run_nextflow.sh index 04c18910e1..c35e103a26 100755 --- a/src/batch_integration/workflows/test/run_nextflow.sh +++ b/src/batch_integration/workflows/test/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|utils' +# bin/viash_build -q 'batch_integration' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) From 3fcad2e504fb9e5a9c46ab1a1f581b5dadb17b0a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 26 Oct 2022 14:59:26 +0200 Subject: [PATCH 0260/1233] fix version to 0.6.0 Former-commit-id: 115e4f28abb02a50adf0a57da0228bdeeba5251f --- bin/init | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bin/init b/bin/init index 5cd42d8bcf..9f175e3437 100755 --- a/bin/init +++ b/bin/init @@ -10,8 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.5.15 \ - --nextflow_variant vdsl3 + --tag 0.6.0 cd bin From 5ab1489500a818779c5b9a986d4c335e807404a8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 06:44:08 +0100 Subject: [PATCH 0261/1233] wip adding contributing guidelines Former-commit-id: 7fb3447e738b7fa1eaa09fee6b95d342de9ed6a1 --- CODE_OF_CONDUCT.md | 133 ++++++++++++ CONTRIBUTING.md | 502 +++++++++++++++++++++++++++++++++++++++++++++ CONTRIBUTING.qmd | 446 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 1081 insertions(+) create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md create mode 100644 CONTRIBUTING.qmd diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000000..45d257b29a --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,133 @@ + +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or advances of + any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email address, + without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +[INSERT CONTACT METHOD]. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][Mozilla CoC]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[homepage]: https://www.contributor-covenant.org +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html +[Mozilla CoC]: https://github.com/mozilla/diversity +[FAQ]: https://www.contributor-covenant.org/faq +[translations]: https://www.contributor-covenant.org/translations diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000000..20c07522cc --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,502 @@ +Contributing to OpenProblems +================ + +[OpenProblems](https://openproblems.bio) is a community effort, and +everyone is welcome to contribute. This project is hosted on +[github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). + +## Code of conduct + +We as members, contributors, and leaders pledge to make participation in +our community a harassment-free experience for everyone, regardless of +age, body size, visible or invisible disability, ethnicity, sex +characteristics, gender identity and expression, level of experience, +education, socio-economic status, nationality, personal appearance, +race, caste, color, religion, or sexual identity and orientation. + +We pledge to act and interact in ways that contribute to an open, +welcoming, diverse, inclusive, and healthy community. + +Our [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the +\[Contributor Covenant\]\[homepage\], version 2.1, available at +\[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html\]\[v2.1\]. + +## Ways to contribute + +There are many ways to contribute to OpenProblems, with the most common +ones being contribution of code or documentation to the project. + +Contributing new functionality usually comes in the form of new +[datasets](#adding-a-new-dataset), [methods](#adding-a-new-method), +[metric](#adding-a-new-metric), or even entire new +[tasks](#adding-a-new-task). + +Improving the documentation is no less important than improving the +library itself. If you find a typo in the documentation, or have made +improvements, do not hesitate to submit a [GitHub pull +request](https://github.com/openproblems-bio/openproblems-v2/pulls). + +But there are many other ways to help. In particular helping to +[improve, triage, and investigate issues](#bug-triaging) and [reviewing +other developers’ pull requests](#code-review) are very valuable +contributions that decrease the burden on the project maintainers. + +Another way to contribute is to report [issues you’re +facing](#submitting-a-bug-report-or-feature-request), and give a “thumbs +up” on issues that others reported and that are relevant to you. It also +helps us if you spread the word: reference the project from your blog +and articles, link to it from your website, or simply star to say “I use +it”: + +Star + + +## Submitting New Features + +To submit new features to Open Problems for Single Cell Analysis, follow +the steps below: + +1. Search through the [GitHub + Issues](https://github.com/openproblems-bio/openproblems-v2/issues) + tracker to make sure there isn’t someone already working on the + feature you’d like to add. If someone is working on this, post in + that issue that you’d like to help or reach out to one of the + contributors working on the issue directly. + +2. If there isn’t an existing issue tracking this feature, create one! + There are several templates you can choose one depending on what + type of feature you’d like to add. + +3. Fork into your + account. If you’re new to `git`, you might find the [Fork a + repo](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) + documentation helpful. \[\](” + width=400px\> + +4. Set up [tower.nf](https://tower.nf) and make sure you have access to + [`openproblems-bio`](https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch). + If you do not have access, please contact us at + . + +5. Create repository secrets (*not environment secrets*) + + + - *AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are included in + your AWS login details. If you do not have these, please contact + us at .* + - *TOWER_ACCESS_KEY: log in with GitHub to and + create a token at .* + - When you are done with this step, your page should look like + this: ![AWS secrets success](static/img/AWS_secret.png) + +6. Enable workflows at + . + +7. Set up your git repository to fetch branches from `base` at + `openproblems-bio/openproblems` + + ``` shell + git clone git@github.com:/openproblems.git + cd openproblems + git remote add base git@github.com:openproblems-bio/openproblems.git + git fetch --all + git branch --set-upstream-to base/main + git pull + ``` + + **Note:** If you haven’t set up SSH keys with your GitHub account, + you may see this error message when adding `base` to your + repository: + + ``` text + git@github.com: Permission denied (publickey). + fatal: Could not read from remote repository. + Please make sure you have the correct access rights + ``` + + To generate an SSH key and add it to your GitHub account, follow + [this tutorial from + GitHub](https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account). + +8. Create a new branch for your task (**no underscores or spaces + allowed**). It is best to coordinate with other people working on + the same feature as you so that there aren’t clases in images + uploaded to our ECR. Here we’re creating a branch called + `method-method-name-task-name`, but if you were creating a new + metric you might use `metric-metric-name-task-name`. In practice you + should actually use the name of your method or metric, like + `method-meld-differential-abundance` or + `metric-mse-label-projection`. + + **Note:** This pushes the branch to your fork, *not to* `base`. You + will create a PR to merge your branch to `base` only after all tests + are passing. + + **Warning:** Do not edit the `main` branch on your fork! This will + not work as expected, and will never pass tests. + + ``` shell + # IMPORTANT: choose a new branch name, e.g. + git checkout -b method-method-name-task-name # or metric-new-metric-name, etc + git push -u origin method-method-name-task-name + ``` + +9. Sometimes, changes might be made to the openproblems `base` + repository that you want to incorporate into your fork. To sync your + fork from `base`, use the following code adapted from the [Syncing a + Fork](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork) + tutorial from GitHub. + + ``` shell + # Fetch the branches and their respective commits from the upstream repository + git fetch base + + # Check out your fork's local default branch + git checkout main + + # Merge the changes from the upstream default branch + git merge base/main + + # Push the changes to your fork + git push -u origin + ``` + + You can now create a [Pull + Request](https://guides.github.com/activities/hello-world/#pr) from + the default branch on your fork, `main`, into your working branch, + e.g. `method-method-name-task-name`. + +10. Wait for all tests to pass on your new branch before pushing changes + (as this will allow GitHub Actions to cache the workflow setup, + which speeds up testing.) + +## API + +Each task consists of datasets, methods, and metrics. + +Datasets should take no arguments and return an AnnData object. If +`test is True`, then the method should load the full dataset, but only +return a small version of the same data (preferably \<200 cells and +\<500 genes) for faster downstream analysis. + +``` text +function dataset(bool test=False) -> AnnData adata +``` + +Methods should take an AnnData object and store a) the output in +`adata.obs` / `adata.obsm` / etc., according to the specification of the +task and b) the version of the package used to run the method in +`adata.uns["method_code_version"]`. If `test is True`, you may modify +hyperparameters (e.g. number of iterations) to make the method run +faster. + +``` text +function method(AnnData adata, bool test=False) -> AnnData adata +``` + +If your method takes hyperparameters, set them as keyword arguments in +the method definition. If the hyperparameters change depending on the +value of `test`, set the keyword argument to `None` and set them to your +chosen defaults only if the passed value is `None`. For an example, see +[harmonic +alignment](openproblems/tasks/multimodal_data_integration/methods/harmonic_alignment.py). + +Metrics should take an AnnData object and return a `float`. + +``` text +function metric(AnnData adata) -> float +``` + +Task-specific APIs are described in the README for each task. + +- [Label Projection](openproblems/tasks/label_projection) +- [Multimodal Data + Integration](openproblems/tasks/multimodal_data_integration) + +### Writing functions in R + +Metrics and methods can also be written in R. AnnData Python objects are +converted to and from `SingleCellExperiment` R objects using +[`anndata2ri`](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/). +R methods should be written in a `.R` file which assumes the existence +of a `SingleCellExperiment` object called `sce`, and should return the +same object. A simple method implemented in R could be written as +follows: + +``` r +### tasks//methods/pca.R +# Dependencies +library(SingleCellExperiment) +library(stats) + +# Method body +n_pca <- 10 +counts <- t(assay(sce, "X")) +reducedDim(sce, "pca") <- prcomp(counts)[,1:n_pca] + +# Return +sce +``` + +``` python +### tasks//methods/pca.py +from ....tools.conversion import r_function +from ....tools.decorators import method +from ....tools.utils import check_r_version + +_pca = r_function("pca.R") + + +@method( + method_name="PCA", + paper_name="On lines and planes of closest fit to systems of points in space", + paper_url="https://www.tandfonline.com/doi/abs/10.1080/14786440109462720", + paper_year=1901, + code_url="https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp", + image="openproblems-r-base", +) +def pca(adata): + adata.uns["method_code_version"] = check_r_version("stats"), + return _pca(adata) +``` + +See the [`anndata2ri` +docs](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/) for API +details. For a more detailed example of how to use this functionality, +see our implementation of fastMNN batch correction +([mnn.R](openproblems/tasks/multimodal_data_integration/methods/mnn.R), +[mnn.py](openproblems/tasks/multimodal_data_integration/methods/mnn.py)). + +### Adding package dependencies + +If you are unable to write your method using our base dependencies, you +may add to our existing Docker images, or create your own. The image you +wish to use (if you are not using the base image) should be specified in +the `image` keyword argument of the method/metric decorator. See the +[Docker images README](docker/README.md) for details. + +For the target method or metric, image-specific packages can then be +imported in the associated python file (i.e. `f2.py`). Importantly, the +import statement must be located in the function that calls the method +or metric. If this is the `f2` function, the first few lines of the +function may be structured as follows: + +``` python +def f2(adata): + import package1 + import package2 +``` + +### Adding a new dataset + +Datasets are loaded under `openproblems/data`. Each data loading +function should download the appropriate dataset from a stable location +(e.g. from Figshare) be decorated with +`openproblems.data.utils.loader(data_url="https://data.link", data_reference="https://doi.org/10.0/123")` +in order to cache the result. + +Data should be provided in a raw count format. We assume that `adata.X` +contains the raw (count) data for the primary modality; this will also +be copied to `adata.layers["counts"]` for permanent access to the raw +data. Additional modalities should be stored in `adata.obsm`. +Prenormalized data (if available) can be stored in `adata.layers`, +preferably using a name corresponding to the equivalent [normalization +function](./openproblems/tools/normalize.py) (e.g., +`adata.layers["log_scran_pooling"]`). + +To see a gold standard loader, look at +[openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py](./openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py) + +This file name should match +`[First Author Last Name]_[Year Published]_short_Description_of_data.py`. +E.g. the dataset of zebrafish embryos perturbed with CRISPR published in +2018 by Wagner *et al.* becomes `Wagner_2018_zebrafish_embryo_CRISPR.py` + +### Adding a dataset / method / metric to a task + +To add a dataset, method, or metric to a task, simply create a new `.py` +file corresponding to your proposed new functionality and import the +main function in the corresponding `__init__.py`. E.g., to add a “F2” +metric to the label projection task, we would create +`openproblems/tasks/label_projection/metrics/f2.py` and add a line + +``` python +from .f2 import f2 +``` + +to +[`openproblems/tasks/label_projection/metrics/__init__.py`](openproblems/tasks/label_projection/metrics/__init__.py). + +For datasets in particular, these should be loaded using a `loader` +function from `openproblems.data`, with only task-specific annotations +added in the task-specific data file. + +Datasets, methods, and metrics should all be decorated with the +appropriate function in `openproblems.tools.decorators` to include +metadata required for the evaluation and presentation of results. + +Note that data is not normalized in the data loader; normalization +should be performed as part of each method or in the task dataset +function if stated in the task API. For ease of use, we provide a +collection of common normalization functions in +[`openproblems.tools.normalize`](openproblems/tools/normalize.py). The +original data stored in `adata.X` is automatically stored in +`adata.layers["counts"]` for later reference in the case the a metric +needs to access the unnormalized data. + +#### Testing method performance + +To test the performance of a dataset, method, or metric, you can use the +command-line interface `openproblems-cli test`. + +First, you must launch a Docker image containing the relevant +dependencies for the dataset/method/metric you wish to test. You can +then run `openproblems-cli test` with any/all of `--dataset`, +`--method`, and `--metric` as desired. E.g., + +``` bash +cd openproblems +docker run \ + -v $(pwd):/usr/src/singlecellopenproblems -v /tmp:/tmp \ + -it singlecellopenproblems/openproblems-python-extras bash +openproblems-cli test \ + --task label_projection \ + --dataset zebrafish_labels \ + --method logistic_regression_log_cpm \ + --metric f1 +``` + +which will print the benchmark score for the method evaluated by the +metric on the dataset you chose. + +Notes: + +- If you have updated Docker images to run your method, you must first + rebuild the images – see the [Docker README](docker/README.md) for + details. +- If your dataset/method/metric cannot be run on the same docker + image, you may wish to `load`, `run`, and `evaluate` separately. You + can do this using each of these commands independently; however, + this workflow is not documented. +- These commands are not guaranteed to work with Apple silicon (M1 + chip). +- If your local machine cannot run the test due to memory constraints + or OS incompatibility, you may use your AWS credentials to launch a + VM for testing purposes. See the [EC2 README](./EC2.md) for details. + +### Adding a new task + +The task directory structure is as follows + +``` text +openproblems/ + - tasks/ + - task_name/ + - README.md + - __init__.py + - api.py + - datasets/ + - __init__.py + - dataset1.py + - ... + - methods/ + - __init__.py + - method1.py + - ... + - metrics/ + - __init__.py + - metric1.py + - ... +``` + +`task_name/__init__.py` can be copied from an existing task. + +`api.py` should implement the following functions: + + + +``` text +check_dataset(AnnData adata) -> bool # checks that a dataset fits the task-specific schema +check_method(AnnData adata) -> bool # checks that the output from a method fits the task-specific schema +sample_dataset() -> AnnData adata # generates a simple dataset the fits the expected API +sample_method(AnnData adata) -> AnnData adata # applies a simple modification that fits the method API +``` + + + +`README.md` should contain a description of the task as will be +displayed on the website, followed by a description of the task API for +dataset/method/metric authors. Note: everything after `## API` will be +discarded in generating the webpage for the task. + +For adding datasets, methods and metrics, see above. + +### Adding a new Docker container + +Datasets, methods and metrics run inside Docker containers. We provide a +few to start with, but if you have specific requirements, you may need +to modify an existing image or add a new one. See the [Docker +README](docker/README.md) for details. + +## Code Style and Testing + +`openproblems` is maintained at close to 100% code coverage. For +datasets, methods, and metrics, tests are generated programatically from +each task’s `api.py`. See the [Adding a new task](#adding-a-new-task) +section for instructions on creating this file. + +For additions outside this core functionality, contributors are +encouraged to write tests for their code – but if you do not know how to +do so, please do not feel discouraged from contributing code! Others can +always help you test your contribution. + +Code is tested by GitHub Actions when you push your changes. However, if +you wish to test locally, you can do so with the following command: + +``` shell +cd openproblems +pip install --editable .[test,r] +pytest -v +``` + +You may run specific tests quickly with + +``` shell +PYTEST_MAX_RETRIES=0 pytest -k my_task +``` + +The test suite also requires Python\>=3.7, R\>=4.0, and Docker to be +installed. + +The benchmarking suite is tested by GitHub Actions when you push your +changes. However, if you wish to test locally, you can do so with the +following command: + +``` shell +cd workflow +snakemake -j 4 docker +cd .. +nextflow run -resume -profile test,docker openproblems-bio/nf-openproblems +``` + +The benchmarking suite also requires Python\>=3.7, snakemake, nextflow, +and Docker to be installed. + +Code style is dictated by +[`black`](https://pypi.org/project/black/#installation-and-usage) and +[`flake8`](https://flake8.pycqa.org/en/latest/) with +[`hacking`](https://github.com/openstack/hacking). Code is automatically +reformatted by [`pre-commit`](https://pre-commit.com/) when you push to +GitHub. + +## Code of Conduct + +We abide by the principles of openness, respect, and consideration of +others of the Python Software Foundation: + and by the Contributor +Covenant. See our [Code of Conduct](CODE_OF_CONDUCT.md) for details. + +## Attribution + +This `CONTRIBUTING.md` was adapted from +[scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/main/CONTRIBUTING.md). diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd new file mode 100644 index 0000000000..85b702220d --- /dev/null +++ b/CONTRIBUTING.qmd @@ -0,0 +1,446 @@ +--- +title: Contributing to OpenProblems +engine: knitr +format: gfm +--- + +```{r setup, echo=FALSE} +repo="https://github.com/openproblems-bio/openproblems-v2" +``` + +[OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). + +## Code of conduct {#code-of-conduct} + +We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. + +Our [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + + +## Ways to contribute + +There are many ways to contribute to OpenProblems, with the most common ones being contribution of code or documentation to the project. + +Contributing new functionality usually comes in the form of new [datasets](#adding-a-new-dataset), [methods](#adding-a-new-method), [metric](#adding-a-new-metric), or even entire new [tasks](#adding-a-new-task). + +Improving the documentation is no less important than improving the library itself. If you find a typo in the documentation, or have made improvements, do not hesitate to submit a [GitHub pull request](https://github.com/openproblems-bio/openproblems-v2/pulls). + +But there are many other ways to help. In particular helping to [improve, triage, and investigate issues](#bug-triaging) and [reviewing other developers' pull requests](#code-review) are very valuable contributions that decrease the burden on the project maintainers. + +Another way to contribute is to report [issues you're facing](#submitting-a-bug-report-or-feature-request), and give a "thumbs up" on issues that others reported and that are relevant to you. It also helps us if you spread the word: reference the project from your blog and articles, link to it from your website, or simply star to say "I use it": + +Star + + + +## Submitting New Features + +To submit new features to Open Problems for Single Cell Analysis, follow the steps +below: + +1. Search through the [GitHub + Issues](https://github.com/openproblems-bio/openproblems-v2/issues) tracker to make sure + there isn't someone already working on the feature you'd like to add. If someone is + working on this, post in that issue that you'd like to help or reach out to one of + the contributors working on the issue directly. +2. If there isn't an existing issue tracking this feature, create one! There are several + templates you can choose one depending on what type of feature you'd like to add. +3. Fork into your account. If you're + new to `git`, you might find the [Fork a + repo](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) + documentation helpful. + ![](" width=400px> +4. Set up [tower.nf](https://tower.nf) and make sure you have access to + [`openproblems-bio`](https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch). + If you do not have access, please contact us at + [singlecellopenproblems@protonmail.com](mailto:singlecellopenproblems@protonmail.com). +5. Create repository secrets (*not environment secrets*) + [https://github.com/USERNAME/openproblems/settings/secrets](https://github.com/USERNAME/openproblems/settings/secrets) + * *AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are included in your AWS login + details. If you do not have these, please contact us at + [singlecellopenproblems@protonmail.com](mailto:singlecellopenproblems@protonmail.com).* + * *TOWER_ACCESS_KEY: log in with GitHub to and create a token at + .* + * When you are done with this step, your page should look like this: + ![AWS secrets success](static/img/AWS_secret.png) + +6. Enable workflows at + [https://github.com/USERNAME/openproblems/actions](https://github.com/USERNAME/openproblems/actions). +7. Set up your git repository to fetch branches from `base` at + `openproblems-bio/openproblems` + + ```shell + git clone git@github.com:/openproblems.git + cd openproblems + git remote add base git@github.com:openproblems-bio/openproblems.git + git fetch --all + git branch --set-upstream-to base/main + git pull + ``` + + **Note:** If you haven't set up SSH keys with your GitHub account, you may see this + error message when adding `base` to your repository: + + ```text + git@github.com: Permission denied (publickey). + fatal: Could not read from remote repository. + Please make sure you have the correct access rights + ``` + + To generate an SSH key and add it to your GitHub account, follow [this tutorial from + GitHub](https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account). + +8. Create a new branch for your task (**no underscores or spaces allowed**). It is best + to coordinate with other people working on the same feature as you so that there + aren't clases in images uploaded to our ECR. Here we're creating a branch called + `method-method-name-task-name`, but if you were creating a new metric you might use + `metric-metric-name-task-name`. In practice you should actually use the name of your + method or metric, like `method-meld-differential-abundance` or + `metric-mse-label-projection`. + + **Note:** This pushes the branch to your fork, *not to* `base`. You will create a PR + to merge your branch to `base` only after all tests are passing. + + **Warning:** Do not edit the `main` branch on your fork! This will not work as + expected, and will never pass tests. + + ```shell + # IMPORTANT: choose a new branch name, e.g. + git checkout -b method-method-name-task-name # or metric-new-metric-name, etc + git push -u origin method-method-name-task-name + ``` + +9. Sometimes, changes might be made to the openproblems `base` repository that you want + to incorporate into your fork. To sync your fork from `base`, use the following code + adapted from the [Syncing a + Fork](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork) + tutorial from GitHub. + + ```shell + # Fetch the branches and their respective commits from the upstream repository + git fetch base + + # Check out your fork's local default branch + git checkout main + + # Merge the changes from the upstream default branch + git merge base/main + + # Push the changes to your fork + git push -u origin + ``` + + You can now create a [Pull + Request](https://guides.github.com/activities/hello-world/#pr) from the default + branch on your fork, `main`, into your working branch, e.g. + `method-method-name-task-name`. + +10. Wait for all tests to pass on your new branch before pushing changes (as this will + allow GitHub Actions to cache the workflow setup, which speeds up testing.) + +## API + +Each task consists of datasets, methods, and metrics. + +Datasets should take no arguments and return an AnnData object. If `test is True`, then +the method should load the full dataset, but only return a small version of the same +data (preferably <200 cells and <500 genes) for faster downstream analysis. + +```text +function dataset(bool test=False) -> AnnData adata +``` + +Methods should take an AnnData object and store a) the output in `adata.obs` / +`adata.obsm` / etc., according to the specification of the task and b) the version of +the package used to run the method in `adata.uns["method_code_version"]`. If `test is +True`, you may modify hyperparameters (e.g. number of iterations) to make the method run +faster. + +```text +function method(AnnData adata, bool test=False) -> AnnData adata +``` + +If your method takes hyperparameters, set them as keyword arguments in the method +definition. If the hyperparameters change depending on the value of `test`, set the +keyword argument to `None` and set them to your chosen defaults only if the passed value +is `None`. For an example, see [harmonic +alignment](openproblems/tasks/multimodal_data_integration/methods/harmonic_alignment.py). + +Metrics should take an AnnData object and return a `float`. + +```text +function metric(AnnData adata) -> float +``` + +Task-specific APIs are described in the README for each task. + +* [Label Projection](openproblems/tasks/label_projection) +* [Multimodal Data Integration](openproblems/tasks/multimodal_data_integration) + +### Writing functions in R + +Metrics and methods can also be written in R. AnnData Python objects are converted to +and from `SingleCellExperiment` R objects using +[`anndata2ri`](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/). R methods +should be written in a `.R` file which assumes the existence of a `SingleCellExperiment` +object called `sce`, and should return the same object. A simple method implemented in R +could be written as follows: + +```R +### tasks//methods/pca.R +# Dependencies +library(SingleCellExperiment) +library(stats) + +# Method body +n_pca <- 10 +counts <- t(assay(sce, "X")) +reducedDim(sce, "pca") <- prcomp(counts)[,1:n_pca] + +# Return +sce +``` + +```python +### tasks//methods/pca.py +from ....tools.conversion import r_function +from ....tools.decorators import method +from ....tools.utils import check_r_version + +_pca = r_function("pca.R") + + +@method( + method_name="PCA", + paper_name="On lines and planes of closest fit to systems of points in space", + paper_url="https://www.tandfonline.com/doi/abs/10.1080/14786440109462720", + paper_year=1901, + code_url="https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp", + image="openproblems-r-base", +) +def pca(adata): + adata.uns["method_code_version"] = check_r_version("stats"), + return _pca(adata) +``` + +See the [`anndata2ri` docs](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/) +for API details. For a more detailed example of how to use this functionality, see our +implementation of fastMNN batch correction +([mnn.R](openproblems/tasks/multimodal_data_integration/methods/mnn.R), +[mnn.py](openproblems/tasks/multimodal_data_integration/methods/mnn.py)). + +### Adding package dependencies + +If you are unable to write your method using our base dependencies, you may add to our +existing Docker images, or create your own. The image you wish to use (if you are not +using the base image) should be specified in the `image` keyword argument of the +method/metric decorator. See the [Docker images README](docker/README.md) for details. + +For the target method or metric, image-specific packages can then be imported in the +associated python file (i.e. `f2.py`). Importantly, the import statement must be located +in the function that calls the method or metric. If this is the `f2` function, the first +few lines of the function may be structured as follows: + +```python +def f2(adata): + import package1 + import package2 +``` + +### Adding a new dataset + +Datasets are loaded under `openproblems/data`. Each data loading function should +download the appropriate dataset from a stable location (e.g. from Figshare) be +decorated with `openproblems.data.utils.loader(data_url="https://data.link", +data_reference="https://doi.org/10.0/123")` in order to cache the result. + +Data should be provided in a raw count format. We assume that `adata.X` contains the raw +(count) data for the primary modality; this will also be copied to +`adata.layers["counts"]` for permanent access to the raw data. Additional modalities +should be stored in `adata.obsm`. Prenormalized data (if available) can be stored in +`adata.layers`, preferably using a name corresponding to the equivalent [normalization +function](./openproblems/tools/normalize.py) (e.g., +`adata.layers["log_scran_pooling"]`). + +To see a gold standard loader, look at +[openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py](./openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py) + +This file name should match +`[First Author Last Name]_[Year Published]_short_Description_of_data.py`. E.g. the +dataset of zebrafish embryos perturbed with CRISPR published in 2018 by Wagner *et al.* +becomes `Wagner_2018_zebrafish_embryo_CRISPR.py` + +### Adding a dataset / method / metric to a task + +To add a dataset, method, or metric to a task, simply create a new `.py` file +corresponding to your proposed new functionality and import the main function in the +corresponding `__init__.py`. E.g., to add a "F2" metric to the label projection task, we +would create `openproblems/tasks/label_projection/metrics/f2.py` and add a line + +```python +from .f2 import f2 +``` + +to +[`openproblems/tasks/label_projection/metrics/__init__.py`](openproblems/tasks/label_projection/metrics/__init__.py). + +For datasets in particular, these should be loaded using a `loader` function from +`openproblems.data`, with only task-specific annotations added in the task-specific data +file. + +Datasets, methods, and metrics should all be decorated with the appropriate function in +`openproblems.tools.decorators` to include metadata required for the evaluation and +presentation of results. + +Note that data is not normalized in the data loader; normalization should be performed +as part of each method or in the task dataset function if stated in the task API. For +ease of use, we provide a collection of common normalization functions in +[`openproblems.tools.normalize`](openproblems/tools/normalize.py). The original data +stored in `adata.X` is automatically stored in `adata.layers["counts"]` for later +reference in the case the a metric needs to access the unnormalized data. + +#### Testing method performance + +To test the performance of a dataset, method, or metric, you can use the command-line +interface `openproblems-cli test`. + +First, you must launch a Docker image containing the relevant dependencies for the +dataset/method/metric you wish to test. You can then run `openproblems-cli test` with +any/all of `--dataset`, `--method`, and `--metric` as desired. E.g., + +```bash +cd openproblems +docker run \ + -v $(pwd):/usr/src/singlecellopenproblems -v /tmp:/tmp \ + -it singlecellopenproblems/openproblems-python-extras bash +openproblems-cli test \ + --task label_projection \ + --dataset zebrafish_labels \ + --method logistic_regression_log_cpm \ + --metric f1 +``` + +which will print the benchmark score for the method evaluated by the metric on the +dataset you chose. + +Notes: + +* If you have updated Docker images to run your method, you must first rebuild the + images -- see the [Docker README](docker/README.md) for details. +* If your dataset/method/metric cannot be run on the same docker image, you may wish to + `load`, `run`, and `evaluate` separately. You can do this using each of these commands + independently; however, this workflow is not documented. +* These commands are not guaranteed to work with Apple silicon (M1 chip). +* If your local machine cannot run the test due to memory constraints or OS + incompatibility, you may use your AWS credentials to launch a VM for testing purposes. + See the [EC2 README](./EC2.md) for details. + +### Adding a new task + +The task directory structure is as follows + +```text +openproblems/ + - tasks/ + - task_name/ + - README.md + - __init__.py + - api.py + - datasets/ + - __init__.py + - dataset1.py + - ... + - methods/ + - __init__.py + - method1.py + - ... + - metrics/ + - __init__.py + - metric1.py + - ... +``` + +`task_name/__init__.py` can be copied from an existing task. + +`api.py` should implement the following functions: + + +```text +check_dataset(AnnData adata) -> bool # checks that a dataset fits the task-specific schema +check_method(AnnData adata) -> bool # checks that the output from a method fits the task-specific schema +sample_dataset() -> AnnData adata # generates a simple dataset the fits the expected API +sample_method(AnnData adata) -> AnnData adata # applies a simple modification that fits the method API +``` + + +`README.md` should contain a description of the task as will be displayed on the +website, followed by a description of the task API for dataset/method/metric authors. +Note: everything after `## API` will be discarded in generating the webpage for the +task. + +For adding datasets, methods and metrics, see above. + +### Adding a new Docker container + +Datasets, methods and metrics run inside Docker containers. We provide a few to start +with, but if you have specific requirements, you may need to modify an existing image or +add a new one. See the [Docker README](docker/README.md) for details. + +## Code Style and Testing + +`openproblems` is maintained at close to 100% code coverage. For datasets, methods, and +metrics, tests are generated programatically from each task's `api.py`. See the [Adding +a new task](#adding-a-new-task) section for instructions on creating this file. + +For additions outside this core functionality, contributors are encouraged to write +tests for their code -- but if you do not know how to do so, please do not feel +discouraged from contributing code! Others can always help you test your contribution. + +Code is tested by GitHub Actions when you push your changes. However, if you wish to +test locally, you can do so with the following command: + +```shell +cd openproblems +pip install --editable .[test,r] +pytest -v +``` + +You may run specific tests quickly with + +```shell +PYTEST_MAX_RETRIES=0 pytest -k my_task +``` + +The test suite also requires Python>=3.7, R>=4.0, and Docker to be installed. + +The benchmarking suite is tested by GitHub Actions when you push your changes. However, +if you wish to test locally, you can do so with the following command: + +```shell +cd workflow +snakemake -j 4 docker +cd .. +nextflow run -resume -profile test,docker openproblems-bio/nf-openproblems +``` + +The benchmarking suite also requires Python>=3.7, snakemake, nextflow, and Docker to be +installed. + +Code style is dictated by +[`black`](https://pypi.org/project/black/#installation-and-usage) and +[`flake8`](https://flake8.pycqa.org/en/latest/) with +[`hacking`](https://github.com/openstack/hacking). Code is automatically reformatted by +[`pre-commit`](https://pre-commit.com/) when you push to GitHub. + +## Code of Conduct + +We abide by the principles of openness, respect, and consideration of others +of the Python Software Foundation: and by +the Contributor Covenant. See our [Code of Conduct](CODE_OF_CONDUCT.md) for details. + +## Attribution + +This `CONTRIBUTING.md` was adapted from +[scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/main/CONTRIBUTING.md). From eb796281c58c7e03d5b3b3ae0bc63dd94ebeb85d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 08:30:53 +0100 Subject: [PATCH 0262/1233] update Former-commit-id: 8c78ba0df513445e7947f97ac2a7d0360109b900 --- CONTRIBUTING.md | 7 ++++--- CONTRIBUTING.qmd | 7 ++----- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 20c07522cc..79dbe4a392 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -17,9 +17,9 @@ race, caste, color, religion, or sexual identity and orientation. We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. -Our [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the -\[Contributor Covenant\]\[homepage\], version 2.1, available at -\[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html\]\[v2.1\]. +Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the +[Contributor Covenant](https://www.contributor-covenant.org), version +2.1. ## Ways to contribute @@ -50,6 +50,7 @@ it”: Star + ## Submitting New Features diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 85b702220d..649f42e3c7 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -4,10 +4,6 @@ engine: knitr format: gfm --- -```{r setup, echo=FALSE} -repo="https://github.com/openproblems-bio/openproblems-v2" -``` - [OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). ## Code of conduct {#code-of-conduct} @@ -16,7 +12,7 @@ We as members, contributors, and leaders pledge to make participation in our com We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community. -Our [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant][homepage], version 2.1, available at [https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. +Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1. ## Ways to contribute @@ -34,6 +30,7 @@ Another way to contribute is to report [issues you're facing](#submitting-a-bug- Star + ## Submitting New Features From 52c6ddd77650719060cfd512f0ecc2df3bc9fd44 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 08:57:45 +0100 Subject: [PATCH 0263/1233] Rename random_celltype to random_labels, fix metadata Former-commit-id: 358db55bfb0f68f6afc4853fa8d91718eb9d5179 --- .../config.vsh.yaml | 11 ++++------- .../{random_celltype => random_labels}/script.py | 0 .../{random_celltype => random_labels}/test_script.py | 0 src/label_projection/workflows/run/main.nf | 4 ++-- 4 files changed, 6 insertions(+), 9 deletions(-) rename src/label_projection/control_methods/{random_celltype => random_labels}/config.vsh.yaml (81%) rename src/label_projection/control_methods/{random_celltype => random_labels}/script.py (100%) rename src/label_projection/control_methods/{random_celltype => random_labels}/test_script.py (100%) diff --git a/src/label_projection/control_methods/random_celltype/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml similarity index 81% rename from src/label_projection/control_methods/random_celltype/config.vsh.yaml rename to src/label_projection/control_methods/random_labels/config.vsh.yaml index cc5e44bcba..f4a77636f5 100644 --- a/src/label_projection/control_methods/random_celltype/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: "random_celltype" + name: "random_labels" namespace: "label_projection/control_methods" version: "dev" description: "Random Labels dummy" @@ -7,12 +7,9 @@ functionality: type: negative_control label: Random prediction authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } + - name: "Nikolay Markov" + roles: [ author, maintainer ] + props: { github: mxposed } arguments: - name: "--input" type: "file" diff --git a/src/label_projection/control_methods/random_celltype/script.py b/src/label_projection/control_methods/random_labels/script.py similarity index 100% rename from src/label_projection/control_methods/random_celltype/script.py rename to src/label_projection/control_methods/random_labels/script.py diff --git a/src/label_projection/control_methods/random_celltype/test_script.py b/src/label_projection/control_methods/random_labels/test_script.py similarity index 100% rename from src/label_projection/control_methods/random_celltype/test_script.py rename to src/label_projection/control_methods/random_labels/test_script.py diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index c73d97b1ef..06e632a00b 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -17,7 +17,7 @@ include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/ // import methods include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" -include { random_celltype } from "$targetDir/label_projection/control_methods/random_celltype/main.nf" +include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" @@ -106,7 +106,7 @@ workflow { | (log_cpm & log_scran_pooling) | mix | map { unique_file_name(it) } - | (knn_classifier & mlp0 & lr0 & random_celltype & majority_vote & all_correct) + | (knn_classifier & mlp0 & lr0 & random_labels & majority_vote & all_correct) | mix | map { unique_file_name(it) } | (accuracy & f1a) From 6f1131ee1a5c8a0cfc4551ce04a871a16f94e4cd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 10:57:30 +0100 Subject: [PATCH 0264/1233] bump viash version Former-commit-id: 331e73c232be9a05aecb728469a9946a29fcfafd --- bin/init | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bin/init b/bin/init index 5cd42d8bcf..9654ac84d1 100755 --- a/bin/init +++ b/bin/init @@ -10,8 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.5.15 \ - --nextflow_variant vdsl3 + --tag develop cd bin From 5230ebc2d9d44e7df8b9f7a9a6cca84c33dc01ed Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 13:32:09 +0100 Subject: [PATCH 0265/1233] rename tests to test resources Former-commit-id: 71d18ec80d3068b312a8a597015e445f2c13ccd5 --- src/common/dataset_concatenate/config.vsh.yaml | 2 +- src/common/dataset_loader/download/config.vsh.yaml | 2 +- .../control_methods/all_correct/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../data_processing/normalize/log_cpm/config.vsh.yaml | 2 +- .../data_processing/normalize/scran/config.vsh.yaml | 2 +- src/label_projection/data_processing/subsample/config.vsh.yaml | 2 +- src/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/modality_alignment/datasets/sample_dataset/config.vsh.yaml | 2 +- src/modality_alignment/datasets/scprep_csv/config.vsh.yaml | 2 +- .../methods/harmonic_alignment/config.vsh.yaml | 2 +- src/modality_alignment/methods/mnn/config.vsh.yaml | 2 +- src/modality_alignment/methods/sample_method/config.vsh.yaml | 2 +- src/modality_alignment/methods/scot/config.vsh.yaml | 2 +- src/modality_alignment/metrics/knn_auc/config.vsh.yaml | 2 +- src/modality_alignment/metrics/mse/config.vsh.yaml | 2 +- 18 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index d6dbd6a7a3..6b4d1af962 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index f11782ef8a..1332668397 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py platforms: diff --git a/src/label_projection/control_methods/all_correct/config.vsh.yaml b/src/label_projection/control_methods/all_correct/config.vsh.yaml index c5cf7ecf0e..d2eea25541 100644 --- a/src/label_projection/control_methods/all_correct/config.vsh.yaml +++ b/src/label_projection/control_methods/all_correct/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 751b6ce77f..4d5f0ecdf2 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index f4a77636f5..f886407b04 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml index 606c122850..ff9d1107f4 100644 --- a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml index 24b46e76e2..11cae6217d 100644 --- a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: resources: - type: r_script path: script.R - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index 23c595a9b1..f786fb7d14 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - type: file diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 151e55c940..c688a31831 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 920865c28e..6d25194538 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test_script.py - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" diff --git a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml index 8d388d82b2..04d9c26a80 100644 --- a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml +++ b/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: - type: python_script path: script.py - path: "../../utils/utils.py" - tests: + test_resources: - type: python_script path: test.py platforms: diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml index e8efc7423c..799336bbf9 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: - type: python_script path: script.py - path: "../../utils/utils.py" - tests: + test_resources: - type: python_script path: test.py platforms: diff --git a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml index 4cb6eadc62..acad005672 100644 --- a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml +++ b/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: - type: python_script path: ./script.py - path: "../../utils/preprocessing.py" - tests: + test_resources: - type: python_script path: test.py - path: "../../resources/sample_dataset.h5ad" diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/modality_alignment/methods/mnn/config.vsh.yaml index 58acdcf477..98598cbb3b 100644 --- a/src/modality_alignment/methods/mnn/config.vsh.yaml +++ b/src/modality_alignment/methods/mnn/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: resources: - type: r_script path: ./script.R - tests: + test_resources: - type: python_script path: test.py - path: "../../resources/sample_dataset.h5ad" diff --git a/src/modality_alignment/methods/sample_method/config.vsh.yaml b/src/modality_alignment/methods/sample_method/config.vsh.yaml index 21a4f1ef32..f83d4a16ba 100644 --- a/src/modality_alignment/methods/sample_method/config.vsh.yaml +++ b/src/modality_alignment/methods/sample_method/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: resources: - type: python_script path: ./script.py - tests: + test_resources: - type: python_script path: test.py - path: "../../resources/sample_dataset.h5ad" diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/modality_alignment/methods/scot/config.vsh.yaml index f4b193ead1..2bb4f829f5 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/modality_alignment/methods/scot/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: - type: python_script path: script.py - path: "../../utils/preprocessing.py" - tests: + test_resources: - type: python_script path: test.py - path: "../../resources/sample_dataset.h5ad" diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index e96966dd7f..5a1106b865 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - path: ../../resources/sample_output.h5ad diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml index 6c7eecd29c..e5f01eac99 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: resources: - type: python_script path: ./script.py - tests: + test_resources: - type: python_script path: test.py - path: ../../resources/sample_output.h5ad From d494a59b74af57400ea0ff8dc502b0638fdd6273 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 13:55:47 +0100 Subject: [PATCH 0266/1233] refactor dataset_loader component Former-commit-id: 9f8712bd6b3bfd5f66bab39e265b628901802152 --- .../dataset_loader/download/config.vsh.yaml | 46 +++++++++++++++---- src/common/dataset_loader/download/script.py | 5 +- src/common/dataset_loader/download/test.py | 11 +++-- 3 files changed, 47 insertions(+), 15 deletions(-) diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 1332668397..db25164f5b 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -4,17 +4,10 @@ functionality: version: "dev" description: "Download a dataset." authors: - - name: "Michaela Mueller " + - name: "Michaela Mueller" roles: [ maintainer, author ] props: { github: mumichae } arguments: - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file of the cleaned dataset" - required: true - name: "--url" type: "string" description: "URL of dataset" @@ -33,6 +26,42 @@ functionality: - name: "--obs_tissue" type: "string" description: "Location of where to find the observation tissue information." + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output h5ad file of the cleaned dataset" + required: true + info: + slots: + X: + type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: celltype + description: Cell type labels + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: false + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + required: false resources: - type: python_script path: script.py @@ -47,5 +76,4 @@ platforms: packages: - scanpy - "anndata<0.8" - - type: native - type: nextflow diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index a95b85ffaf..ced84d1c69 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -30,14 +30,17 @@ print("Reading file") adata = sc.read_h5ad(filepath) -print("Copying .layers['counts'] to .X") if "counts" in adata.layers: + print("Copying .layers['counts'] to .X") adata.X = adata.layers["counts"] del adata.layers["counts"] print("Setting .uns['dataset_id']") adata.uns["dataset_id"] = par["name"] +print("Setting .uns['raw_dataset_id']") +adata.uns["raw_dataset_id"] = par["name"] + print("Setting .obs['celltype']") if par["obs_celltype"]: if par["obs_celltype"] in adata.obs: diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py index 427acbac5c..af8028a26e 100644 --- a/src/common/dataset_loader/download/test.py +++ b/src/common/dataset_loader/download/test.py @@ -3,28 +3,29 @@ import scanpy as sc name = "pancreas" -anndata_file = "dataset.h5ad" +output = "dataset.h5ad" url = "https://ndownloader.figshare.com/files/24539828" obs_celltype = "celltype" obs_batch = "tech" print(">> Running script") out = subprocess.check_output([ - f"./{meta['functionality_name']}", + meta["executable"], "--url", url, "--name", name, "--obs_celltype", obs_celltype, "--obs_batch", obs_batch, - "--output", anndata_file + "--output", output ]).decode("utf-8") print(">> Checking whether file exists") -assert path.exists(anndata_file) +assert path.exists(output) print(">> Read output anndata") -adata = sc.read_h5ad(anndata_file) +adata = sc.read_h5ad(output) print(">> Check that output fits expected API") +assert adata.X is not None assert "counts" not in adata.layers assert adata.uns["dataset_id"] == name if obs_celltype: From 31b6eec4b63d14c2994a3e627815767a221c601e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 14:16:08 +0100 Subject: [PATCH 0267/1233] Allow changing the destination layer of the raw counts; refactor resource test script Former-commit-id: f55d2bc468a8faa27b63146b0c26d7a37ebf5995 --- .../dataset_loader/download/config.vsh.yaml | 8 +++- src/common/dataset_loader/download/script.py | 5 +++ src/common/dataset_loader/download/test.py | 12 +++++- src/common/resources_test_scripts/pancreas.sh | 37 ++++------------- .../resources_test_scripts/pancreas.sh | 41 +++++++++++++++++++ 5 files changed, 70 insertions(+), 33 deletions(-) create mode 100755 src/label_projection/data_processing/resources_test_scripts/pancreas.sh diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index db25164f5b..fc51daf02e 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -26,6 +26,10 @@ functionality: - name: "--obs_tissue" type: "string" description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "Location of where to store the counts data. Leave undefined to store in `.X`, else it will be stored in `.layers[par['layer_counts']]`." + example: counts - name: "--output" alternatives: ["-o"] type: "file" @@ -37,9 +41,9 @@ functionality: slots: X: type: integer - name: counts + name: counts # todo: this should depend on the value of 'layer_counts' description: Raw counts - required: true + required: false obs: - type: string name: celltype diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index ced84d1c69..f12fc00ee3 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -66,5 +66,10 @@ sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) +if par["layer_counts"]: + print(f"Copying .X back to .layers['{par['layer_counts']}']") + adata.layers[par["layer_counts"]] = adata.X + del adata.X + print("Writing adata to file") adata.write(par["output"], compression="gzip") diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py index af8028a26e..4fc48dfb40 100644 --- a/src/common/dataset_loader/download/test.py +++ b/src/common/dataset_loader/download/test.py @@ -7,6 +7,7 @@ url = "https://ndownloader.figshare.com/files/24539828" obs_celltype = "celltype" obs_batch = "tech" +layer_counts = "foobar" print(">> Running script") out = subprocess.check_output([ @@ -15,6 +16,7 @@ "--name", name, "--obs_celltype", obs_celltype, "--obs_batch", obs_batch, + "--layer_counts", layer_counts, "--output", output ]).decode("utf-8") @@ -24,9 +26,15 @@ print(">> Read output anndata") adata = sc.read_h5ad(output) +print(adata) + print(">> Check that output fits expected API") -assert adata.X is not None -assert "counts" not in adata.layers +if layer_counts is not None: + assert adata.X is None + assert layer_counts in adata.layers +else: + assert adata.X is not None + assert layer_counts not in adata.layers assert adata.uns["dataset_id"] == name if obs_celltype: assert "celltype" in adata.obs.columns diff --git a/src/common/resources_test_scripts/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh index 3f5a699413..9815b66bd4 100755 --- a/src/common/resources_test_scripts/pancreas.sh +++ b/src/common/resources_test_scripts/pancreas.sh @@ -9,35 +9,14 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -DATASET_DIR=resources_test/label_projection/pancreas +DATASET_DIR=resources_test/common/pancreas mkdir -p $DATASET_DIR -target/docker/common/dataset_loader/download/download\ - --url "https://ndownloader.figshare.com/files/24539828"\ - --obs_celltype "celltype"\ - --obs_batch "tech"\ - --name "pancreas"\ - --output $DATASET_DIR/raw_data.h5ad - -target/docker/label_projection/data_processing/subsample/subsample\ - --input $DATASET_DIR/raw_data.h5ad\ - --celltype_categories "acinar:beta"\ - --tech_categories "celseq:inDrop4:smarter"\ - --output $DATASET_DIR/toy_data.h5ad - -target/docker/label_projection/data_processing/randomize/randomize\ - --input $DATASET_DIR/toy_data.h5ad\ - --output $DATASET_DIR/toy_preprocessed_data.h5ad - -target/docker/label_projection/data_processing/normalize/log_cpm/log_cpm\ - --input $DATASET_DIR/toy_preprocessed_data.h5ad\ - --output $DATASET_DIR/toy_normalized_log_cpm_data.h5ad - -target/docker/label_projection/data_processing/normalize/scran/log_scran_pooling/log_scran_pooling\ - --input $DATASET_DIR/toy_preprocessed_data.h5ad\ - --output $DATASET_DIR/toy_normalized_log_scran_pooling_data.h5ad - -target/docker/label_projection/methods/baseline/majority_vote/majority_vote\ - --input $DATASET_DIR/toy_normalized_log_cpm_data.h5ad\ - --output $DATASET_DIR/toy_baseline_pred_data.h5ad +bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ + --url "https://ndownloader.figshare.com/files/24539828" \ + --obs_celltype "celltype" \ + --obs_batch "tech" \ + --name "pancreas" \ + --layer_counts "counts" \ + --output $DATASET_DIR/dataset.h5ad \ No newline at end of file diff --git a/src/label_projection/data_processing/resources_test_scripts/pancreas.sh b/src/label_projection/data_processing/resources_test_scripts/pancreas.sh new file mode 100755 index 0000000000..49ac510ba4 --- /dev/null +++ b/src/label_projection/data_processing/resources_test_scripts/pancreas.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/label_projection/pancreas + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +mkdir -p $DATASET_DIR + +bin/viash run src/label_projection/data_processing/subsample/config.vsh.yaml -- \ + --input $RAW_DATA \ + --celltype_categories "acinar:beta" \ + --tech_categories "celseq:inDrop4:smarter" \ + --output $DATASET_DIR/dataset_subsampled.h5ad + +bin/viash run src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset_subsampled.h5ad \ + --output $DATASET_DIR/dataset_subsampled_cpm.h5ad + +bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset_subsampled_cpm.h5ad \ + --output_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ + --output_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ + --output_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad + +bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ + --input_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ + --input_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ + --output $DATASET_DIR/dataset_subsampled_cpm_prediction.h5ad From ff8e82c331b8be680961a36d5e50eec7e6a4899d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 14:24:41 +0100 Subject: [PATCH 0268/1233] update subsample component Former-commit-id: 3166c44c0c47884f95f26c36101a24a757a6137c --- .../data_processing/subsample/config.vsh.yaml | 10 ++---- .../data_processing/subsample/script.py | 12 +++++-- .../data_processing/subsample/test_script.py | 35 +++++++++++-------- 3 files changed, 31 insertions(+), 26 deletions(-) diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index f786fb7d14..44a63ee97c 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -3,13 +3,6 @@ functionality: namespace: "label_projection/data_processing" version: "dev" description: "Component to generate a toy data for tests finality" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Saraiva Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } arguments: - name: "--input" type: "file" @@ -27,6 +20,7 @@ functionality: required: false - name: "--even" type: "boolean_true" + description: Evenly subsamples from different batches - name: "--output" alternatives: ["-o"] type: "file" @@ -41,7 +35,7 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../../resources_test/label_projection/pancreas" + path: "../../../../resources_test/common/pancreas" platforms: - type: native - type: docker diff --git a/src/label_projection/data_processing/subsample/script.py b/src/label_projection/data_processing/subsample/script.py index 46e6c3327b..80ba8b0492 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/label_projection/data_processing/subsample/script.py @@ -1,11 +1,11 @@ import scanpy as sc ### VIASH START par = { - "input": "../../../../resources_test/label_projection/pancreas/raw_data.h5ad", + "input": "resources_test/common/pancreas/dataset.h5ad", # "keep_celltype_categories": ["acinar", "beta"], # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], "even": True, - "ouput": "./toy_data.h5ad" + "ouput": "toy_data.h5ad" } ### VIASH END @@ -13,12 +13,15 @@ def filter_genes_cells(adata): """Remove empty cells and genes.""" sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) - return adata print(">> Load data") adata = sc.read(par['input']) + +# copy counts to .X because otherwise filter_genes and filter_cells won't work +adata.X = adata.layers["counts"] + if par.get('even'): keep_batch_categories = adata.obs["batch"].unique() adata_out = None @@ -53,5 +56,8 @@ def filter_genes_cells(adata): filter_genes_cells(adata) adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" +# remove previously copied .X +del adata.X + print(">> Writing data") adata.write(par['output']) diff --git a/src/label_projection/data_processing/subsample/test_script.py b/src/label_projection/data_processing/subsample/test_script.py index 4677a71539..f6a449783e 100644 --- a/src/label_projection/data_processing/subsample/test_script.py +++ b/src/label_projection/data_processing/subsample/test_script.py @@ -3,35 +3,40 @@ from os import path ### VIASH START +meta = { + "resources_dir": "resources_test/label_projection" +} ### VIASH END -INPUT = f"{meta['resources_dir']}/pancreas/raw_data.h5ad" -OUTPUT = "toy_data.h5ad" -print(">> Runing script as test for even") +input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" +output_path = "toy_data.h5ad" + +print(">> Running script as test for even") out = subprocess.check_output([ - "./" + meta["functionality_name"], - "--input", INPUT, - "--output", OUTPUT, + meta["executable"], + "--input", input_path, + "--output", output_path, "--even" ]).decode("utf-8") + print(">> Checking whether file exists") -assert path.exists(OUTPUT) +assert path.exists(output_path) print(">> Check that test output fits expected API") -adata = sc.read_h5ad(OUTPUT) -assert (495, 467) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) +adata = sc.read_h5ad(output_path) +assert (495, 467) == adata.layers["counts"].shape, "processed result data shape {}".format(adata.layers["counts"].shape) print(">> Runing script as test for specific batch and celltype categories") out = subprocess.check_output([ - "./" + meta["functionality_name"], - "--input", INPUT, + meta["executable"], + "--input", input_path, "--keep_celltype_categories", "acinar:beta", "--keep_batch_categories", "celseq:inDrop4:smarter", - "--output", OUTPUT + "--output", output_path ]).decode("utf-8") print(">> Checking whether file exists") -assert path.exists(OUTPUT) +assert path.exists(output_path) print(">> Check that test output fits expected API") -adata = sc.read_h5ad(OUTPUT) -assert (500, 443) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) +adata = sc.read_h5ad(output_path) +assert (500, 443) == adata.layers["counts"].shape, "processed result data shape {}".format(adata.layers["counts"].shape) From 2a95066466fb4aa0f3152b036ff658b72d4edf87 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 15:57:45 +0100 Subject: [PATCH 0269/1233] initial attempt at api Former-commit-id: 224b683a41d991ba61a000ea91b7a4427a628d7c --- .../api/anndata_prediction.yaml | 20 +++ .../api/anndata_preprocessed.yaml | 27 +++ .../api/anndata_raw_dataset.yaml | 21 +++ src/label_projection/api/anndata_score.yaml | 24 +++ .../api/anndata_solution.yaml | 27 +++ src/label_projection/api/anndata_test.yaml | 24 +++ src/label_projection/api/anndata_train.yaml | 27 +++ .../api/dataset_censoring.yaml | 160 +++--------------- .../api/dataset_preprocessing.yaml | 56 ------ src/label_projection/api/method.yaml | 129 ++++---------- src/label_projection/api/metric.yaml | 128 +++----------- src/label_projection/api/normalization.yaml | 48 ++++++ 12 files changed, 304 insertions(+), 387 deletions(-) create mode 100644 src/label_projection/api/anndata_prediction.yaml create mode 100644 src/label_projection/api/anndata_preprocessed.yaml create mode 100644 src/label_projection/api/anndata_raw_dataset.yaml create mode 100644 src/label_projection/api/anndata_score.yaml create mode 100644 src/label_projection/api/anndata_solution.yaml create mode 100644 src/label_projection/api/anndata_test.yaml create mode 100644 src/label_projection/api/anndata_train.yaml delete mode 100644 src/label_projection/api/dataset_preprocessing.yaml create mode 100644 src/label_projection/api/normalization.yaml diff --git a/src/label_projection/api/anndata_prediction.yaml b/src/label_projection/api/anndata_prediction.yaml new file mode 100644 index 0000000000..ef661079ed --- /dev/null +++ b/src/label_projection/api/anndata_prediction.yaml @@ -0,0 +1,20 @@ +type: file +description: "The prediction file" +example: "prediction.h5ad" +info: + short_description: "Prediction" + slots: + obs: + - type: string + name: label_pred + description: Predicted labels for the test cells. + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: method_id + description: "A unique identifier for the method" \ No newline at end of file diff --git a/src/label_projection/api/anndata_preprocessed.yaml b/src/label_projection/api/anndata_preprocessed.yaml new file mode 100644 index 0000000000..1b061a6579 --- /dev/null +++ b/src/label_projection/api/anndata_preprocessed.yaml @@ -0,0 +1,27 @@ +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: label + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/label_projection/api/anndata_raw_dataset.yaml b/src/label_projection/api/anndata_raw_dataset.yaml new file mode 100644 index 0000000000..fd7627d8d5 --- /dev/null +++ b/src/label_projection/api/anndata_raw_dataset.yaml @@ -0,0 +1,21 @@ +type: file +description: "A raw dataset" +example: "raw_dataset.h5ad" +info: + short_description: "Raw dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: string + name: label + description: Ground truth cell type labels + - type: string + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/label_projection/api/anndata_score.yaml b/src/label_projection/api/anndata_score.yaml new file mode 100644 index 0000000000..5d906e2e61 --- /dev/null +++ b/src/label_projection/api/anndata_score.yaml @@ -0,0 +1,24 @@ +type: file +description: "Metric score file" +example: "output.h5ad" +info: + short_description: "Score" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" + - type: string + name: method_id + description: "A unique identifier for the method" + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true \ No newline at end of file diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml new file mode 100644 index 0000000000..72e24bd13f --- /dev/null +++ b/src/label_projection/api/anndata_solution.yaml @@ -0,0 +1,27 @@ +type: file +description: "The solution for the test data" +example: "solution.h5ad" +info: + short_description: "Solution" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: string + name: label + description: Ground truth cell type labels + - type: string + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml new file mode 100644 index 0000000000..c73e26f2ad --- /dev/null +++ b/src/label_projection/api/anndata_test.yaml @@ -0,0 +1,24 @@ +type: file +description: "The censored test data" +example: "test.h5ad" +info: + short_description: "Test data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: string + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml new file mode 100644 index 0000000000..a0ea982043 --- /dev/null +++ b/src/label_projection/api/anndata_train.yaml @@ -0,0 +1,27 @@ +type: file +description: "The training data" +example: "training.h5ad" +info: + short_description: "Training data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: string + name: label + description: Ground truth cell type labels + - type: string + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/label_projection/api/dataset_censoring.yaml b/src/label_projection/api/dataset_censoring.yaml index 10e6e682b9..d764e76251 100644 --- a/src/label_projection/api/dataset_censoring.yaml +++ b/src/label_projection/api/dataset_censoring.yaml @@ -1,146 +1,42 @@ functionality: - name: dataset_censoring - meta: - label: "Dataset censoring" arguments: - name: "--input" - type: h5ad_file - description: "A preprocessed dataset" - example: "preprocessed.h5ad" - meta: - from: dataset_preprocessing__output - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_preprocessed.yaml - name: "--output_train" - type: h5ad_file - description: "The training data" - example: "training.h5ad" - meta: - short_description: "Training data" - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_train.yaml direction: output - name: "--output_test" - type: h5ad_file - description: "The censored test data" - example: "test.h5ad" - meta: - short_description: "Test data" - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_test.yaml direction: output - name: "--output_solution" - type: h5ad_file - description: "The solution for the test data" - example: "solution.h5ad" - meta: - short_description: "Solution" - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_solution.yaml direction: output - resources: - # A custom python script with additional checks - - type: python_script - path: format_check.py - text: | - import anndata as ad + # test_resources: + # # A custom python script with additional checks + # - type: python_script + # path: format_check.py + # text: | + # import anndata as ad - input = ad.read_h5ad(par["input"]) - output_train = ad.read_h5ad(par["output_train"]) - output_test = ad.read_h5ad(par["output_test"]) - output_solution = ad.read_h5ad(par["output_solution"]) + # input = ad.read_h5ad(par["input"]) + # output_train = ad.read_h5ad(par["output_train"]) + # output_test = ad.read_h5ad(par["output_test"]) + # output_solution = ad.read_h5ad(par["output_solution"]) - print("Checking dimensions") - assert input.n_obs == output_train.n_obs + output_test.n_obs - assert output_test.n_obs == output_solution.n_obs - assert input.n_vars == output_train.n_vars - assert input.n_vars == output_test.n_vars + # print("Checking dimensions") + # assert input.n_obs == output_train.n_obs + output_test.n_obs + # assert output_test.n_obs == output_solution.n_obs + # assert input.n_vars == output_train.n_vars + # assert input.n_vars == output_test.n_vars - print("Checking whether data from input was copied properly to output") - assert input.uns["dataset_id"] == output_train.uns["dataset_id"] - assert input.uns["raw_dataset_id"] == output_train.uns["raw_dataset_id"] - assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - assert input.uns["raw_dataset_id"] == output_test.uns["raw_dataset_id"] - assert input.uns["dataset_id"] == output_solution.uns["dataset_id"] - assert input.uns["raw_dataset_id"] == output_solution.uns["raw_dataset_id"] + # print("Checking whether data from input was copied properly to output") + # assert input.uns["dataset_id"] == output_train.uns["dataset_id"] + # assert input.uns["raw_dataset_id"] == output_train.uns["raw_dataset_id"] + # assert input.uns["dataset_id"] == output_test.uns["dataset_id"] + # assert input.uns["raw_dataset_id"] == output_test.uns["raw_dataset_id"] + # assert input.uns["dataset_id"] == output_solution.uns["dataset_id"] + # assert input.uns["raw_dataset_id"] == output_solution.uns["raw_dataset_id"] - # todo: check .obs and .layers + # # todo: check .obs and .layers - print("All checks succeeded!") + # print("All checks succeeded!") diff --git a/src/label_projection/api/dataset_preprocessing.yaml b/src/label_projection/api/dataset_preprocessing.yaml deleted file mode 100644 index e2aaa6bf9a..0000000000 --- a/src/label_projection/api/dataset_preprocessing.yaml +++ /dev/null @@ -1,56 +0,0 @@ -functionality: - name: dataset_preprocessing - meta: - label: "Dataset preprocessing" - arguments: - - name: "--input" - type: h5ad_file - description: "An unprocessed dataset." - example: "unprocessed.h5ad" - meta: - short_description: "Raw dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - name: "--output" - type: h5ad_file - description: "A preprocessed dataset" - example: "preprocessed.h5ad" - meta: - short_description: "Pre-processed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" - direction: output diff --git a/src/label_projection/api/method.yaml b/src/label_projection/api/method.yaml index d4d8d0ea1e..fccf491d21 100644 --- a/src/label_projection/api/method.yaml +++ b/src/label_projection/api/method.yaml @@ -1,106 +1,49 @@ functionality: - name: method - meta: - # Short descriptive label of the method, ideally 10 characters at most. - label: "Method" - - # The method name, ideally four words at most - name: "Method foo param bar" - - # The type of method. Must be one of: method, positive_control, negative_control, baseline - type: method - - # The doi of an associated paper (optional). - # paper_doi: "10.1234/s56789-012-3456-7" - - # URL to the main codebase of this method (optional). - # code_url: "https://github.com/foo/bar" arguments: - name: "--input_train" - type: h5ad_file - description: "The training data" - example: "training.h5ad" - meta: - from: dataset_censoring__output_train - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset_id - description: "A unique identifier for the dataset" + __inherits__: anndata_train.yaml - name: "--input_test" - type: h5ad_file - description: "The censored test data" - example: "test.h5ad" - meta: - from: dataset_censoring__output_test - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_test.yaml - name: "--output" - type: h5ad_file - description: "The prediction file" - example: "prediction.h5ad" - meta: - short_description: "Prediction" - slots: - obs: - - type: double - name: labels_pred - description: Predicted labels for the test cells. - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: method_id - description: "A unique identifier for the method" + __inherits__: anndata_prediction.yaml direction: output - resources: - # A custom python script with additional checks + test_resources: + - path: ../../../../resources_test/label_projection/pancreas - type: python_script - path: format_check.py + path: generic_test.py text: | import anndata as ad - # input_train = ad.read_h5ad(par["input_train"]) - input_test = ad.read_h5ad(par["input_test"]) - output = ad.read_h5ad(par["output"]) + import subprocess + import scanpy as sc + from os import path + + input_train_path = meta["resources_dir"] + "/pancreas/toy_train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/toy_test.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--input_test", input_test_path, + "--output", output_path + ] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + print("input_test:", input_test) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "celltype_pred" in adata.obs + assert meta['functionality_name'] == adata.uns["method_id"] print("Checking whether data from input was copied properly to output") assert input_test.n_obs == output.n_obs diff --git a/src/label_projection/api/metric.yaml b/src/label_projection/api/metric.yaml index 2141f967f1..54fc6a0bd9 100644 --- a/src/label_projection/api/metric.yaml +++ b/src/label_projection/api/metric.yaml @@ -1,112 +1,28 @@ functionality: - name: metric - meta: - # pretty version of the functionality.name - label: "Metric" - - # The unique identifier(s) of metrics contained in this component - metric_ids: [ "my_metric" ] - - # The minimum value of each metric - metric_mins: [ 0 ] - - # The maximum value of each metric - metric_maxs: [ 1 ] - - # Whether a higher value is better - metric_maximise: [ true ] - arguments: - name: "--input_solution" - type: h5ad_file - description: "The solution for the test data" - example: "solution.h5ad" - meta: - from: dataset_censoring__output_solution - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: lognorm - description: Log-transformed normalised counts - obs: - - type: double - name: labels - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: dataset - description: "A unique identifier for the dataset" + __inherits__: anndata_solution.yaml - name: "--input_prediction" - type: h5ad_file - description: "The prediction file" - example: "prediction.h5ad" - meta: - from: method__output - slots: - obs: - - type: double - name: labels_pred - description: Predicted labels for the test cells. - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: method_id - description: "A unique identifier for the method" + __inherits__: anndata_prediction.yaml - name: "--output" - description: "Metric score file" - example: "output.h5ad" - meta: - short_description: "Scores" - slots: - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - - type: string - name: method_id - description: "A unique identifier for the method" - - type: string - name: metric_ids - description: "One or more unique metric identifiers" - multiple: true - - type: double - name: metric_values - description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." - multiple: true + __inherits__: anndata_score.yaml direction: output - resources: - # A custom python script with additional checks - - type: python_script - path: format_check.py - text: | - import anndata as ad - - input_solution = ad.read_h5ad(par["input_solution"]) - input_prediction = ad.read_h5ad(par["input_prediction"]) - output = ad.read_h5ad(par["output"]) - - print("Checking whether data from input was copied properly to output") - assert input_solution.uns["dataset_id"] == input_prediction.uns["dataset_id"] - assert input_solution.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] - assert input_prediction.uns["dataset_id"] == output.uns["dataset_id"] - assert input_prediction.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] - assert input_prediction.uns["method_id"] == output.uns["method_id"] - - print("All checks succeeded!") + # test_resources: + # # A custom python script with additional checks + # - type: python_script + # path: format_check.py + # text: | + # import anndata as ad + + # input_solution = ad.read_h5ad(par["input_solution"]) + # input_prediction = ad.read_h5ad(par["input_prediction"]) + # output = ad.read_h5ad(par["output"]) + + # print("Checking whether data from input was copied properly to output") + # assert input_solution.uns["dataset_id"] == input_prediction.uns["dataset_id"] + # assert input_solution.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] + # assert input_prediction.uns["dataset_id"] == output.uns["dataset_id"] + # assert input_prediction.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] + # assert input_prediction.uns["method_id"] == output.uns["method_id"] + + # print("All checks succeeded!") diff --git a/src/label_projection/api/normalization.yaml b/src/label_projection/api/normalization.yaml new file mode 100644 index 0000000000..f1a71f3eda --- /dev/null +++ b/src/label_projection/api/normalization.yaml @@ -0,0 +1,48 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_raw_dataset.yaml + - name: "--output" + __inherits__: anndata_preprocessed.yaml + direction: output + test_resources: + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset_subsampled.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + print("input:", input) + print("output:", output) + + print(">> Checking whether output data structures were added") + assert "lognorm" in output.layers + assert output.uns["normalization_method"] == meta['functionality_name'].removeprefix("normalize_") + + print("Checking whether data from input was copied properly to output") + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + assert input.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] + + print("All checks succeeded!") + - path: ../../../../resources_test/label_projection/pancreas + From e0b913d786fcd438f081888643d1cf03b2edbaac Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 15:58:00 +0100 Subject: [PATCH 0270/1233] refactor normalisation methods Former-commit-id: d93b94b190ea8d44294927322d7b9b2977e4b6cb --- .../normalize/log_cpm/config.vsh.yaml | 43 ------------------ .../normalize/log_cpm/script.py | 20 --------- .../normalize/log_cpm/test_script.py | 20 --------- .../normalize/scran/config.vsh.yaml | 45 ------------------- .../data_processing/normalize/scran/script.R | 23 ---------- .../normalize/scran/test_script.py | 20 --------- .../normalize_log_cpm/config.vsh.yaml | 17 +++++++ .../normalize_log_cpm/script.py | 26 +++++++++++ .../config.vsh.yaml | 19 ++++++++ .../normalize_log_scran_pooling/script.R | 31 +++++++++++++ 10 files changed, 93 insertions(+), 171 deletions(-) delete mode 100644 src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml delete mode 100644 src/label_projection/data_processing/normalize/log_cpm/script.py delete mode 100644 src/label_projection/data_processing/normalize/log_cpm/test_script.py delete mode 100644 src/label_projection/data_processing/normalize/scran/config.vsh.yaml delete mode 100644 src/label_projection/data_processing/normalize/scran/script.R delete mode 100644 src/label_projection/data_processing/normalize/scran/test_script.py create mode 100644 src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml create mode 100644 src/label_projection/data_processing/normalize_log_cpm/script.py create mode 100644 src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml create mode 100644 src/label_projection/data_processing/normalize_log_scran_pooling/script.R diff --git a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml deleted file mode 100644 index ff9d1107f4..0000000000 --- a/src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml +++ /dev/null @@ -1,43 +0,0 @@ -functionality: - name: "log_cpm" - namespace: "label_projection/data_processing/normalize" - version: "dev" - description: "Normalize data" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data labeled" - required: true - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - "anndata<0.8" - - type: nextflow diff --git a/src/label_projection/data_processing/normalize/log_cpm/script.py b/src/label_projection/data_processing/normalize/log_cpm/script.py deleted file mode 100644 index e272c4d027..0000000000 --- a/src/label_projection/data_processing/normalize/log_cpm/script.py +++ /dev/null @@ -1,20 +0,0 @@ -##VIASH START -par = { - 'input': "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad", - 'output': "output.h5ad" -} -##VIASH END - -import scanpy as sc - -print(">> Load data") -adata = sc.read(par['input']) - -print(">> Normalize data") -adata.layers["counts"] = adata.X.copy() -sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") -sc.pp.log1p(adata) -adata.uns["normalization_method"] = "log_cpm" - -print(">> Write data") -adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/data_processing/normalize/log_cpm/test_script.py b/src/label_projection/data_processing/normalize/log_cpm/test_script.py deleted file mode 100644 index 8cae3c0f3a..0000000000 --- a/src/label_projection/data_processing/normalize/log_cpm/test_script.py +++ /dev/null @@ -1,20 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.logcpm.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./log_cpm", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "log_cpm" == adata.uns["normalization_method"] diff --git a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml b/src/label_projection/data_processing/normalize/scran/config.vsh.yaml deleted file mode 100644 index 11cae6217d..0000000000 --- a/src/label_projection/data_processing/normalize/scran/config.vsh.yaml +++ /dev/null @@ -1,45 +0,0 @@ -functionality: - name: "log_scran_pooling" - namespace: "label_projection/data_processing/normalize/scran" - version: "dev" - description: "Normalize data" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be normalized" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data labeled" - required: true - resources: - - type: r_script - path: script.R - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: eddelbuettel/r2u:22.04 - setup: - - type: r - cran: [ Matrix, scran, BiocParallel, rlang, anndata] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [anndata<0.8, scanpy] - - type: nextflow diff --git a/src/label_projection/data_processing/normalize/scran/script.R b/src/label_projection/data_processing/normalize/scran/script.R deleted file mode 100644 index 4e1b514dd8..0000000000 --- a/src/label_projection/data_processing/normalize/scran/script.R +++ /dev/null @@ -1,23 +0,0 @@ -## VIASH START -par <- list( - input = "src/label_projection/resources/pancreas/toy_preprocessed_data.h5ad", - output = "output.scran.h5ad" -) -## VIASH END - -cat(">> Loading dependencies\n") -library(anndata, warn.conflicts = FALSE) -library(scran, warn.conflicts = FALSE) -library(BiocParallel, warn.conflicts = FALSE) - -cat(">> Load data\n") -adata <- anndata::read_h5ad(par$input) - -cat(">> Normalizing data\n") -sce <- scran::calculateSumFactors(as.matrix(t(adata$X)), min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) -adata$obs[["size_factors"]] <- sce -adata$X <- log1p(sce * adata$X) - -cat(">> Writing to file\n") -adata$uns["normalization_method"] <- "log_scran_pooling" -zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/label_projection/data_processing/normalize/scran/test_script.py b/src/label_projection/data_processing/normalize/scran/test_script.py deleted file mode 100644 index 7b75372d87..0000000000 --- a/src/label_projection/data_processing/normalize/scran/test_script.py +++ /dev/null @@ -1,20 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.scran.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - "./log_scran_pooling", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "log_scran_pooling" == adata.uns["normalization_method"] diff --git a/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..445ceda54e --- /dev/null +++ b/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml @@ -0,0 +1,17 @@ +__inherits__: ../../api/normalization.yaml +functionality: + name: "normalize_log_cpm" + namespace: "label_projection/data_processing" + description: "Normalize data using Log CPM" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/data_processing/normalize_log_cpm/script.py b/src/label_projection/data_processing/normalize_log_cpm/script.py new file mode 100644 index 0000000000..909deb355f --- /dev/null +++ b/src/label_projection/data_processing/normalize_log_cpm/script.py @@ -0,0 +1,26 @@ +import scanpy as sc + +## VIASH START +par = { + 'input': "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", + 'output': "output.h5ad" +} +meta = { + "functionality_name": "normalize_log_cpm" +} +## VIASH END + +print(">> Load data") +adata = sc.read_h5ad(par['input']) + +print(">> Normalize data") +norm = sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors", layer="counts", inplace=False) +lognorm = sc.pp.log1p(norm["X"]) + +print(">> Store output in adata") +adata.layers["lognorm"] = lognorm +adata.obs["norm_factor"] = norm["norm_factor"] +adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") + +print(">> Write data") +adata.write(par['output'], compression="gzip") diff --git a/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml b/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml new file mode 100644 index 0000000000..4436cae547 --- /dev/null +++ b/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml @@ -0,0 +1,19 @@ +__inherits__: ../../api/normalization.yaml +functionality: + name: "normalize_log_scran_pooling" + namespace: "label_projection/data_processing" + description: "Normalize data" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ Matrix, scran, BiocParallel, rlang, anndata] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [anndata<0.8, scanpy] + - type: nextflow diff --git a/src/label_projection/data_processing/normalize_log_scran_pooling/script.R b/src/label_projection/data_processing/normalize_log_scran_pooling/script.R new file mode 100644 index 0000000000..f04b81e174 --- /dev/null +++ b/src/label_projection/data_processing/normalize_log_scran_pooling/script.R @@ -0,0 +1,31 @@ +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(scran, warn.conflicts = FALSE) +library(BiocParallel, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input = "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", + output = "output.scran.h5ad" +) +meta <- list( + functionality_name = "normalize_log_scran_pooling" +) +## VIASH END + +cat(">> Load data\n") +adata <- anndata::read_h5ad(par$input) +counts <- as.matrix(t(adata$layers[["counts"]])) + +cat(">> Normalizing data\n") +size_factors <- scran::calculateSumFactors(counts, min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) +lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) + +cat(">> Storing in anndata\n") +adata$obs[["size_factors"]] <- size_factors +adata$layers[["lognorm"]] <- lognorm + +cat(">> Writing to file\n") +adata$uns["normalization_method"] <- gsub("^normalize_", "", meta["functionality_name"]) +zzz <- adata$write_h5ad(par$output, compression = "gzip") From 14378b971a41a1289433c2a6c3639699b70c3339 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 15:58:57 +0100 Subject: [PATCH 0271/1233] move and update test resource script Former-commit-id: a2bb3ccf1adf54cfe26a21cbf033d4a736f42893 --- .../resources_test_scripts/pancreas.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename src/label_projection/{data_processing => }/resources_test_scripts/pancreas.sh (89%) diff --git a/src/label_projection/data_processing/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh similarity index 89% rename from src/label_projection/data_processing/resources_test_scripts/pancreas.sh rename to src/label_projection/resources_test_scripts/pancreas.sh index 49ac510ba4..7610c8318e 100755 --- a/src/label_projection/data_processing/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -21,11 +21,11 @@ mkdir -p $DATASET_DIR bin/viash run src/label_projection/data_processing/subsample/config.vsh.yaml -- \ --input $RAW_DATA \ - --celltype_categories "acinar:beta" \ - --tech_categories "celseq:inDrop4:smarter" \ + --keep_celltype_categories "acinar:beta" \ + --keep_batch_categories "celseq:inDrop4:smarter" \ --output $DATASET_DIR/dataset_subsampled.h5ad -bin/viash run src/label_projection/data_processing/normalize/log_cpm/config.vsh.yaml -- \ +bin/viash run src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/dataset_subsampled.h5ad \ --output $DATASET_DIR/dataset_subsampled_cpm.h5ad From b1e80b44f56999ae191f3589c8e152c00140a4db Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 15:59:33 +0100 Subject: [PATCH 0272/1233] fix usage of meta variables Former-commit-id: 081f4218bf751f4f288762a6d2fb87367fc5e139 --- src/common/dataset_concatenate/test_script.py | 2 +- src/label_projection/control_methods/all_correct/test_script.py | 2 +- .../control_methods/majority_vote/test_script.py | 2 +- .../control_methods/random_labels/test_script.py | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/common/dataset_concatenate/test_script.py b/src/common/dataset_concatenate/test_script.py index f97356527a..6b4844af5b 100644 --- a/src/common/dataset_concatenate/test_script.py +++ b/src/common/dataset_concatenate/test_script.py @@ -10,7 +10,7 @@ print(">> Runing script as test") out = subprocess.check_output([ - "./" + meta["functionality_name"], + meta["executable"], "--inputs", INPUTS, "--output", OUTPUT ]).decode("utf-8") diff --git a/src/label_projection/control_methods/all_correct/test_script.py b/src/label_projection/control_methods/all_correct/test_script.py index ae82a8b75b..9bb8c2c0d8 100644 --- a/src/label_projection/control_methods/all_correct/test_script.py +++ b/src/label_projection/control_methods/all_correct/test_script.py @@ -8,7 +8,7 @@ print(">> Running script as test") out = subprocess.check_output([ - "./" + meta["functionality_name"], + meta["executable"], "--input", INPUT, "--output", OUTPUT ]).decode("utf-8") diff --git a/src/label_projection/control_methods/majority_vote/test_script.py b/src/label_projection/control_methods/majority_vote/test_script.py index b961f3cce0..dc9fc15788 100644 --- a/src/label_projection/control_methods/majority_vote/test_script.py +++ b/src/label_projection/control_methods/majority_vote/test_script.py @@ -8,7 +8,7 @@ print(">> Running script as test") out = subprocess.check_output([ - "./" + meta["functionality_name"], + meta["executable"], "--input", INPUT, "--output", OUTPUT ]).decode("utf-8") diff --git a/src/label_projection/control_methods/random_labels/test_script.py b/src/label_projection/control_methods/random_labels/test_script.py index b961f3cce0..dc9fc15788 100644 --- a/src/label_projection/control_methods/random_labels/test_script.py +++ b/src/label_projection/control_methods/random_labels/test_script.py @@ -8,7 +8,7 @@ print(">> Running script as test") out = subprocess.check_output([ - "./" + meta["functionality_name"], + meta["executable"], "--input", INPUT, "--output", OUTPUT ]).decode("utf-8") From 2f67876c3e90321d465f85f6186141f6d4243eaf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 16:15:58 +0100 Subject: [PATCH 0273/1233] add censoring componet Former-commit-id: 6e17f815d3c3677901ab01d6b2279e9dba4ee43f --- .../data_processing/censoring/config.vsh.yaml | 30 +++++++++ .../data_processing/censoring/script.py | 67 +++++++++++++++++++ .../data_processing/randomize/config.vsh.yaml | 49 -------------- .../data_processing/randomize/script.py | 39 ----------- .../data_processing/randomize/test_script.py | 28 -------- 5 files changed, 97 insertions(+), 116 deletions(-) create mode 100644 src/label_projection/data_processing/censoring/config.vsh.yaml create mode 100644 src/label_projection/data_processing/censoring/script.py delete mode 100644 src/label_projection/data_processing/randomize/config.vsh.yaml delete mode 100644 src/label_projection/data_processing/randomize/script.py delete mode 100644 src/label_projection/data_processing/randomize/test_script.py diff --git a/src/label_projection/data_processing/censoring/config.vsh.yaml b/src/label_projection/data_processing/censoring/config.vsh.yaml new file mode 100644 index 0000000000..41a8a3ac7c --- /dev/null +++ b/src/label_projection/data_processing/censoring/config.vsh.yaml @@ -0,0 +1,30 @@ +__inherits__: ../../api/dataset_censoring.yaml +functionality: + name: "censoring" + namespace: "label_projection/data_processing" + arguments: + - name: "--method" + type: "string" + description: "The process method to assign train/test." + choices: ["batch", "random"] + default: "batch" + - name: "--obs_label" + type: "string" + description: "Which .obs slot to use as label." + default: "celltype" + - name: "--obs_batch" + type: "string" + description: "Which .obs slot to use as batch covariate." + default: "batch" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/data_processing/censoring/script.py b/src/label_projection/data_processing/censoring/script.py new file mode 100644 index 0000000000..372ed61c78 --- /dev/null +++ b/src/label_projection/data_processing/censoring/script.py @@ -0,0 +1,67 @@ +import numpy as np +import scanpy as sc + +## VIASH START +par = { + 'input': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm.h5ad', + 'method': 'batch', + 'obs_batch': 'batch', + 'obs_label': 'celltype', + 'output_train': 'train.h5ad', + 'output_test': 'test.h5ad', + 'output_solution': 'solution.h5ad' +} +meta = { + 'resources_dir': 'src/label_projection/data_processing/censoring' +} +## VIASH END + +print(">> Load data") +adata = sc.read(par["input"]) + +print("adata:", adata) + +print(f">> Process data using {par['method']} method") + +if par["method"] == "batch": + test_batches = adata.obs[par["obs_batch"]].dtype.categories[[-3, -1]] + is_test = [ + True if adata.obs[par["obs_batch"]][idx] in test_batches else False + for idx in adata.obs_names + ] +elif par["method"] == "random": + is_test = np.random.choice( + [False, True], adata.shape[0], replace=True, p=[0.8, 0.2] + ) + +# create new anndata objects according to api spec +def subset_anndata(adata_sub, layers, obs, uns): + return sc.AnnData( + layers={key: adata_sub.layers[key] for key in layers}, + obs=adata_sub.obs[obs.values()].rename({v:n for n,v in obs.items()}, axis=1), + var=adata.var.drop(adata.var.columns, axis=1), + uns={key: adata_sub.uns[key] for key in uns} + ) +output_train = subset_anndata( + adata_sub = adata[[not x for x in is_test]], + layers=["counts", "lognorm"], + obs={"label": par["obs_label"], "batch": par["obs_batch"]}, + uns=["raw_dataset_id", "dataset_id"] +) +output_test = subset_anndata( + adata[is_test], + layers=["counts", "lognorm"], + obs={"batch": par["obs_batch"]}, # do NOT copy label to test obs! + uns=["raw_dataset_id", "dataset_id"] +) +output_solution = subset_anndata( + adata[is_test], + layers=["counts", "lognorm"], + obs={"label": par["obs_label"], "batch": par["obs_batch"]}, + uns=["raw_dataset_id", "dataset_id"] +) + +print(">> Writing data") +output_train.write_h5ad(par["output_train"]) +output_test.write_h5ad(par["output_test"]) +output_solution.write_h5ad(par["output_solution"]) diff --git a/src/label_projection/data_processing/randomize/config.vsh.yaml b/src/label_projection/data_processing/randomize/config.vsh.yaml deleted file mode 100644 index 8c2a6d78cc..0000000000 --- a/src/label_projection/data_processing/randomize/config.vsh.yaml +++ /dev/null @@ -1,49 +0,0 @@ -functionality: - name: "randomize" - namespace: "label_projection/data_processing" - version: "dev" - description: "Label_projection component to preprocess pancreas data" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Saraiva Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - type: "file" - description: "Input data to be processed" - required: true - - name: "--method" - description: "The process method to assign train/test. Options: ['batch', 'random', 'random_with_noise']" - type: "string" - choices: ['batch', 'random', 'random_with_noise'] - required: false - default: "batch" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file preprocessed" - required: true - resources: - - type: python_script - path: script.py - - path: "../utils/noise.py" - tests: - - type: python_script - path: test_script.py - - type: file - path: "../../../../resources_test/label_projection/pancreas" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - scanpy - - "anndata<0.8" - - type: nextflow diff --git a/src/label_projection/data_processing/randomize/script.py b/src/label_projection/data_processing/randomize/script.py deleted file mode 100644 index 6538ef0c12..0000000000 --- a/src/label_projection/data_processing/randomize/script.py +++ /dev/null @@ -1,39 +0,0 @@ -## VIASH START -par = { - "input": "../../../raw_data.h5ad", - "method": 'batch', - "output": "./test/preprocess.h5ad" -} -## VIASH END -import sys -sys.path.append(meta["resources_dir"]) -import noise -import numpy as np -import scanpy as sc - -print(">> Load data") -adata = sc.read(par['input']) - -print(">> Process data using {} method".format(par['method'])) -# Remove empty cells and genes. -sc.pp.filter_genes(adata, min_cells=1) -sc.pp.filter_cells(adata, min_counts=2) - -if par["method"] == "batch": - test_batches = adata.obs["batch"].dtype.categories[[-3, -1]] - adata.obs["is_train"] = [ - False if adata.obs["batch"][idx] in test_batches else True - for idx in adata.obs_names - ] -elif par["method"] == "random": - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) -elif par["method"] == "random_with_noise": - adata.obs["is_train"] = np.random.choice( - [True, False], adata.shape[0], replace=True, p=[0.8, 0.2] - ) - adata = noise.add_celltype_noise(adata, noise_prob=0.2) - -print(">> Writing data") -adata.write(par['output']) diff --git a/src/label_projection/data_processing/randomize/test_script.py b/src/label_projection/data_processing/randomize/test_script.py deleted file mode 100644 index 838c00adee..0000000000 --- a/src/label_projection/data_processing/randomize/test_script.py +++ /dev/null @@ -1,28 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -## VIASH START -## VIASH END - -INPUT = f"{meta['resources_dir']}/pancreas/toy_preprocessed_data.h5ad" -OUTPUT = "preprocessed.h5ad" -METHODS = ["batch", "random", "random_with_noise"] - -for method in METHODS: - print(">> Running script for {} method".format(method)) - out = subprocess.check_output([ - "./" + meta["functionality_name"], - "--input", INPUT, - "--method", method, - "--output", OUTPUT - ]).decode("utf-8") - - print(">> Checking whether file exists") - assert path.exists(OUTPUT) - - print(">> Check that test output fits expected API") - adata = sc.read_h5ad(OUTPUT) - assert (500, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) - assert "batch" in adata.obs - assert "is_train" in adata.obs From 31213c4ef9e10e5eec50883c23c10fbf6332c42a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 16:16:16 +0100 Subject: [PATCH 0274/1233] remove old scripts Former-commit-id: 718b2fa35d485cf479846644c6e9c4bff08a38ed --- .../data_processing/utils/noise.py | 41 ------------------ .../methods/scvi/unit_tests/test_method.py | 42 ------------------- .../methods/unit_tests/test_method.py | 29 ------------- 3 files changed, 112 deletions(-) delete mode 100644 src/label_projection/data_processing/utils/noise.py delete mode 100644 src/label_projection/methods/scvi/unit_tests/test_method.py delete mode 100644 src/label_projection/methods/unit_tests/test_method.py diff --git a/src/label_projection/data_processing/utils/noise.py b/src/label_projection/data_processing/utils/noise.py deleted file mode 100644 index 0673985c89..0000000000 --- a/src/label_projection/data_processing/utils/noise.py +++ /dev/null @@ -1,41 +0,0 @@ -import numpy as np - - -def add_celltype_noise(adata, noise_prob): - """Inject random celltype noise in the dataset . - This is done by permuting a fraction of the celltypes in the training set. - By adding different levels of celltype noise metrics can be evaluated to show - generalization trends from training data even if ground truth is uncertain. - Parameters - ------- - adata : AnnData - A dataset with the required fields for the celltype_projection task. - noise_prob : Float - The probability of celltype noise in the training data. - Returns - ------- - new_adata : AnnData - Dataset where training celltypes have been permuted by specified probability. - """ - - old_celltype = adata.obs["celltype"].pipe(np.array) - old_celltype_train = old_celltype[adata.obs["is_train"]].copy() - new_celltype_train = old_celltype_train.copy() - - celltype_names = np.unique(new_celltype_train) - - n_celltype = celltype_names.shape[0] - - reassign_probs = (noise_prob / (n_celltype - 1)) * np.ones((n_celltype, n_celltype)) - - np.fill_diagonal(reassign_probs, 1 - noise_prob) - - for k, celltype in enumerate(celltype_names): - celltype_indices = np.where(old_celltype_train == celltype)[0] - new_celltype_train[celltype_indices] = np.random.choice( - celltype_names, celltype_indices.shape[0], p=reassign_probs[:, k] - ) - - adata.obs.loc[adata.obs["is_train"], "celltype"] = new_celltype_train - - return adata diff --git a/src/label_projection/methods/scvi/unit_tests/test_method.py b/src/label_projection/methods/scvi/unit_tests/test_method.py deleted file mode 100644 index 438d67b70b..0000000000 --- a/src/label_projection/methods/scvi/unit_tests/test_method.py +++ /dev/null @@ -1,42 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "result.scvimethod.h5ad" - -methods_params = { - "./scarches_scanvi_all_genes": ['--n_hidden', "32", '--n_layers', "1", - '--n_latent', "10", '--max_epochs', "1", - '--limit_train_batches', "10", - '--limit_val_batches', "10"], - "./scarches_scanvi_hvg": ['--n_hidden', "32", '--n_layers', "1", - '--n_latent', "10", '--span', "0.8", - '--n_top_genes', "2000", '--max_epochs', "1", - '--limit_train_batches', "10", '--limit_val_batches', "10"], - "./scanvi_hvg": ['--n_hidden', "32", '--n_layers', "1", - '--n_latent', "10", '--span', "0.8", - '--n_top_genes', "2000", '--max_epochs', "1", - '--limit_train_batches', "10", '--limit_val_batches', "10"], - "./scanvi_all_genes": ['--n_hidden', "32", '--n_layers', "1", - '--n_latent', "10", '--max_epochs', "1", - '--limit_train_batches', "10", '--limit_val_batches', "10"] - } - - -_command = "./" + meta['functionality_name'] -method_param = methods_params[_command] - -default_params = ["--input", INPUT, "--output", OUTPUT] -params = [_command] + default_params + method_param - -print(">> Running script as test") -out = subprocess.check_output(params).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert meta['functionality_name'] == adata.uns["method_id"] diff --git a/src/label_projection/methods/unit_tests/test_method.py b/src/label_projection/methods/unit_tests/test_method.py deleted file mode 100644 index 1fa355bf0d..0000000000 --- a/src/label_projection/methods/unit_tests/test_method.py +++ /dev/null @@ -1,29 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -INPUT = ["toy_normalized_log_cpm_data.h5ad", "toy_normalized_log_scran_pooling_data.h5ad"] -OUTPUT = ["result.logcpm.h5ad", "result.lrscran.h5ad"] -methods_params = { - "./mlp": ["--hidden_layer_sizes", "20", "--max_iter", "100"], - "./logistic_regression": ["--max_iter", "100"], - "./knn_classifier": [] - } - - -_command = "./" + meta['functionality_name'] -method_param = methods_params[_command] - -for input, output in zip(INPUT, OUTPUT): - default_params = ["--input", input, "--output", output] - params = [_command] + default_params + method_param - print(">> Running script as test") - out = subprocess.check_output(params).decode("utf-8") - - print(">> Checking if output file exists") - assert path.exists(output) - - print(">> Checking if predictions were added") - adata = sc.read_h5ad(output) - assert "celltype_pred" in adata.obs - assert meta['functionality_name'] == adata.uns["method_id"] From b8ebc4e855e055d0921fce06203729387d3a739d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 8 Nov 2022 16:16:42 +0100 Subject: [PATCH 0275/1233] wip refactor methods Former-commit-id: 7a6d3d40e01dccdb68b58e7bc48f2d5996c45904 --- .../data_processing/subsample/config.vsh.yaml | 2 -- .../methods/knn_classifier/config.vsh.yaml | 27 +------------------ .../methods/knn_classifier/script.py | 5 ++-- .../logistic_regression/config.vsh.yaml | 26 +----------------- .../methods/mlp/config.vsh.yaml | 27 +------------------ .../scvi/scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- 9 files changed, 10 insertions(+), 85 deletions(-) diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index 44a63ee97c..565d8b5feb 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -37,13 +37,11 @@ functionality: - type: file path: "../../../../resources_test/common/pancreas" platforms: - - type: native - type: docker image: "python:3.8" setup: - type: python packages: - - scprep - scanpy - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 9b22dc2bd2..2eacaa212e 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,3 +1,4 @@ +__inherits__: ../../api/method.yaml functionality: name: "knn_classifier" namespace: "label_projection/methods" @@ -6,36 +7,10 @@ functionality: info: type: method label: KNN - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true resources: - type: python_script path: script.py - path: "../../utils.py" - tests: - - type: python_script - path: ../unit_tests/test_method.py - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index e0dd20dd68..3842e085cd 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -3,13 +3,14 @@ 'input': '../../../data/test_data_preprocessed.h5ad', 'output': 'output.knnscran.h5ad' } +meta = { + 'resources_dir' +} ## VIASH END resources_dir = "../../../../common/tools/" utils_dir = "../../../" import sys -sys.path.append(resources_dir) -sys.path.append(utils_dir) sys.path.append(meta['resources_dir']) import scanpy as sc from utils import classifier diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index a32883ce50..bcbe49aff7 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,3 +1,4 @@ +__inherits__: ../../api/method.yaml functionality: name: "logistic_regression" namespace: "label_projection/methods" @@ -6,41 +7,16 @@ functionality: info: type: method label: Logistic Regression - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - name: "--max_iter" type: "integer" example: "100" description: "Maximum number of iterations" required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true resources: - type: python_script path: script.py - path: "../../utils.py" - tests: - - type: python_script - path: ../unit_tests/test_method.py - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 0a2b56a0d0..6b22ed9174 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,3 +1,4 @@ +__inherits__: ../../api/method.yaml functionality: name: "mlp" namespace: "label_projection/methods" @@ -6,20 +7,7 @@ functionality: info: type: method label: Multilayer perceptron - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - name: "--hidden_layer_sizes" type: "integer" multiple: true @@ -30,22 +18,10 @@ functionality: example: "100" description: "Maximum number of iterations" required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data contatining predictions" - required: true resources: - type: python_script path: script.py - path: "../../utils.py" - tests: - - type: python_script - path: ../unit_tests/test_method.py - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_scran_pooling_data.h5ad - - path: ../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad platforms: - type: docker image: "python:3.8" @@ -55,5 +31,4 @@ platforms: - scanpy - sklearn - "anndata<0.8" - - type: native - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index dbd568d0a4..96cd856e1b 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -52,7 +52,7 @@ functionality: - type: python_script path: script.py - path: "../tools.py" - tests: + test_resources: - type: python_script path: ../unit_tests/test_method.py - type: file diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index 5c8a618825..d018f88e85 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -59,7 +59,7 @@ functionality: - type: python_script path: script.py - path: "../tools.py" - tests: + test_resources: - type: python_script path: ../unit_tests/test_method.py - type: file diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index e4259ffa53..6e5b503ae4 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -52,7 +52,7 @@ functionality: - type: python_script path: script.py - path: "../tools.py" - tests: + test_resources: - type: python_script path: ../unit_tests/test_method.py - type: file diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index 027a6e28a5..dc98238b69 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -59,7 +59,7 @@ functionality: - type: python_script path: script.py - path: "../tools.py" - tests: + test_resources: - type: python_script path: ../unit_tests/test_method.py - type: file From 76c5068fd93d7ca36056281870d2d25c75a08be6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 05:30:49 +0100 Subject: [PATCH 0276/1233] refactor censoring Former-commit-id: 4458556314c21974ab4713f2e48408164d7210dc --- .../api/dataset_censoring.yaml | 93 +++++++++++++------ .../data_processing/censoring/test.py | 30 ++++++ .../data_processing/subsample/config.vsh.yaml | 5 +- 3 files changed, 100 insertions(+), 28 deletions(-) create mode 100644 src/label_projection/data_processing/censoring/test.py diff --git a/src/label_projection/api/dataset_censoring.yaml b/src/label_projection/api/dataset_censoring.yaml index d764e76251..d52c906669 100644 --- a/src/label_projection/api/dataset_censoring.yaml +++ b/src/label_projection/api/dataset_censoring.yaml @@ -11,32 +11,73 @@ functionality: - name: "--output_solution" __inherits__: anndata_solution.yaml direction: output - # test_resources: - # # A custom python script with additional checks - # - type: python_script - # path: format_check.py - # text: | - # import anndata as ad - - # input = ad.read_h5ad(par["input"]) - # output_train = ad.read_h5ad(par["output_train"]) - # output_test = ad.read_h5ad(par["output_test"]) - # output_solution = ad.read_h5ad(par["output_solution"]) - - # print("Checking dimensions") - # assert input.n_obs == output_train.n_obs + output_test.n_obs - # assert output_test.n_obs == output_solution.n_obs - # assert input.n_vars == output_train.n_vars - # assert input.n_vars == output_test.n_vars + test_resources: + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm.h5ad" + output_train_path = "output_train.h5ad" + output_test_path = "output_test.h5ad" + output_solution_path = "output_solution.h5ad" + + cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path, + "--output_solution", output_solution_path + ] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_train_path) + assert path.exists(output_test_path) + assert path.exists(output_solution_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output_train = ad.read_h5ad(output_train_path) + output_test = ad.read_h5ad(output_test_path) + output_solution = ad.read_h5ad(output_solution_path) + + print("input:", input) + print("output_train:", output_train) + print("output_test:", output_test) + print("output_solution:", output_solution) + + print(">> Checking dimensions, make sure no cells were dropped") + assert input.n_obs == output_train.n_obs + output_test.n_obs + assert output_test.n_obs == output_solution.n_obs + assert input.n_vars == output_train.n_vars + assert input.n_vars == output_test.n_vars - # print("Checking whether data from input was copied properly to output") - # assert input.uns["dataset_id"] == output_train.uns["dataset_id"] - # assert input.uns["raw_dataset_id"] == output_train.uns["raw_dataset_id"] - # assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - # assert input.uns["raw_dataset_id"] == output_test.uns["raw_dataset_id"] - # assert input.uns["dataset_id"] == output_solution.uns["dataset_id"] - # assert input.uns["raw_dataset_id"] == output_solution.uns["raw_dataset_id"] + print(">> Checking whether data from input was copied properly to output") + assert output_train.uns["dataset_id"] == input.uns["dataset_id"] + assert output_train.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] + assert output_test.uns["dataset_id"] == input.uns["dataset_id"] + assert output_test.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] + assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] + assert output_solution.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] - # # todo: check .obs and .layers + print(">> Check whether certain slots exist") + assert "counts" in output_train.layers + assert "lognorm" in output_train.layers + assert "label" in output_train.obs + assert "batch" in output_train.obs + assert "counts" in output_test.layers + assert "lognorm" in output_test.layers + assert "label" not in output_test.obs # make sure label is /not/ here + assert "batch" in output_test.obs + assert "counts" in output_solution.layers + assert "lognorm" in output_solution.layers + assert "label" in output_solution.obs + assert "batch" in output_solution.obs - # print("All checks succeeded!") + print(">> All checks succeeded!") + - path: ../../../../resources_test/label_projection/pancreas diff --git a/src/label_projection/data_processing/censoring/test.py b/src/label_projection/data_processing/censoring/test.py new file mode 100644 index 0000000000..bb6e01fe40 --- /dev/null +++ b/src/label_projection/data_processing/censoring/test.py @@ -0,0 +1,30 @@ +import subprocess +import scanpy as sc +from os import path + +## VIASH START +## VIASH END + +# TODO: update + +INPUT = f"{meta['resources_dir']}/pancreas/toy_preprocessed_data.h5ad" +OUTPUT = "preprocessed.h5ad" +METHODS = ["batch", "random", "random_with_noise"] + +for method in METHODS: + print(">> Running script for {} method".format(method)) + out = subprocess.check_output([ + meta["executable"], + "--input", INPUT, + "--method", method, + "--output", OUTPUT + ]).decode("utf-8") + + print(">> Checking whether file exists") + assert path.exists(OUTPUT) + + print(">> Check that test output fits expected API") + adata = sc.read_h5ad(OUTPUT) + assert (500, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) + assert "batch" in adata.obs + assert "is_train" in adata.obs diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/label_projection/data_processing/subsample/config.vsh.yaml index 565d8b5feb..d3a8a4ce7f 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/label_projection/data_processing/subsample/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: type: "file" description: "Input data to be resized" required: true + example: input.h5ad - name: "--keep_celltype_categories" type: "string" multiple: true @@ -20,12 +21,12 @@ functionality: required: false - name: "--even" type: "boolean_true" - description: Evenly subsamples from different batches + description: Subsample evenly from different batches - name: "--output" alternatives: ["-o"] type: "file" direction: "output" - default: "toy_data.h5ad" + example: "output.h5ad" description: "Output h5ad file resized" required: true resources: From 0ab88113b1dbf7ef8dd646f09179ee23ef07f4c9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 05:30:58 +0100 Subject: [PATCH 0277/1233] add authors api spec Former-commit-id: d852ce966483e7a39da8b2d77a96ab5ca3909dc1 --- src/label_projection/api/authors.yaml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 src/label_projection/api/authors.yaml diff --git a/src/label_projection/api/authors.yaml b/src/label_projection/api/authors.yaml new file mode 100644 index 0000000000..5487b223ef --- /dev/null +++ b/src/label_projection/api/authors.yaml @@ -0,0 +1,14 @@ +functionality: + authors: + - name: "Nikolay Markov" + roles: [ author, maintainer ] + props: { github: mxposed } + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: Robrecht Cannoodt + roles: [ author ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + - name: "Vinicius Chagas" + roles: [ contributor ] + props: { github: chagasVinicius } \ No newline at end of file From 0fab043a5e0d2d9d336af7b3484e06ed4ee86564 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 06:00:18 +0100 Subject: [PATCH 0278/1233] refactor dummy methods Former-commit-id: 0ea59a32442d27814c97e57e0ff20ff84e4dd9d2 --- src/label_projection/api/method.yaml | 16 ++++--- .../all_correct/config.vsh.yaml | 45 ------------------- .../control_methods/all_correct/script.py | 20 --------- .../all_correct/test_script.py | 23 ---------- .../majority_vote/config.vsh.yaml | 36 +++------------ .../control_methods/majority_vote/script.py | 28 +++++++----- .../majority_vote/test_script.py | 22 --------- .../random_labels/config.vsh.yaml | 30 +++---------- .../control_methods/random_labels/script.py | 39 +++++++++------- .../random_labels/test_script.py | 22 --------- .../true_labels/config.vsh.yaml | 24 ++++++++++ .../control_methods/true_labels/script.py | 25 +++++++++++ 12 files changed, 108 insertions(+), 222 deletions(-) delete mode 100644 src/label_projection/control_methods/all_correct/config.vsh.yaml delete mode 100644 src/label_projection/control_methods/all_correct/script.py delete mode 100644 src/label_projection/control_methods/all_correct/test_script.py delete mode 100644 src/label_projection/control_methods/majority_vote/test_script.py delete mode 100644 src/label_projection/control_methods/random_labels/test_script.py create mode 100644 src/label_projection/control_methods/true_labels/config.vsh.yaml create mode 100644 src/label_projection/control_methods/true_labels/script.py diff --git a/src/label_projection/api/method.yaml b/src/label_projection/api/method.yaml index fccf491d21..5d02b53490 100644 --- a/src/label_projection/api/method.yaml +++ b/src/label_projection/api/method.yaml @@ -13,13 +13,12 @@ functionality: path: generic_test.py text: | import anndata as ad - import subprocess - import scanpy as sc from os import path - input_train_path = meta["resources_dir"] + "/pancreas/toy_train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/toy_test.h5ad" + input_train_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_test.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_solution.h5ad" output_path = "output.h5ad" cmd = [ @@ -29,6 +28,11 @@ functionality: "--output", output_path ] + # todo: if we could access the viash config, we could check whether + # .functionality.info.type == "positive_control" + if meta['functionality_name'] == 'true_labels': + cmd = cmd + ["--input_solution", input_solution_path] + print(">> Running script as test") out = subprocess.check_output(cmd).decode("utf-8") @@ -42,8 +46,8 @@ functionality: print("output:", output) print(">> Checking whether predictions were added") - assert "celltype_pred" in adata.obs - assert meta['functionality_name'] == adata.uns["method_id"] + assert "label_pred" in output.obs + assert meta['functionality_name'] == output.uns["method_id"] print("Checking whether data from input was copied properly to output") assert input_test.n_obs == output.n_obs diff --git a/src/label_projection/control_methods/all_correct/config.vsh.yaml b/src/label_projection/control_methods/all_correct/config.vsh.yaml deleted file mode 100644 index d2eea25541..0000000000 --- a/src/label_projection/control_methods/all_correct/config.vsh.yaml +++ /dev/null @@ -1,45 +0,0 @@ -functionality: - name: "all_correct" - namespace: "label_projection/control_methods" - version: "dev" - description: "Positive control method" - info: - type: positive_control - label: All predictions are correct - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - type: "file" - description: "Input data to predict" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - description: "Ouput data containing predictions" - direction: "output" - example: "output.mv.h5ad" - required: true - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: native - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - "anndata<0.8" - - type: nextflow diff --git a/src/label_projection/control_methods/all_correct/script.py b/src/label_projection/control_methods/all_correct/script.py deleted file mode 100644 index ce2b1178e5..0000000000 --- a/src/label_projection/control_methods/all_correct/script.py +++ /dev/null @@ -1,20 +0,0 @@ -## VIASH START -par = { - 'input': '../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm_data.h5ad', - 'output': 'output.mv.h5ad' -} -## VIASH END -import numpy as np -import scanpy as sc - - -print("Load data") -adata = sc.read(par['input']) - -print("Add celltype prediction") -adata.obs["celltype_pred"] = adata.obs.celltype - - -print("Write output to file") -adata.uns["method_id"] = meta["functionality_name"] -adata.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/all_correct/test_script.py b/src/label_projection/control_methods/all_correct/test_script.py deleted file mode 100644 index 9bb8c2c0d8..0000000000 --- a/src/label_projection/control_methods/all_correct/test_script.py +++ /dev/null @@ -1,23 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.mv.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - meta["executable"], - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert (adata.obs.celltype_pred == adata.obs.celltype).all() -assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 4d5f0ecdf2..aa43e4a3d0 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -1,45 +1,21 @@ +__inherits__: ../../api/method.yaml functionality: name: "majority_vote" namespace: "label_projection/control_methods" - version: "dev" - description: "Majority vote dummy" + description: "Baseline method using majority voting" info: - type: negative_control - label: Random prediction - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - type: "file" - description: "Input data to predict" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - description: "Ouput data containing predictions" - direction: "output" - example: "output.mv.h5ad" - required: true + type: baseline + label: Majority Vote + v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - - type: native - type: docker image: "python:3.8" setup: - type: python packages: - - scanpy - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/control_methods/majority_vote/script.py b/src/label_projection/control_methods/majority_vote/script.py index 05a8f40296..3f48ae22b4 100644 --- a/src/label_projection/control_methods/majority_vote/script.py +++ b/src/label_projection/control_methods/majority_vote/script.py @@ -1,22 +1,26 @@ +import anndata as ad + ## VIASH START par = { - 'input': '../../../../resources_test/label_projection/pancreas/toy_normalized_log_cpm.h5ad', - 'output': 'output.mv.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' } ## VIASH END -import numpy as np -import scanpy as sc - print("Load data") -adata = sc.read(par['input']) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) -print("Add celltype prediction") -majority = adata.obs.celltype[adata.obs.is_train].value_counts().index[0] -adata.obs["celltype_pred"] = np.nan -adata.obs.loc[~adata.obs.is_train, "celltype_pred"] = majority +print("Compute majority vote") +majority = input_train.obs.label.value_counts().index[0] +print("Create prediction object") +input_test.obs["label_pred"] = majority print("Write output to file") -adata.uns["method_id"] = meta["functionality_name"] -adata.write(par["output"], compression="gzip") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/majority_vote/test_script.py b/src/label_projection/control_methods/majority_vote/test_script.py deleted file mode 100644 index dc9fc15788..0000000000 --- a/src/label_projection/control_methods/majority_vote/test_script.py +++ /dev/null @@ -1,22 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.mv.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - meta["executable"], - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index f886407b04..26dbb54754 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,37 +1,17 @@ +__inherits__: ../../api/method.yaml functionality: name: "random_labels" namespace: "label_projection/control_methods" - version: "dev" - description: "Random Labels dummy" + description: "Negative control method which generates random labels" info: type: negative_control - label: Random prediction - authors: - - name: "Nikolay Markov" - roles: [ author, maintainer ] - props: { github: mxposed } - arguments: - - name: "--input" - type: "file" - description: "Input data to predict" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - description: "Ouput data containing predictions" - direction: "output" - example: "output.mv.h5ad" - required: true + label: Random Labels + v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" platforms: - - type: native - type: docker image: "python:3.8" setup: diff --git a/src/label_projection/control_methods/random_labels/script.py b/src/label_projection/control_methods/random_labels/script.py index 5b2dc04c79..8a7b33bc75 100644 --- a/src/label_projection/control_methods/random_labels/script.py +++ b/src/label_projection/control_methods/random_labels/script.py @@ -1,28 +1,33 @@ +import anndata as ad +import numpy as np + ## VIASH START par = { - 'input': 'ouput.h5ad', - 'output': 'output.mv.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' } ## VIASH END -import numpy as np -import scanpy as sc - print("Load data") -adata = sc.read(par['input']) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Compute label distribution") +label_distribution = input_train.obs.label.value_counts() +label_distribution = label_distribution / label_distribution.sum() -print("Add celltype prediction") -celltype_distribution = adata.obs.celltype[adata.obs.is_train].value_counts() -celltype_distribution = celltype_distribution / celltype_distribution.sum() -adata.obs["celltype_pred"] = np.nan -adata.obs.loc[~adata.obs.is_train, "celltype_pred"] = np.random.choice( - celltype_distribution.index, - size=(~adata.obs.is_train).sum(), +print("Create prediction object") +input_test.obs["label_pred"] = np.random.choice( + label_distribution.index, + size=input_test.n_obs, replace=True, - p=celltype_distribution + p=label_distribution ) - print("Write output to file") -adata.uns["method_id"] = meta["functionality_name"] -adata.write(par["output"], compression="gzip") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/random_labels/test_script.py b/src/label_projection/control_methods/random_labels/test_script.py deleted file mode 100644 index dc9fc15788..0000000000 --- a/src/label_projection/control_methods/random_labels/test_script.py +++ /dev/null @@ -1,22 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - - -INPUT = "toy_preprocessed_data.h5ad" -OUTPUT = "output.mv.h5ad" - -print(">> Running script as test") -out = subprocess.check_output([ - meta["executable"], - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking if output file exists") -assert path.exists(OUTPUT) - -print(">> Checking if predictions were added") -adata = sc.read_h5ad(OUTPUT) -assert "celltype_pred" in adata.obs -assert meta["functionality_name"] == adata.uns["method_id"] diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml new file mode 100644 index 0000000000..dfd45da123 --- /dev/null +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -0,0 +1,24 @@ +__inherits__: ../../api/method.yaml +functionality: + name: "true_labels" + namespace: "label_projection/control_methods" + description: "Positive control method by returning the true labels" + info: + type: positive_control + label: True labels + v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + arguments: + - name: "--input_solution" + __inherits__: ../../api/anndata_solution.yaml + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - "anndata<0.8" + - type: nextflow diff --git a/src/label_projection/control_methods/true_labels/script.py b/src/label_projection/control_methods/true_labels/script.py new file mode 100644 index 0000000000..71023a05c0 --- /dev/null +++ b/src/label_projection/control_methods/true_labels/script.py @@ -0,0 +1,25 @@ +import anndata as ad + +## VIASH START +par = { + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' +} +## VIASH END + +print("Load data") +# input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) +input_solution = ad.read_h5ad(par['input_solution']) + +print("Create prediction object") +input_test.obs["label_pred"] = input_solution.obs["label"] + +print("Write output to file") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write(par["output"], compression="gzip") From 64cf5bf047a9a84bdac4a5d2f0f14cd67050a8a6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 07:07:17 +0100 Subject: [PATCH 0279/1233] update api Former-commit-id: 29d00575648fe7e62d89191f15b1398a556d0050 --- src/label_projection/api/anndata_prediction.yaml | 2 +- src/label_projection/api/anndata_preprocessed.yaml | 2 +- src/label_projection/api/anndata_raw_dataset.yaml | 2 +- src/label_projection/api/anndata_score.yaml | 2 +- src/label_projection/api/anndata_solution.yaml | 2 +- src/label_projection/api/anndata_test.yaml | 2 +- src/label_projection/api/anndata_train.yaml | 2 +- src/label_projection/api/authors.yaml | 2 +- .../api/{dataset_censoring.yaml => comp_censoring.yaml} | 0 src/label_projection/api/{method.yaml => comp_method.yaml} | 0 src/label_projection/api/{metric.yaml => comp_metric.yaml} | 0 .../api/{normalization.yaml => comp_normalization.yaml} | 0 12 files changed, 8 insertions(+), 8 deletions(-) rename src/label_projection/api/{dataset_censoring.yaml => comp_censoring.yaml} (100%) rename src/label_projection/api/{method.yaml => comp_method.yaml} (100%) rename src/label_projection/api/{metric.yaml => comp_metric.yaml} (100%) rename src/label_projection/api/{normalization.yaml => comp_normalization.yaml} (100%) diff --git a/src/label_projection/api/anndata_prediction.yaml b/src/label_projection/api/anndata_prediction.yaml index ef661079ed..829200ea93 100644 --- a/src/label_projection/api/anndata_prediction.yaml +++ b/src/label_projection/api/anndata_prediction.yaml @@ -17,4 +17,4 @@ info: description: "A unique identifier for the original dataset (before preprocessing)" - type: string name: method_id - description: "A unique identifier for the method" \ No newline at end of file + description: "A unique identifier for the method" diff --git a/src/label_projection/api/anndata_preprocessed.yaml b/src/label_projection/api/anndata_preprocessed.yaml index 1b061a6579..85c85f1abc 100644 --- a/src/label_projection/api/anndata_preprocessed.yaml +++ b/src/label_projection/api/anndata_preprocessed.yaml @@ -24,4 +24,4 @@ info: description: "A unique identifier for the dataset" - type: string name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_raw_dataset.yaml b/src/label_projection/api/anndata_raw_dataset.yaml index fd7627d8d5..988a8a4027 100644 --- a/src/label_projection/api/anndata_raw_dataset.yaml +++ b/src/label_projection/api/anndata_raw_dataset.yaml @@ -18,4 +18,4 @@ info: uns: - type: string name: dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_score.yaml b/src/label_projection/api/anndata_score.yaml index 5d906e2e61..dcc750dd4c 100644 --- a/src/label_projection/api/anndata_score.yaml +++ b/src/label_projection/api/anndata_score.yaml @@ -21,4 +21,4 @@ info: - type: double name: metric_values description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." - multiple: true \ No newline at end of file + multiple: true diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index 72e24bd13f..c8bc73ab61 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -24,4 +24,4 @@ info: description: "A unique identifier for the dataset" - type: string name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index c73e26f2ad..d9f5dd62d5 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -21,4 +21,4 @@ info: description: "A unique identifier for the dataset" - type: string name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index a0ea982043..3e5bb89dd1 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -24,4 +24,4 @@ info: description: "A unique identifier for the dataset" - type: string name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/authors.yaml b/src/label_projection/api/authors.yaml index 5487b223ef..b98caf5771 100644 --- a/src/label_projection/api/authors.yaml +++ b/src/label_projection/api/authors.yaml @@ -11,4 +11,4 @@ functionality: props: { github: rcannood, orcid: "0000-0003-3641-729X" } - name: "Vinicius Chagas" roles: [ contributor ] - props: { github: chagasVinicius } \ No newline at end of file + props: { github: chagasVinicius } diff --git a/src/label_projection/api/dataset_censoring.yaml b/src/label_projection/api/comp_censoring.yaml similarity index 100% rename from src/label_projection/api/dataset_censoring.yaml rename to src/label_projection/api/comp_censoring.yaml diff --git a/src/label_projection/api/method.yaml b/src/label_projection/api/comp_method.yaml similarity index 100% rename from src/label_projection/api/method.yaml rename to src/label_projection/api/comp_method.yaml diff --git a/src/label_projection/api/metric.yaml b/src/label_projection/api/comp_metric.yaml similarity index 100% rename from src/label_projection/api/metric.yaml rename to src/label_projection/api/comp_metric.yaml diff --git a/src/label_projection/api/normalization.yaml b/src/label_projection/api/comp_normalization.yaml similarity index 100% rename from src/label_projection/api/normalization.yaml rename to src/label_projection/api/comp_normalization.yaml From 51e3626e1060e1fd78dc14f9e8e9571a9d290810 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 07:07:36 +0100 Subject: [PATCH 0280/1233] update methods Former-commit-id: a30ebd60b484b0c08851aa8920f9fc34fa301001 --- .../majority_vote/config.vsh.yaml | 4 +- .../control_methods/majority_vote/script.py | 2 +- .../random_labels/config.vsh.yaml | 4 +- .../control_methods/random_labels/script.py | 2 +- .../true_labels/config.vsh.yaml | 4 +- .../control_methods/true_labels/script.py | 2 +- .../data_processing/censoring/config.vsh.yaml | 2 +- .../normalize_log_cpm/config.vsh.yaml | 2 +- .../normalize_log_cpm/script.py | 2 +- .../config.vsh.yaml | 2 +- .../data_processing/subsample/script.py | 2 +- .../methods/knn_classifier/config.vsh.yaml | 19 ++--- .../methods/knn_classifier/script.py | 63 ++++++++++++----- .../logistic_regression/config.vsh.yaml | 22 +++--- .../methods/logistic_regression/script.py | 67 +++++++++++++----- .../methods/mlp/config.vsh.yaml | 19 ++--- src/label_projection/methods/mlp/script.py | 70 +++++++++++++------ 17 files changed, 190 insertions(+), 98 deletions(-) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index aa43e4a3d0..6f9b3678bc 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "majority_vote" namespace: "label_projection/control_methods" @@ -6,7 +6,7 @@ functionality: info: type: baseline label: Majority Vote - v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c resources: - type: python_script diff --git a/src/label_projection/control_methods/majority_vote/script.py b/src/label_projection/control_methods/majority_vote/script.py index 3f48ae22b4..d847c419a3 100644 --- a/src/label_projection/control_methods/majority_vote/script.py +++ b/src/label_projection/control_methods/majority_vote/script.py @@ -23,4 +23,4 @@ print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] -input_test.write(par["output"], compression="gzip") +input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 26dbb54754..dbbca8219b 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "random_labels" namespace: "label_projection/control_methods" @@ -6,7 +6,7 @@ functionality: info: type: negative_control label: Random Labels - v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c resources: - type: python_script diff --git a/src/label_projection/control_methods/random_labels/script.py b/src/label_projection/control_methods/random_labels/script.py index 8a7b33bc75..8a65bd7b32 100644 --- a/src/label_projection/control_methods/random_labels/script.py +++ b/src/label_projection/control_methods/random_labels/script.py @@ -30,4 +30,4 @@ print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] -input_test.write(par["output"], compression="gzip") +input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index dfd45da123..48266b54df 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "true_labels" namespace: "label_projection/control_methods" @@ -6,7 +6,7 @@ functionality: info: type: positive_control label: True labels - v1_url: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/label_projection/methods/baseline.py + v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c arguments: - name: "--input_solution" diff --git a/src/label_projection/control_methods/true_labels/script.py b/src/label_projection/control_methods/true_labels/script.py index 71023a05c0..32b668a14b 100644 --- a/src/label_projection/control_methods/true_labels/script.py +++ b/src/label_projection/control_methods/true_labels/script.py @@ -22,4 +22,4 @@ print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] -input_test.write(par["output"], compression="gzip") +input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/label_projection/data_processing/censoring/config.vsh.yaml b/src/label_projection/data_processing/censoring/config.vsh.yaml index 41a8a3ac7c..4d876d5fe7 100644 --- a/src/label_projection/data_processing/censoring/config.vsh.yaml +++ b/src/label_projection/data_processing/censoring/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/dataset_censoring.yaml +__inherits__: ../../api/comp_dataset_censoring.yaml functionality: name: "censoring" namespace: "label_projection/data_processing" diff --git a/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml b/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml index 445ceda54e..d11aa501d5 100644 --- a/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/normalization.yaml +__inherits__: ../../api/comp_normalization.yaml functionality: name: "normalize_log_cpm" namespace: "label_projection/data_processing" diff --git a/src/label_projection/data_processing/normalize_log_cpm/script.py b/src/label_projection/data_processing/normalize_log_cpm/script.py index 909deb355f..0f7f2e9ad2 100644 --- a/src/label_projection/data_processing/normalize_log_cpm/script.py +++ b/src/label_projection/data_processing/normalize_log_cpm/script.py @@ -23,4 +23,4 @@ adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") print(">> Write data") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml b/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml index 4436cae547..d47f06a32e 100644 --- a/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml +++ b/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/normalization.yaml +__inherits__: ../../api/comp_normalization.yaml functionality: name: "normalize_log_scran_pooling" namespace: "label_projection/data_processing" diff --git a/src/label_projection/data_processing/subsample/script.py b/src/label_projection/data_processing/subsample/script.py index 80ba8b0492..c33215a863 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/label_projection/data_processing/subsample/script.py @@ -60,4 +60,4 @@ def filter_genes_cells(adata): del adata.X print(">> Writing data") -adata.write(par['output']) +adata.write_h5ad(par['output']) diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 2eacaa212e..0b3f493ccd 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,24 +1,27 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "knn_classifier" namespace: "label_projection/methods" - version: "dev" - description: "Nearest neighbor pattern classification" + description: "K-Nearest Neighbors classifier" info: type: method label: KNN + # paper_name: "Nearest neighbor pattern classification" + # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" + # paper_year: 1967 + paper_doi: "10.1109/TIT.1967.1053964" + code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" + v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py + v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d resources: - type: python_script path: script.py - - path: "../../utils.py" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - scanpy - - scprep - - sklearn + - scikit-learn - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index 3842e085cd..70b7142b4a 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -1,27 +1,56 @@ +import anndata as ad +import sklearn.neighbors +import sklearn.pipeline +import sklearn.preprocessing +import sklearn.decomposition +import scipy.sparse + ## VIASH START par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.knnscran.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad', } meta = { - 'resources_dir' + 'functionality_name': 'foo', } ## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../../" - -import sys -sys.path.append(meta['resources_dir']) -import scanpy as sc -from utils import classifier -import sklearn.neighbors print("Load input data") -adata = sc.read(par['input']) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Set up classifier pipeline") +def pca_op(adata_train, adata_test, n_components=100): + is_sparse = scipy.sparse.issparse(adata_train.X) + + min_components = min( + [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + ) + if is_sparse: + min_components -= 1 + n_components = min([n_components, min_components]) + if is_sparse: + pca_op = sklearn.decomposition.TruncatedSVD + else: + pca_op = sklearn.decomposition.PCA + return pca_op(n_components=n_components) + +classifier = sklearn.neighbors.KNeighborsClassifier() +pipeline = sklearn.pipeline.Pipeline( + [ + ("pca", pca_op(input_train, input_test, n_components=100)), + ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), + ("regression", classifier), + ] +) + +print("Fit to train data") +pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) -print("Run classifier") -adata = classifier(adata, estimator=sklearn.neighbors.KNeighborsClassifier) -adata.uns["method_id"] = meta["functionality_name"] +print("Predict on test data") +input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) -print("Write data") -adata.write(par['output'], compression="gzip") +print("Write output to file") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index bcbe49aff7..9a4edba1c7 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,31 +1,31 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "logistic_regression" namespace: "label_projection/methods" - version: "dev" - description: "Applied Logistic Regression" + description: "Logistic regression method" info: type: method label: Logistic Regression + # paper_name: "Applied Logistic Regression" + # paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" + # paper_year: 2013 + code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" + v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py + v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d arguments: - name: "--max_iter" type: "integer" - example: "100" + default: 1000 description: "Maximum number of iterations" - required: true resources: - type: python_script path: script.py - - path: "../../utils.py" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - scanpy - - scprep - - sklearn + - scikit-learn - "anndata<0.8" - - type: native - type: nextflow diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 0f44a543bd..2d7d25fabe 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -1,25 +1,58 @@ +import anndata as ad +import sklearn.linear_model +import sklearn.pipeline +import sklearn.preprocessing +import sklearn.decomposition +import scipy.sparse + ## VIASH START par = { - 'input': '../../../data/test_data_preprocessed.h5ad', - 'output': 'output.knnscran.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', } ## VIASH END -utils_dir = "../../" - -import sys -sys.path.append(utils_dir) -sys.path.append(meta['resources_dir']) -import scanpy as sc -from utils import classifier -import sklearn.linear_model print("Load input data") -adata = sc.read(par['input']) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Set up classifier pipeline") +def pca_op(adata_train, adata_test, n_components=100): + is_sparse = scipy.sparse.issparse(adata_train.X) + + min_components = min( + [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + ) + if is_sparse: + min_components -= 1 + n_components = min([n_components, min_components]) + if is_sparse: + pca_op = sklearn.decomposition.TruncatedSVD + else: + pca_op = sklearn.decomposition.PCA + return pca_op(n_components=n_components) + +classifier = sklearn.linear_model.LogisticRegression( + max_iter=par["max_iter"] +) +pipeline = sklearn.pipeline.Pipeline( + [ + ("pca", pca_op(input_train, input_test, n_components=100)), + ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), + ("regression", classifier), + ] +) + +print("Fit to train data") +classifipipelineer.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) -print("Run classifier") -max_iter = par['max_iter'] -adata = classifier(adata, estimator=sklearn.linear_model.LogisticRegression, max_iter=max_iter) -adata.uns["method_id"] = meta["functionality_name"] +print("Predict on test data") +input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) -print("Write data") -adata.write(par['output'], compression="gzip") +print("Write output to file") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 6b22ed9174..f166f6a755 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,34 +1,35 @@ -__inherits__: ../../api/method.yaml +__inherits__: ../../api/comp_method.yaml functionality: name: "mlp" namespace: "label_projection/methods" - version: "dev" description: "Multilayer perceptron" info: type: method label: Multilayer perceptron + # paper_name: "Connectionist learning procedures" + # paper_url: "https://doi.org/10.1016/0004-3702(89)90049-0" + # paper_year: 1990 + paper_doi: "10.1016/0004-3702(89)90049-0" + code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" arguments: - name: "--hidden_layer_sizes" type: "integer" multiple: true description: "The ith element represents the number of neurons in the ith hidden layer." - required: true + default: [100, 100] - name: "--max_iter" type: "integer" - example: "100" + default: 1000 description: "Maximum number of iterations" - required: true resources: - type: python_script path: script.py - - path: "../../utils.py" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - scanpy - - sklearn + - scikit-learn - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index be3abe07a1..a5872cf999 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -1,33 +1,59 @@ +import anndata as ad +from sklearn.neural_network import MLPClassifier +import sklearn.pipeline +import sklearn.preprocessing +import sklearn.decomposition +import scipy.sparse + ## VIASH START par = { - 'input': '../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad', - 'output': 'output.mlplogcpm.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', } ## VIASH END -resources_dir = "../../../../common/tools/" -utils_dir = "../../" -import sys -sys.path.append(resources_dir) -sys.path.append(utils_dir) -sys.path.append(meta['resources_dir']) -import scanpy as sc -from utils import classifier -import sklearn.neural_network +print("Load input data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) +print("Set up classifier pipeline") +def pca_op(adata_train, adata_test, n_components=100): + is_sparse = scipy.sparse.issparse(adata_train.X) -print("Load input data") -adata = sc.read(par['input']) + min_components = min( + [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + ) + if is_sparse: + min_components -= 1 + n_components = min([n_components, min_components]) + if is_sparse: + pca_op = sklearn.decomposition.TruncatedSVD + else: + pca_op = sklearn.decomposition.PCA + return pca_op(n_components=n_components) -if "normalization_method" not in adata.uns: - print("Warning: trying to predict for a not normalized data") +classifier = MLPClassifier( + max_iter=par["max_iter"], + hidden_layer_sizes=tuple(par["hidden_layer_sizes"]) +) +pipeline = sklearn.pipeline.Pipeline( + [ + ("pca", pca_op(input_train, input_test, n_components=100)), + ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), + ("regression", classifier), + ] +) +print("Fit to train data") +pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) -print("Run classifier") -hidden_layer_sizes = tuple(par['hidden_layer_sizes']) -max_iter = par['max_iter'] -adata = classifier(adata, estimator=sklearn.neural_network.MLPClassifier, hidden_layer_sizes=hidden_layer_sizes, max_iter=max_iter) -adata.uns["method_id"] = meta["functionality_name"] +print("Predict on test data") +input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) -print("Write data") -adata.write(par['output'], compression="gzip") +print("Write output to file") +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 8ee316b48ad5362186d5ba186a421a30795a916a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 07:07:44 +0100 Subject: [PATCH 0281/1233] update write calls Former-commit-id: 3851e398c1f413470e56c5ae145cbebd7342f89a --- src/common/dataset_concatenate/script.py | 2 +- src/common/dataset_loader/download/script.py | 4 ++-- src/label_projection/methods/scvi/scanvi_all_genes/script.py | 2 +- src/label_projection/methods/scvi/scanvi_hvg/script.py | 2 +- .../methods/scvi/scarches_scanvi_all_genes/script.py | 2 +- .../methods/scvi/scarches_scanvi_hvg/script.py | 2 +- src/label_projection/metrics/accuracy/script.py | 2 +- src/label_projection/metrics/f1/script.py | 2 +- src/modality_alignment/datasets/sample_dataset/script.py | 2 +- src/modality_alignment/datasets/scprep_csv/script.py | 2 +- src/modality_alignment/methods/harmonic_alignment/script.py | 2 +- src/modality_alignment/methods/sample_method/script.py | 2 +- src/modality_alignment/methods/scot/script.py | 2 +- src/modality_alignment/metrics/knn_auc/script.py | 2 +- src/modality_alignment/metrics/mse/script.py | 2 +- 15 files changed, 16 insertions(+), 16 deletions(-) diff --git a/src/common/dataset_concatenate/script.py b/src/common/dataset_concatenate/script.py index 2d4e375f65..4084b96d63 100644 --- a/src/common/dataset_concatenate/script.py +++ b/src/common/dataset_concatenate/script.py @@ -18,4 +18,4 @@ adata = adata_list[0].concatenate(adata_list[1:]) print("Writing result file") -adata.write(par["output"], compression="gzip") +adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index f12fc00ee3..bd6ecea249 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -25,7 +25,7 @@ opener.addheaders = _FAKE_HEADERS urllib.request.install_opener(opener) with urllib.request.urlopen(par["url"]) as urlhandle: - filehandle.write(urlhandle.read()) + filehandle.write_h5ad(urlhandle.read()) print("Reading file") adata = sc.read_h5ad(filepath) @@ -72,4 +72,4 @@ del adata.X print("Writing adata to file") -adata.write(par["output"], compression="gzip") +adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py index cf3b26d4e4..f1ca53fb06 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scanvi_all_genes/script.py @@ -36,4 +36,4 @@ adata.uns["method_id"] = meta["functionality_name"] print("Write data") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_hvg/script.py b/src/label_projection/methods/scvi/scanvi_hvg/script.py index cdc4a6f4f1..50f4ae82c9 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scanvi_hvg/script.py @@ -48,4 +48,4 @@ adata.uns["method_id"] = meta["functionality_name"] print("Write data") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py index d51a6d6a3f..afb5a467f5 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py @@ -39,4 +39,4 @@ adata.uns["method_id"] = meta["functionality_name"] print("Write data") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py index 6342978248..54f39d1bfa 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py @@ -54,4 +54,4 @@ adata.uns["method_id"] = meta["functionality_name"] print("Write data") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index 3798037c6c..07fde62536 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -26,4 +26,4 @@ adata.uns["metric_value"] = accuracy print("Writing adata to file") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 31f88d5e3f..0733bbae53 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -29,4 +29,4 @@ adata.uns["metric_value"] = metrics print("Writing adata to file") -adata.write(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/modality_alignment/datasets/sample_dataset/script.py b/src/modality_alignment/datasets/sample_dataset/script.py index c81093b0df..1d0a3cdefc 100644 --- a/src/modality_alignment/datasets/sample_dataset/script.py +++ b/src/modality_alignment/datasets/sample_dataset/script.py @@ -81,4 +81,4 @@ adata.uns["dataset_id"] = "sample_dataset_test" print("Writing adata to file") -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/datasets/scprep_csv/script.py b/src/modality_alignment/datasets/scprep_csv/script.py index 78de2926fb..c6d4fef450 100644 --- a/src/modality_alignment/datasets/scprep_csv/script.py +++ b/src/modality_alignment/datasets/scprep_csv/script.py @@ -49,4 +49,4 @@ adata.uns["dataset_id"] = par["id"] + "_test" print("Writing adata to file") -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/modality_alignment/methods/harmonic_alignment/script.py index cdf29c75e9..d524f47665 100644 --- a/src/modality_alignment/methods/harmonic_alignment/script.py +++ b/src/modality_alignment/methods/harmonic_alignment/script.py @@ -56,4 +56,4 @@ print("Write output to file") adata.uns["method_id"] = "harmonic_alignment" -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/sample_method/script.py b/src/modality_alignment/methods/sample_method/script.py index 5a75ad7614..c9d8d6d35d 100644 --- a/src/modality_alignment/methods/sample_method/script.py +++ b/src/modality_alignment/methods/sample_method/script.py @@ -12,4 +12,4 @@ print("Write output to file") adata.uns["method_id"] = "sample_method" -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/methods/scot/script.py b/src/modality_alignment/methods/scot/script.py index 58fa078cea..1427ea9f4f 100644 --- a/src/modality_alignment/methods/scot/script.py +++ b/src/modality_alignment/methods/scot/script.py @@ -50,4 +50,4 @@ print("Write output to file") adata.uns["method_id"] = "scot" -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/metrics/knn_auc/script.py b/src/modality_alignment/metrics/knn_auc/script.py index 594a749365..48569c0e9e 100644 --- a/src/modality_alignment/metrics/knn_auc/script.py +++ b/src/modality_alignment/metrics/knn_auc/script.py @@ -62,4 +62,4 @@ adata.uns["metric_value"] = area_under_curve print("Writing adata to file") -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/modality_alignment/metrics/mse/script.py b/src/modality_alignment/metrics/mse/script.py index 59dee3c81e..740b49cdc6 100644 --- a/src/modality_alignment/metrics/mse/script.py +++ b/src/modality_alignment/metrics/mse/script.py @@ -37,4 +37,4 @@ def _square(X): adata.uns["metric_value"] = metric_value print("Writing adata to file") -adata.write(par["output"], compression = "gzip") +adata.write_h5ad(par["output"], compression = "gzip") From 01a3d2fd22c9a63584c58e854659b7865d53e28b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 07:07:50 +0100 Subject: [PATCH 0282/1233] update readme Former-commit-id: 9e1cec2963c74ba396b3ff3dc96dc84a97a9e78d --- src/label_projection/README.md | 192 ++++++++++++++------------------ src/label_projection/README.qmd | 111 +++++++++--------- 2 files changed, 134 insertions(+), 169 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 99717870df..7e1e46dfef 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -48,59 +48,53 @@ correctly assigns cell type labels to cells in the test set. ``` mermaid %%| column: screen-inset-shaded flowchart LR - dataset_censoring__output_train(Training data) - dataset_censoring__output_test(Test data) - dataset_censoring__output_solution(Solution) - dataset_preprocessing__input(Raw dataset) - dataset_preprocessing__output(Pre-processed dataset) - method__output(Prediction) - metric__output(Scores) - dataset_censoring[/Dataset censoring/] - dataset_preprocessing[/Dataset preprocessing/] - method[/Method/] - metric[/Metric/] - dataset_preprocessing__output---dataset_censoring - dataset_preprocessing__input---dataset_preprocessing - dataset_censoring__output_train---method - dataset_censoring__output_test---method - dataset_censoring__output_solution---metric - method__output---metric - dataset_censoring-->dataset_censoring__output_train - dataset_censoring-->dataset_censoring__output_test - dataset_censoring-->dataset_censoring__output_solution - dataset_preprocessing-->dataset_preprocessing__output - method-->method__output - metric-->metric__output + anndata_prediction(prediction) + anndata_preprocessed(preprocessed) + anndata_raw_dataset(raw dataset) + anndata_score(score) + anndata_solution(solution) + anndata_test(test) + anndata_train(train) + comp_censoring[/censoring/] + comp_method[/method/] + comp_metric[/metric/] + comp_normalization[/normalization/] + anndata_preprocessed---comp_censoring + anndata_train---comp_method + anndata_test---comp_method + anndata_solution---comp_metric + anndata_prediction---comp_metric + anndata_raw_dataset---comp_normalization + comp_censoring-->anndata_train + comp_censoring-->anndata_test + comp_censoring-->anndata_solution + comp_method-->anndata_prediction + comp_metric-->anndata_score + comp_normalization-->anndata_preprocessed ``` -### Training data - -The training data +### prediction Used in: -- dataset_censoring: output_train (as output) -- method: input_train (as input) +- method: output (as output) +- metric: input_prediction (as input) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | labels | double | Ground truth cell type labels | -| obs | batch | double | Batch information | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | dataset | string | A unique identifier for the dataset | - -### Test data +| struct | name | type | description | +|:-------|:---------------|:-------|:--------------------------------------------------------------------| +| obs | label_pred | string | Predicted labels for the test cells. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | method_id | string | A unique identifier for the method | -The censored test data +### preprocessed Used in: -- dataset_censoring: output_test (as output) -- method: input_test (as input) +- censoring: input (as input) +- normalization: output (as output) Slots: @@ -108,55 +102,48 @@ Slots: |:-------|:---------------|:--------|:--------------------------------------------------------------------| | layers | counts | integer | Raw counts | | layers | lognorm | double | Log-transformed normalised counts | +| obs | label | double | Ground truth cell type labels | | obs | batch | double | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | dataset | string | A unique identifier for the dataset | - -### Solution -The solution for the test data +### raw dataset Used in: -- dataset_censoring: output_solution (as output) -- metric: input_solution (as input) +- normalization: input (as input) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | labels | double | Ground truth cell type labels | -| obs | batch | double | Batch information | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | dataset | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### Raw dataset - -An unprocessed dataset. +### score Used in: -- dataset_preprocessing: input (as input) +- metric: output (as output) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| obs | labels | double | Ground truth cell type labels | -| obs | batch | double | Batch information | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | - -### Pre-processed dataset +| struct | name | type | description | +|:-------|:---------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | -A preprocessed dataset +### solution Used in: -- dataset_censoring: input (as input) -- dataset_preprocessing: output (as output) +- censoring: output_solution (as output) +- metric: input_solution (as input) Slots: @@ -164,59 +151,42 @@ Slots: |:-------|:---------------|:--------|:--------------------------------------------------------------------| | layers | counts | integer | Raw counts | | layers | lognorm | double | Log-transformed normalised counts | -| obs | labels | double | Ground truth cell type labels | -| obs | batch | double | Batch information | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | dataset | string | A unique identifier for the dataset | -### Prediction - -The prediction file +### test Used in: -- method: output (as output) -- metric: input_prediction (as input) +- censoring: output_test (as output) +- method: input_test (as input) Slots: -| struct | name | type | description | -|:-------|:---------------|:-------|:--------------------------------------------------------------------| -| obs | labels_pred | double | Predicted labels for the test cells. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | method_id | string | A unique identifier for the method | - -### Scores +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -Metric score file +### train Used in: -- metric: output (as output) +- censoring: output_train (as output) +- method: input_train (as input) Slots: -| struct | name | type | description | -|:-------|:---------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - - +| struct | name | type | description | +|:-------|:---------------|:--------|:--------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | lognorm | double | Log-transformed normalised counts | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index e3b8eface7..a00211e33e 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -30,6 +30,11 @@ Here, we compare methods for annotation based on a reference dataset. The datase Metrics for label projection aim to characterize how well each classifer correctly assigns cell type labels to cells in the test set. +```{r metrics, include=FALSE} +metric_yamls <- list.files(paste0(dir, "/metrics"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) +# todo +``` + * **Accuracy**: Average number of correctly applied labels. * **F1 score**: The [F1 score](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html) is a weighted average of the precision and recall over all class labels, where an F1 score reaches its best value at 1 and worst score at 0, where each class contributes to the score relative to its frequency in the dataset. * **Macro F1 score**: The macro F1 score is an unweighted F1 score, where each class contributes equally, regardless of its frequency. @@ -37,57 +42,57 @@ Metrics for label projection aim to characterize how well each classifer correct ## API ```{r data, include=FALSE} -yaml_files <- list.files(paste0(dir, "/api"), full.names = TRUE) +comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) -file_arg_info <- map_df(yaml_files, function(yaml_file) { +comp_file <- map_df(comp_yamls, function(yaml_file) { conf <- yaml::read_yaml(yaml_file) map_df(conf$functionality$arguments, function(arg) { tibble( - comp = conf$functionality$name, + comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), arg_name = str_replace_all(arg$name, "^-*", ""), - id = paste0(comp, "__", arg_name), - short_description = arg$meta$short_description, - description = arg$description, direction = arg$direction %||% "input", - from = arg$meta$from + file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) ) }) }) -comp_info <- map_df(yaml_files, function(yaml_file) { +comp_info <- map_df(comp_yamls, function(yaml_file) { conf <- yaml::read_yaml(yaml_file) tibble( - name = conf$functionality$name, - label = conf$functionality$meta$label %||% str_replace_all(name, "_", " ") + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) ) }) -slot_info <- map_df(yaml_files, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) +file_info <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + ) +}) - map_df(conf$functionality$arguments, function(arg) { - out <- map2_df(names(arg$slots), arg$slots, function(group_name, slot) { - df <- map_df(slot, as.data.frame) - df$struct <- group_name - as_tibble(df) - }) - out$component <- conf$functionality$name - out$argument <- str_replace_all(arg$name, "^-*", "") - out$direction <- arg$direction %||% "input" - out +file_slot <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) + as_tibble(df) }) }) %>% - select(component, argument, struct, name, everything()) %>% - mutate(multiple = multiple %|% FALSE, id = paste0(component, "__", argument)) + mutate(multiple = multiple %|% FALSE) ``` ```{r flow, echo=FALSE,warning=FALSE,error=FALSE} nodes <- bind_rows( - file_arg_info %>% - filter(!is.na(short_description)) %>% - transmute(id, label = short_description, is_comp = FALSE), + file_info %>% + transmute(id = name, label, is_comp = FALSE), comp_info %>% transmute(id = name, label, is_comp = TRUE) ) %>% @@ -99,12 +104,20 @@ nodes <- bind_rows( ifelse(is_comp, "/]", ")") )) edges <- bind_rows( - file_arg_info %>% + comp_file %>% filter(direction == "input") %>% - transmute(from = ifelse(!is.na(from), from, id), to = comp, arrow = "---"), - file_arg_info %>% + transmute( + from = file_name, + to = comp_name, + arrow = "---" + ), + comp_file %>% filter(direction == "output") %>% - transmute(from = comp, to = id, arrow = "-->") + transmute( + from = comp_name, + to = file_name, + arrow = "-->" + ) ) %>% mutate(str = paste0(" ", from, arrow, to)) @@ -121,21 +134,19 @@ knitr::asis_output(out_str) ``` ```{r api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -obj_ids <- file_arg_info %>% filter(!is.na(short_description)) %>% pull(id) -for (obj_id in obj_ids) { - arg_info <- file_arg_info %>% filter(id == obj_id) - sub_out <- slot_info %>% - filter(id == obj_id) %>% +for (file_name in file_info$name) { + arg_info <- file_info %>% filter(name == file_name) + sub_out <- file_slot %>% + filter(file_name == !!file_name) %>% select(struct, name, type, description) - used_in <- file_arg_info %>% - filter(id == obj_id | from == obj_id) %>% - mutate(str = paste0("* ", comp, ": ", arg_name, " (as ", direction, ")")) %>% + used_in <- comp_file %>% + filter(file_name == !!file_name) %>% + left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% + mutate(str = paste0("* ", comp_label, ": ", arg_name, " (as ", direction, ")")) %>% pull(str) out_str <- strip_margin(glue::glue(" - §### {arg_info$short_description} - § - §{arg_info$description} + §### {arg_info$label} § §Used in: § @@ -148,19 +159,3 @@ for (obj_id in obj_ids) { cat(out_str) } ``` - - \ No newline at end of file From 8f7200dbe6d1415a7193d9896303ef7d69512691 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 10:15:24 +0100 Subject: [PATCH 0283/1233] add seed to censor component Former-commit-id: ff230f7505f155a8ee8df40c5c5cfd9679753b13 --- .../data_processing/censoring/config.vsh.yaml | 4 ++++ .../data_processing/censoring/script.py | 17 +++++++++++------ .../resources_test_scripts/pancreas.sh | 13 ++++++++++++- 3 files changed, 27 insertions(+), 7 deletions(-) diff --git a/src/label_projection/data_processing/censoring/config.vsh.yaml b/src/label_projection/data_processing/censoring/config.vsh.yaml index 4d876d5fe7..e48f46800f 100644 --- a/src/label_projection/data_processing/censoring/config.vsh.yaml +++ b/src/label_projection/data_processing/censoring/config.vsh.yaml @@ -16,6 +16,10 @@ functionality: type: "string" description: "Which .obs slot to use as batch covariate." default: "batch" + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 resources: - type: python_script path: script.py diff --git a/src/label_projection/data_processing/censoring/script.py b/src/label_projection/data_processing/censoring/script.py index 372ed61c78..814f39ffbe 100644 --- a/src/label_projection/data_processing/censoring/script.py +++ b/src/label_projection/data_processing/censoring/script.py @@ -1,10 +1,12 @@ import numpy as np -import scanpy as sc +import anndata as ad +import random ## VIASH START par = { 'input': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm.h5ad', 'method': 'batch', + 'seed': None, 'obs_batch': 'batch', 'obs_label': 'celltype', 'output_train': 'train.h5ad', @@ -16,8 +18,12 @@ } ## VIASH END +if par["seed"]: + print(f">> Setting seed to {par['seed']}") + random.seed(par["seed"]) + print(">> Load data") -adata = sc.read(par["input"]) +adata = ad.read_h5ad(par["input"]) print("adata:", adata) @@ -30,13 +36,12 @@ for idx in adata.obs_names ] elif par["method"] == "random": - is_test = np.random.choice( - [False, True], adata.shape[0], replace=True, p=[0.8, 0.2] - ) + train_ix = np.random.choice(adata.n_obs, round(adata.n_obs * 0.8), replace=False) + is_test = [ not x in train_ix for x in range(0, adata.n_obs) ] # create new anndata objects according to api spec def subset_anndata(adata_sub, layers, obs, uns): - return sc.AnnData( + return ad.AnnData( layers={key: adata_sub.layers[key] for key in layers}, obs=adata_sub.obs[obs.values()].rename({v:n for n,v in obs.items()}, axis=1), var=adata.var.drop(adata.var.columns, axis=1), diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 7610c8318e..e6b1ef5284 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -19,23 +19,34 @@ fi mkdir -p $DATASET_DIR +# subsample dataset bin/viash run src/label_projection/data_processing/subsample/config.vsh.yaml -- \ --input $RAW_DATA \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ --output $DATASET_DIR/dataset_subsampled.h5ad +# run one normalisation bin/viash run src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/dataset_subsampled.h5ad \ --output $DATASET_DIR/dataset_subsampled_cpm.h5ad +# censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ --input $DATASET_DIR/dataset_subsampled_cpm.h5ad \ --output_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ --output_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ - --output_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad + --output_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad \ + --seed 123 +# run one method bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ --input_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ --input_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ --output $DATASET_DIR/dataset_subsampled_cpm_prediction.h5ad + +# run one metric +bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ + --input_prediction $DATASET_DIR/dataset_subsampled_cpm_prediction.h5ad \ + --input_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad \ + --output $DATASET_DIR/dataset_subsampled_cpm_score.h5ad From f960a8e680e4b8b8d8663ef9823449d4f37defcd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 10:45:27 +0100 Subject: [PATCH 0284/1233] move subsample component Former-commit-id: 016de7f317937f557b0d3989a17a8aad40d64fc4 --- src/common/dataset_loader/download/script.py | 1 + src/common/resources_test_scripts/pancreas.sh | 11 ++++++++++- .../subsample/config.vsh.yaml | 13 ++++++++----- .../data_processing => common}/subsample/script.py | 12 ++++++++++-- .../subsample/test_script.py | 0 5 files changed, 29 insertions(+), 8 deletions(-) rename src/{label_projection/data_processing => common}/subsample/config.vsh.yaml (79%) rename src/{label_projection/data_processing => common}/subsample/script.py (90%) rename src/{label_projection/data_processing => common}/subsample/test_script.py (100%) diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index bd6ecea249..a563e97148 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -12,6 +12,7 @@ "name": "pancreas", "obs_celltype": "celltype", "obs_batch": "tech", + "layer_counts": "counts", "output": "test_data.h5ad" } ## VIASH END diff --git a/src/common/resources_test_scripts/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh index 9815b66bd4..807d368c65 100755 --- a/src/common/resources_test_scripts/pancreas.sh +++ b/src/common/resources_test_scripts/pancreas.sh @@ -13,10 +13,19 @@ DATASET_DIR=resources_test/common/pancreas mkdir -p $DATASET_DIR +# download dataset bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ --url "https://ndownloader.figshare.com/files/24539828" \ --obs_celltype "celltype" \ --obs_batch "tech" \ --name "pancreas" \ --layer_counts "counts" \ - --output $DATASET_DIR/dataset.h5ad \ No newline at end of file + --output $DATASET_DIR/temp_full_dataset.h5ad + +# subsample +bin/viash run src/common/subsample/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_full_dataset.h5ad \ + --keep_celltype_categories "acinar:beta" \ + --keep_batch_categories "celseq:inDrop4:smarter" \ + --output $DATASET_DIR/dataset.h5ad \ + --seed 123 \ No newline at end of file diff --git a/src/label_projection/data_processing/subsample/config.vsh.yaml b/src/common/subsample/config.vsh.yaml similarity index 79% rename from src/label_projection/data_processing/subsample/config.vsh.yaml rename to src/common/subsample/config.vsh.yaml index d3a8a4ce7f..6cea15b145 100644 --- a/src/label_projection/data_processing/subsample/config.vsh.yaml +++ b/src/common/subsample/config.vsh.yaml @@ -1,8 +1,8 @@ functionality: name: "subsample" - namespace: "label_projection/data_processing" + namespace: "common" version: "dev" - description: "Component to generate a toy data for tests finality" + description: "Subsample an anndata file" arguments: - name: "--input" type: "file" @@ -27,16 +27,19 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output h5ad file resized" + description: "Output h5ad file" required: true + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 resources: - type: python_script path: script.py test_resources: - type: python_script path: test_script.py - - type: file - path: "../../../../resources_test/common/pancreas" + - path: "../../../resources_test/common/pancreas" platforms: - type: docker image: "python:3.8" diff --git a/src/label_projection/data_processing/subsample/script.py b/src/common/subsample/script.py similarity index 90% rename from src/label_projection/data_processing/subsample/script.py rename to src/common/subsample/script.py index c33215a863..b3b19cff30 100644 --- a/src/label_projection/data_processing/subsample/script.py +++ b/src/common/subsample/script.py @@ -1,21 +1,29 @@ import scanpy as sc +import random + ### VIASH START par = { "input": "resources_test/common/pancreas/dataset.h5ad", + "keep_celltype_categories": None, + "keep_batch_categories": None, # "keep_celltype_categories": ["acinar", "beta"], # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], "even": True, - "ouput": "toy_data.h5ad" + "output": "toy_data.h5ad", + "seed": 123 } ### VIASH END +if par["seed"]: + print(f">> Setting seed to {par['seed']}") + random.seed(par["seed"]) + def filter_genes_cells(adata): """Remove empty cells and genes.""" sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) return adata - print(">> Load data") adata = sc.read(par['input']) diff --git a/src/label_projection/data_processing/subsample/test_script.py b/src/common/subsample/test_script.py similarity index 100% rename from src/label_projection/data_processing/subsample/test_script.py rename to src/common/subsample/test_script.py From fc02055ea4b7a80a9abbd91251aeb541dd494419 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:03:30 +0100 Subject: [PATCH 0285/1233] Fix refactoring issue Former-commit-id: b5f98b0c062f4a43fcfd6ef4decc22567c4b22ea --- src/common/dataset_loader/download/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index a563e97148..c2834106ff 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -26,7 +26,7 @@ opener.addheaders = _FAKE_HEADERS urllib.request.install_opener(opener) with urllib.request.urlopen(par["url"]) as urlhandle: - filehandle.write_h5ad(urlhandle.read()) + filehandle.write(urlhandle.read()) print("Reading file") adata = sc.read_h5ad(filepath) From 58ec125e20394c9ac25d5e95e3a35aa133a71ed2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:04:18 +0100 Subject: [PATCH 0286/1233] update test resource naming Former-commit-id: ffa29f3f352e42984d79617ace66dc0636c5d8f5 --- src/label_projection/api/comp_censoring.yaml | 2 +- src/label_projection/api/comp_method.yaml | 6 +-- .../control_methods/majority_vote/script.py | 4 +- .../control_methods/random_labels/script.py | 4 +- .../control_methods/true_labels/script.py | 6 +-- .../data_processing/censoring/config.vsh.yaml | 2 +- .../data_processing/censoring/script.py | 2 +- .../methods/knn_classifier/script.py | 4 +- .../methods/logistic_regression/script.py | 4 +- src/label_projection/methods/mlp/script.py | 4 +- .../resources_test_scripts/pancreas.sh | 37 ++++++++----------- 11 files changed, 34 insertions(+), 41 deletions(-) diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_censoring.yaml index d52c906669..d97e7ca231 100644 --- a/src/label_projection/api/comp_censoring.yaml +++ b/src/label_projection/api/comp_censoring.yaml @@ -19,7 +19,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm.h5ad" + input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" output_train_path = "output_train.h5ad" output_test_path = "output_test.h5ad" output_solution_path = "output_solution.h5ad" diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 5d02b53490..518611fcdf 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -16,9 +16,9 @@ functionality: import subprocess from os import path - input_train_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_test.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/dataset_subsampled_cpm_solution.h5ad" + input_train_path = meta["resources_dir"] + "/pancreas/dataset_cpm_train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/dataset_cpm_test.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/dataset_cpm_solution.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/label_projection/control_methods/majority_vote/script.py b/src/label_projection/control_methods/majority_vote/script.py index d847c419a3..f813afe7c7 100644 --- a/src/label_projection/control_methods/majority_vote/script.py +++ b/src/label_projection/control_methods/majority_vote/script.py @@ -2,8 +2,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/control_methods/random_labels/script.py b/src/label_projection/control_methods/random_labels/script.py index 8a65bd7b32..7526568389 100644 --- a/src/label_projection/control_methods/random_labels/script.py +++ b/src/label_projection/control_methods/random_labels/script.py @@ -3,8 +3,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/control_methods/true_labels/script.py b/src/label_projection/control_methods/true_labels/script.py index 32b668a14b..cc3731563c 100644 --- a/src/label_projection/control_methods/true_labels/script.py +++ b/src/label_projection/control_methods/true_labels/script.py @@ -2,9 +2,9 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', - 'input_solution': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/data_processing/censoring/config.vsh.yaml b/src/label_projection/data_processing/censoring/config.vsh.yaml index e48f46800f..cf2d170b3f 100644 --- a/src/label_projection/data_processing/censoring/config.vsh.yaml +++ b/src/label_projection/data_processing/censoring/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_dataset_censoring.yaml +__inherits__: ../../api/comp_censoring.yaml functionality: name: "censoring" namespace: "label_projection/data_processing" diff --git a/src/label_projection/data_processing/censoring/script.py b/src/label_projection/data_processing/censoring/script.py index 814f39ffbe..bb0f44e8b6 100644 --- a/src/label_projection/data_processing/censoring/script.py +++ b/src/label_projection/data_processing/censoring/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm.h5ad', + 'input': 'resources_test/label_projection/pancreas/dataset_cpm.h5ad', 'method': 'batch', 'seed': None, 'obs_batch': 'batch', diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index 70b7142b4a..5083b9b22e 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 2d7d25fabe..73952b734a 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index a5872cf999..47f2be50e0 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_subsampled_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index e6b1ef5284..8067f40bf5 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -19,34 +19,27 @@ fi mkdir -p $DATASET_DIR -# subsample dataset -bin/viash run src/label_projection/data_processing/subsample/config.vsh.yaml -- \ - --input $RAW_DATA \ - --keep_celltype_categories "acinar:beta" \ - --keep_batch_categories "celseq:inDrop4:smarter" \ - --output $DATASET_DIR/dataset_subsampled.h5ad - # run one normalisation bin/viash run src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset_subsampled.h5ad \ - --output $DATASET_DIR/dataset_subsampled_cpm.h5ad + --input $RAW_DATA \ + --output $DATASET_DIR/dataset_cpm.h5ad # censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset_subsampled_cpm.h5ad \ - --output_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ - --output_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ - --output_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad \ + --input $DATASET_DIR/dataset_cpm.h5ad \ + --output_train $DATASET_DIR/dataset_cpm_train.h5ad \ + --output_test $DATASET_DIR/dataset_cpm_test.h5ad \ + --output_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ --seed 123 # run one method bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ - --input_train $DATASET_DIR/dataset_subsampled_cpm_train.h5ad \ - --input_test $DATASET_DIR/dataset_subsampled_cpm_test.h5ad \ - --output $DATASET_DIR/dataset_subsampled_cpm_prediction.h5ad - -# run one metric -bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/dataset_subsampled_cpm_prediction.h5ad \ - --input_solution $DATASET_DIR/dataset_subsampled_cpm_solution.h5ad \ - --output $DATASET_DIR/dataset_subsampled_cpm_score.h5ad + --input_train $DATASET_DIR/dataset_cpm_train.h5ad \ + --input_test $DATASET_DIR/dataset_cpm_test.h5ad \ + --output $DATASET_DIR/dataset_cpm_prediction.h5ad + +# # run one metric +# bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ +# --input_prediction $DATASET_DIR/dataset_cpm_prediction.h5ad \ +# --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ +# --output $DATASET_DIR/dataset_cpm_score.h5ad From 008e486703fa4c006e264dbacdf57ec73447e49b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:15:34 +0100 Subject: [PATCH 0287/1233] update changelog Former-commit-id: 80c8d0289ae8f8d472c88f73778851e623c6163f --- CHANGELOG.md | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a4bc7e0b8e..cb09c82aaf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,8 +8,30 @@ * `extract_scores`: Summarise a metrics output tsv. -* `dataset_concatenate`: concatenate N AnnData datasets +* `dataset_concatenate`: Concatenate N AnnData datasets. -* `label_projection`: all components for **label_projection** task +* `subsample`: Subsample an anndata file. -## +* Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. + +## label_projection + +### NEW FUNCTIONALITY + +* API: Created an explicit api definition for the censor, normalisation, method and metric components. + +* Created censoring component `data_processing/censoring`. + +* Created test data `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. + +### V1 MIGRATION + +* Ported normalisation method `data_processing/normalise_log_cpm`. + +* Ported normalisation method `data_processing/normalise_log_scran_pooling`. + +* Ported method `methods/knn_classifier`. + +* Ported method `methods/logistic_regression`. + +* Ported method `methods/mlp`. \ No newline at end of file From f039c3386b8dad8b64e7980786f5979a0f00b94b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:31:13 +0100 Subject: [PATCH 0288/1233] update changelog Former-commit-id: b18aed9d2500a0763549ae7d580dcc08808e36d1 --- CHANGELOG.md | 10 +++---- .../api/anndata_normalized_dataset.yaml} | 0 .../api/anndata_raw_dataset.yaml | 0 .../api/comp_normalization.yaml | 4 +-- .../normalization/log_cpm}/config.vsh.yaml | 4 +-- .../normalization/log_cpm}/script.py | 0 .../log_scran_pooling}/config.vsh.yaml | 4 +-- .../normalization/log_scran_pooling}/script.R | 0 src/common/resources_test_scripts/pancreas.sh | 7 ++++- src/label_projection/api/anndata_dataset.yaml | 27 +++++++++++++++++++ src/label_projection/api/comp_censoring.yaml | 2 +- .../resources_test_scripts/pancreas.sh | 5 ---- 12 files changed, 45 insertions(+), 18 deletions(-) rename src/{label_projection/api/anndata_preprocessed.yaml => common/api/anndata_normalized_dataset.yaml} (100%) rename src/{label_projection => common}/api/anndata_raw_dataset.yaml (100%) rename src/{label_projection => common}/api/comp_normalization.yaml (91%) rename src/{label_projection/data_processing/normalize_log_cpm => common/normalization/log_cpm}/config.vsh.yaml (81%) rename src/{label_projection/data_processing/normalize_log_cpm => common/normalization/log_cpm}/script.py (100%) rename src/{label_projection/data_processing/normalize_log_scran_pooling => common/normalization/log_scran_pooling}/config.vsh.yaml (85%) rename src/{label_projection/data_processing/normalize_log_scran_pooling => common/normalization/log_scran_pooling}/script.R (100%) create mode 100644 src/label_projection/api/anndata_dataset.yaml diff --git a/CHANGELOG.md b/CHANGELOG.md index cb09c82aaf..9d9cdaf260 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,11 +14,15 @@ * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. +* Created normalization method `common/normalise_log_cpm`. + +* Created normalization method `common/normalise_log_scran_pooling`. + ## label_projection ### NEW FUNCTIONALITY -* API: Created an explicit api definition for the censor, normalisation, method and metric components. +* API: Created an explicit api definition for the censor, method and metric components. * Created censoring component `data_processing/censoring`. @@ -26,10 +30,6 @@ ### V1 MIGRATION -* Ported normalisation method `data_processing/normalise_log_cpm`. - -* Ported normalisation method `data_processing/normalise_log_scran_pooling`. - * Ported method `methods/knn_classifier`. * Ported method `methods/logistic_regression`. diff --git a/src/label_projection/api/anndata_preprocessed.yaml b/src/common/api/anndata_normalized_dataset.yaml similarity index 100% rename from src/label_projection/api/anndata_preprocessed.yaml rename to src/common/api/anndata_normalized_dataset.yaml diff --git a/src/label_projection/api/anndata_raw_dataset.yaml b/src/common/api/anndata_raw_dataset.yaml similarity index 100% rename from src/label_projection/api/anndata_raw_dataset.yaml rename to src/common/api/anndata_raw_dataset.yaml diff --git a/src/label_projection/api/comp_normalization.yaml b/src/common/api/comp_normalization.yaml similarity index 91% rename from src/label_projection/api/comp_normalization.yaml rename to src/common/api/comp_normalization.yaml index f1a71f3eda..f4e18b841a 100644 --- a/src/label_projection/api/comp_normalization.yaml +++ b/src/common/api/comp_normalization.yaml @@ -3,7 +3,7 @@ functionality: - name: "--input" __inherits__: anndata_raw_dataset.yaml - name: "--output" - __inherits__: anndata_preprocessed.yaml + __inherits__: anndata_normalized_dataset.yaml direction: output test_resources: - type: python_script @@ -13,7 +13,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/pancreas/dataset_subsampled.h5ad" + input_path = meta["resources_dir"] + "/common/dataset.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml b/src/common/normalization/log_cpm/config.vsh.yaml similarity index 81% rename from src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml rename to src/common/normalization/log_cpm/config.vsh.yaml index d11aa501d5..3bdfd4b09e 100644 --- a/src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml +++ b/src/common/normalization/log_cpm/config.vsh.yaml @@ -1,7 +1,7 @@ __inherits__: ../../api/comp_normalization.yaml functionality: - name: "normalize_log_cpm" - namespace: "label_projection/data_processing" + name: "log_cpm" + namespace: "common/normalization" description: "Normalize data using Log CPM" resources: - type: python_script diff --git a/src/label_projection/data_processing/normalize_log_cpm/script.py b/src/common/normalization/log_cpm/script.py similarity index 100% rename from src/label_projection/data_processing/normalize_log_cpm/script.py rename to src/common/normalization/log_cpm/script.py diff --git a/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml b/src/common/normalization/log_scran_pooling/config.vsh.yaml similarity index 85% rename from src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml rename to src/common/normalization/log_scran_pooling/config.vsh.yaml index d47f06a32e..44ac762979 100644 --- a/src/label_projection/data_processing/normalize_log_scran_pooling/config.vsh.yaml +++ b/src/common/normalization/log_scran_pooling/config.vsh.yaml @@ -1,7 +1,7 @@ __inherits__: ../../api/comp_normalization.yaml functionality: - name: "normalize_log_scran_pooling" - namespace: "label_projection/data_processing" + name: "log_scran_pooling" + namespace: "common/normalization" description: "Normalize data" resources: - type: r_script diff --git a/src/label_projection/data_processing/normalize_log_scran_pooling/script.R b/src/common/normalization/log_scran_pooling/script.R similarity index 100% rename from src/label_projection/data_processing/normalize_log_scran_pooling/script.R rename to src/common/normalization/log_scran_pooling/script.R diff --git a/src/common/resources_test_scripts/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh index 807d368c65..999e782279 100755 --- a/src/common/resources_test_scripts/pancreas.sh +++ b/src/common/resources_test_scripts/pancreas.sh @@ -28,4 +28,9 @@ bin/viash run src/common/subsample/config.vsh.yaml -- \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ --output $DATASET_DIR/dataset.h5ad \ - --seed 123 \ No newline at end of file + --seed 123 + +# run one normalisation +bin/viash run src/common/normalization/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset.h5ad \ + --output $DATASET_DIR/dataset_cpm.h5ad diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml new file mode 100644 index 0000000000..85c85f1abc --- /dev/null +++ b/src/label_projection/api/anndata_dataset.yaml @@ -0,0 +1,27 @@ +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + - type: double + name: lognorm + description: Log-transformed normalised counts + obs: + - type: double + name: label + description: Ground truth cell type labels + - type: double + name: batch + description: Batch information + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_censoring.yaml index d97e7ca231..b09e4abd32 100644 --- a/src/label_projection/api/comp_censoring.yaml +++ b/src/label_projection/api/comp_censoring.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_preprocessed.yaml + __inherits__: anndata_dataset.yaml - name: "--output_train" __inherits__: anndata_train.yaml direction: output diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 8067f40bf5..80dbc1b987 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -19,11 +19,6 @@ fi mkdir -p $DATASET_DIR -# run one normalisation -bin/viash run src/label_projection/data_processing/normalize_log_cpm/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output $DATASET_DIR/dataset_cpm.h5ad - # censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ --input $DATASET_DIR/dataset_cpm.h5ad \ From 1df96815ed88297bf5fe9dfb0e5741cbf5e77f96 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:34:16 +0100 Subject: [PATCH 0289/1233] update resources Former-commit-id: 2e5a6c4ab43468a2f63b31242d38bb23147b1197 --- .../resources_test_scripts/pancreas.sh | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 80dbc1b987..c0442a2b16 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad +RAW_DATA=resources_test/common/pancreas/dataset_cpm.h5ad DATASET_DIR=resources_test/label_projection/pancreas if [ ! -f $RAW_DATA ]; then @@ -21,20 +21,20 @@ mkdir -p $DATASET_DIR # censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset_cpm.h5ad \ - --output_train $DATASET_DIR/dataset_cpm_train.h5ad \ - --output_test $DATASET_DIR/dataset_cpm_test.h5ad \ - --output_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ + --input $RAW_DATA \ + --output_train $DATASET_DIR/pancreas_cpm_train.h5ad \ + --output_test $DATASET_DIR/pancreas_cpm_test.h5ad \ + --output_solution $DATASET_DIR/pancreas_cpm_solution.h5ad \ --seed 123 # run one method bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ - --input_train $DATASET_DIR/dataset_cpm_train.h5ad \ - --input_test $DATASET_DIR/dataset_cpm_test.h5ad \ - --output $DATASET_DIR/dataset_cpm_prediction.h5ad + --input_train $DATASET_DIR/pancreas_cpm_train.h5ad \ + --input_test $DATASET_DIR/pancreas_cpm_test.h5ad \ + --output $DATASET_DIR/pancreas_cpm_knn.h5ad # # run one metric # bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ -# --input_prediction $DATASET_DIR/dataset_cpm_prediction.h5ad \ -# --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ -# --output $DATASET_DIR/dataset_cpm_score.h5ad +# --input_prediction $DATASET_DIR/pancreas_cpm_knn.h5ad \ +# --input_solution $DATASET_DIR/pancreas_cpm_solution.h5ad \ +# --output $DATASET_DIR/pancreas_cpm_knn_accuracy.h5ad From a131c8f8750c708ba1063210b5084663f03074e4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:38:13 +0100 Subject: [PATCH 0290/1233] undo dataset renaming Former-commit-id: 05335885283d4030dd5a9d1cce28a4d630210ced --- src/label_projection/api/comp_censoring.yaml | 4 ++-- .../resources_test_scripts/pancreas.sh | 18 +++++++++--------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_censoring.yaml index b09e4abd32..db7c545f28 100644 --- a/src/label_projection/api/comp_censoring.yaml +++ b/src/label_projection/api/comp_censoring.yaml @@ -19,7 +19,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" + input_path = meta["resources_dir"] + "/common/dataset_cpm.h5ad" output_train_path = "output_train.h5ad" output_test_path = "output_test.h5ad" output_solution_path = "output_solution.h5ad" @@ -80,4 +80,4 @@ functionality: assert "batch" in output_solution.obs print(">> All checks succeeded!") - - path: ../../../../resources_test/label_projection/pancreas + - path: ../../../../resources_test/common/pancreas diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index c0442a2b16..867d288f81 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -22,19 +22,19 @@ mkdir -p $DATASET_DIR # censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ --input $RAW_DATA \ - --output_train $DATASET_DIR/pancreas_cpm_train.h5ad \ - --output_test $DATASET_DIR/pancreas_cpm_test.h5ad \ - --output_solution $DATASET_DIR/pancreas_cpm_solution.h5ad \ + --output_train $DATASET_DIR/dataset_cpm_train.h5ad \ + --output_test $DATASET_DIR/dataset_cpm_test.h5ad \ + --output_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ --seed 123 # run one method bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ - --input_train $DATASET_DIR/pancreas_cpm_train.h5ad \ - --input_test $DATASET_DIR/pancreas_cpm_test.h5ad \ - --output $DATASET_DIR/pancreas_cpm_knn.h5ad + --input_train $DATASET_DIR/dataset_cpm_train.h5ad \ + --input_test $DATASET_DIR/dataset_cpm_test.h5ad \ + --output $DATASET_DIR/dataset_cpm_knn.h5ad # # run one metric # bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ -# --input_prediction $DATASET_DIR/pancreas_cpm_knn.h5ad \ -# --input_solution $DATASET_DIR/pancreas_cpm_solution.h5ad \ -# --output $DATASET_DIR/pancreas_cpm_knn_accuracy.h5ad +# --input_prediction $DATASET_DIR/dataset_cpm_knn.h5ad \ +# --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ +# --output $DATASET_DIR/dataset_cpm_knn_accuracy.h5ad From f32aa5b13fbfe13be36c59066315a66fd9040c62 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:49:17 +0100 Subject: [PATCH 0291/1233] speed up container build Former-commit-id: 0e2694a9a1a51e1b1e9b3543571600eaafbfd2ca --- src/common/extract_scores/config.vsh.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index e8225bc863..f6a8154236 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -23,13 +23,15 @@ functionality: description: "Output tsv" resources: - type: r_script - path: ./script.R + path: script.R platforms: - type: docker - image: "ghcr.io/data-intuitive/randpy:r4.1_py3.10" + image: eddelbuettel/r2u:22.04 setup: - type: r - cran: anndata + cran: [ anndata] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pypi: anndata + pip: [ anndata<0.8 ] - type: nextflow From ad05eeadbb42ad6e095aafa200421ac57fc5f5ac Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 11:53:18 +0100 Subject: [PATCH 0292/1233] fix readme and api Former-commit-id: e57b821e34ff13a91240bda863dc76d079320f23 --- src/label_projection/README.md | 44 ++++++-------------- src/label_projection/api/comp_censoring.yaml | 2 +- 2 files changed, 13 insertions(+), 33 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 7e1e46dfef..289d638083 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -48,9 +48,8 @@ correctly assigns cell type labels to cells in the test set. ``` mermaid %%| column: screen-inset-shaded flowchart LR + anndata_dataset(dataset) anndata_prediction(prediction) - anndata_preprocessed(preprocessed) - anndata_raw_dataset(raw dataset) anndata_score(score) anndata_solution(solution) anndata_test(test) @@ -58,43 +57,23 @@ flowchart LR comp_censoring[/censoring/] comp_method[/method/] comp_metric[/metric/] - comp_normalization[/normalization/] - anndata_preprocessed---comp_censoring + anndata_dataset---comp_censoring anndata_train---comp_method anndata_test---comp_method anndata_solution---comp_metric anndata_prediction---comp_metric - anndata_raw_dataset---comp_normalization comp_censoring-->anndata_train comp_censoring-->anndata_test comp_censoring-->anndata_solution comp_method-->anndata_prediction comp_metric-->anndata_score - comp_normalization-->anndata_preprocessed ``` -### prediction - -Used in: - -- method: output (as output) -- metric: input_prediction (as input) - -Slots: - -| struct | name | type | description | -|:-------|:---------------|:-------|:--------------------------------------------------------------------| -| obs | label_pred | string | Predicted labels for the test cells. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | method_id | string | A unique identifier for the method | - -### preprocessed +### dataset Used in: - censoring: input (as input) -- normalization: output (as output) Slots: @@ -107,20 +86,21 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### raw dataset +### prediction Used in: -- normalization: input (as input) +- method: output (as output) +- metric: input_prediction (as input) Slots: -| struct | name | type | description | -|:-------|:-----------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| struct | name | type | description | +|:-------|:---------------|:-------|:--------------------------------------------------------------------| +| obs | label_pred | string | Predicted labels for the test cells. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| uns | method_id | string | A unique identifier for the method | ### score diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_censoring.yaml index db7c545f28..2ac49996e5 100644 --- a/src/label_projection/api/comp_censoring.yaml +++ b/src/label_projection/api/comp_censoring.yaml @@ -19,7 +19,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/common/dataset_cpm.h5ad" + input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" output_train_path = "output_train.h5ad" output_test_path = "output_test.h5ad" output_solution_path = "output_solution.h5ad" From 2decbcf016eb9823b5242b4723a9086233a6cbef Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 12:06:12 +0100 Subject: [PATCH 0293/1233] fix script Former-commit-id: a7a0f0d841531959b4a6e4965fc0bd81665b6acb --- src/label_projection/methods/logistic_regression/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 73952b734a..9c4ae95cdb 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -48,7 +48,7 @@ def pca_op(adata_train, adata_test, n_components=100): ) print("Fit to train data") -classifipipelineer.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) +pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) print("Predict on test data") input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) From 06854e15d022982b5f3f05d0c1cb91d8577c2cd3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:29:47 +0100 Subject: [PATCH 0294/1233] update readme Former-commit-id: af7e49f3f039c684ef55d22302910f8a1687f725 --- README.Rmd | 8 +++++- README.md | 80 ++++++++++++++++++++++++++++++++++++++++-------------- 2 files changed, 66 insertions(+), 22 deletions(-) diff --git a/README.Rmd b/README.Rmd index c0d00878c9..a08ec2a3c6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,7 @@ Proof Of Concept in adapting [Open Problems repository](https://github.com/openp To use this repository, please install the following dependencies: * Bash -* Java (Java 8 or higher) +* Java (Java 11 or higher) * Docker (Instructions [here](https://docs.docker.com/get-docker/)) * Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) @@ -44,6 +44,12 @@ bin/init > Done, happy viash-ing! > Nextflow installation completed. +**Step 0b, download test resources:** by running the following command. + +```bash +bin/viash run src/common/sync_test_resources/config.vsh.yaml +``` + **Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. ```bash diff --git a/README.md b/README.md index 7ad2466921..d6abfd55fe 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ Nextflow and viash. Documentation for viash is available at To use this repository, please install the following dependencies: - Bash -- Java (Java 8 or higher) +- Java (Java 11 or higher) - Docker (Instructions [here](https://docs.docker.com/get-docker/)) - Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) @@ -46,6 +46,12 @@ bin/init > Done, happy viash-ing! > Nextflow installation completed. +**Step 0b, download test resources:** by running the following command. + +``` bash +bin/viash run src/common/sync_test_resources/config.vsh.yaml +``` + **Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. @@ -136,15 +142,18 @@ viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -h ``` foo 0.0.1 + Replace this with a (multiline) description of your component. - Options: + Arguments: -i, --input type: file, required parameter + example: input.txt Describe the input file. -o, --output type: file, required parameter, output + example: output.txt Describe the output file. --option @@ -158,10 +167,13 @@ You can **run the component** as follows: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt ``` + [notice] Checking if Docker image is available at 'modality_alignment/methods_foo:0.0.1' + [warning] Could not pull from 'modality_alignment/methods_foo:0.0.1'. Docker image doesn't exist or is not accessible. + [notice] Building container 'modality_alignment/methods_foo:0.0.1' with Dockerfile This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE + - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - option: default- ## Building a component @@ -192,15 +204,18 @@ target/docker/modality_alignment/methods/foo/foo -h ``` foo 0.0.1 + Replace this with a (multiline) description of your component. - Options: + Arguments: -i, --input type: file, required parameter + example: input.txt Describe the input file. -o, --output type: file, required parameter, output + example: output.txt Describe the output file. --option @@ -216,8 +231,8 @@ target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE + - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - option: default- ## Unit testing a component @@ -230,21 +245,41 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711/build_executable/foo --verbosity 6 ---setup cachedbuild - [notice] Running 'docker build -t modality_alignment/methods_foo:da7Qhr5nLi6A /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-4h6urx' - Sending build context to Docker daemon 22.53kB + +/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'modality_alignment/methods_foo:test_FI4Ch4' with Dockerfile + [info] Running 'docker build -t modality_alignment/methods_foo:test_FI4Ch4 /home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable/tmp/dockerbuild-foo-RlMhS8/Dockerfile' + Sending build context to Docker daemon 38.91kB - Step 1/2 : FROM python:3.9.3-buster + Step 1/7 : FROM python:3.9.3-buster ---> 05034335a2e3 - Step 2/2 : RUN pip install --upgrade pip && pip install --no-cache-dir "numpy" + Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "numpy" ---> Using cache - ---> 45db33ebb9de - Successfully built 45db33ebb9de - Successfully tagged modality_alignment/methods_foo:da7Qhr5nLi6A + ---> ddeebf641d36 + Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component modality_alignment/methods foo" + ---> Using cache + ---> c1c0f5ae9c7d + Step 4/7 : LABEL org.opencontainers.image.created="2022-11-09T13:22:17+01:00" + ---> Running in fa0c5209aade + Removing intermediate container fa0c5209aade + ---> b2db5789cac5 + Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" + ---> Running in d1f880f7a935 + Removing intermediate container d1f880f7a935 + ---> 30128c9999fd + Step 6/7 : LABEL org.opencontainers.image.revision="a7a0f0d841531959b4a6e4965fc0bd81665b6acb" + ---> Running in 4407f6fc3929 + Removing intermediate container 4407f6fc3929 + ---> ae4cc7922a61 + Step 7/7 : LABEL org.opencontainers.image.version="test_FI4Ch4" + ---> Running in 2e07476da268 + Removing intermediate container 2e07476da268 + ---> c95b24408e60 + Successfully built c95b24408e60 + Successfully tagged modality_alignment/methods_foo:test_FI4Ch4 ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo18431554913355206711/test_test.py/test.py + +/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/test_test/test_executable >> Writing test file >> Running component >> Checking whether output file exists @@ -382,7 +417,7 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email ./foo_by_email ---setup cachedbuild ``` - [notice] Running 'docker build -t modality_alignment/methods_foo:0.0.1 /home/rcannood/workspace/viash_temp/viashsetupdocker-foo-TsNVGL' + [notice] Building container 'modality_alignment/methods_foo:0.0.1' with Dockerfile ``` bash # view help @@ -390,15 +425,18 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email ``` foo 0.0.1 + Replace this with a (multiline) description of your component. - Options: + Arguments: -i, --input type: file, required parameter + example: input.txt Describe the input file. -o, --output type: file, required parameter, output + example: output.txt Describe the output file. --option @@ -413,8 +451,8 @@ cp target/docker/modality_alignment/methods/foo/foo foo_by_email This is a skeleton component The arguments are: - - input: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/LICENSE - - output: /viash_automount/home/rcannood/workspace/opsca/opsca-viash/foo_output.txt + - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE + - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - option: default- ### Reprodicible components on Docker Hub From 4b2d937d914ab5cb01cd7a86e6406a4c30e97802 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:30:04 +0100 Subject: [PATCH 0295/1233] temporarily disable scanvi methods Former-commit-id: df14513bb437fba0610cd2c588c0fa3b5ad80b1b --- .../methods/scvi/scanvi_all_genes/config.vsh.yaml | 3 ++- src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml | 3 ++- .../methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml | 3 ++- .../methods/scvi/scarches_scanvi_hvg/config.vsh.yaml | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 96cd856e1b..5d05a6263a 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scanvi_all_genes" namespace: "label_projection/methods/scvi" version: "dev" @@ -65,7 +66,7 @@ platforms: packages: - scanpy - scprep - - sklearn + - scikit-learn - "anndata<0.8" - scvi-tools - type: native diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index d018f88e85..69f4eb8052 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scanvi_hvg" namespace: "label_projection/methods/scvi" version: "dev" @@ -72,7 +73,7 @@ platforms: packages: - scanpy - scprep - - sklearn + - scikit-learn - "anndata<0.8" - scvi-tools - scikit-misc diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index 6e5b503ae4..de4dfc8662 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scarches_scanvi_all_genes" namespace: "label_projection/methods/scvi" version: "dev" @@ -65,7 +66,7 @@ platforms: packages: - scanpy - scprep - - sklearn + - scikit-learn - "anndata<0.8" - scvi-tools - type: native diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index dc98238b69..14e28ff538 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scarches_scanvi_hvg" namespace: "label_projection/methods/scvi" version: "dev" @@ -72,7 +73,7 @@ platforms: packages: - scanpy - scprep - - sklearn + - scikit-learn - "anndata<0.8" - scvi-tools - scikit-misc From 4fd57a3ca77e3b0379aebf235e01c7ca7d3686e9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:35:22 +0100 Subject: [PATCH 0296/1233] fix metrics Former-commit-id: 2538037b79a88b69179742a0f71392b26279d538 --- src/label_projection/api/comp_metric.yaml | 51 +++++++++++++------ .../metrics/accuracy/config.vsh.yaml | 33 ++---------- .../metrics/accuracy/script.py | 38 ++++++++------ .../metrics/accuracy/test_script.py | 30 ----------- .../metrics/f1/config.vsh.yaml | 41 +++++---------- src/label_projection/metrics/f1/script.py | 42 ++++++++------- .../metrics/f1/test_script.py | 32 ------------ .../resources_test_scripts/pancreas.sh | 10 ++-- 8 files changed, 103 insertions(+), 174 deletions(-) delete mode 100644 src/label_projection/metrics/accuracy/test_script.py delete mode 100644 src/label_projection/metrics/f1/test_script.py diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 54fc6a0bd9..5bda5e0583 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -7,22 +7,41 @@ functionality: - name: "--output" __inherits__: anndata_score.yaml direction: output - # test_resources: - # # A custom python script with additional checks - # - type: python_script - # path: format_check.py - # text: | - # import anndata as ad + test_resources: + - path: ../../../../resources_test/label_projection/pancreas + - type: python_script + path: format_check.py + text: | + import anndata as ad + import subprocess + from os import path - # input_solution = ad.read_h5ad(par["input_solution"]) - # input_prediction = ad.read_h5ad(par["input_prediction"]) - # output = ad.read_h5ad(par["output"]) + input_prediction_path = meta["resources_dir"] + "/pancreas/dataset_cpm_knn.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/dataset_cpm_solution.h5ad" + output_path = "output.h5ad" - # print("Checking whether data from input was copied properly to output") - # assert input_solution.uns["dataset_id"] == input_prediction.uns["dataset_id"] - # assert input_solution.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] - # assert input_prediction.uns["dataset_id"] == output.uns["dataset_id"] - # assert input_prediction.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] - # assert input_prediction.uns["method_id"] == output.uns["method_id"] + cmd = [ + meta['executable'], + "--input_prediction", input_prediction_path, + "--input_solution", input_solution_path, + "--output", output_path + ] - # print("All checks succeeded!") + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + input_solution = ad.read_h5ad(input_solution_path) + input_prediction = ad.read_h5ad(input_prediction_path) + output = ad.read_h5ad(output_path) + + print("Checking whether data from input was copied properly to output") + assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] + assert output.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] + assert output.uns["method_id"] == input_prediction.uns["method_id"] + assert output.uns["metric_id"] + assert output.uns["metric_value"] + + print("All checks succeeded!") diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index c688a31831..9d04cb4aae 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -1,42 +1,17 @@ +__inherits__: ../../api/comp_metric.yaml functionality: name: "accuracy" namespace: "label_projection/metrics" - version: "dev" - description: "Accuracy of predictions" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - type: "file" - description: "Input data to get accuracy" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - description: "Ouput data with metric value" - direction: "output" - example: "output.mv.h5ad" - required: true + description: "The percentage of correctly predicted labels." resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test_script.py - - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" platforms: - - type: native - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - sklearn - - scanpy + - scikit-learn - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index 07fde62536..a89d559d40 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -1,29 +1,35 @@ +import numpy as np +import sklearn.preprocessing +import anndata as ad + ## VIASH START par = { - 'input': 'ouput.h5ad', - 'output': 'output.mv.h5ad' + 'input_prediction': 'resources_test/label_projection/pancreas/dataset_cpm_knn.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_solution.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'accuracy' } ## VIASH END -import numpy as np -import sklearn.preprocessing -import scanpy as sc - print("Load data") -adata = sc.read(par['input']) +input_prediction = ad.read_h5ad(par['input_prediction']) +input_solution = ad.read_h5ad(par['input_solution']) -print("Get prediction accuracy") -encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["celltype"]) -test_data = adata[~adata.obs["is_train"]] +assert (input_prediction.obs_names == input_solution.obs_names).all() -test_data.obs["celltype"] = encoder.transform(test_data.obs["celltype"]) -test_data.obs["celltype_pred"] = encoder.transform(test_data.obs["celltype_pred"]) +print("Encode labels") +encoder = sklearn.preprocessing.LabelEncoder().fit(input_solution.obs["label"]) +input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) +input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) -accuracy = np.mean(test_data.obs["celltype"] == test_data.obs["celltype_pred"]) +print("Compute prediction accuracy") +accuracy = np.mean(input_solution.obs["label"] == input_prediction.obs["label_pred"]) print("Store metric value") -adata.uns["metric_id"] = meta["functionality_name"] -adata.uns["metric_value"] = accuracy +input_prediction.uns["metric_id"] = meta["functionality_name"] +input_prediction.uns["metric_value"] = accuracy print("Writing adata to file") -adata.write_h5ad(par['output'], compression="gzip") +input_prediction.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/accuracy/test_script.py b/src/label_projection/metrics/accuracy/test_script.py deleted file mode 100644 index f437cc715f..0000000000 --- a/src/label_projection/metrics/accuracy/test_script.py +++ /dev/null @@ -1,30 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import numpy as np - -INPUT = "toy_baseline_pred_data.h5ad" -OUTPUT = "output.accuracy.h5ad" - -print(">> Running accuracy component") -out = subprocess.check_output([ - "./accuracy", - "--input", INPUT, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(OUTPUT) - -print(">> Check that dataset fits expected API") -adata = sc.read_h5ad(OUTPUT) - -# check id -assert "metric_id" in adata.uns -assert adata.uns["metric_id"] == "accuracy" -assert "metric_value" in adata.uns -assert type(adata.uns["metric_value"]) is np.float64 - -print(">> All tests passed successfully") diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 6d25194538..683327c3eb 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -1,46 +1,29 @@ +__inherits__: ../../api/comp_metric.yaml functionality: name: "f1" namespace: "label_projection/metrics" - version: "dev" description: "balanced F-score or F-measure" - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } arguments: - - name: "--input" - type: "file" - description: "Input data with predictions to get f1-score" - required: true - name: "--average" type: "string" - example: "weighted" - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - description: "Ouput data with metric value" - direction: "output" - example: "output.mv.h5ad" - required: true + default: "weighted" + choices: ['micro', 'macro', 'samples', 'weighted'] + description: | + Determines the type of averaging performed on the data. + + - 'micro': Calculate metrics globally by counting the total true positives, false negatives and false positives. + - 'macro': Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. + - 'weighted': Calculate metrics for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. + - 'samples': Calculate metrics for each instance, and find their average (only meaningful for multilabel classification where this differs from accuracy_score). resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test_script.py - - path: "../../../../resources_test/label_projection/pancreas/toy_baseline_pred_data.h5ad" platforms: - - type: native - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - sklearn - - scanpy + - scikit-learn - "anndata<0.8" - type: nextflow diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 0733bbae53..8d6c6872d2 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -1,32 +1,40 @@ +import sklearn.metrics +import sklearn.preprocessing +import anndata as ad + ## VIASH START par = { - 'input': 'ouput.h5ad', + 'input_prediction': 'resources_test/label_projection/pancreas/dataset_cpm_knn.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_solution.h5ad', 'average': 'weighted', - 'output': 'output.mv.h5ad' + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'f1' } ## VIASH END -import sklearn.metrics -import sklearn.preprocessing -import scanpy as sc - print("Load data") -adata = sc.read(par['input']) +input_prediction = ad.read_h5ad(par['input_prediction']) +input_solution = ad.read_h5ad(par['input_solution']) -print("Get prediction accuracy") -encoder = sklearn.preprocessing.LabelEncoder().fit(adata.obs["celltype"]) -test_data = adata[~adata.obs["is_train"]] +assert (input_prediction.obs_names == input_solution.obs_names).all() -test_data.obs["celltype"] = encoder.transform(test_data.obs["celltype"]) -test_data.obs["celltype_pred"] = encoder.transform(test_data.obs["celltype_pred"]) +print("Encode labels") +encoder = sklearn.preprocessing.LabelEncoder().fit(input_solution.obs["label"]) +input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) +input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) -metrics = sklearn.metrics.f1_score( - test_data.obs["celltype"], test_data.obs["celltype_pred"], average=par["average"] +print("Compute F1 score") +metric_value = sklearn.metrics.f1_score( + input_solution.obs["label"], + input_prediction.obs["label_pred"], + average=par["average"] ) print("Store metric value") -adata.uns["metric_id"] = meta["functionality_name"] -adata.uns["metric_value"] = metrics +input_prediction.uns["metric_id"] = meta["functionality_name"] +input_prediction.uns["metric_value"] = metric_value print("Writing adata to file") -adata.write_h5ad(par['output'], compression="gzip") +input_prediction.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/f1/test_script.py b/src/label_projection/metrics/f1/test_script.py deleted file mode 100644 index 1b291939b3..0000000000 --- a/src/label_projection/metrics/f1/test_script.py +++ /dev/null @@ -1,32 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import numpy as np - -INPUT = "toy_baseline_pred_data.h5ad" -OUTPUT = "output.accuracy.h5ad" -AVG = "weighted" - -print(">> Running f1 component") -out = subprocess.check_output([ - "./f1", - "--input", INPUT, - "--average", AVG, - "--output", OUTPUT -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(OUTPUT) - -print(">> Check that dataset fits expected API") -adata = sc.read_h5ad(OUTPUT) - -# check id -assert "metric_id" in adata.uns -assert adata.uns["metric_id"] == "f1" -assert "metric_value" in adata.uns -assert type(adata.uns["metric_value"]) is np.float64 - -print(">> All tests passed successfully") diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 867d288f81..1a16651c78 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -33,8 +33,8 @@ bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ --input_test $DATASET_DIR/dataset_cpm_test.h5ad \ --output $DATASET_DIR/dataset_cpm_knn.h5ad -# # run one metric -# bin/viash run src/label_projection/metric/accuracy/config.vsh.yaml -- \ -# --input_prediction $DATASET_DIR/dataset_cpm_knn.h5ad \ -# --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ -# --output $DATASET_DIR/dataset_cpm_knn_accuracy.h5ad +# run one metric +bin/viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ + --input_prediction $DATASET_DIR/dataset_cpm_knn.h5ad \ + --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ + --output $DATASET_DIR/dataset_cpm_knn_accuracy.h5ad From 32d58d513486b96ebccad0cf74ba371a1369bbe0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:35:44 +0100 Subject: [PATCH 0297/1233] update changelog Former-commit-id: 05ecf88725cca47cf9d66ca93db2d6372eca5e2b --- CHANGELOG.md | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9d9cdaf260..97db115a1b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,9 +14,9 @@ * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. -* Created normalization method `common/normalise_log_cpm`. +* `common/normalization/log_cpm`: A log CPM normalization method. -* Created normalization method `common/normalise_log_scran_pooling`. +* `common/normalization/log_scran_pooling`: A log scran pooling normalization method. ## label_projection @@ -24,14 +24,20 @@ * API: Created an explicit api definition for the censor, method and metric components. -* Created censoring component `data_processing/censoring`. +* `data_processing/censoring`: Added a censoring component. -* Created test data `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. +* `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. ### V1 MIGRATION -* Ported method `methods/knn_classifier`. +* `methods/knn_classifier`: Migrated from v1. -* Ported method `methods/logistic_regression`. +* `methods/logistic_regression`: Migrated from v1. -* Ported method `methods/mlp`. \ No newline at end of file +* `methods/mlp`: Migrated from v1. + +* Temporarily disable `scanvi` / `scarches_scanvi`. + +* `metric/accuracy`: Migrated from v1. + +* `metric/f1`: Migrated from v1. \ No newline at end of file From 121c578f8b5a2f800cddcc217adc5493eb600ee5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:49:23 +0100 Subject: [PATCH 0298/1233] Fix concatenate component, only works with anndata>=0.8 when X is undefined Former-commit-id: f598e810786f293c67d55db6e623f9ea962b687e --- .../dataset_concatenate/config.vsh.yaml | 23 +++++-------------- src/common/dataset_concatenate/script.py | 20 ++++++++-------- src/common/dataset_concatenate/test_script.py | 22 ++++++++++-------- 3 files changed, 29 insertions(+), 36 deletions(-) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index 6b4d1af962..5008eb5acf 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -1,15 +1,7 @@ functionality: name: "dataset_concatenate" - namespace: "label_projection/data_processing" - version: "dev" - description: "Concatenate datasets." - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas " - roles: [ maintainer ] - props: { github: chagasVinicius } + namespace: "common/data_processing" + description: "Concatenate datasets" arguments: - name: "--inputs" alternatives: ["-i"] @@ -21,9 +13,8 @@ functionality: type: "file" direction: "output" example: "output.h5ad" - description: "Output h5ad file of the cleaned dataset" + description: "Output h5ad file" required: true - resources: - type: python_script path: script.py @@ -31,14 +22,12 @@ functionality: - type: python_script path: test_script.py - type: file - path: "../../../resources_test/label_projection/pancreas" + path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - scanpy - - "anndata<0.8" - - type: native + - "anndata>=0.8" - type: nextflow diff --git a/src/common/dataset_concatenate/script.py b/src/common/dataset_concatenate/script.py index 4084b96d63..a89a80df40 100644 --- a/src/common/dataset_concatenate/script.py +++ b/src/common/dataset_concatenate/script.py @@ -1,21 +1,21 @@ -import scanpy as sc +import anndata as ad -###VIASH START +## VIASH START par = { - "inputs": ["../resources/pancreas/toy_data.h5ad", "../resources/pancreas/toy_data.h5ad"], + "inputs": ["resources_test/common/pancreas/dataset_cpm.h5ad", "resources_test/common/pancreas/dataset_cpm.h5ad"], "output": "output.h5ad" } -###VIASH END +## VIASH END adata_list = [] -for i in par["inputs"]: - print("Loading {}".format(i)) - adata_list.append( - sc.read_h5ad(i) - ) +for input in par["inputs"]: + print("Loading {}".format(input)) + adata_list.append(ad.read_h5ad(input)) print("Concatenate anndatas") -adata = adata_list[0].concatenate(adata_list[1:]) +adata = ad.concat(adata_list) + +print("Concatenated anndata: ", adata) print("Writing result file") adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/common/dataset_concatenate/test_script.py b/src/common/dataset_concatenate/test_script.py index 6b4844af5b..8a0eea0b4e 100644 --- a/src/common/dataset_concatenate/test_script.py +++ b/src/common/dataset_concatenate/test_script.py @@ -1,22 +1,26 @@ import subprocess -import scanpy as sc +import anndata as ad from os import path ## VIASH START ## VIASH END -INPUT = f"{meta['resources_dir']}/pancreas/toy_data.h5ad" -INPUTS = f"{INPUT}:{INPUT}" -OUTPUT = "toy_data_concatenated.h5ad" + +input_path = f"{meta['resources_dir']}/pancreas/dataset_cpm.h5ad" +output_path = "toy_data_concatenated.h5ad" print(">> Runing script as test") out = subprocess.check_output([ meta["executable"], - "--inputs", INPUTS, - "--output", OUTPUT + "--inputs", f"{input_path}:{input_path}", + "--output", output_path ]).decode("utf-8") + print(">> Checking whether file exists") -assert path.exists(OUTPUT) +assert path.exists(output_path) print(">> Check that test output fits expected API") -adata = sc.read_h5ad(OUTPUT) -assert (1000, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +assert output.n_obs == input.n_obs * 2 +assert output.n_vars == input.n_vars From fd8984ac08fd6949dc5591de7a1cca9e86fcb1fd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 13:53:21 +0100 Subject: [PATCH 0299/1233] upgrade viash test ci Former-commit-id: e6662b956bec6c362becd1ac027b275174822555 --- .github/workflows/viash-test.yml | 102 +++++++++++++++++++++++-------- 1 file changed, 76 insertions(+), 26 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 2cf6676ff1..bb86edc52a 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -1,34 +1,50 @@ -name: viash test CI +name: viash test on: + pull_request: push: branches: [ '**' ] jobs: - cancel: - name: 'Cancel Previous Runs' - runs-on: ubuntu-latest - timeout-minutes: 3 - if: github.ref != 'refs/heads/main' - steps: - - uses: styfle/cancel-workflow-action@0.10.0 - with: - all_but_latest: true - access_token: ${{ github.token }} + run_ci_check_job: + if: "!contains(github.event.head_commit.message, 'ci skip')" + runs-on: ubuntu-latest + outputs: + run_ci: ${{ steps.github_cli.outputs.check }} + steps: + - name: 'Check if branch has an existing pull request and the trigger was a push' + id: github_cli + run: | + pull_request=$(gh pr list -R openpipelines-bio/openpipeline -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') + # If the branch has a PR and this run was triggered by a push event, do not run + if [[ "$pull_request" != "null" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then + echo "check=false" >> $GITHUB_OUTPUT + else + echo "check=true" >> $GITHUB_OUTPUT + fi + env: + GITHUB_TOKEN: ${{ secrets.GTHB_PAT }} + # phase 1 list_components: + needs: run_ci_check_job env: s3_bucket: s3://openproblems-data/ runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" - + if: "(!contains(github.event.head_commit.message, 'ci skip')) && needs.run_ci_check_job.outputs.run_ci == 'true'" + outputs: + matrix: ${{ steps.set_matrix.outputs.matrix }} + cachehash: ${{ steps.cachehash.outputs.cachehash }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 + with: + fetch-depth: 0 - name: Fetch viash run: | bin/init + tree . bin/viash -h # create cachehash key @@ -36,7 +52,7 @@ jobs: id: cachehash run: | AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT # initialize cache - name: Cache resources data @@ -56,21 +72,51 @@ jobs: --delete tree resources_test/ -L 3 + - name: Get changed files + id: changed-files + uses: tj-actions/changed-files@v34.0.5 + with: + separator: ";" + diff_relative: true + # store component locations - - id: set_matrix + - name: Set matrix to only run tests for components that had their config or resources changed. + id: set_matrix run: | - json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') - echo "::set-output name=matrix::$json" - outputs: - matrix: ${{ steps.set_matrix.outputs.matrix }} - cachehash: ${{ steps.cachehash.outputs.cachehash }} + IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" + echo "Changed files: "${changed_files[*]}"" + readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | + (.info.config | capture("^(?

.*\/)").dir) as $dir | + { "name": .functionality.name, + "config": .info.config, + "resources": ([.info.config] + + ([.functionality.resources[].path?, + .functionality.test_resources[].path?] | + map($dir + .) + ) + ) + } + ][]') + declare -a result_array_matrix=() + for component in "${components[@]}"; do + readarray -t resources < <(jq -cr '.resources[]' <<< "$component") + for resource_rel_path in "${resources[@]}"; do + resource_project_path=$(realpath --relative-to="$GITHUB_WORKSPACE" "$resource_rel_path") + echo "Checking path $resource_project_path" + if [[ " ${changed_files[*]} " =~ " ${resource_project_path} " || "$GITHUB_REF" == "refs/heads/main" || "${{ contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then + result_array_matrix+="$component" + break + fi + done + done + json=$(jq -cs '.' <<< "${result_array_matrix[*]}") + echo "matrix=$json" >> $GITHUB_OUTPUT # phase 2 viash_test: needs: list_components - + if: ${{ needs.list_components.outputs.matrix != '[]' && needs.list_components.outputs.matrix != '' }} runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" strategy: fail-fast: false @@ -78,21 +124,25 @@ jobs: component: ${{ fromJson(needs.list_components.outputs.matrix) }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | - bin/init + bin/init -n bin/viash -h # use cache - name: Cache resources data uses: actions/cache@v3 + timeout-minutes: 5 with: path: resources_test key: ${{ needs.list_components.outputs.cachehash }} - name: Run test + timeout-minutes: 30 run: | - bin/viash test -p docker ${{ matrix.component.config }} + bin/viash test -p docker ${{ matrix.component.config }} \ + -c '.functionality.requirements.cpus := 2' \ + -c '.functionality.requirements.memory := "5gb"' From 8c2f2d95ca42c7803365cb7f833c98ddb9e01a6e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 14:00:50 +0100 Subject: [PATCH 0300/1233] fixes to tests Former-commit-id: 42d4bfb1f23b0645dce30cbf7456f9950e1abb13 --- src/common/api/comp_normalization.yaml | 4 ++-- src/common/subsample/test_script.py | 26 ++++++++++++++++++-------- 2 files changed, 20 insertions(+), 10 deletions(-) diff --git a/src/common/api/comp_normalization.yaml b/src/common/api/comp_normalization.yaml index f4e18b841a..adaa9aad2a 100644 --- a/src/common/api/comp_normalization.yaml +++ b/src/common/api/comp_normalization.yaml @@ -13,7 +13,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/common/dataset.h5ad" + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" output_path = "output.h5ad" cmd = [ @@ -44,5 +44,5 @@ functionality: assert input.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] print("All checks succeeded!") - - path: ../../../../resources_test/label_projection/pancreas + - path: ../../../../resources_test/common/pancreas diff --git a/src/common/subsample/test_script.py b/src/common/subsample/test_script.py index f6a449783e..2cf9b791e3 100644 --- a/src/common/subsample/test_script.py +++ b/src/common/subsample/test_script.py @@ -9,34 +9,44 @@ ### VIASH END input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" -output_path = "toy_data.h5ad" +input = sc.read_h5ad(input_path) print(">> Running script as test for even") +output_path = "output.h5ad" out = subprocess.check_output([ meta["executable"], "--input", input_path, "--output", output_path, - "--even" + "--even", + "--seed", "123" ]).decode("utf-8") print(">> Checking whether file exists") assert path.exists(output_path) print(">> Check that test output fits expected API") -adata = sc.read_h5ad(output_path) -assert (495, 467) == adata.layers["counts"].shape, "processed result data shape {}".format(adata.layers["counts"].shape) +output = sc.read_h5ad(output_path) + +assert input.n_obs >= output.n_obs +assert input.n_vars == output.n_vars + + print(">> Runing script as test for specific batch and celltype categories") +output2_path = "output.h5ad" out = subprocess.check_output([ meta["executable"], "--input", input_path, "--keep_celltype_categories", "acinar:beta", "--keep_batch_categories", "celseq:inDrop4:smarter", - "--output", output_path + "--output", output_path, + "--seed", "123" ]).decode("utf-8") print(">> Checking whether file exists") -assert path.exists(output_path) +assert path.exists(output2_path) print(">> Check that test output fits expected API") -adata = sc.read_h5ad(output_path) -assert (500, 443) == adata.layers["counts"].shape, "processed result data shape {}".format(adata.layers["counts"].shape) +output2 = sc.read_h5ad(output2_path) + +assert input.n_obs >= output2.n_obs +assert input.n_vars == output2.n_vars From a15bad3b0f61c4ef16e41dad54f3e2d067060812 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 14:41:28 +0100 Subject: [PATCH 0301/1233] add bit64 to the dependencies? Former-commit-id: 45f28d04af4c6bf79dcb0ef77bc52645286ce563 --- src/common/normalization/log_scran_pooling/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/normalization/log_scran_pooling/config.vsh.yaml b/src/common/normalization/log_scran_pooling/config.vsh.yaml index 44ac762979..7dbe6b2182 100644 --- a/src/common/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/common/normalization/log_scran_pooling/config.vsh.yaml @@ -11,9 +11,9 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ Matrix, scran, BiocParallel, rlang, anndata] + cran: [ Matrix, scran, BiocParallel, rlang, anndata, bit64 ] - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [anndata<0.8, scanpy] + pip: [ anndata<0.8, scanpy ] - type: nextflow From bb7ce31a821783e65891a8927d2bbb4b56817d5c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 14:43:56 +0100 Subject: [PATCH 0302/1233] suppress unintential output Former-commit-id: e533addc7be47a172ca75e435aa27b4e76a12bde --- src/common/normalization/log_scran_pooling/script.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/normalization/log_scran_pooling/script.R b/src/common/normalization/log_scran_pooling/script.R index f04b81e174..6e1a5bf5c6 100644 --- a/src/common/normalization/log_scran_pooling/script.R +++ b/src/common/normalization/log_scran_pooling/script.R @@ -1,7 +1,7 @@ cat(">> Loading dependencies\n") library(anndata, warn.conflicts = FALSE) -library(scran, warn.conflicts = FALSE) -library(BiocParallel, warn.conflicts = FALSE) +requireNamespace("scran", quietly = TRUE) +requireNamespace("BiocParallel", quietly = TRUE) library(Matrix, warn.conflicts = FALSE) ## VIASH START From 826f26982ab5ea94a6768bbd6f0dad964ae656b9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 15:14:04 +0100 Subject: [PATCH 0303/1233] annotate metrics Former-commit-id: da453f3af1f354159fd48f321f412aa33fdbc385 --- src/label_projection/api/comp_metric.yaml | 6 ++-- .../metrics/accuracy/config.vsh.yaml | 10 ++++++ .../metrics/accuracy/script.py | 4 +-- .../metrics/f1/config.vsh.yaml | 34 ++++++++++++------- src/label_projection/metrics/f1/script.py | 18 +++++----- 5 files changed, 48 insertions(+), 24 deletions(-) diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 5bda5e0583..e3530706c5 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -41,7 +41,9 @@ functionality: assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] assert output.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] assert output.uns["method_id"] == input_prediction.uns["method_id"] - assert output.uns["metric_id"] - assert output.uns["metric_value"] + assert output.uns["metric_ids"] is not None + assert output.uns["metric_values"] is not None + + # TODO: check whether the metric ids are all in .functionality.info print("All checks succeeded!") diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 9d04cb4aae..7c17213d81 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -3,6 +3,16 @@ functionality: name: "accuracy" namespace: "label_projection/metrics" description: "The percentage of correctly predicted labels." + info: + v1_url: openproblems/tasks/label_projection/metrics/accuracy.py + v1_commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 + metrics: + - id: accuracy + label: Accuracy + description: The percentage of correctly predicted labels. + min: 0 + max: 1 + maximise: true resources: - type: python_script path: script.py diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index a89d559d40..ba54eec185 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -28,8 +28,8 @@ accuracy = np.mean(input_solution.obs["label"] == input_prediction.obs["label_pred"]) print("Store metric value") -input_prediction.uns["metric_id"] = meta["functionality_name"] -input_prediction.uns["metric_value"] = accuracy +input_prediction.uns["metric_ids"] = "accuracy" +input_prediction.uns["metric_values"] = accuracy print("Writing adata to file") input_prediction.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 683327c3eb..acfd6e8dde 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -3,18 +3,28 @@ functionality: name: "f1" namespace: "label_projection/metrics" description: "balanced F-score or F-measure" - arguments: - - name: "--average" - type: "string" - default: "weighted" - choices: ['micro', 'macro', 'samples', 'weighted'] - description: | - Determines the type of averaging performed on the data. - - - 'micro': Calculate metrics globally by counting the total true positives, false negatives and false positives. - - 'macro': Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. - - 'weighted': Calculate metrics for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. - - 'samples': Calculate metrics for each instance, and find their average (only meaningful for multilabel classification where this differs from accuracy_score). + info: + v1_url: openproblems/tasks/label_projection/metrics/f1.py + v1_commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 + metrics: + - id: f1_weighted + label: F1 weighted + description: Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall. + min: 0 + max: 1 + maximise: true + - id: f1_macro + label: F1 macro + description: Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. + min: 0 + max: 1 + maximise: true + - id: f1_micro + label: F1 micro + description: Calculates the F1 score globally by counting the total true positives, false negatives and false positives. + min: 0 + max: 1 + maximise: true resources: - type: python_script path: script.py diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 8d6c6872d2..9132a4e934 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -1,4 +1,4 @@ -import sklearn.metrics +from sklearn.metrics import f1_score import sklearn.preprocessing import anndata as ad @@ -26,15 +26,17 @@ input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) print("Compute F1 score") -metric_value = sklearn.metrics.f1_score( - input_solution.obs["label"], - input_prediction.obs["label_pred"], - average=par["average"] -) +metric_type = [ "macro", "micro", "weighted" ] +metric_id = [ "f1_" + x for x in metric_type] +metric_value = [ f1_score( + input_solution.obs["label"], + input_prediction.obs["label_pred"], + average=x + ) for x in metric_type ] print("Store metric value") -input_prediction.uns["metric_id"] = meta["functionality_name"] -input_prediction.uns["metric_value"] = metric_value +input_prediction.uns["metric_ids"] = metric_id +input_prediction.uns["metric_values"] = metric_value print("Writing adata to file") input_prediction.write_h5ad(par['output'], compression="gzip") From dbc2bf168f14b0bebb60aee6af70f38e78188b2c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 15:26:15 +0100 Subject: [PATCH 0304/1233] autogenerate metrics from yamls Former-commit-id: 218fdac58177a54ba657c493a62dc8a3b758bd5a --- src/label_projection/README.md | 22 +++++++++++++--------- src/label_projection/README.qmd | 27 +++++++++++++++++++++------ 2 files changed, 34 insertions(+), 15 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 289d638083..c09f296809 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -33,15 +33,19 @@ labels onto the test set. Metrics for label projection aim to characterize how well each classifer correctly assigns cell type labels to cells in the test set. -- **Accuracy**: Average number of correctly applied labels. -- **F1 score**: The [F1 - score](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html) - is a weighted average of the precision and recall over all class - labels, where an F1 score reaches its best value at 1 and worst score - at 0, where each class contributes to the score relative to its - frequency in the dataset. -- **Macro F1 score**: The macro F1 score is an unweighted F1 score, - where each class contributes equally, regardless of its frequency. +- **[Accuracy](./metrics/accuracy/config.vsh.yaml)**: The percentage of + correctly predicted labels. Range: \[0, 1\]. Higher is better. +- **[F1 weighted](./metrics/f1/config.vsh.yaml)**: Calculates the F1 + score for each label, and find their average weighted by support (the + number of true instances for each label). This alters ‘macro’ to + account for label imbalance; it can result in an F-score that is not + between precision and recall. Range: \[0, 1\]. Higher is better. +- **[F1 macro](./metrics/f1/config.vsh.yaml)**: Calculates the F1 score + for each label, and find their unweighted mean. This does not take + label imbalance into account. Range: \[0, 1\]. Higher is better. +- **[F1 micro](./metrics/f1/config.vsh.yaml)**: Calculates the F1 score + globally by counting the total true positives, false negatives and + false positives. Range: \[0, 1\]. Higher is better. ## API diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index a00211e33e..8c519d30a3 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -30,14 +30,29 @@ Here, we compare methods for annotation based on a reference dataset. The datase Metrics for label projection aim to characterize how well each classifer correctly assigns cell type labels to cells in the test set. -```{r metrics, include=FALSE} +```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} metric_yamls <- list.files(paste0(dir, "/metrics"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) -# todo -``` +metric_yaml <- metric_yamls[[1]] +metric_info <- map_df(metric_yamls, function(metric_yaml) { + out <- system(paste0("viash config view ", metric_yaml), intern = TRUE, ignore.stderr = TRUE) + config <- yaml::yaml.load(out) + metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) + metric_info$comp_yaml <- metric_yaml + metric_info$comp_name <- config$functionality$name + metric_info$comp_namespace <- config$functionality$namespace + metric_info +}) + +metric_info_view <- + metric_info %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Description = paste0(description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")), + str = paste0("* **[", label, "](", comp_yaml, ")**: ", description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")) + ) -* **Accuracy**: Average number of correctly applied labels. -* **F1 score**: The [F1 score](https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html) is a weighted average of the precision and recall over all class labels, where an F1 score reaches its best value at 1 and worst score at 0, where each class contributes to the score relative to its frequency in the dataset. -* **Macro F1 score**: The macro F1 score is an unweighted F1 score, where each class contributes equally, regardless of its frequency. +cat(paste(metric_info_view$str, collapse = '\n')) +``` ## API From 69d5eb846ee9e4cbaa2cc4dc5698e23e352a2134 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 15:55:56 +0100 Subject: [PATCH 0305/1233] update readmes Former-commit-id: ffd5843643350e6d03b4a8c07d536d7462bfaa92 --- README.md | 99 +++++++++++-------- README.Rmd => README.qmd | 9 +- src/label_projection/README.md | 35 ++++++- src/label_projection/README.qmd | 53 ++++++++-- .../data_processing/anndata_loader.tsv | 2 +- 5 files changed, 139 insertions(+), 59 deletions(-) rename README.Rmd => README.qmd (99%) diff --git a/README.md b/README.md index d6abfd55fe..84b0cf2f98 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,36 @@ -opsca-viash +OpenProblems v2 ================ -- [Requirements](#requirements) -- [Quick start](#quick-start) -- [Project structure](#project-structure) -- [Adding a viash component](#adding-a-viash-component) -- [Running a component from CLI](#running-a-component-from-cli) -- [Building a component](#building-a-component) -- [Unit testing a component](#unit-testing-a-component) -- [Frequently asked questions](#frequently-asked-questions) -- [Benefits of using Nextflow + - viash](#benefits-of-using-nextflow--viash) +- Requirements +- Quick start +- Project + structure +- Adding a viash component +- Running a component from CLI +- Building a + component +- Unit testing a component +- Frequently asked questions + - My + component doesn’t work! +- Benefits of using Nextflow + + viash + - The pipeline is + language-agnostic + - One Docker container per + component + - Reproducible components + - Reprodicible components + on Docker Hub Proof Of Concept in adapting [Open Problems repository](https://github.com/openproblems-bio/openproblems) with @@ -21,11 +41,11 @@ Nextflow and viash. Documentation for viash is available at To use this repository, please install the following dependencies: -- Bash -- Java (Java 11 or higher) -- Docker (Instructions [here](https://docs.docker.com/get-docker/)) -- Nextflow (Optional, though [very easy to - install](https://www.nextflow.io/index.html#GetStarted)) +- Bash +- Java (Java 11 or higher) +- Docker (Instructions [here](https://docs.docker.com/get-docker/)) +- Nextflow (Optional, though [very easy to + install](https://www.nextflow.io/index.html#GetStarted)) ## Quick start @@ -167,9 +187,6 @@ You can **run the component** as follows: viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt ``` - [notice] Checking if Docker image is available at 'modality_alignment/methods_foo:0.0.1' - [warning] Could not pull from 'modality_alignment/methods_foo:0.0.1'. Docker image doesn't exist or is not accessible. - [notice] Building container 'modality_alignment/methods_foo:0.0.1' with Dockerfile This is a skeleton component The arguments are: - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE @@ -245,11 +262,11 @@ functionality of a component, you can run the tests by using the viash test src/modality_alignment/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'modality_alignment/methods_foo:test_FI4Ch4' with Dockerfile - [info] Running 'docker build -t modality_alignment/methods_foo:test_FI4Ch4 /home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/build_executable/tmp/dockerbuild-foo-RlMhS8/Dockerfile' + +/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'modality_alignment/methods_foo:test_HeBJG6' with Dockerfile + [info] Running 'docker build -t modality_alignment/methods_foo:test_HeBJG6 /home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable/tmp/dockerbuild-foo-alcpr9/Dockerfile' Sending build context to Docker daemon 38.91kB Step 1/7 : FROM python:3.9.3-buster @@ -260,26 +277,26 @@ viash test src/modality_alignment/methods/foo/config.vsh.yaml Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component modality_alignment/methods foo" ---> Using cache ---> c1c0f5ae9c7d - Step 4/7 : LABEL org.opencontainers.image.created="2022-11-09T13:22:17+01:00" - ---> Running in fa0c5209aade - Removing intermediate container fa0c5209aade - ---> b2db5789cac5 + Step 4/7 : LABEL org.opencontainers.image.created="2022-11-09T15:53:27+01:00" + ---> Running in 70b7c0e821f0 + Removing intermediate container 70b7c0e821f0 + ---> a9d3ced02d38 Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" - ---> Running in d1f880f7a935 - Removing intermediate container d1f880f7a935 - ---> 30128c9999fd - Step 6/7 : LABEL org.opencontainers.image.revision="a7a0f0d841531959b4a6e4965fc0bd81665b6acb" - ---> Running in 4407f6fc3929 - Removing intermediate container 4407f6fc3929 - ---> ae4cc7922a61 - Step 7/7 : LABEL org.opencontainers.image.version="test_FI4Ch4" - ---> Running in 2e07476da268 - Removing intermediate container 2e07476da268 - ---> c95b24408e60 - Successfully built c95b24408e60 - Successfully tagged modality_alignment/methods_foo:test_FI4Ch4 + ---> Running in 4b3f0db79860 + Removing intermediate container 4b3f0db79860 + ---> 42a0cb2e8f14 + Step 6/7 : LABEL org.opencontainers.image.revision="0b182c07fb8cc9306829c068d4ea600ee26891fc" + ---> Running in 5cc029947710 + Removing intermediate container 5cc029947710 + ---> fdc11be13f2e + Step 7/7 : LABEL org.opencontainers.image.version="test_HeBJG6" + ---> Running in 58757ca3bece + Removing intermediate container 58757ca3bece + ---> eea37ebd4ea2 + Successfully built eea37ebd4ea2 + Successfully tagged modality_alignment/methods_foo:test_HeBJG6 ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo5306251997508180162/test_test/test_executable + +/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/test_test/test_executable >> Writing test file >> Running component >> Checking whether output file exists diff --git a/README.Rmd b/README.qmd similarity index 99% rename from README.Rmd rename to README.qmd index a08ec2a3c6..fb1f166136 100644 --- a/README.Rmd +++ b/README.qmd @@ -1,10 +1,7 @@ --- -title: "opsca-viash" -output: - github_document: - toc: true - toc_depth: 2 - html_preview: false +title: "OpenProblems v2" +format: gfm +toc: true --- ```{r, setup, include=FALSE} diff --git a/src/label_projection/README.md b/src/label_projection/README.md index c09f296809..cade84eea5 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -1,4 +1,19 @@ +- Label + Projection + - The task + - Methods + - Metrics + - Pipeline + topology + - File format API + - dataset + - prediction + - score + - solution + - test + - train + # Label Projection ## The task @@ -28,10 +43,20 @@ then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. -## The metrics +## Methods + +Methods for assigning cell labels from a reference dataset to a + +| Name | Description | DOI | URL | +|:---------------------------------------------------------------------|:-------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| +| [KNN](./methods/knn_classifier/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | +| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | +| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | -Metrics for label projection aim to characterize how well each classifer -correctly assigns cell type labels to cells in the test set. +## Metrics + +Metrics for label projection aim to characterize how well each +classifier correctly assigns cell type labels to cells in the test set. - **[Accuracy](./metrics/accuracy/config.vsh.yaml)**: The percentage of correctly predicted labels. Range: \[0, 1\]. Higher is better. @@ -47,7 +72,7 @@ correctly assigns cell type labels to cells in the test set. globally by counting the total true positives, false negatives and false positives. Range: \[0, 1\]. Higher is better. -## API +## Pipeline topology ``` mermaid %%| column: screen-inset-shaded @@ -73,6 +98,8 @@ flowchart LR comp_metric-->anndata_score ``` +## File format API + ### dataset Used in: diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 8c519d30a3..fff5bbeae3 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -1,7 +1,9 @@ --- format: gfm info: - migration_date: "2022-10-17 12:49:00 GMT" + v1_url: openproblems/tasks/label_projection/README.md + v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +toc: true --- ```{r setup, include=FALSE} @@ -26,13 +28,47 @@ To ensure that the cell type labels in newly generated datasets match existing r Here, we compare methods for annotation based on a reference dataset. The datasets consist of two or more samples of single cell profiles that have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. -## The metrics -Metrics for label projection aim to characterize how well each classifer correctly assigns cell type labels to cells in the test set. + +## Methods + +Methods for assigning cell labels from a reference dataset to a + +```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +method_yamls <- list.files(paste0(dir, "/methods"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) + +method_info <- map_df(method_yamls, function(method_yaml) { + out <- system(paste0("viash config view ", method_yaml), intern = TRUE, ignore.stderr = TRUE) + config <- yaml::yaml.load(out) + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) + info <- as_tibble(config$functionality$info) + info$comp_yaml <- method_yaml + info$name <- config$functionality$name + info$namespace <- config$functionality$namespace + info$description <- config$functionality$description + info +}) + +method_info_view <- + method_info %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Description = description, + DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), + URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") + ) + +cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) +``` + + +## Metrics + +Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. ```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} metric_yamls <- list.files(paste0(dir, "/metrics"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) -metric_yaml <- metric_yamls[[1]] + metric_info <- map_df(metric_yamls, function(metric_yaml) { out <- system(paste0("viash config view ", metric_yaml), intern = TRUE, ignore.stderr = TRUE) config <- yaml::yaml.load(out) @@ -46,15 +82,16 @@ metric_info <- map_df(metric_yamls, function(metric_yaml) { metric_info_view <- metric_info %>% transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")), + # Name = paste0("[", label, "](", comp_yaml, ")"), + # Description = paste0(description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")), str = paste0("* **[", label, "](", comp_yaml, ")**: ", description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")) ) cat(paste(metric_info_view$str, collapse = '\n')) ``` -## API + +## Pipeline topology ```{r data, include=FALSE} comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) @@ -148,6 +185,8 @@ out_str <- strip_margin(glue::glue(" knitr::asis_output(out_str) ``` +## File format API + ```{r api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} for (file_name in file_info$name) { arg_info <- file_info %>% filter(name == file_name) diff --git a/src/label_projection/data_processing/anndata_loader.tsv b/src/label_projection/data_processing/anndata_loader.tsv index 92b362c170..968aba81dd 100644 --- a/src/label_projection/data_processing/anndata_loader.tsv +++ b/src/label_projection/data_processing/anndata_loader.tsv @@ -1,4 +1,4 @@ -processor name url obs_celltype obs_batch obs_tissue +processor name url obs_label obs_batch obs_tissue anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA anndata_loader cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue anndata_loader zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA From b21a07185efdeb698a29a24c14f31d13764c02e9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 15:58:37 +0100 Subject: [PATCH 0306/1233] update readme Former-commit-id: 3716bf44bed9b3d87f233e9562998784e623dfaf --- src/label_projection/README.md | 39 ++++++++++++++++++--------------- src/label_projection/README.qmd | 4 ++-- 2 files changed, 23 insertions(+), 20 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index cade84eea5..aa7d0242a9 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -7,12 +7,15 @@ - Pipeline topology - File format API - - dataset - - prediction - - score - - solution - - test - - train + - dataset.h5ad + - prediction.h5ad + - score.h5ad + - solution.h5ad + - test.h5ad + - train.h5ad # Label Projection @@ -77,12 +80,12 @@ classifier correctly assigns cell type labels to cells in the test set. ``` mermaid %%| column: screen-inset-shaded flowchart LR - anndata_dataset(dataset) - anndata_prediction(prediction) - anndata_score(score) - anndata_solution(solution) - anndata_test(test) - anndata_train(train) + anndata_dataset(dataset.h5ad) + anndata_prediction(prediction.h5ad) + anndata_score(score.h5ad) + anndata_solution(solution.h5ad) + anndata_test(test.h5ad) + anndata_train(train.h5ad) comp_censoring[/censoring/] comp_method[/method/] comp_metric[/metric/] @@ -100,7 +103,7 @@ flowchart LR ## File format API -### dataset +### `dataset.h5ad` Used in: @@ -117,7 +120,7 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### prediction +### `prediction.h5ad` Used in: @@ -133,7 +136,7 @@ Slots: | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | | uns | method_id | string | A unique identifier for the method | -### score +### `score.h5ad` Used in: @@ -149,7 +152,7 @@ Slots: | uns | metric_ids | string | One or more unique metric identifiers | | uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | -### solution +### `solution.h5ad` Used in: @@ -167,7 +170,7 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### test +### `test.h5ad` Used in: @@ -184,7 +187,7 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### train +### `train.h5ad` Used in: diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index fff5bbeae3..99f5ee5918 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -144,7 +144,7 @@ file_slot <- map_df(file_yamls, function(yaml_file) { ```{r flow, echo=FALSE,warning=FALSE,error=FALSE} nodes <- bind_rows( file_info %>% - transmute(id = name, label, is_comp = FALSE), + transmute(id = name, label = paste0(label, ".h5ad"), is_comp = FALSE), comp_info %>% transmute(id = name, label, is_comp = TRUE) ) %>% @@ -200,7 +200,7 @@ for (file_name in file_info$name) { pull(str) out_str <- strip_margin(glue::glue(" - §### {arg_info$label} + §### `{arg_info$label}.h5ad` § §Used in: § From d16bf83c095567d185a075bbfa725d31244421be Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 16:25:03 +0100 Subject: [PATCH 0307/1233] pin to viash 0.6.3; update label projection readme Former-commit-id: 762a01f229309e6bb68ac63f529babfdf21e261f --- bin/init | 2 +- src/label_projection/README.md | 104 ++++++++++++++++++++++++-------- src/label_projection/README.qmd | 45 ++++++++++++-- 3 files changed, 120 insertions(+), 31 deletions(-) diff --git a/bin/init b/bin/init index 9654ac84d1..5d38303842 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag develop + --tag 0.6.3 cd bin diff --git a/src/label_projection/README.md b/src/label_projection/README.md index aa7d0242a9..93f879f0f4 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -7,15 +7,22 @@ - Pipeline topology - File format API - - dataset.h5ad - - prediction.h5ad - - score.h5ad - - solution.h5ad - - test.h5ad - - train.h5ad + - dataset.h5ad: + Preprocessed dataset + - prediction.h5ad: Prediction + - score.h5ad: + Score + - solution.h5ad: Solution + - test.h5ad: Test + data + - train.h5ad: + Training data + - Component API + - censoring + - method + - metric # Label Projection @@ -48,7 +55,7 @@ labels onto the test set. ## Methods -Methods for assigning cell labels from a reference dataset to a +Methods for assigning labels from a reference dataset to a new dataset. | Name | Description | DOI | URL | |:---------------------------------------------------------------------|:-------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| @@ -103,11 +110,13 @@ flowchart LR ## File format API -### `dataset.h5ad` +### `dataset.h5ad`: Preprocessed dataset + +A preprocessed dataset Used in: -- censoring: input (as input) +- [censoring](#censoring): input (as input) Slots: @@ -120,12 +129,14 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### `prediction.h5ad` +### `prediction.h5ad`: Prediction + +The prediction file Used in: -- method: output (as output) -- metric: input_prediction (as input) +- [method](#method): output (as output) +- [metric](#metric): input_prediction (as input) Slots: @@ -136,11 +147,13 @@ Slots: | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | | uns | method_id | string | A unique identifier for the method | -### `score.h5ad` +### `score.h5ad`: Score + +Metric score file Used in: -- metric: output (as output) +- [metric](#metric): output (as output) Slots: @@ -152,12 +165,14 @@ Slots: | uns | metric_ids | string | One or more unique metric identifiers | | uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | -### `solution.h5ad` +### `solution.h5ad`: Solution + +The solution for the test data Used in: -- censoring: output_solution (as output) -- metric: input_solution (as input) +- [censoring](#censoring): output_solution (as output) +- [metric](#metric): input_solution (as input) Slots: @@ -170,12 +185,14 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### `test.h5ad` +### `test.h5ad`: Test data + +The censored test data Used in: -- censoring: output_test (as output) -- method: input_test (as input) +- [censoring](#censoring): output_test (as output) +- [method](#method): input_test (as input) Slots: @@ -187,12 +204,14 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -### `train.h5ad` +### `train.h5ad`: Training data + +The training data Used in: -- censoring: output_train (as output) -- method: input_train (as input) +- [censoring](#censoring): output_train (as output) +- [method](#method): input_train (as input) Slots: @@ -204,3 +223,36 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | | uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | + +## Component API + +### `censoring` + +Arguments: + +| Name | File format | Direction | Description | +|:--------------------|:--------------------------------|:----------|:---------------------| +| `--input` | [dataset.h5ad](#file-dataset) | input | Preprocessed dataset | +| `--output_train` | [train.h5ad](#file-train) | output | Training data | +| `--output_test` | [test.h5ad](#file-test) | output | Test data | +| `--output_solution` | [solution.h5ad](#file-solution) | output | Solution | + +### `method` + +Arguments: + +| Name | File format | Direction | Description | +|:----------------|:------------------------------------|:----------|:--------------| +| `--input_train` | [train.h5ad](#file-train) | input | Training data | +| `--input_test` | [test.h5ad](#file-test) | input | Test data | +| `--output` | [prediction.h5ad](#file-prediction) | output | Prediction | + +### `metric` + +Arguments: + +| Name | File format | Direction | Description | +|:---------------------|:------------------------------------|:----------|:------------| +| `--input_solution` | [solution.h5ad](#file-solution) | input | Solution | +| `--input_prediction` | [prediction.h5ad](#file-prediction) | input | Prediction | +| `--output` | [score.h5ad](#file-score) | output | Score | diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 99f5ee5918..a71fea8bb7 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -32,7 +32,7 @@ Here, we compare methods for annotation based on a reference dataset. The datase ## Methods -Methods for assigning cell labels from a reference dataset to a +Methods for assigning labels from a reference dataset to a new dataset. ```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} method_yamls <- list.files(paste0(dir, "/methods"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) @@ -124,6 +124,9 @@ file_info <- map_df(file_yamls, function(yaml_file) { tibble( name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + description = arg$description, + short_description = arg$info$short_description, + example = arg$example, label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) ) }) @@ -187,7 +190,7 @@ knitr::asis_output(out_str) ## File format API -```{r api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} for (file_name in file_info$name) { arg_info <- file_info %>% filter(name == file_name) sub_out <- file_slot %>% @@ -196,11 +199,13 @@ for (file_name in file_info$name) { used_in <- comp_file %>% filter(file_name == !!file_name) %>% left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% - mutate(str = paste0("* ", comp_label, ": ", arg_name, " (as ", direction, ")")) %>% + mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% pull(str) out_str <- strip_margin(glue::glue(" - §### `{arg_info$label}.h5ad` + §### `{arg_info$label}.h5ad`: {arg_info$short_description} {{#file-{arg_info$label}}} + § + §{arg_info$description} § §Used in: § @@ -213,3 +218,35 @@ for (file_name in file_info$name) { cat(out_str) } ``` + + + +## Component API + +```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +# todo: add description +# todo: add required info fields +for (comp_name in comp_info$name) { + comp <- comp_info %>% filter(name == comp_name) + sub_out <- comp_file %>% + filter(comp_name == !!comp_name) %>% + left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% + transmute( + Name = paste0("`--", arg_name, "`"), + `File format` = paste0("[", file_label, ".h5ad](#file-", file_label, ")"), + Direction = direction, + Description = file_sdesc + ) + + out_str <- strip_margin(glue::glue(" + §### `{comp$label}` + § + §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} + § + §Arguments: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + §"), symbol = "§") + cat(out_str) +} +``` \ No newline at end of file From 3eed4dd1b717a4410cf9a4240c5f78940cb34f53 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 9 Nov 2022 16:31:31 +0100 Subject: [PATCH 0308/1233] update readme Former-commit-id: 8268cf55172fc8191e127849be7eb2caa07b2edf --- src/label_projection/README.md | 55 +++++++++++++++++---------------- src/label_projection/README.qmd | 4 +-- 2 files changed, 31 insertions(+), 28 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 93f879f0f4..617e953dac 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -7,18 +7,21 @@ - Pipeline topology - File format API - - dataset.h5ad: + - dataset.h5ad: Preprocessed dataset - - prediction.h5ad: Prediction - - score.h5ad: - Score - - solution.h5ad: Solution - - test.h5ad: Test + - prediction.h5ad: + Prediction + - score.h5ad: Score + - solution.h5ad: Solution + - test.h5ad: Test data + - train.h5ad: Training data - - train.h5ad: - Training data - Component API - censoring - method @@ -230,29 +233,29 @@ Slots: Arguments: -| Name | File format | Direction | Description | -|:--------------------|:--------------------------------|:----------|:---------------------| -| `--input` | [dataset.h5ad](#file-dataset) | input | Preprocessed dataset | -| `--output_train` | [train.h5ad](#file-train) | output | Training data | -| `--output_test` | [test.h5ad](#file-test) | output | Test data | -| `--output_solution` | [solution.h5ad](#file-solution) | output | Solution | +| Name | File format | Direction | Description | +|:--------------------|:--------------|:----------|:---------------------| +| `--input` | dataset.h5ad | input | Preprocessed dataset | +| `--output_train` | train.h5ad | output | Training data | +| `--output_test` | test.h5ad | output | Test data | +| `--output_solution` | solution.h5ad | output | Solution | ### `method` Arguments: -| Name | File format | Direction | Description | -|:----------------|:------------------------------------|:----------|:--------------| -| `--input_train` | [train.h5ad](#file-train) | input | Training data | -| `--input_test` | [test.h5ad](#file-test) | input | Test data | -| `--output` | [prediction.h5ad](#file-prediction) | output | Prediction | +| Name | File format | Direction | Description | +|:----------------|:----------------|:----------|:--------------| +| `--input_train` | train.h5ad | input | Training data | +| `--input_test` | test.h5ad | input | Test data | +| `--output` | prediction.h5ad | output | Prediction | ### `metric` Arguments: -| Name | File format | Direction | Description | -|:---------------------|:------------------------------------|:----------|:------------| -| `--input_solution` | [solution.h5ad](#file-solution) | input | Solution | -| `--input_prediction` | [prediction.h5ad](#file-prediction) | input | Prediction | -| `--output` | [score.h5ad](#file-score) | output | Score | +| Name | File format | Direction | Description | +|:---------------------|:----------------|:----------|:------------| +| `--input_solution` | solution.h5ad | input | Solution | +| `--input_prediction` | prediction.h5ad | input | Prediction | +| `--output` | score.h5ad | output | Score | diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index a71fea8bb7..249feb37c3 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -203,7 +203,7 @@ for (file_name in file_info$name) { pull(str) out_str <- strip_margin(glue::glue(" - §### `{arg_info$label}.h5ad`: {arg_info$short_description} {{#file-{arg_info$label}}} + §### `{arg_info$label}.h5ad`: {arg_info$short_description} § §{arg_info$description} § @@ -233,7 +233,7 @@ for (comp_name in comp_info$name) { left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% transmute( Name = paste0("`--", arg_name, "`"), - `File format` = paste0("[", file_label, ".h5ad](#file-", file_label, ")"), + `File format` = paste0(file_label, ".h5ad"), Direction = direction, Description = file_sdesc ) From 039a146e112eb00238b3abede42622ef2ba9a5eb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 06:27:27 +0100 Subject: [PATCH 0309/1233] add nxf utils Former-commit-id: e91d9defb39053cb6ab8d477f2c9564beaf69866 --- .gitignore | 1 + bin/init | 6 + src/nxf_utils/ProfilesHelper.config | 64 +++ src/nxf_utils/WorkflowHelper.nf | 602 ++++++++++++++++++++++++++++ 4 files changed, 673 insertions(+) create mode 100644 src/nxf_utils/ProfilesHelper.config create mode 100644 src/nxf_utils/WorkflowHelper.nf diff --git a/.gitignore b/.gitignore index d4e373c1e6..01cb71bac3 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ target/ check_results/ log.txt .viash* +resources/ resources_test/ # nextflow specific ignores diff --git a/bin/init b/bin/init index 5d38303842..019ac17ac8 100755 --- a/bin/init +++ b/bin/init @@ -12,6 +12,12 @@ curl -fsSL get.viash.io | bash -s -- \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ --tag 0.6.3 +# automatically export the workflow helper +NXF_UTILS=src/nxf_utils +[[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS +bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config +bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf + cd bin curl -s https://get.nextflow.io | bash diff --git a/src/nxf_utils/ProfilesHelper.config b/src/nxf_utils/ProfilesHelper.config new file mode 100644 index 0000000000..35442065c6 --- /dev/null +++ b/src/nxf_utils/ProfilesHelper.config @@ -0,0 +1,64 @@ +process.container = 'nextflow/bash:latest' + +// detect tempdir +tempDir = java.nio.file.Paths.get( + System.getenv('NXF_TEMP') ?: + System.getenv('VIASH_TEMP') ?: + System.getenv('TEMPDIR') ?: + System.getenv('TMPDIR') ?: + '/tmp' +).toAbsolutePath() + +profiles { + no_publish { + process { + withName: '.*' { + publishDir = [ + enabled: false + ] + } + } + } + mount_temp { + docker.temp = tempDir + podman.temp = tempDir + charliecloud.temp = tempDir + } + docker { + docker.enabled = true + // docker.userEmulation = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + singularity { + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + podman { + podman.enabled = true + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + shifter { + shifter.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + } + charliecloud { + charliecloud.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + } +} diff --git a/src/nxf_utils/WorkflowHelper.nf b/src/nxf_utils/WorkflowHelper.nf new file mode 100644 index 0000000000..e86ee64cd2 --- /dev/null +++ b/src/nxf_utils/WorkflowHelper.nf @@ -0,0 +1,602 @@ +///////////////////////////////////// +// Viash Workflow helper functions // +///////////////////////////////////// + +import java.util.regex.Pattern +import java.io.BufferedReader +import java.io.FileReader +import java.nio.file.Paths +import groovy.json.JsonSlurper +import groovy.text.SimpleTemplateEngine +import org.yaml.snakeyaml.Yaml + +// param helpers // +def paramExists(name) { + return params.containsKey(name) && params[name] != "" +} + +def assertParamExists(name, description) { + if (!paramExists(name)) { + exit 1, "ERROR: Please provide a --${name} parameter ${description}" + } +} + +// helper functions for reading params from file // +def getChild(parent, child) { + if (child.contains("://") || Paths.get(child).isAbsolute()) { + child + } else { + parent.replaceAll('/[^/]*$', "/") + child + } +} + +def readCsv(file) { + def output = [] + def inputFile = file !instanceof File ? new File(file) : file + + // todo: allow escaped quotes in string + // todo: allow single quotes? + def splitRegex = Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') + def removeQuote = Pattern.compile('''"(.*)"''') + + def br = new BufferedReader(new FileReader(inputFile)) + + def row = -1 + def header = null + while (br.ready() && header == null) { + def line = br.readLine() + row++ + if (!line.startsWith("#")) { + header = splitRegex.split(line, -1).collect{field -> + m = removeQuote.matcher(field) + m.find() ? m.replaceFirst('$1') : field + } + } + } + assert header != null: "CSV file should contain a header" + + while (br.ready()) { + def line = br.readLine() + row++ + if (!line.startsWith("#")) { + def predata = splitRegex.split(line, -1) + def data = predata.collect{field -> + if (field == "") { + return null + } + m = removeQuote.matcher(field) + if (m.find()) { + return m.replaceFirst('$1') + } else { + return field + } + } + assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" + + def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} + output.add(dataMap) + } + } + + output +} + +def readJsonBlob(str) { + def jsonSlurper = new JsonSlurper() + jsonSlurper.parseText(str) +} + +def readJson(file) { + def inputFile = file !instanceof File ? new File(file) : file + def jsonSlurper = new JsonSlurper() + jsonSlurper.parse(inputFile) +} + +def readYamlBlob(str) { + def yamlSlurper = new Yaml() + yamlSlurper.load(str) +} + +def readYaml(file) { + def inputFile = file !instanceof File ? new File(file) : file + def yamlSlurper = new Yaml() + yamlSlurper.load(inputFile) +} + +// helper functions for reading a viash config in groovy // + +// based on how Functionality.scala is implemented +def processArgument(arg) { + arg.multiple = arg.multiple ?: false + arg.required = arg.required ?: false + arg.direction = arg.direction ?: "input" + arg.multiple_sep = arg.multiple_sep ?: ":" + arg.plainName = arg.name.replaceAll("^-*", "") + + if (arg.type == "file" && arg.direction == "output") { + def mult = arg.multiple ? "_*" : "" + def extSearch = "" + if (arg.default != null) { + extSearch = arg.default + } else if (arg.example != null) { + extSearch = arg.example + } + if (extSearch instanceof List) { + extSearch = extSearch[0] + } + def ext = extSearch.find("\\.[^\\.]+\$") ?: "" + arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" + } + + if (!arg.multiple) { + if (arg.default != null && arg.default instanceof List) { + arg.default = arg.default[0] + } + if (arg.example != null && arg.example instanceof List) { + arg.example = arg.example[0] + } + } + + if (arg.type == "boolean_true") { + arg.default = false + } + if (arg.type == "boolean_false") { + arg.default = true + } + + arg +} + +// based on how Functionality.scala is implemented +def processArgumentGroup(argumentGroups, name, arguments) { + def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() + + // Check if 'arguments' is in 'argumentGroups'. + def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} + + // Check whether an argument group of 'name' exists. + def existing = argumentGroups.find{gr -> name == gr.name} + + // if there are no arguments missing from the argument group, just return the existing group (if any) + if (argumentsNotInGroup.isEmpty()) { + return existing == null ? [] : [existing] + + // if there are missing arguments and there is an existing group, add the missing arguments to it + } else if (existing != null) { + def newEx = existing.clone() + newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) + return [newEx] + + // else create a new group + } else { + def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] + return [newEx] + } +} + +// based on how Functionality.scala is implemented +def processConfig(config) { + // TODO: assert .functionality etc. + if (config.functionality.inputs) { + System.err.println("Warning: .functionality.inputs is deprecated. Please use .functionality.arguments instead.") + } + if (config.functionality.outputs) { + System.err.println("Warning: .functionality.outputs is deprecated. Please use .functionality.arguments instead.") + } + + // set defaults for inputs + config.functionality.inputs = + (config.functionality.inputs ?: []).collect{arg -> + arg.type = arg.type ?: "file" + arg.direction = "input" + processArgument(arg) + } + // set defaults for outputs + config.functionality.outputs = + (config.functionality.outputs ?: []).collect{arg -> + arg.type = arg.type ?: "file" + arg.direction = "output" + processArgument(arg) + } + // set defaults for arguments + config.functionality.arguments = + (config.functionality.arguments ?: []).collect{arg -> + processArgument(arg) + } + // set defaults for argument_group arguments + config.functionality.argument_groups = + (config.functionality.argument_groups ?: []).collect{grp -> + grp.arguments = (grp.arguments ?: []).collect{arg -> + arg instanceof String ? arg.replaceAll("^-*", "") : processArgument(arg) + } + grp + } + + // create combined arguments list + config.functionality.allArguments = + config.functionality.inputs + + config.functionality.outputs + + config.functionality.arguments + + config.functionality.argument_groups.collectMany{ group -> + group.arguments.findAll{ it !instanceof String } + } + + // add missing argument groups (based on Functionality::allArgumentGroups()) + def argGroups = config.functionality.argument_groups + def inputGroup = processArgumentGroup(argGroups, "Inputs", config.functionality.inputs) + def outputGroup = processArgumentGroup(argGroups, "Outputs", config.functionality.outputs) + def defaultGroup = processArgumentGroup(argGroups, "Arguments", config.functionality.arguments) + def groupsFiltered = argGroups.findAll(gr -> !(["Inputs", "Outputs", "Arguments"].contains(gr.name))) + config.functionality.allArgumentGroups = inputGroup + outputGroup + defaultGroup + groupsFiltered + + config +} + +def readConfig(file) { + def config = readYaml(file) + processConfig(config) +} + +// recursively merge two maps +def mergeMap(Map lhs, Map rhs) { + return rhs.inject(lhs.clone()) { map, entry -> + if (map[entry.key] instanceof Map && entry.value instanceof Map) { + map[entry.key] = mergeMap(map[entry.key], entry.value) + } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { + map[entry.key] += entry.value + } else { + map[entry.key] = entry.value + } + return map + } +} + +def addGlobalParams(config) { + def localConfig = [ + "functionality" : [ + "argument_groups": [ + [ + "name": "Nextflow input-output arguments", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "arguments" : [ + [ + 'name': '--publish_dir', + 'required': true, + 'type': 'string', + 'description': 'Path to an output directory.', + 'example': 'output/', + 'multiple': false + ], + [ + 'name': '--param_list', + 'required': false, + 'type': 'string', + 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. + | + |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. + |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. + |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. + |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. + | + |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), + 'example': 'my_params.yaml', + 'multiple': false, + 'hidden': true + ], + ] + ] + ] + ] + ] + + return processConfig(mergeMap(config, localConfig)) +} + +// helper functions for generating help // + +// based on io.viash.helpers.Format.wordWrap +def formatWordWrap(str, maxLength) { + def words = str.split("\\s").toList() + + def word = null + def line = "" + def lines = [] + while(!words.isEmpty()) { + word = words.pop() + if (line.length() + word.length() + 1 <= maxLength) { + line = line + " " + word + } else { + lines.add(line) + line = word + } + if (words.isEmpty()) { + lines.add(line) + } + } + return lines +} + +// based on Format.paragraphWrap +def paragraphWrap(str, maxLength) { + def outLines = [] + str.split("\n").each{par -> + def words = par.split("\\s").toList() + + def word = null + def line = words.pop() + while(!words.isEmpty()) { + word = words.pop() + if (line.length() + word.length() + 1 <= maxLength) { + line = line + " " + word + } else { + outLines.add(line) + line = word + } + } + if (words.isEmpty()) { + outLines.add(line) + } + } + return outLines +} + +def generateArgumentHelp(param) { + // alternatives are not supported + // def names = param.alternatives ::: List(param.name) + + def unnamedProps = [ + ["required parameter", param.required], + ["multiple values allowed", param.multiple], + ["output", param.direction.toLowerCase() == "output"], + ["file must exist", param.type == "file" && param.must_exist] + ].findAll{it[1]}.collect{it[0]} + + def dflt = null + if (param.default != null) { + if (param.default instanceof List) { + dflt = param.default.join(param.multiple_sep ?: ", ") + } else { + dflt = param.default.toString() + } + } + def example = null + if (param.example != null) { + if (param.example instanceof List) { + example = param.example.join(param.multiple_sep ?: ", ") + } else { + example = param.example.toString() + } + } + def min = param.min?.toString() + def max = param.max?.toString() + + def escapeChoice = { choice -> + def s1 = choice.replaceAll("\\n", "\\\\n") + def s2 = s1.replaceAll("\"", """\\\"""") + s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 + } + def choices = param.choices == null ? + null : + "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" + + def namedPropsStr = [ + ["type", ([param.type] + unnamedProps).join(", ")], + ["default", dflt], + ["example", example], + ["choices", choices], + ["min", min], + ["max", max] + ] + .findAll{it[1]} + .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} + .join("") + + def descStr = param.description == null ? + "" : + paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") + + "\n --" + param.plainName + + namedPropsStr + + descStr +} + +// Based on Helper.generateHelp() in Helper.scala +def generateHelp(config) { + def fun = config.functionality + + // PART 1: NAME AND VERSION + def nameStr = fun.name + + (fun.version == null ? "" : " " + fun.version) + + // PART 2: DESCRIPTION + def descrStr = fun.description == null ? + "" : + "\n\n" + paragraphWrap(fun.description.trim(), 80).join("\n") + + // PART 3: Usage + def usageStr = fun.usage == null ? + "" : + "\n\nUsage:\n" + fun.usage.trim() + + // PART 4: Options + def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> + def name = argGroup.name + def descriptionStr = argGroup.description == null ? + "" : + "\n " + paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" + def arguments = argGroup.arguments.collect{arg -> + arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg + }.findAll{it != null} + def argumentStrs = arguments.collect{param -> generateArgumentHelp(param)} + + "\n\n$name:" + + descriptionStr + + argumentStrs.join("\n") + } + + // FINAL: combine + def out = nameStr + + descrStr + + usageStr + + argGroupStrs.join("") + + return out +} + +def helpMessage(config) { + if (paramExists("help")) { + def mergedConfig = addGlobalParams(config) + def helpStr = generateHelp(mergedConfig) + println(helpStr) + exit 0 + } +} + +def guessMultiParamFormat(params) { + if (!params.containsKey("param_list") || params.param_list == null) { + "none" + } else { + def param_list = params.param_list + + if (param_list !instanceof String) { + "asis" + } else if (param_list.endsWith(".csv")) { + "csv" + } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { + "json" + } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { + "yaml" + } else { + "yaml_blob" + } + } +} + +def paramsToList(params, config) { + // fetch default params from functionality + def defaultArgs = config.functionality.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // fetch overrides in params + def paramArgs = config.functionality.allArguments + .findAll { params.containsKey(it.plainName) } + .collectEntries { [ it.plainName, params[it.plainName] ] } + + // check multi input params + // objects should be closures and not functions, thanks to FunctionDef + def multiParamFormat = guessMultiParamFormat(params) + + def multiOptionFunctions = [ + "csv": {[it, readCsv(it)]}, + "json": {[it, readJson(it)]}, + "yaml": {[it, readYaml(it)]}, + "yaml_blob": {[null, readYamlBlob(it)]}, + "asis": {[null, it]}, + "none": {[null, [[:]]]} + ] + assert multiOptionFunctions.containsKey(multiParamFormat): + "Format of provided --param_list not recognised.\n" + + "You can use '--param_list_format' to manually specify the format.\n" + + "Found: '$multiParamFormat'. Expected: one of 'csv', 'json', 'yaml', 'yaml_blob', 'asis' or 'none'" + + // fetch multi param inputs + def multiOptionFun = multiOptionFunctions.get(multiParamFormat) + // todo: add try catch + def multiOptionOut = multiOptionFun(params.containsKey("param_list") ? params.param_list : "") + def paramList = multiOptionOut[1] + def multiFile = multiOptionOut[0] + + // data checks + assert paramList instanceof List: "--param_list should contain a list of maps" + for (value in paramList) { + assert value instanceof Map: "--param_list should contain a list of maps" + } + + // combine parameters + def processedParams = paramList.collect{ multiParam -> + // combine params + def combinedArgs = defaultArgs + paramArgs + multiParam + + // check whether required arguments exist + config.functionality.allArguments + .findAll { it.required } + .forEach { par -> + assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" + } + + // process arguments + def inputs = config.functionality.allArguments + .findAll{ par -> combinedArgs.containsKey(par.plainName) } + .collectEntries { par -> + // split on 'multiple_sep' + if (par.multiple) { + parData = combinedArgs[par.plainName] + if (parData instanceof List) { + parData = parData.collect{it instanceof String ? it.split(par.multiple_sep) : it } + } else if (parData instanceof String) { + parData = parData.split(par.multiple_sep) + } else if (parData == null) { + parData = [] + } else { + parData = [ parData ] + } + } else { + parData = [ combinedArgs[par.plainName] ] + } + + // flatten + parData = parData.flatten() + + // cast types + if (par.type == "file" && ((par.direction ?: "input") == "input")) { + parData = parData.collect{path -> + if (path !instanceof String) { + path + } else if (multiFile) { + file(getChild(multiFile, path)) + } else { + file(path) + } + }.flatten() + } else if (par.type == "integer") { + parData = parData.collect{it as Integer} + } else if (par.type == "double") { + parData = parData.collect{it as Double} + } else if (par.type == "boolean" || par.type == "boolean_true" || par.type == "boolean_false") { + parData = parData.collect{it as Boolean} + } + // simplify list to value if need be + if (!par.multiple) { + assert parData.size() == 1 : + "Error: argument ${par.plainName} has too many values.\n" + + " Expected amount: 1. Found: ${parData.size()}" + parData = parData[0] + } + + // return pair + [ par.plainName, parData ] + } + // remove parameters which were explicitly set to null + .findAll{ par -> par != null } + } + + + // check processed params + processedParams.forEach { args -> + assert args.containsKey("id"): "Each argument set should have an 'id'. Argument set: $args" + } + def ppIds = processedParams.collect{it.id} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" + + processedParams +} + +def paramsToChannel(params, config) { + Channel.fromList(paramsToList(params, config)) +} + +def viashChannel(params, config) { + paramsToChannel(params, config) + | map{tup -> [tup.id, tup]} +} From f9037596a7c453cfbd55922513b95e4b570f92e4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 06:27:47 +0100 Subject: [PATCH 0310/1233] allow choosing input/output layers in dataset loader Former-commit-id: 0aa77145ce203cd086f843dd8309f9bc439b29a5 --- .../dataset_loader/download/config.vsh.yaml | 122 +++++++++--------- src/common/dataset_loader/download/script.py | 24 ++-- src/common/dataset_loader/download/test.py | 12 +- 3 files changed, 82 insertions(+), 76 deletions(-) diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index fc51daf02e..86dce2f07c 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -7,65 +7,69 @@ functionality: - name: "Michaela Mueller" roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: "--url" - type: "string" - description: "URL of dataset" - required: true - - name: "--name" - type: "string" - example: "pbmc" - description: "Name of dataset" - required: true - - name: "--obs_celltype" - type: "string" - description: "Location of where to find the observation cell types." - - name: "--obs_batch" - type: "string" - description: "Location of where to find the observation batch IDs." - - name: "--obs_tissue" - type: "string" - description: "Location of where to find the observation tissue information." - - name: "--layer_counts" - type: "string" - description: "Location of where to store the counts data. Leave undefined to store in `.X`, else it will be stored in `.layers[par['layer_counts']]`." - example: counts - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file of the cleaned dataset" - required: true - info: - slots: - X: - type: integer - name: counts # todo: this should depend on the value of 'layer_counts' - description: Raw counts - required: false - obs: - - type: string - name: celltype - description: Cell type labels - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: false - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - required: false + argument_groups: + - name: Inputs + arguments: + - name: "--url" + type: "string" + description: "URL of dataset" + required: true + - name: "--name" + type: "string" + example: "pbmc" + description: "Name of dataset" + required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "In which layer to find the counts matrix. Leave undefined to use `.X`." + example: counts + - name: Outputs + arguments: + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output h5ad file of the cleaned dataset" + required: true + info: + slots: + layers: + - type: integer + name: $par_layer_counts_output + description: Raw counts + required: false + obs: + - type: string + name: celltype + description: Cell type labels + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: false + - name: "--layer_counts_output" + type: "string" + description: "Location of where to store the counts data. Leave undefined to store in `.X`, else it will be stored in `.layers[par['layer_counts_output']]`." + example: counts resources: - type: python_script path: script.py diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py index c2834106ff..48e340f95f 100644 --- a/src/common/dataset_loader/download/script.py +++ b/src/common/dataset_loader/download/script.py @@ -13,7 +13,8 @@ "obs_celltype": "celltype", "obs_batch": "tech", "layer_counts": "counts", - "output": "test_data.h5ad" + "output": "test_data.h5ad", + "layer_counts_output": "counts" } ## VIASH END @@ -31,17 +32,9 @@ print("Reading file") adata = sc.read_h5ad(filepath) -if "counts" in adata.layers: - print("Copying .layers['counts'] to .X") - adata.X = adata.layers["counts"] - del adata.layers["counts"] - print("Setting .uns['dataset_id']") adata.uns["dataset_id"] = par["name"] -print("Setting .uns['raw_dataset_id']") -adata.uns["raw_dataset_id"] = par["name"] - print("Setting .obs['celltype']") if par["obs_celltype"]: if par["obs_celltype"] in adata.obs: @@ -64,12 +57,19 @@ print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") print("Remove cells or genes with 0 counts") +if par["layer_counts"] and par["layer_counts"] in adata.layers: + print(f" Temporarily copying .layers['{par['layer_counts']}'] to .X") + adata.X = adata.layers[par["layer_counts"]] + del adata.layers[par["layer_counts"]] + +print(" Removing empty genes") sc.pp.filter_genes(adata, min_cells=1) +print(" Removing empty cells") sc.pp.filter_cells(adata, min_counts=2) -if par["layer_counts"]: - print(f"Copying .X back to .layers['{par['layer_counts']}']") - adata.layers[par["layer_counts"]] = adata.X +if par["layer_counts_output"]: + print(f" Copying .X back to .layers['{par['layer_counts_output']}']") + adata.layers[par["layer_counts_output"]] = adata.X del adata.X print("Writing adata to file") diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py index 4fc48dfb40..a52ca203cb 100644 --- a/src/common/dataset_loader/download/test.py +++ b/src/common/dataset_loader/download/test.py @@ -7,7 +7,8 @@ url = "https://ndownloader.figshare.com/files/24539828" obs_celltype = "celltype" obs_batch = "tech" -layer_counts = "foobar" + +layer_counts_output = "foobar" print(">> Running script") out = subprocess.check_output([ @@ -16,7 +17,8 @@ "--name", name, "--obs_celltype", obs_celltype, "--obs_batch", obs_batch, - "--layer_counts", layer_counts, + "--layer_counts", "counts", + "--layer_counts_output", layer_counts_output, "--output", output ]).decode("utf-8") @@ -29,12 +31,12 @@ print(adata) print(">> Check that output fits expected API") -if layer_counts is not None: +if layer_counts_output is not None: assert adata.X is None - assert layer_counts in adata.layers + assert layer_counts_output in adata.layers else: assert adata.X is not None - assert layer_counts not in adata.layers + assert layer_counts_output not in adata.layers assert adata.uns["dataset_id"] == name if obs_celltype: assert "celltype" in adata.obs.columns From 0797e13159e27cfa3df0d8029daa8e18f0806edf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 06:28:11 +0100 Subject: [PATCH 0311/1233] add multiple normalisations to the same dataset Former-commit-id: 1e4e2a52640000e6d52e86ea4562b9bd2f31bbd6 --- src/common/api/anndata_normalized_dataset.yaml | 5 +---- src/common/api/anndata_raw_dataset.yaml | 2 +- src/common/api/comp_normalization.yaml | 14 ++++++++++---- .../normalization/log_cpm/config.vsh.yaml | 9 +++++++++ src/common/normalization/log_cpm/script.py | 18 ++++++++++++------ .../log_scran_pooling/config.vsh.yaml | 11 ++++++++++- .../normalization/log_scran_pooling/script.R | 12 +++++------- src/common/resources_test_scripts/pancreas.sh | 18 ++++++++++++------ 8 files changed, 60 insertions(+), 29 deletions(-) diff --git a/src/common/api/anndata_normalized_dataset.yaml b/src/common/api/anndata_normalized_dataset.yaml index 85c85f1abc..34dc402035 100644 --- a/src/common/api/anndata_normalized_dataset.yaml +++ b/src/common/api/anndata_normalized_dataset.yaml @@ -9,7 +9,7 @@ info: name: counts description: Raw counts - type: double - name: lognorm + name: $par_layer_output description: Log-transformed normalised counts obs: - type: double @@ -22,6 +22,3 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/common/api/anndata_raw_dataset.yaml b/src/common/api/anndata_raw_dataset.yaml index 988a8a4027..c2583eaa28 100644 --- a/src/common/api/anndata_raw_dataset.yaml +++ b/src/common/api/anndata_raw_dataset.yaml @@ -18,4 +18,4 @@ info: uns: - type: string name: dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" + description: "A unique identifier for the dataset" diff --git a/src/common/api/comp_normalization.yaml b/src/common/api/comp_normalization.yaml index adaa9aad2a..411270fc66 100644 --- a/src/common/api/comp_normalization.yaml +++ b/src/common/api/comp_normalization.yaml @@ -5,6 +5,12 @@ functionality: - name: "--output" __inherits__: anndata_normalized_dataset.yaml direction: output + + # not including this because we need to override the default + # - name: "--layer_output" + # type: string + # default: "log_cpm" + # description: The name of the layer in which to store the log normalized data. test_resources: - type: python_script path: generic_test.py @@ -15,11 +21,13 @@ functionality: input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" output_path = "output.h5ad" + output_layer = "norm_layer" cmd = [ meta['executable'], "--input", input_path, - "--output", output_path + "--output", output_path, + "--layer_output", output_layer ] print(">> Running script as test") @@ -35,13 +43,11 @@ functionality: print("output:", output) print(">> Checking whether output data structures were added") - assert "lognorm" in output.layers - assert output.uns["normalization_method"] == meta['functionality_name'].removeprefix("normalize_") + assert output_layer in output.layers print("Checking whether data from input was copied properly to output") assert input.n_obs == output.n_obs assert input.uns["dataset_id"] == output.uns["dataset_id"] - assert input.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] print("All checks succeeded!") - path: ../../../../resources_test/common/pancreas diff --git a/src/common/normalization/log_cpm/config.vsh.yaml b/src/common/normalization/log_cpm/config.vsh.yaml index 3bdfd4b09e..6b7121a1a7 100644 --- a/src/common/normalization/log_cpm/config.vsh.yaml +++ b/src/common/normalization/log_cpm/config.vsh.yaml @@ -3,6 +3,15 @@ functionality: name: "log_cpm" namespace: "common/normalization" description: "Normalize data using Log CPM" + arguments: + - name: "--layer_output" + type: string + default: "log_cpm" + description: The name of the layer in which to store the log normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors_log_cpm" + description: In which .obs slot to store the size factors. resources: - type: python_script path: script.py diff --git a/src/common/normalization/log_cpm/script.py b/src/common/normalization/log_cpm/script.py index 0f7f2e9ad2..a080fdc643 100644 --- a/src/common/normalization/log_cpm/script.py +++ b/src/common/normalization/log_cpm/script.py @@ -2,8 +2,10 @@ ## VIASH START par = { - 'input': "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", - 'output': "output.h5ad" + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output': "output.h5ad", + 'layer_output': "log_cpm", + 'obs_size_factors': "log_cpm_size_factors" } meta = { "functionality_name": "normalize_log_cpm" @@ -14,13 +16,17 @@ adata = sc.read_h5ad(par['input']) print(">> Normalize data") -norm = sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors", layer="counts", inplace=False) +norm = sc.pp.normalize_total( + adata, + target_sum=1e6, + layer="counts", + inplace=False +) lognorm = sc.pp.log1p(norm["X"]) print(">> Store output in adata") -adata.layers["lognorm"] = lognorm -adata.obs["norm_factor"] = norm["norm_factor"] -adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") +adata.layers[par["layer_output"]] = lognorm +adata.obs[par["obs_size_factors"]] = norm["norm_factor"] print(">> Write data") adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/common/normalization/log_scran_pooling/config.vsh.yaml b/src/common/normalization/log_scran_pooling/config.vsh.yaml index 7dbe6b2182..ad0eea1ca6 100644 --- a/src/common/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/common/normalization/log_scran_pooling/config.vsh.yaml @@ -2,7 +2,16 @@ __inherits__: ../../api/comp_normalization.yaml functionality: name: "log_scran_pooling" namespace: "common/normalization" - description: "Normalize data" + description: "Normalize data using scran pooling" + arguments: + - name: "--layer_output" + type: string + default: "log_scran_pooling" + description: The name of the layer in which to store the log normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors_log_scran_pooling" + description: In which .obs slot to store the size factors. resources: - type: r_script path: script.R diff --git a/src/common/normalization/log_scran_pooling/script.R b/src/common/normalization/log_scran_pooling/script.R index 6e1a5bf5c6..5885785d96 100644 --- a/src/common/normalization/log_scran_pooling/script.R +++ b/src/common/normalization/log_scran_pooling/script.R @@ -7,10 +7,9 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( input = "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", - output = "output.scran.h5ad" -) -meta <- list( - functionality_name = "normalize_log_scran_pooling" + output = "output.scran.h5ad", + layer_output = "log_scran_pooling", + obs_size_factors = "size_factors_log_scran_pooling" ) ## VIASH END @@ -23,9 +22,8 @@ size_factors <- scran::calculateSumFactors(counts, min.mean=0.1, BPPARAM=BiocPar lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) cat(">> Storing in anndata\n") -adata$obs[["size_factors"]] <- size_factors -adata$layers[["lognorm"]] <- lognorm +adata$obs[[par$obs_size_factors]] <- size_factors +adata$layers[[par$layer_output]] <- lognorm cat(">> Writing to file\n") -adata$uns["normalization_method"] <- gsub("^normalize_", "", meta["functionality_name"]) zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/common/resources_test_scripts/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh index 999e782279..04a134154b 100755 --- a/src/common/resources_test_scripts/pancreas.sh +++ b/src/common/resources_test_scripts/pancreas.sh @@ -20,17 +20,23 @@ bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ --obs_batch "tech" \ --name "pancreas" \ --layer_counts "counts" \ - --output $DATASET_DIR/temp_full_dataset.h5ad + --layer_counts_output "counts" \ + --output $DATASET_DIR/temp_dataset_full.h5ad # subsample bin/viash run src/common/subsample/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_full_dataset.h5ad \ + --input $DATASET_DIR/temp_dataset_full.h5ad \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ - --output $DATASET_DIR/dataset.h5ad \ + --output $DATASET_DIR/temp_dataset_sampled.h5ad \ --seed 123 -# run one normalisation +# run log cpm normalisation bin/viash run src/common/normalization/log_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/dataset_cpm.h5ad + --input $DATASET_DIR/temp_dataset_sampled.h5ad \ + --output $DATASET_DIR/temp_dataset_cpm.h5ad + +# run scran pooling normalisation +bin/viash run src/common/normalization/log_scran_pooling/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset_cpm.h5ad \ + --output $DATASET_DIR/dataset.h5ad From 7001d7a162f5a63fe180544a6335b417a717c10e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 12:56:34 +0100 Subject: [PATCH 0312/1233] add multiple normalisation methods to one dataset Former-commit-id: dc7d674876b3b6bf150cbe61303a2e3adaaad6a8 --- src/common/api/anndata_dataset.yaml | 35 +++++++++++++++++++ .../api/anndata_normalized_dataset.yaml | 24 ------------- src/common/api/anndata_raw_dataset.yaml | 12 +++++-- src/common/api/comp_normalization.yaml | 33 ++++++++++++++++- src/common/dataset_concatenate/script.py | 2 +- src/common/dataset_concatenate/test_script.py | 2 +- src/label_projection/api/anndata_dataset.yaml | 10 +++--- .../api/anndata_prediction.yaml | 3 -- src/label_projection/api/anndata_score.yaml | 3 -- .../api/anndata_solution.yaml | 10 +++--- src/label_projection/api/anndata_test.yaml | 10 +++--- src/label_projection/api/anndata_train.yaml | 10 +++--- src/label_projection/api/comp_censoring.yaml | 14 ++++---- src/label_projection/api/comp_method.yaml | 12 ++++--- src/label_projection/api/comp_metric.yaml | 5 ++- .../majority_vote/config.vsh.yaml | 5 +++ .../control_methods/majority_vote/script.py | 4 +-- .../random_labels/config.vsh.yaml | 5 +++ .../control_methods/random_labels/script.py | 4 +-- .../true_labels/config.vsh.yaml | 4 +++ .../control_methods/true_labels/script.py | 6 ++-- .../data_processing/censoring/script.py | 14 ++++---- .../methods/knn_classifier/config.vsh.yaml | 5 +++ .../methods/knn_classifier/script.py | 10 +++--- .../logistic_regression/config.vsh.yaml | 4 +++ .../methods/logistic_regression/script.py | 10 +++--- .../methods/mlp/config.vsh.yaml | 4 +++ src/label_projection/methods/mlp/script.py | 10 +++--- .../metrics/accuracy/script.py | 4 +-- src/label_projection/metrics/f1/script.py | 4 +-- .../resources_test_scripts/pancreas.sh | 20 +++++------ 31 files changed, 189 insertions(+), 109 deletions(-) create mode 100644 src/common/api/anndata_dataset.yaml delete mode 100644 src/common/api/anndata_normalized_dataset.yaml diff --git a/src/common/api/anndata_dataset.yaml b/src/common/api/anndata_dataset.yaml new file mode 100644 index 0000000000..21694f6745 --- /dev/null +++ b/src/common/api/anndata_dataset.yaml @@ -0,0 +1,35 @@ +type: file +description: "A dataset" +example: "dataset.h5ad" +info: + short_description: "Dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/common/api/anndata_normalized_dataset.yaml b/src/common/api/anndata_normalized_dataset.yaml deleted file mode 100644 index 34dc402035..0000000000 --- a/src/common/api/anndata_normalized_dataset.yaml +++ /dev/null @@ -1,24 +0,0 @@ -type: file -description: "A preprocessed dataset" -example: "preprocessed.h5ad" -info: - short_description: "Preprocessed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - - type: double - name: $par_layer_output - description: Log-transformed normalised counts - obs: - - type: double - name: label - description: Ground truth cell type labels - - type: double - name: batch - description: Batch information - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" diff --git a/src/common/api/anndata_raw_dataset.yaml b/src/common/api/anndata_raw_dataset.yaml index c2583eaa28..37c41a3003 100644 --- a/src/common/api/anndata_raw_dataset.yaml +++ b/src/common/api/anndata_raw_dataset.yaml @@ -8,14 +8,22 @@ info: - type: integer name: counts description: Raw counts + required: true obs: - type: string - name: label - description: Ground truth cell type labels + name: celltype + description: Cell type information + required: false - type: string name: batch description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true diff --git a/src/common/api/comp_normalization.yaml b/src/common/api/comp_normalization.yaml index 411270fc66..f0c786e115 100644 --- a/src/common/api/comp_normalization.yaml +++ b/src/common/api/comp_normalization.yaml @@ -3,7 +3,38 @@ functionality: - name: "--input" __inherits__: anndata_raw_dataset.yaml - name: "--output" - __inherits__: anndata_normalized_dataset.yaml + type: file + description: "A preprocessed dataset" + example: "preprocessed.h5ad" + info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: $par_layer_output + description: Log-transformed normalised counts + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true direction: output # not including this because we need to override the default diff --git a/src/common/dataset_concatenate/script.py b/src/common/dataset_concatenate/script.py index a89a80df40..78faf143ca 100644 --- a/src/common/dataset_concatenate/script.py +++ b/src/common/dataset_concatenate/script.py @@ -2,7 +2,7 @@ ## VIASH START par = { - "inputs": ["resources_test/common/pancreas/dataset_cpm.h5ad", "resources_test/common/pancreas/dataset_cpm.h5ad"], + "inputs": ["resources_test/common/pancreas/dataset.h5ad", "resources_test/common/pancreas/dataset.h5ad"], "output": "output.h5ad" } ## VIASH END diff --git a/src/common/dataset_concatenate/test_script.py b/src/common/dataset_concatenate/test_script.py index 8a0eea0b4e..12c26a8501 100644 --- a/src/common/dataset_concatenate/test_script.py +++ b/src/common/dataset_concatenate/test_script.py @@ -5,7 +5,7 @@ ## VIASH START ## VIASH END -input_path = f"{meta['resources_dir']}/pancreas/dataset_cpm.h5ad" +input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" output_path = "toy_data_concatenated.h5ad" print(">> Runing script as test") diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml index 85c85f1abc..f79db388e7 100644 --- a/src/label_projection/api/anndata_dataset.yaml +++ b/src/label_projection/api/anndata_dataset.yaml @@ -9,8 +9,11 @@ info: name: counts description: Raw counts - type: double - name: lognorm - description: Log-transformed normalised counts + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed obs: - type: double name: label @@ -22,6 +25,3 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_prediction.yaml b/src/label_projection/api/anndata_prediction.yaml index 829200ea93..d7695dcdaf 100644 --- a/src/label_projection/api/anndata_prediction.yaml +++ b/src/label_projection/api/anndata_prediction.yaml @@ -12,9 +12,6 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - type: string name: method_id description: "A unique identifier for the method" diff --git a/src/label_projection/api/anndata_score.yaml b/src/label_projection/api/anndata_score.yaml index dcc750dd4c..a3f1af8399 100644 --- a/src/label_projection/api/anndata_score.yaml +++ b/src/label_projection/api/anndata_score.yaml @@ -8,9 +8,6 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" - type: string name: method_id description: "A unique identifier for the method" diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index c8bc73ab61..d711347996 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -9,8 +9,11 @@ info: name: counts description: Raw counts - type: double - name: lognorm - description: Log-transformed normalised counts + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed obs: - type: string name: label @@ -22,6 +25,3 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index d9f5dd62d5..94e23b6d90 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -9,8 +9,11 @@ info: name: counts description: Raw counts - type: double - name: lognorm - description: Log-transformed normalised counts + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed obs: - type: string name: batch @@ -19,6 +22,3 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index 3e5bb89dd1..87181e24f7 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -9,8 +9,11 @@ info: name: counts description: Raw counts - type: double - name: lognorm - description: Log-transformed normalised counts + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed obs: - type: string name: label @@ -22,6 +25,3 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_censoring.yaml index 2ac49996e5..e935e7135c 100644 --- a/src/label_projection/api/comp_censoring.yaml +++ b/src/label_projection/api/comp_censoring.yaml @@ -19,7 +19,7 @@ functionality: import subprocess from os import path - input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" output_train_path = "output_train.h5ad" output_test_path = "output_test.h5ad" output_solution_path = "output_solution.h5ad" @@ -59,23 +59,23 @@ functionality: print(">> Checking whether data from input was copied properly to output") assert output_train.uns["dataset_id"] == input.uns["dataset_id"] - assert output_train.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - assert output_test.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] - assert output_solution.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] print(">> Check whether certain slots exist") assert "counts" in output_train.layers - assert "lognorm" in output_train.layers + assert "log_cpm" in output_train.layers + assert "log_scran_pooling" in output_train.layers assert "label" in output_train.obs assert "batch" in output_train.obs assert "counts" in output_test.layers - assert "lognorm" in output_test.layers + assert "log_cpm" in output_test.layers + assert "log_scran_pooling" in output_test.layers assert "label" not in output_test.obs # make sure label is /not/ here assert "batch" in output_test.obs assert "counts" in output_solution.layers - assert "lognorm" in output_solution.layers + assert "log_cpm" in output_solution.layers + assert "log_scran_pooling" in output_solution.layers assert "label" in output_solution.obs assert "batch" in output_solution.obs diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 518611fcdf..682e7660f1 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -7,6 +7,11 @@ functionality: - name: "--output" __inherits__: anndata_prediction.yaml direction: output + # TODO: currently needs to be manually specified since the default value needs to be overrideable + # - name: "--layer_input" + # type: string + # default: "log_cpm" + # description: Which layer to use as input. test_resources: - path: ../../../../resources_test/label_projection/pancreas - type: python_script @@ -16,9 +21,9 @@ functionality: import subprocess from os import path - input_train_path = meta["resources_dir"] + "/pancreas/dataset_cpm_train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/dataset_cpm_test.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/dataset_cpm_solution.h5ad" + input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" output_path = "output.h5ad" cmd = [ @@ -52,6 +57,5 @@ functionality: print("Checking whether data from input was copied properly to output") assert input_test.n_obs == output.n_obs assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - assert input_test.uns["raw_dataset_id"] == output.uns["raw_dataset_id"] print("All checks succeeded!") diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index e3530706c5..481d206919 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -16,8 +16,8 @@ functionality: import subprocess from os import path - input_prediction_path = meta["resources_dir"] + "/pancreas/dataset_cpm_knn.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/dataset_cpm_solution.h5ad" + input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" output_path = "output.h5ad" cmd = [ @@ -39,7 +39,6 @@ functionality: print("Checking whether data from input was copied properly to output") assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] - assert output.uns["raw_dataset_id"] == input_prediction.uns["raw_dataset_id"] assert output.uns["method_id"] == input_prediction.uns["method_id"] assert output.uns["metric_ids"] is not None assert output.uns["metric_values"] is not None diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 6f9b3678bc..a2e6ca3bef 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -8,6 +8,11 @@ functionality: label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/majority_vote/script.py b/src/label_projection/control_methods/majority_vote/script.py index f813afe7c7..2a29fdaa80 100644 --- a/src/label_projection/control_methods/majority_vote/script.py +++ b/src/label_projection/control_methods/majority_vote/script.py @@ -2,8 +2,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index dbbca8219b..e1e9b9f9e2 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -8,6 +8,11 @@ functionality: label: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/random_labels/script.py b/src/label_projection/control_methods/random_labels/script.py index 7526568389..6733c4957d 100644 --- a/src/label_projection/control_methods/random_labels/script.py +++ b/src/label_projection/control_methods/random_labels/script.py @@ -3,8 +3,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 48266b54df..35e5432b33 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -11,6 +11,10 @@ functionality: arguments: - name: "--input_solution" __inherits__: ../../api/anndata_solution.yaml + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/true_labels/script.py b/src/label_projection/control_methods/true_labels/script.py index cc3731563c..b0f205b2fe 100644 --- a/src/label_projection/control_methods/true_labels/script.py +++ b/src/label_projection/control_methods/true_labels/script.py @@ -2,9 +2,9 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', - 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/data_processing/censoring/script.py b/src/label_projection/data_processing/censoring/script.py index bb0f44e8b6..5830fbab04 100644 --- a/src/label_projection/data_processing/censoring/script.py +++ b/src/label_projection/data_processing/censoring/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/label_projection/pancreas/dataset_cpm.h5ad', + 'input': 'resources_test/label_projection/pancreas/dataset.h5ad', 'method': 'batch', 'seed': None, 'obs_batch': 'batch', @@ -49,21 +49,21 @@ def subset_anndata(adata_sub, layers, obs, uns): ) output_train = subset_anndata( adata_sub = adata[[not x for x in is_test]], - layers=["counts", "lognorm"], + layers=["counts", "log_cpm", "log_scran_pooling"], obs={"label": par["obs_label"], "batch": par["obs_batch"]}, - uns=["raw_dataset_id", "dataset_id"] + uns=["dataset_id"] ) output_test = subset_anndata( adata[is_test], - layers=["counts", "lognorm"], + layers=["counts", "log_cpm", "log_scran_pooling"], obs={"batch": par["obs_batch"]}, # do NOT copy label to test obs! - uns=["raw_dataset_id", "dataset_id"] + uns=["dataset_id"] ) output_solution = subset_anndata( adata[is_test], - layers=["counts", "lognorm"], + layers=["counts", "log_cpm", "log_scran_pooling"], obs={"label": par["obs_label"], "batch": par["obs_batch"]}, - uns=["raw_dataset_id", "dataset_id"] + uns=["dataset_id"] ) print(">> Writing data") diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 0b3f493ccd..d5bbf4535f 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -13,6 +13,11 @@ functionality: code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d + arguments: + - name: "--layer_input" + type: string + default: "log_cpm" + description: Which layer to use as input. resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index 5083b9b22e..012efe6d8b 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', } meta = { @@ -45,11 +45,13 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) +input_layer = par["layer_input"] + print("Fit to train data") -pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) +pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) +input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 9a4edba1c7..1d3693b0ba 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -13,6 +13,10 @@ functionality: v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d arguments: + - name: "--layer_input" + type: string + default: "log_cpm" + description: Which layer to use as input. - name: "--max_iter" type: "integer" default: 1000 diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 9c4ae95cdb..4211459c4a 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', } meta = { @@ -47,11 +47,13 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) +input_layer = par["layer_input"] + print("Fit to train data") -pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) +pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) +input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index f166f6a755..4e116a7f1e 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -12,6 +12,10 @@ functionality: paper_doi: "10.1016/0004-3702(89)90049-0" code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" arguments: + - name: "--layer_input" + type: string + default: "log_cpm" + description: Which layer to use as input. - name: "--hidden_layer_sizes" type: "integer" multiple: true diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 47f2be50e0..4c5dd4e60e 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/dataset_cpm_train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/dataset_cpm_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', } meta = { @@ -48,11 +48,13 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) +input_layer = par["layer_input"] + print("Fit to train data") -pipeline.fit(input_train.layers["lognorm"], input_train.obs["label"].astype(str)) +pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers["lognorm"]) +input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index ba54eec185..0d73e7324d 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - 'input_prediction': 'resources_test/label_projection/pancreas/dataset_cpm_knn.h5ad', - 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_solution.h5ad', + 'input_prediction': 'resources_test/label_projection/pancreas/knn.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/solution.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 9132a4e934..50aad56d94 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - 'input_prediction': 'resources_test/label_projection/pancreas/dataset_cpm_knn.h5ad', - 'input_solution': 'resources_test/label_projection/pancreas/dataset_cpm_solution.h5ad', + 'input_prediction': 'resources_test/label_projection/pancreas/knn.h5ad', + 'input_solution': 'resources_test/label_projection/pancreas/solution.h5ad', 'average': 'weighted', 'output': 'output.h5ad' } diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 1a16651c78..95e548c4a0 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset_cpm.h5ad +RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/label_projection/pancreas if [ ! -f $RAW_DATA ]; then @@ -22,19 +22,19 @@ mkdir -p $DATASET_DIR # censor dataset bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ --input $RAW_DATA \ - --output_train $DATASET_DIR/dataset_cpm_train.h5ad \ - --output_test $DATASET_DIR/dataset_cpm_test.h5ad \ - --output_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ + --output_train $DATASET_DIR/train.h5ad \ + --output_test $DATASET_DIR/test.h5ad \ + --output_solution $DATASET_DIR/solution.h5ad \ --seed 123 # run one method bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ - --input_train $DATASET_DIR/dataset_cpm_train.h5ad \ - --input_test $DATASET_DIR/dataset_cpm_test.h5ad \ - --output $DATASET_DIR/dataset_cpm_knn.h5ad + --input_train $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output $DATASET_DIR/knn.h5ad # run one metric bin/viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/dataset_cpm_knn.h5ad \ - --input_solution $DATASET_DIR/dataset_cpm_solution.h5ad \ - --output $DATASET_DIR/dataset_cpm_knn_accuracy.h5ad + --input_prediction $DATASET_DIR/knn.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output $DATASET_DIR/knn_accuracy.h5ad From 1fe2f3388fbbfa3ead240919f6159008d0113262 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 12:56:48 +0100 Subject: [PATCH 0313/1233] delete unused files Former-commit-id: 3c85e86b195ffb5a02dee84ac565d12ce912a0e8 --- src/common/workflows/utils.nf | 57 ------------------- .../data_processing/censoring/test.py | 30 ---------- 2 files changed, 87 deletions(-) delete mode 100644 src/common/workflows/utils.nf delete mode 100644 src/label_projection/data_processing/censoring/test.py diff --git a/src/common/workflows/utils.nf b/src/common/workflows/utils.nf deleted file mode 100644 index b985fcdc3b..0000000000 --- a/src/common/workflows/utils.nf +++ /dev/null @@ -1,57 +0,0 @@ -// helper functions -// set id of event to basename of input file -//def updateID = { [ it[1].baseName, it[1], it[2] ] } -def updateID(triplet) { - return [ triplet[1].baseName, triplet[1], triplet[2] ] - } - - -// turn list of triplets into triplet of list -//def combineResults = { it -> [ "combined", it.collect{ a -> a[1] }, params ] } -def combineResults(list) { - return [ "combined", list.collect{ a -> a[1] }, params ] - } - - -// A functional approach to 'updating' a value for an option in the params Map. -def overrideOptionValue(triplet, _key, _option, _value) { - mapCopy = triplet[2].toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy - - return [ - triplet[0], - triplet[1], - triplet[2].collectEntries{ function, v1 -> - (function == _key) - ? [ (function) : v1.collectEntries{ k2, v2 -> - (k2 == "arguments") - ? [ (k2) : v2.collectEntries{ k3, v3 -> - (k3 == _option) - ? [ (k3) : v3 + [ "value" : _value ] ] - : [ (k3) : v3 ] - } ] - : [ (k2) : v2 ] - } ] - : [ (function), v1 ] - } - ] -} - -// A functional approach to 'updating' a value for an option in the params Map. -def overrideParams(params, _key, _option, _value) { - mapCopy = params.toConfigObject().toMap() // As mentioned on https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/groovy/nextflow/config/CascadingConfig.groovy - - return params.collectEntries{ function, v1 -> - (function == _key) - ? [ (function) : v1.collectEntries{ k2, v2 -> - (k2 == "arguments") - ? [ (k2) : v2.collectEntries{ k3, v3 -> - (k3 == _option) - ? [ (k3) : v3 + [ "value" : _value ] ] - : [ (k3) : v3 ] - } ] - : [ (k2) : v2 ] - } ] - : [ (function), v1 ] - } - -} \ No newline at end of file diff --git a/src/label_projection/data_processing/censoring/test.py b/src/label_projection/data_processing/censoring/test.py deleted file mode 100644 index bb6e01fe40..0000000000 --- a/src/label_projection/data_processing/censoring/test.py +++ /dev/null @@ -1,30 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -## VIASH START -## VIASH END - -# TODO: update - -INPUT = f"{meta['resources_dir']}/pancreas/toy_preprocessed_data.h5ad" -OUTPUT = "preprocessed.h5ad" -METHODS = ["batch", "random", "random_with_noise"] - -for method in METHODS: - print(">> Running script for {} method".format(method)) - out = subprocess.check_output([ - meta["executable"], - "--input", INPUT, - "--method", method, - "--output", OUTPUT - ]).decode("utf-8") - - print(">> Checking whether file exists") - assert path.exists(OUTPUT) - - print(">> Check that test output fits expected API") - adata = sc.read_h5ad(OUTPUT) - assert (500, 468) == adata.X.shape, "processed result data shape {}".format(adata.X.shape) - assert "batch" in adata.obs - assert "is_train" in adata.obs From 967b6456db1bfa8e28da5aafec44cdbb636a42ef Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 10 Nov 2022 12:57:26 +0100 Subject: [PATCH 0314/1233] Switch to develop again Former-commit-id: 193d859b2d46c2fe4378773d4e52b8eea08e197d --- bin/init | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/init b/bin/init index 019ac17ac8..8a276b14ee 100755 --- a/bin/init +++ b/bin/init @@ -10,7 +10,7 @@ curl -fsSL get.viash.io | bash -s -- \ --registry ghcr.io \ --organisation openproblems-bio \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag 0.6.3 + --tag develop # automatically export the workflow helper NXF_UTILS=src/nxf_utils From e8bd580a9854987cdd7bd33a60dd3635d7f40cfe Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 14 Nov 2022 16:43:22 +0100 Subject: [PATCH 0315/1233] rename censor to split Former-commit-id: 11c62765b69bb96ccff3c1558c0c651d07c348a2 --- CHANGELOG.md | 4 +- src/label_projection/README.md | 130 +++++++++--------- src/label_projection/api/anndata_test.yaml | 2 +- .../{comp_censoring.yaml => comp_split.yaml} | 0 .../data_processing/anndata_loader.tsv | 6 - .../methods/knn_classifier/config.vsh.yaml | 1 - .../resources_test_scripts/pancreas.sh | 4 +- .../censoring => split}/config.vsh.yaml | 6 +- .../censoring => split}/script.py | 2 +- src/label_projection/workflows/run/main.nf | 40 +++--- .../workflows/run/nextflow.config | 13 +- 11 files changed, 97 insertions(+), 111 deletions(-) rename src/label_projection/api/{comp_censoring.yaml => comp_split.yaml} (100%) delete mode 100644 src/label_projection/data_processing/anndata_loader.tsv rename src/label_projection/{data_processing/censoring => split}/config.vsh.yaml (87%) rename src/label_projection/{data_processing/censoring => split}/script.py (96%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 97db115a1b..430ec26d96 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,9 +22,9 @@ ### NEW FUNCTIONALITY -* API: Created an explicit api definition for the censor, method and metric components. +* API: Created an explicit api definition for the split, method and metric components. -* `data_processing/censoring`: Added a censoring component. +* `data_processing/split`: Added a component for splitting raw datasets into task-ready dataset objects. * `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 617e953dac..de39eceadd 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -23,9 +23,9 @@ id="toc-train.h5ad-training-data">train.h5ad: Training data - Component API - - censoring - method - metric + - split # Label Projection @@ -96,19 +96,19 @@ flowchart LR anndata_solution(solution.h5ad) anndata_test(test.h5ad) anndata_train(train.h5ad) - comp_censoring[/censoring/] comp_method[/method/] comp_metric[/metric/] - anndata_dataset---comp_censoring + comp_split[/split/] anndata_train---comp_method anndata_test---comp_method anndata_solution---comp_metric anndata_prediction---comp_metric - comp_censoring-->anndata_train - comp_censoring-->anndata_test - comp_censoring-->anndata_solution + anndata_dataset---comp_split comp_method-->anndata_prediction comp_metric-->anndata_score + comp_split-->anndata_train + comp_split-->anndata_test + comp_split-->anndata_solution ``` ## File format API @@ -119,18 +119,18 @@ A preprocessed dataset Used in: -- [censoring](#censoring): input (as input) +- [split](#split): input (as input) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | label | double | Ground truth cell type labels | -| obs | batch | double | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| struct | name | type | description | +|:-------|:------------------|:--------|:-------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | log_cpm | double | CPM normalized counts, log transformed | +| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| obs | label | double | Ground truth cell type labels | +| obs | batch | double | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | ### `prediction.h5ad`: Prediction @@ -143,12 +143,11 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:---------------|:-------|:--------------------------------------------------------------------| -| obs | label_pred | string | Predicted labels for the test cells. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | method_id | string | A unique identifier for the method | +| struct | name | type | description | +|:-------|:-----------|:-------|:-------------------------------------| +| obs | label_pred | string | Predicted labels for the test cells. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | ### `score.h5ad`: Score @@ -160,13 +159,12 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:---------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | +| struct | name | type | description | +|:-------|:--------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | ### `solution.h5ad`: Solution @@ -174,38 +172,38 @@ The solution for the test data Used in: -- [censoring](#censoring): output_solution (as output) - [metric](#metric): input_solution (as input) +- [split](#split): output_solution (as output) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| struct | name | type | description | +|:-------|:------------------|:--------|:-------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | log_cpm | double | CPM normalized counts, log transformed | +| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | ### `test.h5ad`: Test data -The censored test data +The test data (without labels) Used in: -- [censoring](#censoring): output_test (as output) - [method](#method): input_test (as input) +- [split](#split): output_test (as output) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| struct | name | type | description | +|:-------|:------------------|:--------|:-------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | log_cpm | double | CPM normalized counts, log transformed | +| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | ### `train.h5ad`: Training data @@ -213,33 +211,22 @@ The training data Used in: -- [censoring](#censoring): output_train (as output) - [method](#method): input_train (as input) +- [split](#split): output_train (as output) Slots: -| struct | name | type | description | -|:-------|:---------------|:--------|:--------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | lognorm | double | Log-transformed normalised counts | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | raw_dataset_id | string | A unique identifier for the original dataset (before preprocessing) | +| struct | name | type | description | +|:-------|:------------------|:--------|:-------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | log_cpm | double | CPM normalized counts, log transformed | +| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| uns | dataset_id | string | A unique identifier for the dataset | ## Component API -### `censoring` - -Arguments: - -| Name | File format | Direction | Description | -|:--------------------|:--------------|:----------|:---------------------| -| `--input` | dataset.h5ad | input | Preprocessed dataset | -| `--output_train` | train.h5ad | output | Training data | -| `--output_test` | test.h5ad | output | Test data | -| `--output_solution` | solution.h5ad | output | Solution | - ### `method` Arguments: @@ -259,3 +246,14 @@ Arguments: | `--input_solution` | solution.h5ad | input | Solution | | `--input_prediction` | prediction.h5ad | input | Prediction | | `--output` | score.h5ad | output | Score | + +### `split` + +Arguments: + +| Name | File format | Direction | Description | +|:--------------------|:--------------|:----------|:---------------------| +| `--input` | dataset.h5ad | input | Preprocessed dataset | +| `--output_train` | train.h5ad | output | Training data | +| `--output_test` | test.h5ad | output | Test data | +| `--output_solution` | solution.h5ad | output | Solution | diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index 94e23b6d90..3b506675d1 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -1,5 +1,5 @@ type: file -description: "The censored test data" +description: "The test data (without labels)" example: "test.h5ad" info: short_description: "Test data" diff --git a/src/label_projection/api/comp_censoring.yaml b/src/label_projection/api/comp_split.yaml similarity index 100% rename from src/label_projection/api/comp_censoring.yaml rename to src/label_projection/api/comp_split.yaml diff --git a/src/label_projection/data_processing/anndata_loader.tsv b/src/label_projection/data_processing/anndata_loader.tsv deleted file mode 100644 index 968aba81dd..0000000000 --- a/src/label_projection/data_processing/anndata_loader.tsv +++ /dev/null @@ -1,6 +0,0 @@ -processor name url obs_label obs_batch obs_tissue -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA -anndata_loader cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue -anndata_loader zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA -anndata_loader tabula_muris_senis_facs_lung https://ndownloader.figshare.com/files/23872619 free_annotation mouse.id NA -anndata_loader tabula_muris_senis_droplet_lung https://ndownloader.figshare.com/files/23873012 free_annotation mouse.id NA diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index d5bbf4535f..90a92ab978 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,7 +1,6 @@ __inherits__: ../../api/comp_method.yaml functionality: name: "knn_classifier" - namespace: "label_projection/methods" description: "K-Nearest Neighbors classifier" info: type: method diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 95e548c4a0..dc7f9c4a19 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -19,8 +19,8 @@ fi mkdir -p $DATASET_DIR -# censor dataset -bin/viash run src/label_projection/data_processing/censoring/config.vsh.yaml -- \ +# split dataset +bin/viash run src/label_projection/split/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ diff --git a/src/label_projection/data_processing/censoring/config.vsh.yaml b/src/label_projection/split/config.vsh.yaml similarity index 87% rename from src/label_projection/data_processing/censoring/config.vsh.yaml rename to src/label_projection/split/config.vsh.yaml index cf2d170b3f..0e76bd7447 100644 --- a/src/label_projection/data_processing/censoring/config.vsh.yaml +++ b/src/label_projection/split/config.vsh.yaml @@ -1,7 +1,7 @@ -__inherits__: ../../api/comp_censoring.yaml +__inherits__: ../../api/comp_split.yaml functionality: - name: "censoring" - namespace: "label_projection/data_processing" + name: "split" + namespace: "label_projection" arguments: - name: "--method" type: "string" diff --git a/src/label_projection/data_processing/censoring/script.py b/src/label_projection/split/script.py similarity index 96% rename from src/label_projection/data_processing/censoring/script.py rename to src/label_projection/split/script.py index 5830fbab04..38bd9a2e3d 100644 --- a/src/label_projection/data_processing/censoring/script.py +++ b/src/label_projection/split/script.py @@ -14,7 +14,7 @@ 'output_solution': 'solution.h5ad' } meta = { - 'resources_dir': 'src/label_projection/data_processing/censoring' + 'resources_dir': 'src/label_projection/split' } ## VIASH END diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 06e632a00b..22281f1d31 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -2,33 +2,33 @@ nextflow.enable.dsl=2 targetDir = "${params.rootDir}/target/nextflow" -// import dataset loaders -include { download } from "$targetDir/common/dataset_loader/download/main.nf" +// // import dataset loaders +// include { download } from "$targetDir/common/dataset_loader/download/main.nf" -// import preprocess -include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" -// for tests -include { subsample } from "$targetDir/label_projection/data_processing/subsample/main.nf" +// // import preprocess +// include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" +// // for tests +// include { subsample } from "$targetDir/label_projection/data_processing/subsample/main.nf" -// import normalization -include { log_scran_pooling } from "$targetDir/label_projection/data_processing/normalize/scran/log_scran_pooling/main.nf" -include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" +// // import normalization +// include { log_scran_pooling } from "$targetDir/label_projection/data_processing/normalize/scran/log_scran_pooling/main.nf" +// include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" // import methods -include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" -include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" -include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" -include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" -include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" +include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" +include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" +include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" +include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" +include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" -include { scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scanvi_hvg/main.nf" -include { scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scanvi_all_genes/main.nf" -include { scarches_scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_all_genes/main.nf" -include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_hvg/main.nf" +// include { scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scanvi_hvg/main.nf" +// include { scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scanvi_all_genes/main.nf" +// include { scarches_scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_all_genes/main.nf" +// include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_hvg/main.nf" // import metrics -include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" -include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" +include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" +include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" // import helper functions include { extract_scores } from "$targetDir/common/extract_scores/main.nf" diff --git a/src/label_projection/workflows/run/nextflow.config b/src/label_projection/workflows/run/nextflow.config index 4e1452b19d..425fb92fed 100644 --- a/src/label_projection/workflows/run/nextflow.config +++ b/src/label_projection/workflows/run/nextflow.config @@ -2,15 +2,10 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } -// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() } -// set default container & default labels -process { - container = 'nextflow/bash:latest' - - withLabel: highmem { memory = 50.Gb } - withLabel: highcpu { cpus = 20 } -} +// include common settings +includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/workflows/utils/labels.config") From 5f1ee3418f5b712136f66c7b1a6b7354c13a81df Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 16:02:13 +0100 Subject: [PATCH 0316/1233] move normalisation methods Former-commit-id: 573b9df16ba8a8815cd3af9d6dfeec6db9549ade --- src/datasets/api/anndata_dataset.yaml | 35 ++++++++ src/datasets/api/anndata_raw_dataset.yaml | 29 +++++++ src/datasets/api/comp_dataset_loader.yaml | 6 ++ src/datasets/api/comp_normalization.yaml | 85 +++++++++++++++++++ .../normalization/log_cpm/config.vsh.yaml | 26 ++++++ src/datasets/normalization/log_cpm/script.py | 32 +++++++ .../log_scran_pooling/config.vsh.yaml | 28 ++++++ .../normalization/log_scran_pooling/script.R | 29 +++++++ 8 files changed, 270 insertions(+) create mode 100644 src/datasets/api/anndata_dataset.yaml create mode 100644 src/datasets/api/anndata_raw_dataset.yaml create mode 100644 src/datasets/api/comp_dataset_loader.yaml create mode 100644 src/datasets/api/comp_normalization.yaml create mode 100644 src/datasets/normalization/log_cpm/config.vsh.yaml create mode 100644 src/datasets/normalization/log_cpm/script.py create mode 100644 src/datasets/normalization/log_scran_pooling/config.vsh.yaml create mode 100644 src/datasets/normalization/log_scran_pooling/script.R diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml new file mode 100644 index 0000000000..21694f6745 --- /dev/null +++ b/src/datasets/api/anndata_dataset.yaml @@ -0,0 +1,35 @@ +type: file +description: "A dataset" +example: "dataset.h5ad" +info: + short_description: "Dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: log_cpm + description: CPM normalized counts, log transformed + - type: double + name: log_scran_pooling + description: Scran pooling normalized counts, log transformed + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/datasets/api/anndata_raw_dataset.yaml b/src/datasets/api/anndata_raw_dataset.yaml new file mode 100644 index 0000000000..37c41a3003 --- /dev/null +++ b/src/datasets/api/anndata_raw_dataset.yaml @@ -0,0 +1,29 @@ +type: file +description: "A raw dataset" +example: "raw_dataset.h5ad" +info: + short_description: "Raw dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml new file mode 100644 index 0000000000..5e8e85d226 --- /dev/null +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -0,0 +1,6 @@ +functionality: + arguments: + - name: "--output" + direction: output + __inherits__: anndata_raw_dataset.yaml + diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml new file mode 100644 index 0000000000..f0c786e115 --- /dev/null +++ b/src/datasets/api/comp_normalization.yaml @@ -0,0 +1,85 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_raw_dataset.yaml + - name: "--output" + type: file + description: "A preprocessed dataset" + example: "preprocessed.h5ad" + info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: $par_layer_output + description: Log-transformed normalised counts + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + direction: output + + # not including this because we need to override the default + # - name: "--layer_output" + # type: string + # default: "log_cpm" + # description: The name of the layer in which to store the log normalized data. + test_resources: + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + output_path = "output.h5ad" + output_layer = "norm_layer" + + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, + "--layer_output", output_layer + ] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + print("input:", input) + print("output:", output) + + print(">> Checking whether output data structures were added") + assert output_layer in output.layers + + print("Checking whether data from input was copied properly to output") + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") + - path: ../../../../resources_test/common/pancreas + diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml new file mode 100644 index 0000000000..6b7121a1a7 --- /dev/null +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -0,0 +1,26 @@ +__inherits__: ../../api/comp_normalization.yaml +functionality: + name: "log_cpm" + namespace: "common/normalization" + description: "Normalize data using Log CPM" + arguments: + - name: "--layer_output" + type: string + default: "log_cpm" + description: The name of the layer in which to store the log normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors_log_cpm" + description: In which .obs slot to store the size factors. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/datasets/normalization/log_cpm/script.py b/src/datasets/normalization/log_cpm/script.py new file mode 100644 index 0000000000..a080fdc643 --- /dev/null +++ b/src/datasets/normalization/log_cpm/script.py @@ -0,0 +1,32 @@ +import scanpy as sc + +## VIASH START +par = { + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output': "output.h5ad", + 'layer_output': "log_cpm", + 'obs_size_factors': "log_cpm_size_factors" +} +meta = { + "functionality_name": "normalize_log_cpm" +} +## VIASH END + +print(">> Load data") +adata = sc.read_h5ad(par['input']) + +print(">> Normalize data") +norm = sc.pp.normalize_total( + adata, + target_sum=1e6, + layer="counts", + inplace=False +) +lognorm = sc.pp.log1p(norm["X"]) + +print(">> Store output in adata") +adata.layers[par["layer_output"]] = lognorm +adata.obs[par["obs_size_factors"]] = norm["norm_factor"] + +print(">> Write data") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml new file mode 100644 index 0000000000..ad0eea1ca6 --- /dev/null +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -0,0 +1,28 @@ +__inherits__: ../../api/comp_normalization.yaml +functionality: + name: "log_scran_pooling" + namespace: "common/normalization" + description: "Normalize data using scran pooling" + arguments: + - name: "--layer_output" + type: string + default: "log_scran_pooling" + description: The name of the layer in which to store the log normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors_log_scran_pooling" + description: In which .obs slot to store the size factors. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ Matrix, scran, BiocParallel, rlang, anndata, bit64 ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata<0.8, scanpy ] + - type: nextflow diff --git a/src/datasets/normalization/log_scran_pooling/script.R b/src/datasets/normalization/log_scran_pooling/script.R new file mode 100644 index 0000000000..5885785d96 --- /dev/null +++ b/src/datasets/normalization/log_scran_pooling/script.R @@ -0,0 +1,29 @@ +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +requireNamespace("scran", quietly = TRUE) +requireNamespace("BiocParallel", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input = "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", + output = "output.scran.h5ad", + layer_output = "log_scran_pooling", + obs_size_factors = "size_factors_log_scran_pooling" +) +## VIASH END + +cat(">> Load data\n") +adata <- anndata::read_h5ad(par$input) +counts <- as.matrix(t(adata$layers[["counts"]])) + +cat(">> Normalizing data\n") +size_factors <- scran::calculateSumFactors(counts, min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) +lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) + +cat(">> Storing in anndata\n") +adata$obs[[par$obs_size_factors]] <- size_factors +adata$layers[[par$layer_output]] <- lognorm + +cat(">> Writing to file\n") +zzz <- adata$write_h5ad(par$output, compression = "gzip") From 17cb09db9c94352af8774cc0b60e2daa533c5853 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 16:03:02 +0100 Subject: [PATCH 0317/1233] add sqrt_cpm Former-commit-id: ea5b4bfb8907bf3dc521ed54464b3c7818e2ad86 --- .../normalization/sqrt_cpm/config.vsh.yaml | 26 +++++++++++++++ src/datasets/normalization/sqrt_cpm/script.py | 33 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 src/datasets/normalization/sqrt_cpm/config.vsh.yaml create mode 100644 src/datasets/normalization/sqrt_cpm/script.py diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml new file mode 100644 index 0000000000..3cc9f4dae3 --- /dev/null +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -0,0 +1,26 @@ +__inherits__: ../../api/comp_normalization.yaml +functionality: + name: "sqrt_cpm" + namespace: "common/normalization" + description: "Normalize data using Log Sqrt" + arguments: + - name: "--layer_output" + type: string + default: "sqrt_cpm" + description: The name of the layer in which to store the log normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors_sqrt_cpm" + description: In which .obs slot to store the size factors. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/datasets/normalization/sqrt_cpm/script.py b/src/datasets/normalization/sqrt_cpm/script.py new file mode 100644 index 0000000000..517d3cdcce --- /dev/null +++ b/src/datasets/normalization/sqrt_cpm/script.py @@ -0,0 +1,33 @@ +import scanpy as sc +import numpy as np + +## VIASH START +par = { + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output': "output.h5ad", + 'layer_output': "sqrt_cpm", + 'obs_size_factors': "size_factors_sqrt_cpm" +} +meta = { + "functionality_name": "normalize_sqrt_cpm" +} +## VIASH END + +print(">> Load data") +adata = sc.read_h5ad(par['input']) + +print(">> Normalize data") +norm = sc.pp.normalize_total( + adata, + target_sum=1e6, + layer="counts", + inplace=False +) +lognorm = np.sqrt(norm["X"]) + +print(">> Store output in adata") +adata.layers[par["layer_output"]] = lognorm +adata.obs[par["obs_size_factors"]] = norm["norm_factor"] + +print(">> Write data") +adata.write_h5ad(par['output'], compression="gzip") From f262803a0e158c284a47508667aa3508260d02ab Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 16:04:59 +0100 Subject: [PATCH 0318/1233] initial attempt at an openproblemsv1 dataloader Former-commit-id: 17cebeb8a794ed691a743f5c5df0e0e696131be6 --- .../loaders/openproblems_v1/config.vsh.yaml | 50 ++++++++++++ .../loaders/openproblems_v1/datasets.tsv | 9 +++ .../loaders/openproblems_v1/script.py | 81 +++++++++++++++++++ src/datasets/loaders/openproblems_v1/test.py | 44 ++++++++++ 4 files changed, 184 insertions(+) create mode 100644 src/datasets/loaders/openproblems_v1/config.vsh.yaml create mode 100644 src/datasets/loaders/openproblems_v1/datasets.tsv create mode 100644 src/datasets/loaders/openproblems_v1/script.py create mode 100644 src/datasets/loaders/openproblems_v1/test.py diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml new file mode 100644 index 0000000000..8016e749de --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -0,0 +1,50 @@ +functionality: + name: "openproblems_v1" + namespace: "datasets/loaders/dataset_loader" + description: "Fetch a dataset from OpenProblems v1" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "In which layer to find the counts matrix. Leave undefined to use `.X`." + example: counts + - name: "--sparse" + type: boolean + default: true + description: Convert layers to a sparse CSR format. + - name: Outputs + arguments: + - name: "--output" + __inherits__: ../../api/anndata_raw_dataset.yaml + direction: "output" + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + github: + - openproblems-bio/openproblems + - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/datasets.tsv b/src/datasets/loaders/openproblems_v1/datasets.tsv new file mode 100644 index 0000000000..1965ee50d2 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/datasets.tsv @@ -0,0 +1,9 @@ +id url obs_celltype obs_batch obs_tissue +pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA +immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue +pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA +tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA +cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue +zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA +tabula_muris_senis_facs_lung https://ndownloader.figshare.com/files/23872619 free_annotation mouse.id NA +tabula_muris_senis_droplet_lung https://ndownloader.figshare.com/files/23873012 free_annotation mouse.id NA diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py new file mode 100644 index 0000000000..37d9863148 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -0,0 +1,81 @@ +print("Importing libraries") +import openproblems as op +import scanpy as sc +import scipy + +## VIASH START +par = { + "id": "pancreas", + "obs_celltype": "celltype", + "obs_batch": "tech", + "obs_tissue": "tissue", + "layer_counts": "counts", + "output": "test_data.h5ad", + "layer_counts_output": "counts" +} +## VIASH END + +dataset_funs = { + 'allen_brain_atlas': op.data.allen_brain_atlas.load_mouse_brain_atlas, + 'cengen': op.data.cengen.load_cengen, + 'immune_cells': op.data.immune_cells.load_immune, + 'mouse_blood_olssen_labelled': op.data.mouse_blood_olssen_labelled.load_olsson_2016_mouse_blood, + 'mouse_hspc_nestorowa2016': op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, + 'pancreas': op.data.pancreas.load_pancreas, + 'tabula_muris_senis': op.data.tabula_muris_senis.load_tabula_muris_senis, + 'tenx_5k_pbmc': op.data.tenx.load_tenx_1k_pbmc, + 'tenx_5k_pbmc': op.data.tenx.load_tenx_5k_pbmc, + 'tnbc_wu2021': op.data.tnbc_wu2021.load_tnbc_data, + # 'Wagner_2018_zebrafish_embryo_CRISPR': op.data.Wagner_2018_zebrafish_embryo_CRISPR.load_zebrafish_chd_tyr, + 'zebrafish': op.data.zebrafish.load_zebrafish +} + +adata = dataset_funs[par['id']]() + +print("Setting .uns['dataset_id']") +adata.uns["dataset_id"] = par["id"] + +print("Setting .obs['celltype']") +if par["obs_celltype"]: + if par["obs_celltype"] in adata.obs: + adata.obs["celltype"] = adata.obs[par["obs_celltype"]] + else: + print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.") + +print("Setting .obs['batch']") +if par["obs_batch"]: + if par["obs_batch"] in adata.obs: + adata.obs["batch"] = adata.obs[par["obs_batch"]] + else: + print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.") + +print("Setting .obs['tissue']") +if par["obs_tissue"]: + if par["obs_tissue"] in adata.obs: + adata.obs["tissue"] = adata.obs[par["obs_tissue"]] + else: + print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") + +if par["layer_counts"] and par["layer_counts"] in adata.layers: + print(f" Temporarily copying .layers['{par['layer_counts']}'] to .X") + adata.X = adata.layers[par["layer_counts"]] + del adata.layers[par["layer_counts"]] + +if par["sparse"] and not scipy.sparse.issparse(adata.X): + print(" Make counts sparse") + adata.X = scipy.sparse.csr_matrix(adata.X) + +print(" Removing empty genes") +sc.pp.filter_genes(adata, min_cells=1) + +print(" Removing empty cells") +sc.pp.filter_cells(adata, min_counts=2) + +if par["layer_counts_output"]: + print(f" Copying .X back to .layers['{par['layer_counts_output']}']") + adata.layers[par["layer_counts_output"]] = adata.X + # todo: make sure X is sparse + del adata.X + +print("Writing adata to file") +adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py new file mode 100644 index 0000000000..274cf8510b --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -0,0 +1,44 @@ +from os import path +import subprocess +import scanpy as sc + +name = "pancreas" +output = "dataset.h5ad" +obs_celltype = "celltype" +obs_batch = "tech" + +layer_counts_output = "foobar" + +print(">> Running script") +out = subprocess.check_output([ + meta["executable"], + "--id", name, + "--obs_celltype", obs_celltype, + "--obs_batch", obs_batch, + "--layer_counts", "counts", + "--layer_counts_output", layer_counts_output, + "--output", output +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output) + +print(">> Read output anndata") +adata = sc.read_h5ad(output) + +print(adata) + +print(">> Check that output fits expected API") +if layer_counts_output is not None: + assert adata.X is None + assert layer_counts_output in adata.layers +else: + assert adata.X is not None + assert layer_counts_output not in adata.layers +assert adata.uns["dataset_id"] == name +if obs_celltype: + assert "celltype" in adata.obs.columns +if obs_batch: + assert "batch" in adata.obs.columns + +print(">> All tests passed successfully") From 99c6dbde408cd08d26fdd46ab9561c9669092c1d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 16:09:35 +0100 Subject: [PATCH 0319/1233] fix split componet Former-commit-id: 656f62c5d8c0b5cb6fa7f6b36f2aee54677db457 --- src/label_projection/split/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/split/config.vsh.yaml b/src/label_projection/split/config.vsh.yaml index 0e76bd7447..bab16ab739 100644 --- a/src/label_projection/split/config.vsh.yaml +++ b/src/label_projection/split/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_split.yaml +__inherits__: ../api/comp_split.yaml functionality: name: "split" namespace: "label_projection" From 9ed6629a739735a13be61c18b183ffa9ffba54cd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 16:18:09 +0100 Subject: [PATCH 0320/1233] attempt to run openproblemsv1 in batch Former-commit-id: c8dff200ff8988595ccc2b6b441d30b23639aedf --- .../loaders/openproblems_v1/config.vsh.yaml | 2 +- .../loaders/openproblems_v1/datasets.csv | 7 +++++++ src/datasets/loaders/openproblems_v1/run.sh | 17 +++++++++++++++++ src/datasets/loaders/openproblems_v1/script.py | 2 +- 4 files changed, 26 insertions(+), 2 deletions(-) create mode 100644 src/datasets/loaders/openproblems_v1/datasets.csv create mode 100755 src/datasets/loaders/openproblems_v1/run.sh diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 8016e749de..2be7e4be1b 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "openproblems_v1" - namespace: "datasets/loaders/dataset_loader" + namespace: "datasets/loaders" description: "Fetch a dataset from OpenProblems v1" argument_groups: - name: Inputs diff --git a/src/datasets/loaders/openproblems_v1/datasets.csv b/src/datasets/loaders/openproblems_v1/datasets.csv new file mode 100644 index 0000000000..12c76e64c1 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/datasets.csv @@ -0,0 +1,7 @@ +id,obs_celltype,obs_batch,obs_tissue,layer_counts +pancreas,celltype,tech,,counts +immune_cells,final_annotation,batch,tissue,counts +tenx_1k_pbmc,,,,counts +tenx_5k_pbmc,,,,counts +cengen,cell_type,experiment_code,tissue,counts +zebrafish,cell_type,lab,,counts \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/run.sh b/src/datasets/loaders/openproblems_v1/run.sh new file mode 100755 index 0000000000..db158b7521 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/run.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script target/nextflow/datasets/loaders/openproblems_v1/main.nf \ + -resume \ + -profile docker \ + --param_list src/datasets/loaders/openproblems_v1/datasets.csv \ + --publish_dir output/datasets \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 37d9863148..416cd2fc87 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -23,7 +23,7 @@ 'mouse_hspc_nestorowa2016': op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, 'pancreas': op.data.pancreas.load_pancreas, 'tabula_muris_senis': op.data.tabula_muris_senis.load_tabula_muris_senis, - 'tenx_5k_pbmc': op.data.tenx.load_tenx_1k_pbmc, + 'tenx_1k_pbmc': op.data.tenx.load_tenx_1k_pbmc, 'tenx_5k_pbmc': op.data.tenx.load_tenx_5k_pbmc, 'tnbc_wu2021': op.data.tnbc_wu2021.load_tnbc_data, # 'Wagner_2018_zebrafish_embryo_CRISPR': op.data.Wagner_2018_zebrafish_embryo_CRISPR.load_zebrafish_chd_tyr, From 4553e201af535ad977bf00e33f5b6b9794832f4b Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 15 Nov 2022 17:50:47 +0100 Subject: [PATCH 0321/1233] add api files Former-commit-id: be2ca9b8a1635d034c8a0c9bd501872c0d57915f --- .../api/anndata_raw_dataset.yaml | 14 +++++++++++ .../api/anndata_reduced.yaml | 25 +++++++++++++++++++ .../api/anndata_score.yaml | 24 ++++++++++++++++++ .../api/comp_method.yaml | 7 ++++++ .../api/comp_metric.yaml | 7 ++++++ 5 files changed, 77 insertions(+) create mode 100644 src/dimensionality_reduction/api/anndata_raw_dataset.yaml create mode 100644 src/dimensionality_reduction/api/anndata_reduced.yaml create mode 100644 src/dimensionality_reduction/api/anndata_score.yaml create mode 100644 src/dimensionality_reduction/api/comp_method.yaml create mode 100644 src/dimensionality_reduction/api/comp_metric.yaml diff --git a/src/dimensionality_reduction/api/anndata_raw_dataset.yaml b/src/dimensionality_reduction/api/anndata_raw_dataset.yaml new file mode 100644 index 0000000000..781304f5e9 --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_raw_dataset.yaml @@ -0,0 +1,14 @@ +type: file +description: A raw dataset +example: "raw_dataset.h5ad" +info: + short_description: "Raw dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" \ No newline at end of file diff --git a/src/dimensionality_reduction/api/anndata_reduced.yaml b/src/dimensionality_reduction/api/anndata_reduced.yaml new file mode 100644 index 0000000000..de772c35ec --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_reduced.yaml @@ -0,0 +1,25 @@ +type: file +description: "A dimensionality reduced dataset" +example: "reduced.h5ad" +info: + short_description: "2D reduced" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obsm: + - type: double + name: dim_red + description: dimensionally-reduced 2D embedding coordinates + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: method_id + description: "A unique identifier for the method" + - type: string + name: param_set_id + description: "A unique identifier for the parameter set" + diff --git a/src/dimensionality_reduction/api/anndata_score.yaml b/src/dimensionality_reduction/api/anndata_score.yaml new file mode 100644 index 0000000000..309918348c --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_score.yaml @@ -0,0 +1,24 @@ +type: file +description: "Metric score file" +example: "score.h5ad" +info: + short_description: "Score" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: method_id + description: "A unique identifier for the method" + - type: string + name: param_set_id + description: "A unique identifier for the parameter set" + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml new file mode 100644 index 0000000000..1bcfdf1cdf --- /dev/null +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -0,0 +1,7 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_dataset.yaml + - name: "--output" + __inherits__: anndata_reduced.yaml + direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml new file mode 100644 index 0000000000..d0624226f6 --- /dev/null +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -0,0 +1,7 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_reduced.yaml + - name: "--output" + __inherits__: anndata_score.yaml + direction: output \ No newline at end of file From 58a01f2442f867493240d6eafbe67cca91614a58 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 15 Nov 2022 17:56:14 +0100 Subject: [PATCH 0322/1233] add authors Former-commit-id: 0f61c13dd07267305386db754eae77a6cb98071a --- src/dimensionality_reduction/api/authors.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 src/dimensionality_reduction/api/authors.yaml diff --git a/src/dimensionality_reduction/api/authors.yaml b/src/dimensionality_reduction/api/authors.yaml new file mode 100644 index 0000000000..d5a676935d --- /dev/null +++ b/src/dimensionality_reduction/api/authors.yaml @@ -0,0 +1,9 @@ +functionality: + authors: + - name: "Juan A. Cordero Varela" + roles: [ contributor ] + props: { github: jacorvar, orcid: 0000-0002-7373-5433} + - name: Robrecht Cannoodt + roles: [ author ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + From c686d9d94b6b322c2b111b49c4bc67b4d620e868 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:11:56 +0100 Subject: [PATCH 0323/1233] delete old components Former-commit-id: 34611b4dfa9e22342359f0ea5cb80dc9a5e8afd1 --- src/common/api/anndata_dataset.yaml | 35 -------- src/common/api/anndata_raw_dataset.yaml | 29 ------- src/common/api/comp_normalization.yaml | 85 ------------------- .../normalization/log_cpm/config.vsh.yaml | 26 ------ src/common/normalization/log_cpm/script.py | 32 ------- .../log_scran_pooling/config.vsh.yaml | 28 ------ .../normalization/log_scran_pooling/script.R | 29 ------- src/common/subsample/config.vsh.yaml | 51 ----------- src/common/subsample/script.py | 71 ---------------- src/common/subsample/test_script.py | 52 ------------ 10 files changed, 438 deletions(-) delete mode 100644 src/common/api/anndata_dataset.yaml delete mode 100644 src/common/api/anndata_raw_dataset.yaml delete mode 100644 src/common/api/comp_normalization.yaml delete mode 100644 src/common/normalization/log_cpm/config.vsh.yaml delete mode 100644 src/common/normalization/log_cpm/script.py delete mode 100644 src/common/normalization/log_scran_pooling/config.vsh.yaml delete mode 100644 src/common/normalization/log_scran_pooling/script.R delete mode 100644 src/common/subsample/config.vsh.yaml delete mode 100644 src/common/subsample/script.py delete mode 100644 src/common/subsample/test_script.py diff --git a/src/common/api/anndata_dataset.yaml b/src/common/api/anndata_dataset.yaml deleted file mode 100644 index 21694f6745..0000000000 --- a/src/common/api/anndata_dataset.yaml +++ /dev/null @@ -1,35 +0,0 @@ -type: file -description: "A dataset" -example: "dataset.h5ad" -info: - short_description: "Dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true \ No newline at end of file diff --git a/src/common/api/anndata_raw_dataset.yaml b/src/common/api/anndata_raw_dataset.yaml deleted file mode 100644 index 37c41a3003..0000000000 --- a/src/common/api/anndata_raw_dataset.yaml +++ /dev/null @@ -1,29 +0,0 @@ -type: file -description: "A raw dataset" -example: "raw_dataset.h5ad" -info: - short_description: "Raw dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true diff --git a/src/common/api/comp_normalization.yaml b/src/common/api/comp_normalization.yaml deleted file mode 100644 index f0c786e115..0000000000 --- a/src/common/api/comp_normalization.yaml +++ /dev/null @@ -1,85 +0,0 @@ -functionality: - arguments: - - name: "--input" - __inherits__: anndata_raw_dataset.yaml - - name: "--output" - type: file - description: "A preprocessed dataset" - example: "preprocessed.h5ad" - info: - short_description: "Preprocessed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: $par_layer_output - description: Log-transformed normalised counts - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - direction: output - - # not including this because we need to override the default - # - name: "--layer_output" - # type: string - # default: "log_cpm" - # description: The name of the layer in which to store the log normalized data. - test_resources: - - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_path = "output.h5ad" - output_layer = "norm_layer" - - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path, - "--layer_output", output_layer - ] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - print("input:", input) - print("output:", output) - - print(">> Checking whether output data structures were added") - assert output_layer in output.layers - - print("Checking whether data from input was copied properly to output") - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") - - path: ../../../../resources_test/common/pancreas - diff --git a/src/common/normalization/log_cpm/config.vsh.yaml b/src/common/normalization/log_cpm/config.vsh.yaml deleted file mode 100644 index 6b7121a1a7..0000000000 --- a/src/common/normalization/log_cpm/config.vsh.yaml +++ /dev/null @@ -1,26 +0,0 @@ -__inherits__: ../../api/comp_normalization.yaml -functionality: - name: "log_cpm" - namespace: "common/normalization" - description: "Normalize data using Log CPM" - arguments: - - name: "--layer_output" - type: string - default: "log_cpm" - description: The name of the layer in which to store the log normalized data. - - name: "--obs_size_factors" - type: string - default: "size_factors_log_cpm" - description: In which .obs slot to store the size factors. - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - scanpy - - "anndata<0.8" - - type: nextflow diff --git a/src/common/normalization/log_cpm/script.py b/src/common/normalization/log_cpm/script.py deleted file mode 100644 index a080fdc643..0000000000 --- a/src/common/normalization/log_cpm/script.py +++ /dev/null @@ -1,32 +0,0 @@ -import scanpy as sc - -## VIASH START -par = { - 'input': "resources_test/common/pancreas/dataset.h5ad", - 'output': "output.h5ad", - 'layer_output': "log_cpm", - 'obs_size_factors': "log_cpm_size_factors" -} -meta = { - "functionality_name": "normalize_log_cpm" -} -## VIASH END - -print(">> Load data") -adata = sc.read_h5ad(par['input']) - -print(">> Normalize data") -norm = sc.pp.normalize_total( - adata, - target_sum=1e6, - layer="counts", - inplace=False -) -lognorm = sc.pp.log1p(norm["X"]) - -print(">> Store output in adata") -adata.layers[par["layer_output"]] = lognorm -adata.obs[par["obs_size_factors"]] = norm["norm_factor"] - -print(">> Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/common/normalization/log_scran_pooling/config.vsh.yaml b/src/common/normalization/log_scran_pooling/config.vsh.yaml deleted file mode 100644 index ad0eea1ca6..0000000000 --- a/src/common/normalization/log_scran_pooling/config.vsh.yaml +++ /dev/null @@ -1,28 +0,0 @@ -__inherits__: ../../api/comp_normalization.yaml -functionality: - name: "log_scran_pooling" - namespace: "common/normalization" - description: "Normalize data using scran pooling" - arguments: - - name: "--layer_output" - type: string - default: "log_scran_pooling" - description: The name of the layer in which to store the log normalized data. - - name: "--obs_size_factors" - type: string - default: "size_factors_log_scran_pooling" - description: In which .obs slot to store the size factors. - resources: - - type: r_script - path: script.R -platforms: - - type: docker - image: eddelbuettel/r2u:22.04 - setup: - - type: r - cran: [ Matrix, scran, BiocParallel, rlang, anndata, bit64 ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata<0.8, scanpy ] - - type: nextflow diff --git a/src/common/normalization/log_scran_pooling/script.R b/src/common/normalization/log_scran_pooling/script.R deleted file mode 100644 index 5885785d96..0000000000 --- a/src/common/normalization/log_scran_pooling/script.R +++ /dev/null @@ -1,29 +0,0 @@ -cat(">> Loading dependencies\n") -library(anndata, warn.conflicts = FALSE) -requireNamespace("scran", quietly = TRUE) -requireNamespace("BiocParallel", quietly = TRUE) -library(Matrix, warn.conflicts = FALSE) - -## VIASH START -par <- list( - input = "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", - output = "output.scran.h5ad", - layer_output = "log_scran_pooling", - obs_size_factors = "size_factors_log_scran_pooling" -) -## VIASH END - -cat(">> Load data\n") -adata <- anndata::read_h5ad(par$input) -counts <- as.matrix(t(adata$layers[["counts"]])) - -cat(">> Normalizing data\n") -size_factors <- scran::calculateSumFactors(counts, min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) -lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) - -cat(">> Storing in anndata\n") -adata$obs[[par$obs_size_factors]] <- size_factors -adata$layers[[par$layer_output]] <- lognorm - -cat(">> Writing to file\n") -zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/common/subsample/config.vsh.yaml b/src/common/subsample/config.vsh.yaml deleted file mode 100644 index 6cea15b145..0000000000 --- a/src/common/subsample/config.vsh.yaml +++ /dev/null @@ -1,51 +0,0 @@ -functionality: - name: "subsample" - namespace: "common" - version: "dev" - description: "Subsample an anndata file" - arguments: - - name: "--input" - type: "file" - description: "Input data to be resized" - required: true - example: input.h5ad - - name: "--keep_celltype_categories" - type: "string" - multiple: true - description: "Categories indexes to be selected" - required: false - - name: "--keep_batch_categories" - type: "string" - multiple: true - description: "Categories indexes to be selected" - required: false - - name: "--even" - type: "boolean_true" - description: Subsample evenly from different batches - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file" - required: true - - name: "--seed" - type: "integer" - description: "A seed for the subsampling." - example: 123 - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test_script.py - - path: "../../../resources_test/common/pancreas" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - "anndata<0.8" - - type: nextflow diff --git a/src/common/subsample/script.py b/src/common/subsample/script.py deleted file mode 100644 index b3b19cff30..0000000000 --- a/src/common/subsample/script.py +++ /dev/null @@ -1,71 +0,0 @@ -import scanpy as sc -import random - -### VIASH START -par = { - "input": "resources_test/common/pancreas/dataset.h5ad", - "keep_celltype_categories": None, - "keep_batch_categories": None, - # "keep_celltype_categories": ["acinar", "beta"], - # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], - "even": True, - "output": "toy_data.h5ad", - "seed": 123 -} -### VIASH END - -if par["seed"]: - print(f">> Setting seed to {par['seed']}") - random.seed(par["seed"]) - -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - return adata - -print(">> Load data") -adata = sc.read(par['input']) - -# copy counts to .X because otherwise filter_genes and filter_cells won't work -adata.X = adata.layers["counts"] - -if par.get('even'): - keep_batch_categories = adata.obs["batch"].unique() - adata_out = None - n_batch_obs_per_value = 500 // len(keep_batch_categories) - for t in keep_batch_categories: - batch_idx = adata.obs["batch"] == t - adata_subset = adata[batch_idx].copy() - sc.pp.subsample(adata_subset, n_obs=min(n_batch_obs_per_value, adata_subset.shape[0])) - if adata_out is None: - adata_out = adata_subset - else: - adata_out = adata_out.concatenate(adata_subset, batch_key="_obs_batch") - adata_out.uns = adata.uns - adata_out.varm = adata.varm - adata_out.varp = adata.varp - adata = adata_out[:, :500].copy() -else: - adata = adata[:, :500].copy() - -filter_genes_cells(adata) - -if par.get('keep_celltype_categories') and par.get('keep_batch_categories'): - print(">> Selecting celltype_categories {categories}".format(categories=par.get('keep_celltype_categories'))) - print(">> Selecting batch_categories {categories}".format(categories=par.get('keep_batch_categories'))) - keep_batch_idx = adata.obs["batch"].isin(par['keep_batch_categories']) - keep_celltype_idx = adata.obs["celltype"].isin(par['keep_celltype_categories']) - adata = adata[keep_celltype_idx & keep_batch_idx].copy() - -# Note: could also use 200-500 HVGs rather than 200 random genes -# Ensure there are no cells or genes with 0 counts -sc.pp.subsample(adata, n_obs=min(500, adata.shape[0])) -filter_genes_cells(adata) -adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" - -# remove previously copied .X -del adata.X - -print(">> Writing data") -adata.write_h5ad(par['output']) diff --git a/src/common/subsample/test_script.py b/src/common/subsample/test_script.py deleted file mode 100644 index 2cf9b791e3..0000000000 --- a/src/common/subsample/test_script.py +++ /dev/null @@ -1,52 +0,0 @@ -import subprocess -import scanpy as sc -from os import path - -### VIASH START -meta = { - "resources_dir": "resources_test/label_projection" -} -### VIASH END - -input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" -input = sc.read_h5ad(input_path) - -print(">> Running script as test for even") -output_path = "output.h5ad" -out = subprocess.check_output([ - meta["executable"], - "--input", input_path, - "--output", output_path, - "--even", - "--seed", "123" -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_path) - -print(">> Check that test output fits expected API") -output = sc.read_h5ad(output_path) - -assert input.n_obs >= output.n_obs -assert input.n_vars == output.n_vars - - - -print(">> Runing script as test for specific batch and celltype categories") -output2_path = "output.h5ad" -out = subprocess.check_output([ - meta["executable"], - "--input", input_path, - "--keep_celltype_categories", "acinar:beta", - "--keep_batch_categories", "celseq:inDrop4:smarter", - "--output", output_path, - "--seed", "123" -]).decode("utf-8") -print(">> Checking whether file exists") -assert path.exists(output2_path) - -print(">> Check that test output fits expected API") -output2 = sc.read_h5ad(output2_path) - -assert input.n_obs >= output2.n_obs -assert input.n_vars == output2.n_vars From 5c8170737f3f531efe839cffd209e55be7e676c6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:12:38 +0100 Subject: [PATCH 0324/1233] deprecate old components Former-commit-id: d6ca5db8fc5eb398eb8f87401b3df4e733bd9119 --- src/common/dataset_concatenate/config.vsh.yaml | 1 + src/common/dataset_loader/download/config.vsh.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml index 5008eb5acf..6800806f11 100644 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ b/src/common/dataset_concatenate/config.vsh.yaml @@ -1,5 +1,6 @@ functionality: name: "dataset_concatenate" + status: deprecated namespace: "common/data_processing" description: "Concatenate datasets" arguments: diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 86dce2f07c..70eddf8359 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -1,5 +1,6 @@ functionality: name: "download" + status: deprecated namespace: "common/dataset_loader" version: "dev" description: "Download a dataset." From 4f15732fa4d64f8833603fb72758eee8b826f8ff Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:12:57 +0100 Subject: [PATCH 0325/1233] update dataset components Former-commit-id: fba83ae9b7568cdff9ad946bad565762c82d30ab --- src/datasets/api/anndata_raw_dataset.yaml | 5 ++ .../loaders/openproblems_v1/config.vsh.yaml | 4 +- .../loaders/openproblems_v1/datasets.csv | 7 -- .../loaders/openproblems_v1/datasets.tsv | 9 --- .../loaders/openproblems_v1/datasets.yaml | 50 +++++++++++++ .../loaders/openproblems_v1/script.py | 18 ++--- .../normalization/log_cpm/config.vsh.yaml | 2 +- .../log_scran_pooling/config.vsh.yaml | 4 +- .../normalization/sqrt_cpm/config.vsh.yaml | 2 +- .../resource_test_scripts/pancreas.sh | 42 +++++++++++ src/datasets/subsample/config.vsh.yaml | 50 +++++++++++++ src/datasets/subsample/script.py | 71 +++++++++++++++++++ src/datasets/subsample/test_script.py | 52 ++++++++++++++ 13 files changed, 286 insertions(+), 30 deletions(-) delete mode 100644 src/datasets/loaders/openproblems_v1/datasets.csv delete mode 100644 src/datasets/loaders/openproblems_v1/datasets.tsv create mode 100644 src/datasets/loaders/openproblems_v1/datasets.yaml create mode 100755 src/datasets/resource_test_scripts/pancreas.sh create mode 100644 src/datasets/subsample/config.vsh.yaml create mode 100644 src/datasets/subsample/script.py create mode 100644 src/datasets/subsample/test_script.py diff --git a/src/datasets/api/anndata_raw_dataset.yaml b/src/datasets/api/anndata_raw_dataset.yaml index 37c41a3003..4a901515b3 100644 --- a/src/datasets/api/anndata_raw_dataset.yaml +++ b/src/datasets/api/anndata_raw_dataset.yaml @@ -27,3 +27,8 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + # todo: ? + # - dataset_label + # - dataset_description + # - dataset_doi + # - dataset_url (if doi not available) diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 2be7e4be1b..5e9d64f437 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -39,12 +39,10 @@ functionality: path: test.py platforms: - type: docker - image: "python:3.10" + image: singlecellopenproblems/openproblems setup: - type: python packages: - scanpy - "anndata<0.8" - github: - - openproblems-bio/openproblems - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/datasets.csv b/src/datasets/loaders/openproblems_v1/datasets.csv deleted file mode 100644 index 12c76e64c1..0000000000 --- a/src/datasets/loaders/openproblems_v1/datasets.csv +++ /dev/null @@ -1,7 +0,0 @@ -id,obs_celltype,obs_batch,obs_tissue,layer_counts -pancreas,celltype,tech,,counts -immune_cells,final_annotation,batch,tissue,counts -tenx_1k_pbmc,,,,counts -tenx_5k_pbmc,,,,counts -cengen,cell_type,experiment_code,tissue,counts -zebrafish,cell_type,lab,,counts \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/datasets.tsv b/src/datasets/loaders/openproblems_v1/datasets.tsv deleted file mode 100644 index 1965ee50d2..0000000000 --- a/src/datasets/loaders/openproblems_v1/datasets.tsv +++ /dev/null @@ -1,9 +0,0 @@ -id url obs_celltype obs_batch obs_tissue -pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA -immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue -pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA -tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA -cengen https://github.com/Munfred/wormcells-data/releases/download/taylor2020/taylor2020.h5ad cell_type experiment_code tissue -zebrafish https://ndownloader.figshare.com/files/24566651?private_link=e3921450ec1bd0587870 cell_type lab NA -tabula_muris_senis_facs_lung https://ndownloader.figshare.com/files/23872619 free_annotation mouse.id NA -tabula_muris_senis_droplet_lung https://ndownloader.figshare.com/files/23873012 free_annotation mouse.id NA diff --git a/src/datasets/loaders/openproblems_v1/datasets.yaml b/src/datasets/loaders/openproblems_v1/datasets.yaml new file mode 100644 index 0000000000..b3bc2535f0 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/datasets.yaml @@ -0,0 +1,50 @@ +param_list: + - id: allen_brain_atlas + obs_celltype: label + layer_counts: counts + + - id: cengen + obs_celltype: cell_type + obs_batch: experiment_code + obs_tissue: tissue + layer_counts: counts + + - id: immune_cells + obs_celltype: final_annotation + obs_batch: batch + obs_tissue: tissue + layer_counts: counts + + - id: mouse_blood_olssen_labelled + obs_celltype: celltype + layer_counts: counts + + - id: mouse_hspc_nestorowa2016 + obs_celltype: cell_type_label + layer_counts: counts + + - id: pancreas + obs_celltype: celltype + obs_batch: tech + layer_counts: counts + + - id: tabula_muris_senis_droplet_lung + obs_celltype: cell_type + obs_batch: donor_id + # obs_tissue: tissue + layer_counts: counts + + - id: tenx_1k_pbmc + layer_counts: counts + + - id: tenx_5k_pbmc + layer_counts: counts + + - id: tnbc_wu2021 + obs_celltype: celltype_minor + layer_counts: counts + + - id: zebrafish + obs_celltype: cell_type + obs_batch: lab + layer_counts: counts \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 416cd2fc87..2a5b958427 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -22,7 +22,11 @@ 'mouse_blood_olssen_labelled': op.data.mouse_blood_olssen_labelled.load_olsson_2016_mouse_blood, 'mouse_hspc_nestorowa2016': op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, 'pancreas': op.data.pancreas.load_pancreas, - 'tabula_muris_senis': op.data.tabula_muris_senis.load_tabula_muris_senis, + # 'tabula_muris_senis': op.data.tabula_muris_senis.load_tabula_muris_senis, + 'tabula_muris_senis_droplet_lung': lambda : op.data.tabula_muris_senis.load_tabula_muris_senis( + organ_list=["lung"], + method_list=["droplet"] + ), 'tenx_1k_pbmc': op.data.tenx.load_tenx_1k_pbmc, 'tenx_5k_pbmc': op.data.tenx.load_tenx_5k_pbmc, 'tnbc_wu2021': op.data.tnbc_wu2021.load_tnbc_data, @@ -33,7 +37,7 @@ adata = dataset_funs[par['id']]() print("Setting .uns['dataset_id']") -adata.uns["dataset_id"] = par["id"] +adata.uns["dataset_id"] = "openproblems_v1/" + par["id"] print("Setting .obs['celltype']") if par["obs_celltype"]: @@ -57,7 +61,7 @@ print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") if par["layer_counts"] and par["layer_counts"] in adata.layers: - print(f" Temporarily copying .layers['{par['layer_counts']}'] to .X") + print(f" Temporarily moving .layers['{par['layer_counts']}'] to .X") adata.X = adata.layers[par["layer_counts"]] del adata.layers[par["layer_counts"]] @@ -71,11 +75,9 @@ print(" Removing empty cells") sc.pp.filter_cells(adata, min_counts=2) -if par["layer_counts_output"]: - print(f" Copying .X back to .layers['{par['layer_counts_output']}']") - adata.layers[par["layer_counts_output"]] = adata.X - # todo: make sure X is sparse - del adata.X +print(f" Moving .X to .layers['counts']") +adata.layers["counts"] = adata.X +del adata.X print("Writing adata to file") adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 6b7121a1a7..476c431924 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -1,7 +1,7 @@ __inherits__: ../../api/comp_normalization.yaml functionality: name: "log_cpm" - namespace: "common/normalization" + namespace: "datasets/normalization" description: "Normalize data using Log CPM" arguments: - name: "--layer_output" diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index ad0eea1ca6..23fa2fade0 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -1,7 +1,7 @@ __inherits__: ../../api/comp_normalization.yaml functionality: name: "log_scran_pooling" - namespace: "common/normalization" + namespace: "datasets/normalization" description: "Normalize data using scran pooling" arguments: - name: "--layer_output" @@ -26,3 +26,5 @@ platforms: - type: python pip: [ anndata<0.8, scanpy ] - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 3cc9f4dae3..7f6f65c1b4 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -1,7 +1,7 @@ __inherits__: ../../api/comp_normalization.yaml functionality: name: "sqrt_cpm" - namespace: "common/normalization" + namespace: "datasets/normalization" description: "Normalize data using Log Sqrt" arguments: - name: "--layer_output" diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh new file mode 100755 index 0000000000..04a134154b --- /dev/null +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -0,0 +1,42 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/common/pancreas + +mkdir -p $DATASET_DIR + +# download dataset +bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ + --url "https://ndownloader.figshare.com/files/24539828" \ + --obs_celltype "celltype" \ + --obs_batch "tech" \ + --name "pancreas" \ + --layer_counts "counts" \ + --layer_counts_output "counts" \ + --output $DATASET_DIR/temp_dataset_full.h5ad + +# subsample +bin/viash run src/common/subsample/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset_full.h5ad \ + --keep_celltype_categories "acinar:beta" \ + --keep_batch_categories "celseq:inDrop4:smarter" \ + --output $DATASET_DIR/temp_dataset_sampled.h5ad \ + --seed 123 + +# run log cpm normalisation +bin/viash run src/common/normalization/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset_sampled.h5ad \ + --output $DATASET_DIR/temp_dataset_cpm.h5ad + +# run scran pooling normalisation +bin/viash run src/common/normalization/log_scran_pooling/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset_cpm.h5ad \ + --output $DATASET_DIR/dataset.h5ad diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml new file mode 100644 index 0000000000..fae1697f1a --- /dev/null +++ b/src/datasets/subsample/config.vsh.yaml @@ -0,0 +1,50 @@ +functionality: + name: "subsample" + namespace: "datasets" + description: "Subsample an h5ad file" + arguments: + - name: "--input" + type: "file" + description: "Input data to be resized" + required: true + example: input.h5ad + - name: "--keep_celltype_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--output" + alternatives: ["-o"] + type: "file" + direction: "output" + example: "output.h5ad" + description: "Output h5ad file" + required: true + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test_script.py + - path: "../../../resources_test/common/pancreas" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata<0.8" + - type: nextflow diff --git a/src/datasets/subsample/script.py b/src/datasets/subsample/script.py new file mode 100644 index 0000000000..b3b19cff30 --- /dev/null +++ b/src/datasets/subsample/script.py @@ -0,0 +1,71 @@ +import scanpy as sc +import random + +### VIASH START +par = { + "input": "resources_test/common/pancreas/dataset.h5ad", + "keep_celltype_categories": None, + "keep_batch_categories": None, + # "keep_celltype_categories": ["acinar", "beta"], + # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], + "even": True, + "output": "toy_data.h5ad", + "seed": 123 +} +### VIASH END + +if par["seed"]: + print(f">> Setting seed to {par['seed']}") + random.seed(par["seed"]) + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) + return adata + +print(">> Load data") +adata = sc.read(par['input']) + +# copy counts to .X because otherwise filter_genes and filter_cells won't work +adata.X = adata.layers["counts"] + +if par.get('even'): + keep_batch_categories = adata.obs["batch"].unique() + adata_out = None + n_batch_obs_per_value = 500 // len(keep_batch_categories) + for t in keep_batch_categories: + batch_idx = adata.obs["batch"] == t + adata_subset = adata[batch_idx].copy() + sc.pp.subsample(adata_subset, n_obs=min(n_batch_obs_per_value, adata_subset.shape[0])) + if adata_out is None: + adata_out = adata_subset + else: + adata_out = adata_out.concatenate(adata_subset, batch_key="_obs_batch") + adata_out.uns = adata.uns + adata_out.varm = adata.varm + adata_out.varp = adata.varp + adata = adata_out[:, :500].copy() +else: + adata = adata[:, :500].copy() + +filter_genes_cells(adata) + +if par.get('keep_celltype_categories') and par.get('keep_batch_categories'): + print(">> Selecting celltype_categories {categories}".format(categories=par.get('keep_celltype_categories'))) + print(">> Selecting batch_categories {categories}".format(categories=par.get('keep_batch_categories'))) + keep_batch_idx = adata.obs["batch"].isin(par['keep_batch_categories']) + keep_celltype_idx = adata.obs["celltype"].isin(par['keep_celltype_categories']) + adata = adata[keep_celltype_idx & keep_batch_idx].copy() + +# Note: could also use 200-500 HVGs rather than 200 random genes +# Ensure there are no cells or genes with 0 counts +sc.pp.subsample(adata, n_obs=min(500, adata.shape[0])) +filter_genes_cells(adata) +adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" + +# remove previously copied .X +del adata.X + +print(">> Writing data") +adata.write_h5ad(par['output']) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py new file mode 100644 index 0000000000..2cf9b791e3 --- /dev/null +++ b/src/datasets/subsample/test_script.py @@ -0,0 +1,52 @@ +import subprocess +import scanpy as sc +from os import path + +### VIASH START +meta = { + "resources_dir": "resources_test/label_projection" +} +### VIASH END + +input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" +input = sc.read_h5ad(input_path) + +print(">> Running script as test for even") +output_path = "output.h5ad" +out = subprocess.check_output([ + meta["executable"], + "--input", input_path, + "--output", output_path, + "--even", + "--seed", "123" +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_path) + +print(">> Check that test output fits expected API") +output = sc.read_h5ad(output_path) + +assert input.n_obs >= output.n_obs +assert input.n_vars == output.n_vars + + + +print(">> Runing script as test for specific batch and celltype categories") +output2_path = "output.h5ad" +out = subprocess.check_output([ + meta["executable"], + "--input", input_path, + "--keep_celltype_categories", "acinar:beta", + "--keep_batch_categories", "celseq:inDrop4:smarter", + "--output", output_path, + "--seed", "123" +]).decode("utf-8") +print(">> Checking whether file exists") +assert path.exists(output2_path) + +print(">> Check that test output fits expected API") +output2 = sc.read_h5ad(output2_path) + +assert input.n_obs >= output2.n_obs +assert input.n_vars == output2.n_vars From ae4b5fbd312288f961093df4fad6fe2c441262df Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:13:09 +0100 Subject: [PATCH 0326/1233] add dataset workflow Former-commit-id: a599fbcea1db0b5406ac26ad6c511882c1375fdc --- .../process_openproblems_v1/config.vsh.yaml | 71 +++++++++++++++++++ .../workflows/process_openproblems_v1/main.nf | 57 +++++++++++++++ .../process_openproblems_v1/nextflow.config | 11 +++ .../process_openproblems_v1/run_nextflow.sh | 17 +++++ 4 files changed, 156 insertions(+) create mode 100644 src/datasets/workflows/process_openproblems_v1/config.vsh.yaml create mode 100644 src/datasets/workflows/process_openproblems_v1/main.nf create mode 100644 src/datasets/workflows/process_openproblems_v1/nextflow.config create mode 100755 src/datasets/workflows/process_openproblems_v1/run_nextflow.sh diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml new file mode 100644 index 0000000000..1a5930651d --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -0,0 +1,71 @@ +functionality: + name: process_openproblems_v1 + namespace: datasets/workflows + description: | + Fetch and process legacy OpenProblems v1 datasets + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "In which layer to find the counts matrix. Leave undefined to use `.X`." + example: counts + - name: "--sparse" + type: boolean + default: true + description: Convert layers to a sparse CSR format. + - name: Outputs + arguments: + - name: "--output" + direction: "output" + # todo: fix inherits in nxf + # __inherits__: ../../api/anndata_raw_dataset.yaml + type: file + description: "A raw dataset" + example: "raw_dataset.h5ad" + info: + short_description: "Raw dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + resources: + - type: nextflow_script + path: main.nf + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf new file mode 100644 index 0000000000..0a0d1b5696 --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -0,0 +1,57 @@ +nextflow.enable.dsl=2 + +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/main.nf" +include { log_cpm } from "$targetDir/datasets/normalization/log_cpm/main.nf" +include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" +include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" + +include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from workflowDir + "/utils/DataFlowHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +workflow { + helpMessage(config) + + viashChannel(params, config) + | run_wf +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + openproblems_v1: ["id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse"], + sqrt_cpm: [ "output" ] + ) + + // fetch data from legacy openproblems + | getWorkflowArguments(key: "openproblems_v1") + | openproblems_v1 + + // run cpm normalisation + | log_cpm + + // run scran normalisation + | log_scran_pooling + + // run sqrt normalisation and publish + | getWorkflowArguments(key: "sqrt_cpm") + | sqrt_cpm.run( + auto = [ publish: true ] + ) + + // clean up channel + | pmap{id, data, passthrough -> [id, data]} + + emit: + output_ch +} \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/nextflow.config b/src/datasets/workflows/process_openproblems_v1/nextflow.config new file mode 100644 index 0000000000..0ecebcacc0 --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1/nextflow.config @@ -0,0 +1,11 @@ +manifest { + nextflowVersion = '!>=22.04.5' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/nxf_utils/labels.config") diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh new file mode 100755 index 0000000000..ebd6d9b8e3 --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ + -resume \ + -profile docker \ + -params-file src/datasets/loaders/openproblems_v1/datasets.yaml \ + --publish_dir output/datasets \ No newline at end of file From 9271210647edd255f5acce8f4b22d122c324eba0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:13:20 +0100 Subject: [PATCH 0327/1233] update authors Former-commit-id: 0c5567c60b1af874c653ce3da53d8c8112e8e2f9 --- src/label_projection/api/authors.yaml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/label_projection/api/authors.yaml b/src/label_projection/api/authors.yaml index b98caf5771..23e6587896 100644 --- a/src/label_projection/api/authors.yaml +++ b/src/label_projection/api/authors.yaml @@ -8,7 +8,4 @@ functionality: props: { github: scottgigante } - name: Robrecht Cannoodt roles: [ author ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } - - name: "Vinicius Chagas" - roles: [ contributor ] - props: { github: chagasVinicius } + props: { github: rcannood, orcid: "0000-0003-3641-729X" } \ No newline at end of file From 3a8593279de40da92f140d53abadbae4770d16fe Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:13:35 +0100 Subject: [PATCH 0328/1233] update changelog Former-commit-id: 82601c4168e569bc361e6a0be554c90e5b124b7c --- CHANGELOG.md | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 430ec26d96..fabd769765 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,22 +1,16 @@ + # openproblems-v2 0.1.0 ## common ### NEW FUNCTIONALITY -* `dataset_loader/download`: Download an AnnData dataset from a URL. - * `extract_scores`: Summarise a metrics output tsv. * `dataset_concatenate`: Concatenate N AnnData datasets. -* `subsample`: Subsample an anndata file. - * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. -* `common/normalization/log_cpm`: A log CPM normalization method. - -* `common/normalization/log_scran_pooling`: A log scran pooling normalization method. ## label_projection @@ -40,4 +34,22 @@ * `metric/accuracy`: Migrated from v1. -* `metric/f1`: Migrated from v1. \ No newline at end of file +* `metric/f1`: Migrated from v1. + +## datasets + +### NEW FUNCTIONALITY + +* `workflows/process_openproblems_v1`: Fetch and process legacy OpenProblems v1 datasets + +* `normalization/log_cpm`: A log CPM normalization method. + +* `normalization/log_scran_pooling`: A log scran pooling normalization method. + +* `normalization/sqrt_cpm`: A sqrt CPM normalization method. + +* `subsample`: Subsample an h5ad file. + +### V1 MIGRATION + +* `loaders/openproblems_v1`: Fetch a dataset from OpenProblems v1 From d0bb738f4cfa46aa2bc2cd35a77665b6ef15a581 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:13:42 +0100 Subject: [PATCH 0329/1233] add nextflow helper functions Former-commit-id: 96f626f7a87e541113e5721dd9b2bd5d1a57150a --- src/nxf_utils/DataFlowHelper.nf | 170 ++++++++++++++++++++++++++++++++ src/nxf_utils/labels.config | 8 ++ 2 files changed, 178 insertions(+) create mode 100644 src/nxf_utils/DataFlowHelper.nf create mode 100644 src/nxf_utils/labels.config diff --git a/src/nxf_utils/DataFlowHelper.nf b/src/nxf_utils/DataFlowHelper.nf new file mode 100644 index 0000000000..3c19f0d7ec --- /dev/null +++ b/src/nxf_utils/DataFlowHelper.nf @@ -0,0 +1,170 @@ +/* usage: +| setWorkflowArguments( + pca: [ "input": "input", "obsm_output": "obsm_pca" ] + harmonypy: [ "obs_covariates": "obs_covariates", "obsm_input": "obsm_pca" ], + find_neighbors: [ "obsm_input": "obsm_pca" ], + umap: [ "output": "output" ] +) +*/ + +def setWorkflowArguments(Map args) { + wfKey = args.key ?: "setWorkflowArguments" + args.keySet().removeAll(["key"]) + + + /* + data = [a:1, b:2, c:3] + // args = [foo: ["a", "b"], bar: ["b"]] + args = [foo: [a: 'a', out: "b"], bar: [in: "b"]] + */ + + workflow setWorkflowArgumentsInstance { + take: + input_ + + main: + output_ = input_ + | map{ tup -> + id = tup[0] + data = tup[1] + passthrough = tup.drop(2) + + // determine new data + toRemove = args.collectMany{ _, dataKeys -> + // dataKeys is a map but could also be a list + dataKeys instanceof List ? dataKeys : dataKeys.values() + }.unique() + newData = data.findAll{!toRemove.contains(it.key)} + + // determine splitargs + splitArgs = args. + collectEntries{procKey, dataKeys -> + // dataKeys is a map but could also be a list + newSplitData = dataKeys + .collectEntries{ val -> + newKey = val instanceof String ? val : val.key + origKey = val instanceof String ? val : val.value + [ newKey, data[origKey] ] + } + .findAll{it.value} + [procKey, newSplitData] + } + + // return output + [ id, newData, splitArgs] + passthrough + } + + emit: + output_ + } + + return setWorkflowArgumentsInstance.cloneWithName(wfKey) +} + +/* usage: +| getWorkflowArguments("harmonypy") +*/ + + +def getWorkflowArguments(Map args) { + def inputKey = args.inputKey ?: "input" + def wfKey = "getWorkflowArguments_" + args.key + + workflow getWorkflowArgumentsInstance { + take: + input_ + + main: + output_ = input_ + | map{ tup -> + id = tup[0] + data = tup[1] + splitArgs = tup[2].clone() + + passthrough = tup.drop(3) + + // try to infer arg name + if (data !instanceof Map) { + data = [[ inputKey, data ]].collectEntries() + } + newData = data + splitArgs.remove(args.key) + + [ id, newData, splitArgs] + passthrough + } + + emit: + output_ + } + + return getWorkflowArgumentsInstance.cloneWithName(wfKey) + +} + + +def strictMap(Closure clos) { + def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount + + workflow strictMapWf { + take: + input_ + + main: + output_ = input_ + | map{ tup -> + if (tup.size() != numArgs) { + throw new RuntimeException("Closure does not have the same number of arguments as channel tuple.\nNumber of closure arguments: $numArgs\nChannel tuple: $tup") + } + clos(tup) + } + + emit: + output_ + } + + return strictMapWf +} + +def passthroughMap(Closure clos) { + def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount + + workflow passthroughMapWf { + take: + input_ + + main: + output_ = input_ + | map{ tup -> + out = clos(tup.take(numArgs)) + out + tup.drop(numArgs) + } + + emit: + output_ + } + + return passthroughMapWf +} + +def passthroughFlatMap(Closure clos) { + def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount + + workflow passthroughFlatMapWf { + take: + input_ + + main: + output_ = input_ + | flatMap{ tup -> + out = clos(tup.take(numArgs)) + for (o in out) { + o.addAll(tup.drop(numArgs)) + } + out + } + + emit: + output_ + } + + return passthroughFlatMapWf +} \ No newline at end of file diff --git a/src/nxf_utils/labels.config b/src/nxf_utils/labels.config new file mode 100644 index 0000000000..a7a3cf47ab --- /dev/null +++ b/src/nxf_utils/labels.config @@ -0,0 +1,8 @@ +process { + withLabel: lowmem { memory = 20.Gb } + withLabel: lowcpu { cpus = 5 } + withLabel: midmem { memory = 50.Gb } + withLabel: midcpu { cpus = 15 } + withLabel: highmem { memory = 100.Gb } + withLabel: highcpu { cpus = 30 } +} From 29fc0b959eacb13f336b66366b5abf864b7fba75 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:40:11 +0100 Subject: [PATCH 0330/1233] fix api Former-commit-id: 06cf5079c9b8b0c4651b2fc669a0ab95b2b41781 --- .../{comp_split.yaml => comp_split_dataset.yaml} | 0 .../{split => split_dataset}/config.vsh.yaml | 6 +++--- .../{split => split_dataset}/script.py | 0 src/label_projection/workflows/run/main.nf | 13 ++----------- 4 files changed, 5 insertions(+), 14 deletions(-) rename src/label_projection/api/{comp_split.yaml => comp_split_dataset.yaml} (100%) rename src/label_projection/{split => split_dataset}/config.vsh.yaml (89%) rename src/label_projection/{split => split_dataset}/script.py (100%) diff --git a/src/label_projection/api/comp_split.yaml b/src/label_projection/api/comp_split_dataset.yaml similarity index 100% rename from src/label_projection/api/comp_split.yaml rename to src/label_projection/api/comp_split_dataset.yaml diff --git a/src/label_projection/split/config.vsh.yaml b/src/label_projection/split_dataset/config.vsh.yaml similarity index 89% rename from src/label_projection/split/config.vsh.yaml rename to src/label_projection/split_dataset/config.vsh.yaml index bab16ab739..f4945ace40 100644 --- a/src/label_projection/split/config.vsh.yaml +++ b/src/label_projection/split_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ -__inherits__: ../api/comp_split.yaml +__inherits__: ../api/comp_split_dataset.yaml functionality: - name: "split" + name: "split_dataset" namespace: "label_projection" arguments: - name: "--method" @@ -30,5 +30,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/split/script.py b/src/label_projection/split_dataset/script.py similarity index 100% rename from src/label_projection/split/script.py rename to src/label_projection/split_dataset/script.py diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 22281f1d31..d660f579c1 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -2,17 +2,8 @@ nextflow.enable.dsl=2 targetDir = "${params.rootDir}/target/nextflow" -// // import dataset loaders -// include { download } from "$targetDir/common/dataset_loader/download/main.nf" -// // import preprocess -// include { randomize } from "$targetDir/label_projection/data_processing/randomize/main.nf" -// // for tests -// include { subsample } from "$targetDir/label_projection/data_processing/subsample/main.nf" - -// // import normalization -// include { log_scran_pooling } from "$targetDir/label_projection/data_processing/normalize/scran/log_scran_pooling/main.nf" -// include { log_cpm } from "$targetDir/label_projection/data_processing/normalize/log_cpm/main.nf" +// include { split_dataset } from "$targetDir/label_projection/split_dataset/main.nf" // import methods include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" @@ -31,7 +22,7 @@ include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" // import helper functions -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" /******************************************************* From ca69580de00ab1f10e7c6b7e1fd3fb09faa6d3e6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:40:33 +0100 Subject: [PATCH 0331/1233] update to anndata>=0.8 Former-commit-id: 695925d6da0f00c98ca8a43b7b9cc440be64d615 --- src/common/dataset_loader/download/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- src/datasets/normalization/log_cpm/config.vsh.yaml | 2 +- src/datasets/normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 2 +- src/datasets/subsample/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/label_projection/methods/knn_classifier/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/config.vsh.yaml | 2 +- .../methods/scvi/scanvi_all_genes/config.vsh.yaml | 2 +- src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml | 2 +- .../methods/scvi/scarches_scanvi_hvg/config.vsh.yaml | 2 +- src/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index 70eddf8359..81921b031a 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -84,5 +84,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index f6a8154236..9912e66ccd 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -33,5 +33,5 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata<0.8 ] + pip: [ anndata>=0.8 ] - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 5e9d64f437..a228c95a61 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -44,5 +44,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 476c431924..9e49f04fb5 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -22,5 +22,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 23fa2fade0..0be7a00951 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -24,7 +24,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata<0.8, scanpy ] + pip: [ anndata>=0.8, scanpy ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 7f6f65c1b4..977fa3cc39 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -22,5 +22,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index fae1697f1a..7616039183 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -46,5 +46,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index a2e6ca3bef..00c6736788 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -22,5 +22,5 @@ platforms: setup: - type: python packages: - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index e1e9b9f9e2..f17c11f911 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -23,5 +23,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 35e5432b33..dd338c006c 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -24,5 +24,5 @@ platforms: setup: - type: python packages: - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 90a92ab978..564bbe96a8 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -27,5 +27,5 @@ platforms: - type: python packages: - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 1d3693b0ba..3fa62d1781 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -31,5 +31,5 @@ platforms: - type: python packages: - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 4e116a7f1e..ff100fcaed 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -35,5 +35,5 @@ platforms: - type: python packages: - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml index 5d05a6263a..2b8d33fdd2 100644 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml @@ -67,7 +67,7 @@ platforms: - scanpy - scprep - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - scvi-tools - type: native - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml index 69f4eb8052..5e623c9f12 100644 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml @@ -74,7 +74,7 @@ platforms: - scanpy - scprep - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - scvi-tools - scikit-misc - type: native diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml index de4dfc8662..ecba2bd330 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml @@ -67,7 +67,7 @@ platforms: - scanpy - scprep - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - scvi-tools - type: native - type: nextflow diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml index 14e28ff538..1a1fa05ba4 100644 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml @@ -74,7 +74,7 @@ platforms: - scanpy - scprep - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - scvi-tools - scikit-misc - type: native diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 7c17213d81..a0e2a4b526 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -23,5 +23,5 @@ platforms: - type: python packages: - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index acfd6e8dde..a205fb1350 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -35,5 +35,5 @@ platforms: - type: python packages: - scikit-learn - - "anndata<0.8" + - "anndata>=0.8" - type: nextflow From 078543c6afdff4e02588c2b2562e4074c49daf55 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 21:40:45 +0100 Subject: [PATCH 0332/1233] update workflow Former-commit-id: dac7bca5635b5bfb8e6fe3ac8d5cdbde82ceb3d4 --- src/datasets/workflows/process_openproblems_v1/main.nf | 4 ++-- .../workflows/process_openproblems_v1/run_nextflow.sh | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 0a0d1b5696..3eae19d60e 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -9,7 +9,7 @@ include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_ include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from workflowDir + "/utils/DataFlowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -46,7 +46,7 @@ workflow run_wf { // run sqrt normalisation and publish | getWorkflowArguments(key: "sqrt_cpm") | sqrt_cpm.run( - auto = [ publish: true ] + auto: [ publish: true ] ) // clean up channel diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh index ebd6d9b8e3..eeae35ab16 100755 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -11,7 +11,7 @@ export NXF_VER=22.04.5 bin/nextflow \ run . \ -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ - -resume \ -profile docker \ + -resume \ -params-file src/datasets/loaders/openproblems_v1/datasets.yaml \ --publish_dir output/datasets \ No newline at end of file From 741ef0d2a29b1896ec4d68d168c7535fc4ea814d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 09:57:54 +0100 Subject: [PATCH 0333/1233] move test resources into its own folder Former-commit-id: 7d6682d5dd3274287e0a610770d535d31dd218f7 --- src/common/resources_test_scripts/aws_sync.sh | 2 +- src/common/sync_test_resources/config.vsh.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/common/resources_test_scripts/aws_sync.sh b/src/common/resources_test_scripts/aws_sync.sh index f4de74a125..1bbea6e60d 100644 --- a/src/common/resources_test_scripts/aws_sync.sh +++ b/src/common/resources_test_scripts/aws_sync.sh @@ -3,4 +3,4 @@ echo "Run the command in this script manually" exit 1 -aws s3 sync "resources_test" "s3://openproblems-data" --exclude */temp_* --delete --dryrun \ No newline at end of file +aws s3 sync "resources_test" "s3://openproblems-data/resources_test" --exclude */temp_* --delete --dryrun diff --git a/src/common/sync_test_resources/config.vsh.yaml b/src/common/sync_test_resources/config.vsh.yaml index d5c587f0f4..b920a9d30b 100644 --- a/src/common/sync_test_resources/config.vsh.yaml +++ b/src/common/sync_test_resources/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: Synchronise the test resources from s3 to resources_test usage: | sync_test_resources - sync_test_resources --input s3://openproblems-data --output resources_test + sync_test_resources --input s3://openproblems-data/resources_test --output resources_test authors: - name: Robrecht Cannoodt email: rcannood@gmail.com @@ -16,7 +16,7 @@ functionality: alternatives: ["-i"] type: string description: "Path to the S3 bucket to sync from." - default: "s3://openproblems-data" + default: "s3://openproblems-data/resources_test" - name: "--output" alternatives: ["-o"] type: file From 702d2c1d2492672abd3518402641b8078ca87a75 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 09:58:18 +0100 Subject: [PATCH 0334/1233] matrix doesn't need to be dense for scran Former-commit-id: 762fa71ea4cf7ff4180727d8e3d412233d17a0ad --- src/datasets/normalization/log_scran_pooling/script.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/datasets/normalization/log_scran_pooling/script.R b/src/datasets/normalization/log_scran_pooling/script.R index 5885785d96..6d80c8cadf 100644 --- a/src/datasets/normalization/log_scran_pooling/script.R +++ b/src/datasets/normalization/log_scran_pooling/script.R @@ -15,10 +15,14 @@ par <- list( cat(">> Load data\n") adata <- anndata::read_h5ad(par$input) -counts <- as.matrix(t(adata$layers[["counts"]])) +counts <- as(t(adata$layers[["counts"]]), "CsparseMatrix") cat(">> Normalizing data\n") -size_factors <- scran::calculateSumFactors(counts, min.mean=0.1, BPPARAM=BiocParallel::MulticoreParam()) +size_factors <- scran::calculateSumFactors( + counts, + min.mean = 0.1, + BPPARAM = BiocParallel::MulticoreParam() +) lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) cat(">> Storing in anndata\n") From 74370d9ac1dd99a627f468e11a496c692b252a9f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 10:01:33 +0100 Subject: [PATCH 0335/1233] choose output names Former-commit-id: 87a6d699e013b9f4370c1bafdb9481709df87f2f --- src/datasets/loaders/openproblems_v1/datasets.yaml | 14 ++++++++++++-- .../process_openproblems_v1/run_nextflow.sh | 2 +- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/datasets.yaml b/src/datasets/loaders/openproblems_v1/datasets.yaml index b3bc2535f0..177d850a74 100644 --- a/src/datasets/loaders/openproblems_v1/datasets.yaml +++ b/src/datasets/loaders/openproblems_v1/datasets.yaml @@ -2,49 +2,59 @@ param_list: - id: allen_brain_atlas obs_celltype: label layer_counts: counts + output: allen_brain_atlas.h5ad - id: cengen obs_celltype: cell_type obs_batch: experiment_code obs_tissue: tissue layer_counts: counts + output: cengen.h5ad - id: immune_cells obs_celltype: final_annotation obs_batch: batch obs_tissue: tissue layer_counts: counts + output: immune_cells.h5ad - id: mouse_blood_olssen_labelled obs_celltype: celltype layer_counts: counts + output: mouse_blood_olssen_labelled.h5ad - id: mouse_hspc_nestorowa2016 obs_celltype: cell_type_label layer_counts: counts + output: mouse_hspc_nestorowa2016.h5ad - id: pancreas obs_celltype: celltype obs_batch: tech layer_counts: counts + output: pancreas.h5ad - id: tabula_muris_senis_droplet_lung obs_celltype: cell_type obs_batch: donor_id - # obs_tissue: tissue layer_counts: counts + output: tabula_muris_senis_droplet_lung.h5ad - id: tenx_1k_pbmc layer_counts: counts + output: tenx_1k_pbmc.h5ad - id: tenx_5k_pbmc layer_counts: counts + output: tenx_5k_pbmc.h5ad - id: tnbc_wu2021 obs_celltype: celltype_minor layer_counts: counts + output: tnbc_wu2021.h5ad - id: zebrafish obs_celltype: cell_type obs_batch: lab - layer_counts: counts \ No newline at end of file + layer_counts: counts + output: zebrafish.h5ad \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh index eeae35ab16..ac65504d9b 100755 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -14,4 +14,4 @@ bin/nextflow \ -profile docker \ -resume \ -params-file src/datasets/loaders/openproblems_v1/datasets.yaml \ - --publish_dir output/datasets \ No newline at end of file + --publish_dir resources/datasets/openproblems_v1 \ No newline at end of file From 410a8937683b720127c4e2559f51df155bd3c1e4 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 16 Nov 2022 10:05:13 +0100 Subject: [PATCH 0336/1233] remove docker images Former-commit-id: 5237ba205657593794cc86033ee98b2b13bf27d1 --- .../base_images/scanpy-r-micromamba/Dockerfile | 6 ------ .../base_images/scanpy-r-micromamba/README.md | 13 ------------- .../base_images/scanpy-r-micromamba/env.yaml | 13 ------------- src/common/base_images/scib-base/Dockerfile | 6 ------ src/common/base_images/scib-base/README.md | 13 ------------- src/common/base_images/scib-base/env.yaml | 14 -------------- 6 files changed, 65 deletions(-) delete mode 100644 src/common/base_images/scanpy-r-micromamba/Dockerfile delete mode 100644 src/common/base_images/scanpy-r-micromamba/README.md delete mode 100644 src/common/base_images/scanpy-r-micromamba/env.yaml delete mode 100644 src/common/base_images/scib-base/Dockerfile delete mode 100644 src/common/base_images/scib-base/README.md delete mode 100644 src/common/base_images/scib-base/env.yaml diff --git a/src/common/base_images/scanpy-r-micromamba/Dockerfile b/src/common/base_images/scanpy-r-micromamba/Dockerfile deleted file mode 100644 index aca04a3a35..0000000000 --- a/src/common/base_images/scanpy-r-micromamba/Dockerfile +++ /dev/null @@ -1,6 +0,0 @@ -# version 1.9.1 -FROM mambaorg/micromamba:0.14.0 -COPY env.yaml /tmp/env.yaml -RUN micromamba install -y -n base -f /tmp/env.yaml && \ - micromamba clean --all --yes -WORKDIR /home/micromamba diff --git a/src/common/base_images/scanpy-r-micromamba/README.md b/src/common/base_images/scanpy-r-micromamba/README.md deleted file mode 100644 index 2630f72468..0000000000 --- a/src/common/base_images/scanpy-r-micromamba/README.md +++ /dev/null @@ -1,13 +0,0 @@ -# Scanpy image with R in micromamba - -Build and tag: - -```shell -docker build -t mumichae/scanpy-r-micromamba:1.9.1 . -``` - -Run the image interactively - -```shell -docker run -it mumichae/scanpy-r-micromamba:1.9.1 bash -``` \ No newline at end of file diff --git a/src/common/base_images/scanpy-r-micromamba/env.yaml b/src/common/base_images/scanpy-r-micromamba/env.yaml deleted file mode 100644 index e1d17a36f1..0000000000 --- a/src/common/base_images/scanpy-r-micromamba/env.yaml +++ /dev/null @@ -1,13 +0,0 @@ -name: base -channels: - - conda-forge -dependencies: - - python=3.8 - - pip=22.0 - - rpy2=3.4.2 - - scanpy=1.9.1 - - r-base=4 - - anndata=0.8 - - git - - pip: - - anndata2ri==1.0.6 diff --git a/src/common/base_images/scib-base/Dockerfile b/src/common/base_images/scib-base/Dockerfile deleted file mode 100644 index 3f112f1ef2..0000000000 --- a/src/common/base_images/scib-base/Dockerfile +++ /dev/null @@ -1,6 +0,0 @@ -# version 1.0.2 -FROM mumichae/scanpy-r-micromamba:1.9.1 -COPY env.yaml /tmp/env.yaml -RUN micromamba install -y -n base -f /tmp/env.yaml -RUN Rscript -e "devtools::install_github('theislab/kBET')" -RUN micromamba clean --all --yes diff --git a/src/common/base_images/scib-base/README.md b/src/common/base_images/scib-base/README.md deleted file mode 100644 index 562ea17862..0000000000 --- a/src/common/base_images/scib-base/README.md +++ /dev/null @@ -1,13 +0,0 @@ -# Image with scib based on scanpy-r-micromamba - -Build and tag: - -```shell -docker build -t mumichae/scib-base:1.0.2 . -``` - -Run the image interactively - -```shell -docker run -it mumichae/scib-base:1.0.2 bash -``` \ No newline at end of file diff --git a/src/common/base_images/scib-base/env.yaml b/src/common/base_images/scib-base/env.yaml deleted file mode 100644 index b6604c6b25..0000000000 --- a/src/common/base_images/scib-base/env.yaml +++ /dev/null @@ -1,14 +0,0 @@ -name: base -channels: - - conda-forge -dependencies: - - python=3.8 - - pip=22 - - rpy2=3.4.2 - - scanpy=1.9.1 - - r-base=4 - - r-devtools - - anndata=0.8 - - git - - pip: - - scib==1.0.2 From 27de0c0495eb08ac0bb1975adba960a243ae0928 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 16 Nov 2022 11:03:54 +0100 Subject: [PATCH 0337/1233] update anndata versions and integration method parameters to work with pipeline Former-commit-id: 20644b4561972d672f0832c7fd8108ccdbc08033 --- .gitignore | 3 ++- .../datasets/preprocessing/config.vsh.yaml | 1 - .../datasets/subsample/config.vsh.yaml | 1 - .../datasets/utils/_hvg_batch.py | 2 +- .../graph/methods/bbknn/config.vsh.yaml | 7 ++++--- .../graph/methods/bbknn/script.py | 2 +- .../graph/methods/combat/config.vsh.yaml | 9 +++++---- .../graph/methods/combat/script.py | 2 +- .../methods/scanorama_embed/config.vsh.yaml | 9 +++++---- .../graph/methods/scanorama_embed/script.py | 3 ++- .../methods/scanorama_feature/config.vsh.yaml | 9 +++++---- .../graph/methods/scanorama_feature/script.py | 2 +- .../graph/methods/scvi/config.vsh.yaml | 9 +++++---- .../graph/methods/scvi/script.py | 2 +- .../graph/metrics/ari/config.vsh.yaml | 1 - .../graph/metrics/nmi/config.vsh.yaml | 1 - src/batch_integration/workflows/test/main.nf | 17 ++++++++--------- .../dataset_loader/download/config.vsh.yaml | 3 +-- 18 files changed, 42 insertions(+), 41 deletions(-) diff --git a/.gitignore b/.gitignore index d4e373c1e6..9ffe374284 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +*.DS_Store *__pycache__ *.h5ad @@ -23,4 +24,4 @@ resources_test/ # nextflow specific ignores .nextflow* work -output \ No newline at end of file +output diff --git a/src/batch_integration/datasets/preprocessing/config.vsh.yaml b/src/batch_integration/datasets/preprocessing/config.vsh.yaml index 1b0075a36f..437c5bb26e 100644 --- a/src/batch_integration/datasets/preprocessing/config.vsh.yaml +++ b/src/batch_integration/datasets/preprocessing/config.vsh.yaml @@ -47,5 +47,4 @@ functionality: platforms: - type: docker image: mumichae/scib-base:1.0.2 - - type: native - type: nextflow diff --git a/src/batch_integration/datasets/subsample/config.vsh.yaml b/src/batch_integration/datasets/subsample/config.vsh.yaml index c4be1a57b8..e48ab044aa 100644 --- a/src/batch_integration/datasets/subsample/config.vsh.yaml +++ b/src/batch_integration/datasets/subsample/config.vsh.yaml @@ -43,5 +43,4 @@ functionality: platforms: - type: docker image: mumichae/scib-base:1.0.2 - - type: native - type: nextflow diff --git a/src/batch_integration/datasets/utils/_hvg_batch.py b/src/batch_integration/datasets/utils/_hvg_batch.py index 3cede619c4..ec59bfab49 100644 --- a/src/batch_integration/datasets/utils/_hvg_batch.py +++ b/src/batch_integration/datasets/utils/_hvg_batch.py @@ -5,7 +5,7 @@ def hvg_batch(adata, batch_key, n_hvg): """ Compute highly variable genes by batch """ - if n_hvg > adata.n_vars: + if n_hvg > adata.n_vars or n_hvg == 0: return adata.var_names.tolist() return scib.pp.hvg_batch( adata, diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index 6daa2204fe..b1e707cf92 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -21,11 +21,13 @@ functionality: - name: --hvg type: boolean description: Whether to subset to highly variable genes - required: true + default: false + required: false - name: --scaling type: boolean description: Whether to scale the data or not - required: true + default: false + required: false - name: --debug type: boolean description: Verbose output for debugging @@ -47,5 +49,4 @@ platforms: - type: python packages: - bbknn - - type: native - type: nextflow diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index caf122afc9..90c2aea599 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -22,7 +22,7 @@ scaling = par['scaling'] print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) if hvg: print('Select HVGs') diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml index 4469797fe3..2244d582cb 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -21,11 +21,13 @@ functionality: - name: --hvg type: boolean description: Whether to subset to highly variable genes - required: true + default: true + required: false - name: --scaling type: boolean description: Whether to scale the data or not - required: true + default: false + required: false - name: --debug type: boolean description: Verbose output for debugging @@ -40,6 +42,5 @@ functionality: - path: '../../../datasets/resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 - - type: native + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index 3f69f6f2f9..fe8fac6d98 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -22,7 +22,7 @@ scaling = par['scaling'] print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) if hvg: print('Select HVGs') diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml index c6e68c9dc9..e516ab098e 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -21,11 +21,13 @@ functionality: - name: --hvg type: boolean description: Whether to subset to highly variable genes - required: true + default: false + required: false - name: --scaling type: boolean description: Whether to scale the data or not - required: true + default: false + required: false - name: --debug type: boolean description: Verbose output for debugging @@ -40,10 +42,9 @@ functionality: - path: '../../../datasets/resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 setup: - type: python packages: - scanorama - - type: native - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/graph/methods/scanorama_embed/script.py index 32609ba5f9..f477fa1f8b 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/script.py +++ b/src/batch_integration/graph/methods/scanorama_embed/script.py @@ -22,7 +22,8 @@ scaling = par['scaling'] print('Read adata') -adata = sc.read(adata_file) +print(adata_file) +adata = sc.read_h5ad(adata_file) if hvg: print('Select HVGs') diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index cf7b4acb28..db13afd87f 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -21,11 +21,13 @@ functionality: - name: --hvg type: boolean description: Whether to subset to highly variable genes - required: true + default: false + required: false - name: --scaling type: boolean description: Whether to scale the data or not - required: true + default: false + required: false - name: --debug type: boolean description: Verbose output for debugging @@ -40,10 +42,9 @@ functionality: - path: '../../../datasets/resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 setup: - type: python packages: - scanorama - - type: native - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index ac6dcc0ef6..d752fef3c9 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -22,7 +22,7 @@ scaling = par['scaling'] print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) if hvg: print('Select HVGs') diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml index 174ec9344e..14fc92cb55 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -21,11 +21,13 @@ functionality: - name: --hvg type: boolean description: Whether to subset to highly variable genes - required: true + default: false + required: false - name: --scaling type: boolean description: Whether to scale the data or not - required: true + default: false + required: false - name: --debug type: boolean description: Verbose output for debugging @@ -40,10 +42,9 @@ functionality: - path: '../../../datasets/resources/datasets_pancreas.h5ad' platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 setup: - type: python packages: - scvi - - type: native - type: nextflow diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/graph/methods/scvi/script.py index 2cd2520578..f5485db850 100644 --- a/src/batch_integration/graph/methods/scvi/script.py +++ b/src/batch_integration/graph/methods/scvi/script.py @@ -22,7 +22,7 @@ scaling = par['scaling'] print('Read adata') -adata = sc.read(adata_file) +adata = sc.read_h5ad(adata_file) if hvg: print('Select HVGs') diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 9e470e5feb..5b3e5d1554 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -36,5 +36,4 @@ functionality: platforms: - type: docker image: mumichae/scib-base:1.0.0 - - type: native - type: nextflow diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 950f7da7f9..7521b65424 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -36,5 +36,4 @@ functionality: platforms: - type: docker image: mumichae/scib-base:1.0.0 - - type: native - type: nextflow diff --git a/src/batch_integration/workflows/test/main.nf b/src/batch_integration/workflows/test/main.nf index 01b1af476f..1559ede6b5 100644 --- a/src/batch_integration/workflows/test/main.nf +++ b/src/batch_integration/workflows/test/main.nf @@ -4,6 +4,8 @@ targetDir = "${params.rootDir}/target/nextflow" params.download = "$launchDir/src/batch_integration/workflows/download.tsv" params.preprocessing = "$launchDir/src/batch_integration/workflows/test/preprocessing.tsv" +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) + // import dataset loaders include { download } from "$targetDir/common/dataset_loader/download/main.nf" params(params) include { subsample } from "$targetDir/batch_integration/datasets/subsample/main.nf" params(params) @@ -48,7 +50,6 @@ workflow process_data { additional_params = Channel.fromPath(params.preprocessing) | splitCsv(header: true, sep: "\t") | map { [ it.name, it ] } - | view { "additional_params $it" } subset = channel_in.join(additional_params) | map { id, data, additional -> @@ -60,7 +61,6 @@ workflow process_data { | map { id, data, additional -> [ id, [ input: data ] + additional ] } - | view { "preprocessing $it" } | preprocessing | join(additional_params) | map { id, data, additional -> @@ -78,17 +78,16 @@ workflow process_data { workflow { load_data | process_data - | view{ "process_data: $it" } -/** -| (bbknn & combat & scvi & scanorama_embed & scanorama_feature) -| mix -| toSortedList - | view + | view { "integration input $it" } + | (bbknn & combat & scvi & scanorama_embed & scanorama_feature) + | mix + | toSortedList + | view { "toSortedList $it" } +/* | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } | (ari & nmi) | extract_scores.run( auto: [ publish: true ] ) */ - } diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml index a0f9410c8e..204def0578 100644 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ b/src/common/dataset_loader/download/config.vsh.yaml @@ -45,6 +45,5 @@ platforms: - type: python packages: - scanpy - - "anndata<0.8" - - type: native + - "anndata>=0.8" - type: nextflow From c22aaff4f6ddaae89a8bf45fffccf01ee34e306f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 11:22:04 +0100 Subject: [PATCH 0338/1233] refactor split datasets in label projection Former-commit-id: 19e801d21de2e65a1e91fe3de076897f8e0d9452 --- .../process_openproblems_v1}/datasets.yaml | 12 ++-------- .../process_openproblems_v1/run_nextflow.sh | 2 +- .../api/comp_split_dataset.yaml | 2 +- .../split_dataset/generate_yaml.R | 24 +++++++++++++++++++ .../split_dataset/params.yaml | 12 ++++++++++ .../split_dataset/run_nextflow.sh | 17 +++++++++++++ src/label_projection/split_dataset/script.py | 11 ++++----- 7 files changed, 62 insertions(+), 18 deletions(-) rename src/datasets/{loaders/openproblems_v1 => workflows/process_openproblems_v1}/datasets.yaml (75%) create mode 100644 src/label_projection/split_dataset/generate_yaml.R create mode 100644 src/label_projection/split_dataset/params.yaml create mode 100755 src/label_projection/split_dataset/run_nextflow.sh diff --git a/src/datasets/loaders/openproblems_v1/datasets.yaml b/src/datasets/workflows/process_openproblems_v1/datasets.yaml similarity index 75% rename from src/datasets/loaders/openproblems_v1/datasets.yaml rename to src/datasets/workflows/process_openproblems_v1/datasets.yaml index 177d850a74..85af28c58e 100644 --- a/src/datasets/loaders/openproblems_v1/datasets.yaml +++ b/src/datasets/workflows/process_openproblems_v1/datasets.yaml @@ -9,52 +9,44 @@ param_list: obs_batch: experiment_code obs_tissue: tissue layer_counts: counts - output: cengen.h5ad - id: immune_cells obs_celltype: final_annotation obs_batch: batch obs_tissue: tissue layer_counts: counts - output: immune_cells.h5ad - id: mouse_blood_olssen_labelled obs_celltype: celltype layer_counts: counts - output: mouse_blood_olssen_labelled.h5ad - id: mouse_hspc_nestorowa2016 obs_celltype: cell_type_label layer_counts: counts - output: mouse_hspc_nestorowa2016.h5ad - id: pancreas obs_celltype: celltype obs_batch: tech layer_counts: counts - output: pancreas.h5ad - id: tabula_muris_senis_droplet_lung obs_celltype: cell_type obs_batch: donor_id layer_counts: counts - output: tabula_muris_senis_droplet_lung.h5ad - id: tenx_1k_pbmc layer_counts: counts - output: tenx_1k_pbmc.h5ad - id: tenx_5k_pbmc layer_counts: counts - output: tenx_5k_pbmc.h5ad - id: tnbc_wu2021 obs_celltype: celltype_minor layer_counts: counts - output: tnbc_wu2021.h5ad - id: zebrafish obs_celltype: cell_type obs_batch: lab layer_counts: counts - output: zebrafish.h5ad \ No newline at end of file + +output: '$id.h5ad' \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh index ac65504d9b..02723f7ca1 100755 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -13,5 +13,5 @@ bin/nextflow \ -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ -profile docker \ -resume \ - -params-file src/datasets/loaders/openproblems_v1/datasets.yaml \ + -params-file src/datasets/workflows/process_openproblems_v1/datasets.yaml \ --publish_dir resources/datasets/openproblems_v1 \ No newline at end of file diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_split_dataset.yaml index e935e7135c..eb40423101 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_split_dataset.yaml @@ -80,4 +80,4 @@ functionality: assert "batch" in output_solution.obs print(">> All checks succeeded!") - - path: ../../../../resources_test/common/pancreas + - path: ../../../resources_test/common/pancreas diff --git a/src/label_projection/split_dataset/generate_yaml.R b/src/label_projection/split_dataset/generate_yaml.R new file mode 100644 index 0000000000..6bb1828d83 --- /dev/null +++ b/src/label_projection/split_dataset/generate_yaml.R @@ -0,0 +1,24 @@ +library(tidyverse) +library(anndata) + +h5ad_files <- fs::dir_ls("resources/datasets/openproblems_v1", recurse = TRUE, regexp = "\\.h5ad$") + +param_list <- map(h5ad_files, function(h5ad_file) { + ad <- anndata::read_h5ad(h5ad_file, backed = "r") + if (all(c("batch", "celltype") %in% colnames(ad$obs))) { + list( + id = gsub(".*/", "", ad$uns[["dataset_id"]]), + input = paste0("../../../", h5ad_file) + ) + } else { + NULL + } +}) +output <- list( + param_list = unname(param_list) %>% .[!map_lgl(., is.null)], + obs_label = "celltype", + obs_batch = "batch", + seed = 123L +) + +yaml::write_yaml(output, "src/label_projection/split_dataset/params.yaml") diff --git a/src/label_projection/split_dataset/params.yaml b/src/label_projection/split_dataset/params.yaml new file mode 100644 index 0000000000..be769ed93c --- /dev/null +++ b/src/label_projection/split_dataset/params.yaml @@ -0,0 +1,12 @@ +param_list: +- id: immune_cells + input: resources/datasets/openproblems_v1/immune_cells.h5ad +- id: pancreas + input: resources/datasets/openproblems_v1/pancreas.h5ad +- id: tabula_muris_senis_droplet_lung + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.h5ad +- id: zebrafish + input: resources/datasets/openproblems_v1/zebrafish.h5ad +obs_label: celltype +obs_batch: batch +seed: 123 diff --git a/src/label_projection/split_dataset/run_nextflow.sh b/src/label_projection/split_dataset/run_nextflow.sh new file mode 100755 index 0000000000..5bbfeaaa49 --- /dev/null +++ b/src/label_projection/split_dataset/run_nextflow.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script target/nextflow/label_projection/split_dataset/main.nf \ + -profile docker \ + -resume \ + -params-file src/label_projection/split_dataset/params.yaml \ + --publish_dir resources/label_projection/openproblems_v1 \ No newline at end of file diff --git a/src/label_projection/split_dataset/script.py b/src/label_projection/split_dataset/script.py index 38bd9a2e3d..21ffcb8935 100644 --- a/src/label_projection/split_dataset/script.py +++ b/src/label_projection/split_dataset/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/label_projection/pancreas/dataset.h5ad', + 'input': 'work/b5/46e5081b30a46ab67d074d4c23eb71/zebrafish.h5ad', 'method': 'batch', 'seed': None, 'obs_batch': 'batch', @@ -30,11 +30,10 @@ print(f">> Process data using {par['method']} method") if par["method"] == "batch": - test_batches = adata.obs[par["obs_batch"]].dtype.categories[[-3, -1]] - is_test = [ - True if adata.obs[par["obs_batch"]][idx] in test_batches else False - for idx in adata.obs_names - ] + batch_info = adata.obs[par["obs_batch"]] + batch_categories = batch_info.dtype.categories + test_batches = random.sample(list(batch_categories), 1) + is_test = [ x in test_batches for x in batch_info ] elif par["method"] == "random": train_ix = np.random.choice(adata.n_obs, round(adata.n_obs * 0.8), replace=False) is_test = [ not x in train_ix for x in range(0, adata.n_obs) ] From 8d100ff355584b60feaa8f79d26d347354e43d08 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 12:18:19 +0100 Subject: [PATCH 0339/1233] fix namespace Former-commit-id: 0e2a3adae79bf74ac360c8d57c32879fbc22a3b2 --- src/label_projection/methods/knn_classifier/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn_classifier/config.vsh.yaml index 564bbe96a8..ec2afa296c 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn_classifier/config.vsh.yaml @@ -1,6 +1,7 @@ __inherits__: ../../api/comp_method.yaml functionality: name: "knn_classifier" + namespace: "label_projection/methods" description: "K-Nearest Neighbors classifier" info: type: method From 7cc63ede03814a38944e24b198773f9bc687e582 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 12:18:34 +0100 Subject: [PATCH 0340/1233] fix metric label encoders Former-commit-id: 6d94b66652dbb054609af85cd3c03052fcbec0fc --- src/label_projection/metrics/accuracy/script.py | 3 ++- src/label_projection/metrics/f1/script.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/label_projection/metrics/accuracy/script.py b/src/label_projection/metrics/accuracy/script.py index 0d73e7324d..93002ee4e2 100644 --- a/src/label_projection/metrics/accuracy/script.py +++ b/src/label_projection/metrics/accuracy/script.py @@ -20,7 +20,8 @@ assert (input_prediction.obs_names == input_solution.obs_names).all() print("Encode labels") -encoder = sklearn.preprocessing.LabelEncoder().fit(input_solution.obs["label"]) +cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) +encoder = sklearn.preprocessing.LabelEncoder().fit(cats) input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) diff --git a/src/label_projection/metrics/f1/script.py b/src/label_projection/metrics/f1/script.py index 50aad56d94..58a68341b4 100644 --- a/src/label_projection/metrics/f1/script.py +++ b/src/label_projection/metrics/f1/script.py @@ -21,7 +21,8 @@ assert (input_prediction.obs_names == input_solution.obs_names).all() print("Encode labels") -encoder = sklearn.preprocessing.LabelEncoder().fit(input_solution.obs["label"]) +cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) +encoder = sklearn.preprocessing.LabelEncoder().fit(cats) input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) From ca47e84c82864fa8784d374b6d2c45cf32a6452e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 12:18:50 +0100 Subject: [PATCH 0341/1233] wip update benchmark pipeline Former-commit-id: 2533d6ed8af8ee19d2fba9af03285f799f6d22bd --- bin/init | 2 + .../workflows/run/config.vsh.yaml | 26 ++++ .../workflows/run/generate_yaml.R | 32 ++++ src/label_projection/workflows/run/main.nf | 137 +++++++----------- .../workflows/run/nextflow.config | 8 +- .../workflows/run/params.yaml | 17 +++ .../workflows/run/run_nextflow.sh | 11 +- 7 files changed, 141 insertions(+), 92 deletions(-) create mode 100644 src/label_projection/workflows/run/config.vsh.yaml create mode 100644 src/label_projection/workflows/run/generate_yaml.R create mode 100644 src/label_projection/workflows/run/params.yaml diff --git a/bin/init b/bin/init index 8a276b14ee..bb1a86cf38 100755 --- a/bin/init +++ b/bin/init @@ -12,6 +12,8 @@ curl -fsSL get.viash.io | bash -s -- \ --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ --tag develop +# add --namespace_separator '/' ? + # automatically export the workflow helper NXF_UTILS=src/nxf_utils [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS diff --git a/src/label_projection/workflows/run/config.vsh.yaml b/src/label_projection/workflows/run/config.vsh.yaml new file mode 100644 index 0000000000..4b9785b86d --- /dev/null +++ b/src/label_projection/workflows/run/config.vsh.yaml @@ -0,0 +1,26 @@ +functionality: + name: "run_benchmark" + namespace: "label_projection/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input_train" + type: "file" # todo: replace with includes + - name: "--input_test" + type: "file" # todo: replace with includes + - name: "--input_solution" + type: "file" # todo: replace with includes + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + # todo: fix inherits in nxf + # __inherits__: ../../api/anndata_raw_dataset.yaml + resources: + - type: nextflow_script + path: main.nf diff --git a/src/label_projection/workflows/run/generate_yaml.R b/src/label_projection/workflows/run/generate_yaml.R new file mode 100644 index 0000000000..50d0fa6f86 --- /dev/null +++ b/src/label_projection/workflows/run/generate_yaml.R @@ -0,0 +1,32 @@ +library(tidyverse) +library(anndata) + +h5ad_files <- fs::dir_ls("resources/label_projection/openproblems_v1", recurse = TRUE, regexp = "\\.h5ad$") + +regex <- ".*/([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.h5ad" + +df <- tibble( + path = as.character(h5ad_files), + id = gsub(regex, "\\1", path), + comp = gsub(regex, "\\2", path), + arg_name = gsub(regex, "\\3", path) +) %>% + spread(arg_name, path) + +param_list <- pmap(df, function(id, comp, output_solution, output_test, output_train) { + list( + id = id, + input_train = output_train, + input_test = output_test, + input_solution = output_solution + ) +}) + +output <- list( + param_list = param_list + # obs_label = "celltype", + # obs_batch = "batch", + # seed = 123L +) + +yaml::write_yaml(output, "src/label_projection/workflows/run/params.yaml") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index d660f579c1..5688e8ce8c 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -1,14 +1,14 @@ nextflow.enable.dsl=2 -targetDir = "${params.rootDir}/target/nextflow" +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" - -// include { split_dataset } from "$targetDir/label_projection/split_dataset/main.nf" - -// import methods -include { all_correct } from "$targetDir/label_projection/control_methods/all_correct/main.nf" +// import control methods +include { true_labels } from "$targetDir/label_projection/control_methods/true_labels/main.nf" include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" + +// import methods include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" @@ -21,91 +21,66 @@ include { logistic_regression } from "$targetDir/label_projection/methods/logist include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" -// import helper functions +// tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" +// import helper functions +include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" -/******************************************************* -* Dataset processor workflows * -*******************************************************/ -// This workflow reads in a tsv containing some metadata about each dataset. -// For each entry in the metadata, a dataset is generated, usually by downloading -// and processing some files. The end result of each of these workflows -// should be simply a channel of [id, h5adfile] triplets. -// -// If the need arises, these workflows could be split off into a separate file. +config = readConfig("$projectDir/config.vsh.yaml") -params.tsv = "$launchDir/src/label_projection/data_processing/anndata_loader.tsv" +workflow { + helpMessage(config) -workflow load_data { - main: - output_ = Channel.fromPath(params.tsv) - | splitCsv(header: true, sep: "\t") - | filter{ it.name != "tabula_muris_senis_facs_lung" || it.name != "tabula_muris_senis_droplet_lung" } //TODO - | map{ [ it.name, it ] } - | download - emit: - output_ + viashChannel(params, config) + | run_wf } -def mlp0 = mlp.run( - args: [max_iter: 100, hidden_layer_sizes: 20] -) - -def lr0 = logistic_regression.run( - args: [max_iter: 100] -) -def scvi_hvg0 = scanvi_hvg.run( - args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, - span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] -) +workflow run_wf { + take: + input_ch -def scvi_allgns0 = scanvi_all_genes.run( - args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, - span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] -) + main: + output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + method: ["input_train", "input_test"], + metric: [ "input_solution" ] + ) -def scarches_hvg0 = scarches_scanvi_hvg.run( - args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, - span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] -) + // run method + | getWorkflowArguments(key: "method") + | majority_vote -def scarches_allgns0 = scarches_scanvi_all_genes.run( - args: [n_hidden: 32, n_layers: 1, n_latent: 10, n_top_genes: 2000, - span: 0.8, max_epochs: 1, limit_train_batches: 10, limit_val_batches: 10] -) + // run metric + | getWorkflowArguments(key: "metric", inputKey: "input_prediction") + | (accuracy & f1) + | mix -def f1a = f1.run( - args: [average: "weighted"] -) - -def unique_file_name(tuple) { - return [tuple[1].baseName.replaceAll('\\.output$', ''), tuple[1]] -} - -/******************************************************* -* Main workflow * -*******************************************************/ - -workflow { - load_data - | randomize - | subsample.run( - map: { [it[0], [input: it[1], even: true]] } - ) - | (log_cpm & log_scran_pooling) - | mix - | map { unique_file_name(it) } - | (knn_classifier & mlp0 & lr0 & random_labels & majority_vote & all_correct) - | mix - | map { unique_file_name(it) } - | (accuracy & f1a) - | mix - | toSortedList - | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - | extract_scores.run( - args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"], - auto: [ publish: true ] - ) + emit: + output_ch } +// workflow { +// load_data +// | randomize +// | subsample.run( +// map: { [it[0], [input: it[1], even: true]] } +// ) +// | (log_cpm & log_scran_pooling) +// | mix +// | map { unique_file_name(it) } +// | (knn_classifier & mlp0 & lr0 & random_labels & majority_vote & true_labels) +// | mix +// | map { unique_file_name(it) } +// | (accuracy & f1a) +// | mix +// | toSortedList +// | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } +// | extract_scores.run( +// args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"], +// auto: [ publish: true ] +// ) +// } diff --git a/src/label_projection/workflows/run/nextflow.config b/src/label_projection/workflows/run/nextflow.config index 425fb92fed..0ecebcacc0 100644 --- a/src/label_projection/workflows/run/nextflow.config +++ b/src/label_projection/workflows/run/nextflow.config @@ -1,11 +1,11 @@ manifest { - nextflowVersion = '!>=20.12.1-edge' + nextflowVersion = '!>=22.04.5' } params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() } // include common settings -includeConfig("${params.rootDir}/workflows/utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/workflows/utils/labels.config") +includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/nxf_utils/labels.config") diff --git a/src/label_projection/workflows/run/params.yaml b/src/label_projection/workflows/run/params.yaml new file mode 100644 index 0000000000..5bab1a89a3 --- /dev/null +++ b/src/label_projection/workflows/run/params.yaml @@ -0,0 +1,17 @@ +param_list: +- id: immune_cells + input_train: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_solution.h5ad +- id: pancreas + input_train: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_solution.h5ad +- id: tabula_muris_senis_droplet_lung + input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_solution.h5ad +- id: zebrafish + input_train: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_solution.h5ad diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_nextflow.sh index 2c244104d1..cf6cde2d29 100755 --- a/src/label_projection/workflows/run/run_nextflow.sh +++ b/src/label_projection/workflows/run/run_nextflow.sh @@ -1,20 +1,17 @@ #!/bin/bash -# Run this prior to executing this script: -# bin/viash_build -q 'label_projection|common' - # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -# choose a particular version of nextflow -export NXF_VER=21.10.6 +export NXF_VER=22.04.5 bin/nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ - --publishDir output/label_projection \ + -profile docker \ -resume \ - -with-docker + -params-file src/label_projection/workflows/run/params.yaml \ + --publish_dir output/label_projection \ No newline at end of file From 49be0fe6f333bce3261b3e93debd1c03d9ac1b6b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 12:41:47 +0100 Subject: [PATCH 0342/1233] fix extract scores Former-commit-id: 8f80a343d43f7582ab27e2d582b7bc91453e0372 --- src/common/extract_scores/config.vsh.yaml | 4 ++-- src/common/extract_scores/script.R | 20 ++++++++++---------- src/label_projection/workflows/run/main.nf | 7 +++++++ 3 files changed, 19 insertions(+), 12 deletions(-) diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 9912e66ccd..3e1a336106 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: - name: "--column_names" type: "string" multiple: true - default: [ "dataset_id", "method_id", "metric_id", "metric_value" ] + default: [ "dataset_id", "method_id", "metric_ids", "metric_values" ] description: "Which fields from adata.uns to extract and store as a data frame." - name: "--output" alternatives: ["-o"] @@ -29,7 +29,7 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata] + cran: [ anndata, tidyverse ] - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python diff --git a/src/common/extract_scores/script.R b/src/common/extract_scores/script.R index 670ccf2aea..6b540380ab 100644 --- a/src/common/extract_scores/script.R +++ b/src/common/extract_scores/script.R @@ -1,18 +1,18 @@ -## VIASH START -par <- list( - input = list.files("work", full.names = TRUE, pattern = "*.h5ad"), - output = "out_bash/modality_alignment/scores.tsv" -) -inp <- par$input[[2]] -## VIASH END - cat("Loading dependencies\n") library(anndata, warn.conflicts = FALSE) options(tidyverse.quiet = TRUE) library(tidyverse) library(assertthat) -cat("Reading input h5ad files") +## VIASH START +par <- list( + input = "resources_test/label_projection/pancreas/knn_accuracy.h5ad", + output = "scores.tsv" +) +inp <- par$input[[1]] +## VIASH END + +cat("Reading input h5ad files\n") scores <- map_df(par$input, function(inp) { cat("Reading '", inp, "'\n", sep = "") ad <- read_h5ad(inp) @@ -24,7 +24,7 @@ scores <- map_df(par$input, function(inp) { ) } - as_tibble(ad$uns[par$column_names]) + data.frame(ad$uns[par$column_names]) }) write_tsv(scores, par$output) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 5688e8ce8c..e40716142d 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -60,6 +60,13 @@ workflow run_wf { | (accuracy & f1) | mix + // convert to tsv + | toSortedList + | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + | extract_scores.run( + auto: [ publish: true ] + ) + emit: output_ch } From f1650c1035823584d4ac87c2656ea9ce0f2beeeb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 12:57:32 +0100 Subject: [PATCH 0343/1233] extend pipeline Former-commit-id: a186905e6d311b417bdd5febfc1837300e910436 --- src/label_projection/workflows/run/main.nf | 55 +++++++++++----------- 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index e40716142d..bc46fc53b7 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -43,6 +43,12 @@ workflow run_wf { input_ch main: + def addSolution = { tup -> + out = tup.clone() + out[1] = out[1] + [input_solution: out[2].metric.input_solution] + out + } + output_ch = input_ch // split params for downstream components @@ -51,43 +57,38 @@ workflow run_wf { metric: [ "input_solution" ] ) - // run method + // run methods | getWorkflowArguments(key: "method") - | majority_vote + | ( + true_labels.run(map: addSolution) & + random_labels & + majority_vote & + knn_classifier & + logistic_regression & + mlp + ) + | mix - // run metric - | getWorkflowArguments(key: "metric", inputKey: "input_prediction") + // construct tuples for metrics + | pmap{ id, file, passthrough -> + // derive unique ids from output filenames + def newId = file.getName().replaceAll(".output.*", "") + // combine prediction with solution + def newData = [ input_prediction: file, input_solution: passthrough.metric.input_solution ] + [ newId, newData ] + } + + // run metrics | (accuracy & f1) | mix // convert to tsv | toSortedList - | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } + | map{ it -> [ "combined", it.collect{ it[1] } ] } | extract_scores.run( auto: [ publish: true ] ) emit: output_ch -} -// workflow { -// load_data -// | randomize -// | subsample.run( -// map: { [it[0], [input: it[1], even: true]] } -// ) -// | (log_cpm & log_scran_pooling) -// | mix -// | map { unique_file_name(it) } -// | (knn_classifier & mlp0 & lr0 & random_labels & majority_vote & true_labels) -// | mix -// | map { unique_file_name(it) } -// | (accuracy & f1a) -// | mix -// | toSortedList -// | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } -// | extract_scores.run( -// args: [column_names: "dataset_id:normalization_method:method_id:metric_id:metric_value"], -// auto: [ publish: true ] -// ) -// } +} \ No newline at end of file From 2c537596a55ec9b2a0aba2c841b8821d8f6df3d2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 13:11:14 +0100 Subject: [PATCH 0344/1233] fix pca operations Former-commit-id: f9e2cc0f4df7ff0733a6486bfa205084fed0c75f --- .../methods/knn_classifier/script.py | 12 ++++++------ .../methods/logistic_regression/script.py | 12 ++++++------ src/label_projection/methods/mlp/script.py | 12 ++++++------ 3 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn_classifier/script.py index 012efe6d8b..7edbeca922 100644 --- a/src/label_projection/methods/knn_classifier/script.py +++ b/src/label_projection/methods/knn_classifier/script.py @@ -7,9 +7,10 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', + 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', 'output': 'output.h5ad', + 'layer_input': 'counts' } meta = { 'functionality_name': 'foo', @@ -19,13 +20,14 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) +input_layer = par["layer_input"] print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.X) + is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) min_components = min( - [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] ) if is_sparse: min_components -= 1 @@ -45,8 +47,6 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) -input_layer = par["layer_input"] - print("Fit to train data") pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 4211459c4a..6f62694824 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -7,9 +7,10 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', + 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', 'output': 'output.h5ad', + 'layer_input': 'counts' } meta = { 'functionality_name': 'foo', @@ -19,13 +20,14 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) +input_layer = par["layer_input"] print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.X) + is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) min_components = min( - [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] ) if is_sparse: min_components -= 1 @@ -47,8 +49,6 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) -input_layer = par["layer_input"] - print("Fit to train data") pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 4c5dd4e60e..1fea2a5555 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -7,9 +7,10 @@ ## VIASH START par = { - 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', - 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', + 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', 'output': 'output.h5ad', + 'layer_input': 'counts' } meta = { 'functionality_name': 'foo', @@ -19,13 +20,14 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) +input_layer = par["layer_input"] print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.X) + is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) min_components = min( - [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] + [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] ) if is_sparse: min_components -= 1 @@ -48,8 +50,6 @@ def pca_op(adata_train, adata_test, n_components=100): ] ) -input_layer = par["layer_input"] - print("Fit to train data") pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) From 33847f08b8e8687c1e1628b5c65ef115a3794634 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 13:21:37 +0100 Subject: [PATCH 0345/1233] fix api Former-commit-id: 183eeb8c4d893fd6a14b24bda3f9e70ea2681687 --- src/datasets/api/anndata_dataset.yaml | 3 +++ src/label_projection/api/anndata_dataset.yaml | 3 +++ src/label_projection/api/anndata_solution.yaml | 3 +++ src/label_projection/api/anndata_test.yaml | 3 +++ src/label_projection/api/anndata_train.yaml | 3 +++ 5 files changed, 15 insertions(+) diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index 21694f6745..92337723d7 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -15,6 +15,9 @@ info: - type: double name: log_scran_pooling description: Scran pooling normalized counts, log transformed + - type: double + name: sqrt_cpm + description: CPM normalized counts, sqrt transformed obs: - type: string name: celltype diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml index f79db388e7..98e7fc7ba7 100644 --- a/src/label_projection/api/anndata_dataset.yaml +++ b/src/label_projection/api/anndata_dataset.yaml @@ -14,6 +14,9 @@ info: - type: double name: log_scran_pooling description: Scran pooling normalized counts, log transformed + - type: double + name: sqrt_cpm + description: CPM normalized counts, sqrt transformed obs: - type: double name: label diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index d711347996..a43c01ac34 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -14,6 +14,9 @@ info: - type: double name: log_scran_pooling description: Scran pooling normalized counts, log transformed + - type: double + name: sqrt_cpm + description: CPM normalized counts, sqrt transformed obs: - type: string name: label diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index 3b506675d1..03add01c3d 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -14,6 +14,9 @@ info: - type: double name: log_scran_pooling description: Scran pooling normalized counts, log transformed + - type: double + name: sqrt_cpm + description: CPM normalized counts, sqrt transformed obs: - type: string name: batch diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index 87181e24f7..e50255af15 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -14,6 +14,9 @@ info: - type: double name: log_scran_pooling description: Scran pooling normalized counts, log transformed + - type: double + name: sqrt_cpm + description: CPM normalized counts, sqrt transformed obs: - type: string name: label From 90309bd03cd3da9b052af899d92d90a508443238 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Nov 2022 14:47:57 +0100 Subject: [PATCH 0346/1233] add initial analysis script Former-commit-id: 8923077ef8b8eb3be53fabdada7fcc4d58636743 --- README.qmd | 1 + src/common/resources_test_scripts/aws_sync.sh | 1 + .../analysis_scripts/script.R | 61 +++++++++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 src/label_projection/analysis_scripts/script.R diff --git a/README.qmd b/README.qmd index fb1f166136..f24bae47ff 100644 --- a/README.qmd +++ b/README.qmd @@ -45,6 +45,7 @@ bin/init ```bash bin/viash run src/common/sync_test_resources/config.vsh.yaml +bin/viash run src/common/sync_test_resources/config.vsh.yaml -- --input s3://openproblems-data/resources --output resources ``` **Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. diff --git a/src/common/resources_test_scripts/aws_sync.sh b/src/common/resources_test_scripts/aws_sync.sh index 1bbea6e60d..d146cd3caf 100644 --- a/src/common/resources_test_scripts/aws_sync.sh +++ b/src/common/resources_test_scripts/aws_sync.sh @@ -4,3 +4,4 @@ echo "Run the command in this script manually" exit 1 aws s3 sync "resources_test" "s3://openproblems-data/resources_test" --exclude */temp_* --delete --dryrun +aws s3 sync "resources" "s3://openproblems-data/resources" --exclude */temp_* --delete --dryrun diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R new file mode 100644 index 0000000000..7faecd957e --- /dev/null +++ b/src/label_projection/analysis_scripts/script.R @@ -0,0 +1,61 @@ +library(tidyverse) + +scores <- read_tsv("output/label_projection/combined.extract_scores.output.tsv") %>% + rename(metric_id = metric_ids, metric_value = metric_values) + +ns_list_methods <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*methods"))$stdout) + +method_info <- map_df(ns_list_methods, function(conf) { + tryCatch({ + info <- c( + list( + id = conf$functionality$name, + namespace = conf$functionality$namespace, + description = conf$functionality$description + ), + conf$functionality$info + ) + as.data.frame(info) + }, error = function(err) { + cat(err$message, "\n", sep = "") + data.frame(id = conf$functionality$name) + }) +}) + +ns_list_metrics <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*metrics"))$stdout) + +metric_info <- map_df(ns_list_metrics, function(conf) { + tryCatch({ + map_df(conf$functionality$info$metrics, as.data.frame) + }, error = function(err) { + cat(err$message, "\n", sep = "") + data.frame(id = conf$functionality$name) + }) +}) + + + +df <- scores %>% + left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") %>% + left_join(metric_info %>% select(id, label, min, max, maximise) %>% rename_all(function(x) paste0("metric_", x)), by = "metric_id") %>% + mutate(method_label = factor(method_label, levels = c("True labels", "Multilayer perceptron"))) + +ordering <- df %>% + group_by(metric_id, dataset_id) %>% + mutate(rank = rank(ifelse(metric_maximise, -metric_value, metric_value))) %>% + ungroup() %>% + group_by(method_id, method_label) %>% + summarise(mean_rank = mean(rank)) %>% + arrange(mean_rank) + +df$method_label <- factor(df$method_label, levels = rev(ordering$method_label)) + +g <- ggplot(df %>% arrange(method_label)) + + geom_path(aes(metric_value, method_label, group = dataset_id), alpha = .2) + + geom_point(aes(metric_value, method_label, colour = method_type)) + + facet_wrap(~metric_label, ncol = 1) + + theme_bw() + + labs(title = "OpenProblems v2 - Label projection v0.1") + +ggsave("output/label_projection/plot.pdf", g, width = 6, height = 8) +ggsave("output/label_projection/plot.png", g, width = 6, height = 8) From 3862beeb6797caef2ab09163e99cbdfac9c65dd0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 07:41:14 +0100 Subject: [PATCH 0347/1233] update docs Former-commit-id: 2cae9eaca605b01ef4b20aee66e5546ba9355261 --- CONTRIBUTING.md | 881 +++++++++--------- CONTRIBUTING.qmd | 651 ++++++------- README.md | 523 +---------- README.qmd | 328 +------ .../{params.yaml => params_benchmark.yaml} | 0 .../workflows/run/params_test.yaml | 5 + .../workflows/run/run_benchmark.sh | 17 + .../run/{run_nextflow.sh => run_test.sh} | 2 +- 8 files changed, 797 insertions(+), 1610 deletions(-) rename src/label_projection/workflows/run/{params.yaml => params_benchmark.yaml} (100%) create mode 100644 src/label_projection/workflows/run/params_test.yaml create mode 100755 src/label_projection/workflows/run/run_benchmark.sh rename src/label_projection/workflows/run/{run_nextflow.sh => run_test.sh} (83%) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 79dbe4a392..703bbe403d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,6 +1,22 @@ Contributing to OpenProblems ================ +- Code of conduct +- Requirements +- Quick start +- Project + structure +- Adding a Viash component +- Running a component from CLI +- Building a + component +- Unit testing a component +- More + information + [OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). @@ -21,483 +37,512 @@ Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1. -## Ways to contribute - -There are many ways to contribute to OpenProblems, with the most common -ones being contribution of code or documentation to the project. - -Contributing new functionality usually comes in the form of new -[datasets](#adding-a-new-dataset), [methods](#adding-a-new-method), -[metric](#adding-a-new-metric), or even entire new -[tasks](#adding-a-new-task). - -Improving the documentation is no less important than improving the -library itself. If you find a typo in the documentation, or have made -improvements, do not hesitate to submit a [GitHub pull -request](https://github.com/openproblems-bio/openproblems-v2/pulls). - -But there are many other ways to help. In particular helping to -[improve, triage, and investigate issues](#bug-triaging) and [reviewing -other developers’ pull requests](#code-review) are very valuable -contributions that decrease the burden on the project maintainers. - -Another way to contribute is to report [issues you’re -facing](#submitting-a-bug-report-or-feature-request), and give a “thumbs -up” on issues that others reported and that are relevant to you. It also -helps us if you spread the word: reference the project from your blog -and articles, link to it from your website, or simply star to say “I use -it”: - -Star - - - -## Submitting New Features - -To submit new features to Open Problems for Single Cell Analysis, follow -the steps below: - -1. Search through the [GitHub - Issues](https://github.com/openproblems-bio/openproblems-v2/issues) - tracker to make sure there isn’t someone already working on the - feature you’d like to add. If someone is working on this, post in - that issue that you’d like to help or reach out to one of the - contributors working on the issue directly. - -2. If there isn’t an existing issue tracking this feature, create one! - There are several templates you can choose one depending on what - type of feature you’d like to add. - -3. Fork into your - account. If you’re new to `git`, you might find the [Fork a - repo](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) - documentation helpful. \[\](” - width=400px\> - -4. Set up [tower.nf](https://tower.nf) and make sure you have access to - [`openproblems-bio`](https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch). - If you do not have access, please contact us at - . - -5. Create repository secrets (*not environment secrets*) - - - - *AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are included in - your AWS login details. If you do not have these, please contact - us at .* - - *TOWER_ACCESS_KEY: log in with GitHub to and - create a token at .* - - When you are done with this step, your page should look like - this: ![AWS secrets success](static/img/AWS_secret.png) - -6. Enable workflows at - . - -7. Set up your git repository to fetch branches from `base` at - `openproblems-bio/openproblems` - - ``` shell - git clone git@github.com:/openproblems.git - cd openproblems - git remote add base git@github.com:openproblems-bio/openproblems.git - git fetch --all - git branch --set-upstream-to base/main - git pull - ``` - - **Note:** If you haven’t set up SSH keys with your GitHub account, - you may see this error message when adding `base` to your - repository: - - ``` text - git@github.com: Permission denied (publickey). - fatal: Could not read from remote repository. - Please make sure you have the correct access rights - ``` - - To generate an SSH key and add it to your GitHub account, follow - [this tutorial from - GitHub](https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account). - -8. Create a new branch for your task (**no underscores or spaces - allowed**). It is best to coordinate with other people working on - the same feature as you so that there aren’t clases in images - uploaded to our ECR. Here we’re creating a branch called - `method-method-name-task-name`, but if you were creating a new - metric you might use `metric-metric-name-task-name`. In practice you - should actually use the name of your method or metric, like - `method-meld-differential-abundance` or - `metric-mse-label-projection`. - - **Note:** This pushes the branch to your fork, *not to* `base`. You - will create a PR to merge your branch to `base` only after all tests - are passing. - - **Warning:** Do not edit the `main` branch on your fork! This will - not work as expected, and will never pass tests. - - ``` shell - # IMPORTANT: choose a new branch name, e.g. - git checkout -b method-method-name-task-name # or metric-new-metric-name, etc - git push -u origin method-method-name-task-name - ``` - -9. Sometimes, changes might be made to the openproblems `base` - repository that you want to incorporate into your fork. To sync your - fork from `base`, use the following code adapted from the [Syncing a - Fork](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork) - tutorial from GitHub. - - ``` shell - # Fetch the branches and their respective commits from the upstream repository - git fetch base - - # Check out your fork's local default branch - git checkout main - - # Merge the changes from the upstream default branch - git merge base/main - - # Push the changes to your fork - git push -u origin - ``` - - You can now create a [Pull - Request](https://guides.github.com/activities/hello-world/#pr) from - the default branch on your fork, `main`, into your working branch, - e.g. `method-method-name-task-name`. - -10. Wait for all tests to pass on your new branch before pushing changes - (as this will allow GitHub Actions to cache the workflow setup, - which speeds up testing.) - -## API - -Each task consists of datasets, methods, and metrics. - -Datasets should take no arguments and return an AnnData object. If -`test is True`, then the method should load the full dataset, but only -return a small version of the same data (preferably \<200 cells and -\<500 genes) for faster downstream analysis. - -``` text -function dataset(bool test=False) -> AnnData adata -``` +## Requirements -Methods should take an AnnData object and store a) the output in -`adata.obs` / `adata.obsm` / etc., according to the specification of the -task and b) the version of the package used to run the method in -`adata.uns["method_code_version"]`. If `test is True`, you may modify -hyperparameters (e.g. number of iterations) to make the method run -faster. +To use this repository, please install the following dependencies: -``` text -function method(AnnData adata, bool test=False) -> AnnData adata -``` +- Bash +- Java (Java 11 or higher) +- Docker (Instructions [here](https://docs.docker.com/get-docker/)) +- Nextflow (Optional, though [very easy to + install](https://www.nextflow.io/index.html#GetStarted)) -If your method takes hyperparameters, set them as keyword arguments in -the method definition. If the hyperparameters change depending on the -value of `test`, set the keyword argument to `None` and set them to your -chosen defaults only if the passed value is `None`. For an example, see -[harmonic -alignment](openproblems/tasks/multimodal_data_integration/methods/harmonic_alignment.py). +## Quick start -Metrics should take an AnnData object and return a `float`. - -``` text -function metric(AnnData adata) -> float -``` +The `src/` folder contains modular software components for running a +modality alignment benchmark. Running the full pipeline is quite easy. -Task-specific APIs are described in the README for each task. +**Step 0, fetch viash and nextflow:** run the `bin/init` executable. -- [Label Projection](openproblems/tasks/label_projection) -- [Multimodal Data - Integration](openproblems/tasks/multimodal_data_integration) +``` bash +bin/init +``` -### Writing functions in R + > Using tag develop + > Cleanup + > Downloading Viash source code @develop + > Building Viash from source + > Building Viash helper scripts from source + > Done, happy viash-ing! -Metrics and methods can also be written in R. AnnData Python objects are -converted to and from `SingleCellExperiment` R objects using -[`anndata2ri`](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/). -R methods should be written in a `.R` file which assumes the existence -of a `SingleCellExperiment` object called `sce`, and should return the -same object. A simple method implemented in R could be written as -follows: +**Step 1, download test resources:** by running the following command. -``` r -### tasks//methods/pca.R -# Dependencies -library(SingleCellExperiment) -library(stats) +``` bash +bin/viash run src/common/sync_test_resources/config.vsh.yaml +``` -# Method body -n_pca <- 10 -counts <- t(assay(sce, "X")) -reducedDim(sce, "pca") <- prcomp(counts)[,1:n_pca] + Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining + Completed 512.0 KiB/7.2 MiB (595.8 KiB/s) with 6 file(s) remaining + Completed 768.0 KiB/7.2 MiB (880.3 KiB/s) with 6 file(s) remaining + Completed 1.0 MiB/7.2 MiB (1.1 MiB/s) with 6 file(s) remaining + Completed 1.2 MiB/7.2 MiB (1.3 MiB/s) with 6 file(s) remaining + ... -# Return -sce -``` +**Step 2, build all the components:** in the `src/` folder as standalone +executables in the `target/` folder. Use the `-q 'xxx'` parameter to +build a subset of components in the repository. -``` python -### tasks//methods/pca.py -from ....tools.conversion import r_function -from ....tools.decorators import method -from ....tools.utils import check_r_version - -_pca = r_function("pca.R") - - -@method( - method_name="PCA", - paper_name="On lines and planes of closest fit to systems of points in space", - paper_url="https://www.tandfonline.com/doi/abs/10.1080/14786440109462720", - paper_year=1901, - code_url="https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp", - image="openproblems-r-base", -) -def pca(adata): - adata.uns["method_code_version"] = check_r_version("stats"), - return _pca(adata) +``` bash +bin/viash_build -q 'label_projection|common' ``` -See the [`anndata2ri` -docs](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/) for API -details. For a more detailed example of how to use this functionality, -see our implementation of fastMNN batch correction -([mnn.R](openproblems/tasks/multimodal_data_integration/methods/mnn.R), -[mnn.py](openproblems/tasks/multimodal_data_integration/methods/mnn.py)). - -### Adding package dependencies + In development mode with 'dev'. + Exporting split_dataset (label_projection) =docker=> target/docker/label_projection/split_dataset + Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy + Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels + [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile + [notice] Building container 'common/data_processing_dataset_concatenate:dev' with Dockerfile + [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile + ... -If you are unable to write your method using our base dependencies, you -may add to our existing Docker images, or create your own. The image you -wish to use (if you are not using the base image) should be specified in -the `image` keyword argument of the method/metric decorator. See the -[Docker images README](docker/README.md) for details. +These standalone executables you can give to somebody else, and they +will be able to run it, provided that they have Bash and Docker +installed. The command might take a while to run, since it is building a +docker container for each of the components. -For the target method or metric, image-specific packages can then be -imported in the associated python file (i.e. `f2.py`). Importantly, the -import statement must be located in the function that calls the method -or metric. If this is the `f2` function, the first few lines of the -function may be structured as follows: +**Step 3, run the pipeline with nextflow.** To do so, run the bash +script located at `src/label_projection/workflows/run_nextflow.sh`: -``` python -def f2(adata): - import package1 - import package2 +``` bash +src/label_projection/workflows/run/run_test.sh ``` -### Adding a new dataset - -Datasets are loaded under `openproblems/data`. Each data loading -function should download the appropriate dataset from a stable location -(e.g. from Figshare) be decorated with -`openproblems.data.utils.loader(data_url="https://data.link", data_reference="https://doi.org/10.0/123")` -in order to cache the result. - -Data should be provided in a raw count format. We assume that `adata.X` -contains the raw (count) data for the primary modality; this will also -be copied to `adata.layers["counts"]` for permanent access to the raw -data. Additional modalities should be stored in `adata.obsm`. -Prenormalized data (if available) can be stored in `adata.layers`, -preferably using a name corresponding to the equivalent [normalization -function](./openproblems/tools/normalize.py) (e.g., -`adata.layers["log_scran_pooling"]`). + N E X T F L O W ~ version 22.04.5 + Launching `src/label_projection/workflows/run/main.nf` [small_becquerel] DSL2 - revision: ece87259df + executor > local (19) + [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ + [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ + [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ + [fd/92edc7] process > run_wf:knn_classifier:knn_classifier_process (1) [100%] 1 of 1 ✔ + [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ + [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ + [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ + [72/5076e8] process > run_wf:f1:f1_process (6) [100%] 6 of 6 ✔ + [cf/eccd48] process > run_wf:extract_scores:extract_scores_process [100%] 1 of 1 ✔ + +## Project structure + + . + ├── bin Helper scripts for building the project and developing a new component. + ├── resources_test Datasets for testing components. If you don't have this folder, run **Step 1** above. + ├── src Source files for each component in the pipeline. + │ ├── common Common processing components. + │ ├── datasets Components for ingesting datasets from a source. + │ ├── label_projection Source files related to the 'Label projection' task. + │ └── ... Other tasks. + └── target Executables generated by viash based on the components listed under `src/`. + ├── docker Bash executables which can be used from a terminal. + └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. + + + bin/ Helper scripts for building the project and developing a new component. + resources_test/ Datasets for testing components. + src/ Source files for each component in the pipeline. + common/ Common processing components. + datasets/ Components related to ingesting datasets into OpenProblems v2. + api/ Specs for the data loaders and normalisation methods. + loaders/ Components for ingesting datasets from a source. + normalization/ Common normalization methods. + label_projection/ Source files related to the 'Label projection' task. + datasets/ Dataset downloader components. + methods/ Modality alignment method components. + metrics/ Modality alignment metric components. + utils/ Utils functions. + workflow/ The pipeline workflow for this task. + target/ Executables generated by viash based on the components listed under `src/`. + docker/ Bash executables which can be used from a terminal. + nextflow/ Nextflow modules which can be used in a Nextflow pipeline. + work/ A working directory used by Nextflow. + output/ Output generated by the pipeline. + +The `src/datasets` folder + +src/datasets/ ├── api Specs for the data loaders and normalisation +methods. ├── loaders Components for ingesting datasets from a source. +├── normalization Common normalization methods. ├── +resource_test_scripts Scripts for generating the objects in the +`resources_test` folder. └── workflows A set of Nextflow workflows which +tie together various components. + +The `src/label_projection` folder + +src/label_projection/ ├── api Specs for the split_dataset, methods and +metrics in this task. ├── control_methods Positive and negative control +methods for quality control. ├── methods Method components. ├── metrics +Metric components. ├── [README.md](src/label_projection/) More +information on how this task works. ├── resources_test_scripts Scripts +for generating the objects in the `resources_test` folder. ├── +split_dataset A component for splitting a common dataset into a `train`, +`test` and `solution` object. └── workflows A set of Nextflow workflows +which tie together various components. + +## Adding a Viash component + +[Viash](https://viash.io) allows you to create pipelines in Bash or +Nextflow by wrapping Python, R, or Bash scripts into reusable +components. + +You can start creating a new component by [creating a Viash +component](https://viash.io/guide/component/creation/docker.html). + +For example, to create a new Python-based method named `foo`, create a +Viash config at `src/label_projection/methods/foo/config.vsh.yaml`: + +``` yaml +__inherits__: ../../api/comp_method.yaml +functionality: + name: "foo" + namespace: "label_projection/methods" + # A multiline description of your method. + description: "Todo: fill in" + info: + type: method + + # a short label of your method + label: Foo + + paper_doi: "10.1234/1234.5678.1234567890" + + # if you don't have a Doi, you can specify a name, url and year manually: + # paper_name: "Nearest neighbor pattern classification" + # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" + # paper_year: 1967 + + code_url: "https://github.com/my_organisation/foo" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - anndata>=0.8 + - scikit-learn + - type: nextflow +``` -To see a gold standard loader, look at -[openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py](./openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py) +And create a script at `src/label_projection/methods/foo/script.py`: -This file name should match -`[First Author Last Name]_[Year Published]_short_Description_of_data.py`. -E.g. the dataset of zebrafish embryos perturbed with CRISPR published in -2018 by Wagner *et al.* becomes `Wagner_2018_zebrafish_embryo_CRISPR.py` +``` python +import anndata as ad +import numpy as np + +## VIASH START +# This code-block will automatically be replaced by Viash at runtime. +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' +} +## VIASH END + +print("Load data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Create predictions") +input_test.obs["label_pred"] = "foo" + +print("Add method name to uns") +input_test.uns["method_id"] = meta["functionality_name"] + +print("Write output to file") +input_test.write_h5ad(par["output"], compression="gzip") +``` -### Adding a dataset / method / metric to a task +## Running a component from CLI -To add a dataset, method, or metric to a task, simply create a new `.py` -file corresponding to your proposed new functionality and import the -main function in the corresponding `__init__.py`. E.g., to add a “F2” -metric to the label projection task, we would create -`openproblems/tasks/label_projection/metrics/f2.py` and add a line +You can view the interface of the executable by running the executable +with the `-h` or `--help` parameter. -``` python -from .f2 import f2 +``` bash +bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` -to -[`openproblems/tasks/label_projection/metrics/__init__.py`](openproblems/tasks/label_projection/metrics/__init__.py). - -For datasets in particular, these should be loaded using a `loader` -function from `openproblems.data`, with only task-specific annotations -added in the task-specific data file. + Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + foo -Datasets, methods, and metrics should all be decorated with the -appropriate function in `openproblems.tools.decorators` to include -metadata required for the evaluation and presentation of results. + Todo: fill in -Note that data is not normalized in the data loader; normalization -should be performed as part of each method or in the task dataset -function if stated in the task API. For ease of use, we provide a -collection of common normalization functions in -[`openproblems.tools.normalize`](openproblems/tools/normalize.py). The -original data stored in `adata.X` is automatically stored in -`adata.layers["counts"]` for later reference in the case the a metric -needs to access the unnormalized data. + Arguments: + --input_train + type: file + example: training.h5ad + The training data -#### Testing method performance + --input_test + type: file + example: test.h5ad + The test data (without labels) -To test the performance of a dataset, method, or metric, you can use the -command-line interface `openproblems-cli test`. + --output + type: file, output + example: prediction.h5ad + The prediction file -First, you must launch a Docker image containing the relevant -dependencies for the dataset/method/metric you wish to test. You can -then run `openproblems-cli test` with any/all of `--dataset`, -`--method`, and `--metric` as desired. E.g., +You can **run the component** as follows: ``` bash -cd openproblems -docker run \ - -v $(pwd):/usr/src/singlecellopenproblems -v /tmp:/tmp \ - -it singlecellopenproblems/openproblems-python-extras bash -openproblems-cli test \ - --task label_projection \ - --dataset zebrafish_labels \ - --method logistic_regression_log_cpm \ - --metric f1 +bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ + --input_train resources_test/label_projection/pancreas/train.h5ad \ + --input_test resources_test/label_projection/pancreas/test.h5ad \ + --output resources_test/label_projection/pancreas/prediction.h5ad ``` -which will print the benchmark score for the method evaluated by the -metric on the dataset you chose. - -Notes: - -- If you have updated Docker images to run your method, you must first - rebuild the images – see the [Docker README](docker/README.md) for - details. -- If your dataset/method/metric cannot be run on the same docker - image, you may wish to `load`, `run`, and `evaluate` separately. You - can do this using each of these commands independently; however, - this workflow is not documented. -- These commands are not guaranteed to work with Apple silicon (M1 - chip). -- If your local machine cannot run the test due to memory constraints - or OS incompatibility, you may use your AWS credentials to launch a - VM for testing purposes. See the [EC2 README](./EC2.md) for details. - -### Adding a new task - -The task directory structure is as follows - -``` text -openproblems/ - - tasks/ - - task_name/ - - README.md - - __init__.py - - api.py - - datasets/ - - __init__.py - - dataset1.py - - ... - - methods/ - - __init__.py - - method1.py - - ... - - metrics/ - - __init__.py - - metric1.py - - ... -``` + Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Load data + Create predictions + Add method name to uns + Write output to file -`task_name/__init__.py` can be copied from an existing task. +## Building a component -`api.py` should implement the following functions: +`viash` has several helper functions to help you quickly develop a +component. - +With **`viash build`**, you can turn the component into a standalone +executable. This standalone executable you can give to somebody else, +and they will be able to run it, provided that they have Bash and Docker +installed. -``` text -check_dataset(AnnData adata) -> bool # checks that a dataset fits the task-specific schema -check_method(AnnData adata) -> bool # checks that the output from a method fits the task-specific schema -sample_dataset() -> AnnData adata # generates a simple dataset the fits the expected API -sample_method(AnnData adata) -> AnnData adata # applies a simple modification that fits the method API +``` bash +bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ + -o target/docker/label_projection/methods/foo ``` - + Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. -`README.md` should contain a description of the task as will be -displayed on the website, followed by a description of the task API for -dataset/method/metric authors. Note: everything after `## API` will be -discarded in generating the webpage for the task. +
-For adding datasets, methods and metrics, see above. +> **Note** +> +> The `bin/viash_build` component does a much better job of setting up a +> collection of components. -### Adding a new Docker container +
-Datasets, methods and metrics run inside Docker containers. We provide a -few to start with, but if you have specific requirements, you may need -to modify an existing image or add a new one. See the [Docker -README](docker/README.md) for details. +You can now view the same interface of the executable by running the +executable with the `-h` parameter. -## Code Style and Testing +``` bash +target/docker/label_projection/methods/foo/foo -h +``` -`openproblems` is maintained at close to 100% code coverage. For -datasets, methods, and metrics, tests are generated programatically from -each task’s `api.py`. See the [Adding a new task](#adding-a-new-task) -section for instructions on creating this file. + foo -For additions outside this core functionality, contributors are -encouraged to write tests for their code – but if you do not know how to -do so, please do not feel discouraged from contributing code! Others can -always help you test your contribution. + Todo: fill in -Code is tested by GitHub Actions when you push your changes. However, if -you wish to test locally, you can do so with the following command: + Arguments: + --input_train + type: file + example: training.h5ad + The training data -``` shell -cd openproblems -pip install --editable .[test,r] -pytest -v -``` + --input_test + type: file + example: test.h5ad + The test data (without labels) + + --output + type: file, output + example: prediction.h5ad + The prediction file -You may run specific tests quickly with +Or **run the component** as follows: -``` shell -PYTEST_MAX_RETRIES=0 pytest -k my_task +``` bash +target/docker/label_projection/methods/foo/foo \ + --input_train resources_test/label_projection/pancreas/train.h5ad \ + --input_test resources_test/label_projection/pancreas/test.h5ad \ + --output resources_test/label_projection/pancreas/prediction.h5ad ``` -The test suite also requires Python\>=3.7, R\>=4.0, and Docker to be -installed. + Load data + Create predictions + Add method name to uns + Write output to file -The benchmarking suite is tested by GitHub Actions when you push your -changes. However, if you wish to test locally, you can do so with the -following command: +## Unit testing a component -``` shell -cd workflow -snakemake -j 4 docker -cd .. -nextflow run -resume -profile test,docker openproblems-bio/nf-openproblems -``` +The [method API +specifications](src/label_projection/api/comp_method.yaml) comes with a +generic unit test for free. This means you can unit test your component +using the **`viash test`** command. -The benchmarking suite also requires Python\>=3.7, snakemake, nextflow, -and Docker to be installed. +``` bash +bin/viash test src/label_projection/methods/foo/config.vsh.yaml +``` -Code style is dictated by -[`black`](https://pypi.org/project/black/#installation-and-usage) and -[`flake8`](https://flake8.pycqa.org/en/latest/) with -[`hacking`](https://github.com/openstack/hacking). Code is automatically -reformatted by [`pre-commit`](https://pre-commit.com/) when you push to -GitHub. + Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818' + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'label_projection/methods_foo:test_rIrBSI' with Dockerfile + [info] Running 'docker build -t label_projection/methods_foo:test_rIrBSI /home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable/tmp/dockerbuild-foo-y7Hdos/Dockerfile' + Sending build context to Docker daemon 37.89kB + + Step 1/7 : FROM python:3.10 + ---> ecbdd6bafdb5 + Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" + ---> Using cache + ---> f1fbd09c8ccd + Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" + ---> Using cache + ---> 063049300b14 + Step 4/7 : LABEL org.opencontainers.image.created="2022-11-17T07:37:39+01:00" + ---> Running in 5d3bda2ec79c + Removing intermediate container 5d3bda2ec79c + ---> e77cbb1b5502 + Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" + ---> Running in fed5d3371cea + Removing intermediate container fed5d3371cea + ---> 9db7959fd7af + Step 6/7 : LABEL org.opencontainers.image.revision="8f9371ddfa5f5c20df01612342040a2003274da3" + ---> Running in 9a2f654aedb9 + Removing intermediate container 9a2f654aedb9 + ---> 912628903c90 + Step 7/7 : LABEL org.opencontainers.image.version="test_rIrBSI" + ---> Running in 82b6f860d949 + Removing intermediate container 82b6f860d949 + ---> e0720a8407a9 + Successfully built e0720a8407a9 + Successfully tagged label_projection/methods_foo:test_rIrBSI + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/test_generic_test/test_executable + >> Running script as test + >> Checking whether output file exists + >> Reading h5ad files + input_test: AnnData object with n_obs × n_vars = 307 × 443 + obs: 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling' + output: AnnData object with n_obs × n_vars = 307 × 443 + obs: 'batch', 'label_pred' + uns: 'dataset_id', 'method_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling' + >> Checking whether predictions were added + Checking whether data from input was copied properly to output + All checks succeeded! + ==================================================================== + SUCCESS! All 1 out of 1 test scripts succeeded! + Cleaning up temporary directory + +Let’s introduce a bug in the script and try running the test again. For +instance: -## Code of Conduct +``` python +import anndata as ad +import numpy as np + +## VIASH START +# This code-block will automatically be replaced by Viash at runtime. +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' +} +## VIASH END + +print("Load data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Not creating any predictions!!!") +# input_test.obs["label_pred"] = "foo" + +print("Not adding method name to uns!!!") +# input_test.uns["method_id"] = meta["functionality_name"] + +print("Write output to file") +input_test.write_h5ad(par["output"], compression="gzip") +``` -We abide by the principles of openness, respect, and consideration of -others of the Python Software Foundation: - and by the Contributor -Covenant. See our [Code of Conduct](CODE_OF_CONDUCT.md) for details. +If we now run the test, we should get an error since we didn’t create +all of the required output slots. -## Attribution +``` bash +bin/viash test src/label_projection/methods/foo/config.vsh.yaml +``` -This `CONTRIBUTING.md` was adapted from -[scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/main/CONTRIBUTING.md). + Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789' + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'label_projection/methods_foo:test_5q5NGA' with Dockerfile + [info] Running 'docker build -t label_projection/methods_foo:test_5q5NGA /home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable/tmp/dockerbuild-foo-GRvLt9/Dockerfile' + Sending build context to Docker daemon 37.89kB + + Step 1/7 : FROM python:3.10 + ---> ecbdd6bafdb5 + Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" + ---> Using cache + ---> f1fbd09c8ccd + Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" + ---> Using cache + ---> 063049300b14 + Step 4/7 : LABEL org.opencontainers.image.created="2022-11-17T07:38:03+01:00" + ---> Running in 2211c2f3d253 + Removing intermediate container 2211c2f3d253 + ---> 4a7607ecb7b4 + Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" + ---> Running in 21c85f7d64bc + Removing intermediate container 21c85f7d64bc + ---> ad15f8b03066 + Step 6/7 : LABEL org.opencontainers.image.revision="8f9371ddfa5f5c20df01612342040a2003274da3" + ---> Running in 94c15d5c9736 + Removing intermediate container 94c15d5c9736 + ---> 423d9a6d04e2 + Step 7/7 : LABEL org.opencontainers.image.version="test_5q5NGA" + ---> Running in d31d99d449ef + Removing intermediate container d31d99d449ef + ---> 7f9635195fe8 + Successfully built 7f9635195fe8 + Successfully tagged label_projection/methods_foo:test_5q5NGA + ==================================================================== + +/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/test_generic_test/test_executable + Traceback (most recent call last): + >> Running script as test + File "/viash_automount/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/test_generic_test/tmp//viash-run-foo-j6Jfba", line 56, in + >> Checking whether output file exists + assert "label_pred" in output.obs + >> Reading h5ad files + AssertionError + input_test: AnnData object with n_obs × n_vars = 307 × 443 + obs: 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling' + output: AnnData object with n_obs × n_vars = 307 × 443 + obs: 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling' + >> Checking whether predictions were added + ==================================================================== + ERROR! Only 0 out of 1 test scripts succeeded! + Unexpected error occurred! If you think this is a bug, please post + create an issue at https://github.com/viash-io/viash/issues containing + a reproducible example and the stack trace below. + + viash - 0.6.3 + Stacktrace: + java.lang.RuntimeException: Only 0 out of 1 test scripts succeeded! + at io.viash.ViashTest$.apply(ViashTest.scala:110) + at io.viash.Main$.internalMain(Main.scala:99) + at io.viash.Main$.main(Main.scala:39) + at io.viash.Main.main(Main.scala) + +## More information + +The [Viash reference docs](https://viash.io/reference/config/) page +provides information on all of the available fields in a Viash config, +and the [Guide](https://viash.io/guide/) will help you get started with +creating components from scratch. + + diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 649f42e3c7..e78745fc46 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -1,7 +1,8 @@ --- title: Contributing to OpenProblems -engine: knitr format: gfm +toc: true +engine: knitr --- [OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). @@ -15,429 +16,343 @@ We pledge to act and interact in ways that contribute to an open, welcoming, div Our full [Code of Conduct](CODE_OF_CONDUCT.md) is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1. -## Ways to contribute - -There are many ways to contribute to OpenProblems, with the most common ones being contribution of code or documentation to the project. - -Contributing new functionality usually comes in the form of new [datasets](#adding-a-new-dataset), [methods](#adding-a-new-method), [metric](#adding-a-new-metric), or even entire new [tasks](#adding-a-new-task). - -Improving the documentation is no less important than improving the library itself. If you find a typo in the documentation, or have made improvements, do not hesitate to submit a [GitHub pull request](https://github.com/openproblems-bio/openproblems-v2/pulls). - -But there are many other ways to help. In particular helping to [improve, triage, and investigate issues](#bug-triaging) and [reviewing other developers' pull requests](#code-review) are very valuable contributions that decrease the burden on the project maintainers. - -Another way to contribute is to report [issues you're facing](#submitting-a-bug-report-or-feature-request), and give a "thumbs up" on issues that others reported and that are relevant to you. It also helps us if you spread the word: reference the project from your blog and articles, link to it from your website, or simply star to say "I use it": - -Star - - - - -## Submitting New Features - -To submit new features to Open Problems for Single Cell Analysis, follow the steps -below: - -1. Search through the [GitHub - Issues](https://github.com/openproblems-bio/openproblems-v2/issues) tracker to make sure - there isn't someone already working on the feature you'd like to add. If someone is - working on this, post in that issue that you'd like to help or reach out to one of - the contributors working on the issue directly. -2. If there isn't an existing issue tracking this feature, create one! There are several - templates you can choose one depending on what type of feature you'd like to add. -3. Fork into your account. If you're - new to `git`, you might find the [Fork a - repo](https://docs.github.com/en/github/getting-started-with-github/fork-a-repo) - documentation helpful. - ![](" width=400px> -4. Set up [tower.nf](https://tower.nf) and make sure you have access to - [`openproblems-bio`](https://tower.nf/orgs/openproblems-bio/workspaces/openproblems-bio/watch). - If you do not have access, please contact us at - [singlecellopenproblems@protonmail.com](mailto:singlecellopenproblems@protonmail.com). -5. Create repository secrets (*not environment secrets*) - [https://github.com/USERNAME/openproblems/settings/secrets](https://github.com/USERNAME/openproblems/settings/secrets) - * *AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are included in your AWS login - details. If you do not have these, please contact us at - [singlecellopenproblems@protonmail.com](mailto:singlecellopenproblems@protonmail.com).* - * *TOWER_ACCESS_KEY: log in with GitHub to and create a token at - .* - * When you are done with this step, your page should look like this: - ![AWS secrets success](static/img/AWS_secret.png) - -6. Enable workflows at - [https://github.com/USERNAME/openproblems/actions](https://github.com/USERNAME/openproblems/actions). -7. Set up your git repository to fetch branches from `base` at - `openproblems-bio/openproblems` - - ```shell - git clone git@github.com:/openproblems.git - cd openproblems - git remote add base git@github.com:openproblems-bio/openproblems.git - git fetch --all - git branch --set-upstream-to base/main - git pull - ``` - - **Note:** If you haven't set up SSH keys with your GitHub account, you may see this - error message when adding `base` to your repository: - - ```text - git@github.com: Permission denied (publickey). - fatal: Could not read from remote repository. - Please make sure you have the correct access rights - ``` - - To generate an SSH key and add it to your GitHub account, follow [this tutorial from - GitHub](https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account). - -8. Create a new branch for your task (**no underscores or spaces allowed**). It is best - to coordinate with other people working on the same feature as you so that there - aren't clases in images uploaded to our ECR. Here we're creating a branch called - `method-method-name-task-name`, but if you were creating a new metric you might use - `metric-metric-name-task-name`. In practice you should actually use the name of your - method or metric, like `method-meld-differential-abundance` or - `metric-mse-label-projection`. - - **Note:** This pushes the branch to your fork, *not to* `base`. You will create a PR - to merge your branch to `base` only after all tests are passing. - - **Warning:** Do not edit the `main` branch on your fork! This will not work as - expected, and will never pass tests. - - ```shell - # IMPORTANT: choose a new branch name, e.g. - git checkout -b method-method-name-task-name # or metric-new-metric-name, etc - git push -u origin method-method-name-task-name - ``` - -9. Sometimes, changes might be made to the openproblems `base` repository that you want - to incorporate into your fork. To sync your fork from `base`, use the following code - adapted from the [Syncing a - Fork](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork) - tutorial from GitHub. - - ```shell - # Fetch the branches and their respective commits from the upstream repository - git fetch base - - # Check out your fork's local default branch - git checkout main - - # Merge the changes from the upstream default branch - git merge base/main - - # Push the changes to your fork - git push -u origin - ``` - - You can now create a [Pull - Request](https://guides.github.com/activities/hello-world/#pr) from the default - branch on your fork, `main`, into your working branch, e.g. - `method-method-name-task-name`. - -10. Wait for all tests to pass on your new branch before pushing changes (as this will - allow GitHub Actions to cache the workflow setup, which speeds up testing.) - -## API - -Each task consists of datasets, methods, and metrics. - -Datasets should take no arguments and return an AnnData object. If `test is True`, then -the method should load the full dataset, but only return a small version of the same -data (preferably <200 cells and <500 genes) for faster downstream analysis. - -```text -function dataset(bool test=False) -> AnnData adata -``` +## Requirements -Methods should take an AnnData object and store a) the output in `adata.obs` / -`adata.obsm` / etc., according to the specification of the task and b) the version of -the package used to run the method in `adata.uns["method_code_version"]`. If `test is -True`, you may modify hyperparameters (e.g. number of iterations) to make the method run -faster. +To use this repository, please install the following dependencies: -```text -function method(AnnData adata, bool test=False) -> AnnData adata -``` +* Bash +* Java (Java 11 or higher) +* Docker (Instructions [here](https://docs.docker.com/get-docker/)) +* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) -If your method takes hyperparameters, set them as keyword arguments in the method -definition. If the hyperparameters change depending on the value of `test`, set the -keyword argument to `None` and set them to your chosen defaults only if the passed value -is `None`. For an example, see [harmonic -alignment](openproblems/tasks/multimodal_data_integration/methods/harmonic_alignment.py). +## Quick start -Metrics should take an AnnData object and return a `float`. +The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. -```text -function metric(AnnData adata) -> float -``` - -Task-specific APIs are described in the README for each task. +**Step 0, fetch viash and nextflow:** run the `bin/init` executable. -* [Label Projection](openproblems/tasks/label_projection) -* [Multimodal Data Integration](openproblems/tasks/multimodal_data_integration) +```bash +bin/init +``` -### Writing functions in R + > Using tag develop + > Cleanup + > Downloading Viash source code @develop + > Building Viash from source + > Building Viash helper scripts from source + > Done, happy viash-ing! -Metrics and methods can also be written in R. AnnData Python objects are converted to -and from `SingleCellExperiment` R objects using -[`anndata2ri`](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/). R methods -should be written in a `.R` file which assumes the existence of a `SingleCellExperiment` -object called `sce`, and should return the same object. A simple method implemented in R -could be written as follows: +**Step 1, download test resources:** by running the following command. -```R -### tasks//methods/pca.R -# Dependencies -library(SingleCellExperiment) -library(stats) +```bash +bin/viash run src/common/sync_test_resources/config.vsh.yaml +``` -# Method body -n_pca <- 10 -counts <- t(assay(sce, "X")) -reducedDim(sce, "pca") <- prcomp(counts)[,1:n_pca] + Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining + Completed 512.0 KiB/7.2 MiB (595.8 KiB/s) with 6 file(s) remaining + Completed 768.0 KiB/7.2 MiB (880.3 KiB/s) with 6 file(s) remaining + Completed 1.0 MiB/7.2 MiB (1.1 MiB/s) with 6 file(s) remaining + Completed 1.2 MiB/7.2 MiB (1.3 MiB/s) with 6 file(s) remaining + ... -# Return -sce -``` +**Step 2, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. -```python -### tasks//methods/pca.py -from ....tools.conversion import r_function -from ....tools.decorators import method -from ....tools.utils import check_r_version - -_pca = r_function("pca.R") - - -@method( - method_name="PCA", - paper_name="On lines and planes of closest fit to systems of points in space", - paper_url="https://www.tandfonline.com/doi/abs/10.1080/14786440109462720", - paper_year=1901, - code_url="https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/prcomp", - image="openproblems-r-base", -) -def pca(adata): - adata.uns["method_code_version"] = check_r_version("stats"), - return _pca(adata) +```bash +bin/viash_build -q 'label_projection|common' ``` -See the [`anndata2ri` docs](https://icb-anndata2ri.readthedocs-hosted.com/en/latest/) -for API details. For a more detailed example of how to use this functionality, see our -implementation of fastMNN batch correction -([mnn.R](openproblems/tasks/multimodal_data_integration/methods/mnn.R), -[mnn.py](openproblems/tasks/multimodal_data_integration/methods/mnn.py)). + In development mode with 'dev'. + Exporting split_dataset (label_projection) =docker=> target/docker/label_projection/split_dataset + Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy + Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels + [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile + [notice] Building container 'common/data_processing_dataset_concatenate:dev' with Dockerfile + [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile + ... -### Adding package dependencies +These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. +The command might take a while to run, since it is building a docker container for each of the components. -If you are unable to write your method using our base dependencies, you may add to our -existing Docker images, or create your own. The image you wish to use (if you are not -using the base image) should be specified in the `image` keyword argument of the -method/metric decorator. See the [Docker images README](docker/README.md) for details. +**Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/label_projection/workflows/run_nextflow.sh`: -For the target method or metric, image-specific packages can then be imported in the -associated python file (i.e. `f2.py`). Importantly, the import statement must be located -in the function that calls the method or metric. If this is the `f2` function, the first -few lines of the function may be structured as follows: +```bash +src/label_projection/workflows/run/run_test.sh +``` -```python -def f2(adata): - import package1 - import package2 + N E X T F L O W ~ version 22.04.5 + Launching `src/label_projection/workflows/run/main.nf` [small_becquerel] DSL2 - revision: ece87259df + executor > local (19) + [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ + [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ + [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ + [fd/92edc7] process > run_wf:knn_classifier:knn_classifier_process (1) [100%] 1 of 1 ✔ + [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ + [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ + [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ + [72/5076e8] process > run_wf:f1:f1_process (6) [100%] 6 of 6 ✔ + [cf/eccd48] process > run_wf:extract_scores:extract_scores_process [100%] 1 of 1 ✔ + +## Project structure + + . + ├── bin Helper scripts for building the project and developing a new component. + ├── resources_test Datasets for testing components. If you don't have this folder, run **Step 1** above. + ├── src Source files for each component in the pipeline. + │ ├── common Common processing components. + │ ├── datasets Components for ingesting datasets from a source. + │ ├── label_projection Source files related to the 'Label projection' task. + │ └── ... Other tasks. + └── target Executables generated by viash based on the components listed under `src/`. + ├── docker Bash executables which can be used from a terminal. + └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. + + + bin/ Helper scripts for building the project and developing a new component. + resources_test/ Datasets for testing components. + src/ Source files for each component in the pipeline. + common/ Common processing components. + datasets/ Components related to ingesting datasets into OpenProblems v2. + api/ Specs for the data loaders and normalisation methods. + loaders/ Components for ingesting datasets from a source. + normalization/ Common normalization methods. + label_projection/ Source files related to the 'Label projection' task. + datasets/ Dataset downloader components. + methods/ Modality alignment method components. + metrics/ Modality alignment metric components. + utils/ Utils functions. + workflow/ The pipeline workflow for this task. + target/ Executables generated by viash based on the components listed under `src/`. + docker/ Bash executables which can be used from a terminal. + nextflow/ Nextflow modules which can be used in a Nextflow pipeline. + work/ A working directory used by Nextflow. + output/ Output generated by the pipeline. + +The `src/datasets` folder + +src/datasets/ +├── api Specs for the data loaders and normalisation methods. +├── loaders Components for ingesting datasets from a source. +├── normalization Common normalization methods. +├── resource_test_scripts Scripts for generating the objects in the `resources_test` folder. +└── workflows A set of Nextflow workflows which tie together various components. + +The `src/label_projection` folder + +src/label_projection/ +├── api Specs for the split_dataset, methods and metrics in this task. +├── control_methods Positive and negative control methods for quality control. +├── methods Method components. +├── metrics Metric components. +├── [README.md](src/label_projection/) More information on how this task works. +├── resources_test_scripts Scripts for generating the objects in the `resources_test` folder. +├── split_dataset A component for splitting a common dataset into a `train`, `test` and `solution` object. +└── workflows A set of Nextflow workflows which tie together various components. + +## Adding a Viash component + +[Viash](https://viash.io) allows you to create pipelines +in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. + + +You can start creating a new component by [creating a Viash component](https://viash.io/guide/component/creation/docker.html). + + +```{bash, include=FALSE} +# bin/viash_skeleton --name foo --namespace "label_projection/methods" --language python + +mkdir -p src/label_projection/methods/foo + +cat > src/label_projection/methods/foo/config.vsh.yaml << HERE +__inherits__: ../../api/comp_method.yaml +functionality: + name: "foo" + namespace: "label_projection/methods" + # A multiline description of your method. + description: "Todo: fill in" + info: + type: method + + # a short label of your method + label: Foo + + paper_doi: "10.1234/1234.5678.1234567890" + + # if you don't have a Doi, you can specify a name, url and year manually: + # paper_name: "Nearest neighbor pattern classification" + # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" + # paper_year: 1967 + + code_url: "https://github.com/my_organisation/foo" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - anndata>=0.8 + - scikit-learn + - type: nextflow +HERE + +cat > src/label_projection/methods/foo/script.py << HERE +import anndata as ad +import numpy as np + +## VIASH START +# This code-block will automatically be replaced by Viash at runtime. +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' +} +## VIASH END + +print("Load data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Create predictions") +input_test.obs["label_pred"] = "foo" + +print("Add method name to uns") +input_test.uns["method_id"] = meta["functionality_name"] + +print("Write output to file") +input_test.write_h5ad(par["output"], compression="gzip") +HERE ``` -### Adding a new dataset +For example, to create a new Python-based method named `foo`, create a Viash config at `src/label_projection/methods/foo/config.vsh.yaml`: -Datasets are loaded under `openproblems/data`. Each data loading function should -download the appropriate dataset from a stable location (e.g. from Figshare) be -decorated with `openproblems.data.utils.loader(data_url="https://data.link", -data_reference="https://doi.org/10.0/123")` in order to cache the result. +```{embed lang="yaml"} +src/label_projection/methods/foo/config.vsh.yaml +``` -Data should be provided in a raw count format. We assume that `adata.X` contains the raw -(count) data for the primary modality; this will also be copied to -`adata.layers["counts"]` for permanent access to the raw data. Additional modalities -should be stored in `adata.obsm`. Prenormalized data (if available) can be stored in -`adata.layers`, preferably using a name corresponding to the equivalent [normalization -function](./openproblems/tools/normalize.py) (e.g., -`adata.layers["log_scran_pooling"]`). +And create a script at `src/label_projection/methods/foo/script.py`: -To see a gold standard loader, look at -[openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py](./openproblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py) +```{embed lang="python"} +src/label_projection/methods/foo/script.py +``` -This file name should match -`[First Author Last Name]_[Year Published]_short_Description_of_data.py`. E.g. the -dataset of zebrafish embryos perturbed with CRISPR published in 2018 by Wagner *et al.* -becomes `Wagner_2018_zebrafish_embryo_CRISPR.py` -### Adding a dataset / method / metric to a task +## Running a component from CLI -To add a dataset, method, or metric to a task, simply create a new `.py` file -corresponding to your proposed new functionality and import the main function in the -corresponding `__init__.py`. E.g., to add a "F2" metric to the label projection task, we -would create `openproblems/tasks/label_projection/metrics/f2.py` and add a line +You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. -```python -from .f2 import f2 +```{bash} +bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` -to -[`openproblems/tasks/label_projection/metrics/__init__.py`](openproblems/tasks/label_projection/metrics/__init__.py). - -For datasets in particular, these should be loaded using a `loader` function from -`openproblems.data`, with only task-specific annotations added in the task-specific data -file. - -Datasets, methods, and metrics should all be decorated with the appropriate function in -`openproblems.tools.decorators` to include metadata required for the evaluation and -presentation of results. +You can **run the component** as follows: -Note that data is not normalized in the data loader; normalization should be performed -as part of each method or in the task dataset function if stated in the task API. For -ease of use, we provide a collection of common normalization functions in -[`openproblems.tools.normalize`](openproblems/tools/normalize.py). The original data -stored in `adata.X` is automatically stored in `adata.layers["counts"]` for later -reference in the case the a metric needs to access the unnormalized data. - -#### Testing method performance +```{bash} +bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ + --input_train resources_test/label_projection/pancreas/train.h5ad \ + --input_test resources_test/label_projection/pancreas/test.h5ad \ + --output resources_test/label_projection/pancreas/prediction.h5ad +``` -To test the performance of a dataset, method, or metric, you can use the command-line -interface `openproblems-cli test`. +## Building a component -First, you must launch a Docker image containing the relevant dependencies for the -dataset/method/metric you wish to test. You can then run `openproblems-cli test` with -any/all of `--dataset`, `--method`, and `--metric` as desired. E.g., +`viash` has several helper functions to help you quickly develop a component. -```bash -cd openproblems -docker run \ - -v $(pwd):/usr/src/singlecellopenproblems -v /tmp:/tmp \ - -it singlecellopenproblems/openproblems-python-extras bash -openproblems-cli test \ - --task label_projection \ - --dataset zebrafish_labels \ - --method logistic_regression_log_cpm \ - --metric f1 -``` +With **`viash build`**, you can turn the component into a standalone executable. +This standalone executable you can give to somebody else, and they will be able to +run it, provided that they have Bash and Docker installed. -which will print the benchmark score for the method evaluated by the metric on the -dataset you chose. - -Notes: - -* If you have updated Docker images to run your method, you must first rebuild the - images -- see the [Docker README](docker/README.md) for details. -* If your dataset/method/metric cannot be run on the same docker image, you may wish to - `load`, `run`, and `evaluate` separately. You can do this using each of these commands - independently; however, this workflow is not documented. -* These commands are not guaranteed to work with Apple silicon (M1 chip). -* If your local machine cannot run the test due to memory constraints or OS - incompatibility, you may use your AWS credentials to launch a VM for testing purposes. - See the [EC2 README](./EC2.md) for details. - -### Adding a new task - -The task directory structure is as follows - -```text -openproblems/ - - tasks/ - - task_name/ - - README.md - - __init__.py - - api.py - - datasets/ - - __init__.py - - dataset1.py - - ... - - methods/ - - __init__.py - - method1.py - - ... - - metrics/ - - __init__.py - - metric1.py - - ... +```{bash} +bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ + -o target/docker/label_projection/methods/foo ``` -`task_name/__init__.py` can be copied from an existing task. +:::{.callout-note} +The `bin/viash_build` component does a much better job of setting up +a collection of components. +::: -`api.py` should implement the following functions: +You can now view the same interface of the executable by running the executable with the `-h` parameter. - -```text -check_dataset(AnnData adata) -> bool # checks that a dataset fits the task-specific schema -check_method(AnnData adata) -> bool # checks that the output from a method fits the task-specific schema -sample_dataset() -> AnnData adata # generates a simple dataset the fits the expected API -sample_method(AnnData adata) -> AnnData adata # applies a simple modification that fits the method API +```{bash} +target/docker/label_projection/methods/foo/foo -h ``` - - -`README.md` should contain a description of the task as will be displayed on the -website, followed by a description of the task API for dataset/method/metric authors. -Note: everything after `## API` will be discarded in generating the webpage for the -task. -For adding datasets, methods and metrics, see above. +Or **run the component** as follows: -### Adding a new Docker container - -Datasets, methods and metrics run inside Docker containers. We provide a few to start -with, but if you have specific requirements, you may need to modify an existing image or -add a new one. See the [Docker README](docker/README.md) for details. +```{bash} +target/docker/label_projection/methods/foo/foo \ + --input_train resources_test/label_projection/pancreas/train.h5ad \ + --input_test resources_test/label_projection/pancreas/test.h5ad \ + --output resources_test/label_projection/pancreas/prediction.h5ad +``` -## Code Style and Testing -`openproblems` is maintained at close to 100% code coverage. For datasets, methods, and -metrics, tests are generated programatically from each task's `api.py`. See the [Adding -a new task](#adding-a-new-task) section for instructions on creating this file. +## Unit testing a component -For additions outside this core functionality, contributors are encouraged to write -tests for their code -- but if you do not know how to do so, please do not feel -discouraged from contributing code! Others can always help you test your contribution. +The [method API specifications](src/label_projection/api/comp_method.yaml) comes with a generic unit test for free. +This means you can unit test your component using the **`viash test`** command. -Code is tested by GitHub Actions when you push your changes. However, if you wish to -test locally, you can do so with the following command: +```{bash} +bin/viash test src/label_projection/methods/foo/config.vsh.yaml +``` -```shell -cd openproblems -pip install --editable .[test,r] -pytest -v +```{bash include=FALSE} +cat > src/label_projection/methods/foo/script.py << HERE +import anndata as ad +import numpy as np + +## VIASH START +# This code-block will automatically be replaced by Viash at runtime. +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo' +} +## VIASH END + +print("Load data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Not creating any predictions!!!") +# input_test.obs["label_pred"] = "foo" + +print("Not adding method name to uns!!!") +# input_test.uns["method_id"] = meta["functionality_name"] + +print("Write output to file") +input_test.write_h5ad(par["output"], compression="gzip") +HERE ``` -You may run specific tests quickly with +Let's introduce a bug in the script and try running the test again. For instance: -```shell -PYTEST_MAX_RETRIES=0 pytest -k my_task +```{embed lang="python"} +src/label_projection/methods/foo/script.py ``` -The test suite also requires Python>=3.7, R>=4.0, and Docker to be installed. - -The benchmarking suite is tested by GitHub Actions when you push your changes. However, -if you wish to test locally, you can do so with the following command: +If we now run the test, we should get an error since we didn't create all of the required output slots. -```shell -cd workflow -snakemake -j 4 docker -cd .. -nextflow run -resume -profile test,docker openproblems-bio/nf-openproblems +```{bash error=TRUE} +bin/viash test src/label_projection/methods/foo/config.vsh.yaml ``` -The benchmarking suite also requires Python>=3.7, snakemake, nextflow, and Docker to be -installed. -Code style is dictated by -[`black`](https://pypi.org/project/black/#installation-and-usage) and -[`flake8`](https://flake8.pycqa.org/en/latest/) with -[`hacking`](https://github.com/openstack/hacking). Code is automatically reformatted by -[`pre-commit`](https://pre-commit.com/) when you push to GitHub. +## More information -## Code of Conduct +The [Viash reference docs](https://viash.io/reference/config/) page provides information on all of the available fields in a Viash config, and the [Guide](https://viash.io/guide/) will help you get started with creating components from scratch. -We abide by the principles of openness, respect, and consideration of others -of the Python Software Foundation: and by -the Contributor Covenant. See our [Code of Conduct](CODE_OF_CONDUCT.md) for details. -## Attribution + -This `CONTRIBUTING.md` was adapted from -[scikit-learn](https://github.com/scikit-learn/scikit-learn/blob/main/CONTRIBUTING.md). +```{bash, echo=FALSE} +rm -r src/label_projection/methods/foo target/docker/label_projection/methods/foo +``` diff --git a/README.md b/README.md index 84b0cf2f98..1dbb8d6abb 100644 --- a/README.md +++ b/README.md @@ -1,520 +1,35 @@ OpenProblems v2 ================ -- Requirements -- Quick start -- Project - structure -- Adding a viash component -- Running a component from CLI -- Building a - component -- Unit testing a component -- Frequently asked questions - - My - component doesn’t work! -- Benefits of using Nextflow + - viash - - The pipeline is - language-agnostic - - One Docker container per - component - - Reproducible components - - Reprodicible components - on Docker Hub +Formalizing and benchmarking open problems in single-cell genomics. -Proof Of Concept in adapting [Open Problems -repository](https://github.com/openproblems-bio/openproblems) with -Nextflow and viash. Documentation for viash is available at -[viash.io](https://viash.io). +[**Visit the Open Problems Website.**](https://openproblems.bio/) -## Requirements +To get started with developing a new method or metric, please see the +[Contribution guidelines](CONTRIBUTING.md). -To use this repository, please install the following dependencies: - -- Bash -- Java (Java 11 or higher) -- Docker (Instructions [here](https://docs.docker.com/get-docker/)) -- Nextflow (Optional, though [very easy to - install](https://www.nextflow.io/index.html#GetStarted)) - -## Quick start - -The `src/` folder contains modular software components for running a -modality alignment benchmark. Running the full pipeline is quite easy. - -**Step 0, fetch viash and nextflow:** run the `bin/init` executable. - -``` bash -bin/init -``` - - > Using tag develop - > Cleanup - > Install viash develop under /viash_automount/home/rcannood/workspace/opsca/opsca-viash/bin/ - > Fetching components sources (version develop) - > Building components - > Done, happy viash-ing! - > Nextflow installation completed. - -**Step 0b, download test resources:** by running the following command. - -``` bash -bin/viash run src/common/sync_test_resources/config.vsh.yaml -``` - -**Step 1, build all the components:** in the `src/` folder as standalone -executables in the `target/` folder. Use the `-q 'xxx'` parameter to -build only several components of the repository. - -``` bash -bin/viash_build -q 'modality_alignment|common' -``` - - Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc - Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot - Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn - ... - -These standalone executables you can give to somebody else, and they -will be able to run it, provided that they have Bash and Docker -installed. The command might take a while to run, since it is building a -docker container for each of the components. If you’re interested in -building only a subset of components, you can apply a regex to the -selected components. For example: -`bin/viash_build -q 'common|modality_alignment'`. - -**Step 2, run the pipeline with nextflow.** To do so, run the bash -script located at `src/modality_alignment/workflows/run_nextflow.sh`: - -``` bash -src/modality_alignment/workflows/run_nextflow.sh -``` - - [15/84d27c] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [2f/318ad9] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [6f/dd22c1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [c6/6e0999] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [73/f6dffa] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [54/c89b95] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - Completed at: 20-Apr-2021 06:52:19 - Duration : 3m 40s - CPU hours : 0.1 - Succeeded : 8 - -## Project structure - - bin/ Helper scripts for building the project and developing a new component. - src/ Source files for each component in the pipeline. - modality_alignment/ Source files related to the 'Modality alignment' task. - datasets/ Dataset downloader components. - methods/ Modality alignment method components. - metrics/ Modality alignment metric components. - utils/ Utils functions. - workflow/ The pipeline workflow for this task. - common/ Helper files. - target/ Executables generated by viash based on the components listed under `src/`. - docker/ Bash executables which can be used from a terminal. - nextflow/ Nextflow modules which can be used in a Nextflow pipeline. - work/ A working directory used by Nextflow. - output/ Output generated by the pipeline. - -## Adding a viash component - -[`viash`](https://github.com/data-intuitive/viash) allows you to create -pipelines in Bash or Nextflow by wrapping Python, R, or Bash scripts -into reusable components. You can start creating a new component using -`bin/skeleton`. For example to create a new Python-based viash component -in the `src/modality_alignment/methods/foo` folder, run: You can start -creating a new component by using the `bin/skeleton` command: - -``` bash -bin/viash_skeleton --name foo --namespace "modality_alignment/methods" --language python -``` - -This should create a few files in this folder: - - script.py A python script for you to edit. - config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. - test.py A python script with which you can start unit testing your component. - -The [Getting started](http://www.data-intuitive.com/viash_docs/) page on -the viash documentation site provides some information on how a basic -viash component works, or on the specifications of the `config.vsh.yaml` -[config file](http://www.data-intuitive.com/viash_docs/config/). - -## Running a component from CLI - -You can view the interface of the executable by running the executable -with the `-h` parameter. - -``` bash -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -h -``` - - foo 0.0.1 - - Replace this with a (multiline) description of your component. - - Arguments: - -i, --input - type: file, required parameter - example: input.txt - Describe the input file. - - -o, --output - type: file, required parameter, output - example: output.txt - Describe the output file. - - --option - type: string - default: default- - Describe an optional parameter. - -You can **run the component** as follows: - -``` bash -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt -``` - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE - - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - - option: default- - -## Building a component - -`viash` has several helper functions to help you quickly develop a -component. - -With **`viash build`**, you can turn the component into a standalone -executable. This standalone executable you can give to somebody else, -and they will be able to run it, provided that they have Bash and Docker -installed. - -``` bash -viash build src/modality_alignment/methods/foo/config.vsh.yaml \ - -o target/docker/modality_alignment/methods/foo -``` - -Note that the `bin/viash_build` component does a much better job of -setting up a collection of components. You can filter which components -will be built by providing a regex to the `-q` parameter, -e.g. `bin/viash_build -q 'common|modality_alignment'`. - -You can now view the same interface of the executable by running the -executable with the `-h` parameter. - -``` bash -target/docker/modality_alignment/methods/foo/foo -h -``` - - foo 0.0.1 - - Replace this with a (multiline) description of your component. - - Arguments: - -i, --input - type: file, required parameter - example: input.txt - Describe the input file. - - -o, --output - type: file, required parameter, output - example: output.txt - Describe the output file. - - --option - type: string - default: default- - Describe an optional parameter. - -Or **run the component** as follows: - -``` bash -target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt -``` - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE - - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - - option: default- - -## Unit testing a component - -Provided that you wrote a script that allows you to test the -functionality of a component, you can run the tests by using the -**`viash test`** command. - -``` bash -viash test src/modality_alignment/methods/foo/config.vsh.yaml -``` - - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811' - ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'modality_alignment/methods_foo:test_HeBJG6' with Dockerfile - [info] Running 'docker build -t modality_alignment/methods_foo:test_HeBJG6 /home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/build_executable/tmp/dockerbuild-foo-alcpr9/Dockerfile' - Sending build context to Docker daemon 38.91kB - - Step 1/7 : FROM python:3.9.3-buster - ---> 05034335a2e3 - Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "numpy" - ---> Using cache - ---> ddeebf641d36 - Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component modality_alignment/methods foo" - ---> Using cache - ---> c1c0f5ae9c7d - Step 4/7 : LABEL org.opencontainers.image.created="2022-11-09T15:53:27+01:00" - ---> Running in 70b7c0e821f0 - Removing intermediate container 70b7c0e821f0 - ---> a9d3ced02d38 - Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" - ---> Running in 4b3f0db79860 - Removing intermediate container 4b3f0db79860 - ---> 42a0cb2e8f14 - Step 6/7 : LABEL org.opencontainers.image.revision="0b182c07fb8cc9306829c068d4ea600ee26891fc" - ---> Running in 5cc029947710 - Removing intermediate container 5cc029947710 - ---> fdc11be13f2e - Step 7/7 : LABEL org.opencontainers.image.version="test_HeBJG6" - ---> Running in 58757ca3bece - Removing intermediate container 58757ca3bece - ---> eea37ebd4ea2 - Successfully built eea37ebd4ea2 - Successfully tagged modality_alignment/methods_foo:test_HeBJG6 - ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo14025213034981140811/test_test/test_executable - >> Writing test file - >> Running component - >> Checking whether output file exists - >> Checking contents of output file - >> All tests succeeded successfully! - ==================================================================== - SUCCESS! All 1 out of 1 test scripts succeeded! - Cleaning up temporary directory - -To run all the unit tests of all the components in the repository, use -`bin/viash_test`. - -## Frequently asked questions - -### My component doesn’t work! - -Debugging your component based on the output from a Nextflow pipeline is -easier than you might realise. For example, the error message below -tells you that the ‘mse’ component failed: - -``` bash -src/modality_alignment/workflows/run_nextflow.sh -``` - - N E X T F L O W ~ version 20.10.0 - [f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ - [22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - [3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored - Completed at: 19-Apr-2021 20:09:22 - Duration : 3m 46s - CPU hours : 0.1 (2.7% failed) - Succeeded : 6 - Ignored : 2 - Failed : 2 - -Looking at this output reveals in which step of the pipeline the ‘mse’ -component failed, namely `3d/0d6afe`. This means we should check a -folder called `work/3d/0d6afe...`: - -``` bash -ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ -``` - - total 28 - drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . - drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. - lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad - -rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin - -rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err - -rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log - -rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out - -rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run - -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh - -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode - -``` bash -cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err -``` - - Traceback (most recent call last): - File "/tmp/viash-run-mse-WausLu", line 39, in - adata.uns["metric_value"] = area_under_curve - NameError: name 'area_under_curve' is not defined - -It seems that some error occurred within the Python script. Luckiky, the -input file of this process is in this directory. We can manually run the -component by running: - -``` bash -viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- \ - -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad -``` - -Alternatively, you can edit -`src/modality_alignment/metrics/mse/script.py` and replace the header -by: - -``` python -## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. -par = { - "input": "work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad", - "output": "test.h5ad" -} -## VIASH END - -## ... the rest of the script ... -``` - -Now you can work on the `script.py` file in your preferred editor -(vim?). For easy prototyping, viash will automatically strip away -anything between the `## VIASH START` and `## VIASH END` codeblock at -runtime. - -## Benefits of using Nextflow + viash +## Benefits of using Viash ### The pipeline is **language-agnostic** This means that each component can be written in whatever scripting -language the user desires. Here are examples of a -[Python](src/modality_alignment/methods/scot/) and an -[R](src/modality_alignment/methods/mnn) component. - -By default, viash supports wrapping the following scripting languages: -Bash, Python, R, JavaScript, and Scala. If viash doesn’t support your -preferred scripting language, feel free to ask the developers to [add -it](https://github.com/data-intuitive/viash/issues). Alternatively, you -can write a Bash script which calls your desired programming language. +language the user desires. By default, Viash supports wrapping the +following scripting languages: Bash, Python, R, JavaScript, and Scala. +If Viash doesn’t support your preferred scripting language, you can +still write a Bash script which calls your desired programming language. ### One Docker container per component -By running the `bin/viash_build` command, viash will build one Docker -container per component. While this results in some initial -computational overhead, this makes it a lot easier to add a new -component to the pipeline with dependencies which might conflict with -those of other components. +Viash builds one Docker container per component. While this results in +some initial computational overhead, this makes it a lot easier to add a +new component to the pipeline with dependencies which might conflict +with those of other components. ### Reproducible components -A component built by viash is meant to be reproducible. If you send the -`target/docker/modality_alignment/methods/foo/foo` file to someone, they -can run `./foo ---setup cachedbuild` and then will be able to use the -`foo` component however they like. - -``` bash -# pretend to send the component to someone through 'cp' -cp target/docker/modality_alignment/methods/foo/foo foo_by_email - -# build container -./foo_by_email ---setup cachedbuild -``` - - [notice] Building container 'modality_alignment/methods_foo:0.0.1' with Dockerfile - -``` bash -# view help -./foo_by_email -h -``` - - foo 0.0.1 - - Replace this with a (multiline) description of your component. - - Arguments: - -i, --input - type: file, required parameter - example: input.txt - Describe the input file. - - -o, --output - type: file, required parameter, output - example: output.txt - Describe the output file. - - --option - type: string - default: default- - Describe an optional parameter. - -``` bash -# run component -./foo_by_email -i LICENSE -o foo_output.txt -``` - - This is a skeleton component - The arguments are: - - input: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/LICENSE - - output: /viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/foo_output.txt - - option: default- - -### Reprodicible components on Docker Hub - -You might notice that the `---setup cachedbuild` builds the docker -container from scratch, rather than pulling it from Docker hub. - -With `bin/viash_build`, you can build a versioned release of all the -components in the repository and push it to Docker hub. - -``` bash -bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems -``` - - In release mode... - Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn - Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot - Exporting src/common/extract_scores/ (common) =docker=> target/docker/common/extract_scores - Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc - Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv - Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse - > docker build -t singlecellopenproblems/common_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS - > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO - > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 - > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 - > docker build -t singlecellopenproblems/modality_alignment/methods_scot:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scot-xUKof3 - > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc - -The images themselves can be pushed to Docker Hub with the -`bin/viash_push` command. I’d have to make a small change to viash to -ensure that the component names don’t contain any slashes because the -images listed above can’t be pushed to Docker hub. However, the output -would look something like this: - -``` bash -bin/viash_push -m release -v '0.1.0' -r openproblems -In release mode... -Using version 0.1.0 to tag containers -``` - - > openproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > openproblems/common_extract_scores:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! - - +A component built by viash is meant to be reproducible. All executables +and Nextflow modules in the `target/` folder in one of the +[releases](https://github.com/openproblems-bio/openproblems-v2/releases) +is fully reproducible, since all containers are published on the [GitHub +Container +Registry](https://github.com/orgs/openproblems-bio/packages?repo_name=openproblems-v2). diff --git a/README.qmd b/README.qmd index f24bae47ff..6d8bc5ea1d 100644 --- a/README.qmd +++ b/README.qmd @@ -1,337 +1,27 @@ --- title: "OpenProblems v2" format: gfm -toc: true +toc: false +engine: knitr --- -```{r, setup, include=FALSE} -knitr::opts_chunk$set( - warning=FALSE, - message=FALSE, - error=FALSE, - comment="" -) -``` -Proof Of Concept in adapting [Open Problems repository](https://github.com/openproblems-bio/openproblems) with Nextflow and viash. Documentation for viash is available at [viash.io](https://viash.io). +Formalizing and benchmarking open problems in single-cell genomics. -## Requirements +[**Visit the Open Problems Website.**](https://openproblems.bio/) -To use this repository, please install the following dependencies: +To get started with developing a new method or metric, please see the [Contribution guidelines](CONTRIBUTING.md). -* Bash -* Java (Java 11 or higher) -* Docker (Instructions [here](https://docs.docker.com/get-docker/)) -* Nextflow (Optional, though [very easy to install](https://www.nextflow.io/index.html#GetStarted)) -## Quick start - -The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. - -**Step 0, fetch viash and nextflow:** run the `bin/init` executable. - -```bash -bin/init -``` - - > Using tag develop - > Cleanup - > Install viash develop under /viash_automount/home/rcannood/workspace/opsca/opsca-viash/bin/ - > Fetching components sources (version develop) - > Building components - > Done, happy viash-ing! - > Nextflow installation completed. - -**Step 0b, download test resources:** by running the following command. - -```bash -bin/viash run src/common/sync_test_resources/config.vsh.yaml -bin/viash run src/common/sync_test_resources/config.vsh.yaml -- --input s3://openproblems-data/resources --output resources -``` - -**Step 1, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build only several components of the repository. - -```bash -bin/viash_build -q 'modality_alignment|common' -``` - - Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =nextflow=> target/nextflow/modality_alignment/metrics/knn_auc - Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =nextflow=> target/nextflow/modality_alignment/methods/scot - Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn - ... - -These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. -The command might take a while to run, since it is building a docker container for each of the components. -If you're interested in building only a subset of components, you can apply a regex to the selected components. -For example: `bin/viash_build -q 'common|modality_alignment'`. - -**Step 2, run the pipeline with nextflow.** To do so, run the bash script located at `src/modality_alignment/workflows/run_nextflow.sh`: - -```bash -src/modality_alignment/workflows/run_nextflow.sh -``` - - [15/84d27c] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [2f/318ad9] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [6f/dd22c1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [c6/6e0999] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [73/f6dffa] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [54/c89b95] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - Completed at: 20-Apr-2021 06:52:19 - Duration : 3m 40s - CPU hours : 0.1 - Succeeded : 8 - -## Project structure - - bin/ Helper scripts for building the project and developing a new component. - src/ Source files for each component in the pipeline. - modality_alignment/ Source files related to the 'Modality alignment' task. - datasets/ Dataset downloader components. - methods/ Modality alignment method components. - metrics/ Modality alignment metric components. - utils/ Utils functions. - workflow/ The pipeline workflow for this task. - common/ Helper files. - target/ Executables generated by viash based on the components listed under `src/`. - docker/ Bash executables which can be used from a terminal. - nextflow/ Nextflow modules which can be used in a Nextflow pipeline. - work/ A working directory used by Nextflow. - output/ Output generated by the pipeline. - - -## Adding a viash component - -[`viash`](https://github.com/data-intuitive/viash) allows you to create pipelines -in Bash or Nextflow by wrapping Python, R, or Bash scripts into reusable components. -You can start creating a new component using `bin/skeleton`. For example to create -a new Python-based viash component in the `src/modality_alignment/methods/foo` folder, run: -You can start creating a new component by using the `bin/skeleton` command: - -```{bash} -bin/viash_skeleton --name foo --namespace "modality_alignment/methods" --language python -``` - -This should create a few files in this folder: - - script.py A python script for you to edit. - config.vsh.yaml Metadata for the script containing info on the input/output arguments of the component. - test.py A python script with which you can start unit testing your component. - -The [Getting started](http://www.data-intuitive.com/viash_docs/) page on the viash documentation site -provides some information on how a basic viash component works, or on the specifications of the `config.vsh.yaml` [config file](http://www.data-intuitive.com/viash_docs/config/). - -## Running a component from CLI - -You can view the interface of the executable by running the executable with the `-h` parameter. - -```{bash} -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -h -``` - -You can **run the component** as follows: - -```{bash} -viash run src/modality_alignment/methods/foo/config.vsh.yaml -- -i LICENSE -o foo_output.txt -``` - -## Building a component - -`viash` has several helper functions to help you quickly develop a component. - -With **`viash build`**, you can turn the component into a standalone executable. -This standalone executable you can give to somebody else, and they will be able to -run it, provided that they have Bash and Docker installed. - -```{bash} -viash build src/modality_alignment/methods/foo/config.vsh.yaml \ - -o target/docker/modality_alignment/methods/foo -``` - -Note that the `bin/viash_build` component does a much better job of setting up -a collection of components. You can filter which components will be built by -providing a regex to the `-q` parameter, e.g. `bin/viash_build -q 'common|modality_alignment'`. - -You can now view the same interface of the executable by running the executable with the `-h` parameter. - -```{bash} -target/docker/modality_alignment/methods/foo/foo -h -``` - -Or **run the component** as follows: - -```{bash} -target/docker/modality_alignment/methods/foo/foo -i LICENSE -o foo_output.txt -``` - - -## Unit testing a component -Provided that you wrote a script that allows you to test the functionality of a component, -you can run the tests by using the **`viash test`** command. - -```{bash} -viash test src/modality_alignment/methods/foo/config.vsh.yaml -``` - -To run all the unit tests of all the components in the repository, use `bin/viash_test`. - -## Frequently asked questions - -### My component doesn't work! - -Debugging your component based on the output from a Nextflow pipeline is easier than you might realise. For example, the error message below tells you that the 'mse' component failed: - -``` bash -src/modality_alignment/workflows/run_nextflow.sh -``` - - N E X T F L O W ~ version 20.10.0 - [f8/2acb9f] process > get_scprep_csv_datasets:scprep_csv:scprep_csv_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [6e/0cb81b] process > mnn:mnn_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [43/edc9a1] process > scot:scot_process (CBMC_8K_13AB_10x) [100%] 1 of 1 ✔ - [00/41ee55] process > knn_auc:knn_auc_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2 ✔ - [3d/0d6afe] process > mse:mse_process (CBMC_8K_13AB_10x.scot) [100%] 2 of 2, failed: 2 ✔ - [22/5899a9] process > extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ - [3d/0d6afe] NOTE: Process `mse:mse_process (CBMC_8K_13AB_10x.scot)` terminated with an error exit status (1) -- Error is ignored - Completed at: 19-Apr-2021 20:09:22 - Duration : 3m 46s - CPU hours : 0.1 (2.7% failed) - Succeeded : 6 - Ignored : 2 - Failed : 2 - - -Looking at this output reveals in which step of the pipeline the 'mse' component failed, namely `3d/0d6afe`. This means we should check a folder called `work/3d/0d6afe...`: - -``` bash -ls -la work/3d/0d6afe9c27ab68d3f10551c3d3104c/ -``` - - total 28 - drwxrwxr-x. 1 rcannood rcannood 216 Apr 19 20:09 . - drwxrwxr-x. 1 rcannood rcannood 60 Apr 19 20:09 .. - lrwxrwxrwx. 1 rcannood rcannood 108 Apr 19 20:09 CBMC_8K_13AB_10x.scot.h5ad - -rw-rw-r--. 1 rcannood rcannood 0 Apr 19 20:09 .command.begin - -rw-rw-r--. 1 rcannood rcannood 191 Apr 19 20:09 .command.err - -rw-rw-r--. 1 rcannood rcannood 262 Apr 19 20:09 .command.log - -rw-rw-r--. 1 rcannood rcannood 71 Apr 19 20:09 .command.out - -rw-rw-r--. 1 rcannood rcannood 3224 Apr 19 20:09 .command.run - -rw-rw-r--. 1 rcannood rcannood 463 Apr 19 20:09 .command.sh - -rw-rw-r--. 1 rcannood rcannood 1 Apr 19 20:09 .exitcode - -```bash -cat work/3d/0d6afe9c27ab68d3f10551c3d3104c/.command.err -``` - - Traceback (most recent call last): - File "/tmp/viash-run-mse-WausLu", line 39, in - adata.uns["metric_value"] = area_under_curve - NameError: name 'area_under_curve' is not defined - -It seems that some error occurred within the Python script. Luckiky, the input file of this process is in this directory. We can manually run the component by running: - -``` bash -viash run src/modality_alignment/metrics/mse/config.vsh.yaml -- \ - -i work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad -o test.h5ad -``` - -Alternatively, you can edit `src/modality_alignment/metrics/mse/script.py` and replace the header by: -```python -## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. -par = { - "input": "work/3d/0d6afe9c27ab68d3f10551c3d3104c/CBMC_8K_13AB_10x.scot.h5ad", - "output": "test.h5ad" -} -## VIASH END - -## ... the rest of the script ... -``` - -Now you can work on the `script.py` file in your preferred editor (vim?). For easy prototyping, viash will automatically strip -away anything between the `## VIASH START` and `## VIASH END` codeblock at runtime. - - -## Benefits of using Nextflow + viash +## Benefits of using Viash ### The pipeline is **language-agnostic** -This means that each component can be written in whatever scripting language the user desires. -Here are examples of a [Python](src/modality_alignment/methods/scot/) and an [R](src/modality_alignment/methods/mnn) component. - -By default, viash supports wrapping the following scripting languages: Bash, Python, R, JavaScript, and Scala. -If viash doesn't support your preferred scripting language, feel free to ask the developers to [add it](https://github.com/data-intuitive/viash/issues). -Alternatively, you can write a Bash script which calls your desired programming language. +This means that each component can be written in whatever scripting language the user desires. By default, Viash supports wrapping the following scripting languages: Bash, Python, R, JavaScript, and Scala. If Viash doesn't support your preferred scripting language, you can still write a Bash script which calls your desired programming language. ### One Docker container per component -By running the `bin/viash_build` command, viash will build one Docker container per component. While this results in some initial computational overhead, -this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with those of other components. +Viash builds one Docker container per component. While this results in some initial computational overhead, this makes it a lot easier to add a new component to the pipeline with dependencies which might conflict with those of other components. ### Reproducible components -A component built by viash is meant to be reproducible. If you send the `target/docker/modality_alignment/methods/foo/foo` file to someone, -they can run `./foo ---setup cachedbuild` and then will be able to use the `foo` component however they like. - -```{bash} -# pretend to send the component to someone through 'cp' -cp target/docker/modality_alignment/methods/foo/foo foo_by_email - -# build container -./foo_by_email ---setup cachedbuild -``` - -```{bash} -# view help -./foo_by_email -h -``` - -```{bash} -# run component -./foo_by_email -i LICENSE -o foo_output.txt -``` - -### Reprodicible components on Docker Hub -You might notice that the `---setup cachedbuild` builds the docker container from scratch, rather than pulling it from Docker hub. - -With `bin/viash_build`, you can build a versioned release of all the components in the repository and push it to Docker hub. - -```bash -bin/viash_build -m release -v '0.1.0' -r singlecellopenproblems -``` - - In release mode... - Exporting src/modality_alignment/methods/mnn/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/mnn - Exporting src/modality_alignment/methods/scot/ (modality_alignment/methods) =docker=> target/docker/modality_alignment/methods/scot - Exporting src/common/extract_scores/ (common) =docker=> target/docker/common/extract_scores - Exporting src/modality_alignment/metrics/knn_auc/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/knn_auc - Exporting src/modality_alignment/datasets/scprep_csv/ (modality_alignment/datasets) =docker=> target/docker/modality_alignment/datasets/scprep_csv - Exporting src/modality_alignment/metrics/mse/ (modality_alignment/metrics) =docker=> target/docker/modality_alignment/metrics/mse - > docker build -t singlecellopenproblems/common_extract_scores:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-extract_scores-FyHtgS - > docker build -t singlecellopenproblems/modality_alignment/metrics_mse:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mse-r2LSpO - > docker build -t singlecellopenproblems/modality_alignment/metrics_knn_auc:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-knn_auc-S8dJP5 - > docker build -t singlecellopenproblems/modality_alignment/datasets_scprep_csv:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scprep_csv-lItAG1 - > docker build -t singlecellopenproblems/modality_alignment/methods_scot:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-scot-xUKof3 - > docker build -t singlecellopenproblems/modality_alignment/methods_mnn:0.1.0 --no-cache /home/rcannood/workspace/viash_temp/viashsetupdocker-mnn-0rjhKc - -The images themselves can be pushed to Docker Hub with the `bin/viash_push` command. I'd have to make a small change to viash to ensure that the component names don't contain any slashes because the images listed above can't be pushed to Docker hub. However, the output would look something like this: - -```bash -bin/viash_push -m release -v '0.1.0' -r openproblems -In release mode... -Using version 0.1.0 to tag containers -``` - > openproblems/modality_alignment_metrics_knn_auc:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_methods_scot:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_metrics_mse:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_datasets_scprep_csv:0.1.0 does not exist, try pushing ... OK! - > openproblems/common_extract_scores:0.1.0 does not exist, try pushing ... OK! - > openproblems/modality_alignment_methods_mnn:0.1.0 does not exist, try pushing ... OK! - - - -```{bash, echo=FALSE} -# remove example files -rm -r src/modality_alignment/methods/foo target/docker/modality_alignment/methods/foo -rm foo_output.txt foo_by_email -``` +A component built by viash is meant to be reproducible. All executables and Nextflow modules in the `target/` folder in one of the [releases](https://github.com/openproblems-bio/openproblems-v2/releases) is fully reproducible, since all containers are published on the [GitHub Container Registry](https://github.com/orgs/openproblems-bio/packages?repo_name=openproblems-v2). diff --git a/src/label_projection/workflows/run/params.yaml b/src/label_projection/workflows/run/params_benchmark.yaml similarity index 100% rename from src/label_projection/workflows/run/params.yaml rename to src/label_projection/workflows/run/params_benchmark.yaml diff --git a/src/label_projection/workflows/run/params_test.yaml b/src/label_projection/workflows/run/params_test.yaml new file mode 100644 index 0000000000..7485ad2b6c --- /dev/null +++ b/src/label_projection/workflows/run/params_test.yaml @@ -0,0 +1,5 @@ +param_list: +- id: pancreas + input_train: resources_test/label_projection/pancreas/train.h5ad + input_test: resources_test/label_projection/pancreas/test.h5ad + input_solution: resources_test/label_projection/pancreas/solution.h5ad \ No newline at end of file diff --git a/src/label_projection/workflows/run/run_benchmark.sh b/src/label_projection/workflows/run/run_benchmark.sh new file mode 100755 index 0000000000..7e378a1af1 --- /dev/null +++ b/src/label_projection/workflows/run/run_benchmark.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/label_projection/workflows/run/main.nf \ + -profile docker \ + -resume \ + -params-file src/label_projection/workflows/run/params_benchmark.yaml \ + --publish_dir output/label_projection \ No newline at end of file diff --git a/src/label_projection/workflows/run/run_nextflow.sh b/src/label_projection/workflows/run/run_test.sh similarity index 83% rename from src/label_projection/workflows/run/run_nextflow.sh rename to src/label_projection/workflows/run/run_test.sh index cf6cde2d29..2afdd9bfb2 100755 --- a/src/label_projection/workflows/run/run_nextflow.sh +++ b/src/label_projection/workflows/run/run_test.sh @@ -13,5 +13,5 @@ bin/nextflow \ -main-script src/label_projection/workflows/run/main.nf \ -profile docker \ -resume \ - -params-file src/label_projection/workflows/run/params.yaml \ + -params-file src/label_projection/workflows/run/params_test.yaml \ --publish_dir output/label_projection \ No newline at end of file From 33c2d0256f85c4b2c1352eef3362da3fb0958071 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:26:34 +0100 Subject: [PATCH 0348/1233] update test resources Former-commit-id: 210bb604bd9a1e9f89a501f24ef700b09f3b41a1 --- .../normalization/log_scran_pooling/script.R | 2 +- .../resource_test_scripts/pancreas.sh | 27 ++++++----- .../resources_test_scripts/pancreas.sh | 2 +- src/label_projection/utils.py | 48 ------------------- 4 files changed, 18 insertions(+), 61 deletions(-) delete mode 100644 src/label_projection/utils.py diff --git a/src/datasets/normalization/log_scran_pooling/script.R b/src/datasets/normalization/log_scran_pooling/script.R index 6d80c8cadf..e67ad6bdd5 100644 --- a/src/datasets/normalization/log_scran_pooling/script.R +++ b/src/datasets/normalization/log_scran_pooling/script.R @@ -6,7 +6,7 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( - input = "resources_test/label_projection/pancreas/dataset_subsampled.h5ad", + input = "resources_test/label_projection/pancreas/datas.h5ad", output = "output.scran.h5ad", layer_output = "log_scran_pooling", obs_size_factors = "size_factors_log_scran_pooling" diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 04a134154b..e7035affca 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -14,29 +14,34 @@ DATASET_DIR=resources_test/common/pancreas mkdir -p $DATASET_DIR # download dataset -bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ - --url "https://ndownloader.figshare.com/files/24539828" \ +bin/viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ + --id "pancreas" \ --obs_celltype "celltype" \ --obs_batch "tech" \ - --name "pancreas" \ --layer_counts "counts" \ - --layer_counts_output "counts" \ --output $DATASET_DIR/temp_dataset_full.h5ad # subsample -bin/viash run src/common/subsample/config.vsh.yaml -- \ +bin/viash run src/datasets/subsample/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset_full.h5ad \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ - --output $DATASET_DIR/temp_dataset_sampled.h5ad \ + --output $DATASET_DIR/temp_dataset0.h5ad \ --seed 123 # run log cpm normalisation -bin/viash run src/common/normalization/log_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_sampled.h5ad \ - --output $DATASET_DIR/temp_dataset_cpm.h5ad +bin/viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset0.h5ad \ + --output $DATASET_DIR/temp_dataset1.h5ad + +# run sqrt cpm normalisation +bin/viash run src/datasets/normalization/sqrt_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset1.h5ad \ + --output $DATASET_DIR/temp_dataset2.h5ad # run scran pooling normalisation -bin/viash run src/common/normalization/log_scran_pooling/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_cpm.h5ad \ +bin/viash run src/datasets/normalization/log_scran_pooling/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset2.h5ad \ --output $DATASET_DIR/dataset.h5ad + +rm -r $DATASET_DIR/temp_* \ No newline at end of file diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index dc7f9c4a19..8a2bb62bd0 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -20,7 +20,7 @@ fi mkdir -p $DATASET_DIR # split dataset -bin/viash run src/label_projection/split/config.vsh.yaml -- \ +bin/viash run src/label_projection/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ diff --git a/src/label_projection/utils.py b/src/label_projection/utils.py deleted file mode 100644 index 30c6851742..0000000000 --- a/src/label_projection/utils.py +++ /dev/null @@ -1,48 +0,0 @@ -import numpy as np -import sklearn.pipeline -import sklearn.preprocessing -import scipy.sparse -import sklearn.decomposition - - -def pca_op(adata_train, adata_test, n_components=100): - - is_sparse = scipy.sparse.issparse(adata_train.X) - - min_components = min( - [adata_train.shape[0], adata_test.shape[0], adata_train.shape[1]] - ) - if is_sparse: - min_components -= 1 - n_components = min([n_components, min_components]) - if is_sparse: - pca_op = sklearn.decomposition.TruncatedSVD - else: - pca_op = sklearn.decomposition.PCA - return pca_op(n_components=n_components) - - -def classifier(adata, estimator, n_pca=100, **kwargs): - """Run a generic scikit-learn classifier.""" - adata_train = adata[adata.obs["is_train"]] - adata_test = adata[~adata.obs["is_train"]].copy() - - classifier = sklearn.pipeline.Pipeline( - [ - ("pca", pca_op(adata_train, adata_test, n_components=n_pca)), - ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), - ("regression", estimator(**kwargs)), - ] - ) - - # Fit to train data - classifier.fit(adata_train.X, adata_train.obs["celltype"].astype(str)) - - # Predict on test data - adata_test.obs["celltype_pred"] = classifier.predict(adata_test.X) - - adata.obs["celltype_pred"] = [ - adata_test.obs["celltype_pred"][idx] if idx in adata_test.obs_names else np.nan - for idx in adata.obs_names - ] - return adata From 6a5ea891a63f0ffe5acf0e71480eeaba84746c41 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:31:49 +0100 Subject: [PATCH 0349/1233] change the majority vote method in a negative control Former-commit-id: 7d33aaf4e070f9e1cee1ea35f04b4097e45a2c58 --- .../control_methods/majority_vote/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 00c6736788..7e1cf0167b 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "label_projection/control_methods" description: "Baseline method using majority voting" info: - type: baseline + type: negative_control label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c From cd3b716ee97c4e35bf330bb305b8efff57f77f5f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:33:58 +0100 Subject: [PATCH 0350/1233] rename knn_classifier to knn Former-commit-id: c1a463978fd5c76b0ba0cab44f8a8a376321b47c --- CONTRIBUTING.md | 2 +- CONTRIBUTING.qmd | 2 +- src/label_projection/README.md | 2 +- .../methods/{knn_classifier => knn}/config.vsh.yaml | 2 +- .../methods/{knn_classifier => knn}/script.py | 0 src/label_projection/resources_test_scripts/pancreas.sh | 2 +- src/label_projection/workflows/run/main.nf | 4 ++-- 7 files changed, 7 insertions(+), 7 deletions(-) rename src/label_projection/methods/{knn_classifier => knn}/config.vsh.yaml (97%) rename src/label_projection/methods/{knn_classifier => knn}/script.py (100%) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 703bbe403d..b9a2d2dfcd 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -113,7 +113,7 @@ src/label_projection/workflows/run/run_test.sh [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ - [fd/92edc7] process > run_wf:knn_classifier:knn_classifier_process (1) [100%] 1 of 1 ✔ + [fd/92edc7] process > run_wf:knn:knn_process (1) [100%] 1 of 1 ✔ [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index e78745fc46..f7616fd049 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -85,7 +85,7 @@ src/label_projection/workflows/run/run_test.sh [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ - [fd/92edc7] process > run_wf:knn_classifier:knn_classifier_process (1) [100%] 1 of 1 ✔ + [fd/92edc7] process > run_wf:knn:knn_process (1) [100%] 1 of 1 ✔ [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ diff --git a/src/label_projection/README.md b/src/label_projection/README.md index de39eceadd..7ccfe12a46 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -62,7 +62,7 @@ Methods for assigning labels from a reference dataset to a new dataset. | Name | Description | DOI | URL | |:---------------------------------------------------------------------|:-------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| -| [KNN](./methods/knn_classifier/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | +| [KNN](./methods/knn/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | | [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | | [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | diff --git a/src/label_projection/methods/knn_classifier/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml similarity index 97% rename from src/label_projection/methods/knn_classifier/config.vsh.yaml rename to src/label_projection/methods/knn/config.vsh.yaml index ec2afa296c..eeaddf9b40 100644 --- a/src/label_projection/methods/knn_classifier/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -1,6 +1,6 @@ __inherits__: ../../api/comp_method.yaml functionality: - name: "knn_classifier" + name: "knn" namespace: "label_projection/methods" description: "K-Nearest Neighbors classifier" info: diff --git a/src/label_projection/methods/knn_classifier/script.py b/src/label_projection/methods/knn/script.py similarity index 100% rename from src/label_projection/methods/knn_classifier/script.py rename to src/label_projection/methods/knn/script.py diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 8a2bb62bd0..35bbc9f2e6 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -28,7 +28,7 @@ bin/viash run src/label_projection/split_dataset/config.vsh.yaml -- \ --seed 123 # run one method -bin/viash run src/label_projection/methods/knn_classifier/config.vsh.yaml -- \ +bin/viash run src/label_projection/methods/knn/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/knn.h5ad diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index bc46fc53b7..b5807111a9 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -9,7 +9,7 @@ include { majority_vote } from "$targetDir/label_projection/control_methods/majo include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" // import methods -include { knn_classifier } from "$targetDir/label_projection/methods/knn_classifier/main.nf" +include { knn } from "$targetDir/label_projection/methods/knn/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" // include { scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scanvi_hvg/main.nf" @@ -63,7 +63,7 @@ workflow run_wf { true_labels.run(map: addSolution) & random_labels & majority_vote & - knn_classifier & + knn & logistic_regression & mlp ) From ce3b6467f7cc766c38cb7602779ac0dcbbece0a4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:34:13 +0100 Subject: [PATCH 0351/1233] update changelog Former-commit-id: 98de0438fddbeccc3cd55acf31e732bdc9bca0ff --- CHANGELOG.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fabd769765..2e5fdaad92 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,20 +16,28 @@ ### NEW FUNCTIONALITY -* API: Created an explicit api definition for the split, method and metric components. +* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. -* `data_processing/split`: Added a component for splitting raw datasets into task-ready dataset objects. +* `api/comp_*`: Created an api definition for the split, method and metric components. + +* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. * `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. ### V1 MIGRATION -* `methods/knn_classifier`: Migrated from v1. +* `methods/knn`: Migrated from v1. * `methods/logistic_regression`: Migrated from v1. * `methods/mlp`: Migrated from v1. +* `control_methods/majority_vote`: Migrated from v1. + +* `control_methods/random_labels`: Migrated from v1. + +* `control_methods/true_labels`: Migrated from v1. + * Temporarily disable `scanvi` / `scarches_scanvi`. * `metric/accuracy`: Migrated from v1. From 8e46906312abb3a0663ead066ba5a2e202905a10 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:34:23 +0100 Subject: [PATCH 0352/1233] fix script Former-commit-id: 94ec57d471089a5c8cf0adeb22e2070f8b6933a9 --- src/label_projection/analysis_scripts/script.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index 7faecd957e..756f01b187 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -37,8 +37,7 @@ metric_info <- map_df(ns_list_metrics, function(conf) { df <- scores %>% left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") %>% - left_join(metric_info %>% select(id, label, min, max, maximise) %>% rename_all(function(x) paste0("metric_", x)), by = "metric_id") %>% - mutate(method_label = factor(method_label, levels = c("True labels", "Multilayer perceptron"))) + left_join(metric_info %>% select(id, label, min, max, maximise) %>% rename_all(function(x) paste0("metric_", x)), by = "metric_id") ordering <- df %>% group_by(metric_id, dataset_id) %>% From cf8c6333fe6e26c1a7f71221d05785eccb4fea8d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 09:59:01 +0100 Subject: [PATCH 0353/1233] copy task description to separate file Former-commit-id: eda650d2e16e5402547b5e04ebf1275fb4676551 --- src/label_projection/README.md | 43 +++++++++++-------- src/label_projection/README.qmd | 14 +++--- src/label_projection/docs/task_description.md | 7 +++ 3 files changed, 37 insertions(+), 27 deletions(-) create mode 100644 src/label_projection/docs/task_description.md diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 7ccfe12a46..277af4cc3a 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -1,7 +1,8 @@ - Label Projection - - The task + - Task + description - Methods - Metrics - Pipeline @@ -25,11 +26,12 @@ - Component API - method - metric - - split + - split dataset # Label Projection -## The task +## Task description A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common @@ -60,11 +62,12 @@ labels onto the test set. Methods for assigning labels from a reference dataset to a new dataset. -| Name | Description | DOI | URL | -|:---------------------------------------------------------------------|:-------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| -| [KNN](./methods/knn/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | -| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | -| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | +| Name | Description | DOI | URL | +|:---------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| +| [KNN](./methods/knn/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | +| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | +| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | +| [Scanvi](./methods/scanvi/config.vsh.yaml) | Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | ## Metrics @@ -98,17 +101,17 @@ flowchart LR anndata_train(train.h5ad) comp_method[/method/] comp_metric[/metric/] - comp_split[/split/] + comp_split_dataset[/split dataset/] anndata_train---comp_method anndata_test---comp_method anndata_solution---comp_metric anndata_prediction---comp_metric - anndata_dataset---comp_split + anndata_dataset---comp_split_dataset comp_method-->anndata_prediction comp_metric-->anndata_score - comp_split-->anndata_train - comp_split-->anndata_test - comp_split-->anndata_solution + comp_split_dataset-->anndata_train + comp_split_dataset-->anndata_test + comp_split_dataset-->anndata_solution ``` ## File format API @@ -119,7 +122,7 @@ A preprocessed dataset Used in: -- [split](#split): input (as input) +- [split dataset](#split%20dataset): input (as input) Slots: @@ -128,6 +131,7 @@ Slots: | layers | counts | integer | Raw counts | | layers | log_cpm | double | CPM normalized counts, log transformed | | layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | | obs | label | double | Ground truth cell type labels | | obs | batch | double | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | @@ -173,7 +177,7 @@ The solution for the test data Used in: - [metric](#metric): input_solution (as input) -- [split](#split): output_solution (as output) +- [split dataset](#split%20dataset): output_solution (as output) Slots: @@ -182,6 +186,7 @@ Slots: | layers | counts | integer | Raw counts | | layers | log_cpm | double | CPM normalized counts, log transformed | | layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | | obs | label | string | Ground truth cell type labels | | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | @@ -193,7 +198,7 @@ The test data (without labels) Used in: - [method](#method): input_test (as input) -- [split](#split): output_test (as output) +- [split dataset](#split%20dataset): output_test (as output) Slots: @@ -202,6 +207,7 @@ Slots: | layers | counts | integer | Raw counts | | layers | log_cpm | double | CPM normalized counts, log transformed | | layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | @@ -212,7 +218,7 @@ The training data Used in: - [method](#method): input_train (as input) -- [split](#split): output_train (as output) +- [split dataset](#split%20dataset): output_train (as output) Slots: @@ -221,6 +227,7 @@ Slots: | layers | counts | integer | Raw counts | | layers | log_cpm | double | CPM normalized counts, log transformed | | layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | +| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | | obs | label | string | Ground truth cell type labels | | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | @@ -247,7 +254,7 @@ Arguments: | `--input_prediction` | prediction.h5ad | input | Prediction | | `--output` | score.h5ad | output | Score | -### `split` +### `split dataset` Arguments: diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 249feb37c3..2479d5b5e9 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -20,15 +20,11 @@ dir <- "." # Label Projection -## The task - -A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) whereby cells are aggregated into clusters based on feature similarity and then manually characterized based on differential gene expression or previously identified marker genes. Recently, methods have emerged to build on this strategy and annotate cells using [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. - -To ensure that the cell type labels in newly generated datasets match existing reference datasets, some methods align cells to a previously annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) and then _project_ labels from the reference to the new dataset. - -Here, we compare methods for annotation based on a reference dataset. The datasets consist of two or more samples of single cell profiles that have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. - - +```{r description, echo=FALSE} +lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) +lines2 <- gsub("^#", "##", lines) +knitr::asis_output(lines2) +``` ## Methods diff --git a/src/label_projection/docs/task_description.md b/src/label_projection/docs/task_description.md new file mode 100644 index 0000000000..be120e2b88 --- /dev/null +++ b/src/label_projection/docs/task_description.md @@ -0,0 +1,7 @@ +# Task description + +A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) whereby cells are aggregated into clusters based on feature similarity and then manually characterized based on differential gene expression or previously identified marker genes. Recently, methods have emerged to build on this strategy and annotate cells using [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. + +To ensure that the cell type labels in newly generated datasets match existing reference datasets, some methods align cells to a previously annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) and then _project_ labels from the reference to the new dataset. + +Here, we compare methods for annotation based on a reference dataset. The datasets consist of two or more samples of single cell profiles that have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. \ No newline at end of file From 0339d730be5fbe6091c2945a8783afce83c0d622 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 10:26:15 +0100 Subject: [PATCH 0354/1233] update readme Former-commit-id: 11eb289f10759bd896176e8d8095e1ad08093136 --- src/label_projection/README.md | 97 ++++++++++++++------------------- src/label_projection/README.qmd | 36 ++++++------ 2 files changed, 60 insertions(+), 73 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 277af4cc3a..28f5d1ad0b 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -8,26 +8,17 @@ - Pipeline topology - File format API - - dataset.h5ad: - Preprocessed dataset - - prediction.h5ad: - Prediction - - score.h5ad: Score - - solution.h5ad: Solution - - test.h5ad: Test data - - train.h5ad: Training - data + - Dataset + - Prediction + - Score + - Solution + - Test + - Train - Component API - - method - - metric + - Method + - Metric - split dataset + id="toc-split-dataset">Split Dataset # Label Projection @@ -62,46 +53,42 @@ labels onto the test set. Methods for assigning labels from a reference dataset to a new dataset. -| Name | Description | DOI | URL | -|:---------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| -| [KNN](./methods/knn/config.vsh.yaml) | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | -| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | -| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | -| [Scanvi](./methods/scanvi/config.vsh.yaml) | Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | +| Name | Type | Description | DOI | URL | +|:---------------------------------------------------------------------|:-----------------|:------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| +| [KNN](./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | +| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | +| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | +| [Scanvi](./methods/scanvi/config.vsh.yaml) | method | Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | +| [Majority Vote](./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | +| [Random Labels](./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | +| [True labels](./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | ## Metrics Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. -- **[Accuracy](./metrics/accuracy/config.vsh.yaml)**: The percentage of - correctly predicted labels. Range: \[0, 1\]. Higher is better. -- **[F1 weighted](./metrics/f1/config.vsh.yaml)**: Calculates the F1 - score for each label, and find their average weighted by support (the - number of true instances for each label). This alters ‘macro’ to - account for label imbalance; it can result in an F-score that is not - between precision and recall. Range: \[0, 1\]. Higher is better. -- **[F1 macro](./metrics/f1/config.vsh.yaml)**: Calculates the F1 score - for each label, and find their unweighted mean. This does not take - label imbalance into account. Range: \[0, 1\]. Higher is better. -- **[F1 micro](./metrics/f1/config.vsh.yaml)**: Calculates the F1 score - globally by counting the total true positives, false negatives and - false positives. Range: \[0, 1\]. Higher is better. +| Name | Description | Range | +|:-----------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------| +| [Accuracy](./metrics/accuracy/config.vsh.yaml) | The percentage of correctly predicted labels. Higher is better. | \[0, 1\] | +| [F1 weighted](./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. Higher is better. | \[0, 1\] | +| [F1 macro](./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. Higher is better. | \[0, 1\] | +| [F1 micro](./metrics/f1/config.vsh.yaml) | Calculates the F1 score globally by counting the total true positives, false negatives and false positives. Higher is better. | \[0, 1\] | ## Pipeline topology ``` mermaid %%| column: screen-inset-shaded flowchart LR - anndata_dataset(dataset.h5ad) - anndata_prediction(prediction.h5ad) - anndata_score(score.h5ad) - anndata_solution(solution.h5ad) - anndata_test(test.h5ad) - anndata_train(train.h5ad) - comp_method[/method/] - comp_metric[/metric/] - comp_split_dataset[/split dataset/] + anndata_dataset(Dataset) + anndata_prediction(Prediction) + anndata_score(Score) + anndata_solution(Solution) + anndata_test(Test) + anndata_train(Train) + comp_method[/Method/] + comp_metric[/Metric/] + comp_split_dataset[/Split Dataset/] anndata_train---comp_method anndata_test---comp_method anndata_solution---comp_metric @@ -116,7 +103,7 @@ flowchart LR ## File format API -### `dataset.h5ad`: Preprocessed dataset +### `Dataset` A preprocessed dataset @@ -136,7 +123,7 @@ Slots: | obs | batch | double | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | -### `prediction.h5ad`: Prediction +### `Prediction` The prediction file @@ -153,7 +140,7 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | method_id | string | A unique identifier for the method | -### `score.h5ad`: Score +### `Score` Metric score file @@ -170,7 +157,7 @@ Slots: | uns | metric_ids | string | One or more unique metric identifiers | | uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | -### `solution.h5ad`: Solution +### `Solution` The solution for the test data @@ -191,7 +178,7 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | -### `test.h5ad`: Test data +### `Test` The test data (without labels) @@ -211,7 +198,7 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | -### `train.h5ad`: Training data +### `Train` The training data @@ -234,7 +221,7 @@ Slots: ## Component API -### `method` +### `Method` Arguments: @@ -244,7 +231,7 @@ Arguments: | `--input_test` | test.h5ad | input | Test data | | `--output` | prediction.h5ad | output | Prediction | -### `metric` +### `Metric` Arguments: @@ -254,7 +241,7 @@ Arguments: | `--input_prediction` | prediction.h5ad | input | Prediction | | `--output` | score.h5ad | output | Score | -### `split dataset` +### `Split Dataset` Arguments: diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 2479d5b5e9..0fa9c55ce4 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -31,14 +31,13 @@ knitr::asis_output(lines2) Methods for assigning labels from a reference dataset to a new dataset. ```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -method_yamls <- list.files(paste0(dir, "/methods"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) +method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) +method_configs <- yaml::yaml.load(method_ns_list$stdout) -method_info <- map_df(method_yamls, function(method_yaml) { - out <- system(paste0("viash config view ", method_yaml), intern = TRUE, ignore.stderr = TRUE) - config <- yaml::yaml.load(out) +method_info <- map_df(method_configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(config$functionality$info) - info$comp_yaml <- method_yaml + info$comp_yaml <- config$info$config info$name <- config$functionality$name info$namespace <- config$functionality$namespace info$description <- config$functionality$description @@ -47,8 +46,10 @@ method_info <- map_df(method_yamls, function(method_yaml) { method_info_view <- method_info %>% + arrange(type, label) %>% transmute( Name = paste0("[", label, "](", comp_yaml, ")"), + Type = type, Description = description, DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") @@ -63,13 +64,12 @@ cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. ```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -metric_yamls <- list.files(paste0(dir, "/metrics"), pattern = "config.vsh.yaml", full.names = TRUE, recursive = TRUE) +metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) +metric_configs <- yaml::yaml.load(metric_ns_list$stdout) -metric_info <- map_df(metric_yamls, function(metric_yaml) { - out <- system(paste0("viash config view ", metric_yaml), intern = TRUE, ignore.stderr = TRUE) - config <- yaml::yaml.load(out) +metric_info <- map_df(metric_configs, function(config) { metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - metric_info$comp_yaml <- metric_yaml + metric_info$comp_yaml <- config$info$config metric_info$comp_name <- config$functionality$name metric_info$comp_namespace <- config$functionality$namespace metric_info @@ -78,12 +78,12 @@ metric_info <- map_df(metric_yamls, function(metric_yaml) { metric_info_view <- metric_info %>% transmute( - # Name = paste0("[", label, "](", comp_yaml, ")"), - # Description = paste0(description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")), - str = paste0("* **[", label, "](", comp_yaml, ")**: ", description, " Range: [", min, ", ", max, "]. ", ifelse(maximise, "Higher is better.", "Lower is better.")) + Name = paste0("[", label, "](", comp_yaml, ")"), + Description = paste0(description, " ", ifelse(maximise, "Higher is better.", "Lower is better.")), + Range = paste0("[", min, ", ", max, "]") ) -cat(paste(metric_info_view$str, collapse = '\n')) +cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) ``` @@ -143,9 +143,9 @@ file_slot <- map_df(file_yamls, function(yaml_file) { ```{r flow, echo=FALSE,warning=FALSE,error=FALSE} nodes <- bind_rows( file_info %>% - transmute(id = name, label = paste0(label, ".h5ad"), is_comp = FALSE), + transmute(id = name, label = str_to_title(label), is_comp = FALSE), comp_info %>% - transmute(id = name, label, is_comp = TRUE) + transmute(id = name, label = str_to_title(label), is_comp = TRUE) ) %>% mutate(str = paste0( " ", @@ -199,7 +199,7 @@ for (file_name in file_info$name) { pull(str) out_str <- strip_margin(glue::glue(" - §### `{arg_info$label}.h5ad`: {arg_info$short_description} + §### `{str_to_title(arg_info$label)}` § §{arg_info$description} § @@ -235,7 +235,7 @@ for (comp_name in comp_info$name) { ) out_str <- strip_margin(glue::glue(" - §### `{comp$label}` + §### `{str_to_title(comp$label)}` § §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} § From 35976deefa3dfd4ebc57201cb51e5f8ccb4af1a9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 11:06:39 +0100 Subject: [PATCH 0355/1233] update readme Former-commit-id: 320c8aff0444c553f96a996a02e4f2e0fce24136 --- src/label_projection/README.md | 71 +++++++++++++++++++++++++-------- src/label_projection/README.qmd | 17 +++++++- 2 files changed, 71 insertions(+), 17 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 28f5d1ad0b..ba08e1f7e7 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -123,6 +123,13 @@ Slots: | obs | batch | double | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | +Example: + + AnnData object + obs: 'label', 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + ### `Prediction` The prediction file @@ -140,6 +147,12 @@ Slots: | uns | dataset_id | string | A unique identifier for the dataset | | uns | method_id | string | A unique identifier for the method | +Example: + + AnnData object + obs: 'label_pred' + uns: 'dataset_id', 'method_id' + ### `Score` Metric score file @@ -157,6 +170,11 @@ Slots: | uns | metric_ids | string | One or more unique metric identifiers | | uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | +Example: + + AnnData object + uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + ### `Solution` The solution for the test data @@ -178,6 +196,13 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | +Example: + + AnnData object + obs: 'label', 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + ### `Test` The test data (without labels) @@ -198,6 +223,13 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | +Example: + + AnnData object + obs: 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + ### `Train` The training data @@ -219,35 +251,42 @@ Slots: | obs | batch | string | Batch information | | uns | dataset_id | string | A unique identifier for the dataset | +Example: + + AnnData object + obs: 'label', 'batch' + uns: 'dataset_id' + layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + ## Component API ### `Method` Arguments: -| Name | File format | Direction | Description | -|:----------------|:----------------|:----------|:--------------| -| `--input_train` | train.h5ad | input | Training data | -| `--input_test` | test.h5ad | input | Test data | -| `--output` | prediction.h5ad | output | Prediction | +| Name | File format | Direction | Description | +|:----------------|:--------------------------|:----------|:--------------| +| `--input_train` | [Train](#train) | input | Training data | +| `--input_test` | [Test](#test) | input | Test data | +| `--output` | [Prediction](#prediction) | output | Prediction | ### `Metric` Arguments: -| Name | File format | Direction | Description | -|:---------------------|:----------------|:----------|:------------| -| `--input_solution` | solution.h5ad | input | Solution | -| `--input_prediction` | prediction.h5ad | input | Prediction | -| `--output` | score.h5ad | output | Score | +| Name | File format | Direction | Description | +|:---------------------|:--------------------------|:----------|:------------| +| `--input_solution` | [Solution](#solution) | input | Solution | +| `--input_prediction` | [Prediction](#prediction) | input | Prediction | +| `--output` | [Score](#score) | output | Score | ### `Split Dataset` Arguments: -| Name | File format | Direction | Description | -|:--------------------|:--------------|:----------|:---------------------| -| `--input` | dataset.h5ad | input | Preprocessed dataset | -| `--output_train` | train.h5ad | output | Training data | -| `--output_test` | test.h5ad | output | Test data | -| `--output_solution` | solution.h5ad | output | Solution | +| Name | File format | Direction | Description | +|:--------------------|:----------------------|:----------|:---------------------| +| `--input` | [Dataset](#dataset) | input | Preprocessed dataset | +| `--output_train` | [Train](#train) | output | Training data | +| `--output_test` | [Test](#test) | output | Test data | +| `--output_solution` | [Solution](#solution) | output | Solution | diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 0fa9c55ce4..df3b739f6a 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -192,11 +192,21 @@ for (file_name in file_info$name) { sub_out <- file_slot %>% filter(file_name == !!file_name) %>% select(struct, name, type, description) + used_in <- comp_file %>% filter(file_name == !!file_name) %>% left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% pull(str) + + example <- sub_out %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) + + example_str <- c(" AnnData object", paste0(" ", example$str)) out_str <- strip_margin(glue::glue(" §### `{str_to_title(arg_info$label)}` @@ -210,6 +220,11 @@ for (file_name in file_info$name) { §Slots: § §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + § + §Example: + § + §{paste(example_str, collapse = '\n')} + § §"), symbol = "§") cat(out_str) } @@ -229,7 +244,7 @@ for (comp_name in comp_info$name) { left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% transmute( Name = paste0("`--", arg_name, "`"), - `File format` = paste0(file_label, ".h5ad"), + `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), Direction = direction, Description = file_sdesc ) From 27504eb1abecd59cf490eed4d2e0dc792191e884 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:00:53 +0100 Subject: [PATCH 0356/1233] run only one normalization method per dataset Former-commit-id: 90b16a3f66e45e5b177596b1fecc1d8274db9f33 --- src/datasets/api/anndata_dataset.yaml | 14 +++--- src/datasets/api/anndata_normalized.yaml | 40 +++++++++++++++ ...data_raw_dataset.yaml => anndata_raw.yaml} | 0 src/datasets/api/comp_dataset_loader.yaml | 2 +- src/datasets/api/comp_normalization.yaml | 49 ++++--------------- .../loaders/openproblems_v1/config.vsh.yaml | 2 +- .../normalization/log_cpm/config.vsh.yaml | 9 ---- .../log_scran_pooling/config.vsh.yaml | 9 ---- .../normalization/sqrt_cpm/config.vsh.yaml | 9 ---- .../process_openproblems_v1/config.vsh.yaml | 2 +- .../workflows/process_openproblems_v1/main.nf | 18 +++++-- 11 files changed, 72 insertions(+), 82 deletions(-) create mode 100644 src/datasets/api/anndata_normalized.yaml rename src/datasets/api/{anndata_raw_dataset.yaml => anndata_raw.yaml} (100%) diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index 92337723d7..0dee2ee98d 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -10,14 +10,8 @@ info: description: Raw counts required: true - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - - type: double - name: sqrt_cpm - description: CPM normalized counts, sqrt transformed + name: normalized + description: Normalised expression values obs: - type: string name: celltype @@ -35,4 +29,8 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" required: true \ No newline at end of file diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/anndata_normalized.yaml new file mode 100644 index 0000000000..96b29db247 --- /dev/null +++ b/src/datasets/api/anndata_normalized.yaml @@ -0,0 +1,40 @@ +type: file +description: "A dataset" +example: "dataset.h5ad" +info: + short_description: "Normalized dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalised expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true \ No newline at end of file diff --git a/src/datasets/api/anndata_raw_dataset.yaml b/src/datasets/api/anndata_raw.yaml similarity index 100% rename from src/datasets/api/anndata_raw_dataset.yaml rename to src/datasets/api/anndata_raw.yaml diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 5e8e85d226..4b15d566f5 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -2,5 +2,5 @@ functionality: arguments: - name: "--output" direction: output - __inherits__: anndata_raw_dataset.yaml + __inherits__: anndata_raw.yaml diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index f0c786e115..b720c9bf83 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,47 +1,18 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_raw_dataset.yaml + __inherits__: anndata_raw.yaml - name: "--output" - type: file - description: "A preprocessed dataset" - example: "preprocessed.h5ad" - info: - short_description: "Preprocessed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: $par_layer_output - description: Log-transformed normalised counts - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true direction: output - - # not including this because we need to override the default - # - name: "--layer_output" - # type: string - # default: "log_cpm" - # description: The name of the layer in which to store the log normalized data. + __inherits__: anndata_normalized.yaml + - name: "--layer_output" + type: string + default: "normalized" + description: The name of the layer in which to store the normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors" + description: In which .obs slot to store the size factors (if any). test_resources: - type: python_script path: generic_test.py diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index a228c95a61..7c2ebcda1e 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: - name: Outputs arguments: - name: "--output" - __inherits__: ../../api/anndata_raw_dataset.yaml + __inherits__: ../../api/anndata_raw.yaml direction: "output" resources: - type: python_script diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 9e49f04fb5..1685944df9 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -3,15 +3,6 @@ functionality: name: "log_cpm" namespace: "datasets/normalization" description: "Normalize data using Log CPM" - arguments: - - name: "--layer_output" - type: string - default: "log_cpm" - description: The name of the layer in which to store the log normalized data. - - name: "--obs_size_factors" - type: string - default: "size_factors_log_cpm" - description: In which .obs slot to store the size factors. resources: - type: python_script path: script.py diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 0be7a00951..4af63dba94 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -3,15 +3,6 @@ functionality: name: "log_scran_pooling" namespace: "datasets/normalization" description: "Normalize data using scran pooling" - arguments: - - name: "--layer_output" - type: string - default: "log_scran_pooling" - description: The name of the layer in which to store the log normalized data. - - name: "--obs_size_factors" - type: string - default: "size_factors_log_scran_pooling" - description: In which .obs slot to store the size factors. resources: - type: r_script path: script.R diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 977fa3cc39..48aa7562b8 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -3,15 +3,6 @@ functionality: name: "sqrt_cpm" namespace: "datasets/normalization" description: "Normalize data using Log Sqrt" - arguments: - - name: "--layer_output" - type: string - default: "sqrt_cpm" - description: The name of the layer in which to store the log normalized data. - - name: "--obs_size_factors" - type: string - default: "size_factors_sqrt_cpm" - description: In which .obs slot to store the size factors. resources: - type: python_script path: script.py diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 1a5930651d..64db3042a8 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: - name: "--output" direction: "output" # todo: fix inherits in nxf - # __inherits__: ../../api/anndata_raw_dataset.yaml + # __inherits__: ../../api/anndata_raw.yaml type: file description: "A raw dataset" example: "raw_dataset.h5ad" diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 3eae19d60e..b77a66def7 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -29,16 +29,24 @@ workflow run_wf { // split params for downstream components | setWorkflowArguments( - openproblems_v1: ["id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse"], - sqrt_cpm: [ "output" ] + loader: ["id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse"], + output: [ "output" ] ) // fetch data from legacy openproblems - | getWorkflowArguments(key: "openproblems_v1") + | getWorkflowArguments(key: "loader") | openproblems_v1 - // run cpm normalisation - | log_cpm + // run normalization methods + | (log_cpm & log_scran_pooling & sqrt_cpm) + | mix + + // make id unique again + | pmap{ id, file -> + // derive unique ids from output filenames + def newId = file.getName().replaceAll(".output.*", "") + [ newId, file ] + } // run scran normalisation | log_scran_pooling From eb561e5e8aaacaddfe4c75325c396d1d2f43f3eb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:01:33 +0100 Subject: [PATCH 0357/1233] add hvg and pca components Former-commit-id: 7c2cc3636b6fc493645d116bee471922a14aa50a --- src/datasets/api/anndata_dataset.yaml | 14 ++++ src/datasets/api/comp_processor_hvg.yaml | 15 ++++ src/datasets/api/comp_processor_pca.yaml | 15 ++++ src/datasets/processors/hvg/config.vsh.yaml | 60 ++++++++++++++++ src/datasets/processors/hvg/script.py | 36 ++++++++++ src/datasets/processors/pca/config.vsh.yaml | 70 +++++++++++++++++++ src/datasets/processors/pca/script.py | 39 +++++++++++ .../workflows/process_openproblems_v1/main.nf | 10 +-- 8 files changed, 254 insertions(+), 5 deletions(-) create mode 100644 src/datasets/api/comp_processor_hvg.yaml create mode 100644 src/datasets/api/comp_processor_pca.yaml create mode 100644 src/datasets/processors/hvg/config.vsh.yaml create mode 100644 src/datasets/processors/hvg/script.py create mode 100644 src/datasets/processors/pca/config.vsh.yaml create mode 100644 src/datasets/processors/pca/script.py diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index 0dee2ee98d..e4b969803a 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -25,6 +25,15 @@ info: name: tissue description: Tissue information required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_ranking + description: A ranking of the features by hvg. + required: true uns: - type: string name: dataset_id @@ -33,4 +42,9 @@ info: - type: string name: normalization_id description: "Which normalization was used" + required: true + obsm: + - type: double + name: X_pca + description: A PCA embedding of the normalized data. required: true \ No newline at end of file diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml new file mode 100644 index 0000000000..fa490e7007 --- /dev/null +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -0,0 +1,15 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_raw.yaml + - name: "--output" + direction: output + __inherits__: anndata_normalized.yaml + - name: "--layer_output" + type: string + default: "normalized" + description: The name of the layer in which to store the normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors" + description: In which .obs slot to store the size factors (if any). \ No newline at end of file diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml new file mode 100644 index 0000000000..fa490e7007 --- /dev/null +++ b/src/datasets/api/comp_processor_pca.yaml @@ -0,0 +1,15 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_raw.yaml + - name: "--output" + direction: output + __inherits__: anndata_normalized.yaml + - name: "--layer_output" + type: string + default: "normalized" + description: The name of the layer in which to store the normalized data. + - name: "--obs_size_factors" + type: string + default: "size_factors" + description: In which .obs slot to store the size factors (if any). \ No newline at end of file diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml new file mode 100644 index 0000000000..d445e30599 --- /dev/null +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -0,0 +1,60 @@ + +functionality: + name: "hvg" + namespace: "datasets/processors" + description: "Compute HVG" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __inherits__: ../../api/anndata_normalized.yaml + - name: "--layer_input" + type: string + default: "normalized" + description: Which layer to use as input for the PCA. + - name: Outputs + arguments: + - name: "--output" + direction: output + __inherits__: ../../api/anndata_normalized.yaml + info: + slots: + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_ranking + description: A ranking of the features by hvg. + required: true + - name: "--var_hvg" + type: string + default: "hvg" + description: "In which .var slot to store whether a feature is considered to be hvg." + - name: "--var_hvg_ranking" + type: string + default: "hvg_ranking" + description: "In which .var slot to store whether a ranking of the features by variance." + - name: Arguments + arguments: + - name: "--num_features" + type: integer + default: 1000 + description: "The number of HVG to select" + resources: + - type: python_script + path: script.py + # test_resources: + # - type: python_script + # path: test_script.py + # - path: "../../../resources_test/common/pancreas" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - type: nextflow diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py new file mode 100644 index 0000000000..17d42a471b --- /dev/null +++ b/src/datasets/processors/hvg/script.py @@ -0,0 +1,36 @@ + +import scanpy as sc + +### VIASH START +par = { + 'input': 'work/ca/0751ff85df6f9478cb7bda5a705cad/zebrafish.sqrt_cpm.pca.output.h5ad', + 'layer_input': 'normalized', + 'output': 'dataset.h5ad', + 'var_hvg': 'hvg', + 'var_hvg_ranking': 'hvg_ranking', + 'num_features': 100 +} +### VIASH END + +print(">> Load data") +adata = sc.read(par['input']) + +print(">> Look for layer") +layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] + +print(">> Run PCA") +out = sc.pp.highly_variable_genes( + adata, + layer=par["layer_input"], + n_top_genes=par["num_features"], + flavor='cell_ranger', + inplace=False +) + +print(">> Storing output") +adata.var[par["var_hvg"]] = out['highly_variable'].values +adata.var[par["var_hvg_ranking"]] = out['dispersions'].values + +print(">> Writing data") +adata.write_h5ad(par['output']) + diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml new file mode 100644 index 0000000000..ad41445cc0 --- /dev/null +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -0,0 +1,70 @@ + +functionality: + name: "pca" + namespace: "datasets/processors" + description: "Compute PCA" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __inherits__: ../../api/anndata_normalized.yaml + - name: "--layer_input" + type: string + default: "normalized" + description: Which layer to use as input for the PCA. + - name: Outputs + arguments: + - name: "--output" + direction: output + __inherits__: ../../api/anndata_normalized.yaml + info: + slots: + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true + uns: + - type: double + name: pca_variance + description: The PCA variance objects. + required: true + - name: "--obsm_embedding" + type: string + default: "X_pca" + description: "In which .obsm slot to store the resulting embedding." + - name: "--varm_loadings" + type: string + default: "pca_loadings" + description: "In which .varm slot to store the resulting loadings matrix." + - name: "--uns_variance" + type: string + default: "pca_variance" + description: "In which .uns slot to store the resulting variance objects." + - name: Arguments + arguments: + - name: "--num_components" + type: integer + example: 25 + description: Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. + resources: + - type: python_script + path: script.py + # test_resources: + # - type: python_script + # path: test_script.py + # - path: "../../../resources_test/common/pancreas" +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - type: nextflow diff --git a/src/datasets/processors/pca/script.py b/src/datasets/processors/pca/script.py new file mode 100644 index 0000000000..ca0bd5ed10 --- /dev/null +++ b/src/datasets/processors/pca/script.py @@ -0,0 +1,39 @@ + +import scanpy as sc + +### VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'layer_input': 'log_cpm', + 'output': 'dataset.h5ad', + 'obsm_embedding': 'X_pca', + 'varm_loadings': 'pca_loadings', + 'uns_variance': 'pca_variance', + 'num_components': 25 +} +### VIASH END + +print(">> Load data") +adata = sc.read(par['input']) + +print(">> Look for layer") +layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] + +print(">> Run PCA") +X_pca, loadings, variance, variance_ratio = sc.tl.pca( + layer, + n_comps=par["num_components"], + return_info=True +) + +print(">> Storing output") +adata.obsm[par["obsm_embedding"]] = X_pca +adata.varm[par["varm_loadings"]] = loadings.T +adata.uns[par["uns_variance"]] = { + "variance": variance, + "variance_ratio": variance_ratio +} + +print(">> Writing data") +adata.write_h5ad(par['output']) + diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index b77a66def7..4c0506cfb6 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -7,6 +7,8 @@ include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/ma include { log_cpm } from "$targetDir/datasets/normalization/log_cpm/main.nf" include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" +include { pca } from "$targetDir/datasets/processors/pca/main.nf" +include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" @@ -48,12 +50,10 @@ workflow run_wf { [ newId, file ] } - // run scran normalisation - | log_scran_pooling + | pca - // run sqrt normalisation and publish - | getWorkflowArguments(key: "sqrt_cpm") - | sqrt_cpm.run( + | getWorkflowArguments(key: "output") + | hvg.run( auto: [ publish: true ] ) From 2ca9cc5edacec24e12e3d57db5d9c6a5bac67145 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:01:46 +0100 Subject: [PATCH 0358/1233] fix datasets yaml Former-commit-id: f4c88b02a5501d4fff9f100543e742dae0828806 --- src/datasets/workflows/process_openproblems_v1/datasets.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/datasets/workflows/process_openproblems_v1/datasets.yaml b/src/datasets/workflows/process_openproblems_v1/datasets.yaml index 85af28c58e..16d65b368d 100644 --- a/src/datasets/workflows/process_openproblems_v1/datasets.yaml +++ b/src/datasets/workflows/process_openproblems_v1/datasets.yaml @@ -2,7 +2,6 @@ param_list: - id: allen_brain_atlas obs_celltype: label layer_counts: counts - output: allen_brain_atlas.h5ad - id: cengen obs_celltype: cell_type From 7a0b2f961ea1a5c207de7350bda155ddbb300ddf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:15:04 +0100 Subject: [PATCH 0359/1233] update formats Former-commit-id: 729df43c38fad46fcfa8d1300984df9478e38b50 --- src/datasets/README.md | 219 ++++++++++++++++++ src/datasets/README.qmd | 199 ++++++++++++++++ ...{anndata_dataset.yaml => anndata_hvg.yaml} | 23 +- src/datasets/api/anndata_normalized.yaml | 2 +- src/datasets/api/anndata_pca.yaml | 54 +++++ src/datasets/api/comp_dataset_loader.yaml | 1 - src/datasets/api/comp_normalization.yaml | 1 - src/datasets/api/comp_processor_hvg.yaml | 24 +- src/datasets/api/comp_processor_pca.yaml | 28 ++- src/datasets/processors/hvg/config.vsh.yaml | 41 +--- src/datasets/processors/pca/config.vsh.yaml | 51 +--- 11 files changed, 529 insertions(+), 114 deletions(-) create mode 100644 src/datasets/README.md create mode 100644 src/datasets/README.qmd rename src/datasets/api/{anndata_dataset.yaml => anndata_hvg.yaml} (70%) create mode 100644 src/datasets/api/anndata_pca.yaml diff --git a/src/datasets/README.md b/src/datasets/README.md new file mode 100644 index 0000000000..2d67d8da15 --- /dev/null +++ b/src/datasets/README.md @@ -0,0 +1,219 @@ + +- Common datasets + - Pipeline + topology + - File format API + - Hvg + - Normalized + - Pca + - Raw + - Component API + - Dataset Loader + - Normalization + - Processor Hvg + - Processor Pca + +# Common datasets + +TODO: fill in + +## Pipeline topology + +``` mermaid +%%| column: screen-inset-shaded +flowchart LR + anndata_hvg(Hvg) + anndata_normalized(Normalized) + anndata_pca(Pca) + anndata_raw(Raw) + comp_dataset_loader[/Dataset Loader/] + comp_normalization[/Normalization/] + comp_processor_hvg[/Processor Hvg/] + comp_processor_pca[/Processor Pca/] + anndata_raw---comp_normalization + anndata_pca---comp_processor_hvg + anndata_normalized---comp_processor_pca + comp_dataset_loader-->anndata_raw + comp_normalization-->anndata_normalized + comp_processor_hvg-->anndata_hvg + comp_processor_pca-->anndata_pca +``` + +## File format API + +### `Hvg` + +A dataset + +Used in: + +- [processor hvg](#processor%20hvg): output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalised expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalisation method, if any. | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_ranking | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| varm | pca_loadings | double | The PCA loadings matrix. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | pca_variance | double | The PCA variance objects. | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_ranking' + uns: 'dataset_id', 'normalization_id', 'pca_variance' + obsm: 'X_pca' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + +### `Normalized` + +A dataset + +Used in: + +- [normalization](#normalization): output (as output) +- [processor pca](#processor%20pca): input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:--------|:--------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalised expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalisation method, if any. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + uns: 'dataset_id', 'normalization_id' + layers: 'counts', 'normalized' + +### `Pca` + +A dataset + +Used in: + +- [processor hvg](#processor%20hvg): input (as input) +- [processor pca](#processor%20pca): output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:--------|:--------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalised expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalisation method, if any. | +| obsm | X_pca | double | The resulting PCA embedding. | +| varm | pca_loadings | double | The PCA loadings matrix. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | pca_variance | double | The PCA variance objects. | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + uns: 'dataset_id', 'normalization_id', 'pca_variance' + obsm: 'X_pca' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + +### `Raw` + +A raw dataset + +Used in: + +- [dataset loader](#dataset%20loader): output (as output) +- [normalization](#normalization): input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue' + uns: 'dataset_id' + layers: 'counts' + +## Component API + +### `Dataset Loader` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------|:------------|:----------|:------------| +| `--output` | [Raw](#raw) | output | Raw dataset | + +### `Normalization` + +Arguments: + +| Name | File format | Direction | Description | +|:---------------------|:--------------------------|:----------|:-------------------| +| `--input` | [Raw](#raw) | input | Raw dataset | +| `--output` | [Normalized](#normalized) | output | Normalized dataset | +| `--layer_output` | [NA](#NA) | input | NA | +| `--obs_size_factors` | [NA](#NA) | input | NA | + +### `Processor Hvg` + +Arguments: + +| Name | File format | Direction | Description | +|:--------------------|:------------|:----------|:----------------| +| `--input` | [Pca](#pca) | input | Dataset+PCA | +| `--layer_input` | [NA](#NA) | input | NA | +| `--output` | [Hvg](#hvg) | output | Dataset+PCA+HVG | +| `--var_hvg` | [NA](#NA) | input | NA | +| `--var_hvg_ranking` | [NA](#NA) | input | NA | +| `--num_features` | [NA](#NA) | input | NA | + +### `Processor Pca` + +Arguments: + +| Name | File format | Direction | Description | +|:-------------------|:--------------------------|:----------|:-------------------| +| `--input` | [Normalized](#normalized) | input | Normalized dataset | +| `--layer_input` | [NA](#NA) | input | NA | +| `--output` | [Pca](#pca) | output | Dataset+PCA | +| `--obsm_embedding` | [NA](#NA) | input | NA | +| `--varm_loadings` | [NA](#NA) | input | NA | +| `--uns_variance` | [NA](#NA) | input | NA | +| `--num_components` | [NA](#NA) | input | NA | diff --git a/src/datasets/README.qmd b/src/datasets/README.qmd new file mode 100644 index 0000000000..fd53ccdbf4 --- /dev/null +++ b/src/datasets/README.qmd @@ -0,0 +1,199 @@ +--- +format: gfm +toc: true +--- + +```{r setup, include=FALSE} +library(tidyverse) +library(rlang) + +strip_margin <- function(text, symbol = "\\|") { + str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") +} + +dir <- "src/datasets" +dir <- "." +``` + +# Common datasets + +TODO: fill in + + +## Pipeline topology + +```{r data, include=FALSE} +comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) + +comp_file <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + df <- tibble( + comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + arg_name = str_replace_all(arg$name, "^-*", ""), + direction = arg$direction %||% "input" + ) + if ("__inherits__" %in% names(arg)) { + df$file_name <- basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + } + df + }) +}) + +comp_info <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_info <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + description = arg$description, + short_description = arg$info$short_description, + example = arg$example, + label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_slot <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + df$file_name <- basename(yaml_file) %>% gsub("\\.yaml", "", .) + df$multiple <- df$multiple %||% FALSE %|% FALSE + as_tibble(df) + }) +}) +``` + +```{r flow, echo=FALSE,warning=FALSE,error=FALSE} +nodes <- bind_rows( + file_info %>% + transmute(id = name, label = str_to_title(label), is_comp = FALSE), + comp_info %>% + transmute(id = name, label = str_to_title(label), is_comp = TRUE) +) %>% + mutate(str = paste0( + " ", + id, + ifelse(is_comp, "[/", "("), + label, + ifelse(is_comp, "/]", ")") + )) +edges <- bind_rows( + comp_file %>% + filter(direction == "input", !is.na(file_name)) %>% + transmute( + from = file_name, + to = comp_name, + arrow = "---" + ), + comp_file %>% + filter(direction == "output", !is.na(file_name)) %>% + transmute( + from = comp_name, + to = file_name, + arrow = "-->" + ) +) %>% + mutate(str = paste0(" ", from, arrow, to)) + +# note: use ```{mermaid} instead of ```mermaid when rendering to html +out_str <- strip_margin(glue::glue(" + §```mermaid + §%%| column: screen-inset-shaded + §flowchart LR + §{paste(nodes$str, collapse = '\n')} + §{paste(edges$str, collapse = '\n')} + §``` + §"), symbol = "§") +knitr::asis_output(out_str) +``` + +## File format API + +```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +for (file_name in file_info$name) { + arg_info <- file_info %>% filter(name == file_name) + sub_out <- file_slot %>% + filter(file_name == !!file_name) %>% + select(struct, name, type, description) + + used_in <- comp_file %>% + filter(file_name == !!file_name) %>% + left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% + mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% + pull(str) + + example <- sub_out %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) + + example_str <- c(" AnnData object", paste0(" ", example$str)) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(arg_info$label)}` + § + §{arg_info$description} + § + §Used in: + § + §{paste(used_in, collapse = '\n')} + § + §Slots: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + § + §Example: + § + §{paste(example_str, collapse = '\n')} + § + §"), symbol = "§") + cat(out_str) +} +``` + + + +## Component API + +```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +# todo: add description +# todo: add required info fields +for (comp_name in comp_info$name) { + comp <- comp_info %>% filter(name == comp_name) + sub_out <- comp_file %>% + filter(comp_name == !!comp_name) %>% + left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% + transmute( + Name = paste0("`--", arg_name, "`"), + `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), + Direction = direction, + Description = file_sdesc + ) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(comp$label)}` + § + §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} + § + §Arguments: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + §"), symbol = "§") + cat(out_str) +} +``` \ No newline at end of file diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_hvg.yaml similarity index 70% rename from src/datasets/api/anndata_dataset.yaml rename to src/datasets/api/anndata_hvg.yaml index e4b969803a..0752e13d85 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_hvg.yaml @@ -2,7 +2,7 @@ type: file description: "A dataset" example: "dataset.h5ad" info: - short_description: "Dataset" + short_description: "Dataset+PCA+HVG" slots: layers: - type: integer @@ -25,6 +25,10 @@ info: name: tissue description: Tissue information required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false var: - type: boolean name: hvg @@ -34,6 +38,16 @@ info: name: hvg_ranking description: A ranking of the features by hvg. required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true uns: - type: string name: dataset_id @@ -43,8 +57,7 @@ info: name: normalization_id description: "Which normalization was used" required: true - obsm: - type: double - name: X_pca - description: A PCA embedding of the normalized data. - required: true \ No newline at end of file + name: pca_variance + description: The PCA variance objects. + required: true diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/anndata_normalized.yaml index 96b29db247..b3abf0e9bd 100644 --- a/src/datasets/api/anndata_normalized.yaml +++ b/src/datasets/api/anndata_normalized.yaml @@ -37,4 +37,4 @@ info: - type: string name: normalization_id description: "Which normalization was used" - required: true \ No newline at end of file + required: true diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/anndata_pca.yaml new file mode 100644 index 0000000000..334183913f --- /dev/null +++ b/src/datasets/api/anndata_pca.yaml @@ -0,0 +1,54 @@ +type: file +description: "A dataset" +example: "dataset.h5ad" +info: + short_description: "Dataset+PCA" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalised expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: double + name: pca_variance + description: The PCA variance objects. + required: true diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 4b15d566f5..1840cab99d 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -3,4 +3,3 @@ functionality: - name: "--output" direction: output __inherits__: anndata_raw.yaml - diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index b720c9bf83..eebb0fb7f5 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -53,4 +53,3 @@ functionality: print("All checks succeeded!") - path: ../../../../resources_test/common/pancreas - diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index fa490e7007..9d464f673b 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,15 +1,23 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_raw.yaml + __inherits__: api/anndata_pca.yaml + - name: "--layer_input" + type: string + default: "normalized" + description: Which layer to use as input for the PCA. - name: "--output" direction: output - __inherits__: anndata_normalized.yaml - - name: "--layer_output" + __inherits__: api/anndata_hvg.yaml + - name: "--var_hvg" type: string - default: "normalized" - description: The name of the layer in which to store the normalized data. - - name: "--obs_size_factors" + default: "hvg" + description: "In which .var slot to store whether a feature is considered to be hvg." + - name: "--var_hvg_ranking" type: string - default: "size_factors" - description: In which .obs slot to store the size factors (if any). \ No newline at end of file + default: "hvg_ranking" + description: "In which .var slot to store whether a ranking of the features by variance." + - name: "--num_features" + type: integer + default: 1000 + description: "The number of HVG to select" diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index fa490e7007..6276ebd305 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -1,15 +1,27 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_raw.yaml - - name: "--output" - direction: output __inherits__: anndata_normalized.yaml - - name: "--layer_output" + - name: "--layer_input" type: string default: "normalized" - description: The name of the layer in which to store the normalized data. - - name: "--obs_size_factors" + description: Which layer to use as input for the PCA. + - name: "--output" + direction: output + __inherits__: anndata_pca.yaml + - name: "--obsm_embedding" + type: string + default: "X_pca" + description: "In which .obsm slot to store the resulting embedding." + - name: "--varm_loadings" + type: string + default: "pca_loadings" + description: "In which .varm slot to store the resulting loadings matrix." + - name: "--uns_variance" type: string - default: "size_factors" - description: In which .obs slot to store the size factors (if any). \ No newline at end of file + default: "pca_variance" + description: "In which .uns slot to store the resulting variance objects." + - name: "--num_components" + type: integer + example: 25 + description: Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index d445e30599..25470f8586 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -1,47 +1,8 @@ - +__inherits__: ../../api/comp_processor_hvg.yaml functionality: name: "hvg" namespace: "datasets/processors" description: "Compute HVG" - argument_groups: - - name: Inputs - arguments: - - name: "--input" - __inherits__: ../../api/anndata_normalized.yaml - - name: "--layer_input" - type: string - default: "normalized" - description: Which layer to use as input for the PCA. - - name: Outputs - arguments: - - name: "--output" - direction: output - __inherits__: ../../api/anndata_normalized.yaml - info: - slots: - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_ranking - description: A ranking of the features by hvg. - required: true - - name: "--var_hvg" - type: string - default: "hvg" - description: "In which .var slot to store whether a feature is considered to be hvg." - - name: "--var_hvg_ranking" - type: string - default: "hvg_ranking" - description: "In which .var slot to store whether a ranking of the features by variance." - - name: Arguments - arguments: - - name: "--num_features" - type: integer - default: 1000 - description: "The number of HVG to select" resources: - type: python_script path: script.py diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index ad41445cc0..1e1e569091 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -1,57 +1,8 @@ - +__inherits__: ../../api/comp_processor_pca.yaml functionality: name: "pca" namespace: "datasets/processors" description: "Compute PCA" - argument_groups: - - name: Inputs - arguments: - - name: "--input" - __inherits__: ../../api/anndata_normalized.yaml - - name: "--layer_input" - type: string - default: "normalized" - description: Which layer to use as input for the PCA. - - name: Outputs - arguments: - - name: "--output" - direction: output - __inherits__: ../../api/anndata_normalized.yaml - info: - slots: - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true - uns: - - type: double - name: pca_variance - description: The PCA variance objects. - required: true - - name: "--obsm_embedding" - type: string - default: "X_pca" - description: "In which .obsm slot to store the resulting embedding." - - name: "--varm_loadings" - type: string - default: "pca_loadings" - description: "In which .varm slot to store the resulting loadings matrix." - - name: "--uns_variance" - type: string - default: "pca_variance" - description: "In which .uns slot to store the resulting variance objects." - - name: Arguments - arguments: - - name: "--num_components" - type: integer - example: 25 - description: Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. resources: - type: python_script path: script.py From 54becc1263c483bf5abe258f431b60e6db1d54b9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:23:29 +0100 Subject: [PATCH 0360/1233] update api docs Former-commit-id: 1ccb916ec9486643e84c08fa074a75807202d5cb --- src/datasets/README.md | 62 ++++++++++++------------ src/datasets/README.qmd | 16 +++--- src/datasets/api/anndata_hvg.yaml | 4 +- src/datasets/api/anndata_normalized.yaml | 4 +- src/datasets/api/anndata_pca.yaml | 4 +- src/datasets/api/anndata_raw.yaml | 4 +- 6 files changed, 48 insertions(+), 46 deletions(-) diff --git a/src/datasets/README.md b/src/datasets/README.md index 2d67d8da15..d56f52547d 100644 --- a/src/datasets/README.md +++ b/src/datasets/README.md @@ -19,8 +19,6 @@ # Common datasets -TODO: fill in - ## Pipeline topology ``` mermaid @@ -47,7 +45,7 @@ flowchart LR ### `Hvg` -A dataset +A normalised data with a PCA embedding and HVG selection Used in: @@ -83,7 +81,7 @@ Example: ### `Normalized` -A dataset +A normalized dataset Used in: @@ -112,7 +110,7 @@ Example: ### `Pca` -A dataset +A normalised data with a PCA embedding Used in: @@ -146,7 +144,7 @@ Example: ### `Raw` -A raw dataset +An unprocessed dataset as output by a dataset loader. Used in: @@ -176,44 +174,44 @@ Example: Arguments: -| Name | File format | Direction | Description | -|:-----------|:------------|:----------|:------------| -| `--output` | [Raw](#raw) | output | Raw dataset | +| Name | Type | Direction | Description | +|:-----------|:------------|:----------|:------------------------------------------------------| +| `--output` | [Raw](#raw) | output | An unprocessed dataset as output by a dataset loader. | ### `Normalization` Arguments: -| Name | File format | Direction | Description | -|:---------------------|:--------------------------|:----------|:-------------------| -| `--input` | [Raw](#raw) | input | Raw dataset | -| `--output` | [Normalized](#normalized) | output | Normalized dataset | -| `--layer_output` | [NA](#NA) | input | NA | -| `--obs_size_factors` | [NA](#NA) | input | NA | +| Name | Type | Direction | Description | +|:---------------------|:--------------------------|:----------|:-------------------------------------------------------------| +| `--input` | [Raw](#raw) | input | An unprocessed dataset as output by a dataset loader. | +| `--output` | [Normalized](#normalized) | output | A normalized dataset | +| `--layer_output` | `string` | input | The name of the layer in which to store the normalized data. | +| `--obs_size_factors` | `string` | input | In which .obs slot to store the size factors (if any). | ### `Processor Hvg` Arguments: -| Name | File format | Direction | Description | -|:--------------------|:------------|:----------|:----------------| -| `--input` | [Pca](#pca) | input | Dataset+PCA | -| `--layer_input` | [NA](#NA) | input | NA | -| `--output` | [Hvg](#hvg) | output | Dataset+PCA+HVG | -| `--var_hvg` | [NA](#NA) | input | NA | -| `--var_hvg_ranking` | [NA](#NA) | input | NA | -| `--num_features` | [NA](#NA) | input | NA | +| Name | Type | Direction | Description | +|:--------------------|:------------|:----------|:---------------------------------------------------------------------------| +| `--input` | [Pca](#pca) | input | A normalised data with a PCA embedding | +| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | +| `--output` | [Hvg](#hvg) | output | A normalised data with a PCA embedding and HVG selection | +| `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | +| `--var_hvg_ranking` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | +| `--num_features` | `integer` | input | The number of HVG to select | ### `Processor Pca` Arguments: -| Name | File format | Direction | Description | -|:-------------------|:--------------------------|:----------|:-------------------| -| `--input` | [Normalized](#normalized) | input | Normalized dataset | -| `--layer_input` | [NA](#NA) | input | NA | -| `--output` | [Pca](#pca) | output | Dataset+PCA | -| `--obsm_embedding` | [NA](#NA) | input | NA | -| `--varm_loadings` | [NA](#NA) | input | NA | -| `--uns_variance` | [NA](#NA) | input | NA | -| `--num_components` | [NA](#NA) | input | NA | +| Name | Type | Direction | Description | +|:-------------------|:--------------------------|:----------|:---------------------------------------------------------------------------------------------------------------------| +| `--input` | [Normalized](#normalized) | input | A normalized dataset | +| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | +| `--output` | [Pca](#pca) | output | A normalised data with a PCA embedding | +| `--obsm_embedding` | `string` | input | In which .obsm slot to store the resulting embedding. | +| `--varm_loadings` | `string` | input | In which .varm slot to store the resulting loadings matrix. | +| `--uns_variance` | `string` | input | In which .uns slot to store the resulting variance objects. | +| `--num_components` | `integer` | input | Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. | diff --git a/src/datasets/README.qmd b/src/datasets/README.qmd index fd53ccdbf4..2cfe0d2522 100644 --- a/src/datasets/README.qmd +++ b/src/datasets/README.qmd @@ -17,7 +17,6 @@ dir <- "." # Common datasets -TODO: fill in ## Pipeline topology @@ -32,8 +31,10 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { map_df(conf$functionality$arguments, function(arg) { df <- tibble( comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + type = arg$type, arg_name = str_replace_all(arg$name, "^-*", ""), - direction = arg$direction %||% "input" + direction = arg$direction %||% "input", + description = arg$description ) if ("__inherits__" %in% names(arg)) { df$file_name <- basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) @@ -57,7 +58,6 @@ file_info <- map_df(file_yamls, function(yaml_file) { tibble( name = basename(yaml_file) %>% gsub("\\.yaml", "", .), description = arg$description, - short_description = arg$info$short_description, example = arg$example, label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) ) @@ -177,12 +177,16 @@ for (comp_name in comp_info$name) { comp <- comp_info %>% filter(name == comp_name) sub_out <- comp_file %>% filter(comp_name == !!comp_name) %>% - left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% + left_join(file_info %>% select(file_name = name, file_desc = description, file_label = label), by = "file_name") %>% transmute( Name = paste0("`--", arg_name, "`"), - `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), + Type = ifelse( + is.na(file_label), + paste0("`", type, "`"), + paste0("[", str_to_title(file_label), "](#", file_label, ")") + ), Direction = direction, - Description = file_sdesc + Description = description %|% file_desc ) out_str <- strip_margin(glue::glue(" diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_hvg.yaml index 0752e13d85..bd461fd330 100644 --- a/src/datasets/api/anndata_hvg.yaml +++ b/src/datasets/api/anndata_hvg.yaml @@ -1,8 +1,8 @@ type: file -description: "A dataset" +description: "A normalised data with a PCA embedding and HVG selection" example: "dataset.h5ad" info: - short_description: "Dataset+PCA+HVG" + label: "Dataset+PCA+HVG" slots: layers: - type: integer diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/anndata_normalized.yaml index b3abf0e9bd..58aaa077ad 100644 --- a/src/datasets/api/anndata_normalized.yaml +++ b/src/datasets/api/anndata_normalized.yaml @@ -1,8 +1,8 @@ type: file -description: "A dataset" +description: "A normalized dataset" example: "dataset.h5ad" info: - short_description: "Normalized dataset" + label: "Normalized dataset" slots: layers: - type: integer diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/anndata_pca.yaml index 334183913f..fd3b19d250 100644 --- a/src/datasets/api/anndata_pca.yaml +++ b/src/datasets/api/anndata_pca.yaml @@ -1,8 +1,8 @@ type: file -description: "A dataset" +description: "A normalised data with a PCA embedding" example: "dataset.h5ad" info: - short_description: "Dataset+PCA" + label: "Dataset+PCA" slots: layers: - type: integer diff --git a/src/datasets/api/anndata_raw.yaml b/src/datasets/api/anndata_raw.yaml index 4a901515b3..2e46e64cff 100644 --- a/src/datasets/api/anndata_raw.yaml +++ b/src/datasets/api/anndata_raw.yaml @@ -1,8 +1,8 @@ type: file -description: "A raw dataset" +description: "An unprocessed dataset as output by a dataset loader." example: "raw_dataset.h5ad" info: - short_description: "Raw dataset" + label: "Raw dataset" slots: layers: - type: integer From 4ada684d86c53fcf17a9f0d422d6292bd2fa4407 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:26:15 +0100 Subject: [PATCH 0361/1233] update readme Former-commit-id: 82b1cdb36478dd6331007ba99fbc0cec562a75c6 --- src/datasets/README.md | 78 +++++++++++++++++++++-------------------- src/datasets/README.qmd | 2 +- 2 files changed, 41 insertions(+), 39 deletions(-) diff --git a/src/datasets/README.md b/src/datasets/README.md index d56f52547d..07714db16e 100644 --- a/src/datasets/README.md +++ b/src/datasets/README.md @@ -3,10 +3,12 @@ - Pipeline topology - File format API - - Hvg - - Normalized - - Pca - - Raw + - Dataset+Pca+Hvg + - Normalized Dataset + - Dataset+Pca + - Raw Dataset - Component API - Dataset Loader @@ -24,10 +26,10 @@ ``` mermaid %%| column: screen-inset-shaded flowchart LR - anndata_hvg(Hvg) - anndata_normalized(Normalized) - anndata_pca(Pca) - anndata_raw(Raw) + anndata_hvg(Dataset+Pca+Hvg) + anndata_normalized(Normalized Dataset) + anndata_pca(Dataset+Pca) + anndata_raw(Raw Dataset) comp_dataset_loader[/Dataset Loader/] comp_normalization[/Normalization/] comp_processor_hvg[/Processor Hvg/] @@ -43,7 +45,7 @@ flowchart LR ## File format API -### `Hvg` +### `Dataset+Pca+Hvg` A normalised data with a PCA embedding and HVG selection @@ -79,7 +81,7 @@ Example: varm: 'pca_loadings' layers: 'counts', 'normalized' -### `Normalized` +### `Normalized Dataset` A normalized dataset @@ -108,7 +110,7 @@ Example: uns: 'dataset_id', 'normalization_id' layers: 'counts', 'normalized' -### `Pca` +### `Dataset+Pca` A normalised data with a PCA embedding @@ -142,7 +144,7 @@ Example: varm: 'pca_loadings' layers: 'counts', 'normalized' -### `Raw` +### `Raw Dataset` An unprocessed dataset as output by a dataset loader. @@ -174,44 +176,44 @@ Example: Arguments: -| Name | Type | Direction | Description | -|:-----------|:------------|:----------|:------------------------------------------------------| -| `--output` | [Raw](#raw) | output | An unprocessed dataset as output by a dataset loader. | +| Name | Type | Direction | Description | +|:-----------|:------------------------------|:----------|:------------------------------------------------------| +| `--output` | [Raw Dataset](#Raw%20dataset) | output | An unprocessed dataset as output by a dataset loader. | ### `Normalization` Arguments: -| Name | Type | Direction | Description | -|:---------------------|:--------------------------|:----------|:-------------------------------------------------------------| -| `--input` | [Raw](#raw) | input | An unprocessed dataset as output by a dataset loader. | -| `--output` | [Normalized](#normalized) | output | A normalized dataset | -| `--layer_output` | `string` | input | The name of the layer in which to store the normalized data. | -| `--obs_size_factors` | `string` | input | In which .obs slot to store the size factors (if any). | +| Name | Type | Direction | Description | +|:---------------------|:--------------------------------------------|:----------|:-------------------------------------------------------------| +| `--input` | [Raw Dataset](#Raw%20dataset) | input | An unprocessed dataset as output by a dataset loader. | +| `--output` | [Normalized Dataset](#Normalized%20dataset) | output | A normalized dataset | +| `--layer_output` | `string` | input | The name of the layer in which to store the normalized data. | +| `--obs_size_factors` | `string` | input | In which .obs slot to store the size factors (if any). | ### `Processor Hvg` Arguments: -| Name | Type | Direction | Description | -|:--------------------|:------------|:----------|:---------------------------------------------------------------------------| -| `--input` | [Pca](#pca) | input | A normalised data with a PCA embedding | -| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | -| `--output` | [Hvg](#hvg) | output | A normalised data with a PCA embedding and HVG selection | -| `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | -| `--var_hvg_ranking` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | -| `--num_features` | `integer` | input | The number of HVG to select | +| Name | Type | Direction | Description | +|:--------------------|:------------------------------------|:----------|:---------------------------------------------------------------------------| +| `--input` | [Dataset+Pca](#Dataset+PCA) | input | A normalised data with a PCA embedding | +| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | +| `--output` | [Dataset+Pca+Hvg](#Dataset+PCA+HVG) | output | A normalised data with a PCA embedding and HVG selection | +| `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | +| `--var_hvg_ranking` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | +| `--num_features` | `integer` | input | The number of HVG to select | ### `Processor Pca` Arguments: -| Name | Type | Direction | Description | -|:-------------------|:--------------------------|:----------|:---------------------------------------------------------------------------------------------------------------------| -| `--input` | [Normalized](#normalized) | input | A normalized dataset | -| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | -| `--output` | [Pca](#pca) | output | A normalised data with a PCA embedding | -| `--obsm_embedding` | `string` | input | In which .obsm slot to store the resulting embedding. | -| `--varm_loadings` | `string` | input | In which .varm slot to store the resulting loadings matrix. | -| `--uns_variance` | `string` | input | In which .uns slot to store the resulting variance objects. | -| `--num_components` | `integer` | input | Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. | +| Name | Type | Direction | Description | +|:-------------------|:--------------------------------------------|:----------|:---------------------------------------------------------------------------------------------------------------------| +| `--input` | [Normalized Dataset](#Normalized%20dataset) | input | A normalized dataset | +| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | +| `--output` | [Dataset+Pca](#Dataset+PCA) | output | A normalised data with a PCA embedding | +| `--obsm_embedding` | `string` | input | In which .obsm slot to store the resulting embedding. | +| `--varm_loadings` | `string` | input | In which .varm slot to store the resulting loadings matrix. | +| `--uns_variance` | `string` | input | In which .uns slot to store the resulting variance objects. | +| `--num_components` | `integer` | input | Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. | diff --git a/src/datasets/README.qmd b/src/datasets/README.qmd index 2cfe0d2522..1dd60faf7c 100644 --- a/src/datasets/README.qmd +++ b/src/datasets/README.qmd @@ -59,7 +59,7 @@ file_info <- map_df(file_yamls, function(yaml_file) { name = basename(yaml_file) %>% gsub("\\.yaml", "", .), description = arg$description, example = arg$example, - label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + label = arg$info$label %||% (name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .)) ) }) From 27721129d26db17458da967edb694f52c69be43f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 15:58:55 +0100 Subject: [PATCH 0362/1233] rename hvg_ranking to hvg_score Former-commit-id: 4b75b4ef358b98d397d28647c4a17aec3db2445f --- src/datasets/README.md | 6 +++--- src/datasets/api/anndata_hvg.yaml | 2 +- src/datasets/api/comp_processor_hvg.yaml | 4 ++-- src/datasets/processors/hvg/script.py | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/datasets/README.md b/src/datasets/README.md index 07714db16e..02e6813996 100644 --- a/src/datasets/README.md +++ b/src/datasets/README.md @@ -64,7 +64,7 @@ Slots: | obs | tissue | string | Tissue information | | obs | size_factors | double | The size factors created by the normalisation method, if any. | | var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_ranking | integer | A ranking of the features by hvg. | +| var | hvg_score | integer | A ranking of the features by hvg. | | obsm | X_pca | double | The resulting PCA embedding. | | varm | pca_loadings | double | The PCA loadings matrix. | | uns | dataset_id | string | A unique identifier for the dataset | @@ -75,7 +75,7 @@ Example: AnnData object obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_ranking' + var: 'hvg', 'hvg_score' uns: 'dataset_id', 'normalization_id', 'pca_variance' obsm: 'X_pca' varm: 'pca_loadings' @@ -201,7 +201,7 @@ Arguments: | `--layer_input` | `string` | input | Which layer to use as input for the PCA. | | `--output` | [Dataset+Pca+Hvg](#Dataset+PCA+HVG) | output | A normalised data with a PCA embedding and HVG selection | | `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | -| `--var_hvg_ranking` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | +| `--var_hvg_score` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | | `--num_features` | `integer` | input | The number of HVG to select | ### `Processor Pca` diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_hvg.yaml index bd461fd330..9a65630b80 100644 --- a/src/datasets/api/anndata_hvg.yaml +++ b/src/datasets/api/anndata_hvg.yaml @@ -35,7 +35,7 @@ info: description: Whether or not the feature is considered to be a 'highly variable gene' required: true - type: integer - name: hvg_ranking + name: hvg_score description: A ranking of the features by hvg. required: true obsm: diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index 9d464f673b..b82df3e09e 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -13,9 +13,9 @@ functionality: type: string default: "hvg" description: "In which .var slot to store whether a feature is considered to be hvg." - - name: "--var_hvg_ranking" + - name: "--var_hvg_score" type: string - default: "hvg_ranking" + default: "hvg_score" description: "In which .var slot to store whether a ranking of the features by variance." - name: "--num_features" type: integer diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index 17d42a471b..0f97161529 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -7,7 +7,7 @@ 'layer_input': 'normalized', 'output': 'dataset.h5ad', 'var_hvg': 'hvg', - 'var_hvg_ranking': 'hvg_ranking', + 'var_hvg_score': 'hvg_score', 'num_features': 100 } ### VIASH END @@ -29,7 +29,7 @@ print(">> Storing output") adata.var[par["var_hvg"]] = out['highly_variable'].values -adata.var[par["var_hvg_ranking"]] = out['dispersions'].values +adata.var[par["var_hvg_score"]] = out['dispersions'].values print(">> Writing data") adata.write_h5ad(par['output']) From d5d0eaab4be2cc0bac5c7cc53a8346840eb29434 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 16:05:53 +0100 Subject: [PATCH 0363/1233] use tower for logging Former-commit-id: 040cdcbd66eea3aff28ffaf92f3555d1565691fe --- src/datasets/workflows/process_openproblems_v1/run_nextflow.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh index 02723f7ca1..26001f4cba 100755 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -14,4 +14,5 @@ bin/nextflow \ -profile docker \ -resume \ -params-file src/datasets/workflows/process_openproblems_v1/datasets.yaml \ - --publish_dir resources/datasets/openproblems_v1 \ No newline at end of file + --publish_dir resources/datasets/openproblems_v1 \ + -with-tower From 44e953105d5ecea5a4f7dfa7d5d86776c8a90462 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 16:18:37 +0100 Subject: [PATCH 0364/1233] Fix paths to s3 bucket Former-commit-id: c75035378baaf9b73590d19eab2e50e0667ddbbb --- .github/workflows/main-build.yml | 2 +- .github/workflows/viash-test.yml | 2 +- src/common/resources_test_scripts/pancreas.sh | 42 ------------------- src/common/sync_test_resources/run_test.sh | 2 +- src/common/sync_test_resources/script.sh | 2 +- 5 files changed, 4 insertions(+), 46 deletions(-) delete mode 100755 src/common/resources_test_scripts/pancreas.sh diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 4ac886e4ef..fd38d0f8f4 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -8,7 +8,7 @@ jobs: # phase 1 list_components: env: - s3_bucket: s3://openproblems-data/ + s3_bucket: s3://openproblems-data/resources_test runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, 'ci skip')" diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index bb86edc52a..a7655f54ae 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -30,7 +30,7 @@ jobs: list_components: needs: run_ci_check_job env: - s3_bucket: s3://openproblems-data/ + s3_bucket: s3://openproblems-data/resources_test runs-on: ubuntu-latest if: "(!contains(github.event.head_commit.message, 'ci skip')) && needs.run_ci_check_job.outputs.run_ci == 'true'" outputs: diff --git a/src/common/resources_test_scripts/pancreas.sh b/src/common/resources_test_scripts/pancreas.sh deleted file mode 100755 index 04a134154b..0000000000 --- a/src/common/resources_test_scripts/pancreas.sh +++ /dev/null @@ -1,42 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/common/pancreas - -mkdir -p $DATASET_DIR - -# download dataset -bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ - --url "https://ndownloader.figshare.com/files/24539828" \ - --obs_celltype "celltype" \ - --obs_batch "tech" \ - --name "pancreas" \ - --layer_counts "counts" \ - --layer_counts_output "counts" \ - --output $DATASET_DIR/temp_dataset_full.h5ad - -# subsample -bin/viash run src/common/subsample/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_full.h5ad \ - --keep_celltype_categories "acinar:beta" \ - --keep_batch_categories "celseq:inDrop4:smarter" \ - --output $DATASET_DIR/temp_dataset_sampled.h5ad \ - --seed 123 - -# run log cpm normalisation -bin/viash run src/common/normalization/log_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_sampled.h5ad \ - --output $DATASET_DIR/temp_dataset_cpm.h5ad - -# run scran pooling normalisation -bin/viash run src/common/normalization/log_scran_pooling/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_cpm.h5ad \ - --output $DATASET_DIR/dataset.h5ad diff --git a/src/common/sync_test_resources/run_test.sh b/src/common/sync_test_resources/run_test.sh index 1160a2c34e..40b1b5e58f 100755 --- a/src/common/sync_test_resources/run_test.sh +++ b/src/common/sync_test_resources/run_test.sh @@ -5,7 +5,7 @@ echo ">> Run aws s3 sync" ./$meta_functionality_name \ - --input s3://openproblems-data/label_projection/pancreas \ + --input s3://openproblems-data/resources_test/label_projection/pancreas \ --output foo \ --quiet diff --git a/src/common/sync_test_resources/script.sh b/src/common/sync_test_resources/script.sh index fe86a59c33..c97b9fcdfd 100644 --- a/src/common/sync_test_resources/script.sh +++ b/src/common/sync_test_resources/script.sh @@ -1,7 +1,7 @@ #!/bin/bash ## VIASH START -par_input='s3://openproblems-data' +par_input='s3://openproblems-data/resources_test' par_output='resources_test' ## VIASH END From ba77135775df6477f9f1a22f56bc955c1af411b8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 18:48:48 +0100 Subject: [PATCH 0365/1233] add dependabot Former-commit-id: 6eec81323079cee8d65a96429e38fa108ddcb4ef --- .github/dependabot.yml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000000..909637159a --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,6 @@ +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "daily" \ No newline at end of file From 71bf55ef1971f51cc11717ef8ee5cb0478343d75 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 17 Nov 2022 17:49:21 +0000 Subject: [PATCH 0366/1233] Bump docker/login-action from 1 to 2 Bumps [docker/login-action](https://github.com/docker/login-action) from 1 to 2. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/v1...v2) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Former-commit-id: cac88361e661a32811c16868de78053852ea2382 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/main-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 14afa846df..ab1a3a1aab 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -102,7 +102,7 @@ jobs: bin/viash_build -m release -t integration_build -s "$SRC_DIR" - name: Login to container registry - uses: docker/login-action@v1 + uses: docker/login-action@v2 with: registry: ghcr.io username: ${{ github.actor }} diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index fd38d0f8f4..abbfa70059 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -101,7 +101,7 @@ jobs: bin/viash_build -m release -t main_build -s "$SRC_DIR" - name: Login to container registry - uses: docker/login-action@v1 + uses: docker/login-action@v2 with: registry: ghcr.io username: ${{ github.actor }} From 261a047fb049719909c732a363d4bc8a3cdade8f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 17 Nov 2022 17:49:22 +0000 Subject: [PATCH 0367/1233] Bump actions/checkout from 2 to 3 Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v2...v3) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Former-commit-id: 15940b939a8bc3a442dec8f2905b759179be4f3d --- .github/workflows/integration-test.yml | 6 +++--- .github/workflows/main-build.yml | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 14afa846df..f22386153b 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -14,7 +14,7 @@ jobs: # if: "contains(github.event.head_commit.message, '#integration')" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | @@ -89,7 +89,7 @@ jobs: component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | @@ -125,7 +125,7 @@ jobs: component: ${{ fromJson(needs.list_components.outputs.workflow_matrix) }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index fd38d0f8f4..440b30176d 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -13,7 +13,7 @@ jobs: if: "!contains(github.event.head_commit.message, 'ci skip')" steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | @@ -88,7 +88,7 @@ jobs: component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Fetch viash run: | From 19dc3f0602f2431ef171098cd16d1348d6c0a5db Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 22:08:45 +0100 Subject: [PATCH 0368/1233] update specs Former-commit-id: cc6836cfdfc75e88cfaab36cdc0a2132b90b2ab9 --- src/label_projection/README.md | 39 ++++++++++--- .../api/comp_control_method.yaml | 58 +++++++++++++++++++ src/label_projection/api/comp_method.yaml | 5 -- .../majority_vote/config.vsh.yaml | 8 +-- .../random_labels/config.vsh.yaml | 8 +-- .../true_labels/config.vsh.yaml | 10 +--- .../methods/knn/config.vsh.yaml | 5 +- .../logistic_regression/config.vsh.yaml | 5 +- .../methods/mlp/config.vsh.yaml | 7 +-- .../methods/scanvi/config.vsh.yaml | 57 ++++++++++++++++++ 10 files changed, 156 insertions(+), 46 deletions(-) create mode 100644 src/label_projection/api/comp_control_method.yaml create mode 100644 src/label_projection/methods/scanvi/config.vsh.yaml diff --git a/src/label_projection/README.md b/src/label_projection/README.md index ba08e1f7e7..1a1db6e70e 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -15,6 +15,8 @@ - Test - Train - Component API + - Control Method - Method - Metric - anndata_prediction comp_method-->anndata_prediction comp_metric-->anndata_score comp_split_dataset-->anndata_train @@ -136,6 +142,7 @@ The prediction file Used in: +- [control method](#control%20method): output (as output) - [method](#method): output (as output) - [metric](#metric): input_prediction (as input) @@ -181,6 +188,7 @@ The solution for the test data Used in: +- [control method](#control%20method): input_solution (as input) - [metric](#metric): input_solution (as input) - [split dataset](#split%20dataset): output_solution (as output) @@ -209,6 +217,7 @@ The test data (without labels) Used in: +- [control method](#control%20method): input_test (as input) - [method](#method): input_test (as input) - [split dataset](#split%20dataset): output_test (as output) @@ -236,6 +245,7 @@ The training data Used in: +- [control method](#control%20method): input_train (as input) - [method](#method): input_train (as input) - [split dataset](#split%20dataset): output_train (as output) @@ -260,6 +270,17 @@ Example: ## Component API +### `Control Method` + +Arguments: + +| Name | File format | Direction | Description | +|:-------------------|:--------------------------|:----------|:--------------| +| `--input_train` | [Train](#train) | input | Training data | +| `--input_test` | [Test](#test) | input | Test data | +| `--input_solution` | [Solution](#solution) | input | Solution | +| `--output` | [Prediction](#prediction) | output | Prediction | + ### `Method` Arguments: diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml new file mode 100644 index 0000000000..1daacf3709 --- /dev/null +++ b/src/label_projection/api/comp_control_method.yaml @@ -0,0 +1,58 @@ +functionality: + arguments: + - name: "--input_train" + __inherits__: anndata_train.yaml + - name: "--input_test" + __inherits__: anndata_test.yaml + - name: "--input_solution" + __inherits__: anndata_solution.yaml + - name: "--output" + __inherits__: anndata_prediction.yaml + direction: output + test_resources: + - path: ../../../../resources_test/label_projection/pancreas + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" + input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--input_test", input_test_path, + "--output", output_path + ] + + # todo: if we could access the viash config, we could check whether + # .functionality.info.type == "positive_control" + if meta['functionality_name'] == 'true_labels': + cmd = cmd + ["--input_solution", input_solution_path] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + print("input_test:", input_test) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "label_pred" in output.obs + assert meta['functionality_name'] == output.uns["method_id"] + + print("Checking whether data from input was copied properly to output") + assert input_test.n_obs == output.n_obs + assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 682e7660f1..d225df01a2 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -7,11 +7,6 @@ functionality: - name: "--output" __inherits__: anndata_prediction.yaml direction: output - # TODO: currently needs to be manually specified since the default value needs to be overrideable - # - name: "--layer_input" - # type: string - # default: "log_cpm" - # description: Which layer to use as input. test_resources: - path: ../../../../resources_test/label_projection/pancreas - type: python_script diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 7e1cf0167b..62aa4af7f8 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__inherits__: ../../api/comp_control_method.yaml functionality: name: "majority_vote" namespace: "label_projection/control_methods" @@ -8,11 +8,7 @@ functionality: label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. + preferred_normalization: counts resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index f17c11f911..f0c23ebf2f 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__inherits__: ../../api/comp_control_method.yaml functionality: name: "random_labels" namespace: "label_projection/control_methods" @@ -8,11 +8,7 @@ functionality: label: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. + preferred_normalization: counts resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index dd338c006c..070eb34ce6 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__inherits__: ../../api/comp_control_method.yaml functionality: name: "true_labels" namespace: "label_projection/control_methods" @@ -8,13 +8,7 @@ functionality: label: True labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - arguments: - - name: "--input_solution" - __inherits__: ../../api/anndata_solution.yaml - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. + preferred_normalization: counts resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index eeaddf9b40..c28faf751c 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -13,11 +13,8 @@ functionality: code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d + preferred_normalization: log_cpm arguments: - - name: "--layer_input" - type: string - default: "log_cpm" - description: Which layer to use as input. resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 3fa62d1781..eb35d7edb2 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -12,11 +12,8 @@ functionality: code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d + preferred_normalization: log_cpm arguments: - - name: "--layer_input" - type: string - default: "log_cpm" - description: Which layer to use as input. - name: "--max_iter" type: "integer" default: 1000 diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index ff100fcaed..f7f39da1fd 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -11,11 +11,10 @@ functionality: # paper_year: 1990 paper_doi: "10.1016/0004-3702(89)90049-0" code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" + v1_url: openproblems/tasks/label_projection/methods/mlp.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + preferred_normalization: log_cpm arguments: - - name: "--layer_input" - type: string - default: "log_cpm" - description: Which layer to use as input. - name: "--hidden_layer_sizes" type: "integer" multiple: true diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml new file mode 100644 index 0000000000..6cca91bf16 --- /dev/null +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -0,0 +1,57 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "scanvi" + status: disabled + namespace: "label_projection/methods" + description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." + info: + type: method + label: Scanvi + paper_doi: "10.1101/2020.07.16.205997" + code_url: "https://github.com/YosefLab/scvi-tools" + arguments: + - name: "--n_hidden" + type: "integer" + required: true + default: "10" + - name: "--n_layers" + type: "integer" + required: true + default: "1" + - name: "--n_latent" + type: "integer" + required: true + default: "10" + - name: "--n_top_genes" + type: "integer" + required: true + default: "2000" + - name: "--span" + type: "double" + required: false + - name: "--max_epochs" + type: "integer" + required: false + - name: "--limit_brain_batches" + type: "integer" + required: false + - name: "--limit_val_batches" + type: "integer" + required: false + resources: + - type: python_script + path: script.py + - path: "../tools.py" +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scikit-learn + - "anndata>=0.8" + - scanpy + - scprep + - scvi-tools + - scikit-misc + - type: nextflow From 70274f98fde8aed4c78fffac2bf34a92a6aeb51e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 22:10:01 +0100 Subject: [PATCH 0369/1233] add normalization id to uns Former-commit-id: 1610ebceb0493faef3eac3ca72e6f9dad073955f --- src/datasets/normalization/log_cpm/script.py | 1 + src/datasets/normalization/log_scran_pooling/script.R | 1 + src/datasets/normalization/sqrt_cpm/script.py | 1 + 3 files changed, 3 insertions(+) diff --git a/src/datasets/normalization/log_cpm/script.py b/src/datasets/normalization/log_cpm/script.py index a080fdc643..98034b3fa9 100644 --- a/src/datasets/normalization/log_cpm/script.py +++ b/src/datasets/normalization/log_cpm/script.py @@ -27,6 +27,7 @@ print(">> Store output in adata") adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] +adata.uns["normalization_id"] = meta["functionality_name"] print(">> Write data") adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_scran_pooling/script.R b/src/datasets/normalization/log_scran_pooling/script.R index e67ad6bdd5..d4b36cb754 100644 --- a/src/datasets/normalization/log_scran_pooling/script.R +++ b/src/datasets/normalization/log_scran_pooling/script.R @@ -28,6 +28,7 @@ lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) cat(">> Storing in anndata\n") adata$obs[[par$obs_size_factors]] <- size_factors adata$layers[[par$layer_output]] <- lognorm +adata$uns[["normalization_id"]] <- meta[["functionality_name"]] cat(">> Writing to file\n") zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/datasets/normalization/sqrt_cpm/script.py b/src/datasets/normalization/sqrt_cpm/script.py index 517d3cdcce..f8e96952bf 100644 --- a/src/datasets/normalization/sqrt_cpm/script.py +++ b/src/datasets/normalization/sqrt_cpm/script.py @@ -28,6 +28,7 @@ print(">> Store output in adata") adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] +adata.uns["normalization_id"] = meta["functionality_name"] print(">> Write data") adata.write_h5ad(par['output'], compression="gzip") From 3c4b753066d194b5ca28c3ddb9ce0651841ae2f4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 22:11:14 +0100 Subject: [PATCH 0370/1233] add workspaceid Former-commit-id: d3b8232e9b7a29b3eb8e13a5865a209c8badeea1 --- src/datasets/workflows/process_openproblems_v1/run_nextflow.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh index 26001f4cba..cbdd1348de 100755 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh @@ -7,6 +7,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" export NXF_VER=22.04.5 +export TOWER_WORKSPACE_ID=53907369739130 bin/nextflow \ run . \ From 0a2a54b637d0217ab13c9a66dc5229a987ccd6c0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 22:36:49 +0100 Subject: [PATCH 0371/1233] rework normalization in label projection Former-commit-id: 8e104ee8aedf9909e9c90bc3f532b1c05d2faa37 --- src/label_projection/api/anndata_dataset.yaml | 10 +--- .../api/anndata_solution.yaml | 10 +--- src/label_projection/api/anndata_test.yaml | 10 +--- src/label_projection/api/anndata_train.yaml | 10 +--- .../api/comp_split_dataset.yaml | 9 +-- src/label_projection/methods/scanvi/script.py | 46 ++++++++++++++ .../split_dataset/generate_yaml.R | 6 +- .../split_dataset/params.yaml | 36 ++++++++--- src/label_projection/split_dataset/script.py | 7 ++- .../workflows/run/generate_yaml.R | 17 +++--- .../workflows/run/params.yaml | 60 +++++++++++++++++++ 11 files changed, 163 insertions(+), 58 deletions(-) create mode 100644 src/label_projection/methods/scanvi/script.py create mode 100644 src/label_projection/workflows/run/params.yaml diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml index 98e7fc7ba7..cbac32a823 100644 --- a/src/label_projection/api/anndata_dataset.yaml +++ b/src/label_projection/api/anndata_dataset.yaml @@ -9,14 +9,8 @@ info: name: counts description: Raw counts - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - - type: double - name: sqrt_cpm - description: CPM normalized counts, sqrt transformed + name: normalized + description: Normalized counts obs: - type: double name: label diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index a43c01ac34..6a9fb22dad 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -9,14 +9,8 @@ info: name: counts description: Raw counts - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - - type: double - name: sqrt_cpm - description: CPM normalized counts, sqrt transformed + name: normalized + description: Normalized counts obs: - type: string name: label diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index 03add01c3d..5c6de96597 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -9,14 +9,8 @@ info: name: counts description: Raw counts - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - - type: double - name: sqrt_cpm - description: CPM normalized counts, sqrt transformed + name: normalized + description: Normalized counts obs: - type: string name: batch diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index e50255af15..f20dbcb1e4 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -9,14 +9,8 @@ info: name: counts description: Raw counts - type: double - name: log_cpm - description: CPM normalized counts, log transformed - - type: double - name: log_scran_pooling - description: Scran pooling normalized counts, log transformed - - type: double - name: sqrt_cpm - description: CPM normalized counts, sqrt transformed + name: normalized + description: Normalized counts obs: - type: string name: label diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_split_dataset.yaml index eb40423101..64c9115217 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_split_dataset.yaml @@ -64,18 +64,15 @@ functionality: print(">> Check whether certain slots exist") assert "counts" in output_train.layers - assert "log_cpm" in output_train.layers - assert "log_scran_pooling" in output_train.layers + assert "normalized" in output_train.layers assert "label" in output_train.obs assert "batch" in output_train.obs assert "counts" in output_test.layers - assert "log_cpm" in output_test.layers - assert "log_scran_pooling" in output_test.layers + assert "normalized" in output_test.layers assert "label" not in output_test.obs # make sure label is /not/ here assert "batch" in output_test.obs assert "counts" in output_solution.layers - assert "log_cpm" in output_solution.layers - assert "log_scran_pooling" in output_solution.layers + assert "normalized" in output_solution.layers assert "label" in output_solution.obs assert "batch" in output_solution.obs diff --git a/src/label_projection/methods/scanvi/script.py b/src/label_projection/methods/scanvi/script.py new file mode 100644 index 0000000000..1303d8c480 --- /dev/null +++ b/src/label_projection/methods/scanvi/script.py @@ -0,0 +1,46 @@ +import scvi +import scanpy as sc + +## VIASH START +par = { + 'input': '../../../resources/toy_preprocessed_data.h5ad', + 'n_top_genes': 2000, + 'max_epochs': 1, + 'limit_train_batches': 10, + 'span': 0.8, + 'limit_val_batches': 10, + 'output': 'output.scviallgenes.h5ad' +} +## VIASH END + +print("Load input data") +adata = sc.read(par['input']) + +hvg_kwargs = { + "flavor": "seurat_v3", + "inplace": False, + "n_top_genes": par['n_top_genes'], + "batch_key": "batch", + +} + +# check parameters for test exists +par.get("span") and hvg_kwargs.update({"span": par['span']}) + +train_kwargs = { + "train_size": 0.9, + "early_stopping": True, +} + +# check parameters for test exists +par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) +par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) +par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) + +hvg_df = hvg(adata, **hvg_kwargs) +bdata = adata[:, hvg_df.highly_variable].copy() +adata.obs["celltype_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) +adata.uns["method_id"] = meta["functionality_name"] + +print("Write data") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/split_dataset/generate_yaml.R b/src/label_projection/split_dataset/generate_yaml.R index 6bb1828d83..a1dae37da2 100644 --- a/src/label_projection/split_dataset/generate_yaml.R +++ b/src/label_projection/split_dataset/generate_yaml.R @@ -6,9 +6,11 @@ h5ad_files <- fs::dir_ls("resources/datasets/openproblems_v1", recurse = TRUE, r param_list <- map(h5ad_files, function(h5ad_file) { ad <- anndata::read_h5ad(h5ad_file, backed = "r") if (all(c("batch", "celltype") %in% colnames(ad$obs))) { + dataset_id <- gsub(".*/", "", ad$uns[["dataset_id"]]) + normalization_id <- ad$uns[["normalization_id"]] list( - id = gsub(".*/", "", ad$uns[["dataset_id"]]), - input = paste0("../../../", h5ad_file) + id = paste0(dataset_id, ".", normalization_id), + input = h5ad_file ) } else { NULL diff --git a/src/label_projection/split_dataset/params.yaml b/src/label_projection/split_dataset/params.yaml index be769ed93c..f4f55e5745 100644 --- a/src/label_projection/split_dataset/params.yaml +++ b/src/label_projection/split_dataset/params.yaml @@ -1,12 +1,32 @@ param_list: -- id: immune_cells - input: resources/datasets/openproblems_v1/immune_cells.h5ad -- id: pancreas - input: resources/datasets/openproblems_v1/pancreas.h5ad -- id: tabula_muris_senis_droplet_lung - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.h5ad -- id: zebrafish - input: resources/datasets/openproblems_v1/zebrafish.h5ad +- id: cengen.log_cpm + input: resources/datasets/openproblems_v1/cengen.log_cpm.h5ad +- id: cengen.sqrt_cpm + input: resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad +- id: immune_cells.log_cpm + input: resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad +- id: immune_cells.log_scran_pooling + input: resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad +- id: immune_cells.sqrt_cpm + input: resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad +- id: pancreas.log_cpm + input: resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad +- id: pancreas.log_scran_pooling + input: resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad +- id: pancreas.sqrt_cpm + input: resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad +- id: tabula_muris_senis_droplet_lung.log_cpm + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad +- id: tabula_muris_senis_droplet_lung.log_scran_pooling + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad +- id: tabula_muris_senis_droplet_lung.sqrt_cpm + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad +- id: zebrafish.log_cpm + input: resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad +- id: zebrafish.log_scran_pooling + input: resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad +- id: zebrafish.sqrt_cpm + input: resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad obs_label: celltype obs_batch: batch seed: 123 diff --git a/src/label_projection/split_dataset/script.py b/src/label_projection/split_dataset/script.py index 21ffcb8935..f17a2dc83f 100644 --- a/src/label_projection/split_dataset/script.py +++ b/src/label_projection/split_dataset/script.py @@ -48,22 +48,23 @@ def subset_anndata(adata_sub, layers, obs, uns): ) output_train = subset_anndata( adata_sub = adata[[not x for x in is_test]], - layers=["counts", "log_cpm", "log_scran_pooling"], + layers=["counts", "normalized"], obs={"label": par["obs_label"], "batch": par["obs_batch"]}, uns=["dataset_id"] ) output_test = subset_anndata( adata[is_test], - layers=["counts", "log_cpm", "log_scran_pooling"], + layers=["counts", "normalized"], obs={"batch": par["obs_batch"]}, # do NOT copy label to test obs! uns=["dataset_id"] ) output_solution = subset_anndata( adata[is_test], - layers=["counts", "log_cpm", "log_scran_pooling"], + layers=["counts", "normalized"], obs={"label": par["obs_label"], "batch": par["obs_batch"]}, uns=["dataset_id"] ) +# TODO: use .viash_config.yaml to define these subsets print(">> Writing data") output_train.write_h5ad(par["output_train"]) diff --git a/src/label_projection/workflows/run/generate_yaml.R b/src/label_projection/workflows/run/generate_yaml.R index 50d0fa6f86..526600d007 100644 --- a/src/label_projection/workflows/run/generate_yaml.R +++ b/src/label_projection/workflows/run/generate_yaml.R @@ -3,22 +3,25 @@ library(anndata) h5ad_files <- fs::dir_ls("resources/label_projection/openproblems_v1", recurse = TRUE, regexp = "\\.h5ad$") -regex <- ".*/([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.h5ad" +regex <- ".*/([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.h5ad" df <- tibble( path = as.character(h5ad_files), - id = gsub(regex, "\\1", path), - comp = gsub(regex, "\\2", path), - arg_name = gsub(regex, "\\3", path) + dataset_id = gsub(regex, "\\1", path), + normalization_id = gsub(regex, "\\2", path), + comp = gsub(regex, "\\3", path), + arg_name = gsub(regex, "\\4", path) ) %>% spread(arg_name, path) -param_list <- pmap(df, function(id, comp, output_solution, output_test, output_train) { +param_list <- pmap(df, function(dataset_id, normalization_id, comp, output_solution, output_test, output_train) { list( - id = id, + id = paste0(dataset_id, ".", normalization_id), input_train = output_train, input_test = output_test, - input_solution = output_solution + input_solution = output_solution, + dataset_id = dataset_id, + normalization_id = normalization_id ) }) diff --git a/src/label_projection/workflows/run/params.yaml b/src/label_projection/workflows/run/params.yaml new file mode 100644 index 0000000000..60f8615008 --- /dev/null +++ b/src/label_projection/workflows/run/params.yaml @@ -0,0 +1,60 @@ +param_list: + resources/datasets/openproblems_v1/allen_brain_atlas.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/allen_brain_atlas.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/cengen.log_cpm.h5ad: + id: cengen.log_cpm + input: resources/datasets/openproblems_v1/cengen.log_cpm.h5ad + resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad: + id: cengen.sqrt_cpm + input: resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad + resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad: + id: immune_cells.log_cpm + input: resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad + resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad: + id: immune_cells.log_scran_pooling + input: resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad + resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad: + id: immune_cells.sqrt_cpm + input: resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad + resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.log_scran_pooling.h5ad: ~ + resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.log_scran_pooling.h5ad: ~ + resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad: + id: pancreas.log_cpm + input: resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad + resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad: + id: pancreas.log_scran_pooling + input: resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad + resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad: + id: pancreas.sqrt_cpm + input: resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad + resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad: + id: tabula_muris_senis_droplet_lung.log_cpm + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad + resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad: + id: tabula_muris_senis_droplet_lung.log_scran_pooling + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad + resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad: + id: tabula_muris_senis_droplet_lung.sqrt_cpm + input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad + resources/datasets/openproblems_v1/tenx_1k_pbmc.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/tenx_1k_pbmc.log_scran_pooling.h5ad: ~ + resources/datasets/openproblems_v1/tenx_1k_pbmc.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/tenx_5k_pbmc.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/tenx_5k_pbmc.log_scran_pooling.h5ad: ~ + resources/datasets/openproblems_v1/tenx_5k_pbmc.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/tnbc_wu2021.log_cpm.h5ad: ~ + resources/datasets/openproblems_v1/tnbc_wu2021.log_scran_pooling.h5ad: ~ + resources/datasets/openproblems_v1/tnbc_wu2021.sqrt_cpm.h5ad: ~ + resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad: + id: zebrafish.log_cpm + input: resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad + resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad: + id: zebrafish.log_scran_pooling + input: resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad + resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad: + id: zebrafish.sqrt_cpm + input: resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad From ede374e23cb62c27a8052de28448d0d390523615 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 22:56:15 +0100 Subject: [PATCH 0372/1233] fix pipeline and components Former-commit-id: 96f4c876102e553588327a8f758e6e6d0a8ab921 --- .../methods/knn/config.vsh.yaml | 1 - src/label_projection/methods/knn/script.py | 2 +- .../methods/logistic_regression/script.py | 2 +- src/label_projection/methods/mlp/script.py | 2 +- .../workflows/run/config.vsh.yaml | 8 ++ .../workflows/run/generate_yaml.R | 2 +- src/label_projection/workflows/run/main.nf | 15 +-- .../workflows/run/params.yaml | 60 ----------- .../workflows/run/params_benchmark.yaml | 100 +++++++++++++++--- 9 files changed, 104 insertions(+), 88 deletions(-) delete mode 100644 src/label_projection/workflows/run/params.yaml diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index c28faf751c..10ac11bcf3 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -14,7 +14,6 @@ functionality: v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d preferred_normalization: log_cpm - arguments: resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/knn/script.py b/src/label_projection/methods/knn/script.py index 7edbeca922..84b3d1beb9 100644 --- a/src/label_projection/methods/knn/script.py +++ b/src/label_projection/methods/knn/script.py @@ -20,7 +20,7 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = par["layer_input"] +input_layer = "normalized" print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 6f62694824..9a0f600a43 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -20,7 +20,7 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = par["layer_input"] +input_layer = "normalized" print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 1fea2a5555..facebd892c 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -20,7 +20,7 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = par["layer_input"] +input_layer = "normalized" print("Set up classifier pipeline") def pca_op(adata_train, adata_test, n_components=100): diff --git a/src/label_projection/workflows/run/config.vsh.yaml b/src/label_projection/workflows/run/config.vsh.yaml index 4b9785b86d..74616d6845 100644 --- a/src/label_projection/workflows/run/config.vsh.yaml +++ b/src/label_projection/workflows/run/config.vsh.yaml @@ -5,9 +5,17 @@ functionality: - name: Inputs arguments: - name: "--id" + type: "string" + description: "The ID of the normalized dataset" + required: true + - name: "--dataset_id" type: "string" description: "The ID of the dataset" required: true + - name: "--normalization_id" + type: "string" + description: "The ID of the normalization used" + required: true - name: "--input_train" type: "file" # todo: replace with includes - name: "--input_test" diff --git a/src/label_projection/workflows/run/generate_yaml.R b/src/label_projection/workflows/run/generate_yaml.R index 526600d007..b112681aca 100644 --- a/src/label_projection/workflows/run/generate_yaml.R +++ b/src/label_projection/workflows/run/generate_yaml.R @@ -32,4 +32,4 @@ output <- list( # seed = 123L ) -yaml::write_yaml(output, "src/label_projection/workflows/run/params.yaml") +yaml::write_yaml(output, "src/label_projection/workflows/run/params_benchmark.yaml") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index b5807111a9..718228c959 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -50,22 +50,23 @@ workflow run_wf { } output_ch = input_ch + | filter{it[1].normalization_id == "log_cpm"} // split params for downstream components | setWorkflowArguments( - method: ["input_train", "input_test"], + method: ["input_train", "input_test", "normalization_id", "dataset_id"], metric: [ "input_solution" ] ) // run methods | getWorkflowArguments(key: "method") | ( - true_labels.run(map: addSolution) & - random_labels & - majority_vote & - knn & - logistic_regression & - mlp + true_labels.run(map: addSolution, filter: {it[1].normalization_id == "log_cpm"}) & + random_labels.run(filter: {it[1].normalization_id == "log_cpm"}) & + majority_vote.run(filter: {it[1].normalization_id == "log_cpm"}) & + knn.run(filter: {it[1].normalization_id == "log_cpm"}) & + logistic_regression.run(filter: {it[1].normalization_id == "log_cpm"}) & + mlp.run(filter: {it[1].normalization_id == "log_cpm"}) ) | mix diff --git a/src/label_projection/workflows/run/params.yaml b/src/label_projection/workflows/run/params.yaml deleted file mode 100644 index 60f8615008..0000000000 --- a/src/label_projection/workflows/run/params.yaml +++ /dev/null @@ -1,60 +0,0 @@ -param_list: - resources/datasets/openproblems_v1/allen_brain_atlas.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/allen_brain_atlas.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/cengen.log_cpm.h5ad: - id: cengen.log_cpm - input: resources/datasets/openproblems_v1/cengen.log_cpm.h5ad - resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad: - id: cengen.sqrt_cpm - input: resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad - resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad: - id: immune_cells.log_cpm - input: resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad - resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad: - id: immune_cells.log_scran_pooling - input: resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad - resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad: - id: immune_cells.sqrt_cpm - input: resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad - resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.log_scran_pooling.h5ad: ~ - resources/datasets/openproblems_v1/mouse_blood_olssen_labelled.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.log_scran_pooling.h5ad: ~ - resources/datasets/openproblems_v1/mouse_hspc_nestorowa2016.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad: - id: pancreas.log_cpm - input: resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad - resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad: - id: pancreas.log_scran_pooling - input: resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad - resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad: - id: pancreas.sqrt_cpm - input: resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad - resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad: - id: tabula_muris_senis_droplet_lung.log_cpm - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad - resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad: - id: tabula_muris_senis_droplet_lung.log_scran_pooling - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad - resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad: - id: tabula_muris_senis_droplet_lung.sqrt_cpm - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad - resources/datasets/openproblems_v1/tenx_1k_pbmc.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/tenx_1k_pbmc.log_scran_pooling.h5ad: ~ - resources/datasets/openproblems_v1/tenx_1k_pbmc.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/tenx_5k_pbmc.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/tenx_5k_pbmc.log_scran_pooling.h5ad: ~ - resources/datasets/openproblems_v1/tenx_5k_pbmc.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/tnbc_wu2021.log_cpm.h5ad: ~ - resources/datasets/openproblems_v1/tnbc_wu2021.log_scran_pooling.h5ad: ~ - resources/datasets/openproblems_v1/tnbc_wu2021.sqrt_cpm.h5ad: ~ - resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad: - id: zebrafish.log_cpm - input: resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad - resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad: - id: zebrafish.log_scran_pooling - input: resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad - resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad: - id: zebrafish.sqrt_cpm - input: resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad diff --git a/src/label_projection/workflows/run/params_benchmark.yaml b/src/label_projection/workflows/run/params_benchmark.yaml index 5bab1a89a3..5b75c0788a 100644 --- a/src/label_projection/workflows/run/params_benchmark.yaml +++ b/src/label_projection/workflows/run/params_benchmark.yaml @@ -1,17 +1,85 @@ param_list: -- id: immune_cells - input_train: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/immune_cells.split_dataset.output_solution.h5ad -- id: pancreas - input_train: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_solution.h5ad -- id: tabula_muris_senis_droplet_lung - input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.split_dataset.output_solution.h5ad -- id: zebrafish - input_train: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/zebrafish.split_dataset.output_solution.h5ad +- id: cengen.log_cpm + input_train: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_solution.h5ad + dataset_id: cengen + normalization_id: log_cpm +- id: cengen.sqrt_cpm + input_train: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_solution.h5ad + dataset_id: cengen + normalization_id: sqrt_cpm +- id: immune_cells.log_cpm + input_train: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_solution.h5ad + dataset_id: immune_cells + normalization_id: log_cpm +- id: immune_cells.log_scran_pooling + input_train: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_solution.h5ad + dataset_id: immune_cells + normalization_id: log_scran_pooling +- id: immune_cells.sqrt_cpm + input_train: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_solution.h5ad + dataset_id: immune_cells + normalization_id: sqrt_cpm +- id: pancreas.log_cpm + input_train: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_solution.h5ad + dataset_id: pancreas + normalization_id: log_cpm +- id: pancreas.log_scran_pooling + input_train: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_solution.h5ad + dataset_id: pancreas + normalization_id: log_scran_pooling +- id: pancreas.sqrt_cpm + input_train: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_solution.h5ad + dataset_id: pancreas + normalization_id: sqrt_cpm +- id: tabula_muris_senis_droplet_lung.log_cpm + input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_solution.h5ad + dataset_id: tabula_muris_senis_droplet_lung + normalization_id: log_cpm +- id: tabula_muris_senis_droplet_lung.log_scran_pooling + input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_solution.h5ad + dataset_id: tabula_muris_senis_droplet_lung + normalization_id: log_scran_pooling +- id: tabula_muris_senis_droplet_lung.sqrt_cpm + input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_solution.h5ad + dataset_id: tabula_muris_senis_droplet_lung + normalization_id: sqrt_cpm +- id: zebrafish.log_cpm + input_train: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_solution.h5ad + dataset_id: zebrafish + normalization_id: log_cpm +- id: zebrafish.log_scran_pooling + input_train: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_solution.h5ad + dataset_id: zebrafish + normalization_id: log_scran_pooling +- id: zebrafish.sqrt_cpm + input_train: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_train.h5ad + input_test: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_test.h5ad + input_solution: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_solution.h5ad + dataset_id: zebrafish + normalization_id: sqrt_cpm From 26ad9c711ada0f608edd6e8b5218344f43015e38 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 17 Nov 2022 23:01:45 +0100 Subject: [PATCH 0373/1233] fix method and script Former-commit-id: 7299235904ce7b8b0a5d0f9802457e7b496ac208 --- src/datasets/api/comp_processor_hvg.yaml | 4 ++-- src/datasets/resource_test_scripts/pancreas.sh | 10 ---------- 2 files changed, 2 insertions(+), 12 deletions(-) diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index b82df3e09e..b6c95b2ccc 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,14 +1,14 @@ functionality: arguments: - name: "--input" - __inherits__: api/anndata_pca.yaml + __inherits__: anndata_pca.yaml - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input for the PCA. - name: "--output" direction: output - __inherits__: api/anndata_hvg.yaml + __inherits__: anndata_hvg.yaml - name: "--var_hvg" type: string default: "hvg" diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index e7035affca..12989d894e 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -32,16 +32,6 @@ bin/viash run src/datasets/subsample/config.vsh.yaml -- \ # run log cpm normalisation bin/viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset0.h5ad \ - --output $DATASET_DIR/temp_dataset1.h5ad - -# run sqrt cpm normalisation -bin/viash run src/datasets/normalization/sqrt_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset1.h5ad \ - --output $DATASET_DIR/temp_dataset2.h5ad - -# run scran pooling normalisation -bin/viash run src/datasets/normalization/log_scran_pooling/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset2.h5ad \ --output $DATASET_DIR/dataset.h5ad rm -r $DATASET_DIR/temp_* \ No newline at end of file From a8e262784451cf59b8c991b9cf0e6ad85785cbaf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 13:16:48 +0100 Subject: [PATCH 0374/1233] move scripts around Former-commit-id: 336e63e0aec1c4a734fd7d97958af2cae084fa52 --- .../resources_scripts/run_benchmark.sh | 64 ++++++++++++++ .../resources_scripts/split_datasets.sh | 65 ++++++++++++++ .../resources_test_scripts/pancreas.sh | 17 ++++ .../split_dataset/generate_yaml.R | 26 ------ .../split_dataset/params.yaml | 32 ------- .../split_dataset/run_nextflow.sh | 17 ---- .../workflows/run/config.vsh.yaml | 3 +- .../workflows/run/generate_yaml.R | 35 -------- src/label_projection/workflows/run/main.nf | 8 +- .../workflows/run/params_benchmark.yaml | 85 ------------------- .../workflows/run/params_test.yaml | 5 -- .../workflows/run/run_benchmark.sh | 17 ---- .../workflows/run/run_test.sh | 17 ---- 13 files changed, 152 insertions(+), 239 deletions(-) create mode 100755 src/label_projection/resources_scripts/run_benchmark.sh create mode 100755 src/label_projection/resources_scripts/split_datasets.sh delete mode 100644 src/label_projection/split_dataset/generate_yaml.R delete mode 100644 src/label_projection/split_dataset/params.yaml delete mode 100755 src/label_projection/split_dataset/run_nextflow.sh delete mode 100644 src/label_projection/workflows/run/generate_yaml.R delete mode 100644 src/label_projection/workflows/run/params_benchmark.yaml delete mode 100644 src/label_projection/workflows/run/params_test.yaml delete mode 100755 src/label_projection/workflows/run/run_benchmark.sh delete mode 100755 src/label_projection/workflows/run/run_test.sh diff --git a/src/label_projection/resources_scripts/run_benchmark.sh b/src/label_projection/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..97b75e012a --- /dev/null +++ b/src/label_projection/resources_scripts/run_benchmark.sh @@ -0,0 +1,64 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASETS_DIR="resources/label_projection/datasets/openproblems_v1" +OUTPUT_DIR="resources/label_projection/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import yaml + +dataset_dir = "$DATASETS_DIR" +output_dir = "$OUTPUT_DIR" + +with open(dataset_dir + "/params_split.yaml", "r") as file: + split_list = yaml.safe_load(file) +datasets = split_list['param_list'] + + +param_list = [] + +for dataset in datasets: + id = dataset["id"] + input_train = dataset_dir + "/" + id + ".train.h5ad" + input_test = dataset_dir + "/" + id + ".test.h5ad" + input_solution = dataset_dir + "/" + id + ".solution.h5ad" + + obj = { + 'id': id, + 'dataset_id': dataset["dataset_id"], + 'normalization_id': dataset["normalization_id"], + 'input_train': input_train, + 'input_test': input_test, + 'input_solution': input_solution + } + param_list.append(obj) + +output = { + "param_list": param_list, +} + +with open(output_dir + "/params.yaml", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script src/label_projection/workflows/run/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/label_projection/resources_scripts/split_datasets.sh b/src/label_projection/resources_scripts/split_datasets.sh new file mode 100755 index 0000000000..8cc4217555 --- /dev/null +++ b/src/label_projection/resources_scripts/split_datasets.sh @@ -0,0 +1,65 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +COMMON_DATASETS="resources/datasets/openproblems_v1" +OUTPUT_DIR="resources/label_projection/datasets/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import anndata as ad +import glob +import yaml + +h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") + +param_list = [] + +for h5ad_file in h5ad_files: + print(f"Checking {h5ad_file}") + adata = ad.read_h5ad(h5ad_file, backed=True) + if "batch" in adata.obs and "celltype" in adata.obs: + dataset_id = adata.uns["dataset_id"].replace("/", ".") + normalization_id = adata.uns["normalization_id"] + id = dataset_id + "." + normalization_id + obj = { + 'id': id, + 'input': h5ad_file, + 'dataset_id': dataset_id, + 'normalization_id': normalization_id + } + param_list.append(obj) + +output = { + "param_list": param_list, + "obs_label": "celltype", + "obs_batch": "batch", + "seed": 123, + "output_train": "\$id.train.h5ad", + "output_test": "\$id.test.h5ad", + "output_solution": "\$id.solution.h5ad" +} + +with open("$params_file", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script target/nextflow/label_projection/split_dataset/main.nf \ + -profile docker \ + -resume \ + -params-file $params_file \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 35bbc9f2e6..e8b4064022 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -38,3 +38,20 @@ bin/viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ --input_prediction $DATASET_DIR/knn.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/knn_accuracy.h5ad + +# run benchmark +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/label_projection/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ + --input_train $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/label_projection/split_dataset/generate_yaml.R b/src/label_projection/split_dataset/generate_yaml.R deleted file mode 100644 index a1dae37da2..0000000000 --- a/src/label_projection/split_dataset/generate_yaml.R +++ /dev/null @@ -1,26 +0,0 @@ -library(tidyverse) -library(anndata) - -h5ad_files <- fs::dir_ls("resources/datasets/openproblems_v1", recurse = TRUE, regexp = "\\.h5ad$") - -param_list <- map(h5ad_files, function(h5ad_file) { - ad <- anndata::read_h5ad(h5ad_file, backed = "r") - if (all(c("batch", "celltype") %in% colnames(ad$obs))) { - dataset_id <- gsub(".*/", "", ad$uns[["dataset_id"]]) - normalization_id <- ad$uns[["normalization_id"]] - list( - id = paste0(dataset_id, ".", normalization_id), - input = h5ad_file - ) - } else { - NULL - } -}) -output <- list( - param_list = unname(param_list) %>% .[!map_lgl(., is.null)], - obs_label = "celltype", - obs_batch = "batch", - seed = 123L -) - -yaml::write_yaml(output, "src/label_projection/split_dataset/params.yaml") diff --git a/src/label_projection/split_dataset/params.yaml b/src/label_projection/split_dataset/params.yaml deleted file mode 100644 index f4f55e5745..0000000000 --- a/src/label_projection/split_dataset/params.yaml +++ /dev/null @@ -1,32 +0,0 @@ -param_list: -- id: cengen.log_cpm - input: resources/datasets/openproblems_v1/cengen.log_cpm.h5ad -- id: cengen.sqrt_cpm - input: resources/datasets/openproblems_v1/cengen.sqrt_cpm.h5ad -- id: immune_cells.log_cpm - input: resources/datasets/openproblems_v1/immune_cells.log_cpm.h5ad -- id: immune_cells.log_scran_pooling - input: resources/datasets/openproblems_v1/immune_cells.log_scran_pooling.h5ad -- id: immune_cells.sqrt_cpm - input: resources/datasets/openproblems_v1/immune_cells.sqrt_cpm.h5ad -- id: pancreas.log_cpm - input: resources/datasets/openproblems_v1/pancreas.log_cpm.h5ad -- id: pancreas.log_scran_pooling - input: resources/datasets/openproblems_v1/pancreas.log_scran_pooling.h5ad -- id: pancreas.sqrt_cpm - input: resources/datasets/openproblems_v1/pancreas.sqrt_cpm.h5ad -- id: tabula_muris_senis_droplet_lung.log_cpm - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.h5ad -- id: tabula_muris_senis_droplet_lung.log_scran_pooling - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.h5ad -- id: tabula_muris_senis_droplet_lung.sqrt_cpm - input: resources/datasets/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.h5ad -- id: zebrafish.log_cpm - input: resources/datasets/openproblems_v1/zebrafish.log_cpm.h5ad -- id: zebrafish.log_scran_pooling - input: resources/datasets/openproblems_v1/zebrafish.log_scran_pooling.h5ad -- id: zebrafish.sqrt_cpm - input: resources/datasets/openproblems_v1/zebrafish.sqrt_cpm.h5ad -obs_label: celltype -obs_batch: batch -seed: 123 diff --git a/src/label_projection/split_dataset/run_nextflow.sh b/src/label_projection/split_dataset/run_nextflow.sh deleted file mode 100755 index 5bbfeaaa49..0000000000 --- a/src/label_projection/split_dataset/run_nextflow.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -bin/nextflow \ - run . \ - -main-script target/nextflow/label_projection/split_dataset/main.nf \ - -profile docker \ - -resume \ - -params-file src/label_projection/split_dataset/params.yaml \ - --publish_dir resources/label_projection/openproblems_v1 \ No newline at end of file diff --git a/src/label_projection/workflows/run/config.vsh.yaml b/src/label_projection/workflows/run/config.vsh.yaml index 74616d6845..23a2d1ca51 100644 --- a/src/label_projection/workflows/run/config.vsh.yaml +++ b/src/label_projection/workflows/run/config.vsh.yaml @@ -27,8 +27,7 @@ functionality: - name: "--output" direction: "output" type: file - # todo: fix inherits in nxf - # __inherits__: ../../api/anndata_raw_dataset.yaml + example: output.tsv resources: - type: nextflow_script path: main.nf diff --git a/src/label_projection/workflows/run/generate_yaml.R b/src/label_projection/workflows/run/generate_yaml.R deleted file mode 100644 index b112681aca..0000000000 --- a/src/label_projection/workflows/run/generate_yaml.R +++ /dev/null @@ -1,35 +0,0 @@ -library(tidyverse) -library(anndata) - -h5ad_files <- fs::dir_ls("resources/label_projection/openproblems_v1", recurse = TRUE, regexp = "\\.h5ad$") - -regex <- ".*/([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.([^\\.]*)\\.h5ad" - -df <- tibble( - path = as.character(h5ad_files), - dataset_id = gsub(regex, "\\1", path), - normalization_id = gsub(regex, "\\2", path), - comp = gsub(regex, "\\3", path), - arg_name = gsub(regex, "\\4", path) -) %>% - spread(arg_name, path) - -param_list <- pmap(df, function(dataset_id, normalization_id, comp, output_solution, output_test, output_train) { - list( - id = paste0(dataset_id, ".", normalization_id), - input_train = output_train, - input_test = output_test, - input_solution = output_solution, - dataset_id = dataset_id, - normalization_id = normalization_id - ) -}) - -output <- list( - param_list = param_list - # obs_label = "celltype", - # obs_batch = "batch", - # seed = 123L -) - -yaml::write_yaml(output, "src/label_projection/workflows/run/params_benchmark.yaml") diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 718228c959..932007bcbc 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -55,7 +55,8 @@ workflow run_wf { // split params for downstream components | setWorkflowArguments( method: ["input_train", "input_test", "normalization_id", "dataset_id"], - metric: [ "input_solution" ] + metric: ["input_solution"], + output: ["output"] ) // run methods @@ -76,7 +77,7 @@ workflow run_wf { def newId = file.getName().replaceAll(".output.*", "") // combine prediction with solution def newData = [ input_prediction: file, input_solution: passthrough.metric.input_solution ] - [ newId, newData ] + [ newId, newData, passthrough ] } // run metrics @@ -85,7 +86,8 @@ workflow run_wf { // convert to tsv | toSortedList - | map{ it -> [ "combined", it.collect{ it[1] } ] } + | map{ it -> [ "combined", it.collect{ it[1] } ] + it[0].drop(2) } + | getWorkflowArguments(key: "output") | extract_scores.run( auto: [ publish: true ] ) diff --git a/src/label_projection/workflows/run/params_benchmark.yaml b/src/label_projection/workflows/run/params_benchmark.yaml deleted file mode 100644 index 5b75c0788a..0000000000 --- a/src/label_projection/workflows/run/params_benchmark.yaml +++ /dev/null @@ -1,85 +0,0 @@ -param_list: -- id: cengen.log_cpm - input_train: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/cengen.log_cpm.split_dataset.output_solution.h5ad - dataset_id: cengen - normalization_id: log_cpm -- id: cengen.sqrt_cpm - input_train: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/cengen.sqrt_cpm.split_dataset.output_solution.h5ad - dataset_id: cengen - normalization_id: sqrt_cpm -- id: immune_cells.log_cpm - input_train: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/immune_cells.log_cpm.split_dataset.output_solution.h5ad - dataset_id: immune_cells - normalization_id: log_cpm -- id: immune_cells.log_scran_pooling - input_train: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/immune_cells.log_scran_pooling.split_dataset.output_solution.h5ad - dataset_id: immune_cells - normalization_id: log_scran_pooling -- id: immune_cells.sqrt_cpm - input_train: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/immune_cells.sqrt_cpm.split_dataset.output_solution.h5ad - dataset_id: immune_cells - normalization_id: sqrt_cpm -- id: pancreas.log_cpm - input_train: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/pancreas.log_cpm.split_dataset.output_solution.h5ad - dataset_id: pancreas - normalization_id: log_cpm -- id: pancreas.log_scran_pooling - input_train: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/pancreas.log_scran_pooling.split_dataset.output_solution.h5ad - dataset_id: pancreas - normalization_id: log_scran_pooling -- id: pancreas.sqrt_cpm - input_train: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/pancreas.sqrt_cpm.split_dataset.output_solution.h5ad - dataset_id: pancreas - normalization_id: sqrt_cpm -- id: tabula_muris_senis_droplet_lung.log_cpm - input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_cpm.split_dataset.output_solution.h5ad - dataset_id: tabula_muris_senis_droplet_lung - normalization_id: log_cpm -- id: tabula_muris_senis_droplet_lung.log_scran_pooling - input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.log_scran_pooling.split_dataset.output_solution.h5ad - dataset_id: tabula_muris_senis_droplet_lung - normalization_id: log_scran_pooling -- id: tabula_muris_senis_droplet_lung.sqrt_cpm - input_train: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/tabula_muris_senis_droplet_lung.sqrt_cpm.split_dataset.output_solution.h5ad - dataset_id: tabula_muris_senis_droplet_lung - normalization_id: sqrt_cpm -- id: zebrafish.log_cpm - input_train: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/zebrafish.log_cpm.split_dataset.output_solution.h5ad - dataset_id: zebrafish - normalization_id: log_cpm -- id: zebrafish.log_scran_pooling - input_train: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/zebrafish.log_scran_pooling.split_dataset.output_solution.h5ad - dataset_id: zebrafish - normalization_id: log_scran_pooling -- id: zebrafish.sqrt_cpm - input_train: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_train.h5ad - input_test: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_test.h5ad - input_solution: resources/label_projection/openproblems_v1/zebrafish.sqrt_cpm.split_dataset.output_solution.h5ad - dataset_id: zebrafish - normalization_id: sqrt_cpm diff --git a/src/label_projection/workflows/run/params_test.yaml b/src/label_projection/workflows/run/params_test.yaml deleted file mode 100644 index 7485ad2b6c..0000000000 --- a/src/label_projection/workflows/run/params_test.yaml +++ /dev/null @@ -1,5 +0,0 @@ -param_list: -- id: pancreas - input_train: resources_test/label_projection/pancreas/train.h5ad - input_test: resources_test/label_projection/pancreas/test.h5ad - input_solution: resources_test/label_projection/pancreas/solution.h5ad \ No newline at end of file diff --git a/src/label_projection/workflows/run/run_benchmark.sh b/src/label_projection/workflows/run/run_benchmark.sh deleted file mode 100755 index 7e378a1af1..0000000000 --- a/src/label_projection/workflows/run/run_benchmark.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -bin/nextflow \ - run . \ - -main-script src/label_projection/workflows/run/main.nf \ - -profile docker \ - -resume \ - -params-file src/label_projection/workflows/run/params_benchmark.yaml \ - --publish_dir output/label_projection \ No newline at end of file diff --git a/src/label_projection/workflows/run/run_test.sh b/src/label_projection/workflows/run/run_test.sh deleted file mode 100755 index 2afdd9bfb2..0000000000 --- a/src/label_projection/workflows/run/run_test.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -bin/nextflow \ - run . \ - -main-script src/label_projection/workflows/run/main.nf \ - -profile docker \ - -resume \ - -params-file src/label_projection/workflows/run/params_test.yaml \ - --publish_dir output/label_projection \ No newline at end of file From f1c934595af3fcfad5c206898db730ebfc57af2d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 15:30:54 +0100 Subject: [PATCH 0375/1233] don't forget to run pca and hvg on the pancreas test resource Former-commit-id: 050305fd4c3abf40d2f0743011d54f8a38e4f879 --- src/datasets/resource_test_scripts/pancreas.sh | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 12989d894e..e48a845a24 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -32,6 +32,16 @@ bin/viash run src/datasets/subsample/config.vsh.yaml -- \ # run log cpm normalisation bin/viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset0.h5ad \ + --output $DATASET_DIR/temp_dataset1.h5ad + +# run pca +bin/viash run src/datasets/processors/pca/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset1.h5ad \ + --output $DATASET_DIR/temp_dataset2.h5ad + +# run log cpm normalisation +bin/viash run src/datasets/processors/hvg/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset2.h5ad \ --output $DATASET_DIR/dataset.h5ad rm -r $DATASET_DIR/temp_* \ No newline at end of file From ab771a7f25044b4ef6542fb1ae966f020d9d55ae Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 20:48:20 +0100 Subject: [PATCH 0376/1233] refactor split dataset component to be a little more generic Former-commit-id: 5dbbdcd679aa17e4ca1d14c9f542a2f08a60407f --- .../split_dataset/config.vsh.yaml | 4 +- src/label_projection/split_dataset/script.py | 97 ++++++++++++++----- 2 files changed, 73 insertions(+), 28 deletions(-) diff --git a/src/label_projection/split_dataset/config.vsh.yaml b/src/label_projection/split_dataset/config.vsh.yaml index f4945ace40..88c5ee387d 100644 --- a/src/label_projection/split_dataset/config.vsh.yaml +++ b/src/label_projection/split_dataset/config.vsh.yaml @@ -25,10 +25,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: - - scanpy + - pyyaml - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/split_dataset/script.py b/src/label_projection/split_dataset/script.py index f17a2dc83f..1c71c64d6b 100644 --- a/src/label_projection/split_dataset/script.py +++ b/src/label_projection/split_dataset/script.py @@ -1,10 +1,13 @@ +import re +import yaml +import random import numpy as np import anndata as ad -import random +# Todo: throw error when not all slots are available? ## VIASH START par = { - 'input': 'work/b5/46e5081b30a46ab67d074d4c23eb71/zebrafish.h5ad', + 'input': 'resources_test/common/pancreas/dataset.h5ad', 'method': 'batch', 'seed': None, 'obs_batch': 'batch', @@ -14,21 +17,69 @@ 'output_solution': 'solution.h5ad' } meta = { - 'resources_dir': 'src/label_projection/split' + 'resources_dir': 'src/label_projection/split_dataset', + 'config': 'src/label_projection/split_dataset/.config.vsh.yaml' } ## VIASH END +# read the .config.vsh.yaml to find out which output slots need to be copied to which output file +def read_slots(par, meta): + # read output spec from yaml + with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + + output_struct_slots = {} + + # fetch info on which slots should be copied to which file + for arg in config["functionality"]["arguments"]: + if re.match("--output_", arg["name"]): + file = re.sub("--output_", "", arg["name"]) + + struct_slots = arg['info']['slots'] + out = {} + for (struct, slots) in struct_slots.items(): + out[struct] = { slot['name'] : slot['name'] for slot in slots } + + # rename source keys + if 'obs' in out: + if 'label' in out['obs']: + out['obs']['label'] = par['obs_label'] + if 'batch' in out['obs']: + out['obs']['batch'] = par['obs_batch'] + + output_struct_slots[file] = out + + return output_struct_slots + +# create new anndata objects according to api spec +def subset_anndata(adata_sub, slot_info): + structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] + kwargs = {} + + for struct in structs: + slot_mapping = slot_info.get(struct, {}) + data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} + if len(data) > 0: + if struct in ['obs', 'var']: + data = pd.concat(data, axis=1) + kwargs[struct] = data + elif struct in ['obs', 'var']: + # if no columns need to be copied, we still need an 'obs' and a 'var' + # to help determine the shape of the adata + kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] + + return ad.AnnData(**kwargs) + +# set seed if need be if par["seed"]: print(f">> Setting seed to {par['seed']}") random.seed(par["seed"]) print(">> Load data") adata = ad.read_h5ad(par["input"]) - print("adata:", adata) print(f">> Process data using {par['method']} method") - if par["method"] == "batch": batch_info = adata.obs[par["obs_batch"]] batch_categories = batch_info.dtype.categories @@ -38,33 +89,27 @@ train_ix = np.random.choice(adata.n_obs, round(adata.n_obs * 0.8), replace=False) is_test = [ not x in train_ix for x in range(0, adata.n_obs) ] -# create new anndata objects according to api spec -def subset_anndata(adata_sub, layers, obs, uns): - return ad.AnnData( - layers={key: adata_sub.layers[key] for key in layers}, - obs=adata_sub.obs[obs.values()].rename({v:n for n,v in obs.items()}, axis=1), - var=adata.var.drop(adata.var.columns, axis=1), - uns={key: adata_sub.uns[key] for key in uns} - ) +# subset the different adatas +print(">> Figuring which data needs to be copied to which output file") +slot_info_per_output = read_slots(par, meta) + +print(">> Creating train data") output_train = subset_anndata( - adata_sub = adata[[not x for x in is_test]], - layers=["counts", "normalized"], - obs={"label": par["obs_label"], "batch": par["obs_batch"]}, - uns=["dataset_id"] + adata_sub=adata[[not x for x in is_test]], + slot_info=slot_info_per_output['train'] ) + +print(">> Creating test data") output_test = subset_anndata( - adata[is_test], - layers=["counts", "normalized"], - obs={"batch": par["obs_batch"]}, # do NOT copy label to test obs! - uns=["dataset_id"] + adata_sub=adata[is_test], + slot_info=slot_info_per_output['test'] ) + +print(">> Creating solution data") output_solution = subset_anndata( - adata[is_test], - layers=["counts", "normalized"], - obs={"label": par["obs_label"], "batch": par["obs_batch"]}, - uns=["dataset_id"] + adata_sub=adata[is_test], + slot_info=slot_info_per_output['solution'] ) -# TODO: use .viash_config.yaml to define these subsets print(">> Writing data") output_train.write_h5ad(par["output_train"]) From f5271ac42bbdde6811c69476c4092a56f9c7b7c6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 20:48:28 +0100 Subject: [PATCH 0377/1233] fix placeholders Former-commit-id: 48f2eb834ecd4af035bceba76fa88ca16c9f0a07 --- src/label_projection/methods/knn/script.py | 4 ++-- src/label_projection/methods/logistic_regression/script.py | 4 ++-- src/label_projection/methods/mlp/script.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/label_projection/methods/knn/script.py b/src/label_projection/methods/knn/script.py index 84b3d1beb9..fe2ebb3e92 100644 --- a/src/label_projection/methods/knn/script.py +++ b/src/label_projection/methods/knn/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', - 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', 'layer_input': 'counts' } diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index 9a0f600a43..e44fa598c0 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', - 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', 'layer_input': 'counts' } diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index facebd892c..7283197010 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -7,8 +7,8 @@ ## VIASH START par = { - 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', - 'input_test': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad', + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', 'layer_input': 'counts' } From 6b99e93790bc387ac3850de209c2283f31f4e7c2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 21:07:18 +0100 Subject: [PATCH 0378/1233] fix datasets api Former-commit-id: 9ebc4f5705913950ea76121bc9402fc7e2bc9ac1 --- src/datasets/README.md | 20 +++++++++---------- ...{anndata_hvg.yaml => anndata_dataset.yaml} | 0 src/datasets/api/comp_processor_hvg.yaml | 2 +- 3 files changed, 11 insertions(+), 11 deletions(-) rename src/datasets/api/{anndata_hvg.yaml => anndata_dataset.yaml} (100%) diff --git a/src/datasets/README.md b/src/datasets/README.md index 02e6813996..739febdc10 100644 --- a/src/datasets/README.md +++ b/src/datasets/README.md @@ -26,7 +26,7 @@ ``` mermaid %%| column: screen-inset-shaded flowchart LR - anndata_hvg(Dataset+Pca+Hvg) + anndata_dataset(Dataset+Pca+Hvg) anndata_normalized(Normalized Dataset) anndata_pca(Dataset+Pca) anndata_raw(Raw Dataset) @@ -39,7 +39,7 @@ flowchart LR anndata_normalized---comp_processor_pca comp_dataset_loader-->anndata_raw comp_normalization-->anndata_normalized - comp_processor_hvg-->anndata_hvg + comp_processor_hvg-->anndata_dataset comp_processor_pca-->anndata_pca ``` @@ -64,7 +64,7 @@ Slots: | obs | tissue | string | Tissue information | | obs | size_factors | double | The size factors created by the normalisation method, if any. | | var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | +| var | hvg_score | integer | A ranking of the features by hvg. | | obsm | X_pca | double | The resulting PCA embedding. | | varm | pca_loadings | double | The PCA loadings matrix. | | uns | dataset_id | string | A unique identifier for the dataset | @@ -195,14 +195,14 @@ Arguments: Arguments: -| Name | Type | Direction | Description | -|:--------------------|:------------------------------------|:----------|:---------------------------------------------------------------------------| -| `--input` | [Dataset+Pca](#Dataset+PCA) | input | A normalised data with a PCA embedding | -| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | -| `--output` | [Dataset+Pca+Hvg](#Dataset+PCA+HVG) | output | A normalised data with a PCA embedding and HVG selection | -| `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | +| Name | Type | Direction | Description | +|:------------------|:------------------------------------|:----------|:---------------------------------------------------------------------------| +| `--input` | [Dataset+Pca](#Dataset+PCA) | input | A normalised data with a PCA embedding | +| `--layer_input` | `string` | input | Which layer to use as input for the PCA. | +| `--output` | [Dataset+Pca+Hvg](#Dataset+PCA+HVG) | output | A normalised data with a PCA embedding and HVG selection | +| `--var_hvg` | `string` | input | In which .var slot to store whether a feature is considered to be hvg. | | `--var_hvg_score` | `string` | input | In which .var slot to store whether a ranking of the features by variance. | -| `--num_features` | `integer` | input | The number of HVG to select | +| `--num_features` | `integer` | input | The number of HVG to select | ### `Processor Pca` diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_dataset.yaml similarity index 100% rename from src/datasets/api/anndata_hvg.yaml rename to src/datasets/api/anndata_dataset.yaml diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index b6c95b2ccc..c9f4cf256f 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -8,7 +8,7 @@ functionality: description: Which layer to use as input for the PCA. - name: "--output" direction: output - __inherits__: anndata_hvg.yaml + __inherits__: anndata_dataset.yaml - name: "--var_hvg" type: string default: "hvg" From 2a94b539276ce1a66700e92ab5bc9ca0469ab1a3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 21:13:45 +0100 Subject: [PATCH 0379/1233] fix label_projection api Former-commit-id: bc809dea3f3e0a909a8423d8498f99b47aaeda84 --- src/label_projection/README.md | 151 ++++++++++-------- src/label_projection/api/anndata_dataset.yaml | 55 ++++++- .../api/anndata_prediction.yaml | 5 + src/label_projection/api/anndata_score.yaml | 8 + .../api/anndata_solution.yaml | 19 +++ src/label_projection/api/anndata_test.yaml | 19 +++ src/label_projection/api/anndata_train.yaml | 19 +++ .../api/comp_split_dataset.yaml | 2 +- src/label_projection/split_dataset/script.py | 1 + 9 files changed, 206 insertions(+), 73 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 1a1db6e70e..5654c711fc 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -111,7 +111,7 @@ flowchart LR ### `Dataset` -A preprocessed dataset +A normalised data with a PCA embedding and HVG selection Used in: @@ -119,22 +119,31 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:------------------|:--------|:-------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | log_cpm | double | CPM normalized counts, log transformed | -| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | -| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | -| obs | label | double | Ground truth cell type labels | -| obs | batch | double | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalised expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalisation method, if any. | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| varm | pca_loadings | double | The PCA loadings matrix. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | pca_variance | double | The PCA variance objects. | Example: AnnData object - obs: 'label', 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id', 'pca_variance' + obsm: 'X_pca' + varm: 'pca_loadings' + layers: 'counts', 'normalized' ### `Prediction` @@ -148,17 +157,18 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:-----------|:-------|:-------------------------------------| -| obs | label_pred | string | Predicted labels for the test cells. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | +| struct | name | type | description | +|:-------|:-----------------|:-------|:-------------------------------------| +| obs | label_pred | string | Predicted labels for the test cells. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | method_id | string | A unique identifier for the method | Example: AnnData object obs: 'label_pred' - uns: 'dataset_id', 'method_id' + uns: 'dataset_id', 'normalization_id', 'method_id' ### `Score` @@ -170,17 +180,18 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:--------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | +| struct | name | type | description | +|:-------|:-----------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | Example: AnnData object - uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' ### `Solution` @@ -194,22 +205,26 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:------------------|:--------|:-------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | log_cpm | double | CPM normalized counts, log transformed | -| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | -| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized counts | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | Example: AnnData object obs: 'label', 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' ### `Test` @@ -223,21 +238,25 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:------------------|:--------|:-------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | log_cpm | double | CPM normalized counts, log transformed | -| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | -| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized counts | +| obs | batch | string | Batch information | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | Example: AnnData object obs: 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' ### `Train` @@ -251,22 +270,26 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:------------------|:--------|:-------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | log_cpm | double | CPM normalized counts, log transformed | -| layers | log_scran_pooling | double | Scran pooling normalized counts, log transformed | -| layers | sqrt_cpm | double | CPM normalized counts, sqrt transformed | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized counts | +| obs | label | string | Ground truth cell type labels | +| obs | batch | string | Batch information | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | Example: AnnData object obs: 'label', 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling', 'sqrt_cpm' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' ## Component API @@ -305,9 +328,9 @@ Arguments: Arguments: -| Name | File format | Direction | Description | -|:--------------------|:----------------------|:----------|:---------------------| -| `--input` | [Dataset](#dataset) | input | Preprocessed dataset | -| `--output_train` | [Train](#train) | output | Training data | -| `--output_test` | [Test](#test) | output | Test data | -| `--output_solution` | [Solution](#solution) | output | Solution | +| Name | File format | Direction | Description | +|:--------------------|:----------------------|:----------|:--------------| +| `--input` | [Dataset](#dataset) | input | NA | +| `--output_train` | [Train](#train) | output | Training data | +| `--output_test` | [Test](#test) | output | Test data | +| `--output_solution` | [Solution](#solution) | output | Solution | diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml index cbac32a823..9a65630b80 100644 --- a/src/label_projection/api/anndata_dataset.yaml +++ b/src/label_projection/api/anndata_dataset.yaml @@ -1,24 +1,63 @@ type: file -description: "A preprocessed dataset" -example: "preprocessed.h5ad" +description: "A normalised data with a PCA embedding and HVG selection" +example: "dataset.h5ad" info: - short_description: "Preprocessed dataset" + label: "Dataset+PCA+HVG" slots: layers: - type: integer name: counts description: Raw counts + required: true - type: double name: normalized - description: Normalized counts + description: Normalised expression values obs: - - type: double - name: label - description: Ground truth cell type labels - - type: double + - type: string + name: celltype + description: Cell type information + required: false + - type: string name: batch description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: double + name: pca_variance + description: The PCA variance objects. + required: true diff --git a/src/label_projection/api/anndata_prediction.yaml b/src/label_projection/api/anndata_prediction.yaml index d7695dcdaf..de033195d0 100644 --- a/src/label_projection/api/anndata_prediction.yaml +++ b/src/label_projection/api/anndata_prediction.yaml @@ -12,6 +12,11 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true - type: string name: method_id description: "A unique identifier for the method" diff --git a/src/label_projection/api/anndata_score.yaml b/src/label_projection/api/anndata_score.yaml index a3f1af8399..39181c68ba 100644 --- a/src/label_projection/api/anndata_score.yaml +++ b/src/label_projection/api/anndata_score.yaml @@ -8,14 +8,22 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true - type: string name: method_id description: "A unique identifier for the method" + required: true - type: string name: metric_ids description: "One or more unique metric identifiers" multiple: true + required: true - type: double name: metric_values description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." multiple: true + required: true diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index 6a9fb22dad..bed612a67b 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -18,7 +18,26 @@ info: - type: string name: batch description: Batch information + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index 5c6de96597..0c48edb999 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -15,7 +15,26 @@ info: - type: string name: batch description: Batch information + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index f20dbcb1e4..eece0bb34c 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -18,7 +18,26 @@ info: - type: string name: batch description: Batch information + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_split_dataset.yaml index 64c9115217..7ecd1c1e49 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_split_dataset.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_dataset.yaml + __inherits__: ../../datasets/api/anndata_dataset.yaml - name: "--output_train" __inherits__: anndata_train.yaml direction: output diff --git a/src/label_projection/split_dataset/script.py b/src/label_projection/split_dataset/script.py index 1c71c64d6b..7451c0e97a 100644 --- a/src/label_projection/split_dataset/script.py +++ b/src/label_projection/split_dataset/script.py @@ -1,6 +1,7 @@ import re import yaml import random +import pandas as pd import numpy as np import anndata as ad # Todo: throw error when not all slots are available? From cdd302326a1641009035def9af58680ec1b24c53 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 22:41:43 +0100 Subject: [PATCH 0380/1233] add labels Former-commit-id: 4afe06ab1480fa90e8c18e1f482171a531c12903 --- .../control_methods/majority_vote/config.vsh.yaml | 2 ++ .../control_methods/random_labels/config.vsh.yaml | 2 ++ .../control_methods/true_labels/config.vsh.yaml | 2 ++ src/label_projection/methods/knn/config.vsh.yaml | 2 ++ .../methods/logistic_regression/config.vsh.yaml | 2 ++ src/label_projection/methods/mlp/config.vsh.yaml | 2 ++ 6 files changed, 12 insertions(+) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 62aa4af7f8..de17f0d032 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -20,3 +20,5 @@ platforms: packages: - "anndata>=0.8" - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index f0c23ebf2f..4ba8ba009c 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -21,3 +21,5 @@ platforms: - scanpy - "anndata>=0.8" - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 070eb34ce6..1216e3062f 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -20,3 +20,5 @@ platforms: packages: - "anndata>=0.8" - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 10ac11bcf3..6c84270856 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -26,3 +26,5 @@ platforms: - scikit-learn - "anndata>=0.8" - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index eb35d7edb2..75455cea94 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -30,3 +30,5 @@ platforms: - scikit-learn - "anndata>=0.8" - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index f7f39da1fd..6eb3c210aa 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -36,3 +36,5 @@ platforms: - scikit-learn - "anndata>=0.8" - type: nextflow + directives: + label: [ midmem, lowcpu ] From b879219244a99051c20cacea64db2617ea11c381 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 22:41:54 +0100 Subject: [PATCH 0381/1233] add scanvi Former-commit-id: b9cffd42828dfcabb12aa0f4dfef703b15cf75dc --- .../methods/scanvi/config.vsh.yaml | 56 ++++-------- src/label_projection/methods/scanvi/script.py | 87 +++++++++++-------- .../scvi/scanvi_all_genes/config.vsh.yaml | 73 ---------------- .../methods/scvi/scanvi_all_genes/script.py | 39 --------- .../methods/scvi/scanvi_hvg/config.vsh.yaml | 81 ----------------- .../methods/scvi/scanvi_hvg/script.py | 51 ----------- .../scarches_scanvi_all_genes/config.vsh.yaml | 73 ---------------- .../scvi/scarches_scanvi_all_genes/script.py | 42 --------- .../scvi/scarches_scanvi_hvg/config.vsh.yaml | 81 ----------------- .../scvi/scarches_scanvi_hvg/script.py | 57 ------------ src/label_projection/methods/scvi/tools.py | 72 --------------- src/label_projection/workflows/run/main.nf | 9 +- 12 files changed, 72 insertions(+), 649 deletions(-) delete mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml delete mode 100644 src/label_projection/methods/scvi/scanvi_all_genes/script.py delete mode 100644 src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml delete mode 100644 src/label_projection/methods/scvi/scanvi_hvg/script.py delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml delete mode 100644 src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py delete mode 100644 src/label_projection/methods/scvi/tools.py diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 6cca91bf16..110274fabb 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -1,57 +1,37 @@ __inherits__: ../../api/comp_method.yaml functionality: name: "scanvi" - status: disabled namespace: "label_projection/methods" - description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." + description: | + Probabilistic harmonization and annotation of single-cell + transcriptomics data with deep generative models. info: type: method - label: Scanvi + label: SCANVI paper_doi: "10.1101/2020.07.16.205997" code_url: "https://github.com/YosefLab/scvi-tools" arguments: - - name: "--n_hidden" - type: "integer" - required: true - default: "10" - - name: "--n_layers" - type: "integer" - required: true - default: "1" - - name: "--n_latent" - type: "integer" - required: true - default: "10" - - name: "--n_top_genes" - type: "integer" - required: true - default: "2000" - - name: "--span" - type: "double" - required: false - - name: "--max_epochs" - type: "integer" - required: false - - name: "--limit_brain_batches" - type: "integer" - required: false - - name: "--limit_val_batches" - type: "integer" - required: false + - name: "--hvg" + type: boolean + default: true + description: "Whether or not to reduce the input matrix to the set of HVG genes before training the model." resources: - type: python_script path: script.py - - path: "../tools.py" platforms: - type: docker - image: "python:3.10" + image: nvcr.io/nvidia/pytorch:22.09-py3 setup: - type: python - packages: - - scikit-learn + packages: - "anndata>=0.8" - - scanpy - - scprep - scvi-tools - - scikit-misc + # image: "python:3.10" + # setup: + # - type: python + # packages: + # - "anndata>=0.8" + # - scvi-tools - type: nextflow + directives: + label: [ midmem, highcpu, gpu ] diff --git a/src/label_projection/methods/scanvi/script.py b/src/label_projection/methods/scanvi/script.py index 1303d8c480..09ae1b02ee 100644 --- a/src/label_projection/methods/scanvi/script.py +++ b/src/label_projection/methods/scanvi/script.py @@ -1,46 +1,59 @@ + +import anndata as ad import scvi -import scanpy as sc ## VIASH START par = { - 'input': '../../../resources/toy_preprocessed_data.h5ad', - 'n_top_genes': 2000, - 'max_epochs': 1, - 'limit_train_batches': 10, - 'span': 0.8, - 'limit_val_batches': 10, - 'output': 'output.scviallgenes.h5ad' + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad', + 'hvg': True +} +meta = { + 'functionality_name': 'scanvi' } ## VIASH END print("Load input data") -adata = sc.read(par['input']) - -hvg_kwargs = { - "flavor": "seurat_v3", - "inplace": False, - "n_top_genes": par['n_top_genes'], - "batch_key": "batch", - -} - -# check parameters for test exists -par.get("span") and hvg_kwargs.update({"span": par['span']}) - -train_kwargs = { - "train_size": 0.9, - "early_stopping": True, -} - -# check parameters for test exists -par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) -par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) -par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) - -hvg_df = hvg(adata, **hvg_kwargs) -bdata = adata[:, hvg_df.highly_variable].copy() -adata.obs["celltype_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) -adata.uns["method_id"] = meta["functionality_name"] +input_train_orig = ad.read_h5ad(par['input_train']) +input_test_orig = ad.read_h5ad(par['input_test']) + +print("Subsetting to HVG") +input_train = input_train_orig[:,input_train_orig.var['hvg']] +input_test = input_test_orig[:,input_test_orig.var['hvg']] + +print("Concatenating train and test data") +input_train.obs['is_test'] = False +input_test.obs['is_test'] = True +input_test.obs['label'] = "Unknown" +adata = ad.concat([input_train, input_test], merge = "same") + +print("Setting up adata object") +adata.obs["scanvi_label"] = adata.obs["label"].to_numpy() +scvi.model.SCVI.setup_anndata( + adata, + batch_key="batch", + labels_key="scanvi_label", + layer="normalized" +) + +print("Train SCVI model") +train_kwargs = dict( + train_size=0.9, + early_stopping=True, +) +scvi_model = scvi.model.SCVI(adata) +scvi_model.train(**train_kwargs) + +print("Train SCANVI model") +model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") +model.train(**train_kwargs) + +print("Make predictions") +preds = model.predict(adata) +input_test_orig.obs["label_pred"] = preds[adata.obs['is_test'].values] + +print("Write output to file") +input_test_orig.uns["method_id"] = meta["functionality_name"] +input_test_orig.write_h5ad(par['output'], compression="gzip") -print("Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml deleted file mode 100644 index 2b8d33fdd2..0000000000 --- a/src/label_projection/methods/scvi/scanvi_all_genes/config.vsh.yaml +++ /dev/null @@ -1,73 +0,0 @@ -functionality: - status: disabled - name: "scanvi_all_genes" - namespace: "label_projection/methods/scvi" - version: "dev" - description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." - info: - type: method - label: Scanvi_ALL_GENES - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--n_hidden" - type: "integer" - required: true - default: "10" - - name: "--n_layers" - type: "integer" - required: true - default: "1" - - name: "--n_latent" - type: "integer" - required: true - default: "10" - - name: "--max_epochs" - type: "integer" - required: false - - name: "--limit_brain_batches" - type: "integer" - required: false - - name: "--limit_val_batches" - type: "integer" - required: false - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true - resources: - - type: python_script - path: script.py - - path: "../tools.py" - test_resources: - - type: python_script - path: ../unit_tests/test_method.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - scprep - - scikit-learn - - "anndata>=0.8" - - scvi-tools - - type: native - - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scanvi_all_genes/script.py deleted file mode 100644 index f1ca53fb06..0000000000 --- a/src/label_projection/methods/scvi/scanvi_all_genes/script.py +++ /dev/null @@ -1,39 +0,0 @@ -## VIASH START -par = { - 'input': '../../../resources/toy_preprocessed_data.h5ad', - 'n_latent': 10, - 'n_layers': 1, - 'n_hidden': 32, - 'max_epochs': 1, - 'limit_train_batches': 10, - 'limit_val_batches': 10, - 'output': 'output.scviallgenes.h5ad' -} -## VIASH END -resources_dir="../" - -import sys -sys.path.append(resources_dir) -sys.path.append(meta['resources_dir']) -import scvi -import scanpy as sc -from tools import scanvi - -print("Load input data") -adata = sc.read(par['input']) - -train_kwargs = { - "train_size": 0.9, - "early_stopping": True, -} - -# check if parameters for test exists -par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) -par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) -par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) - -adata.obs["celltype_pred"] = scanvi(adata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) -adata.uns["method_id"] = meta["functionality_name"] - -print("Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml deleted file mode 100644 index 5e623c9f12..0000000000 --- a/src/label_projection/methods/scvi/scanvi_hvg/config.vsh.yaml +++ /dev/null @@ -1,81 +0,0 @@ -functionality: - status: disabled - name: "scanvi_hvg" - namespace: "label_projection/methods/scvi" - version: "dev" - description: "Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models." - info: - type: method - label: Scanvi_HVG - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--n_hidden" - type: "integer" - required: true - default: "10" - - name: "--n_layers" - type: "integer" - required: true - default: "1" - - name: "--n_latent" - type: "integer" - required: true - default: "10" - - name: "--n_top_genes" - type: "integer" - required: true - default: "2000" - - name: "--span" - type: "double" - required: false - - name: "--max_epochs" - type: "integer" - required: false - - name: "--limit_brain_batches" - type: "integer" - required: false - - name: "--limit_val_batches" - type: "integer" - required: false - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true - resources: - - type: python_script - path: script.py - - path: "../tools.py" - test_resources: - - type: python_script - path: ../unit_tests/test_method.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - scprep - - scikit-learn - - "anndata>=0.8" - - scvi-tools - - scikit-misc - - type: native - - type: nextflow diff --git a/src/label_projection/methods/scvi/scanvi_hvg/script.py b/src/label_projection/methods/scvi/scanvi_hvg/script.py deleted file mode 100644 index 50f4ae82c9..0000000000 --- a/src/label_projection/methods/scvi/scanvi_hvg/script.py +++ /dev/null @@ -1,51 +0,0 @@ -## VIASH START -par = { - 'input': '../../../resources/toy_preprocessed_data.h5ad', - 'n_top_genes': 2000, - 'max_epochs': 1, - 'limit_train_batches': 10, - 'span': 0.8, - 'limit_val_batches': 10, - 'output': 'output.scviallgenes.h5ad' -} -## VIASH END -resources_dir="../" - -import sys -sys.path.append(resources_dir) -sys.path.append(meta['resources_dir']) -import scvi -import scanpy as sc -from tools import scanvi, hvg - -print("Load input data") -adata = sc.read(par['input']) - -hvg_kwargs = { - "flavor": "seurat_v3", - "inplace": False, - "n_top_genes": par['n_top_genes'], - "batch_key": "batch", - -} - -# check parameters for test exists -par.get("span") and hvg_kwargs.update({"span": par['span']}) - -train_kwargs = { - "train_size": 0.9, - "early_stopping": True, -} - -# check parameters for test exists -par.get("max_epochs") and train_kwargs.update({"max_epochs": par['max_epochs']}) -par.get("limit_train_batches") and train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) -par.get("limit_val_batches") and train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) - -hvg_df = hvg(adata, **hvg_kwargs) -bdata = adata[:, hvg_df.highly_variable].copy() -adata.obs["celltype_pred"] = scanvi(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], **train_kwargs) -adata.uns["method_id"] = meta["functionality_name"] - -print("Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml deleted file mode 100644 index ecba2bd330..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/config.vsh.yaml +++ /dev/null @@ -1,73 +0,0 @@ -functionality: - status: disabled - name: "scarches_scanvi_all_genes" - namespace: "label_projection/methods/scvi" - version: "dev" - description: "Probabilistic harmonization and annotation of single-cell" - info: - type: method - label: Scarches_scanvi_ALL_GENES - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--n_hidden" - type: "integer" - required: true - default: "10" - - name: "--n_layers" - type: "integer" - required: true - default: "1" - - name: "--n_latent" - type: "integer" - required: true - default: "10" - - name: "--max_epochs" - type: "integer" - required: false - - name: "--limit_brain_batches" - type: "integer" - required: false - - name: "--limit_val_batches" - type: "integer" - required: false - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true - resources: - - type: python_script - path: script.py - - path: "../tools.py" - test_resources: - - type: python_script - path: ../unit_tests/test_method.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - scprep - - scikit-learn - - "anndata>=0.8" - - scvi-tools - - type: native - - type: nextflow diff --git a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py b/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py deleted file mode 100644 index afb5a467f5..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_all_genes/script.py +++ /dev/null @@ -1,42 +0,0 @@ -## VIASH START -par = { - 'input': '../../../resources/toy_preprocessed_data.h5ad', - 'max_epochs': 1, - 'limit_train_batches': 10, - 'limit_val_batches': 10, - 'output': 'output.scviallgenes.h5ad' -} -## VIASH END -resources_dir="../" - -import sys -sys.path.append(resources_dir) -sys.path.append(meta['resources_dir']) -import scvi -import scanpy as sc -from tools import scanvi_scarches - -print("Load input data") -adata = sc.read(par['input']) - -model_train_kwargs = { - "train_size": 0.9, - "early_stopping": True, -} - -query_model_train_kwargs = { - "max_epochs": 200, - "early_stopping": True, -} - -# check parameters for test exists -par.get("max_epochs") and model_train_kwargs.update({"max_epochs": par['max_epochs']}) and query_model_train_kwargs.update({"max_epochs": par['max_epochs']}) -par.get("limit_train_batches") and model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) and query_model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) -par.get("limit_val_batches") and model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) and query_model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) - -adata.obs["celltype_pred"] = scanvi_scarches(adata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, - 'query_model_train_kwargs': query_model_train_kwargs}) -adata.uns["method_id"] = meta["functionality_name"] - -print("Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml b/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml deleted file mode 100644 index 1a1fa05ba4..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/config.vsh.yaml +++ /dev/null @@ -1,81 +0,0 @@ -functionality: - status: disabled - name: "scarches_scanvi_hvg" - namespace: "label_projection/methods/scvi" - version: "dev" - description: "Probabilistic harmonization and annotation of single-cell" - info: - type: method - label: Scarches_scanvi_HVG - authors: - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: "Vinicius Chagas" - roles: [ maintainer ] - props: { github: chagasVinicius } - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - example: "input.h5ad" - description: "Input file that will be used to generate predictions" - required: true - - name: "--n_hidden" - type: "integer" - required: true - default: "10" - - name: "--n_layers" - type: "integer" - required: true - default: "1" - - name: "--n_latent" - type: "integer" - required: true - default: "10" - - name: "--max_epochs" - type: "integer" - required: false - - name: "--limit_brain_batches" - type: "integer" - required: false - - name: "--limit_val_batches" - type: "integer" - required: false - - name: "--n_top_genes" - type: "integer" - required: true - default: "2000" - - name: "--span" - type: "double" - required: false - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output data containing predictions" - required: true - resources: - - type: python_script - path: script.py - - path: "../tools.py" - test_resources: - - type: python_script - path: ../unit_tests/test_method.py - - type: file - path: "../../../../../resources_test/label_projection/pancreas/toy_preprocessed_data.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - scprep - - scikit-learn - - "anndata>=0.8" - - scvi-tools - - scikit-misc - - type: native - - type: nextflow diff --git a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py b/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py deleted file mode 100644 index 54f39d1bfa..0000000000 --- a/src/label_projection/methods/scvi/scarches_scanvi_hvg/script.py +++ /dev/null @@ -1,57 +0,0 @@ -## VIASH START -par = { - 'input': '../../../resources/toy_preprocessed_data.h5ad', - 'span': 0.8, - 'n_top_genes': 2000, - 'max_epochs': 1, - 'limit_train_batches': 10, - 'limit_val_batches': 10, - 'output': 'output.scviallgenes.h5ad' -} -## VIASH END -resources_dir="../" - -import sys -sys.path.append(resources_dir) -sys.path.append(meta['resources_dir']) -import scvi -import scanpy as sc -from tools import scanvi_scarches, hvg - -print("Load input data") -adata = sc.read(par['input']) - -hvg_kwargs = { - "flavor": "seurat_v3", - "inplace": False, - "n_top_genes": par['n_top_genes'], - "batch_key": "batch", - -} - -# check parameters for test exists -par.get("span") and hvg_kwargs.update({"span": par['span']}) - -model_train_kwargs = { - "train_size": 0.9, - "early_stopping": True, -} - -query_model_train_kwargs = { - "max_epochs": 200, - "early_stopping": True, -} - -# check parameters for test exists -par.get("max_epochs") and model_train_kwargs.update({"max_epochs": par['max_epochs']}) and query_model_train_kwargs.update({"max_epochs": par['max_epochs']}) -par.get("limit_train_batches") and model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) and query_model_train_kwargs.update({"limit_train_batches": par['limit_train_batches']}) -par.get("limit_val_batches") and model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) and query_model_train_kwargs.update({"limit_val_batches": par['limit_val_batches']}) - -hvg_df = hvg(adata, **hvg_kwargs) -bdata = adata[:, hvg_df.highly_variable].copy() -adata.obs["celltype_pred"] = scanvi_scarches(bdata, par['n_hidden'], par['n_latent'], par['n_layers'], {'model_train_kwargs': model_train_kwargs, - 'query_model_train_kwargs': query_model_train_kwargs}) -adata.uns["method_id"] = meta["functionality_name"] - -print("Write data") -adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/label_projection/methods/scvi/tools.py b/src/label_projection/methods/scvi/tools.py deleted file mode 100644 index 79674c5201..0000000000 --- a/src/label_projection/methods/scvi/tools.py +++ /dev/null @@ -1,72 +0,0 @@ -import scanpy as sc -import scvi - - -def hvg (adata, **hvg_kwargs): - try: - return sc.pp.highly_variable_genes(adata[adata.obs["is_train"]], **hvg_kwargs) - except ValueError: # loess estimation can fail on small data with seurat_v3 flavor - # in this case we try seurat flavor - # and copy the data because it needs normalized counts - # but later we need raw counts - hvg_kwargs["flavor"] = "seurat" - normdata = adata.copy() - sc.pp.normalize_total(normdata, target_sum=1e4) - sc.pp.log1p(normdata) - return sc.pp.highly_variable_genes( - normdata[normdata.obs["is_train"]], **hvg_kwargs - ) - -def scanvi(adata, n_hidden=None, n_latent=None, n_layers=None, **train_kwargs): - scanvi_labels = adata.obs["celltype"].to_numpy() - # test set labels masked - scanvi_labels[~adata.obs["is_train"].to_numpy()] = "Unknown" - adata.obs["scanvi_labels"] = scanvi_labels - scvi.model.SCVI.setup_anndata(adata, batch_key="batch", labels_key="scanvi_labels") - scvi_model = scvi.model.SCVI( - adata, n_hidden=n_hidden, n_latent=n_latent, n_layers=n_layers - ) - scvi_model.train(**train_kwargs) - model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") - model.train(**train_kwargs) - del adata.obs["scanvi_labels"] - # predictions for train and test - return model.predict(adata) - -def scanvi_scarches(adata, n_hidden=None, n_latent=None, n_layers=None, train_kwargs={}): - model_train_kwargs = train_kwargs['model_train_kwargs'] - query_model_train_kwargs = train_kwargs['query_model_train_kwargs'] - # new obs labels to mask test set - adata_train = adata[adata.obs["is_train"]].copy() - adata_train.obs["scanvi_labels"] = adata_train.obs["celltype"].copy() - adata_test = adata[~adata.obs["is_train"]].copy() - adata_test.obs["scanvi_labels"] = "Unknown" - scvi.model.SCVI.setup_anndata( - adata_train, batch_key="batch", labels_key="scanvi_labels" - ) - - # specific scArches parameters - arches_params = dict( - use_layer_norm="both", - use_batch_norm="none", - encode_covariates=True, - dropout_rate=0.2, - n_hidden=n_hidden, - n_layers=n_layers, - n_latent=n_latent, - ) - scvi_model = scvi.model.SCVI(adata_train, **arches_params) - - scvi_model.train(**model_train_kwargs) - model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") - model.train(**model_train_kwargs) - - query_model = scvi.model.SCANVI.load_query_data(adata_test, model) - query_model.train(plan_kwargs=dict(weight_decay=0.0), **query_model_train_kwargs) - - # this is temporary and won't be used - adata.obs["scanvi_labels"] = "Unknown" - preds = query_model.predict(adata) - del adata.obs["scanvi_labels"] - # predictions for train and test - return preds diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 932007bcbc..c8cf6be485 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -12,10 +12,8 @@ include { random_labels } from "$targetDir/label_projection/control_methods/rand include { knn } from "$targetDir/label_projection/methods/knn/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" -// include { scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scanvi_hvg/main.nf" -// include { scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scanvi_all_genes/main.nf" -// include { scarches_scanvi_all_genes } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_all_genes/main.nf" -// include { scarches_scanvi_hvg } from "$targetDir/label_projection/methods/scvi/scarches_scanvi_hvg/main.nf" +include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" +// include { scarches } from "$targetDir/label_projection/methods/scarches/main.nf" // import metrics include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" @@ -67,7 +65,8 @@ workflow run_wf { majority_vote.run(filter: {it[1].normalization_id == "log_cpm"}) & knn.run(filter: {it[1].normalization_id == "log_cpm"}) & logistic_regression.run(filter: {it[1].normalization_id == "log_cpm"}) & - mlp.run(filter: {it[1].normalization_id == "log_cpm"}) + mlp.run(filter: {it[1].normalization_id == "log_cpm"}) & + scanvi.run(filter: {it[1].normalization_id == "log_cpm"}) ) | mix From aa6c71ee1a9c9770475a2d04251129f41edddb7e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 22:42:56 +0100 Subject: [PATCH 0382/1233] add labels Former-commit-id: 3d29e082e0eb379b7ac3e98a0b7b22a3018a7e25 --- src/datasets/normalization/log_cpm/config.vsh.yaml | 2 ++ src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 1685944df9..87dfa39d4c 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -15,3 +15,5 @@ platforms: - scanpy - "anndata>=0.8" - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 48aa7562b8..4315de267c 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -15,3 +15,5 @@ platforms: - scanpy - "anndata>=0.8" - type: nextflow + directives: + label: [ lowmem, lowcpu ] From 5461efde8ac89aab742422bd92128738d28cf1d6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 22:43:01 +0100 Subject: [PATCH 0383/1233] move scripts Former-commit-id: 6adc8bba7da0140ac8d4aff3be6f72fdc76d4392 --- .../openproblems_v1.sh} | 34 ++++++++++++++++++- .../process_openproblems_v1/run_nextflow.sh | 19 ----------- 2 files changed, 33 insertions(+), 20 deletions(-) rename src/datasets/{workflows/process_openproblems_v1/datasets.yaml => resource_scripts/openproblems_v1.sh} (59%) mode change 100644 => 100755 delete mode 100755 src/datasets/workflows/process_openproblems_v1/run_nextflow.sh diff --git a/src/datasets/workflows/process_openproblems_v1/datasets.yaml b/src/datasets/resource_scripts/openproblems_v1.sh old mode 100644 new mode 100755 similarity index 59% rename from src/datasets/workflows/process_openproblems_v1/datasets.yaml rename to src/datasets/resource_scripts/openproblems_v1.sh index 16d65b368d..fced1e226c --- a/src/datasets/workflows/process_openproblems_v1/datasets.yaml +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -1,3 +1,23 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="resources/datasets/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + cat > "$params_file" << 'HERE' param_list: - id: allen_brain_atlas obs_celltype: label @@ -48,4 +68,16 @@ param_list: obs_batch: lab layer_counts: counts -output: '$id.h5ad' \ No newline at end of file +output: '$id.h5ad' +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" \ + -with-tower diff --git a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh b/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh deleted file mode 100755 index cbdd1348de..0000000000 --- a/src/datasets/workflows/process_openproblems_v1/run_nextflow.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 -export TOWER_WORKSPACE_ID=53907369739130 - -bin/nextflow \ - run . \ - -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ - -profile docker \ - -resume \ - -params-file src/datasets/workflows/process_openproblems_v1/datasets.yaml \ - --publish_dir resources/datasets/openproblems_v1 \ - -with-tower From 004c282b72e7ec64581f5fc4060819da939145fa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 23:15:59 +0100 Subject: [PATCH 0384/1233] fix script Former-commit-id: 578801e7b0711910ce385ba5de3dd7cdd8adae90 --- src/label_projection/resources_scripts/run_benchmark.sh | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/label_projection/resources_scripts/run_benchmark.sh b/src/label_projection/resources_scripts/run_benchmark.sh index 97b75e012a..7c9265baa0 100755 --- a/src/label_projection/resources_scripts/run_benchmark.sh +++ b/src/label_projection/resources_scripts/run_benchmark.sh @@ -6,6 +6,8 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +export TOWER_WORKSPACE_ID=53907369739130 + DATASETS_DIR="resources/label_projection/datasets/openproblems_v1" OUTPUT_DIR="resources/label_projection/benchmarks/openproblems_v1" @@ -22,11 +24,12 @@ import yaml dataset_dir = "$DATASETS_DIR" output_dir = "$OUTPUT_DIR" -with open(dataset_dir + "/params_split.yaml", "r") as file: +# read split datasets yaml +with open(dataset_dir + "/params.yaml", "r") as file: split_list = yaml.safe_load(file) datasets = split_list['param_list'] - +# figure out where train/test/solution files were stored param_list = [] for dataset in datasets: @@ -45,6 +48,7 @@ for dataset in datasets: } param_list.append(obj) +# write as output file output = { "param_list": param_list, } From 2ea040da49f0a69c23670161f11f8085fe32ce8c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 23:21:25 +0100 Subject: [PATCH 0385/1233] add description Former-commit-id: 0a44c02efc9e951a14ff9d4bde655e99d1bcacf3 --- src/label_projection/workflows/run/nextflow.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/label_projection/workflows/run/nextflow.config b/src/label_projection/workflows/run/nextflow.config index 0ecebcacc0..9a59101ea1 100644 --- a/src/label_projection/workflows/run/nextflow.config +++ b/src/label_projection/workflows/run/nextflow.config @@ -1,5 +1,8 @@ manifest { + name = 'label_projection/workflows/run' + mainScript = 'main.nf' nextflowVersion = '!>=22.04.5' + description = 'Label projection' } params { From 5e62be36f03503caf1f3d3fcac7523faf9c33690 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 18 Nov 2022 23:21:36 +0100 Subject: [PATCH 0386/1233] add description Former-commit-id: ff07db46b16c60263fb4977a586bd24936fdb120 --- src/datasets/workflows/process_openproblems_v1/nextflow.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/datasets/workflows/process_openproblems_v1/nextflow.config b/src/datasets/workflows/process_openproblems_v1/nextflow.config index 0ecebcacc0..d189e3cc02 100644 --- a/src/datasets/workflows/process_openproblems_v1/nextflow.config +++ b/src/datasets/workflows/process_openproblems_v1/nextflow.config @@ -1,5 +1,8 @@ manifest { + name = 'datasets/workflows/process_openproblems_v1' + mainScript = 'main.nf' nextflowVersion = '!>=22.04.5' + description = 'Fetch and process legacy OpenProblems v1 datasets' } params { From ef87b5f505cce22d0766cc5190d3c8e60e35a523 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 19 Nov 2022 01:39:13 +0000 Subject: [PATCH 0387/1233] Bump tj-actions/changed-files from 34.0.5 to 34.4.4 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.0.5 to 34.4.4. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.0.5...v34.4.4) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: 3ee1c435a785276d74acc45815607bc172885dbc --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index a7655f54ae..e0b6f6a0b9 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -74,7 +74,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.0.5 + uses: tj-actions/changed-files@v34.4.4 with: separator: ";" diff_relative: true From 68cb3aae1cc8e7be214decd3cc832005bb99bd2c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 19 Nov 2022 08:58:31 +0100 Subject: [PATCH 0388/1233] add tools script Former-commit-id: c7c7a1eac56cb4df7e3079fd61c82b1a1466000d --- bin/.gitignore | 1 + bin/init_tools | 25 +++++++++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100755 bin/init_tools diff --git a/bin/.gitignore b/bin/.gitignore index d00b90146a..042da6f70d 100644 --- a/bin/.gitignore +++ b/bin/.gitignore @@ -1,3 +1,4 @@ fetch viash* nextflow +tools \ No newline at end of file diff --git a/bin/init_tools b/bin/init_tools new file mode 100755 index 0000000000..0f4630aea3 --- /dev/null +++ b/bin/init_tools @@ -0,0 +1,25 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +tmpdir=$(mktemp -d) +function clean_up { + rm -rf "$tmpdir" +} +trap clean_up EXIT + +VERSION=0.1.0 + +if [ $# -eq 2 ]; then + git clone --depth 1 --branch $VERSION https://$1:$2@github.com/viash-io/viash_tools.git $tmpdir/ +else + git clone --depth 1 --branch $VERSION git@github.com:viash-io/viash_tools.git $tmpdir/ +fi + +[ -d bin/tools ] && rm -r bin/tools + +cp -r $tmpdir/target bin/tools \ No newline at end of file From e35adbb6c2f8b24159e00ce5135b7921da4510c7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 19 Nov 2022 08:59:24 +0100 Subject: [PATCH 0389/1233] update scripts Former-commit-id: 6711f9b9f88f6b211dd5776a926bf9b2d2820d7e --- .../analysis_scripts/script.R | 44 ++++++++++++++++--- .../resources_scripts/run_benchmark.sh | 18 +++++++- src/label_projection/workflows/run/main.nf | 1 + 3 files changed, 55 insertions(+), 8 deletions(-) diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index 756f01b187..0744aea082 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -1,8 +1,20 @@ library(tidyverse) -scores <- read_tsv("output/label_projection/combined.extract_scores.output.tsv") %>% +out_dir <- "resources/label_projection/benchmarks/openproblems_v1/" + +scores <- read_tsv(paste0(out_dir, "combined.extract_scores.output.tsv")) %>% rename(metric_id = metric_ids, metric_value = metric_values) +output_regex <- "^(.*)\\.([^\\.]*)\\.output[^\\.]*\\.h5ad" +nxf_log <- read_tsv(paste0(out_dir, "nextflow_log.tsv")) %>% + mutate( + output_file = gsub(".*output=([^,]*).*", "\\1", params), + id = gsub(output_regex, "\\1", output_file), + dataset_id = gsub("^([^\\.]*)\\.([^\\.]*).*", "\\1/\\2", id), + component_id = gsub(output_regex, "\\2", output_file) + ) +nxf_log %>% select(id:component_id) + ns_list_methods <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*methods"))$stdout) method_info <- map_df(ns_list_methods, function(conf) { @@ -33,8 +45,7 @@ metric_info <- map_df(ns_list_metrics, function(conf) { }) }) - - +# make scores plot df <- scores %>% left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") %>% left_join(metric_info %>% select(id, label, min, max, maximise) %>% rename_all(function(x) paste0("metric_", x)), by = "metric_id") @@ -49,12 +60,33 @@ ordering <- df %>% df$method_label <- factor(df$method_label, levels = rev(ordering$method_label)) -g <- ggplot(df %>% arrange(method_label)) + +g1 <- ggplot(df %>% arrange(method_label)) + geom_path(aes(metric_value, method_label, group = dataset_id), alpha = .2) + geom_point(aes(metric_value, method_label, colour = method_type)) + facet_wrap(~metric_label, ncol = 1) + theme_bw() + labs(title = "OpenProblems v2 - Label projection v0.1") -ggsave("output/label_projection/plot.pdf", g, width = 6, height = 8) -ggsave("output/label_projection/plot.png", g, width = 6, height = 8) +# make execution plot +# todo: capture walltime, memory, disk, cpu +execution_info <- nxf_log %>% + filter(component_id %in% method_info$id) %>% + transmute(method_id = component_id, dataset_id, exit, duration = lubridate::duration(toupper(duration)), realtime = lubridate::duration(toupper(realtime))) %>% + left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") + +execution_info$method_label <- factor(execution_info$method_label, levels = rev(ordering$method_label)) + +g2 <- + ggplot(execution_info %>% arrange(method_label)) + + geom_path(aes(duration, method_label, group = dataset_id), alpha = .2) + + geom_point(aes(duration, method_label, colour = method_type)) + + theme_bw() + + labs(title = "Execution time", x = "Log duration (s)") + + scale_x_log10() + +g <- patchwork::wrap_plots(g1, g2, ncol = 1, heights = c(4, 1)) + +ggsave(paste0(out_dir, "plot.pdf"), g, width = 6, height = 10) +ggsave(paste0(out_dir, "plot.png"), g, width = 6, height = 10) + + diff --git a/src/label_projection/resources_scripts/run_benchmark.sh b/src/label_projection/resources_scripts/run_benchmark.sh index 7c9265baa0..6fd51739a0 100755 --- a/src/label_projection/resources_scripts/run_benchmark.sh +++ b/src/label_projection/resources_scripts/run_benchmark.sh @@ -63,6 +63,20 @@ bin/nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ -profile docker \ - -resume \ -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" \ + -with-tower + +bin/tools/docker/nextflow/process_log/process_log \ + --output "$OUTPUT_DIR/nextflow_log.tsv" + +# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' +# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' + +# bin/nextflow run . \ +# -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ +# -profile docker \ +# --input_train resources_test/label_projection/pancreas/train.h5ad \ +# --input_test resources_test/label_projection/pancreas/test.h5ad \ +# --input_solution resources_test/label_projection/pancreas/solution.h5ad \ +# --publish_dir foo \ No newline at end of file diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index c8cf6be485..b4d7c39c32 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -58,6 +58,7 @@ workflow run_wf { ) // run methods + // TODO: these filters don't work atm. | getWorkflowArguments(key: "method") | ( true_labels.run(map: addSolution, filter: {it[1].normalization_id == "log_cpm"}) & From ab642f324b327f45c67362e1fb7f7caae1768ad6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 19 Nov 2022 08:59:49 +0100 Subject: [PATCH 0390/1233] update netadata Former-commit-id: 5006e73b252ec5824ccb94514dc22b48a3210838 --- src/label_projection/methods/scanvi/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 110274fabb..b8ca261988 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: transcriptomics data with deep generative models. info: type: method - label: SCANVI + label: scANVI paper_doi: "10.1101/2020.07.16.205997" code_url: "https://github.com/YosefLab/scvi-tools" arguments: From 5c22d48fdbce724d3d82162acf8334e637eb3901 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 21 Nov 2022 10:27:28 +0100 Subject: [PATCH 0391/1233] update script Former-commit-id: e279e5bccfbee8656f5f9b007e425fb49c920625 --- .../analysis_scripts/script.R | 102 +++++++++++------- 1 file changed, 66 insertions(+), 36 deletions(-) diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index 0744aea082..5d09be3d6a 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -2,9 +2,11 @@ library(tidyverse) out_dir <- "resources/label_projection/benchmarks/openproblems_v1/" +# read scores scores <- read_tsv(paste0(out_dir, "combined.extract_scores.output.tsv")) %>% rename(metric_id = metric_ids, metric_value = metric_values) +# read nxf log output_regex <- "^(.*)\\.([^\\.]*)\\.output[^\\.]*\\.h5ad" nxf_log <- read_tsv(paste0(out_dir, "nextflow_log.tsv")) %>% mutate( @@ -15,6 +17,22 @@ nxf_log <- read_tsv(paste0(out_dir, "nextflow_log.tsv")) %>% ) nxf_log %>% select(id:component_id) +# process execution info +execution_info <- nxf_log %>% + filter(component_id %in% method_info$id) %>% + transmute( + method_id = component_id, + dataset_id, + status, + realtime = lubridate::duration(toupper(realtime)), + pcpu = as.numeric(gsub("%", "", pcpu)), + vmem_gb = as.numeric(gsub(" GB", "", vmem)), + peak_vmem_gb = as.numeric(gsub(" GB", "", peak_vmem)), + read_bytes_mb = as.numeric(gsub(" MB", "", read_bytes)), + write_bytes_mb = as.numeric(gsub(" MB", "", write_bytes)) + ) + +# get method info ns_list_methods <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*methods"))$stdout) method_info <- map_df(ns_list_methods, function(conf) { @@ -34,6 +52,7 @@ method_info <- map_df(ns_list_methods, function(conf) { }) }) +# get metric info ns_list_metrics <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*metrics"))$stdout) metric_info <- map_df(ns_list_metrics, function(conf) { @@ -45,48 +64,59 @@ metric_info <- map_df(ns_list_metrics, function(conf) { }) }) -# make scores plot -df <- scores %>% - left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") %>% - left_join(metric_info %>% select(id, label, min, max, maximise) %>% rename_all(function(x) paste0("metric_", x)), by = "metric_id") - -ordering <- df %>% +# get data table +ranking <- scores %>% + left_join(metric_info %>% select(metric_id = id, maximise), by = "metric_id") %>% + left_join(method_info %>% select(method_id = id, method_label = label), by = "method_id") %>% group_by(metric_id, dataset_id) %>% - mutate(rank = rank(ifelse(metric_maximise, -metric_value, metric_value))) %>% + mutate(rank = rank(ifelse(maximise, -metric_value, metric_value))) %>% ungroup() %>% group_by(method_id, method_label) %>% - summarise(mean_rank = mean(rank)) %>% + summarise(mean_rank = mean(rank), .groups = "drop") %>% arrange(mean_rank) -df$method_label <- factor(df$method_label, levels = rev(ordering$method_label)) - -g1 <- ggplot(df %>% arrange(method_label)) + - geom_path(aes(metric_value, method_label, group = dataset_id), alpha = .2) + - geom_point(aes(metric_value, method_label, colour = method_type)) + - facet_wrap(~metric_label, ncol = 1) + - theme_bw() + - labs(title = "OpenProblems v2 - Label projection v0.1") - -# make execution plot -# todo: capture walltime, memory, disk, cpu -execution_info <- nxf_log %>% - filter(component_id %in% method_info$id) %>% - transmute(method_id = component_id, dataset_id, exit, duration = lubridate::duration(toupper(duration)), realtime = lubridate::duration(toupper(realtime))) %>% - left_join(method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)), by = "method_id") - -execution_info$method_label <- factor(execution_info$method_label, levels = rev(ordering$method_label)) - -g2 <- - ggplot(execution_info %>% arrange(method_label)) + - geom_path(aes(duration, method_label, group = dataset_id), alpha = .2) + - geom_point(aes(duration, method_label, colour = method_type)) + - theme_bw() + - labs(title = "Execution time", x = "Log duration (s)") + - scale_x_log10() +df <- + method_info %>% + select(id, type, label) %>% + rename_all(function(x) paste0("method_", x)) %>% + left_join(scores %>% spread(metric_id, metric_value), by = "method_id") %>% + left_join(execution_info, by = c("dataset_id", "method_id")) %>% + mutate(method_label = factor(method_label, levels = rev(ranking$method_label))) %>% + arrange(method_label) + + +# get feature info +feature_info_exec <- tribble( + ~id, ~label, ~log_x, + "realtime", "Duration (s)", FALSE, + "pcpu", "CPU usage (%)", FALSE, + "vmem_gb", "Memory usage (GB)", FALSE, + "peak_vmem_gb", "Peak memory (GB)", FALSE, + "read_bytes_mb", "Read disk (MB)", FALSE, + "write_bytes_mb", "Write disk (MB)", FALSE +) +feature_info <- bind_rows( + metric_info %>% transmute(id, label, log_x = FALSE), + feature_info_exec +) + +plots <- pmap(feature_info, function(id, label, log_x) { + g <- ggplot(df) + + geom_path(aes_string(id, "method_label", group = "dataset_id"), alpha = .2) + + geom_point(aes_string(id, "method_label", colour = "method_type")) + + theme_bw() + + theme(legend.position = "none") + + labs(x = label, y = NULL) + + expand_limits(x = 0) + if (log_x) { + g <- g + scale_x_log10() + } + g +}) +g <- patchwork::wrap_plots(plots, ncol = 2, byrow = FALSE) -g <- patchwork::wrap_plots(g1, g2, ncol = 1, heights = c(4, 1)) -ggsave(paste0(out_dir, "plot.pdf"), g, width = 6, height = 10) -ggsave(paste0(out_dir, "plot.png"), g, width = 6, height = 10) +ggsave(paste0(out_dir, "plot.pdf"), g, width = 8, height = 12) +ggsave(paste0(out_dir, "plot.png"), g, width = 8, height = 12) From 2eeaecfd390a826e6fcb49d162fee2a5b131ee93 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 15 Nov 2022 09:51:22 +0100 Subject: [PATCH 0392/1233] first commit Former-commit-id: 181444997d6e49b24b853a24f2e9f0ccea230254 --- .../normalization/sqrt_L1/config.vsh.yaml | 19 +++++ src/common/normalization/sqrt_L1/script.py | 32 ++++++++ src/denoising/api/anndata_raw_dataset.yaml | 18 +++++ src/denoising/api/anndata_test.yaml | 21 +++++ src/denoising/api/anndata_train.yaml | 21 +++++ src/denoising/api/comp_split_data.yaml | 80 +++++++++++++++++++ .../split_data/config.vsh.yaml | 32 ++++++++ .../data_processing/split_data/script.py | 62 ++++++++++++++ src/denoising/readme.md | 55 +++++++++++++ 9 files changed, 340 insertions(+) create mode 100644 src/common/normalization/sqrt_L1/config.vsh.yaml create mode 100644 src/common/normalization/sqrt_L1/script.py create mode 100644 src/denoising/api/anndata_raw_dataset.yaml create mode 100644 src/denoising/api/anndata_test.yaml create mode 100644 src/denoising/api/anndata_train.yaml create mode 100644 src/denoising/api/comp_split_data.yaml create mode 100644 src/denoising/data_processing/split_data/config.vsh.yaml create mode 100644 src/denoising/data_processing/split_data/script.py create mode 100644 src/denoising/readme.md diff --git a/src/common/normalization/sqrt_L1/config.vsh.yaml b/src/common/normalization/sqrt_L1/config.vsh.yaml new file mode 100644 index 0000000000..fc9e55432f --- /dev/null +++ b/src/common/normalization/sqrt_L1/config.vsh.yaml @@ -0,0 +1,19 @@ +__inherits__: ../../api/comp_normalization.yaml +functionality: + name: "sqrt" + namespace: "common/normalization" + description: "Normalize data using sqrt L1" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - scprep + - "anndata<0.8" + - numpy + - type: nextflow diff --git a/src/common/normalization/sqrt_L1/script.py b/src/common/normalization/sqrt_L1/script.py new file mode 100644 index 0000000000..0fd638db61 --- /dev/null +++ b/src/common/normalization/sqrt_L1/script.py @@ -0,0 +1,32 @@ +import scanpy as sc +import scprep +import numpy as np + +## VIASH START +par = { + 'input': "output_train.h5ad", + 'output': "output_norm.h5ad" +} +meta = { + "functionality_name": "normalize_sqrt_L1" +} +## VIASH END + +print(">> Load data") +adata = sc.read_h5ad(par['input']) + +print(">> Normalize data") +# libsize and sqrt L1 norm +sqrt_data = scprep.utils.matrix_transform(adata, np.sqrt) +# sqrt_L1, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) +# sqrt_L1 = sqrt_L1.tocsr() + +print(sqrt_data) + +# print(">> Store output in adata") +# adata.layers["sqrtnorm"] = lognorm +# adata.obs["norm_factor"] = norm["norm_factor"] +# adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") + +# print(">> Write data") +# adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/denoising/api/anndata_raw_dataset.yaml b/src/denoising/api/anndata_raw_dataset.yaml new file mode 100644 index 0000000000..de80bf6d09 --- /dev/null +++ b/src/denoising/api/anndata_raw_dataset.yaml @@ -0,0 +1,18 @@ +type: file +description: "A raw dataset" +example: "raw_dataset.h5ad" +info: + short_description: "Raw dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: integer + name: n_counts + description: raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/denoising/api/anndata_test.yaml b/src/denoising/api/anndata_test.yaml new file mode 100644 index 0000000000..3026067d52 --- /dev/null +++ b/src/denoising/api/anndata_test.yaml @@ -0,0 +1,21 @@ +type: file +description: "The test data" +example: "test.h5ad" +info: + short_description: "Test data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: string + name: n_counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/denoising/api/anndata_train.yaml b/src/denoising/api/anndata_train.yaml new file mode 100644 index 0000000000..71df73b898 --- /dev/null +++ b/src/denoising/api/anndata_train.yaml @@ -0,0 +1,21 @@ +type: file +description: "The training data" +example: "training.h5ad" +info: + short_description: "Training data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: string + name: n_counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: raw_dataset_id + description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/denoising/api/comp_split_data.yaml b/src/denoising/api/comp_split_data.yaml new file mode 100644 index 0000000000..5108b6094e --- /dev/null +++ b/src/denoising/api/comp_split_data.yaml @@ -0,0 +1,80 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_dataset.yaml + - name: "--output_train" + __inherits__: anndata_train.yaml + direction: output + - name: "--output_test" + __inherits__: anndata_test.yaml + direction: output + # test_resources: + # - type: python_script + # path: generic_test.py + # text: | + # import anndata as ad + # import subprocess + # from os import path + + # input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" + # output_train_path = "output_train.h5ad" + # output_test_path = "output_test.h5ad" + # output_solution_path = "output_solution.h5ad" + + # cmd = [ + # meta['executable'], + # "--input", input_path, + # "--output_train", output_train_path, + # "--output_test", output_test_path, + # "--output_solution", output_solution_path + # ] + + # print(">> Running script as test") + # out = subprocess.check_output(cmd).decode("utf-8") + + # print(">> Checking whether output file exists") + # assert path.exists(output_train_path) + # assert path.exists(output_test_path) + # assert path.exists(output_solution_path) + + # print(">> Reading h5ad files") + # input = ad.read_h5ad(input_path) + # output_train = ad.read_h5ad(output_train_path) + # output_test = ad.read_h5ad(output_test_path) + # output_solution = ad.read_h5ad(output_solution_path) + + # print("input:", input) + # print("output_train:", output_train) + # print("output_test:", output_test) + # print("output_solution:", output_solution) + + # print(">> Checking dimensions, make sure no cells were dropped") + # assert input.n_obs == output_train.n_obs + output_test.n_obs + # assert output_test.n_obs == output_solution.n_obs + # assert input.n_vars == output_train.n_vars + # assert input.n_vars == output_test.n_vars + + # print(">> Checking whether data from input was copied properly to output") + # assert output_train.uns["dataset_id"] == input.uns["dataset_id"] + # assert output_train.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] + # assert output_test.uns["dataset_id"] == input.uns["dataset_id"] + # assert output_test.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] + # assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] + # assert output_solution.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] + + # print(">> Check whether certain slots exist") + # assert "counts" in output_train.layers + # assert "lognorm" in output_train.layers + # assert "label" in output_train.obs + # assert "batch" in output_train.obs + # assert "counts" in output_test.layers + # assert "lognorm" in output_test.layers + # assert "label" not in output_test.obs # make sure label is /not/ here + # assert "batch" in output_test.obs + # assert "counts" in output_solution.layers + # assert "lognorm" in output_solution.layers + # assert "label" in output_solution.obs + # assert "batch" in output_solution.obs + + # print(">> All checks succeeded!") + # - path: ../../../../resources_test/common/pancreas diff --git a/src/denoising/data_processing/split_data/config.vsh.yaml b/src/denoising/data_processing/split_data/config.vsh.yaml new file mode 100644 index 0000000000..5caae3e315 --- /dev/null +++ b/src/denoising/data_processing/split_data/config.vsh.yaml @@ -0,0 +1,32 @@ +__inherits__: ../../api/comp_split_data.yaml +functionality: + name: "split_data" + namespace: "denoising/data_processing" + arguments: + - name: "--method" + type: "string" + description: "The process method to assign train/test." + choices: ["mcv"] + default: "mcv" + - name: "--train_frac" + type: "float" + description: "The fraction the molecules need to be split to train dataset" + default: 0.9 + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata<0.8" + - numpy + - scipy + - molecular_cross_validation #TODO: custom github package -> how to add? + - type: nextflow diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/data_processing/split_data/script.py new file mode 100644 index 0000000000..62a4347a2e --- /dev/null +++ b/src/denoising/data_processing/split_data/script.py @@ -0,0 +1,62 @@ +import scanpy as sc +import numpy as np +import scipy.sparse +import molecular_cross_validation.util + +## VIASH START +par = { + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output_train': "output_train.h5ad", + 'output_test': "output_test.h5ad", + 'seed': 0 +} +meta = { + "functionality_name": "split_data" +} +## VIASH END +"""Split data using molecular cross-validation. + +Stores "train" and "test" dataset in separate ad files. +""" + +random_state = np.random.RandomState(par['seed']) + +print(">> Load Data") +adata = sc.read_h5ad(par["input"]) + + +X = adata.layers["counts"] + +# for test purposes +X = X.round() + +print(">> process and split data") +if scipy.sparse.issparse(X): + X = np.array(X.todense()) +if np.allclose(X, X.astype(int)): + X = X.astype(int) +else: + raise TypeError("Molecular cross-validation requires integer count data.") + +X_train, X_test = molecular_cross_validation.util.split_molecules( + X, 0.9, 0.0, random_state +) + + + +# copy adata to train_set, test_set + +output_train = adata +output_train.layers["counts"] = scipy.sparse.csr_matrix(X_train).astype(float) + +output_test = adata +output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) + +# TODO: remove zero entries -> uncertain how this is done. below code gives error that matrix size is different +# is_missing = output_train.layers["counts"].sum(axis=0) == 0 +# output_train.layers["counts"], output_test.layers["counts"] = output_train.layers["counts"][:, ~is_missing], output_test.layers["counts"][:, ~is_missing] + +print(">> Writing") + +output_train.write_h5ad(par["output_train"]) +output_test.write_h5ad(par["output_test"]) diff --git a/src/denoising/readme.md b/src/denoising/readme.md new file mode 100644 index 0000000000..1167878998 --- /dev/null +++ b/src/denoising/readme.md @@ -0,0 +1,55 @@ +# Denoising + +## The task + +Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present +in each cell. As a result, the measurements (UMI counts) observed for each gene and each +cell are associated with generally high levels of technical noise ([Grün et al., +2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes the task of +estimating the true expression level of each gene in each cell. In the single-cell +literature, this task is also referred to as *imputation*, a term which is typically +used for missing data problems in statistics. Similar to the use of the terms "dropout", +"missing data", and "technical zeros", this terminology can create confusion about the +underlying measurement process ([Sarkar and Stephens, +2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). + +A key challenge in evaluating denoising methods is the general lack of a ground truth. A +recent benchmark study ([Hou et al., +2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) +relied on flow-sorted datasets, mixture control experiments ([Tian et al., +2019](https://www.nature.com/articles/s41592-019-0425-8)), and comparisons with bulk +RNA-Seq data. Since each of these approaches suffers from specific limitations, it is +difficult to combine these different approaches into a single quantitative measure of +denoising accuracy. Here, we instead rely on an approach termed molecular +cross-validation (MCV), which was specifically developed to quantify denoising accuracy +in the absence of a ground truth ([Batson et al., +2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the observed molecules +in a given scRNA-Seq dataset are first partitioned between a *training* and a *test* +dataset. Next, a denoising method is applied to the training dataset. Finally, denoising +accuracy is measured by comparing the result to the test dataset. The authors show that +both in theory and in practice, the measured denoising accuracy is representative of the +accuracy that would be obtained on a ground truth dataset. + +## The metrics + +Metrics for data denoising aim to assess denoising accuracy by comparing the denoised +*training* set to the randomly sampled *test* set. + +* **MSE**: The mean squared error between the denoised counts of the training dataset + and the true counts of the test dataset after reweighting by the train/test ratio. +* **Poisson**: The Poisson log likelihood of observing the true counts of the test + dataset given the distribution given in the denoised dataset. + +## API + +Datasets should contain the raw UMI counts in `adata.X`, subsampled to training +(`adata.obsm["train"]`) and testing (`adata.obsm["test"]`) datasets using +`openproblems.tasks.denoising.datasets.utils.split_data`. + +The task-specific data loader functions should split the provided raw UMI counts into a +training and a test dataset, as described by [Batson et al., +2019](https://www.biorxiv.org/content/10.1101/786269v1). The training dataset should be +stored in `adata.obsm['train']`, and the test dataset should be stored in +`adata.obsm['test']`. Methods should store the denoising result in +`adata.obsm['denoised']`. Methods should not edit `adata.obsm["train"]` or +`adata.obsm["test"]`. \ No newline at end of file From 02bc0fee9bb6991b907563d44c741be0359218fc Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 12:42:40 +0100 Subject: [PATCH 0393/1233] fix api Former-commit-id: 47df1fff63966a0830a9e7327557e2bae81ed0de --- src/denoising/api/comp_split_data.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/api/comp_split_data.yaml b/src/denoising/api/comp_split_data.yaml index 5108b6094e..08682c23a0 100644 --- a/src/denoising/api/comp_split_data.yaml +++ b/src/denoising/api/comp_split_data.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_dataset.yaml + __inherits__: ../../common/api/anndata_dataset.yaml - name: "--output_train" __inherits__: anndata_train.yaml direction: output From 25d4667bed4f5b017898d55d8db4543b6ebdbd57 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 12:42:49 +0100 Subject: [PATCH 0394/1233] fix config Former-commit-id: 6240d1c996dd1c006d5003cf6dba67729112eb4d --- src/denoising/data_processing/split_data/config.vsh.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/denoising/data_processing/split_data/config.vsh.yaml b/src/denoising/data_processing/split_data/config.vsh.yaml index 5caae3e315..f361a098a7 100644 --- a/src/denoising/data_processing/split_data/config.vsh.yaml +++ b/src/denoising/data_processing/split_data/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: choices: ["mcv"] default: "mcv" - name: "--train_frac" - type: "float" + type: "double" description: "The fraction the molecules need to be split to train dataset" default: 0.9 - name: "--seed" @@ -28,5 +28,6 @@ platforms: - "anndata<0.8" - numpy - scipy - - molecular_cross_validation #TODO: custom github package -> how to add? + github: + - czbiohub/molecular-cross-validation - type: nextflow From b640fd366cc7a8e73cb711e6560599588d14b4d9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 15 Nov 2022 12:48:22 +0100 Subject: [PATCH 0395/1233] add comments Former-commit-id: edb48f4a48630a1bbf1c3f29d091bc6078a4059a --- src/denoising/data_processing/split_data/script.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/data_processing/split_data/script.py index 62a4347a2e..785e0d59b1 100644 --- a/src/denoising/data_processing/split_data/script.py +++ b/src/denoising/data_processing/split_data/script.py @@ -52,10 +52,16 @@ output_test = adata output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) +# TODO: remove cells which have not enough reads +# * first, remove genes with 0 expression +# * then, remove cells with 1 count or less + # TODO: remove zero entries -> uncertain how this is done. below code gives error that matrix size is different # is_missing = output_train.layers["counts"].sum(axis=0) == 0 # output_train.layers["counts"], output_test.layers["counts"] = output_train.layers["counts"][:, ~is_missing], output_test.layers["counts"][:, ~is_missing] +# TODO: Remove other normalisation methods so that they can be recomputed later + print(">> Writing") output_train.write_h5ad(par["output_train"]) From 8113c47df3e3f221342803bdb1d19cdbcbb134c3 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 17 Nov 2022 14:03:27 +0100 Subject: [PATCH 0396/1233] transfer methods from v1 Former-commit-id: f2e5b959bccb4be68946e4e061e60601e3790817 --- src/common/normalization/sqrt_L1/script.py | 32 ---------- .../normalization/sqrt_L1/config.vsh.yaml | 0 src/datasets/normalization/sqrt_L1/script.py | 31 ++++++++++ src/denoising/api/anndata_denoised.yaml | 24 ++++++++ src/denoising/api/anndata_test.yaml | 5 +- src/denoising/api/anndata_train.yaml | 5 +- src/denoising/api/comp_method.yaml | 61 +++++++++++++++++++ .../data_processing/split_data/script.py | 34 ++++++++--- src/denoising/methods/alra/alra.R | 0 src/denoising/methods/alra/config.vsh.yaml | 37 +++++++++++ src/denoising/methods/alra/script.py | 1 + .../methods/baseline/config.vsh.yaml | 36 +++++++++++ src/denoising/methods/baseline/script.py | 35 +++++++++++ src/denoising/methods/dca/config.vsh.yaml | 37 +++++++++++ src/denoising/methods/dca/script.py | 36 +++++++++++ .../methods/knn_smoothing/config.vsh.yaml | 34 +++++++++++ src/denoising/methods/knn_smoothing/script.py | 27 ++++++++ src/denoising/methods/magic/config.vsh.yaml | 43 +++++++++++++ src/denoising/methods/magic/script.py | 53 ++++++++++++++++ 19 files changed, 481 insertions(+), 50 deletions(-) delete mode 100644 src/common/normalization/sqrt_L1/script.py rename src/{common => datasets}/normalization/sqrt_L1/config.vsh.yaml (100%) create mode 100644 src/datasets/normalization/sqrt_L1/script.py create mode 100644 src/denoising/api/anndata_denoised.yaml create mode 100644 src/denoising/api/comp_method.yaml create mode 100644 src/denoising/methods/alra/alra.R create mode 100644 src/denoising/methods/alra/config.vsh.yaml create mode 100644 src/denoising/methods/alra/script.py create mode 100644 src/denoising/methods/baseline/config.vsh.yaml create mode 100644 src/denoising/methods/baseline/script.py create mode 100644 src/denoising/methods/dca/config.vsh.yaml create mode 100644 src/denoising/methods/dca/script.py create mode 100644 src/denoising/methods/knn_smoothing/config.vsh.yaml create mode 100644 src/denoising/methods/knn_smoothing/script.py create mode 100644 src/denoising/methods/magic/config.vsh.yaml create mode 100644 src/denoising/methods/magic/script.py diff --git a/src/common/normalization/sqrt_L1/script.py b/src/common/normalization/sqrt_L1/script.py deleted file mode 100644 index 0fd638db61..0000000000 --- a/src/common/normalization/sqrt_L1/script.py +++ /dev/null @@ -1,32 +0,0 @@ -import scanpy as sc -import scprep -import numpy as np - -## VIASH START -par = { - 'input': "output_train.h5ad", - 'output': "output_norm.h5ad" -} -meta = { - "functionality_name": "normalize_sqrt_L1" -} -## VIASH END - -print(">> Load data") -adata = sc.read_h5ad(par['input']) - -print(">> Normalize data") -# libsize and sqrt L1 norm -sqrt_data = scprep.utils.matrix_transform(adata, np.sqrt) -# sqrt_L1, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) -# sqrt_L1 = sqrt_L1.tocsr() - -print(sqrt_data) - -# print(">> Store output in adata") -# adata.layers["sqrtnorm"] = lognorm -# adata.obs["norm_factor"] = norm["norm_factor"] -# adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") - -# print(">> Write data") -# adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/common/normalization/sqrt_L1/config.vsh.yaml b/src/datasets/normalization/sqrt_L1/config.vsh.yaml similarity index 100% rename from src/common/normalization/sqrt_L1/config.vsh.yaml rename to src/datasets/normalization/sqrt_L1/config.vsh.yaml diff --git a/src/datasets/normalization/sqrt_L1/script.py b/src/datasets/normalization/sqrt_L1/script.py new file mode 100644 index 0000000000..b5faf23536 --- /dev/null +++ b/src/datasets/normalization/sqrt_L1/script.py @@ -0,0 +1,31 @@ +import anndata as ad +import scprep +import numpy as np + +## VIASH START +par = { + 'input': "output_train.h5ad", + 'output': "output_norm.h5ad" +} +meta = { + "functionality_name": "normalize_sqrt_L1" +} +## VIASH END + +print(">> Load data") +adata = ad.read_h5ad(par['input']) + +print(">> Normalize data") +# libsize and sqrt L1 norm +sqrt_data = scprep.utils.matrix_transform(adata.X, np.sqrt) +sqrt_L1, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) +sqrt_L1 = sqrt_L1.tocsr() + +print(">> Store output in adata") +adata.layers["sqrtnorm"] = sqrt_L1 +adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") + +print(adata.to_df(layer="sqrtnorm")) + +print(">> Write data") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/denoising/api/anndata_denoised.yaml b/src/denoising/api/anndata_denoised.yaml new file mode 100644 index 0000000000..db7cdda740 --- /dev/null +++ b/src/denoising/api/anndata_denoised.yaml @@ -0,0 +1,24 @@ +type: file +description: "The denoised data" +example: "denoised.h5ad" +info: + short_description: "Denoised data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: string + name: n_counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: method_id + description: "A unique identifier for the method" + X: + - type: integer + description: denoised data \ No newline at end of file diff --git a/src/denoising/api/anndata_test.yaml b/src/denoising/api/anndata_test.yaml index 3026067d52..55c933409e 100644 --- a/src/denoising/api/anndata_test.yaml +++ b/src/denoising/api/anndata_test.yaml @@ -15,7 +15,4 @@ info: uns: - type: string name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the dataset" \ No newline at end of file diff --git a/src/denoising/api/anndata_train.yaml b/src/denoising/api/anndata_train.yaml index 71df73b898..803457ef73 100644 --- a/src/denoising/api/anndata_train.yaml +++ b/src/denoising/api/anndata_train.yaml @@ -15,7 +15,4 @@ info: uns: - type: string name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: raw_dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file + description: "A unique identifier for the dataset" \ No newline at end of file diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml new file mode 100644 index 0000000000..9cb99ae54b --- /dev/null +++ b/src/denoising/api/comp_method.yaml @@ -0,0 +1,61 @@ +functionality: + arguments: + - name: "--input_train" + __inherits__: anndata_train.yaml + - name: "--input_test" + __inherits__: anndata_test.yaml + - name: "--output" + __inherits__: anndata_denoised.yaml + direction: output + # TODO: currently needs to be manually specified since the default value needs to be overrideable + # - name: "--layer_input" + # type: string + # default: "log_cpm" + # description: Which layer to use as input. + # test_resources: + # - path: ../../../../resources_test/label_projection/pancreas + # - type: python_script + # path: generic_test.py + # text: | + # import anndata as ad + # import subprocess + # from os import path + + # input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" + # input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" + # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" + # output_path = "output.h5ad" + + # cmd = [ + # meta['executable'], + # "--input_train", input_train_path, + # "--input_test", input_test_path, + # "--output", output_path + # ] + + # # todo: if we could access the viash config, we could check whether + # # .functionality.info.type == "positive_control" + # if meta['functionality_name'] == 'true_labels': + # cmd = cmd + ["--input_solution", input_solution_path] + + # print(">> Running script as test") + # out = subprocess.check_output(cmd).decode("utf-8") + + # print(">> Checking whether output file exists") + # assert path.exists(output_path) + + # print(">> Reading h5ad files") + # input_test = ad.read_h5ad(input_test_path) + # output = ad.read_h5ad(output_path) + # print("input_test:", input_test) + # print("output:", output) + + # print(">> Checking whether predictions were added") + # assert "label_pred" in output.obs + # assert meta['functionality_name'] == output.uns["method_id"] + + # print("Checking whether data from input was copied properly to output") + # assert input_test.n_obs == output.n_obs + # assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + + # print("All checks succeeded!") diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/data_processing/split_data/script.py index 785e0d59b1..37f51c8241 100644 --- a/src/denoising/data_processing/split_data/script.py +++ b/src/denoising/data_processing/split_data/script.py @@ -25,7 +25,13 @@ adata = sc.read_h5ad(par["input"]) -X = adata.layers["counts"] +# remove all layers except for counts +for key in list(adata.layers.keys()): + if key != "counts": + del adata.layers[key] + +adata.X = adata.layers["counts"] +X = adata.X # for test purposes X = X.round() @@ -42,25 +48,33 @@ X, 0.9, 0.0, random_state ) +# Remove no cells that do not have enough reads +is_missing = X_train.sum(axis=0) == 0 +X_train, X_test = X_train[:, ~is_missing], X_test[:, ~is_missing] +# copy adata to train_set, test_set -# copy adata to train_set, test_set - -output_train = adata +output_train = adata[:, ~is_missing].copy() +del output_train.layers["counts"] output_train.layers["counts"] = scipy.sparse.csr_matrix(X_train).astype(float) -output_test = adata +output_test = adata[:, ~is_missing].copy() +del output_test.layers["counts"] output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) -# TODO: remove cells which have not enough reads + +# NOTE: remove cells which have not enough reads -> is it possible to remove same cells/genes in test set as in train set a above ? # * first, remove genes with 0 expression # * then, remove cells with 1 count or less -# TODO: remove zero entries -> uncertain how this is done. below code gives error that matrix size is different -# is_missing = output_train.layers["counts"].sum(axis=0) == 0 -# output_train.layers["counts"], output_test.layers["counts"] = output_train.layers["counts"][:, ~is_missing], output_test.layers["counts"][:, ~is_missing] +# def filter_genes_cells(adata): +# """Remove empty cells and genes.""" +# sc.pp.filter_genes(adata, min_cells=1) +# sc.pp.filter_cells(adata, min_counts=1) +# return adata + -# TODO: Remove other normalisation methods so that they can be recomputed later +# filter_genes_cells(output_train) print(">> Writing") diff --git a/src/denoising/methods/alra/alra.R b/src/denoising/methods/alra/alra.R new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml new file mode 100644 index 0000000000..770746784c --- /dev/null +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -0,0 +1,37 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + status: disabled + name: "alra" + namespace: "denoising/methods" + description: "" + info: + type: method + label: DCA + # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" + # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" + # paper_year: 2019 + paper_doi: "0.1038/s41467-018-07931-2" + code_url: "https://github.com/theislab/dca" + v1_url: /openproblems/tasks/denoising/methods/dca.py + v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. + - name: "--epochs" + type: "integer" + default: 300 + description: "Number of total epochs in training" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - "anndata>=0.8" + - dca==0.3.4 + - type: nextflow diff --git a/src/denoising/methods/alra/script.py b/src/denoising/methods/alra/script.py new file mode 100644 index 0000000000..8b13789179 --- /dev/null +++ b/src/denoising/methods/alra/script.py @@ -0,0 +1 @@ + diff --git a/src/denoising/methods/baseline/config.vsh.yaml b/src/denoising/methods/baseline/config.vsh.yaml new file mode 100644 index 0000000000..ede01f5469 --- /dev/null +++ b/src/denoising/methods/baseline/config.vsh.yaml @@ -0,0 +1,36 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "baseline" + namespace: "denoising/methods" + description: "baseline" + info: + type: method + label: baseline + # paper_name: "Molecular Cross-Validation for Single-Cell RNA-seq"" + # paper_url: "https://doi.org/10.1101/786269" + # paper_year: 2019 + paper_doi: "10.1101/786269" + code_url: "https://github.com/czbiohub/molecular-cross-validation" + v1_url: /openproblems/tasks/denoising/methods/baseline.py + v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 + arguments: + - name: "--layer_input" + type: string + default: "denoised" + description: "Which layer to use as input." + - name: "--baseline" + type: "string" + required: true + choices: ["no_denoising", "perfect_denoising"] + description: "wich baseline needs to be created" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - "anndata>=0.8" + - type: nextflow diff --git a/src/denoising/methods/baseline/script.py b/src/denoising/methods/baseline/script.py new file mode 100644 index 0000000000..e30d5c9c77 --- /dev/null +++ b/src/denoising/methods/baseline/script.py @@ -0,0 +1,35 @@ +import anndata as ad + +## VIASH START +par = { + 'input_train': 'output_train.h5ad', + 'input_test': 'output_test.h5ad', + 'output': 'output_baseline_PD.h5ad', + 'layer_input': 'counts', + 'baseline': 'perfect_denoising', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + + +output_denoised = input_train.copy() + +print("process data") +if par['baseline'] == "no_denoising": + """Do nothing.""" + output_denoised.layers["denoised"] = input_train.layers[par['layer_input']].toarray() + +elif par['baseline'] == "perfect_denoising": + """Cheat.""" + output_denoised.layers["denoised"] = input_test.layers[par['layer_input']].toarray() + +output_denoised.uns["method_id"] = meta['functionality_name'] + +print("Write Data") +output_denoised.write_h5ad(par['output'],compression="gzip") diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml new file mode 100644 index 0000000000..3e7f47884a --- /dev/null +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -0,0 +1,37 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + status: disabled + name: "dca" + namespace: "denoising/methods" + description: "Deep Count Autoencoder" + info: + type: method + label: DCA + # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" + # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" + # paper_year: 2019 + paper_doi: "0.1038/s41467-018-07931-2" + code_url: "https://github.com/theislab/dca" + v1_url: /openproblems/tasks/denoising/methods/dca.py + v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. + - name: "--epochs" + type: "integer" + default: 300 + description: "Number of total epochs in training" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - "anndata>=0.8" + - dca==0.3.4 + - type: nextflow diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py new file mode 100644 index 0000000000..2ac92cfde4 --- /dev/null +++ b/src/denoising/methods/dca/script.py @@ -0,0 +1,36 @@ +import anndata as ad +from dca.api import dca + +# NOTE: pickup later. DCA package uses old keras imports ? + +## VIASH START +par = { + 'input_train': 'output_train.h5ad', + 'output': 'output_dca.h5ad', + 'epochs': 300, +} +meta = { + 'functionality_name': 'dca', +} +## VIASH END + +print("load input data") +input_train = ad.read_h5ad(par['input_train']) + +print("process data") + +# make adata object with train counts +# run DCA +dca(input_train, epochs=par["epochs"]) + +# set denoised to Xmat +output_denoised = input_train.copy +output_denoised.X = input_train.X + +print("Writing data") +output_denoised.uns["method_id"] = meta['functionality_name'] +output_denoised.write_h5ad(par['output'], compression="gzip") + + + + diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml new file mode 100644 index 0000000000..51c92cbdc4 --- /dev/null +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -0,0 +1,34 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + status: disabled + name: "KNN_smoothing" + namespace: "denoising/methods" + description: "K-nearest neighbor smoothing" + info: + type: method + label: knn_smooth + # paper_name: "K-nearest neighbor smoothing for high-throughput" + # paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" + # paper_year: 2018 + paper_doi: "10.1101/217737" + code_url: "https://github.com/yanailab/knn-smoothing" + v1_url: /openproblems/tasks/denoising/methods/dca.py + v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + github: + - knn_smooth + - type: nextflow diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py new file mode 100644 index 0000000000..acc879e42b --- /dev/null +++ b/src/denoising/methods/knn_smoothing/script.py @@ -0,0 +1,27 @@ +import knn_smooth #NOTE: not a python package but just a py script on github +import numpy as np +import anndata as ad + +## VIASH START +par = { + 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', + 'output': 'output_knn.h5ad', + 'layer_input': 'counts' +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +input_train = ad.read_h5ad(par["input_train"]) + +print("process data") + +X = input_train.X.transpose().toarray() +output_denoised = input_train.copy() +output_denoised.X = (knn_smooth.knn_smoothing(X, k=10)).transpose() + +print("Writing data") +output_denoised.uns["method_id"] = par["functionality_name"] +output_denoised.write_h5ad(par["output"], compression="gzip") diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml new file mode 100644 index 0000000000..214fd1f893 --- /dev/null +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -0,0 +1,43 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "magic" + namespace: "denoising/methods" + description: "MAGIC: Markov affinity-based graph imputation of cells" + info: + type: method + label: magic + # paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" + # paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" + # paper_year: 2018 + paper_doi: "10.1016/j.cell.2018.05.061" + code_url: "https://github.com/KrishnaswamyLab/MAGIC" + v1_url: /openproblems/tasks/denoising/methods/magic.py + v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e + arguments: + - name: "--layer_input" + type: string + default: "counts" + description: Which layer to use as input. + - name: "--solver" + type: "string" + choices: ["exact", "approximate"] + description: Which solver to use. + required: true + - name: "--norm" + type: string + required: true + choices: ["sqrt", "log"] + description: Normalization method + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + - scprep + - magic + - type: nextflow diff --git a/src/denoising/methods/magic/script.py b/src/denoising/methods/magic/script.py new file mode 100644 index 0000000000..88b9dec39b --- /dev/null +++ b/src/denoising/methods/magic/script.py @@ -0,0 +1,53 @@ +import anndata as ad +import numpy as np +import scprep +from magic import MAGIC + + +## VIASH START +par = { + 'input_train': 'output_train.h5ad', + 'output': 'output_magic.h5ad', + 'layer_input': 'counts', + 'solver': 'exact', + 'norm': 'sqrt' +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + + +print("load data") +input_train = ad.read_h5ad(par['input_train']) + +normtype = par['norm'] + +if normtype == "sqrt": + norm_fn = np.sqrt + denorm_fn = np.square +elif normtype == "log": + norm_fn = np.log1p + denorm_fn = np.expm1 + +print("processing data") + +X, libsize = scprep.normalize.library_size_normalize( + input_train.layers[par['layer_input']], rescale=1, return_library_size=True +) + +X = scprep.utils.matrix_transform(X, norm_fn) +Y = MAGIC(solver=par['solver'], verbose=False).fit_transform( + X, genes="all_genes" +) + +Y = scprep.utils.matrix_transform(Y, denorm_fn) +Y = scprep.utils.matrix_vector_elementwise_multiply(Y, libsize, axis=0) + +output_denoised = input_train.copy() +output_denoised.uns["method_id"] = meta["functionality_name"] +output_denoised.layers["denoised"] = Y + +print("Writing Data") +output_denoised.write_h5ad(par['output'],compression="gzip") + From 88fe16e42a4c279dc8e3bb0175e8b64c209cb414 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 17 Nov 2022 15:33:03 +0100 Subject: [PATCH 0397/1233] Add metrics Former-commit-id: b00ea4389b4f8332e5bb1feb4550f5013fb36b94 --- src/denoising/api/anndata_score.yaml | 21 ++++++++ src/denoising/api/comp_metric.yaml | 48 +++++++++++++++++++ src/denoising/metrics/mse/config.vsh.yaml | 26 ++++++++++ src/denoising/metrics/mse/script.py | 48 +++++++++++++++++++ src/denoising/metrics/possion/config.vsh.yaml | 26 ++++++++++ src/denoising/metrics/possion/script.py | 37 ++++++++++++++ 6 files changed, 206 insertions(+) create mode 100644 src/denoising/api/anndata_score.yaml create mode 100644 src/denoising/api/comp_metric.yaml create mode 100644 src/denoising/metrics/mse/config.vsh.yaml create mode 100644 src/denoising/metrics/mse/script.py create mode 100644 src/denoising/metrics/possion/config.vsh.yaml create mode 100644 src/denoising/metrics/possion/script.py diff --git a/src/denoising/api/anndata_score.yaml b/src/denoising/api/anndata_score.yaml new file mode 100644 index 0000000000..a3f1af8399 --- /dev/null +++ b/src/denoising/api/anndata_score.yaml @@ -0,0 +1,21 @@ +type: file +description: "Metric score file" +example: "output.h5ad" +info: + short_description: "Score" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: method_id + description: "A unique identifier for the method" + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml new file mode 100644 index 0000000000..661cd82c03 --- /dev/null +++ b/src/denoising/api/comp_metric.yaml @@ -0,0 +1,48 @@ +functionality: + arguments: + - name: "--input_test" + __inherits__: anndata_test.yaml + - name: "--input_denoised" + __inherits__: anndata_denoised.yaml + - name: "--output" + __inherits__: anndata_score.yaml + direction: output + # test_resources: + # - path: ../../../../resources_test/label_projection/pancreas + # - type: python_script + # path: format_check.py + # text: | + # import anndata as ad + # import subprocess + # from os import path + + # input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" + # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" + # output_path = "output.h5ad" + + # cmd = [ + # meta['executable'], + # "--input_prediction", input_prediction_path, + # "--input_solution", input_solution_path, + # "--output", output_path + # ] + + # print(">> Running script as test") + # out = subprocess.check_output(cmd).decode("utf-8") + + # print(">> Checking whether output file exists") + # assert path.exists(output_path) + + # input_solution = ad.read_h5ad(input_solution_path) + # input_prediction = ad.read_h5ad(input_prediction_path) + # output = ad.read_h5ad(output_path) + + # print("Checking whether data from input was copied properly to output") + # assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] + # assert output.uns["method_id"] == input_prediction.uns["method_id"] + # assert output.uns["metric_ids"] is not None + # assert output.uns["metric_values"] is not None + + # # TODO: check whether the metric ids are all in .functionality.info + + # print("All checks succeeded!") diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml new file mode 100644 index 0000000000..af4f2a70d9 --- /dev/null +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -0,0 +1,26 @@ +__inherits__: ../../api/comp_metric.yaml +functionality: + name: "mse" + namespace: "denoising/metrics" + description: "Mean Squared Error." + info: + v1_url: openproblems/tasks/denoising/metrics/mse.py + v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 + metrics: + - id: mse + label: mse + description: Mean Squared Error + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scikit-learn + - "anndata>=0.8" + - scanpy + - scprep + - type: nextflow diff --git a/src/denoising/metrics/mse/script.py b/src/denoising/metrics/mse/script.py new file mode 100644 index 0000000000..d3278682c6 --- /dev/null +++ b/src/denoising/metrics/mse/script.py @@ -0,0 +1,48 @@ +import anndata as ad +import scanpy as sc +import sklearn.metrics +import scprep + + +## VIASH START +par = { + 'input_test': 'output_test.h5ad', + 'input_denoised': 'output_magic.h5ad', + 'output': 'output_mse.h5ad' +} +meta = { + 'functionality_name': 'mse' +} +## VIASH END + +print("Load data") +input_denoised = ad.read_h5ad(par['input_denoised']) +input_test = ad.read_h5ad(par['input_test']) + + +test_data = ad.AnnData(X=input_test.layers["counts"], obs=input_test.obs, var=input_test.var, dtype="float32") +denoised_data = ad.AnnData( X=input_denoised.layers["denoised"], obs=input_denoised.obs, var=input_denoised.var, dtype="float32") + +print("Normalize data") + +# scaling and transformation +target_sum = 10000 + +sc.pp.normalize_total(test_data, target_sum) +sc.pp.log1p(test_data) + +sc.pp.normalize_total(denoised_data, target_sum) +sc.pp.log1p(denoised_data) + +print("Compute mse value") +error = sklearn.metrics.mean_squared_error( + scprep.utils.toarray(test_data.X), denoised_data.X +) + +print("Store metric value") +input_denoised.uns["metric_ids"] = meta['functionality_name'] +input_denoised.uns["metric_values"] = error + +print("Write adata to file") +input_denoised.write_h5ad(par['output'], compression="gzip") + diff --git a/src/denoising/metrics/possion/config.vsh.yaml b/src/denoising/metrics/possion/config.vsh.yaml new file mode 100644 index 0000000000..7efa6d8e95 --- /dev/null +++ b/src/denoising/metrics/possion/config.vsh.yaml @@ -0,0 +1,26 @@ +__inherits__: ../../api/comp_metric.yaml +functionality: + name: "poisson" + namespace: "denoising/metrics" + description: "Poisson loss" + info: + v1_url: openproblems/tasks/denoising/metrics/poisson.py + v1_commit: 4524f7bbcc4ea94cfb4acf1bd7f7c93c1ba7d0c9 + metrics: + - id: poisson + label: poisson + description: poisson loss + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + - scprep + github: + - czbiohub/molecular-cross-validation + - type: nextflow diff --git a/src/denoising/metrics/possion/script.py b/src/denoising/metrics/possion/script.py new file mode 100644 index 0000000000..4a7efac1fa --- /dev/null +++ b/src/denoising/metrics/possion/script.py @@ -0,0 +1,37 @@ +import anndata as ad +import scprep +from molecular_cross_validation.mcv_sweep import poisson_nll_loss + +## VIASH START +par = { + 'input_denoised': 'output_magic.h5ad', + 'input_test': 'output_test.h5ad', + 'output': 'output_poisson.h5ad' +} +meta = { + 'functionality_name': 'poisson' +} +## VIASH END + +print("Load Data") +input_denoised = ad.read_h5ad(par['input_denoised']) +input_test = ad.read_h5ad(par['input_test']) + + +test_data = input_test.layers["counts"] +denoised_data = input_denoised.layers["denoised"] + +print("Compute metric value") +# scaling +initial_sum = input_denoised.layers["counts"].sum() +target_sum = test_data.sum() +denoised_data = denoised_data * target_sum / initial_sum + +error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) + +print("Store poission value") +input_denoised.uns["metric_ids"] = meta['functionality_name'] +input_denoised.uns["metric_values"] = error + +print("Write adata to file") +input_denoised.write_h5ad(par['output'], compression="gzip") From 1798756dc7e30840404524f1c36db4c97375fb46 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 17 Nov 2022 17:48:02 +0100 Subject: [PATCH 0398/1233] start workflow files Former-commit-id: f2634a296277645c4f42723c9782fd6481abca2a --- src/denoising/methods/magic/config.vsh.yaml | 2 +- src/denoising/workflows/run/config.vsh.yaml | 26 +++++++++++++++++++++ src/denoising/workflows/run/main.nf | 26 +++++++++++++++++++++ 3 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 src/denoising/workflows/run/config.vsh.yaml create mode 100644 src/denoising/workflows/run/main.nf diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 214fd1f893..87d4fda94c 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -39,5 +39,5 @@ platforms: packages: - "anndata>=0.8" - scprep - - magic + - magic-impute - type: nextflow diff --git a/src/denoising/workflows/run/config.vsh.yaml b/src/denoising/workflows/run/config.vsh.yaml new file mode 100644 index 0000000000..4c5bbab8c4 --- /dev/null +++ b/src/denoising/workflows/run/config.vsh.yaml @@ -0,0 +1,26 @@ +functionality: + name: "run_benchmark" + namespace: "denoising/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input_train" + type: "file" # todo: replace with includes + - name: "--input_test" + type: "file" # todo: replace with includes + - name: "--input_solution" + type: "file" # todo: replace with includes + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + # todo: fix inherits in nxf + # __inherits__: ../../api/anndata_raw_dataset.yaml + resources: + - type: nextflow_script + path: main.nf diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf new file mode 100644 index 0000000000..09c70b62a8 --- /dev/null +++ b/src/denoising/workflows/run/main.nf @@ -0,0 +1,26 @@ +nextflow.enable.dsl=2 + +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "target/nextflow" + +// import methods +include { baseline } from "$targetDir/denoising/methods/baseline/main_nf" +include { magic } from "$targetDir/denoising/methods/magic/main_nf" + + +// import metrics +include { mse } from "$targetDir/denoising/metrics/mse/main_nf" +include { poisson } from "$targetDir/denoising/metrics/poisson/main_nf" + +// import helper functions +include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +workflow { + helpMessage(config) + + viashChannel(params, config) + | run_wf +} \ No newline at end of file From eacd988e61af46fa28d0dc7279b6ba527a8b67f6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 21 Nov 2022 10:55:37 +0100 Subject: [PATCH 0399/1233] add split_data nextflow Former-commit-id: 6dd2588602e72fe7fd0f87fbb467961ec67051fb --- .../normalization/sqrt_L1/config.vsh.yaml | 2 +- src/denoising/api/comp_split_data.yaml | 2 +- .../split_data/config.vsh.yaml | 2 +- .../data_processing/split_data/params.yaml | 4 +++ .../split_data/run_nextflow.sh | 17 ++++++++++++ .../data_processing/split_data/script.py | 11 ++++---- src/denoising/workflows/run/main.nf | 26 ++++++++++++++++++- src/denoising/workflows/run/params.yaml | 4 +++ 8 files changed, 59 insertions(+), 9 deletions(-) create mode 100644 src/denoising/data_processing/split_data/params.yaml create mode 100644 src/denoising/data_processing/split_data/run_nextflow.sh create mode 100644 src/denoising/workflows/run/params.yaml diff --git a/src/datasets/normalization/sqrt_L1/config.vsh.yaml b/src/datasets/normalization/sqrt_L1/config.vsh.yaml index fc9e55432f..c815c7d491 100644 --- a/src/datasets/normalization/sqrt_L1/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_L1/config.vsh.yaml @@ -14,6 +14,6 @@ platforms: packages: - scanpy - scprep - - "anndata<0.8" + - "anndata>=0.8" - numpy - type: nextflow diff --git a/src/denoising/api/comp_split_data.yaml b/src/denoising/api/comp_split_data.yaml index 08682c23a0..97adbd9718 100644 --- a/src/denoising/api/comp_split_data.yaml +++ b/src/denoising/api/comp_split_data.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: ../../common/api/anndata_dataset.yaml + __inherits__: ../../datasets/api/anndata_dataset.yaml - name: "--output_train" __inherits__: anndata_train.yaml direction: output diff --git a/src/denoising/data_processing/split_data/config.vsh.yaml b/src/denoising/data_processing/split_data/config.vsh.yaml index f361a098a7..4b6ab76fbe 100644 --- a/src/denoising/data_processing/split_data/config.vsh.yaml +++ b/src/denoising/data_processing/split_data/config.vsh.yaml @@ -25,7 +25,7 @@ platforms: setup: - type: python packages: - - "anndata<0.8" + - "anndata>=0.8" - numpy - scipy github: diff --git a/src/denoising/data_processing/split_data/params.yaml b/src/denoising/data_processing/split_data/params.yaml new file mode 100644 index 0000000000..025d3946ba --- /dev/null +++ b/src/denoising/data_processing/split_data/params.yaml @@ -0,0 +1,4 @@ +param_list: +- id: pancreas + input: /home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad +seed: 123 diff --git a/src/denoising/data_processing/split_data/run_nextflow.sh b/src/denoising/data_processing/split_data/run_nextflow.sh new file mode 100644 index 0000000000..1eaa4b7af7 --- /dev/null +++ b/src/denoising/data_processing/split_data/run_nextflow.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script target/nextflow/denoising/data_processing/split_data/main.nf \ + -profile docker \ + -resume \ + -params-file src/denoising/data_processing/split_data/params.yaml \ + --publish_dir output/denoising/ \ No newline at end of file diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/data_processing/split_data/script.py index 37f51c8241..d8c3dfc4a2 100644 --- a/src/denoising/data_processing/split_data/script.py +++ b/src/denoising/data_processing/split_data/script.py @@ -5,9 +5,10 @@ ## VIASH START par = { - 'input': "resources_test/common/pancreas/dataset.h5ad", - 'output_train': "output_train.h5ad", - 'output_test': "output_test.h5ad", + 'input': "/home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad", + 'output_train': "output/nextflow/pancreas_split_data_output_train.h5d", + 'output_test': "output/nextflow/pancreas_split_data_output_test.h5d", + 'train_frac': 0.9, 'seed': 0 } meta = { @@ -31,7 +32,7 @@ del adata.layers[key] adata.X = adata.layers["counts"] -X = adata.X +X = np.array(adata.X) # for test purposes X = X.round() @@ -45,7 +46,7 @@ raise TypeError("Molecular cross-validation requires integer count data.") X_train, X_test = molecular_cross_validation.util.split_molecules( - X, 0.9, 0.0, random_state + X, par["train_frac"], 0.0, random_state ) # Remove no cells that do not have enough reads diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index 09c70b62a8..099ce55954 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -3,6 +3,9 @@ nextflow.enable.dsl=2 sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "target/nextflow" +//import data processing +include { split_data } from "$targetDir/denoising/data_processing/split_data/main.nf" + // import methods include { baseline } from "$targetDir/denoising/methods/baseline/main_nf" include { magic } from "$targetDir/denoising/methods/magic/main_nf" @@ -23,4 +26,25 @@ workflow { viashChannel(params, config) | run_wf -} \ No newline at end of file +} + +output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + method: ["input_train", "input_test"], + ) + + // run methods + | getWorkflowArguments(key: "method") + | ( + baseline & + magic + ) + | mix + + // construct tuples for metrics + | pmap{ id, file, passthrough -> + // derive unique ids from output filenames + def newId = file.getName().replaceAll(".output.*", "") + } \ No newline at end of file diff --git a/src/denoising/workflows/run/params.yaml b/src/denoising/workflows/run/params.yaml new file mode 100644 index 0000000000..3b0c0cb3a6 --- /dev/null +++ b/src/denoising/workflows/run/params.yaml @@ -0,0 +1,4 @@ +param_list: +- id: pancreas + input_train: output/nextflow/pancreas_split_data_output_train.h5d + input_test: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad From 092dfc5e51f9f538cc35e2ad6bdb62621d72387a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 21 Nov 2022 13:38:06 +0100 Subject: [PATCH 0400/1233] add seurat transferdata component Former-commit-id: 93ff3ea563211629f77ba3966df9181f56add811 --- .../seurat_transferdata/config.vsh.yaml | 29 +++++++ .../methods/seurat_transferdata/script.R | 79 +++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 src/label_projection/methods/seurat_transferdata/config.vsh.yaml create mode 100644 src/label_projection/methods/seurat_transferdata/script.R diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml new file mode 100644 index 0000000000..ac8a1ea039 --- /dev/null +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -0,0 +1,29 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "seurat_transferdata" + namespace: "label_projection/methods" + description: | + The Seurat v3 anchoring procedure is designed to integrate + diverse single-cell datasets across technologies and modalities. + info: + type: method + label: Seurat TransferData + paper_doi: "10.1101/460147" + code_url: "https://github.com/satijalab/seurat" + doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ Matrix, Seurat, rlang, anndata, bit64 ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/label_projection/methods/seurat_transferdata/script.R b/src/label_projection/methods/seurat_transferdata/script.R new file mode 100644 index 0000000000..d7539cdbc4 --- /dev/null +++ b/src/label_projection/methods/seurat_transferdata/script.R @@ -0,0 +1,79 @@ +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +requireNamespace("Seurat", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE) +library(magrittr, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input_train = "resources_test/label_projection/pancreas/train.h5ad", + input_test = "resources_test/label_projection/pancreas/test.h5ad", + output = "output.h5ad" +) +## VIASH END + +cat(">> Load input data\n") +input_train <- read_h5ad(par$input_train) +input_test <- read_h5ad(par$input_test) + +# sce_train <- zellkonverter::readH5AD(par$input_train) +# obj_train <- Seurat::as.Seurat(sce_train, data = "normalized") +# sce_test <- zellkonverter::readH5AD(par$input_test) +# obj_test <- Seurat::as.Seurat(sce_test, data = "normalized") + +cat(">> Converting AnnData to Seurat\n") +anndataToSeurat <- function(adata) { + # interpreted from https://github.com/satijalab/seurat/blob/v3.1.0/R/objects.R + obj <- + SeuratObject::CreateSeuratObject( + counts = as(Matrix::t(adata$layers[["counts"]]), "CsparseMatrix") + ) %>% + SeuratObject::SetAssayData( + slot = "data", + new.data = as(Matrix::t(adata$layers[["normalized"]]), "CsparseMatrix") + ) %>% + SeuratObject::AddMetaData( + adata$obs + ) + + # set hvg + SeuratObject::VariableFeatures(obj) <- adata$var_names[adata$var[["hvg"]]] + + # set embedding + # could add loadings and stdev + embed <- SeuratObject::CreateDimReducObject( + embeddings = adata$obsm[["X_pca"]], + key = "PC_" + ) + obj[["pca"]] <- embed + + # return + obj +} + +obj_train <- anndataToSeurat(input_train) +obj_test <- anndataToSeurat(input_test) + +cat(">> Find transfer anchors\n") +npcs <- ncol(obj_train[["pca"]]) +anchors <- Seurat::FindTransferAnchors( + reference = obj_train, + query = obj_test, + npcs = npcs, + dims = seq_len(npcs), + verbose = FALSE +) + +cat(">> Predict on test data\n") +query <- Seurat::TransferData( + anchorset = anchors, + reference = obj_train, + query = obj_test, + refdata = list(labels = "label"), + verbose = FALSE +) +input_test$obs[["label_pred"]] <- query$predicted.labels[input_test$obs_names] + +cat(">> Write output to file\n") +input_test$uns[["method_id"]] <- meta[["functionality_name"]] +input_test$write_h5ad(par$output, compression = "gzip") From 99935999860225216870a1a3b0a2be42231c72ea Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 21 Nov 2022 13:38:57 +0100 Subject: [PATCH 0401/1233] add project config Former-commit-id: 12d1f8d1c97ed9e68a98a72bb14828e536363d13 --- _viash.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 _viash.yaml diff --git a/_viash.yaml b/_viash.yaml new file mode 100644 index 0000000000..3ffa165c48 --- /dev/null +++ b/_viash.yaml @@ -0,0 +1,8 @@ +source: src +target: target + +config_mods: | + .functionality.version := 'dev' + .platforms[.type == 'docker'].target_registry := 'ghcr.io' + .platforms[.type == 'docker'].target_organization := 'openproblems-bio' + .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems-v2' \ No newline at end of file From 6273759e52cb409e624c686dd827106b64a82a3d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 21 Nov 2022 13:43:20 +0100 Subject: [PATCH 0402/1233] add seurat to pipeline Former-commit-id: 6ab694bec05758a7b2c11afdfbc153aa4ab31f3c --- src/label_projection/workflows/run/main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index b4d7c39c32..77303183e0 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -13,6 +13,7 @@ include { knn } from "$targetDir/label_projection/methods/knn/main.nf" include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" +include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" // include { scarches } from "$targetDir/label_projection/methods/scarches/main.nf" // import metrics @@ -67,7 +68,8 @@ workflow run_wf { knn.run(filter: {it[1].normalization_id == "log_cpm"}) & logistic_regression.run(filter: {it[1].normalization_id == "log_cpm"}) & mlp.run(filter: {it[1].normalization_id == "log_cpm"}) & - scanvi.run(filter: {it[1].normalization_id == "log_cpm"}) + scanvi.run(filter: {it[1].normalization_id == "log_cpm"}) & + seurat_transferdata.run(filter: {it[1].normalization_id == "log_cpm"}) ) | mix From 441bdb5148935b8fad07aecaf5e145afd24a7142 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 06:25:37 +0100 Subject: [PATCH 0403/1233] add xgboost Former-commit-id: 49307590ffd122d28e7f0d6a30908002fe070f42 --- .../methods/xgboost/config.vsh.yaml | 28 +++++++++++++ .../methods/xgboost/script.py | 39 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 src/label_projection/methods/xgboost/config.vsh.yaml create mode 100644 src/label_projection/methods/xgboost/script.py diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml new file mode 100644 index 0000000000..041f9fe96f --- /dev/null +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -0,0 +1,28 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "xgboost" + namespace: "label_projection/methods" + description: "XGBoost: A Scalable Tree Boosting System" + info: + type: method + label: XGBoost + paper_doi: 10.1145/2939672.2939785 + code_url: "https://github.com/dmlc/xgboost" + doc_url: "https://xgboost.readthedocs.io/en/stable/index.html" + v1_url: openproblems/tasks/label_projection/methods/xgboost.py + v1_commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c + preferred_normalization: log_cpm + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + - xgboost + - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/label_projection/methods/xgboost/script.py b/src/label_projection/methods/xgboost/script.py new file mode 100644 index 0000000000..c56eae59d5 --- /dev/null +++ b/src/label_projection/methods/xgboost/script.py @@ -0,0 +1,39 @@ +import anndata as ad +import xgboost as xgb + +## VIASH START +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data", flush=True) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) +input_layer = "normalized" + +print("Transform into integers", flush=True) +input_train.obs["label_int"] = input_train.obs["label"].cat.codes +categories = input_train.obs["label"].cat.categories + +print("Convert AnnDatas into datasets", flush=True) +xg_train = xgb.DMatrix(input_train.layers[input_layer], label=input_train.obs["label_int"]) +xg_test = xgb.DMatrix(input_test.layers[input_layer]) + +print("Fit on train data", flush=True) +param = {'objective': 'multi:softmax', 'num_class': len(categories)} +watchlist = [(xg_train, "train")] +xgb_op = xgb.train(param, xg_train, evals=watchlist) + +print("Predict on test data", flush=True) +pred = xgb_op.predict(xg_test).astype(int) +input_test.obs["label_pred"] = categories[pred] + +print("Write output to file", flush=True) +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 58b8f6b6c6e366c4151ff7992a0bd996974518e6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 06:44:27 +0100 Subject: [PATCH 0404/1233] refactor scanvi based on docs Former-commit-id: ba57510c8b93facee5bab6a7d4d9903c0527b72d --- .../methods/scanvi/config.vsh.yaml | 9 +-- src/label_projection/methods/scanvi/script.py | 55 +++++++++++-------- 2 files changed, 34 insertions(+), 30 deletions(-) diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index b8ca261988..9259ea4b22 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -7,9 +7,10 @@ functionality: transcriptomics data with deep generative models. info: type: method - label: scANVI + label: SCANVI paper_doi: "10.1101/2020.07.16.205997" code_url: "https://github.com/YosefLab/scvi-tools" + doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html arguments: - name: "--hvg" type: boolean @@ -26,12 +27,6 @@ platforms: packages: - "anndata>=0.8" - scvi-tools - # image: "python:3.10" - # setup: - # - type: python - # packages: - # - "anndata>=0.8" - # - scvi-tools - type: nextflow directives: label: [ midmem, highcpu, gpu ] diff --git a/src/label_projection/methods/scanvi/script.py b/src/label_projection/methods/scanvi/script.py index 09ae1b02ee..18a6580f12 100644 --- a/src/label_projection/methods/scanvi/script.py +++ b/src/label_projection/methods/scanvi/script.py @@ -1,6 +1,9 @@ import anndata as ad -import scvi +import scarches as sca + +# followed procedure from here: +# https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html ## VIASH START par = { @@ -14,46 +17,52 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train_orig = ad.read_h5ad(par['input_train']) input_test_orig = ad.read_h5ad(par['input_test']) -print("Subsetting to HVG") -input_train = input_train_orig[:,input_train_orig.var['hvg']] -input_test = input_test_orig[:,input_test_orig.var['hvg']] +if par["hvg"]: + print("Subsetting to HVG", flush=True) + input_train = input_train_orig[:,input_train_orig.var['hvg']] + input_test = input_test_orig[:,input_test_orig.var['hvg']] +else: + input_train = input_train_orig + input_test = input_test_orig -print("Concatenating train and test data") +print("Concatenating train and test data", flush=True) input_train.obs['is_test'] = False input_test.obs['is_test'] = True input_test.obs['label'] = "Unknown" adata = ad.concat([input_train, input_test], merge = "same") -print("Setting up adata object") -adata.obs["scanvi_label"] = adata.obs["label"].to_numpy() -scvi.model.SCVI.setup_anndata( +print("Create SCANVI model and train it on fully labelled reference dataset", flush=True) +sca.models.SCVI.setup_anndata( adata, - batch_key="batch", - labels_key="scanvi_label", + batch_key="batch", + labels_key="label", layer="normalized" ) -print("Train SCVI model") -train_kwargs = dict( - train_size=0.9, - early_stopping=True, +vae = sca.models.SCVI( + adata, + n_layers=2, + encode_covariates=True, + deeply_inject_covariates=False, + use_layer_norm="both", + use_batch_norm="none", ) -scvi_model = scvi.model.SCVI(adata) -scvi_model.train(**train_kwargs) -print("Train SCANVI model") -model = scvi.model.SCANVI.from_scvi_model(scvi_model, unlabeled_category="Unknown") -model.train(**train_kwargs) +print("Create the SCANVI model instance with ZINB loss", flush=True) +scanvae = sca.models.SCANVI.from_scvi_model(vae, unlabeled_category = "Unknown") + +print("Train SCANVI model", flush=True) +scanvae.train() -print("Make predictions") -preds = model.predict(adata) +print("Make predictions", flush=True) +preds = scanvae.predict(adata) input_test_orig.obs["label_pred"] = preds[adata.obs['is_test'].values] -print("Write output to file") +print("Write output to file", flush=True) input_test_orig.uns["method_id"] = meta["functionality_name"] input_test_orig.write_h5ad(par['output'], compression="gzip") From 647d8df43676d270c6b14526e58f672a221a3f7f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 07:19:15 +0100 Subject: [PATCH 0405/1233] update metadata Former-commit-id: 699d4acb68f640a7a7de0ae6c246c1bc9c3487eb --- src/label_projection/methods/knn/config.vsh.yaml | 3 ++- .../methods/logistic_regression/config.vsh.yaml | 14 +++++--------- src/label_projection/methods/mlp/config.vsh.yaml | 3 ++- .../methods/scanvi/config.vsh.yaml | 3 +++ .../methods/seurat_transferdata/config.vsh.yaml | 3 +++ 5 files changed, 15 insertions(+), 11 deletions(-) diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 6c84270856..4a10110638 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -10,7 +10,8 @@ functionality: # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" # paper_year: 1967 paper_doi: "10.1109/TIT.1967.1053964" - code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" + code_url: https://github.com/scikit-learn/scikit-learn + doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d preferred_normalization: log_cpm diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 75455cea94..d6c44ec918 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -6,18 +6,14 @@ functionality: info: type: method label: Logistic Regression - # paper_name: "Applied Logistic Regression" - # paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" - # paper_year: 2013 - code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" + paper_name: "Applied Logistic Regression" + paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" + paper_year: 2013 + code_url: https://github.com/scikit-learn/scikit-learn + doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d preferred_normalization: log_cpm - arguments: - - name: "--max_iter" - type: "integer" - default: 1000 - description: "Maximum number of iterations" resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 6eb3c210aa..8fe92afca3 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -10,7 +10,8 @@ functionality: # paper_url: "https://doi.org/10.1016/0004-3702(89)90049-0" # paper_year: 1990 paper_doi: "10.1016/0004-3702(89)90049-0" - code_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" + code_url: https://github.com/scikit-learn/scikit-learn + doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1_url: openproblems/tasks/label_projection/methods/mlp.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 9259ea4b22..af029abfc7 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -11,6 +11,9 @@ functionality: paper_doi: "10.1101/2020.07.16.205997" code_url: "https://github.com/YosefLab/scvi-tools" doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html + v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py + v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + preferred_normalization: log_cpm arguments: - name: "--hvg" type: boolean diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index ac8a1ea039..8e66120b4f 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -11,6 +11,9 @@ functionality: paper_doi: "10.1101/460147" code_url: "https://github.com/satijalab/seurat" doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" + v1_url: openproblems/tasks/label_projection/methods/seurat.py + v1_commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 + preferred_normalization: log_cpm resources: - type: r_script path: script.R From fa303512e426c13870d32bdf01e1c1a346e58dd3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 07:20:01 +0100 Subject: [PATCH 0406/1233] simplify sklearn-based components Former-commit-id: 171658eb6d7c3a85ac716335f7da4535a1315c55 --- src/label_projection/methods/knn/script.py | 35 ++---------------- .../methods/logistic_regression/script.py | 37 ++----------------- src/label_projection/methods/mlp/script.py | 35 ++---------------- 3 files changed, 9 insertions(+), 98 deletions(-) diff --git a/src/label_projection/methods/knn/script.py b/src/label_projection/methods/knn/script.py index fe2ebb3e92..54eb74a68f 100644 --- a/src/label_projection/methods/knn/script.py +++ b/src/label_projection/methods/knn/script.py @@ -1,9 +1,5 @@ import anndata as ad import sklearn.neighbors -import sklearn.pipeline -import sklearn.preprocessing -import sklearn.decomposition -import scipy.sparse ## VIASH START par = { @@ -20,38 +16,13 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = "normalized" - -print("Set up classifier pipeline") -def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) - - min_components = min( - [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] - ) - if is_sparse: - min_components -= 1 - n_components = min([n_components, min_components]) - if is_sparse: - pca_op = sklearn.decomposition.TruncatedSVD - else: - pca_op = sklearn.decomposition.PCA - return pca_op(n_components=n_components) - -classifier = sklearn.neighbors.KNeighborsClassifier() -pipeline = sklearn.pipeline.Pipeline( - [ - ("pca", pca_op(input_train, input_test, n_components=100)), - ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), - ("regression", classifier), - ] -) print("Fit to train data") -pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) +classifier = sklearn.neighbors.KNeighborsClassifier() +classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) +input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index e44fa598c0..cee2268ba4 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -1,9 +1,5 @@ import anndata as ad import sklearn.linear_model -import sklearn.pipeline -import sklearn.preprocessing -import sklearn.decomposition -import scipy.sparse ## VIASH START par = { @@ -20,40 +16,13 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = "normalized" - -print("Set up classifier pipeline") -def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) - - min_components = min( - [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] - ) - if is_sparse: - min_components -= 1 - n_components = min([n_components, min_components]) - if is_sparse: - pca_op = sklearn.decomposition.TruncatedSVD - else: - pca_op = sklearn.decomposition.PCA - return pca_op(n_components=n_components) - -classifier = sklearn.linear_model.LogisticRegression( - max_iter=par["max_iter"] -) -pipeline = sklearn.pipeline.Pipeline( - [ - ("pca", pca_op(input_train, input_test, n_components=100)), - ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), - ("regression", classifier), - ] -) print("Fit to train data") -pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) +classifier = sklearn.linear_model.LogisticRegression() +classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) +input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index 7283197010..e5547953ac 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -1,9 +1,5 @@ import anndata as ad from sklearn.neural_network import MLPClassifier -import sklearn.pipeline -import sklearn.preprocessing -import sklearn.decomposition -import scipy.sparse ## VIASH START par = { @@ -20,41 +16,16 @@ print("Load input data") input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -input_layer = "normalized" - -print("Set up classifier pipeline") -def pca_op(adata_train, adata_test, n_components=100): - is_sparse = scipy.sparse.issparse(adata_train.layers[input_layer]) - - min_components = min( - [adata_train.n_obs, adata_test.n_obs, adata_train.n_vars] - ) - if is_sparse: - min_components -= 1 - n_components = min([n_components, min_components]) - if is_sparse: - pca_op = sklearn.decomposition.TruncatedSVD - else: - pca_op = sklearn.decomposition.PCA - return pca_op(n_components=n_components) +print("Fit to train data") classifier = MLPClassifier( max_iter=par["max_iter"], hidden_layer_sizes=tuple(par["hidden_layer_sizes"]) ) -pipeline = sklearn.pipeline.Pipeline( - [ - ("pca", pca_op(input_train, input_test, n_components=100)), - ("scaler", sklearn.preprocessing.StandardScaler(with_mean=True)), - ("regression", classifier), - ] -) - -print("Fit to train data") -pipeline.fit(input_train.layers[input_layer], input_train.obs["label"].astype(str)) +classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) print("Predict on test data") -input_test.obs["label_pred"] = pipeline.predict(input_test.layers[input_layer]) +input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) print("Write output to file") input_test.uns["method_id"] = meta["functionality_name"] From 078358741585fe89774bdd365cf6465916d004b5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 07:20:10 +0100 Subject: [PATCH 0407/1233] update pipelines Former-commit-id: 988bcb4c84fbb6684c242ab78c054941e540a185 --- .../workflows/process_openproblems_v1/config.vsh.yaml | 2 ++ src/label_projection/analysis_scripts/script.R | 4 ++-- src/label_projection/workflows/run/config.vsh.yaml | 6 ++++++ src/label_projection/workflows/run/main.nf | 5 +++-- 4 files changed, 13 insertions(+), 4 deletions(-) diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 64db3042a8..55f57f212f 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -69,3 +69,5 @@ functionality: # - type: nextflow_script # path: main.nf # entrypoint: test_wf +platforms: + - type: nextflow diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index 5d09be3d6a..f86530ead6 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -67,7 +67,7 @@ metric_info <- map_df(ns_list_metrics, function(conf) { # get data table ranking <- scores %>% left_join(metric_info %>% select(metric_id = id, maximise), by = "metric_id") %>% - left_join(method_info %>% select(method_id = id, method_label = label), by = "method_id") %>% + inner_join(method_info %>% select(method_id = id, method_label = label), by = "method_id") %>% group_by(metric_id, dataset_id) %>% mutate(rank = rank(ifelse(maximise, -metric_value, metric_value))) %>% ungroup() %>% @@ -79,7 +79,7 @@ df <- method_info %>% select(id, type, label) %>% rename_all(function(x) paste0("method_", x)) %>% - left_join(scores %>% spread(metric_id, metric_value), by = "method_id") %>% + inner_join(scores %>% spread(metric_id, metric_value), by = "method_id") %>% left_join(execution_info, by = c("dataset_id", "method_id")) %>% mutate(method_label = factor(method_label, levels = rev(ranking$method_label))) %>% arrange(method_label) diff --git a/src/label_projection/workflows/run/config.vsh.yaml b/src/label_projection/workflows/run/config.vsh.yaml index 23a2d1ca51..395a3333ba 100644 --- a/src/label_projection/workflows/run/config.vsh.yaml +++ b/src/label_projection/workflows/run/config.vsh.yaml @@ -31,3 +31,9 @@ functionality: resources: - type: nextflow_script path: main.nf + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 77303183e0..b2949b3861 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -14,7 +14,7 @@ include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" -// include { scarches } from "$targetDir/label_projection/methods/scarches/main.nf" +include { xgboost } from "$targetDir/label_projection/methods/xgboost/main.nf" // import metrics include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" @@ -69,7 +69,8 @@ workflow run_wf { logistic_regression.run(filter: {it[1].normalization_id == "log_cpm"}) & mlp.run(filter: {it[1].normalization_id == "log_cpm"}) & scanvi.run(filter: {it[1].normalization_id == "log_cpm"}) & - seurat_transferdata.run(filter: {it[1].normalization_id == "log_cpm"}) + seurat_transferdata.run(filter: {it[1].normalization_id == "log_cpm"}) & + xgboost.run(filter: {it[1].normalization_id == "log_cpm"}) ) | mix From 125000fb48b9a52b90f3093843089fb7455365cc Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 07:22:52 +0100 Subject: [PATCH 0408/1233] fix scarches setup Former-commit-id: 9de87d33fd8ffb82b271556bc7de9d0f5c48033b --- src/label_projection/methods/scanvi/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index af029abfc7..32e7840222 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -29,7 +29,7 @@ platforms: - type: python packages: - "anndata>=0.8" - - scvi-tools + - scarches - type: nextflow directives: label: [ midmem, highcpu, gpu ] From 4412be53d38814aa60ee823f44a36090ad4f01df Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 07:23:09 +0100 Subject: [PATCH 0409/1233] update changelog Former-commit-id: 6260682718e7e82a1edf28383daa51df922b1b32 --- CHANGELOG.md | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e5fdaad92..28b2f2eb2a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,14 +32,18 @@ * `methods/mlp`: Migrated from v1. +* `methods/scanvi`: Migrated and adapted from v1. + +* `methods/seurat_transferdata`: Migrated and adapted from v1. + +* `methods/xgboost`: Migrated from v1. + * `control_methods/majority_vote`: Migrated from v1. * `control_methods/random_labels`: Migrated from v1. * `control_methods/true_labels`: Migrated from v1. -* Temporarily disable `scanvi` / `scarches_scanvi`. - * `metric/accuracy`: Migrated from v1. * `metric/f1`: Migrated from v1. From a5aedd714425df72e2d9eabe8e94346e8fa0f6cf Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 22 Nov 2022 11:15:26 +0100 Subject: [PATCH 0410/1233] update files for nextflow setup Former-commit-id: bf3f7bcea0eb9c366a0c42bcf2054e715e0b2e6a --- src/denoising/api/anndata_dataset.yaml | 18 ++++++++++++++++++ src/denoising/api/comp_split_data.yaml | 2 +- .../data_processing/split_data/script.py | 4 ++-- src/denoising/methods/magic/config.vsh.yaml | 2 ++ src/denoising/workflows/run/nextflow.config | 7 +++++++ src/denoising/workflows/run/params.yaml | 4 ++-- src/denoising/workflows/run/run_nextflow.sh | 16 ++++++++++++++++ 7 files changed, 48 insertions(+), 5 deletions(-) create mode 100644 src/denoising/api/anndata_dataset.yaml create mode 100644 src/denoising/workflows/run/nextflow.config create mode 100644 src/denoising/workflows/run/run_nextflow.sh diff --git a/src/denoising/api/anndata_dataset.yaml b/src/denoising/api/anndata_dataset.yaml new file mode 100644 index 0000000000..7da5339137 --- /dev/null +++ b/src/denoising/api/anndata_dataset.yaml @@ -0,0 +1,18 @@ +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + obs: + - type: integer + name: n_counts + description: raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" diff --git a/src/denoising/api/comp_split_data.yaml b/src/denoising/api/comp_split_data.yaml index 97adbd9718..5108b6094e 100644 --- a/src/denoising/api/comp_split_data.yaml +++ b/src/denoising/api/comp_split_data.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: ../../datasets/api/anndata_dataset.yaml + __inherits__: anndata_dataset.yaml - name: "--output_train" __inherits__: anndata_train.yaml direction: output diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/data_processing/split_data/script.py index d8c3dfc4a2..6b8ab1ba7f 100644 --- a/src/denoising/data_processing/split_data/script.py +++ b/src/denoising/data_processing/split_data/script.py @@ -6,8 +6,8 @@ ## VIASH START par = { 'input': "/home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad", - 'output_train': "output/nextflow/pancreas_split_data_output_train.h5d", - 'output_test': "output/nextflow/pancreas_split_data_output_test.h5d", + 'output_train': "output/nextflow/pancreas_split_data_output_train.h5ad", + 'output_test': "output/nextflow/pancreas_split_data_output_test.h5ad", 'train_frac': 0.9, 'seed': 0 } diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 87d4fda94c..4c2beb62fc 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -21,12 +21,14 @@ functionality: - name: "--solver" type: "string" choices: ["exact", "approximate"] + default: "exact" description: Which solver to use. required: true - name: "--norm" type: string required: true choices: ["sqrt", "log"] + default: "sqrt" description: Normalization method resources: - type: python_script diff --git a/src/denoising/workflows/run/nextflow.config b/src/denoising/workflows/run/nextflow.config new file mode 100644 index 0000000000..5ded7de645 --- /dev/null +++ b/src/denoising/workflows/run/nextflow.config @@ -0,0 +1,7 @@ +manifest { + nextflowVersion = '!>=22.04.5' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} \ No newline at end of file diff --git a/src/denoising/workflows/run/params.yaml b/src/denoising/workflows/run/params.yaml index 3b0c0cb3a6..e865650cf5 100644 --- a/src/denoising/workflows/run/params.yaml +++ b/src/denoising/workflows/run/params.yaml @@ -1,4 +1,4 @@ param_list: - id: pancreas - input_train: output/nextflow/pancreas_split_data_output_train.h5d - input_test: resources/label_projection/openproblems_v1/pancreas.split_dataset.output_test.h5ad + input_train: output/denoising/pancreas.split_data.output_train.h5ad + input_test: output/denoising/pancreas.split_data.output_test.h5ad diff --git a/src/denoising/workflows/run/run_nextflow.sh b/src/denoising/workflows/run/run_nextflow.sh new file mode 100644 index 0000000000..d61d3f5780 --- /dev/null +++ b/src/denoising/workflows/run/run_nextflow.sh @@ -0,0 +1,16 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/denoising/workflows/run/main.nf \ + -resume \ + -params-file src/denoising/workflows/run/params.yaml \ + --publish_dir output/denoising/ \ No newline at end of file From 992b822d634132a6cc76b547b998399b12ef01c0 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 22 Nov 2022 11:18:49 +0100 Subject: [PATCH 0411/1233] add preferred normalization Former-commit-id: 65e8e8422e5e539d64eac98a16d470262a6c5364 --- src/denoising/methods/baseline/config.vsh.yaml | 4 +++- src/denoising/methods/magic/config.vsh.yaml | 5 +---- src/denoising/methods/magic/script.py | 3 +-- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/denoising/methods/baseline/config.vsh.yaml b/src/denoising/methods/baseline/config.vsh.yaml index ede01f5469..b9cce756e0 100644 --- a/src/denoising/methods/baseline/config.vsh.yaml +++ b/src/denoising/methods/baseline/config.vsh.yaml @@ -13,15 +13,17 @@ functionality: code_url: "https://github.com/czbiohub/molecular-cross-validation" v1_url: /openproblems/tasks/denoising/methods/baseline.py v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 + preferred_normalization: counts arguments: - name: "--layer_input" type: string - default: "denoised" + default: "counts" description: "Which layer to use as input." - name: "--baseline" type: "string" required: true choices: ["no_denoising", "perfect_denoising"] + default: "perfect_denoising" description: "wich baseline needs to be created" resources: - type: python_script diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 4c2beb62fc..268db5af8b 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -13,11 +13,8 @@ functionality: code_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: /openproblems/tasks/denoising/methods/magic.py v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e + preferred_normalization: counts arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. - name: "--solver" type: "string" choices: ["exact", "approximate"] diff --git a/src/denoising/methods/magic/script.py b/src/denoising/methods/magic/script.py index 88b9dec39b..d2b3840364 100644 --- a/src/denoising/methods/magic/script.py +++ b/src/denoising/methods/magic/script.py @@ -8,7 +8,6 @@ par = { 'input_train': 'output_train.h5ad', 'output': 'output_magic.h5ad', - 'layer_input': 'counts', 'solver': 'exact', 'norm': 'sqrt' } @@ -33,7 +32,7 @@ print("processing data") X, libsize = scprep.normalize.library_size_normalize( - input_train.layers[par['layer_input']], rescale=1, return_library_size=True + input_train.layers[par['counts']], rescale=1, return_library_size=True ) X = scprep.utils.matrix_transform(X, norm_fn) From 6354bb7a89cc9811d645cfc4e3c8c5ff549e5d7a Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 13:36:02 +0100 Subject: [PATCH 0412/1233] readapt api files to store normalized data Former-commit-id: ad19fda1637f6f1aaf76bcd9eb9b0ef70993815f --- .../api/anndata_dataset.yaml | 63 +++++++++++++++++++ .../api/anndata_reduced.yaml | 43 +++++++++++-- .../api/anndata_score.yaml | 13 ++-- 3 files changed, 109 insertions(+), 10 deletions(-) create mode 100644 src/dimensionality_reduction/api/anndata_dataset.yaml diff --git a/src/dimensionality_reduction/api/anndata_dataset.yaml b/src/dimensionality_reduction/api/anndata_dataset.yaml new file mode 100644 index 0000000000..d698890866 --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_dataset.yaml @@ -0,0 +1,63 @@ +type: file +description: "A normalised data with a PCA embedding and HVG selection" +example: "dataset.h5ad" +info: + label: "Dataset+PCA+HVG" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalization method, if any. + required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: double + name: pca_variance + description: The PCA variance objects. + required: true diff --git a/src/dimensionality_reduction/api/anndata_reduced.yaml b/src/dimensionality_reduction/api/anndata_reduced.yaml index de772c35ec..4da063c3d3 100644 --- a/src/dimensionality_reduction/api/anndata_reduced.yaml +++ b/src/dimensionality_reduction/api/anndata_reduced.yaml @@ -2,16 +2,46 @@ type: file description: "A dimensionality reduced dataset" example: "reduced.h5ad" info: - short_description: "2D reduced" + label: "Dataset+HVG+X_emb" slots: - layers: + layers: - type: integer name: counts description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalization method, if any. + required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true obsm: - type: double - name: dim_red - description: dimensionally-reduced 2D embedding coordinates + name: X_emb + description: 2D embedding coordinates uns: - type: string name: dataset_id @@ -20,6 +50,7 @@ info: name: method_id description: "A unique identifier for the method" - type: string - name: param_set_id - description: "A unique identifier for the parameter set" + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/dimensionality_reduction/api/anndata_score.yaml b/src/dimensionality_reduction/api/anndata_score.yaml index 309918348c..8c14dc9b1d 100644 --- a/src/dimensionality_reduction/api/anndata_score.yaml +++ b/src/dimensionality_reduction/api/anndata_score.yaml @@ -8,17 +8,22 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true - type: string name: method_id description: "A unique identifier for the method" - - type: string - name: param_set_id - description: "A unique identifier for the parameter set" + required: true - type: string name: metric_ids description: "One or more unique metric identifiers" multiple: true + required: true - type: double name: metric_values description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." - multiple: true \ No newline at end of file + multiple: true + required: true \ No newline at end of file From fc4118c8ece2c4cfbd14a54a68c4c6b0723d7386 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 13:36:48 +0100 Subject: [PATCH 0413/1233] add tsne Former-commit-id: 9e28b4951a15e6111224e937bc6cf68cec2d2cc7 --- .../methods/tsne/config.vsh.yaml | 28 +++++++++++++++++++ .../methods/tsne/script.py | 23 +++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 src/dimensionality_reduction/methods/tsne/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/tsne/script.py diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml new file mode 100644 index 0000000000..6e40f26e3a --- /dev/null +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -0,0 +1,28 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "tsne" + namespace: "dimensionality_reduction/methods" + description: "t-distributed stochastic neighbor embedding" + info: + type: method + label: t-SNE + v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + preferred_normalization: log_cpm + arguments: + - name: "--n_pca" + type: integer + default: 50 + description: Number of principal components of PCA to use. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - anndata<0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py new file mode 100644 index 0000000000..39eecd1fdd --- /dev/null +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -0,0 +1,23 @@ +import anndata as ad +import scanpy as sc + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', + 'n_pca': 50, +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +adata = ad.read_h5ad(par['input']) + +# t-SNE +sc.tl.tsne(adata, use_rep="X_pca", n_pcs=par['n_pca']) +adata.obsm["X_emb"] = adata.obsm["X_tsne"].copy() +del(adata.obsm["X_tsne"]) +adata.uns["method_code_version"] = check_version("MulticoreTSNE") + +adata.write_h5ad(par['output'], compression="gzip") From a1719706b5ed55a4fa755485e989233ec70be270 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 13:37:18 +0100 Subject: [PATCH 0414/1233] remove anndata raw dataset without normalization Former-commit-id: 99cf2151cb80e8fcb3166b9ea4c0b73d998bdbc9 --- .../api/anndata_raw_dataset.yaml | 14 -------------- 1 file changed, 14 deletions(-) delete mode 100644 src/dimensionality_reduction/api/anndata_raw_dataset.yaml diff --git a/src/dimensionality_reduction/api/anndata_raw_dataset.yaml b/src/dimensionality_reduction/api/anndata_raw_dataset.yaml deleted file mode 100644 index 781304f5e9..0000000000 --- a/src/dimensionality_reduction/api/anndata_raw_dataset.yaml +++ /dev/null @@ -1,14 +0,0 @@ -type: file -description: A raw dataset -example: "raw_dataset.h5ad" -info: - short_description: "Raw dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" \ No newline at end of file From dc65e393cddf3201cb8f0ca093b6d2c1b9396a52 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 13:38:14 +0100 Subject: [PATCH 0415/1233] add project config Former-commit-id: f2cd1b86e15861672c02dd77bd0d69d9530d243c --- _viash.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 _viash.yaml diff --git a/_viash.yaml b/_viash.yaml new file mode 100644 index 0000000000..9e65aec838 --- /dev/null +++ b/_viash.yaml @@ -0,0 +1,9 @@ +source: src +target: target + +config_mods: | + .functionality.version := 'dev' + .platforms[.type == 'docker'].target_registry := 'ghcr.io' + .platforms[.type == 'docker'].target_organization := 'openproblems-bio' + .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems-v2' + .platforms[.type == "nextflow"].directives.tag := "$id" \ No newline at end of file From 208b5679b0c61105e6776ec27e5bb6ba7dffb5b5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 13:38:20 +0100 Subject: [PATCH 0416/1233] update ci Former-commit-id: da90864882f8f65e84117f9f93004d2d7da959d6 --- .github/workflows/integration-test.yml | 29 ++-- .github/workflows/main-build.yml | 40 +++-- .github/workflows/release-build.yml | 226 +++++++++++++++++++++++++ .github/workflows/viash-test.yml | 8 +- 4 files changed, 274 insertions(+), 29 deletions(-) create mode 100644 .github/workflows/release-build.yml diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 26de6aa573..da68e81f95 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -1,17 +1,13 @@ -name: integration CI +name: integration test on: workflow_dispatch - # push: - # branches: [ '**' ] - jobs: # phase 1 list_components: env: - s3_bucket: s3://openproblems-data/ + s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest - # if: "contains(github.event.head_commit.message, '#integration')" steps: - uses: actions/checkout@v3 @@ -26,7 +22,7 @@ jobs: id: cachehash run: | AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT # initialize cache - name: Cache resources data @@ -41,7 +37,7 @@ jobs: run: | bin/viash run \ -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ + src/download/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 @@ -68,9 +64,9 @@ jobs: - id: set_matrix run: | component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') - echo "::set-output name=component_matrix::$component_json" + echo "component_matrix=$component_json" >> $GITHUB_OUTPUT workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') - echo "::set-output name=workflow_matrix::$workflow_json" + echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT outputs: component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} @@ -81,7 +77,6 @@ jobs: needs: list_components runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" strategy: fail-fast: false @@ -105,14 +100,15 @@ jobs: uses: docker/login-action@v2 with: registry: ghcr.io - username: ${{ github.actor }} + username: ${{ secrets.GTHB_USER }} password: ${{ secrets.GTHB_PAT }} - name: Push containers run: | - bin/viash_push -m release -t integration_build --force + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_push -m release -t integration_build -s "$SRC_DIR" --force - ###################################3 + ################################### # phase 3 integration_test: needs: [ build_containers, list_components ] @@ -145,17 +141,20 @@ jobs: # use cache - name: Cache resources data uses: actions/cache@v3 + timeout-minutes: 5 with: path: resources_test key: ${{ needs.list_components.outputs.cachehash }} - name: Run integration test + timeout-minutes: 45 run: | # todo: replace with viash test command config_dir=`dirname ${{ matrix.component.config }}` script="$config_dir/${{ matrix.component.test_script }}" + export NXF_VER=22.04.5 bin/nextflow run . \ -main-script "$script" \ -entry ${{ matrix.component.entry }} \ - -profile docker,mount_temp \ + -profile docker,mount_temp,no_publish \ -c workflows/utils/labels_ci.config diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index f16fd33e7a..654cf546c4 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -8,7 +8,7 @@ jobs: # phase 1 list_components: env: - s3_bucket: s3://openproblems-data/resources_test + s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest if: "!contains(github.event.head_commit.message, 'ci skip')" @@ -20,12 +20,18 @@ jobs: bin/init bin/viash -h + - name: Fetch viash tools + run: | + + bin/init_tools ${{ secrets.GTHB_USER }} ${{ secrets.GTHB_PAT }} + tree bin/tools + # create cachehash key - name: Create hash key id: cachehash run: | AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "::set-output name=cachehash::resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" + echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT # initialize cache - name: Cache resources data @@ -40,7 +46,7 @@ jobs: run: | bin/viash run \ -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ + src/download/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 @@ -56,6 +62,22 @@ jobs: # build target dir bin/viash_build -m release -t main_build + - name: Build nextflow schemas & params + run: | + bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) + outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) + outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) + bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + + bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) + outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) + outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) + bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 with: @@ -66,13 +88,10 @@ jobs: # store component locations - id: set_matrix run: | - component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') - echo "::set-output name=component_matrix::$component_json" - workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') - echo "::set-output name=workflow_matrix::$workflow_json" + component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "namespace": .functionality.namespace, "config": .info.config } ]') + echo "component_matrix=$component_json" >> $GITHUB_OUTPUT outputs: component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} cachehash: ${{ steps.cachehash.outputs.cachehash }} # phase 2 @@ -104,9 +123,10 @@ jobs: uses: docker/login-action@v2 with: registry: ghcr.io - username: ${{ github.actor }} + username: ${{ secrets.GTHB_USER }} password: ${{ secrets.GTHB_PAT }} - name: Push containers run: | - bin/viash_push -m release -t main_build --force \ No newline at end of file + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_push -m release -t main_build -s "$SRC_DIR" --force \ No newline at end of file diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml new file mode 100644 index 0000000000..22a2b3e5af --- /dev/null +++ b/.github/workflows/release-build.yml @@ -0,0 +1,226 @@ +name: release build + +on: + workflow_dispatch: + inputs: + version_tag: + description: Version tag + required: true + +jobs: + # phase 1 + list_components: + env: + s3_bucket: s3://openproblems-data/resources_test/ + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + - name: Fetch viash tools + run: | + + bin/init_tools ${{ secrets.GTHB_USER }} ${{ secrets.GTHB_PAT }} + tree bin/tools + + # create cachehash key + - name: Create hash key + id: cachehash + run: | + AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt + echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT + + # initialize cache + - name: Cache resources data + uses: actions/cache@v3 + with: + path: resources_test + key: ${{ steps.cachehash.outputs.cachehash }} + restore-keys: resources_test_ + + # sync if need be + - name: Sync test resources + run: | + bin/viash run \ + -p native \ + src/download/sync_test_resources/config.vsh.yaml -- \ + --input $s3_bucket \ + --delete + tree resources_test/ -L 3 + + - name: Build target dir + run: | + # allow publishing the target folder + sed -i '/^target.*/d' .gitignore + + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} + + - name: Build nextflow schemas & params + run: | + bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) + outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) + outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) + bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + + bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) + outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) + outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) + bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + + - name: Deploy to target branch + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: . + publish_branch: release + full_commit_message: "Deploy for release ${{ github.event.inputs.version_tag }} from ${{ github.sha }}" + + # store component locations + - id: set_matrix + run: | + component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + echo "component_matrix=$component_json" >> $GITHUB_OUTPUT + workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') + echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT + outputs: + component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} + cachehash: ${{ steps.cachehash.outputs.cachehash }} + + # phase 2 + build_containers: + needs: list_components + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + + steps: + - uses: actions/checkout@v3 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + - name: Build container + run: | + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} -s "$SRC_DIR" + + - name: Login to container registry + uses: docker/login-action@v2 + with: + registry: ghcr.io + username: ${{ secrets.GTHB_USER }} + password: ${{ secrets.GTHB_PAT }} + + - name: Push containers + run: | + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_push -m release -t ${{ github.event.inputs.version_tag }} -s "$SRC_DIR" --force + + ###################################3 + # phase 3 + integration_test: + needs: [ build_containers, list_components ] + if: "${{ needs.list_components.outputs.workflow_matrix != '[]' }}" + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.workflow_matrix) }} + + steps: + - uses: actions/checkout@v3 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + # build target dir + # use containers from release branch, hopefully these are available + - name: Build target dir + run: | + # force override viash build strategy to not build containers + sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build + + # build target dir + bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} + + # use cache + - name: Cache resources data + uses: actions/cache@v3 + timeout-minutes: 5 + with: + path: resources_test + key: ${{ needs.list_components.outputs.cachehash }} + + - name: Run integration test + timeout-minutes: 45 + run: | + # todo: replace with viash test command + config_dir=`dirname ${{ matrix.component.config }}` + script="$config_dir/${{ matrix.component.test_script }}" + export NXF_VER=22.04.5 + bin/nextflow run . \ + -main-script "$script" \ + -entry ${{ matrix.component.entry }} \ + -profile docker,mount_temp,no_publish \ + -c workflows/utils/labels_ci.config + + ###################################3 + # phase 4 + component_test: + needs: [ build_containers, list_components ] + + runs-on: ubuntu-latest + + strategy: + fail-fast: false + matrix: + component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + + steps: + - uses: actions/checkout@v3 + + - name: Fetch viash + run: | + bin/init + bin/viash -h + + # use cache + - name: Cache resources data + uses: actions/cache@v3 + timeout-minutes: 5 + with: + path: resources_test + key: ${{ needs.list_components.outputs.cachehash }} + + - name: Test component + timeout-minutes: 30 + run: | + SRC_DIR=`dirname ${{ matrix.component.config }}` + bin/viash_test -m release -t ${{ github.event.inputs.version_tag }} \ + -s "$SRC_DIR" \ + -c '.functionality.requirements.cpus := 2' \ + -c '.functionality.requirements.memory := "5gb"' diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index a7655f54ae..d8df36ccf0 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -30,7 +30,7 @@ jobs: list_components: needs: run_ci_check_job env: - s3_bucket: s3://openproblems-data/resources_test + s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest if: "(!contains(github.event.head_commit.message, 'ci skip')) && needs.run_ci_check_job.outputs.run_ci == 'true'" outputs: @@ -43,7 +43,7 @@ jobs: - name: Fetch viash run: | - bin/init + bin/init -n tree . bin/viash -h @@ -67,14 +67,14 @@ jobs: run: | bin/viash run \ -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ + src/download/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.0.5 + uses: tj-actions/changed-files@v34.4.3 with: separator: ";" diff_relative: true From 80a9303035a9e5c9d82949647d692aad7ece9817 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 13:42:20 +0100 Subject: [PATCH 0417/1233] fix repo name Former-commit-id: 702709bb7aa7c62c299e8c4f92299b5669454ec1 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 4ed3fe5cd9..9a26732072 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -15,7 +15,7 @@ jobs: - name: 'Check if branch has an existing pull request and the trigger was a push' id: github_cli run: | - pull_request=$(gh pr list -R openpipelines-bio/openpipeline -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') + pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') # If the branch has a PR and this run was triggered by a push event, do not run if [[ "$pull_request" != "null" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then echo "check=false" >> $GITHUB_OUTPUT From 07b70317cc3d529913a3253174501fef75b9beab Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 13:50:07 +0100 Subject: [PATCH 0418/1233] don't keep track of python package version Former-commit-id: 102481d5aef6d553ff0e5aacc5f7b77e8aeee2a6 --- src/dimensionality_reduction/methods/tsne/script.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index 39eecd1fdd..ca68f961e2 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -18,6 +18,4 @@ sc.tl.tsne(adata, use_rep="X_pca", n_pcs=par['n_pca']) adata.obsm["X_emb"] = adata.obsm["X_tsne"].copy() del(adata.obsm["X_tsne"]) -adata.uns["method_code_version"] = check_version("MulticoreTSNE") - -adata.write_h5ad(par['output'], compression="gzip") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 34a307656b22e8c38b027e8fbbbc960e6c1b24e3 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 13:50:32 +0100 Subject: [PATCH 0419/1233] use anndata>=0.8 Former-commit-id: 2cae4689317e1eb517ae1e1120323b72729ee661 --- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 6e40f26e3a..0ee7a348c6 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -24,5 +24,5 @@ platforms: - type: python packages: - scanpy - - anndata<0.8" + - anndata>=0.8" - type: nextflow \ No newline at end of file From e6d3a89f6200b8ea432c1df7a2f3431fe183fc2f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 14:01:51 +0100 Subject: [PATCH 0420/1233] try adding config view Former-commit-id: 4460c086e5d459fb82609670ce8a7afd77e8ec27 --- .github/workflows/viash-test.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 9a26732072..7d08865eb3 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -65,6 +65,9 @@ jobs: # sync if need be - name: Sync test resources run: | + bin/viash config view \ + src/download/sync_test_resources/config.vsh.yaml + bin/viash run \ -p native \ src/download/sync_test_resources/config.vsh.yaml -- \ From f14b460add7ac6a0ff3648436dfb5fbea783f399 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 14:04:13 +0100 Subject: [PATCH 0421/1233] remove typo Former-commit-id: 5fd71f8aa9773067677c375520891267e407a65d --- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 0ee7a348c6..e84ad953f0 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -24,5 +24,5 @@ platforms: - type: python packages: - scanpy - - anndata>=0.8" + - "anndata>=0.8" - type: nextflow \ No newline at end of file From 46a0a281daf8377ad1d828b6c13f7b58ad2aae9f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 14:07:38 +0100 Subject: [PATCH 0422/1233] fix ci Former-commit-id: c069d13985f8599d3bc345243ec068e8dc3b6ab7 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/main-build.yml | 2 +- .github/workflows/release-build.yml | 2 +- .github/workflows/viash-test.yml | 5 +---- 4 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index da68e81f95..59a2616e7b 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -37,7 +37,7 @@ jobs: run: | bin/viash run \ -p native \ - src/download/sync_test_resources/config.vsh.yaml -- \ + src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 654cf546c4..8ac662aee4 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -46,7 +46,7 @@ jobs: run: | bin/viash run \ -p native \ - src/download/sync_test_resources/config.vsh.yaml -- \ + src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 22a2b3e5af..a7b38806b3 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -48,7 +48,7 @@ jobs: run: | bin/viash run \ -p native \ - src/download/sync_test_resources/config.vsh.yaml -- \ + src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 7d08865eb3..5e03b15327 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -65,12 +65,9 @@ jobs: # sync if need be - name: Sync test resources run: | - bin/viash config view \ - src/download/sync_test_resources/config.vsh.yaml - bin/viash run \ -p native \ - src/download/sync_test_resources/config.vsh.yaml -- \ + src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ --delete tree resources_test/ -L 3 From b3922ad1c3bed8c3045dcc8ce9c75b266880d3cb Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 22 Nov 2022 15:29:36 +0100 Subject: [PATCH 0423/1233] split baseline to control methods Former-commit-id: d3b0d41d0b88e7475c8755e4eb51d38340a42c5a --- .../no_denoising}/config.vsh.yaml | 25 +++++------------ .../control_methods/no_denoising/script.py | 25 +++++++++++++++++ .../perfect_denoising/config.vsh.yaml | 27 +++++++++++++++++++ .../perfect_denoising}/script.py | 13 ++------- src/denoising/methods/magic/script.py | 2 +- 5 files changed, 62 insertions(+), 30 deletions(-) rename src/denoising/{methods/baseline => control_methods/no_denoising}/config.vsh.yaml (52%) create mode 100644 src/denoising/control_methods/no_denoising/script.py create mode 100644 src/denoising/control_methods/perfect_denoising/config.vsh.yaml rename src/denoising/{methods/baseline => control_methods/perfect_denoising}/script.py (57%) diff --git a/src/denoising/methods/baseline/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml similarity index 52% rename from src/denoising/methods/baseline/config.vsh.yaml rename to src/denoising/control_methods/no_denoising/config.vsh.yaml index b9cce756e0..ee7f4a927c 100644 --- a/src/denoising/methods/baseline/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -1,36 +1,25 @@ __inherits__: ../../api/comp_method.yaml functionality: - name: "baseline" - namespace: "denoising/methods" - description: "baseline" + name: "no_denoising" + namespace: "denoising/control_methods" + description: "negative control by copying train counts" info: - type: method - label: baseline + type: negative_control + label: no denoising # paper_name: "Molecular Cross-Validation for Single-Cell RNA-seq"" # paper_url: "https://doi.org/10.1101/786269" # paper_year: 2019 paper_doi: "10.1101/786269" code_url: "https://github.com/czbiohub/molecular-cross-validation" v1_url: /openproblems/tasks/denoising/methods/baseline.py - v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts - arguments: - - name: "--layer_input" - type: string - default: "counts" - description: "Which layer to use as input." - - name: "--baseline" - type: "string" - required: true - choices: ["no_denoising", "perfect_denoising"] - default: "perfect_denoising" - description: "wich baseline needs to be created" resources: - type: python_script path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/denoising/control_methods/no_denoising/script.py b/src/denoising/control_methods/no_denoising/script.py new file mode 100644 index 0000000000..63c238aa06 --- /dev/null +++ b/src/denoising/control_methods/no_denoising/script.py @@ -0,0 +1,25 @@ +import anndata as ad + +## VIASH START +par = { + 'input_train': 'output_train.h5ad', + 'input_test': 'output_test.h5ad', + 'output': 'output_baseline_ND.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +input_train = ad.read_h5ad(par['input_train']) + +print("Process data") +output_denoised = input_train.copy() + +output_denoised.layers["denoised"] = input_train.layers['counts'].toarray() + +output_denoised.uns["method_id"] = meta['functionality_name'] + +print("Write Data") +output_denoised.write_h5ad(par['output'],compression="gzip") diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml new file mode 100644 index 0000000000..b42a343e67 --- /dev/null +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -0,0 +1,27 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "perfect_denoising" + namespace: "denoising/control_methods" + description: "Negative control by copying the train counts" + info: + type: positive_control + label: perfect denoising + # paper_name: "Molecular Cross-Validation for Single-Cell RNA-seq"" + # paper_url: "https://doi.org/10.1101/786269" + # paper_year: 2019 + paper_doi: "10.1101/786269" + code_url: "https://github.com/czbiohub/molecular-cross-validation" + v1_url: /openproblems/tasks/denoising/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + preferred_normalization: counts + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + - type: nextflow diff --git a/src/denoising/methods/baseline/script.py b/src/denoising/control_methods/perfect_denoising/script.py similarity index 57% rename from src/denoising/methods/baseline/script.py rename to src/denoising/control_methods/perfect_denoising/script.py index e30d5c9c77..cdfa113040 100644 --- a/src/denoising/methods/baseline/script.py +++ b/src/denoising/control_methods/perfect_denoising/script.py @@ -5,8 +5,6 @@ 'input_train': 'output_train.h5ad', 'input_test': 'output_test.h5ad', 'output': 'output_baseline_PD.h5ad', - 'layer_input': 'counts', - 'baseline': 'perfect_denoising', } meta = { 'functionality_name': 'foo', @@ -17,17 +15,10 @@ input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) - +print("Process data") output_denoised = input_train.copy() -print("process data") -if par['baseline'] == "no_denoising": - """Do nothing.""" - output_denoised.layers["denoised"] = input_train.layers[par['layer_input']].toarray() - -elif par['baseline'] == "perfect_denoising": - """Cheat.""" - output_denoised.layers["denoised"] = input_test.layers[par['layer_input']].toarray() +output_denoised.layers["denoised"] = input_test.layers['counts'].toarray() output_denoised.uns["method_id"] = meta['functionality_name'] diff --git a/src/denoising/methods/magic/script.py b/src/denoising/methods/magic/script.py index d2b3840364..0d9174387f 100644 --- a/src/denoising/methods/magic/script.py +++ b/src/denoising/methods/magic/script.py @@ -32,7 +32,7 @@ print("processing data") X, libsize = scprep.normalize.library_size_normalize( - input_train.layers[par['counts']], rescale=1, return_library_size=True + input_train.layers['counts'], rescale=1, return_library_size=True ) X = scprep.utils.matrix_transform(X, norm_fn) From a27a786e5ab4058a131ab556c51f7e685d000b45 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 22 Nov 2022 15:30:06 +0100 Subject: [PATCH 0424/1233] add working nextflow file Former-commit-id: 008c4d0a2da344f632ceeb0eb2d31a51e19bfcd6 --- src/denoising/workflows/run/main.nf | 52 +++++++++++++++++++++++------ 1 file changed, 41 insertions(+), 11 deletions(-) diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index 099ce55954..e8c78197f0 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -1,19 +1,22 @@ nextflow.enable.dsl=2 sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "target/nextflow" +targetDir = params.rootDir + "/target/nextflow" -//import data processing -include { split_data } from "$targetDir/denoising/data_processing/split_data/main.nf" +// import control methods +include { no_denoising } from "$targetDir/denoising/control_methods/no_denoising/main.nf" +include { perfect_denoising } from "$targetDir/denoising/control_methods/perfect_denoising/main.nf" // import methods -include { baseline } from "$targetDir/denoising/methods/baseline/main_nf" -include { magic } from "$targetDir/denoising/methods/magic/main_nf" +include { magic } from "$targetDir/denoising/methods/magic/main.nf" // import metrics -include { mse } from "$targetDir/denoising/metrics/mse/main_nf" -include { poisson } from "$targetDir/denoising/metrics/poisson/main_nf" +include { mse } from "$targetDir/denoising/metrics/mse/main.nf" +include { poisson } from "$targetDir/denoising/metrics/poisson/main.nf" + +// tsv generation component +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" @@ -28,17 +31,25 @@ workflow { | run_wf } -output_ch = input_ch - +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + // split params for downstream components | setWorkflowArguments( method: ["input_train", "input_test"], + metric: ["input_test"], + output: ["output"] ) // run methods | getWorkflowArguments(key: "method") | ( - baseline & + no_denoising & + perfect_denoising & magic ) | mix @@ -47,4 +58,23 @@ output_ch = input_ch | pmap{ id, file, passthrough -> // derive unique ids from output filenames def newId = file.getName().replaceAll(".output.*", "") - } \ No newline at end of file + // combine prediction with solution + def newData = [ input_denoised: file, input_test: passthrough.metric.input_test ] + [ newId, newData, passthrough ] + } + + // run metrics + | (mse & poisson) + | mix + + // convert to tsv + | toSortedList + | map{ it -> [ "combined", it.collect{ it[1] } ] + it[0].drop(2) } + | getWorkflowArguments(key: "output") + | extract_scores.run( + auto: [ publish: true ] + ) + + emit: + output_ch +} \ No newline at end of file From d304cfcf62ee160ad7597d56aeda9a1a2f49dc7a Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 15:51:34 +0100 Subject: [PATCH 0425/1233] add lacking .uns data as in anndata_reduced.yaml Former-commit-id: aaaad5ccc51a875c17221f9bea622a19121f8e57 --- src/dimensionality_reduction/methods/tsne/script.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index ca68f961e2..dc8307ee82 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -17,5 +17,15 @@ # t-SNE sc.tl.tsne(adata, use_rep="X_pca", n_pcs=par['n_pca']) adata.obsm["X_emb"] = adata.obsm["X_tsne"].copy() -del(adata.obsm["X_tsne"]) + +# Update .uns +adata.uns['method_id'] = 'tsne' +adata.uns['normalization_id'] = 'pca' +#del(adata.uns["pca_variance"]) +#del(adata.uns["tsne"]) +# Update .obsm/.varm +#del(adata.obsm["X_tsne"]) +#del(adata.varm["pca_loadings"]) + +# Write output adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From f13b43a5c78fbb801cbcd1866fa7b325fef31d31 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 15:54:13 +0100 Subject: [PATCH 0426/1233] change description Former-commit-id: 7c914437777a68bc5e0f879fc46c1b6e2d1ae185 --- src/dimensionality_reduction/api/anndata_reduced.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/api/anndata_reduced.yaml b/src/dimensionality_reduction/api/anndata_reduced.yaml index 4da063c3d3..fcc7c5f83f 100644 --- a/src/dimensionality_reduction/api/anndata_reduced.yaml +++ b/src/dimensionality_reduction/api/anndata_reduced.yaml @@ -39,9 +39,12 @@ info: description: A ranking of the features by hvg. required: true obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. - type: double name: X_emb - description: 2D embedding coordinates + description: The resulting t-SNE embedding. uns: - type: string name: dataset_id From 70380a5c46abbe8deb2832394b1cec049d5a2bfc Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 22 Nov 2022 16:39:24 +0100 Subject: [PATCH 0427/1233] add preferred normalization & update v1_commit Former-commit-id: a357411194f0a06adb955415bfcb341fb7f03dce --- src/denoising/methods/alra/config.vsh.yaml | 3 ++- src/denoising/methods/dca/config.vsh.yaml | 9 +++------ src/denoising/methods/knn_smoothing/config.vsh.yaml | 12 ++++-------- src/denoising/methods/knn_smoothing/script.py | 6 ++---- 4 files changed, 11 insertions(+), 19 deletions(-) diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 770746784c..6e1fe784e1 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -13,7 +13,8 @@ functionality: paper_doi: "0.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: /openproblems/tasks/denoising/methods/dca.py - v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + preferred_normalization: counts arguments: - name: "--layer_input" type: string diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 3e7f47884a..430b407d8f 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -13,12 +13,9 @@ functionality: paper_doi: "0.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: /openproblems/tasks/denoising/methods/dca.py - v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + preferred_normalization: counts arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. - name: "--epochs" type: "integer" default: 300 @@ -32,6 +29,6 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata<0.8" - dca==0.3.4 - type: nextflow diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 51c92cbdc4..3f3ac06147 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -3,7 +3,7 @@ functionality: status: disabled name: "KNN_smoothing" namespace: "denoising/methods" - description: "K-nearest neighbor smoothing" + description: "iterative K-nearest neighbor smoothing" info: type: method label: knn_smooth @@ -12,13 +12,9 @@ functionality: # paper_year: 2018 paper_doi: "10.1101/217737" code_url: "https://github.com/yanailab/knn-smoothing" - v1_url: /openproblems/tasks/denoising/methods/dca.py - v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 - arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. + v1_url: /openproblems/tasks/denoising/methods/knn_smoothing.py + v1_commit: bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1 + preferred_normalization: counts resources: - type: python_script path: script.py diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py index acc879e42b..948f41e96b 100644 --- a/src/denoising/methods/knn_smoothing/script.py +++ b/src/denoising/methods/knn_smoothing/script.py @@ -6,7 +6,6 @@ par = { 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', 'output': 'output_knn.h5ad', - 'layer_input': 'counts' } meta = { 'functionality_name': 'foo', @@ -17,10 +16,9 @@ input_train = ad.read_h5ad(par["input_train"]) print("process data") - -X = input_train.X.transpose().toarray() +X = input_train.layers["counts"].transpose().toarray() output_denoised = input_train.copy() -output_denoised.X = (knn_smooth.knn_smoothing(X, k=10)).transpose() +output_denoised.layers["counts"] = (knn_smooth.knn_smoothing(X, k=10)).transpose() print("Writing data") output_denoised.uns["method_id"] = par["functionality_name"] From f95b397974a36e02c7217c99014113cda4b5d6fa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 17:31:43 +0100 Subject: [PATCH 0428/1233] clean up header Former-commit-id: 95394ba9623e80393aae1f6b4ef8f6bf6466bf53 --- src/label_projection/methods/knn/script.py | 3 +-- src/label_projection/methods/logistic_regression/script.py | 3 +-- src/label_projection/methods/mlp/script.py | 3 +-- src/label_projection/methods/scanvi/script.py | 1 - 4 files changed, 3 insertions(+), 7 deletions(-) diff --git a/src/label_projection/methods/knn/script.py b/src/label_projection/methods/knn/script.py index 54eb74a68f..e714e01736 100644 --- a/src/label_projection/methods/knn/script.py +++ b/src/label_projection/methods/knn/script.py @@ -5,8 +5,7 @@ par = { 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad', - 'layer_input': 'counts' + 'output': 'output.h5ad' } meta = { 'functionality_name': 'foo', diff --git a/src/label_projection/methods/logistic_regression/script.py b/src/label_projection/methods/logistic_regression/script.py index cee2268ba4..2973e7ecfd 100644 --- a/src/label_projection/methods/logistic_regression/script.py +++ b/src/label_projection/methods/logistic_regression/script.py @@ -5,8 +5,7 @@ par = { 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad', - 'layer_input': 'counts' + 'output': 'output.h5ad' } meta = { 'functionality_name': 'foo', diff --git a/src/label_projection/methods/mlp/script.py b/src/label_projection/methods/mlp/script.py index e5547953ac..1a7d924b77 100644 --- a/src/label_projection/methods/mlp/script.py +++ b/src/label_projection/methods/mlp/script.py @@ -5,8 +5,7 @@ par = { 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', - 'output': 'output.h5ad', - 'layer_input': 'counts' + 'output': 'output.h5ad' } meta = { 'functionality_name': 'foo', diff --git a/src/label_projection/methods/scanvi/script.py b/src/label_projection/methods/scanvi/script.py index 18a6580f12..fef2366a9c 100644 --- a/src/label_projection/methods/scanvi/script.py +++ b/src/label_projection/methods/scanvi/script.py @@ -1,4 +1,3 @@ - import anndata as ad import scarches as sca From 2ae176f2d0088d319543605392da0e0ab6990326 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 22 Nov 2022 17:35:20 +0100 Subject: [PATCH 0429/1233] Remove trajectory inference task for now Former-commit-id: 0f490b1e9e178b611ed2050d72e964eda7b29243 --- src/trajectory_inference/README.md | 69 -- .../datasets/download_datasets/config.vsh.yml | 48 - .../datasets/download_datasets/datasets.tsv | 11 - .../datasets/download_datasets/script.R | 40 - .../download_datasets/write_dataset_table.R | 31 - .../resources/api_discussion.R | 68 -- .../resources/images/format.svg | 698 -------------- .../resources/images/format_delayed.svg | 885 ------------------ .../resources/images/trajectory_inference.png | Bin 676367 -> 0 bytes src/trajectory_inference/workflows/main.nf | 44 - .../workflows/nextflow.config | 32 - .../workflows/run_nextflow.sh | 15 - 12 files changed, 1941 deletions(-) delete mode 100644 src/trajectory_inference/README.md delete mode 100644 src/trajectory_inference/datasets/download_datasets/config.vsh.yml delete mode 100644 src/trajectory_inference/datasets/download_datasets/datasets.tsv delete mode 100644 src/trajectory_inference/datasets/download_datasets/script.R delete mode 100644 src/trajectory_inference/datasets/download_datasets/write_dataset_table.R delete mode 100644 src/trajectory_inference/resources/api_discussion.R delete mode 100644 src/trajectory_inference/resources/images/format.svg delete mode 100644 src/trajectory_inference/resources/images/format_delayed.svg delete mode 100644 src/trajectory_inference/resources/images/trajectory_inference.png delete mode 100644 src/trajectory_inference/workflows/main.nf delete mode 100644 src/trajectory_inference/workflows/nextflow.config delete mode 100755 src/trajectory_inference/workflows/run_nextflow.sh diff --git a/src/trajectory_inference/README.md b/src/trajectory_inference/README.md deleted file mode 100644 index 4899d697d0..0000000000 --- a/src/trajectory_inference/README.md +++ /dev/null @@ -1,69 +0,0 @@ -# Trajectory inference - -## Task description -Trajectory inference (TI) is a computational analysis used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression through the process. -A trajectory is a graph where the nodes represent noteworthy cellular states, and each cell is predicted to be progressing along transitions between the different states (Figure 1A). -Main applications of TI are identifying branch points, end states, predicting the topology of the dynamic process, or identifying genes whose expression varies gradually along the topology (Figure 1B). - -![](resources/images/trajectory_inference.png) -**Figure 1**: Trajectory inference for single-cell omics data. Image borrowed from [1]. **A**: During a dynamic process cells pass through several transitional states, characterized by different waves of transcriptional, morphological, epigenomic and/or surface marker changes [2]. TI methods provide an unbiased approach to identifying and correctly ordering different transitional stages. **B**: By overlaying gene expression levels on a dimensionality reduction, the milestones can be annotated to allow better interpretation of the cellular heterogeneity. - -A comparison of 45 TI methods on 110 real and 229 synthetic datasets found that the different methods are very complementary when comparing different types of input datasets, and that performance of a method can be highly variable even in multiple runs on the same input dataset [3]. - -A persisting issue amongst TI methods is the usage of a standard definition of the task and usage of well-defined input and output data structures in order to make results comparable between methods. -This task assumes a trajectory consists of two data structures: the milestone network and the cell progressions (Figure 2). The milestone network is a data frame that must contain the columns 'from' (milestones), 'to' (milestones) and 'length' (> 0). The progressions is a data frame that must contain the columns 'cell_id' (name of the cell), 'from' and 'to' (transition it is located on), and 'percentage' (its' percentual progression along the transition). - -![](resources/images/format.svg) -**Figure 2**: The data structure for a trajectory. - - -These data structures first used in a the comparison of 45 TI methods [3]. It was also used in a TopCoder competition for Trajectory inference [4]. - -## API via anndata -The interface of the following files are as follows: - -### Dataset generator - -**--output** is a dataset h5ad-file containing: - -* `ad.uns["dataset_id"]`: A unique identifier for the dataset (Required). -* `ad.X`: a normalised expression matrix (Required). A sparse, double/numeric, M-by-N matrix, where M is the number of cells and N is the number of features. -* `ad.obsm["dimred"]`: a dimensionality reduction matrix (Optional). A dense, double/numeric, M-by-P matrix, where P << N. -* `ad.obs["clustering"]`: a clustering vector (Optional). an integer vector of length M. -* `ad.uns["traj_milestone_network"]`: Gold standard network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. -* `ad.uns["traj_progressions"]`: Gold standard cell progressions (Required). A data frame with columns 'cell_id', 'from', 'to', 'percentage'. - -### Method - -**--input** is a dataset h5ad file containing the objets `ad.uns["dataset_id"]` and `ad.X`, and may require `ad.obsm["dimred"]` and `"ad.obs["clustering"]`. Note that, a method should run successfully, **whether or not** a dimensionality reduction or clustering object is passed. - -**--output** is a prediction h5ad file containing: - -* `ad.uns["dataset_id"]`: The unique identifier for the dataset (Required). -* `ad.uns["method"]`: A unique identifier for the method (Required). -* `ad.uns["traj_milestone_network"]`: Predicted network of milestones (Required). A data frame with columns 'from', 'to', 'length' and 'directed'. -* `ad.uns["traj_progressions"]`: Predicted cell progressions (Required). A data frame with columns 'cell_id', 'from', 'to', 'percentage'. - - -## Metric - -**--dataset** is a dataset h5ad file. - -**--prediction** is a prediction h5ad file. - -**--output** is an evaluation h5ad file containing: - -* `ad.uns["evaluation"]`: A data frame containing columns `dataset_id`, `method_id`, `metric_id`, `value`. May contain one or more rows. - -## API via HDF5 - -This description can be provided if necessary, create an issue and mention @LouiseDck and @rcannood. - -## References -1. Robrecht Cannoodt. “Modelling single-cell dynamics with trajectories and gene regulatory networks“. Doctoral dissertation, Ghent University (2019). URL: [cannoodt.dev/files/phdthesis.pdf](https://cannoodt.dev/files/phdthesis.pdf). - -2. Tariq Enver et al. “Stem Cell States, Fates, and the Rules of Attraction”. In: Cell Stem Cell 4.5 (May 8, 2009), pp. 387–397. ISSN: 1875-9777. DOI: [10.1016/j.stem.2009.04.011](https://doi.org/10.1016/j.stem.2009.04.011). pmid: 19427289. - -3. Wouter Saelens, Cannoodt Robrecht et al. “A Comparison of Single-Cell Trajectory Inference Methods“. In: Nature Biotechnology 37 (May 2019). ISSN: 15461696. DOI: [10.1038/s41587-019-0071-9](https://doi.org/10.1038/s41587-019-0071-9). - -4. Luca Pinello et al. “TopCoder Challenge: Single-Cell Trajectory Inference Methods“. URL: [topcoder.com/lp/single-cell](https://www.topcoder.com/lp/single-cell). diff --git a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml b/src/trajectory_inference/datasets/download_datasets/config.vsh.yml deleted file mode 100644 index f2ddd551ef..0000000000 --- a/src/trajectory_inference/datasets/download_datasets/config.vsh.yml +++ /dev/null @@ -1,48 +0,0 @@ -functionality: - name: "download_datasets" - namespace: "trajectory_inference/datasets" - version: "dev" - description: "Download datasets to use for TI, mix of real and synthetic" - authors: - - name: "Louise Deconinck" - roles: [ maintainer, author ] - props: { github: LouiseDck } - arguments: - - name: "--id" - type: "string" - default: "ti_dataset" - description: "The id of the output dataset id" - - name: "--input" - alternatives: ["-i"] - type: "file" - direction: "input" - default: "" - description: "Input download link for the dataset" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing input matrices data" - required: true - resources: - - type: r_script - path: script.R -platforms: - - type: docker - image: "rocker/tidyverse:4.0.4" - setup: - - type: r - packages: - - httr - - anndata # needed by utils.py - github: - - dynverse/dynio - - type: apt - packages: - - python3 - - pip - - type: python - packages: - - anndata - - type: nextflow diff --git a/src/trajectory_inference/datasets/download_datasets/datasets.tsv b/src/trajectory_inference/datasets/download_datasets/datasets.tsv deleted file mode 100644 index 6de2db4c7b..0000000000 --- a/src/trajectory_inference/datasets/download_datasets/datasets.tsv +++ /dev/null @@ -1,11 +0,0 @@ -id url checksum filesize -zenodo_1443566_real_gold_aging-hsc-old_kowalczyk https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/aging-hsc-old_kowalczyk.rds b889d9e24abbd1c6cbd603a8bfbb73c5 7068624 -zenodo_1443566_real_gold_aging-hsc-young_kowalczyk https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/aging-hsc-young_kowalczyk.rds 2ce1033dc76556d0462e1edda3cfd51e 3094540 -zenodo_1443566_real_gold_cellbench-SC1_luyitian https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/cellbench-SC1_luyitian.rds 30e891afc4dded9686efffdf274923bc 276076 -zenodo_1443566_real_gold_cellbench-SC2_luyitian https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/cellbench-SC2_luyitian.rds f07dd1b7cba30c5505f4bd4983bf9bf0 341256 -zenodo_1443566_real_gold_cellbench-SC3_luyitian https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/cellbench-SC3_luyitian.rds f372602b998a86a0fdbf4b3a38b7d5a3 392076 -zenodo_1443566_real_gold_cellbench-SC4_luyitian https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/cellbench-SC4_luyitian.rds 30409d9462e08c43e7bd24fcb7750eea 491332 -zenodo_1443566_real_gold_cell-cycle_buettner https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/cell-cycle_buettner.rds 6ccfc7067c79f5681523f70ca1dad1a6 7184464 -zenodo_1443566_real_gold_developing-dendritic-cells_schlitzer https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/developing-dendritic-cells_schlitzer.rds 1601e5efe29927353ae200db0a13fa1b 2158224 -zenodo_1443566_real_gold_germline-human-both_guo https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/germline-human-both_guo.rds ff530a2b5f5e86c48fc88fb1c44df2c5 7171704 -zenodo_1443566_real_gold_germline-human-female_guo https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/gold/germline-human-female_guo.rds b3c42c7c86a27468faea9e072dd6abae 2471628 diff --git a/src/trajectory_inference/datasets/download_datasets/script.R b/src/trajectory_inference/datasets/download_datasets/script.R deleted file mode 100644 index 4b0805c190..0000000000 --- a/src/trajectory_inference/datasets/download_datasets/script.R +++ /dev/null @@ -1,40 +0,0 @@ -## VIASH START -par <- list( - id = "ti_dataset", - output = "dataset", - input1 = "https://zenodo.org/api/files/8b17ae8e-2fd8-4ab6-9b3b-a1def87cdf34/real/silver/placenta-trophoblast-differentiation-invasive_mca.rds" -) -## VIASH END - -print("> Loading dependencies") - -options(tidyverse.quiet = TRUE) # make sure tidyverse is quiet -library(tidyverse) -requireNamespace("dynio", quietly = TRUE) -requireNamespace("anndata", quietly = TRUE) - -output_dir <- tempfile() -dir.create(output_dir) - -cat("> Checking input parameter\n") - -input_path <- - if (grepl("^https?://", par$input)) { - cat("> Downloading file from remote\n") - # Check if link or local file - tmp <- tempfile() - on.exit(file.remove(tmp)) - utils::download.file(par$input, tmp, quiet = TRUE) - tmp - } else { - par$input - } - -cat("> Reading file\n") -ds <- read_rds(input_path) - -cat("> Converting RDS to h5ad\n") -ad <- dynio::to_h5ad(ds) - -cat("> Writing to h5ad\n") -ad$write_h5ad(paste0(par$output)) diff --git a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R b/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R deleted file mode 100644 index 99c747a88d..0000000000 --- a/src/trajectory_inference/datasets/download_datasets/write_dataset_table.R +++ /dev/null @@ -1,31 +0,0 @@ -library(httr) -library(tidyverse) - -output_dir <- tempfile() -dir.create(output_dir) - -# config -deposit_id <- 1443566 - -cat("Retrieving metadata\n") - -# retrieve file metadata from zenodo -files <- - GET(glue::glue("https://zenodo.org/api/records/{deposit_id}")) %>% - httr::content() %>% - .$files %>% - map_df(function(l) { - as_tibble(t(unlist(l))) - }) %>% - transmute( - id = filename %>% str_replace_all("\\.rds$", "") %>% str_replace_all("/", "_") %>% paste0("zenodo_", deposit_id, "_", .), - url = links.download, - checksum, - filesize - ) - -# subsample dataset -files <- files %>% slice(1:10) - -# TODO rename links.download as header to links_download -write_tsv(files, "src/trajectory_inference/datasets/download_datasets/datasets.tsv") diff --git a/src/trajectory_inference/resources/api_discussion.R b/src/trajectory_inference/resources/api_discussion.R deleted file mode 100644 index 3d8faaeb6e..0000000000 --- a/src/trajectory_inference/resources/api_discussion.R +++ /dev/null @@ -1,68 +0,0 @@ -library(tidyverse) - -# example from: https://github.com/rcannood/phdthesis/blob/master/ch3_dynbenchmark/fig/snote1fig_1.pdf - -cell_ids <- c("a", "b", "c", "d", "e") -milestone_ids <- c("W", "X", "Y", "Z") - -milestone_network <- tribble( - ~from, ~to, ~length, ~directed, - "W", "X", 2, FALSE, - "X", "Y", 3, FALSE, - "X", "Z", 4, FALSE -) - -milestone_percentages <- tribble( - ~cell_id, ~milestone_id, ~percentage, - "a", "W", 0.9, - "a", "X", 0.1, - "b", "W", 0.2, - "b", "X", 0.8, - "c", "X", 0.8, - "c", "Z", 0.2, - "d", "X", 0.2, - "d", "Y", 0.7, - "d", "Z", 0.1, - "e", "X", 0.3, - "e", "Y", 0.2, - "e", "Z", 0.5 -) - -divergence_regions <- tribble( - ~divergence_id, ~milestone_id, ~is_start, - "XYZ", "X", TRUE, - "XYZ", "Y", FALSE, - "XYZ", "Z", FALSE -) - -library(dynwrap) -library(dynplot) - -convert_milestone_percentages_to_progressions( - cell_ids = cell_ids, - milestone_ids = milestone_ids, - milestone_network = milestone_network, - milestone_percentages = milestone_percentages -) - -traj <- - wrap_data(cell_ids = cell_ids) %>% - add_trajectory( - milestone_ids = milestone_ids, - milestone_network = milestone_network, - milestone_percentages = milestone_percentages, - divergence_regions = divergence_regions - ) - -plot_graph(traj) - -traj$progressions - - - - - - - - - diff --git a/src/trajectory_inference/resources/images/format.svg b/src/trajectory_inference/resources/images/format.svg deleted file mode 100644 index e9fbe39e2a..0000000000 --- a/src/trajectory_inference/resources/images/format.svg +++ /dev/null @@ -1,698 +0,0 @@ - - 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a/src/trajectory_inference/workflows/main.nf b/src/trajectory_inference/workflows/main.nf deleted file mode 100644 index d8a5e3a367..0000000000 --- a/src/trajectory_inference/workflows/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -nextflow.enable.dsl=2 - -/* for now, you need to manually specify the - * root directory of this repository as follows. - * (it's a nextflow limitation I'm trying to figure out - * how to resolve.) */ -rootDir = "$projectDir/../../.." - -// target dir containing the nxf modules generated by viash -targetDir = "$rootDir/target/nextflow" - -// import dataset loaders -include { download_datasets } from "$targetDir/trajectory_inference/datasets/download_datasets/main.nf" params(params) - -// import methods - -// import metrics - -// import helper functions -include { overrideOptionValue; overrideParams } from "$launchDir/src/utils/workflows/utils.nf" - -/******************************************************* -* Dataset processor workflows * -*******************************************************/ -// This workflow reads in a tsv containing some metadata about each dataset. -// For each entry in the metadata, a dataset is generated, usually by downloading -// and processing some files. The end result of each of these workflows -// should be simply a channel of [id, h5adfile, params] triplets. -// -// If the need arises, these workflows could be split off into a separate file. - -workflow { - main: - output_ = Channel.fromPath(file("$launchDir/src/trajectory_inference/datasets/download_datasets/datasets.tsv")) \ - | splitCsv(header: true, sep: "\t") \ - | map { row -> - newParams = overrideParams(params, "download_datasets", "id", row.id) - [ row.id, file(row.url), newParams] - } \ - | download_datasets - emit: - output_ -} - diff --git a/src/trajectory_inference/workflows/nextflow.config b/src/trajectory_inference/workflows/nextflow.config deleted file mode 100644 index 630f1b79b0..0000000000 --- a/src/trajectory_inference/workflows/nextflow.config +++ /dev/null @@ -1,32 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -rootDir = "$projectDir/../../.." -targetDir = "$rootDir/target/nextflow" - -// additional includes -includeConfig "$targetDir/trajectory_inference/datasets/download_datasets/nextflow.config" - -// other configs -docker { - runOptions = "-v $rootDir:$rootDir" -} - -process { - maxForks = 30 - cpus = 2 - errorStrategy='ignore' - container = 'nextflow/bash:latest' - - pod = [ [ nodeSelector: 'worker-group = m5s' ] ] - - withLabel: highmem { memory = 50.Gb } - withLabel: highcpu { cpus = 20 } - withLabel: highmem_highcpu { - cpus = 20 - memory = 128.Gb - } -} - - diff --git a/src/trajectory_inference/workflows/run_nextflow.sh b/src/trajectory_inference/workflows/run_nextflow.sh deleted file mode 100755 index 133c32343d..0000000000 --- a/src/trajectory_inference/workflows/run_nextflow.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/project_build -q 'modality_alignment|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -NXF_VER=20.10.0 bin/nextflow run src/trajectory_inference/workflows/main.nf \ - -resume \ - --publish_dir output/trajectory_inference - From 74750c55fc0c78d77138e70912588179f869c833 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 22 Nov 2022 18:37:40 +0100 Subject: [PATCH 0430/1233] add metric: rmse Former-commit-id: 00794f01c04d718e97caca2db5f273ec3f3d3c19 --- .../metrics/rmse/config.vsh.yaml | 24 ++++++++++ .../metrics/rmse/script.py | 46 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 src/dimensionality_reduction/metrics/rmse/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/rmse/script.py diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml new file mode 100644 index 0000000000..7b32035489 --- /dev/null +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -0,0 +1,24 @@ +__inherits__: ../../api/comp_metric.yaml +functionality: + name: "rmse" + namespace: "dimensionality_reduction/metrics" + description: The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices + info: + type: metric + label: RMSE + v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scikit-learn + - numpy + - scipy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py new file mode 100644 index 0000000000..1f28dfceb8 --- /dev/null +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -0,0 +1,46 @@ +import anndata as ad +import scipy.spatial.distance as dist +import numpy as np +from sklearn import decomposition, metrics + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load data") +adata = ad.read_h5ad(par['input']) + +print('Reduce dimensionality of raw data') +adata.obsm['svd'] = decomposition.TruncatedSVD(n_components = 200).fit_transform(adata.layers['counts']) + +print('Compute pairwise distance between points in a matrix and format it into a squared-form vector.') +high_dim_dist_matrix = dist.squareform(dist.pdist(adata.obsm['svd'])) +low_dim_dist_matrix = dist.squareform(dist.pdist(adata.obsm["X_emb"])) + +print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix') +y_actual = high_dim_dist_matrix +y_predict = low_dim_dist_matrix +rmse = np.sqrt(metrics.mean_squared_error(y_actual, y_predict)) + +print('Compute Kruskal stress between the full (or processed) data matrix and a dimensionally-reduced matrix') +diff = high_dim_dist_matrix - low_dim_dist_matrix +kruskal_matrix = np.sqrt(diff**2 / sum(low_dim_dist_matrix**2)) +kruskal_score = np.sqrt(sum(diff**2) / sum(low_dim_dist_matrix**2)) + +print("Store metric value") +if 'metric_ids' not in adata.uns.keys(): + adata.uns['metric_ids'] = [] + adata.uns['metric_values'] = [] + +adata.uns['metric_ids'] += ['kruskal', 'rmse'] +adata.uns['metric_values'] += ['kruskal_score', 'rmse'] +adata.obsm['kruskal'] = kruskal_matrix + +print("Write data to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 858d2740f45efa721618d34f911202b069fab81a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Nov 2022 07:07:10 +0100 Subject: [PATCH 0431/1233] change maximise into maximize Former-commit-id: 48360dc154a8d6668468a3a2fa29eb6450a301a2 --- src/label_projection/README.qmd | 2 +- src/label_projection/analysis_scripts/script.R | 4 ++-- src/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 6 +++--- src/modality_alignment/metrics/knn_auc/config.vsh.yaml | 2 +- src/modality_alignment/metrics/mse/config.vsh.yaml | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index df3b739f6a..a7e5239df3 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -79,7 +79,7 @@ metric_info_view <- metric_info %>% transmute( Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " ", ifelse(maximise, "Higher is better.", "Lower is better.")), + Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), Range = paste0("[", min, ", ", max, "]") ) diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index f86530ead6..eadb5c7639 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -66,10 +66,10 @@ metric_info <- map_df(ns_list_metrics, function(conf) { # get data table ranking <- scores %>% - left_join(metric_info %>% select(metric_id = id, maximise), by = "metric_id") %>% + left_join(metric_info %>% select(metric_id = id, maximize), by = "metric_id") %>% inner_join(method_info %>% select(method_id = id, method_label = label), by = "method_id") %>% group_by(metric_id, dataset_id) %>% - mutate(rank = rank(ifelse(maximise, -metric_value, metric_value))) %>% + mutate(rank = rank(ifelse(maximize, -metric_value, metric_value))) %>% ungroup() %>% group_by(method_id, method_label) %>% summarise(mean_rank = mean(rank), .groups = "drop") %>% diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index a0e2a4b526..fe2a680dca 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: The percentage of correctly predicted labels. min: 0 max: 1 - maximise: true + maximize: true resources: - type: python_script path: script.py diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index a205fb1350..5d761d037f 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -12,19 +12,19 @@ functionality: description: Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall. min: 0 max: 1 - maximise: true + maximize: true - id: f1_macro label: F1 macro description: Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. min: 0 max: 1 - maximise: true + maximize: true - id: f1_micro label: F1 micro description: Calculates the F1 score globally by counting the total true positives, false negatives and false positives. min: 0 max: 1 - maximise: true + maximize: true resources: - type: python_script path: script.py diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml index 5a1106b865..51f8de3f03 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/modality_alignment/metrics/knn_auc/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: info: method_label: "KNN-AUC" metric_name: "kNN Area Under the Curve" - maximise: "true" + maximize: "true" arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/modality_alignment/metrics/mse/config.vsh.yaml index e5f01eac99..97da63adac 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/modality_alignment/metrics/mse/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: info: method_label: "MSE" metric_name: "Mean Squared Error" - maximise: "true" + maximize: "true" arguments: - name: "--input" alternatives: ["-i"] From 66e4ad9045a11069392a4d19c2131c61432b1c7e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Nov 2022 08:37:12 +0100 Subject: [PATCH 0432/1233] add ALRA Former-commit-id: fe4e01ef60f403f71bc95e6eba9d9e616c796e27 --- src/denoising/methods/alra/alra.R | 0 src/denoising/methods/alra/config.vsh.yaml | 42 +++++++++++++--------- src/denoising/methods/alra/script.R | 34 ++++++++++++++++++ src/denoising/methods/alra/script.py | 1 - 4 files changed, 60 insertions(+), 17 deletions(-) delete mode 100644 src/denoising/methods/alra/alra.R create mode 100644 src/denoising/methods/alra/script.R delete mode 100644 src/denoising/methods/alra/script.py diff --git a/src/denoising/methods/alra/alra.R b/src/denoising/methods/alra/alra.R deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 770746784c..4bcb623681 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -1,19 +1,25 @@ __inherits__: ../../api/comp_method.yaml functionality: - status: disabled name: "alra" namespace: "denoising/methods" - description: "" + description: | + Adaptively-thresholded Low Rank Approximation (ALRA). + + ALRA is a method for imputation of missing values in single cell RNA-sequencing data, + described in the preprint, "Zero-preserving imputation of scRNA-seq data using low-rank approximation" + available [here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a + scRNA-seq expression matrix, ALRA first computes its rank-k approximation using randomized SVD. + Next, each row (gene) is thresholded by the magnitude of the most negative value of that gene. + Finally, the matrix is rescaled. info: type: method - label: DCA - # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" - # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" - # paper_year: 2019 - paper_doi: "0.1038/s41467-018-07931-2" - code_url: "https://github.com/theislab/dca" - v1_url: /openproblems/tasks/denoising/methods/dca.py - v1_commit: 903469a532b96b25ef7d727e687c5b4263966323 + label: ALRA + paper_doi: "10.1101/397588" + code_url: "https://github.com/KlugerLab/ALRA" + doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md + v1_url: /openproblems/tasks/denoising/methods/alra.py + v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + preferred_normalization: counts arguments: - name: "--layer_input" type: string @@ -24,14 +30,18 @@ functionality: default: 300 description: "Number of total epochs in training" resources: - - type: python_script - path: script.py + - type: r_script + path: script.R platforms: - type: docker - image: "python:3.8" + image: eddelbuettel/r2u:22.04 setup: + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] - type: python - packages: - - "anndata>=0.8" - - dca==0.3.4 + pip: [ anndata>=0.8 ] + - type: r + cran: [ Matrix, anndata, bit64, rsvd ] + - type: docker + run: git clone https://github.com/KlugerLab/ALRA.git /ALRA - type: nextflow diff --git a/src/denoising/methods/alra/script.R b/src/denoising/methods/alra/script.R new file mode 100644 index 0000000000..2d6f6ba06c --- /dev/null +++ b/src/denoising/methods/alra/script.R @@ -0,0 +1,34 @@ + +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) + +# load alra script from within the Docker container +source("/ALRA/alra.R") + +## VIASH START +# load directly from github when testing locally +source("https://raw.githubusercontent.com/KlugerLab/ALRA/master/alra.R") + +par <- list( + input_train = "resources_test/denoising/pancreas/train.h5ad", + # input_train = "resources_test/common/pancreas/dataset.h5ad", + output = "output.h5ad" +) +## VIASH END + +cat(">> Load input data\n") +adata <- read_h5ad(par$input_train) + +counts <- t(adata$layers[["counts"]]) + +cat(">> Run ALRA\n") +# alra doesn't work with sparce matrices +out <- alra(as.matrix(counts)) + +cat(">> Store output\n") +adata$layers[["denoised"]] <- as(out$A_norm_rank_k_cor_sc, "CsparseMatrix") +adata$uns[["method_id"]] <- meta[["functionality_name"]] + +cat(">> Write output to file\n") +adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/denoising/methods/alra/script.py b/src/denoising/methods/alra/script.py deleted file mode 100644 index 8b13789179..0000000000 --- a/src/denoising/methods/alra/script.py +++ /dev/null @@ -1 +0,0 @@ - From 90d96becfc8ad09749a334bc3fb9314f05a4907b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Nov 2022 10:11:18 +0100 Subject: [PATCH 0433/1233] add generic configuremethod Former-commit-id: c14dcb9e0ddf0e3fd29338c39b457aa6d43e477b --- src/label_projection/workflows/run/main.nf | 57 ++++++++++++++++------ 1 file changed, 41 insertions(+), 16 deletions(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index b2949b3861..220653a33b 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -36,20 +36,46 @@ workflow { | run_wf } +/** + * Helper function for making sure the right data gets passed to a method + */ +def configureMethod = { module -> + // if method is a control method, add the solution to the data field + def methodType = module.config.functionality.info.type + def mapFun = null + if (methodType != "method") { + mapFun = { tup -> + out = tup.clone() + out[1] = out[1] + [input_solution: out[2].metric.input_solution] + out + } + } + + // only let datasets with the right preferred normalization through + // if preferred is 'counts', use any normalization method + def preferred = module.config.functionality.info.preferred_normalization + if (preferred == "counts") { + preferred = "log_cpm" + } + + def filterFun = { tup -> + tup[1].normalization_id == preferred + } + + // return module + module.run( + map: mapFun, + filter: filterFun + ) +} workflow run_wf { take: input_ch main: - def addSolution = { tup -> - out = tup.clone() - out[1] = out[1] + [input_solution: out[2].metric.input_solution] - out - } output_ch = input_ch - | filter{it[1].normalization_id == "log_cpm"} // split params for downstream components | setWorkflowArguments( @@ -59,18 +85,17 @@ workflow run_wf { ) // run methods - // TODO: these filters don't work atm. | getWorkflowArguments(key: "method") | ( - true_labels.run(map: addSolution, filter: {it[1].normalization_id == "log_cpm"}) & - random_labels.run(filter: {it[1].normalization_id == "log_cpm"}) & - majority_vote.run(filter: {it[1].normalization_id == "log_cpm"}) & - knn.run(filter: {it[1].normalization_id == "log_cpm"}) & - logistic_regression.run(filter: {it[1].normalization_id == "log_cpm"}) & - mlp.run(filter: {it[1].normalization_id == "log_cpm"}) & - scanvi.run(filter: {it[1].normalization_id == "log_cpm"}) & - seurat_transferdata.run(filter: {it[1].normalization_id == "log_cpm"}) & - xgboost.run(filter: {it[1].normalization_id == "log_cpm"}) + configureMethod(true_labels) & + configureMethod(random_labels) & + configureMethod(majority_vote) & + configureMethod(knn) & + configureMethod(logistic_regression) & + configureMethod(mlp) & + configureMethod(scanvi) & + configureMethod(seurat_transferdata) & + configureMethod(xgboost) ) | mix From 73ec26cfcf75e373275b7407120df828a13fb825 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Nov 2022 10:16:18 +0100 Subject: [PATCH 0434/1233] make sure script stops when script is cancelled Former-commit-id: ee4aa1a583fbdfe3d03286ef5ed5974597ce029c --- src/label_projection/resources_scripts/run_benchmark.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/label_projection/resources_scripts/run_benchmark.sh b/src/label_projection/resources_scripts/run_benchmark.sh index 6fd51739a0..9aac51109d 100755 --- a/src/label_projection/resources_scripts/run_benchmark.sh +++ b/src/label_projection/resources_scripts/run_benchmark.sh @@ -6,6 +6,8 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + export TOWER_WORKSPACE_ID=53907369739130 DATASETS_DIR="resources/label_projection/datasets/openproblems_v1" From 0d4b800dd30b176f3a21fe68748df836163f9835 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 23 Nov 2022 11:28:40 +0100 Subject: [PATCH 0435/1233] Resolve comments PR #27 Former-commit-id: 08e2048ca4938e52155f9dcd1f1d724623142296 --- src/denoising/README.qmd | 263 ++++++++++++++++++ src/denoising/api/anndata_dataset.yaml | 4 - src/denoising/api/anndata_denoised.yaml | 7 +- src/denoising/api/anndata_raw_dataset.yaml | 18 -- src/denoising/api/comp_control_method.yaml | 61 ++++ src/denoising/api/comp_method.yaml | 2 - ...plit_data.yaml => comp_split_dataset.yaml} | 0 .../no_denoising/config.vsh.yaml | 7 +- .../perfect_denoising/config.vsh.yaml | 7 +- .../data_processing/split_data/params.yaml | 4 - src/denoising/{ => docs}/readme.md | 0 .../{possion => poisson}/config.vsh.yaml | 0 .../metrics/{possion => poisson}/script.py | 0 .../config.vsh.yaml | 6 +- src/denoising/split_dataset/params.yaml | 4 + .../run_nextflow.sh | 4 +- .../split_data => split_dataset}/script.py | 14 - src/denoising/workflows/run/config.vsh.yaml | 2 - 18 files changed, 339 insertions(+), 64 deletions(-) create mode 100644 src/denoising/README.qmd delete mode 100644 src/denoising/api/anndata_raw_dataset.yaml create mode 100644 src/denoising/api/comp_control_method.yaml rename src/denoising/api/{comp_split_data.yaml => comp_split_dataset.yaml} (100%) delete mode 100644 src/denoising/data_processing/split_data/params.yaml rename src/denoising/{ => docs}/readme.md (100%) rename src/denoising/metrics/{possion => poisson}/config.vsh.yaml (100%) rename src/denoising/metrics/{possion => poisson}/script.py (100%) rename src/denoising/{data_processing/split_data => split_dataset}/config.vsh.yaml (87%) create mode 100644 src/denoising/split_dataset/params.yaml rename src/denoising/{data_processing/split_data => split_dataset}/run_nextflow.sh (66%) rename src/denoising/{data_processing/split_data => split_dataset}/script.py (80%) diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd new file mode 100644 index 0000000000..df3b739f6a --- /dev/null +++ b/src/denoising/README.qmd @@ -0,0 +1,263 @@ +--- +format: gfm +info: + v1_url: openproblems/tasks/label_projection/README.md + v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +toc: true +--- + +```{r setup, include=FALSE} +library(tidyverse) +library(rlang) + +strip_margin <- function(text, symbol = "\\|") { + str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") +} + +dir <- "src/label_projection" +dir <- "." +``` + +# Label Projection + +```{r description, echo=FALSE} +lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) +lines2 <- gsub("^#", "##", lines) +knitr::asis_output(lines2) +``` + +## Methods + +Methods for assigning labels from a reference dataset to a new dataset. + +```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) +method_configs <- yaml::yaml.load(method_ns_list$stdout) + +method_info <- map_df(method_configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) + info <- as_tibble(config$functionality$info) + info$comp_yaml <- config$info$config + info$name <- config$functionality$name + info$namespace <- config$functionality$namespace + info$description <- config$functionality$description + info +}) + +method_info_view <- + method_info %>% + arrange(type, label) %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Type = type, + Description = description, + DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), + URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") + ) + +cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) +``` + + +## Metrics + +Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. + +```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) +metric_configs <- yaml::yaml.load(metric_ns_list$stdout) + +metric_info <- map_df(metric_configs, function(config) { + metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) + metric_info$comp_yaml <- config$info$config + metric_info$comp_name <- config$functionality$name + metric_info$comp_namespace <- config$functionality$namespace + metric_info +}) + +metric_info_view <- + metric_info %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Description = paste0(description, " ", ifelse(maximise, "Higher is better.", "Lower is better.")), + Range = paste0("[", min, ", ", max, "]") + ) + +cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) +``` + + +## Pipeline topology + +```{r data, include=FALSE} +comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) + +comp_file <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + tibble( + comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + arg_name = str_replace_all(arg$name, "^-*", ""), + direction = arg$direction %||% "input", + file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + ) + }) +}) + +comp_info <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_info <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + description = arg$description, + short_description = arg$info$short_description, + example = arg$example, + label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_slot <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) + as_tibble(df) + }) +}) %>% + mutate(multiple = multiple %|% FALSE) +``` + +```{r flow, echo=FALSE,warning=FALSE,error=FALSE} +nodes <- bind_rows( + file_info %>% + transmute(id = name, label = str_to_title(label), is_comp = FALSE), + comp_info %>% + transmute(id = name, label = str_to_title(label), is_comp = TRUE) +) %>% + mutate(str = paste0( + " ", + id, + ifelse(is_comp, "[/", "("), + label, + ifelse(is_comp, "/]", ")") + )) +edges <- bind_rows( + comp_file %>% + filter(direction == "input") %>% + transmute( + from = file_name, + to = comp_name, + arrow = "---" + ), + comp_file %>% + filter(direction == "output") %>% + transmute( + from = comp_name, + to = file_name, + arrow = "-->" + ) +) %>% + mutate(str = paste0(" ", from, arrow, to)) + +# note: use ```{mermaid} instead of ```mermaid when rendering to html +out_str <- strip_margin(glue::glue(" + §```mermaid + §%%| column: screen-inset-shaded + §flowchart LR + §{paste(nodes$str, collapse = '\n')} + §{paste(edges$str, collapse = '\n')} + §``` + §"), symbol = "§") +knitr::asis_output(out_str) +``` + +## File format API + +```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +for (file_name in file_info$name) { + arg_info <- file_info %>% filter(name == file_name) + sub_out <- file_slot %>% + filter(file_name == !!file_name) %>% + select(struct, name, type, description) + + used_in <- comp_file %>% + filter(file_name == !!file_name) %>% + left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% + mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% + pull(str) + + example <- sub_out %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) + + example_str <- c(" AnnData object", paste0(" ", example$str)) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(arg_info$label)}` + § + §{arg_info$description} + § + §Used in: + § + §{paste(used_in, collapse = '\n')} + § + §Slots: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + § + §Example: + § + §{paste(example_str, collapse = '\n')} + § + §"), symbol = "§") + cat(out_str) +} +``` + + + +## Component API + +```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +# todo: add description +# todo: add required info fields +for (comp_name in comp_info$name) { + comp <- comp_info %>% filter(name == comp_name) + sub_out <- comp_file %>% + filter(comp_name == !!comp_name) %>% + left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% + transmute( + Name = paste0("`--", arg_name, "`"), + `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), + Direction = direction, + Description = file_sdesc + ) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(comp$label)}` + § + §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} + § + §Arguments: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + §"), symbol = "§") + cat(out_str) +} +``` \ No newline at end of file diff --git a/src/denoising/api/anndata_dataset.yaml b/src/denoising/api/anndata_dataset.yaml index 7da5339137..cf0a3a4eb0 100644 --- a/src/denoising/api/anndata_dataset.yaml +++ b/src/denoising/api/anndata_dataset.yaml @@ -8,10 +8,6 @@ info: - type: integer name: counts description: Raw counts - obs: - - type: integer - name: n_counts - description: raw counts uns: - type: string name: dataset_id diff --git a/src/denoising/api/anndata_denoised.yaml b/src/denoising/api/anndata_denoised.yaml index db7cdda740..66754b81e5 100644 --- a/src/denoising/api/anndata_denoised.yaml +++ b/src/denoising/api/anndata_denoised.yaml @@ -8,6 +8,9 @@ info: - type: integer name: counts description: Raw counts + - type: integer + name: denoised + description: denoised data obs: - type: string name: n_counts @@ -19,6 +22,4 @@ info: - type: string name: method_id description: "A unique identifier for the method" - X: - - type: integer - description: denoised data \ No newline at end of file + \ No newline at end of file diff --git a/src/denoising/api/anndata_raw_dataset.yaml b/src/denoising/api/anndata_raw_dataset.yaml deleted file mode 100644 index de80bf6d09..0000000000 --- a/src/denoising/api/anndata_raw_dataset.yaml +++ /dev/null @@ -1,18 +0,0 @@ -type: file -description: "A raw dataset" -example: "raw_dataset.h5ad" -info: - short_description: "Raw dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - obs: - - type: integer - name: n_counts - description: raw counts - uns: - - type: string - name: dataset_id - description: "A unique identifier for the original dataset (before preprocessing)" \ No newline at end of file diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml new file mode 100644 index 0000000000..9cb99ae54b --- /dev/null +++ b/src/denoising/api/comp_control_method.yaml @@ -0,0 +1,61 @@ +functionality: + arguments: + - name: "--input_train" + __inherits__: anndata_train.yaml + - name: "--input_test" + __inherits__: anndata_test.yaml + - name: "--output" + __inherits__: anndata_denoised.yaml + direction: output + # TODO: currently needs to be manually specified since the default value needs to be overrideable + # - name: "--layer_input" + # type: string + # default: "log_cpm" + # description: Which layer to use as input. + # test_resources: + # - path: ../../../../resources_test/label_projection/pancreas + # - type: python_script + # path: generic_test.py + # text: | + # import anndata as ad + # import subprocess + # from os import path + + # input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" + # input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" + # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" + # output_path = "output.h5ad" + + # cmd = [ + # meta['executable'], + # "--input_train", input_train_path, + # "--input_test", input_test_path, + # "--output", output_path + # ] + + # # todo: if we could access the viash config, we could check whether + # # .functionality.info.type == "positive_control" + # if meta['functionality_name'] == 'true_labels': + # cmd = cmd + ["--input_solution", input_solution_path] + + # print(">> Running script as test") + # out = subprocess.check_output(cmd).decode("utf-8") + + # print(">> Checking whether output file exists") + # assert path.exists(output_path) + + # print(">> Reading h5ad files") + # input_test = ad.read_h5ad(input_test_path) + # output = ad.read_h5ad(output_path) + # print("input_test:", input_test) + # print("output:", output) + + # print(">> Checking whether predictions were added") + # assert "label_pred" in output.obs + # assert meta['functionality_name'] == output.uns["method_id"] + + # print("Checking whether data from input was copied properly to output") + # assert input_test.n_obs == output.n_obs + # assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + + # print("All checks succeeded!") diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 9cb99ae54b..76528d4e8b 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -2,8 +2,6 @@ functionality: arguments: - name: "--input_train" __inherits__: anndata_train.yaml - - name: "--input_test" - __inherits__: anndata_test.yaml - name: "--output" __inherits__: anndata_denoised.yaml direction: output diff --git a/src/denoising/api/comp_split_data.yaml b/src/denoising/api/comp_split_dataset.yaml similarity index 100% rename from src/denoising/api/comp_split_data.yaml rename to src/denoising/api/comp_split_dataset.yaml diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index ee7f4a927c..6966a1366f 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__inherits__: ../../api/comp_control_method.yaml functionality: name: "no_denoising" namespace: "denoising/control_methods" @@ -6,11 +6,6 @@ functionality: info: type: negative_control label: no denoising - # paper_name: "Molecular Cross-Validation for Single-Cell RNA-seq"" - # paper_url: "https://doi.org/10.1101/786269" - # paper_year: 2019 - paper_doi: "10.1101/786269" - code_url: "https://github.com/czbiohub/molecular-cross-validation" v1_url: /openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index b42a343e67..aef8fca288 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__inherits__: ../../api/comp_control_method.yaml functionality: name: "perfect_denoising" namespace: "denoising/control_methods" @@ -6,11 +6,6 @@ functionality: info: type: positive_control label: perfect denoising - # paper_name: "Molecular Cross-Validation for Single-Cell RNA-seq"" - # paper_url: "https://doi.org/10.1101/786269" - # paper_year: 2019 - paper_doi: "10.1101/786269" - code_url: "https://github.com/czbiohub/molecular-cross-validation" v1_url: /openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/denoising/data_processing/split_data/params.yaml b/src/denoising/data_processing/split_data/params.yaml deleted file mode 100644 index 025d3946ba..0000000000 --- a/src/denoising/data_processing/split_data/params.yaml +++ /dev/null @@ -1,4 +0,0 @@ -param_list: -- id: pancreas - input: /home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad -seed: 123 diff --git a/src/denoising/readme.md b/src/denoising/docs/readme.md similarity index 100% rename from src/denoising/readme.md rename to src/denoising/docs/readme.md diff --git a/src/denoising/metrics/possion/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml similarity index 100% rename from src/denoising/metrics/possion/config.vsh.yaml rename to src/denoising/metrics/poisson/config.vsh.yaml diff --git a/src/denoising/metrics/possion/script.py b/src/denoising/metrics/poisson/script.py similarity index 100% rename from src/denoising/metrics/possion/script.py rename to src/denoising/metrics/poisson/script.py diff --git a/src/denoising/data_processing/split_data/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml similarity index 87% rename from src/denoising/data_processing/split_data/config.vsh.yaml rename to src/denoising/split_dataset/config.vsh.yaml index 4b6ab76fbe..7e72d2a8c2 100644 --- a/src/denoising/data_processing/split_data/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -1,7 +1,7 @@ -__inherits__: ../../api/comp_split_data.yaml +__inherits__: ../api/comp_split_dataset.yaml functionality: - name: "split_data" - namespace: "denoising/data_processing" + name: "split_datase" + namespace: "denoising" arguments: - name: "--method" type: "string" diff --git a/src/denoising/split_dataset/params.yaml b/src/denoising/split_dataset/params.yaml new file mode 100644 index 0000000000..d6d333fa88 --- /dev/null +++ b/src/denoising/split_dataset/params.yaml @@ -0,0 +1,4 @@ +param_list: +- id: pancreas + input: resources_test/common/pancreas/dataset.h5ad +seed: 123 diff --git a/src/denoising/data_processing/split_data/run_nextflow.sh b/src/denoising/split_dataset/run_nextflow.sh similarity index 66% rename from src/denoising/data_processing/split_data/run_nextflow.sh rename to src/denoising/split_dataset/run_nextflow.sh index 1eaa4b7af7..d2b6eec0c6 100644 --- a/src/denoising/data_processing/split_data/run_nextflow.sh +++ b/src/denoising/split_dataset/run_nextflow.sh @@ -10,8 +10,8 @@ export NXF_VER=22.04.5 bin/nextflow \ run . \ - -main-script target/nextflow/denoising/data_processing/split_data/main.nf \ + -main-script target/nextflow/denoising/split_data/main.nf \ -profile docker \ -resume \ - -params-file src/denoising/data_processing/split_data/params.yaml \ + -params-file src/denoising/split_data/params.yaml \ --publish_dir output/denoising/ \ No newline at end of file diff --git a/src/denoising/data_processing/split_data/script.py b/src/denoising/split_dataset/script.py similarity index 80% rename from src/denoising/data_processing/split_data/script.py rename to src/denoising/split_dataset/script.py index 6b8ab1ba7f..4113b20484 100644 --- a/src/denoising/data_processing/split_data/script.py +++ b/src/denoising/split_dataset/script.py @@ -64,20 +64,6 @@ output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) -# NOTE: remove cells which have not enough reads -> is it possible to remove same cells/genes in test set as in train set a above ? -# * first, remove genes with 0 expression -# * then, remove cells with 1 count or less - -# def filter_genes_cells(adata): -# """Remove empty cells and genes.""" -# sc.pp.filter_genes(adata, min_cells=1) -# sc.pp.filter_cells(adata, min_counts=1) -# return adata - - -# filter_genes_cells(output_train) - print(">> Writing") - output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) diff --git a/src/denoising/workflows/run/config.vsh.yaml b/src/denoising/workflows/run/config.vsh.yaml index 4c5bbab8c4..07960e56b1 100644 --- a/src/denoising/workflows/run/config.vsh.yaml +++ b/src/denoising/workflows/run/config.vsh.yaml @@ -12,8 +12,6 @@ functionality: type: "file" # todo: replace with includes - name: "--input_test" type: "file" # todo: replace with includes - - name: "--input_solution" - type: "file" # todo: replace with includes - name: Outputs arguments: - name: "--output" From 2f24911321bef714dca20da6b57a59e7ed2c2a79 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Nov 2022 12:08:26 +0100 Subject: [PATCH 0436/1233] update Former-commit-id: b2b4da9fe418587813e8066fb5691dbe07838525 --- src/label_projection/README.md | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 5654c711fc..5f7e8fbc7e 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -55,14 +55,19 @@ labels onto the test set. Methods for assigning labels from a reference dataset to a new dataset. -| Name | Type | Description | DOI | URL | -|:---------------------------------------------------------------------|:-----------------|:------------------------------------------------------|:-----------------------------------------------------|:-------------------------------------------------------------------------------------------------------| -| [KNN](./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html) | -| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html) | -| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html) | -| [Majority Vote](./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | -| [Random Labels](./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | -| [True labels](./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | +| Name | Type | Description | DOI | URL | +|:---------------------------------------------------------------------|:--------------------------------------------------|:-----------------------------------------------------------|:-----------------------------------------------------|:-----------------------------------------------------| +| [KNN](./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://github.com/scikit-learn/scikit-learn) | +| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://github.com/scikit-learn/scikit-learn) | +| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://github.com/scikit-learn/scikit-learn) | +| [SCANVI](./methods/scanvi/config.vsh.yaml) | method | Probabilistic harmonization and annotation of single-cell | | | +| transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | | | +| [Seurat TransferData](./methods/seurat_transferdata/config.vsh.yaml) | method | The Seurat v3 anchoring procedure is designed to integrate | | | +| diverse single-cell datasets across technologies and modalities. | [link](https://doi.org/10.1101/460147) | [link](https://github.com/satijalab/seurat) | | | +| [XGBoost](./methods/xgboost/config.vsh.yaml) | method | XGBoost: A Scalable Tree Boosting System | [link](https://doi.org/10.1145/2939672.2939785) | [link](https://github.com/dmlc/xgboost) | +| [Majority Vote](./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | +| [Random Labels](./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | +| [True labels](./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | ## Metrics From 2d392d692ba02bd29ec97a1f0315dd83f54241dd Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 23 Nov 2022 13:16:54 +0100 Subject: [PATCH 0437/1233] add umap Former-commit-id: 98f83793136fec3553f15fc36e3d0929fb36f478 --- .../methods/umap/config.vsh.yaml | 28 ++++++++++++++ .../methods/umap/script.py | 38 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 src/dimensionality_reduction/methods/umap/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/umap/script.py diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml new file mode 100644 index 0000000000..50437d5011 --- /dev/null +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -0,0 +1,28 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "umap" + namespace: "dimensionality_reduction/methods" + description: "Uniform manifold approximation and projection" + info: + type: method + label: UMAP + v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + preferred_normalization: log_cpm + arguments: + - name: "--n_pca" + type: integer + default: 50 + description: Number of principal components of PCA to use. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py new file mode 100644 index 0000000000..ad8181b1ad --- /dev/null +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -0,0 +1,38 @@ +import anndata as ad +import scanpy as sc + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', + 'n_pca': 50, +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +adata = ad.read_h5ad(par['input']) + +print('Select top 1000 high variable genes') +n_genes = 1000 +idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + +print('Apply PCA with 50 dimensions') +adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") + +print('Calculate a nearest-neighbour graph') +sc.pp.neighbors(adata, use_rep="X_pca_hvg", n_pcs=par['n_pca']) + +print("Run UMAP") +sc.tl.umap(adata) + +adata.obsm["X_emb"] = adata.obsm["X_umap"].copy() + +# Update .uns +adata.uns['method_id'] = 'umap' +adata.uns['normalization_id'] = 'log_cpm' + +print("Write output to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From df36c5be51f56fe6602e35855d44487b827173e5 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 23 Nov 2022 13:17:15 +0100 Subject: [PATCH 0438/1233] recalculate pca from hvg Former-commit-id: 2fb9da453b4a7470248785d9a01c1f13942d1b98 --- .../methods/tsne/script.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index dc8307ee82..cc0a0ea1b6 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -12,20 +12,28 @@ } ## VIASH END +print("Load input data") adata = ad.read_h5ad(par['input']) -# t-SNE -sc.tl.tsne(adata, use_rep="X_pca", n_pcs=par['n_pca']) +print('Select top 1000 high variable genes') +n_genes = 1000 +idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + +print('Apply PCA with 50 dimensions') +adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") + +print('Run t-SNE') +sc.tl.tsne(adata, use_rep="X_pca_hvg", n_pcs=par['n_pca']) adata.obsm["X_emb"] = adata.obsm["X_tsne"].copy() # Update .uns adata.uns['method_id'] = 'tsne' -adata.uns['normalization_id'] = 'pca' +adata.uns['normalization_id'] = 'log_cpm' #del(adata.uns["pca_variance"]) #del(adata.uns["tsne"]) # Update .obsm/.varm #del(adata.obsm["X_tsne"]) #del(adata.varm["pca_loadings"]) -# Write output +print("Write output to file") adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 392cd2261c68331c90c9e99bb31b62fe3610c8af Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 23 Nov 2022 17:29:04 +0100 Subject: [PATCH 0439/1233] add unit testing to methods and control_methods Former-commit-id: 2b44c77acaadc5bcbd1bc4d90ad1667bd6eadbf0 --- src/denoising/api/comp_control_method.yaml | 96 +++++++++---------- src/denoising/api/comp_method.yaml | 91 ++++++++---------- .../methods/knn_smoothing/config.vsh.yaml | 3 +- src/denoising/methods/knn_smoothing/script.py | 11 +-- src/denoising/methods/magic/config.vsh.yaml | 2 - 5 files changed, 89 insertions(+), 114 deletions(-) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 9cb99ae54b..c1cabec5f0 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -7,55 +7,47 @@ functionality: - name: "--output" __inherits__: anndata_denoised.yaml direction: output - # TODO: currently needs to be manually specified since the default value needs to be overrideable - # - name: "--layer_input" - # type: string - # default: "log_cpm" - # description: Which layer to use as input. - # test_resources: - # - path: ../../../../resources_test/label_projection/pancreas - # - type: python_script - # path: generic_test.py - # text: | - # import anndata as ad - # import subprocess - # from os import path - - # input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - # input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - # output_path = "output.h5ad" - - # cmd = [ - # meta['executable'], - # "--input_train", input_train_path, - # "--input_test", input_test_path, - # "--output", output_path - # ] - - # # todo: if we could access the viash config, we could check whether - # # .functionality.info.type == "positive_control" - # if meta['functionality_name'] == 'true_labels': - # cmd = cmd + ["--input_solution", input_solution_path] - - # print(">> Running script as test") - # out = subprocess.check_output(cmd).decode("utf-8") - - # print(">> Checking whether output file exists") - # assert path.exists(output_path) - - # print(">> Reading h5ad files") - # input_test = ad.read_h5ad(input_test_path) - # output = ad.read_h5ad(output_path) - # print("input_test:", input_test) - # print("output:", output) - - # print(">> Checking whether predictions were added") - # assert "label_pred" in output.obs - # assert meta['functionality_name'] == output.uns["method_id"] - - # print("Checking whether data from input was copied properly to output") - # assert input_test.n_obs == output.n_obs - # assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - - # print("All checks succeeded!") + test_resources: + - path: ../../../../output/denoising + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_train_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_train.h5ad" + input_test_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_test.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--output", output_path + ] + + if meta['functionality_name'] == 'perfect_denoising': + cmd = cmd + ["--input_test", input_test_path] + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + print("input_test:", input_test) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "denoised" in output.layers + assert meta['functionality_name'] == output.uns["method_id"] + + print("Checking whether data from input was copied properly to output") + assert input_test.n_obs == output.n_obs + assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 76528d4e8b..2f44b5b088 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -5,55 +5,42 @@ functionality: - name: "--output" __inherits__: anndata_denoised.yaml direction: output - # TODO: currently needs to be manually specified since the default value needs to be overrideable - # - name: "--layer_input" - # type: string - # default: "log_cpm" - # description: Which layer to use as input. - # test_resources: - # - path: ../../../../resources_test/label_projection/pancreas - # - type: python_script - # path: generic_test.py - # text: | - # import anndata as ad - # import subprocess - # from os import path - - # input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - # input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - # output_path = "output.h5ad" - - # cmd = [ - # meta['executable'], - # "--input_train", input_train_path, - # "--input_test", input_test_path, - # "--output", output_path - # ] - - # # todo: if we could access the viash config, we could check whether - # # .functionality.info.type == "positive_control" - # if meta['functionality_name'] == 'true_labels': - # cmd = cmd + ["--input_solution", input_solution_path] - - # print(">> Running script as test") - # out = subprocess.check_output(cmd).decode("utf-8") - - # print(">> Checking whether output file exists") - # assert path.exists(output_path) - - # print(">> Reading h5ad files") - # input_test = ad.read_h5ad(input_test_path) - # output = ad.read_h5ad(output_path) - # print("input_test:", input_test) - # print("output:", output) - - # print(">> Checking whether predictions were added") - # assert "label_pred" in output.obs - # assert meta['functionality_name'] == output.uns["method_id"] - - # print("Checking whether data from input was copied properly to output") - # assert input_test.n_obs == output.n_obs - # assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - - # print("All checks succeeded!") + test_resources: + - path: ../../../../output/denoising + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_train_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_train.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--output", output_path + ] + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + print("input_test:", input_test) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "denoised" in output.layers + assert meta['functionality_name'] == output.uns["method_id"] + + print("Checking whether data from input was copied properly to output") + assert input_test.n_obs == output.n_obs + assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 3f3ac06147..86bba654ba 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -1,6 +1,5 @@ __inherits__: ../../api/comp_method.yaml functionality: - status: disabled name: "KNN_smoothing" namespace: "denoising/methods" description: "iterative K-nearest neighbor smoothing" @@ -26,5 +25,5 @@ platforms: packages: - "anndata>=0.8" github: - - knn_smooth + - scottgigante-immunai/knn-smoothing - type: nextflow diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py index 948f41e96b..b8b16eab03 100644 --- a/src/denoising/methods/knn_smoothing/script.py +++ b/src/denoising/methods/knn_smoothing/script.py @@ -1,10 +1,10 @@ -import knn_smooth #NOTE: not a python package but just a py script on github +import knn_smooth import numpy as np import anndata as ad ## VIASH START par = { - 'input_train': 'resources/label_projection/openproblems_v1/pancreas.split_dataset.output_train.h5ad', + 'input_train': 'output/denoising/pancreas.split_data.output_train.h5ad', 'output': 'output_knn.h5ad', } meta = { @@ -17,9 +17,8 @@ print("process data") X = input_train.layers["counts"].transpose().toarray() -output_denoised = input_train.copy() -output_denoised.layers["counts"] = (knn_smooth.knn_smoothing(X, k=10)).transpose() +input_train.layers["denoised"] = (knn_smooth.knn_smoothing(X, k=10)).transpose() print("Writing data") -output_denoised.uns["method_id"] = par["functionality_name"] -output_denoised.write_h5ad(par["output"], compression="gzip") +input_train.uns["method_id"] = meta["functionality_name"] +input_train.write_h5ad(par["output"], compression="gzip") diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 268db5af8b..fc79b116fb 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -20,10 +20,8 @@ functionality: choices: ["exact", "approximate"] default: "exact" description: Which solver to use. - required: true - name: "--norm" type: string - required: true choices: ["sqrt", "log"] default: "sqrt" description: Normalization method From 05586e6398fe5565dd3b494f8179647ee5b3f1a1 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 23 Nov 2022 20:48:34 +0100 Subject: [PATCH 0440/1233] add densmap Former-commit-id: 8fe9c968002c3571e08f86b29458828cc52d7cf1 --- .../methods/densmap/config.vsh.yaml | 27 +++++++++++++ .../methods/densmap/script.py | 39 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 src/dimensionality_reduction/methods/densmap/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/densmap/script.py diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml new file mode 100644 index 0000000000..7cc0d4a9ee --- /dev/null +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -0,0 +1,27 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "densmap" + namespace: "dimensionality_reduction/methods" + description: "density-preserving based on UMAP" + info: + type: method + label: densMAP + v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py + v1_commit: + preferred_normalization: log_cpm + arguments: + - name: "--no_pca" + type: boolean_true + description: Do not apply PCA with 50 dimensions before running UMAP. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py new file mode 100644 index 0000000000..b9d4212260 --- /dev/null +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -0,0 +1,39 @@ +import anndata as ad +from umap import UMAP +import scanpy as sc + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', + 'no_pca': False, +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +adata = ad.read_h5ad(par['input']) + +print('Select top 1000 high variable genes') +n_genes = 1000 +idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + +print("Run UMAP...") +if par['no_pca']: + print('... using logCPM data') + adata.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(adata.layers['normalized'][:, idx]) +else: + print('... after applying PCA with 50 dimensions to logCPM data') + adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack") + adata.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(adata.obsm['X_pca_hvg']) + +print(adata.obsm['X_emb'][:10,:]) + +# Update .uns +adata.uns['method_id'] = 'densmap' +adata.uns['normalization_id'] = 'log_cpm' + +print("Write output to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From e44c8cae03e09ab1259993bd59ee6481c95339e4 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 24 Nov 2022 11:36:30 +0100 Subject: [PATCH 0441/1233] add metrics unit testing Former-commit-id: b36ab661bff2878760bab474251e47ed4cbbf2d4 --- src/denoising/api/comp_metric.yaml | 78 +++++++++---------- .../perfect_denoising/script.py | 4 +- .../docs/{readme.md => task_description.md} | 0 3 files changed, 41 insertions(+), 41 deletions(-) rename src/denoising/docs/{readme.md => task_description.md} (100%) diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 661cd82c03..a77dc789e7 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -7,42 +7,42 @@ functionality: - name: "--output" __inherits__: anndata_score.yaml direction: output - # test_resources: - # - path: ../../../../resources_test/label_projection/pancreas - # - type: python_script - # path: format_check.py - # text: | - # import anndata as ad - # import subprocess - # from os import path - - # input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" - # input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - # output_path = "output.h5ad" - - # cmd = [ - # meta['executable'], - # "--input_prediction", input_prediction_path, - # "--input_solution", input_solution_path, - # "--output", output_path - # ] - - # print(">> Running script as test") - # out = subprocess.check_output(cmd).decode("utf-8") - - # print(">> Checking whether output file exists") - # assert path.exists(output_path) - - # input_solution = ad.read_h5ad(input_solution_path) - # input_prediction = ad.read_h5ad(input_prediction_path) - # output = ad.read_h5ad(output_path) - - # print("Checking whether data from input was copied properly to output") - # assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] - # assert output.uns["method_id"] == input_prediction.uns["method_id"] - # assert output.uns["metric_ids"] is not None - # assert output.uns["metric_values"] is not None - - # # TODO: check whether the metric ids are all in .functionality.info - - # print("All checks succeeded!") + test_resources: + - path: ../../../../output/denoising/ + - type: python_script + path: format_check.py + text: | + import anndata as ad + import subprocess + from os import path + + input_denoised_path = meta["resources_dir"] + "/denoising/output_baseline_PD.h5ad" + input_test_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_test.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input_denoised", input_denoised_path, + "--input_test", input_test_path, + "--output", output_path + ] + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + input_denoised = ad.read_h5ad(input_denoised_path) + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + + print("Checking whether data from input was copied properly to output") + assert output.uns["dataset_id"] == input_denoised.uns["dataset_id"] + assert output.uns["method_id"] == input_denoised.uns["method_id"] + assert output.uns["metric_ids"] is not None + assert output.uns["metric_values"] is not None + + # TODO: check whether the metric ids are all in .functionality.info + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/denoising/control_methods/perfect_denoising/script.py b/src/denoising/control_methods/perfect_denoising/script.py index cdfa113040..995814faf1 100644 --- a/src/denoising/control_methods/perfect_denoising/script.py +++ b/src/denoising/control_methods/perfect_denoising/script.py @@ -2,8 +2,8 @@ ## VIASH START par = { - 'input_train': 'output_train.h5ad', - 'input_test': 'output_test.h5ad', + 'input_train': 'output/denoising/pancreas.split_data.output_train.h5ad', + 'input_test': 'output/denoising/pancreas.split_data.output_test.h5ad', 'output': 'output_baseline_PD.h5ad', } meta = { diff --git a/src/denoising/docs/readme.md b/src/denoising/docs/task_description.md similarity index 100% rename from src/denoising/docs/readme.md rename to src/denoising/docs/task_description.md From b1b72cfa7c79fdbc8ecc46dcc66f6f19678e4bba Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Nov 2022 13:34:28 +0100 Subject: [PATCH 0442/1233] fixes to dataflowhelper Former-commit-id: 5d7a8df82c9db66e21f34486806fa12f1fc90580 --- src/nxf_utils/DataFlowHelper.nf | 57 ++++++++++++++++++++++++--------- 1 file changed, 42 insertions(+), 15 deletions(-) diff --git a/src/nxf_utils/DataFlowHelper.nf b/src/nxf_utils/DataFlowHelper.nf index 3c19f0d7ec..1057038288 100644 --- a/src/nxf_utils/DataFlowHelper.nf +++ b/src/nxf_utils/DataFlowHelper.nf @@ -25,19 +25,20 @@ def setWorkflowArguments(Map args) { main: output_ = input_ | map{ tup -> - id = tup[0] - data = tup[1] - passthrough = tup.drop(2) + assert tup.size() : "Event should have length 2 or greater. Expected format: [id, data]." + def id = tup[0] + def data = tup[1] + def passthrough = tup.drop(2) // determine new data - toRemove = args.collectMany{ _, dataKeys -> + def toRemove = args.collectMany{ _, dataKeys -> // dataKeys is a map but could also be a list dataKeys instanceof List ? dataKeys : dataKeys.values() }.unique() - newData = data.findAll{!toRemove.contains(it.key)} + def newData = data.findAll{!toRemove.contains(it.key)} // determine splitargs - splitArgs = args. + def splitArgs = args. collectEntries{procKey, dataKeys -> // dataKeys is a map but could also be a list newSplitData = dataKeys @@ -76,18 +77,23 @@ def getWorkflowArguments(Map args) { main: output_ = input_ - | map{ tup -> - id = tup[0] - data = tup[1] - splitArgs = tup[2].clone() + | map{ tup -> + assert tup.size() : "Event should have length 3 or greater. Expected format: [id, data, splitArgs]." + + def id = tup[0] + def data = tup[1] + def splitArgs = tup[2].clone() - passthrough = tup.drop(3) + def passthrough = tup.drop(3) // try to infer arg name if (data !instanceof Map) { data = [[ inputKey, data ]].collectEntries() } - newData = data + splitArgs.remove(args.key) + assert splitArgs instanceof Map: "Third element of event (id: $id) should be a map" + assert splitArgs.containsKey(args.key): "Third element of event (id: $id) should have a key ${args.key}" + + def newData = data + splitArgs.remove(args.key) [ id, newData, splitArgs] + passthrough } @@ -134,7 +140,7 @@ def passthroughMap(Closure clos) { main: output_ = input_ | map{ tup -> - out = clos(tup.take(numArgs)) + def out = clos(tup.take(numArgs)) out + tup.drop(numArgs) } @@ -155,9 +161,10 @@ def passthroughFlatMap(Closure clos) { main: output_ = input_ | flatMap{ tup -> - out = clos(tup.take(numArgs)) + def out = clos(tup.take(numArgs)) + def pt = tup.drop(numArgs) for (o in out) { - o.addAll(tup.drop(numArgs)) + o.addAll(pt) } out } @@ -167,4 +174,24 @@ def passthroughFlatMap(Closure clos) { } return passthroughFlatMapWf +} + +def passthroughFilter(Closure clos) { + def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount + + workflow passthroughFilterWf { + take: + input_ + + main: + output_ = input_ + | filter{ tup -> + clos(tup.take(numArgs)) + } + + emit: + output_ + } + + return passthroughFilterWf } \ No newline at end of file From ded451642fe4bba4191def97f5834b26a6ee5799 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Nov 2022 13:34:41 +0100 Subject: [PATCH 0443/1233] refactor benchmark pipeline Former-commit-id: b929ded1bb766e6d85c05f121a52fd9e82a735c2 --- src/label_projection/workflows/run/main.nf | 172 +++++++++++++-------- 1 file changed, 111 insertions(+), 61 deletions(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 220653a33b..11428d3eed 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -25,10 +25,16 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/nxf_utils/DataFlowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") +// construct a map of methods (id -> method_module) +methods = [ true_labels, majority_vote, random_labels, knn, mlp, logistic_regression, scanvi, seurat_transferdata, xgboost ] + .collectEntries{method -> + [method.config.functionality.name, method] + } + workflow { helpMessage(config) @@ -36,90 +42,134 @@ workflow { | run_wf } -/** - * Helper function for making sure the right data gets passed to a method - */ -def configureMethod = { module -> - // if method is a control method, add the solution to the data field - def methodType = module.config.functionality.info.type - def mapFun = null - if (methodType != "method") { - mapFun = { tup -> - out = tup.clone() - out[1] = out[1] + [input_solution: out[2].metric.input_solution] - out - } - } - - // only let datasets with the right preferred normalization through - // if preferred is 'counts', use any normalization method - def preferred = module.config.functionality.info.preferred_normalization - if (preferred == "counts") { - preferred = "log_cpm" - } - - def filterFun = { tup -> - tup[1].normalization_id == preferred - } - - // return module - module.run( - map: mapFun, - filter: filterFun - ) -} - workflow run_wf { take: input_ch main: - output_ch = input_ch // split params for downstream components | setWorkflowArguments( - method: ["input_train", "input_test", "normalization_id", "dataset_id"], + preprocess: ["normalization_id", "dataset_id"], + method: ["input_train", "input_test"], metric: ["input_solution"], output: ["output"] ) + + // multiply events by the number of method + | getWorkflowArguments(key: "preprocess") + | add_methods + + // filter the normalization methods that a method actually prefers + | check_filtered_normalization_id + + // add input_solution to data for the positive controls + | controls_can_cheat // run methods - | getWorkflowArguments(key: "method") - | ( - configureMethod(true_labels) & - configureMethod(random_labels) & - configureMethod(majority_vote) & - configureMethod(knn) & - configureMethod(logistic_regression) & - configureMethod(mlp) & - configureMethod(scanvi) & - configureMethod(seurat_transferdata) & - configureMethod(xgboost) - ) - | mix + | run_methods + + // run metrics + | run_metrics + + // convert to tsv + | aggregate_results - // construct tuples for metrics - | pmap{ id, file, passthrough -> - // derive unique ids from output filenames - def newId = file.getName().replaceAll(".output.*", "") - // combine prediction with solution - def newData = [ input_prediction: file, input_solution: passthrough.metric.input_solution ] - [ newId, newData, passthrough ] + emit: + output_ch +} + +workflow add_methods { + take: input_ch + main: + output_ch = Channel.fromList(methods.keySet()) + | combine(input_ch) + + // generate combined id for method_id and dataset_id + | pmap{method_id, dataset_id, data -> + def new_id = dataset_id + "." + method_id + def new_data = data.clone() + [method_id: method_id] + new_data.remove("id") + [new_id, new_data] } + emit: output_ch +} - // run metrics +workflow check_filtered_normalization_id { + take: input_ch + main: + output_ch = input_ch + | pfilter{id, data -> + data = data.clone() + def method = methods[data.method_id] + def preferred = method.config.functionality.info.preferred_normalization + // if a method is just using the counts, we can use any normalization method + if (preferred == "counts") { + preferred = "log_cpm" + } + data.normalization_id == preferred + } + emit: output_ch +} + +workflow controls_can_cheat { + take: input_ch + main: + output_ch = input_ch + | pmap{id, data, passthrough -> + def method = methods[data.method_id] + def method_type = method.config.functionality.info.method_type + def new_data = data.clone() + if (method_type != "method") { + new_data = new_data + [input_solution: passthrough.metric.input_solution] + } + [id, new_data, passthrough] + } + emit: output_ch +} + +workflow run_methods { + take: input_ch + main: + // generate one channel per method + method_chs = methods.collect { method_id, method_module -> + input_ch + | filter{it[1].method_id == method_id} + | method_module + } + // mix all results + output_ch = method_chs[0].mix(*method_chs.drop(1)) + + emit: output_ch +} + +workflow run_metrics { + take: input_ch + main: + + output_ch = input_ch + | getWorkflowArguments(key: "metric", inputKey: "input_prediction") | (accuracy & f1) | mix - // convert to tsv + emit: output_ch +} + +workflow aggregate_results { + take: input_ch + main: + + output_ch = input_ch | toSortedList - | map{ it -> [ "combined", it.collect{ it[1] } ] + it[0].drop(2) } + | filter{ it.size() > 0 } + | map{ it -> + [ "combined", it.collect{ it[1] } ] + it[0].drop(2) + } | getWorkflowArguments(key: "output") | extract_scores.run( auto: [ publish: true ] ) - emit: - output_ch + emit: output_ch } \ No newline at end of file From c2cdbefb617eb4a509bc850a9840bc098006935e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Nov 2022 13:36:51 +0100 Subject: [PATCH 0444/1233] fix workflow arguments flow Former-commit-id: cfbb0ddd95999c7ba0f4d9e4a2d6b4d25762915d --- src/label_projection/workflows/run/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 11428d3eed..90b61d922c 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -68,9 +68,11 @@ workflow run_wf { | controls_can_cheat // run methods + | getWorkflowArguments(key: "method") | run_methods // run metrics + | getWorkflowArguments(key: "metric", inputKey: "input_prediction") | run_metrics // convert to tsv @@ -149,7 +151,6 @@ workflow run_metrics { main: output_ch = input_ch - | getWorkflowArguments(key: "metric", inputKey: "input_prediction") | (accuracy & f1) | mix From 819789b80d272704f8d64e2d92e0813be901c5db Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Nov 2022 13:42:17 +0100 Subject: [PATCH 0445/1233] fetch dataflow helper from viash Former-commit-id: c534fccf13a0fac00417b646a599c564d2328111 --- bin/init | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/init b/bin/init index bb1a86cf38..9b5ac7917c 100755 --- a/bin/init +++ b/bin/init @@ -19,6 +19,7 @@ NXF_UTILS=src/nxf_utils [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf +bin/viash export resource platforms/nextflow/DataflowHelper.config > $NXF_UTILS/DataFlowHelper.config cd bin From 6f3acf111002d5171a0cf2be579c3e11a9877c76 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 24 Nov 2022 17:23:19 +0100 Subject: [PATCH 0446/1233] add v1_commit Former-commit-id: 8c82bdc20825787006116032924ce7a6c4f28899 --- src/dimensionality_reduction/methods/densmap/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 7cc0d4a9ee..30852e4603 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: type: method label: densMAP v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py - v1_commit: + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm arguments: - name: "--no_pca" From d4cb4b7288dc6d3aea8ea3002e9f3228b4b0cf8a Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 24 Nov 2022 17:23:34 +0100 Subject: [PATCH 0447/1233] add method: phate Former-commit-id: 008a1f0fd410704b8a4334253a1959ad840506b0 --- .../methods/phate/config.vsh.yaml | 35 +++++++++++++ .../methods/phate/script.py | 49 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 src/dimensionality_reduction/methods/phate/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/phate/script.py diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml new file mode 100644 index 0000000000..145befdae1 --- /dev/null +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -0,0 +1,35 @@ +__inherits__: ../../api/comp_method.yaml +functionality: + name: "phate" + namespace: "dimensionality_reduction/methods" + description: "" + info: + type: method + label: PHATE + v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py + v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 + preferred_normalization: log_cpm + arguments: + - name: '--hvg' + type: boolean_true + description: Use logCPM of 1000 HVGs instead of the square-root CPM transformed expression matrix. + - name: '--n_pca' + type: integer + default: 50 + description: Number of principal components of PCA to use. + - name: '--g0' + type: boolean_true + description: Set informational distance constant to 0. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - "anndata>=0.8" + - phate + - scprep + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py new file mode 100644 index 0000000000..7642d8b3a5 --- /dev/null +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -0,0 +1,49 @@ +import anndata as ad +from phate import PHATE +import scprep as sc +# import yaml + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', + 'n_pca': 50, + 'g0': False, + 'hvg': False +} +meta = { + 'functionality_name': 'foo', + 'config': 'src/dimensionality_reduction/methods/phate/config.vsh.yaml' +} +## VIASH END +# with open(meta['config'], 'r') as config_file: +# config = yaml.safe_load(config_file) + +# config['functionality']['info']['preferred_normalization'] +# print(meta) + +print("Load input data") +adata = ad.read_h5ad(par['input']) + +print("Run PHATE...") +gamma = 0 if par['g0'] else 1 +print('... with gamma=' + str(gamma) + ' and...') +phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=gamma) + +if par['hvg']: + print('... using logCPM data') + n_genes = 1000 + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + adata.obsm["X_emb"] = phate_op.fit_transform(adata.layers['normalized'][:, idx]) + adata.uns['normalization_id'] = 'log_cpm' +else: + print('... using sqrt-CPM data') + adata.layers['sqrt_cpm'] = sc.transform.sqrt(adata.layers['normalized'].expm1()) + adata.obsm["X_emb"] = phate_op.fit_transform(adata.layers['sqrt_cpm']) + adata.uns['normalization_id'] = 'sqrt_cpm' + +# Update .uns +adata.uns['method_id'] = 'phate' + +print("Write output to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From fd47ddc73f40c4a0b685cc81c40bea6d87757d09 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 24 Nov 2022 20:01:16 +0100 Subject: [PATCH 0448/1233] add unit tests Former-commit-id: c62b0f812d2a58926eae3259c5782a6b5f008176 --- .../methods/umap/config.vsh.yaml | 5 ++ .../methods/umap/test.py | 47 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 src/dimensionality_reduction/methods/umap/test.py diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 50437d5011..c2deda27c7 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -17,6 +17,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/methods/umap/test.py b/src/dimensionality_reduction/methods/umap/test.py new file mode 100644 index 0000000000..962fde2cc6 --- /dev/null +++ b/src/dimensionality_reduction/methods/umap/test.py @@ -0,0 +1,47 @@ +import anndata as ad +import subprocess +from os import path + +## VIASH START +meta = { + 'executable': './target/docker/dimensionality_reduction/umap', + 'resources_dir': './resources_test/common/', + 'cpus': 2 +} +## VIASH END + +input_path = meta["resources_dir"] + "/input/dataset.h5ad" +output_path = "output.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether predictions were added") +assert "X_emb" in output.obsm +assert meta['functionality_name'] == output.uns["method_id"] +assert 'normalization_id' in output.uns + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From 23fb666e3d0a293e553ccf6fd465a1eb4bd311ec Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 24 Nov 2022 21:39:36 +0000 Subject: [PATCH 0449/1233] Bump tj-actions/changed-files from 34.4.4 to 34.5.0 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.4.4 to 34.5.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.4.4...v34.5.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: cd0e95aafd996a48e8e6b170d47bccd71333d104 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 5e03b15327..4907a485ca 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -74,7 +74,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.4.4 + uses: tj-actions/changed-files@v34.5.0 with: separator: ";" diff_relative: true From dfc715627f026f066665167ec0577539d1cedafb Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 25 Nov 2022 10:49:29 +0100 Subject: [PATCH 0450/1233] add unit testing for split_dataset Former-commit-id: 4187fe32dcac7f98c620672397c1f572d38ea61e --- src/denoising/api/comp_method.yaml | 8 +- src/denoising/api/comp_split_dataset.yaml | 74 +------------------ .../methods/knn_smoothing/config.vsh.yaml | 4 +- src/denoising/split_dataset/config.vsh.yaml | 2 +- src/denoising/split_dataset/generic_test.py | 40 ++++++++++ src/denoising/split_dataset/script.py | 22 ++++-- 6 files changed, 65 insertions(+), 85 deletions(-) create mode 100644 src/denoising/split_dataset/generic_test.py diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 2f44b5b088..cd6c39e985 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -30,9 +30,9 @@ functionality: assert path.exists(output_path) print(">> Reading h5ad files") - input_test = ad.read_h5ad(input_test_path) + input_train = ad.read_h5ad(input_train_path) output = ad.read_h5ad(output_path) - print("input_test:", input_test) + print("input_train:", input_train) print("output:", output) print(">> Checking whether predictions were added") @@ -40,7 +40,7 @@ functionality: assert meta['functionality_name'] == output.uns["method_id"] print("Checking whether data from input was copied properly to output") - assert input_test.n_obs == output.n_obs - assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + assert input_train.n_obs == output.n_obs + assert input_train.uns["dataset_id"] == output.uns["dataset_id"] print("All checks succeeded!") diff --git a/src/denoising/api/comp_split_dataset.yaml b/src/denoising/api/comp_split_dataset.yaml index 5108b6094e..111e06266e 100644 --- a/src/denoising/api/comp_split_dataset.yaml +++ b/src/denoising/api/comp_split_dataset.yaml @@ -8,73 +8,7 @@ functionality: - name: "--output_test" __inherits__: anndata_test.yaml direction: output - # test_resources: - # - type: python_script - # path: generic_test.py - # text: | - # import anndata as ad - # import subprocess - # from os import path - - # input_path = meta["resources_dir"] + "/pancreas/dataset_cpm.h5ad" - # output_train_path = "output_train.h5ad" - # output_test_path = "output_test.h5ad" - # output_solution_path = "output_solution.h5ad" - - # cmd = [ - # meta['executable'], - # "--input", input_path, - # "--output_train", output_train_path, - # "--output_test", output_test_path, - # "--output_solution", output_solution_path - # ] - - # print(">> Running script as test") - # out = subprocess.check_output(cmd).decode("utf-8") - - # print(">> Checking whether output file exists") - # assert path.exists(output_train_path) - # assert path.exists(output_test_path) - # assert path.exists(output_solution_path) - - # print(">> Reading h5ad files") - # input = ad.read_h5ad(input_path) - # output_train = ad.read_h5ad(output_train_path) - # output_test = ad.read_h5ad(output_test_path) - # output_solution = ad.read_h5ad(output_solution_path) - - # print("input:", input) - # print("output_train:", output_train) - # print("output_test:", output_test) - # print("output_solution:", output_solution) - - # print(">> Checking dimensions, make sure no cells were dropped") - # assert input.n_obs == output_train.n_obs + output_test.n_obs - # assert output_test.n_obs == output_solution.n_obs - # assert input.n_vars == output_train.n_vars - # assert input.n_vars == output_test.n_vars - - # print(">> Checking whether data from input was copied properly to output") - # assert output_train.uns["dataset_id"] == input.uns["dataset_id"] - # assert output_train.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] - # assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - # assert output_test.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] - # assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] - # assert output_solution.uns["raw_dataset_id"] == input.uns["raw_dataset_id"] - - # print(">> Check whether certain slots exist") - # assert "counts" in output_train.layers - # assert "lognorm" in output_train.layers - # assert "label" in output_train.obs - # assert "batch" in output_train.obs - # assert "counts" in output_test.layers - # assert "lognorm" in output_test.layers - # assert "label" not in output_test.obs # make sure label is /not/ here - # assert "batch" in output_test.obs - # assert "counts" in output_solution.layers - # assert "lognorm" in output_solution.layers - # assert "label" in output_solution.obs - # assert "batch" in output_solution.obs - - # print(">> All checks succeeded!") - # - path: ../../../../resources_test/common/pancreas + test_resources: + - type: python_script + path: generic_test.py + - path: ../../../resources_test/common/pancreas \ No newline at end of file diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 86bba654ba..050d51b19c 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -1,6 +1,6 @@ __inherits__: ../../api/comp_method.yaml functionality: - name: "KNN_smoothing" + name: "knn_smoothing" namespace: "denoising/methods" description: "iterative K-nearest neighbor smoothing" info: @@ -25,5 +25,5 @@ platforms: packages: - "anndata>=0.8" github: - - scottgigante-immunai/knn-smoothing + - scottgigante-immunai/knn-smoothing@python_package - type: nextflow diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml index 7e72d2a8c2..478804e461 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ __inherits__: ../api/comp_split_dataset.yaml functionality: - name: "split_datase" + name: "split_dataset" namespace: "denoising" arguments: - name: "--method" diff --git a/src/denoising/split_dataset/generic_test.py b/src/denoising/split_dataset/generic_test.py new file mode 100644 index 0000000000..ca7a29dbbb --- /dev/null +++ b/src/denoising/split_dataset/generic_test.py @@ -0,0 +1,40 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +output_train_path = "output_train.h5ad" +output_test_path = "output_test.h5ad" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_train_path) +assert path.exists(output_test_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output_train = ad.read_h5ad(output_train_path) +output_test = ad.read_h5ad(output_test_path) + +print("input:", input) +print("output_train:", output_train) +print("output_test:", output_test) + +print(">> Checking whether data from input was copied properly to output") +assert output_train.uns["dataset_id"] == input.uns["dataset_id"] +assert output_test.uns["dataset_id"] == input.uns["dataset_id"] + +print(">> Check whether certain slots exist") +assert "counts" in output_train.layers +assert "counts" in output_test.layers + +print(">> All checks succeeded!") \ No newline at end of file diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index 4113b20484..0e825fc9d9 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -1,4 +1,4 @@ -import scanpy as sc +import anndata as ad import numpy as np import scipy.sparse import molecular_cross_validation.util @@ -23,7 +23,7 @@ random_state = np.random.RandomState(par['seed']) print(">> Load Data") -adata = sc.read_h5ad(par["input"]) +adata = ad.read_h5ad(par["input"]) # remove all layers except for counts @@ -55,13 +55,19 @@ # copy adata to train_set, test_set -output_train = adata[:, ~is_missing].copy() -del output_train.layers["counts"] -output_train.layers["counts"] = scipy.sparse.csr_matrix(X_train).astype(float) +new_adata = adata[:, ~is_missing].copy() -output_test = adata[:, ~is_missing].copy() -del output_test.layers["counts"] -output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) +output_train = ad.AnnData(scipy.sparse.csr_matrix(X_train).astype(float)) +output_train.layers["counts"] = output_train.X +output_train.uns["dataset_id"] = adata.uns["dataset_id"] + +output_test = ad.AnnData(scipy.sparse.csr_matrix(X_test).astype(float)) +output_test.layers["counts"] = output_test.X +output_test.uns["dataset_id"] = adata.uns["dataset_id"] + +# output_test = adata[:, ~is_missing].copy() +# del output_test.layers["counts"] +# output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) print(">> Writing") From b896f5b46442b09812c5edc4caccc02493360cd4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 25 Nov 2022 16:40:04 +0100 Subject: [PATCH 0451/1233] fix required fields in metrics Former-commit-id: aea1c8664b3232e3fe22a16ead6ab0bf22e3ecfd --- src/denoising/metrics/mse/config.vsh.yaml | 3 +++ src/denoising/metrics/poisson/config.vsh.yaml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index af4f2a70d9..ba1eadcc12 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -10,6 +10,9 @@ functionality: - id: mse label: mse description: Mean Squared Error + maximize: false + min: 0 + max: +inf resources: - type: python_script path: script.py diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 7efa6d8e95..b37712029c 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -10,6 +10,9 @@ functionality: - id: poisson label: poisson description: poisson loss + maximize: false + min: 0 + max: +inf resources: - type: python_script path: script.py From c00aeb2115cf31abc279b931b27b44bd0fe6b776 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 25 Nov 2022 16:40:29 +0100 Subject: [PATCH 0452/1233] render readme Former-commit-id: b3279f258bb2cd0d56ea7a7fe4471106e0cc45b1 --- src/denoising/README.md | 314 +++++++++++++++++++++++++ src/denoising/README.qmd | 16 +- src/denoising/docs/task_description.md | 2 - 3 files changed, 320 insertions(+), 12 deletions(-) create mode 100644 src/denoising/README.md diff --git a/src/denoising/README.md b/src/denoising/README.md new file mode 100644 index 0000000000..fb654b54be --- /dev/null +++ b/src/denoising/README.md @@ -0,0 +1,314 @@ + +- Denoising + - The task + - The metrics + - API + - Methods + - Metrics + - Pipeline + topology + - File format API + - Dataset + - Denoised + - Score + - Test + - Train + - Component API + - Control Method + - Method + - Metric + - Split Dataset + +# Denoising + +## The task + +Single-cell RNA-Seq protocols only detect a fraction of the mRNA +molecules present in each cell. As a result, the measurements (UMI +counts) observed for each gene and each cell are associated with +generally high levels of technical noise ([Grün et al., +2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes +the task of estimating the true expression level of each gene in each +cell. In the single-cell literature, this task is also referred to as +*imputation*, a term which is typically used for missing data problems +in statistics. Similar to the use of the terms “dropout”, “missing +data”, and “technical zeros”, this terminology can create confusion +about the underlying measurement process ([Sarkar and Stephens, +2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). + +A key challenge in evaluating denoising methods is the general lack of a +ground truth. A recent benchmark study ([Hou et al., +2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) +relied on flow-sorted datasets, mixture control experiments ([Tian et +al., 2019](https://www.nature.com/articles/s41592-019-0425-8)), and +comparisons with bulk RNA-Seq data. Since each of these approaches +suffers from specific limitations, it is difficult to combine these +different approaches into a single quantitative measure of denoising +accuracy. Here, we instead rely on an approach termed molecular +cross-validation (MCV), which was specifically developed to quantify +denoising accuracy in the absence of a ground truth ([Batson et al., +2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the +observed molecules in a given scRNA-Seq dataset are first partitioned +between a *training* and a *test* dataset. Next, a denoising method is +applied to the training dataset. Finally, denoising accuracy is measured +by comparing the result to the test dataset. The authors show that both +in theory and in practice, the measured denoising accuracy is +representative of the accuracy that would be obtained on a ground truth +dataset. + +## The metrics + +Metrics for data denoising aim to assess denoising accuracy by comparing +the denoised *training* set to the randomly sampled *test* set. + +- **MSE**: The mean squared error between the denoised counts of the + training dataset and the true counts of the test dataset after + reweighting by the train/test ratio. +- **Poisson**: The Poisson log likelihood of observing the true counts + of the test dataset given the distribution given in the denoised + dataset. + +## API + +Datasets should contain the raw UMI counts in `adata.X`, subsampled to +training (`adata.obsm["train"]`) and testing (`adata.obsm["test"]`) +datasets using `openproblems.tasks.denoising.datasets.utils.split_data`. + +The task-specific data loader functions should split the provided raw +UMI counts into a training and a test dataset, as described by [Batson +et al., 2019](https://www.biorxiv.org/content/10.1101/786269v1). The +training dataset should be stored in `adata.obsm['train']`, and the test +dataset should be stored in `adata.obsm['test']`. Methods should store +the denoising result in `adata.obsm['denoised']`. Methods should not +edit `adata.obsm["train"]` or `adata.obsm["test"]`. + +## Methods + +Methods for assigning labels from a reference dataset to a new dataset. + +| Name | Type | Description | DOI | URL | +|:-----------------------------------------------------------------------------------------------------------|:-------|:------------------------------------------------------|:----|:----| +| [ALRA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/alra/config.vsh.yaml) | method | Adaptively-thresholded Low Rank Approximation (ALRA). | | | + +ALRA is a method for imputation of missing values in single cell +RNA-sequencing data, described in the preprint, “Zero-preserving +imputation of scRNA-seq data using low-rank approximation” available +[here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a +scRNA-seq expression matrix, ALRA first computes its rank-k +approximation using randomized SVD. Next, each row (gene) is thresholded +by the magnitude of the most negative value of that gene. Finally, the +matrix is +rescaled.\|[link](https://doi.org/10.1101/397588)\|[link](https://github.com/KlugerLab/ALRA)\| +\|[knn_smooth](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/knn_smoothing/config.vsh.yaml)\|method +\|iterative K-nearest neighbor smoothing +\|[link](https://doi.org/10.1101/217737)\|[link](https://github.com/yanailab/knn-smoothing)\| +\|[magic](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/magic/config.vsh.yaml)\|method +\|MAGIC: Markov affinity-based graph imputation of cells +\|[link](https://doi.org/10.1016/j.cell.2018.05.061)\|[link](https://github.com/KrishnaswamyLab/MAGIC)\| +\|[no +denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/no_denoising/config.vsh.yaml)\|negative_control +\|negative control by copying train counts \| \| \| \|[perfect +denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/perfect_denoising/config.vsh.yaml)\|positive_control +\|Negative control by copying the train counts \| \| \| + +## Metrics + +Metrics for label projection aim to characterize how well each +classifier correctly assigns cell type labels to cells in the test set. + +| Name | Description | Range | +|:-----------------------------------------------------------------------------------------------------------------|:------------------------------------|:----------------| +| [mse](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/mse/config.vsh.yaml) | Mean Squared Error Lower is better. | \[0, infinity\] | +| [poisson](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/poisson/config.vsh.yaml) | poisson loss Lower is better. | \[0, +inf\] | + +## Pipeline topology + +``` mermaid +%%| column: screen-inset-shaded +flowchart LR + anndata_dataset(Dataset) + anndata_denoised(Denoised) + anndata_score(Score) + anndata_test(Test) + anndata_train(Train) + comp_control_method[/Control Method/] + comp_method[/Method/] + comp_metric[/Metric/] + comp_split_dataset[/Split Dataset/] + anndata_train---comp_control_method + anndata_test---comp_control_method + anndata_train---comp_method + anndata_test---comp_metric + anndata_denoised---comp_metric + anndata_dataset---comp_split_dataset + comp_control_method-->anndata_denoised + comp_method-->anndata_denoised + comp_metric-->anndata_score + comp_split_dataset-->anndata_train + comp_split_dataset-->anndata_test +``` + +## File format API + +### `Dataset` + +A preprocessed dataset + +Used in: + +- [split dataset](#split%20dataset): input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + uns: 'dataset_id' + layers: 'counts' + +### `Denoised` + +The denoised data + +Used in: + +- [control method](#control%20method): output (as output) +- [method](#method): output (as output) +- [metric](#metric): input_denoised (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| layers | denoised | integer | denoised data | +| obs | n_counts | string | Raw counts | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | + +Example: + + AnnData object + obs: 'n_counts' + uns: 'dataset_id', 'method_id' + layers: 'counts', 'denoised' + +### `Score` + +Metric score file + +Used in: + +- [metric](#metric): output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:--------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +Example: + + AnnData object + uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + +### `Test` + +The test data + +Used in: + +- [control method](#control%20method): input_test (as input) +- [metric](#metric): input_test (as input) +- [split dataset](#split%20dataset): output_test (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| obs | n_counts | string | Raw counts | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + obs: 'n_counts' + uns: 'dataset_id' + layers: 'counts' + +### `Train` + +The training data + +Used in: + +- [control method](#control%20method): input_train (as input) +- [method](#method): input_train (as input) +- [split dataset](#split%20dataset): output_train (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| obs | n_counts | string | Raw counts | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + obs: 'n_counts' + uns: 'dataset_id' + layers: 'counts' + +## Component API + +### `Control Method` + +Arguments: + +| Name | File format | Direction | Description | +|:----------------|:----------------------|:----------|:--------------| +| `--input_train` | [Train](#train) | input | Training data | +| `--input_test` | [Test](#test) | input | Test data | +| `--output` | [Denoised](#denoised) | output | Denoised data | + +### `Method` + +Arguments: + +| Name | File format | Direction | Description | +|:----------------|:----------------------|:----------|:--------------| +| `--input_train` | [Train](#train) | input | Training data | +| `--output` | [Denoised](#denoised) | output | Denoised data | + +### `Metric` + +Arguments: + +| Name | File format | Direction | Description | +|:-------------------|:----------------------|:----------|:--------------| +| `--input_test` | [Test](#test) | input | Test data | +| `--input_denoised` | [Denoised](#denoised) | input | Denoised data | +| `--output` | [Score](#score) | output | Score | + +### `Split Dataset` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------------|:--------------------|:----------|:---------------------| +| `--input` | [Dataset](#dataset) | input | Preprocessed dataset | +| `--output_train` | [Train](#train) | output | Training data | +| `--output_test` | [Test](#test) | output | Test data | diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd index df3b739f6a..45276f884e 100644 --- a/src/denoising/README.qmd +++ b/src/denoising/README.qmd @@ -1,8 +1,8 @@ --- format: gfm info: - v1_url: openproblems/tasks/label_projection/README.md - v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 + v1_url: openproblems/tasks/denoising/README.md + v1_commit: null # todo: fill in toc: true --- @@ -14,17 +14,13 @@ strip_margin <- function(text, symbol = "\\|") { str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") } -dir <- "src/label_projection" +dir <- "src/denoising" dir <- "." ``` -# Label Projection +# Denoising -```{r description, echo=FALSE} -lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) -lines2 <- gsub("^#", "##", lines) -knitr::asis_output(lines2) -``` +{{< include docs/task_description.md >}} ## Methods @@ -79,7 +75,7 @@ metric_info_view <- metric_info %>% transmute( Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " ", ifelse(maximise, "Higher is better.", "Lower is better.")), + Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), Range = paste0("[", min, ", ", max, "]") ) diff --git a/src/denoising/docs/task_description.md b/src/denoising/docs/task_description.md index 1167878998..2bb88ca1b9 100644 --- a/src/denoising/docs/task_description.md +++ b/src/denoising/docs/task_description.md @@ -1,5 +1,3 @@ -# Denoising - ## The task Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present From d41ea29218eea5d46a27457da333dfc33ae126d8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 25 Nov 2022 23:22:06 +0100 Subject: [PATCH 0453/1233] wip creating common components for fetching info Former-commit-id: e393226ea0195b378e8659f33fa1e2cab4bd69ef --- src/common/get_api_info/config.vsh.yaml | 29 ++++++++ src/common/get_api_info/script.R | 71 +++++++++++++++++++ src/common/get_method_info/config.vsh.yaml | 29 ++++++++ src/common/get_method_info/script.R | 30 ++++++++ src/common/get_metric_info/config.vsh.yaml | 29 ++++++++ src/common/get_metric_info/script.R | 28 ++++++++ src/common/get_results/config.vsh.yaml | 34 +++++++++ src/common/get_results/script.R | 42 +++++++++++ .../analysis_scripts/script.R | 70 ++++-------------- 9 files changed, 306 insertions(+), 56 deletions(-) create mode 100644 src/common/get_api_info/config.vsh.yaml create mode 100644 src/common/get_api_info/script.R create mode 100644 src/common/get_method_info/config.vsh.yaml create mode 100644 src/common/get_method_info/script.R create mode 100644 src/common/get_metric_info/config.vsh.yaml create mode 100644 src/common/get_metric_info/script.R create mode 100644 src/common/get_results/config.vsh.yaml create mode 100644 src/common/get_results/script.R diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml new file mode 100644 index 0000000000..fa6c91d34a --- /dev/null +++ b/src/common/get_api_info/config.vsh.yaml @@ -0,0 +1,29 @@ +functionality: + name: "get_api_info" + namespace: "common" + description: "Extract api info" + arguments: + - name: "--input" + type: "file" + multiple: true + example: src/label_projection + description: "A task dir" + - name: "--output" + type: "file" + direction: "output" + default: "output.yaml" + description: "Output yaml" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ anndata, tidyverse ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R new file mode 100644 index 0000000000..dce054cfde --- /dev/null +++ b/src/common/get_api_info/script.R @@ -0,0 +1,71 @@ +library(tidyverse) +library(rlang) + +## VIASH START +par <- list( + input = "src/label_projection", + output = "resources/label_projection/output/api.yaml" +) +## VIASH END + +comp_yamls <- list.files(paste0(par$input, "/api"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste0(par$input, "/api"), pattern = "anndata_", full.names = TRUE) + +# list component - file args links +comp_file <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + tibble( + comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + arg_name = str_replace_all(arg$name, "^-*", ""), + direction = arg$direction %||% "input", + file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + ) + }) +}) + +# get component info +comp_info <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) + ) +}) + +# get file info +file_info <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + description = arg$description, + short_description = arg$info$short_description, + example = arg$example, + label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + ) +}) + +# get file - slot args +file_slot <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + df$file_name <- basename(yaml_file) %>% gsub("\\.yaml", "", .) + as_tibble(df) + }) +}) %>% + mutate(multiple = multiple %|% FALSE) + +out <- list( + comp_info = purrr::transpose(comp_info), + file_info = purrr::transpose(file_info), + comp_file_io = purrr::transpose(comp_file), + file_schema = purrr::transpose(file_slot) +) + +yaml::write_yaml(out, par$output) diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml new file mode 100644 index 0000000000..e596f764a4 --- /dev/null +++ b/src/common/get_method_info/config.vsh.yaml @@ -0,0 +1,29 @@ +functionality: + name: "get_method_info" + namespace: "common" + description: "Extract method info" + arguments: + - name: "--input" + type: "file" + multiple: true + example: src/label_projection + description: "A task dir" + - name: "--output" + type: "file" + direction: "output" + default: "output.yaml" + description: "Output yaml" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ anndata, tidyverse ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R new file mode 100644 index 0000000000..da1abedc78 --- /dev/null +++ b/src/common/get_method_info/script.R @@ -0,0 +1,30 @@ +library(tidyverse) +library(rlang) + +## VIASH START +par <- list( + input = "src/label_projection", + output = "resources/label_projection/output/method_info.yaml" +) +## VIASH END + +ns_list <- processx::run( + "viash", + c("ns", "list", "-q", "methods", "--src", "."), + wd = par$input +) +configs <- yaml::yaml.load(ns_list$stdout) + +df <- map_df(configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) + info <- as_tibble(config$functionality$info) + info$config_path <- gsub(".*\\./", "", config$info$config) + info$id <- config$functionality$name + info$namespace <- config$functionality$namespace + info$description <- config$functionality$description + info +}) %>% + select(id, type, label, everything()) + +yaml::write_yaml(purrr::transpose(df), par$output) + diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml new file mode 100644 index 0000000000..bb709f31f5 --- /dev/null +++ b/src/common/get_metric_info/config.vsh.yaml @@ -0,0 +1,29 @@ +functionality: + name: "get_metric_info" + namespace: "common" + description: "Extract metric info" + arguments: + - name: "--input" + type: "file" + multiple: true + example: src/label_projection + description: "A task dir" + - name: "--output" + type: "file" + direction: "output" + default: "output.yaml" + description: "Output yaml" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ anndata, tidyverse ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R new file mode 100644 index 0000000000..ede6d7b0cc --- /dev/null +++ b/src/common/get_metric_info/script.R @@ -0,0 +1,28 @@ +library(tidyverse) +library(rlang) + +## VIASH START +par <- list( + input = "src/label_projection", + output = "resources/label_projection/output/metric_info.yaml" +) +## VIASH END + +ns_list <- processx::run( + "viash", + c("ns", "list", "-q", "metrics", "--src", "."), + wd = par$input +) +configs <- yaml::yaml.load(ns_list$stdout) + +df <- map_df(configs, function(config) { + info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) + info$config_path <- gsub(".*\\./", "", config$info$config) + info$id <- config$functionality$name + info$namespace <- config$functionality$namespace + info$description <- config$functionality$description + info +}) + +yaml::write_yaml(purrr::transpose(df), par$output) + diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml new file mode 100644 index 0000000000..83a031f21b --- /dev/null +++ b/src/common/get_results/config.vsh.yaml @@ -0,0 +1,34 @@ +functionality: + name: "get_execution_info" + namespace: "common" + description: "Extract execution info" + arguments: + - name: "--input_scores" + type: "file" + multiple: true + example: resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.tsv + description: "Scores file" + - name: "--input_execution" + type: "file" + multiple: true + example: resources/label_projection/benchmarks/openproblems_v1/nextflow_log.tsv + description: "Nextflow log file" + - name: "--output" + type: "file" + direction: "output" + default: "output.yaml" + description: "Output yaml" + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ anndata, tidyverse ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow diff --git a/src/common/get_results/script.R b/src/common/get_results/script.R new file mode 100644 index 0000000000..6abe4ab034 --- /dev/null +++ b/src/common/get_results/script.R @@ -0,0 +1,42 @@ +library(tidyverse) +library(rlang) + +## VIASH START +par <- list( + input_scores = "resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.tsv", + input_execution = "resources/label_projection/benchmarks/openproblems_v1/nextflow_log.tsv", + output = "resources/label_projection/output/results.yaml" +) +## VIASH END + +# read scores +raw_scores <- read_tsv(par$input_scores) %>% + spread(metric_ids, metric_values) + +# read nxf log +id_regex <- "^(.*)\\.([^\\.]*)" +nxf_log <- read_tsv(par$input_execution) %>% + mutate( + id = tag, + dataset_id = gsub("^([^\\.]*)\\.([^\\.]*).*", "\\1/\\2", id), + method_id = gsub(".*\\.", "", id) + ) + +# process execution info +execution_info <- nxf_log %>% + transmute( + method_id, + dataset_id, + status, + realtime = lubridate::duration(toupper(realtime)), + pcpu = as.numeric(gsub("%", "", pcpu)), + vmem_gb = as.numeric(gsub(" GB", "", vmem)), + peak_vmem_gb = as.numeric(gsub(" GB", "", peak_vmem)), + read_bytes_mb = as.numeric(gsub(" MB", "", read_bytes)), + write_bytes_mb = as.numeric(gsub(" MB", "", write_bytes)) + ) + +df <- full_join(raw_scores, execution_info, by = c("method_id", "dataset_id")) + +yaml::write_yaml(purrr::transpose(df), par$output) + diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R index eadb5c7639..80f987e875 100644 --- a/src/label_projection/analysis_scripts/script.R +++ b/src/label_projection/analysis_scripts/script.R @@ -2,67 +2,25 @@ library(tidyverse) out_dir <- "resources/label_projection/benchmarks/openproblems_v1/" -# read scores -scores <- read_tsv(paste0(out_dir, "combined.extract_scores.output.tsv")) %>% - rename(metric_id = metric_ids, metric_value = metric_values) - -# read nxf log -output_regex <- "^(.*)\\.([^\\.]*)\\.output[^\\.]*\\.h5ad" -nxf_log <- read_tsv(paste0(out_dir, "nextflow_log.tsv")) %>% - mutate( - output_file = gsub(".*output=([^,]*).*", "\\1", params), - id = gsub(output_regex, "\\1", output_file), - dataset_id = gsub("^([^\\.]*)\\.([^\\.]*).*", "\\1/\\2", id), - component_id = gsub(output_regex, "\\2", output_file) - ) -nxf_log %>% select(id:component_id) - -# process execution info -execution_info <- nxf_log %>% - filter(component_id %in% method_info$id) %>% - transmute( - method_id = component_id, - dataset_id, - status, - realtime = lubridate::duration(toupper(realtime)), - pcpu = as.numeric(gsub("%", "", pcpu)), - vmem_gb = as.numeric(gsub(" GB", "", vmem)), - peak_vmem_gb = as.numeric(gsub(" GB", "", peak_vmem)), - read_bytes_mb = as.numeric(gsub(" MB", "", read_bytes)), - write_bytes_mb = as.numeric(gsub(" MB", "", write_bytes)) - ) +# read results +results <- map_df( + yaml::read_yaml("resources/label_projection/output/results.yaml"), + as_tibble +) # get method info -ns_list_methods <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*methods"))$stdout) - -method_info <- map_df(ns_list_methods, function(conf) { - tryCatch({ - info <- c( - list( - id = conf$functionality$name, - namespace = conf$functionality$namespace, - description = conf$functionality$description - ), - conf$functionality$info - ) - as.data.frame(info) - }, error = function(err) { - cat(err$message, "\n", sep = "") - data.frame(id = conf$functionality$name) - }) -}) +method_info <- map_df( + yaml::read_yaml("resources/label_projection/output/method_info.yaml"), + as_tibble +) # get metric info -ns_list_metrics <- yaml::yaml.load(processx::run("viash", c("ns", "list", "-q", "label_projection.*metrics"))$stdout) +metric_info <- map_df( + yaml::read_yaml("resources/label_projection/output/metric_info.yaml"), + as_tibble +) + -metric_info <- map_df(ns_list_metrics, function(conf) { - tryCatch({ - map_df(conf$functionality$info$metrics, as.data.frame) - }, error = function(err) { - cat(err$message, "\n", sep = "") - data.frame(id = conf$functionality$name) - }) -}) # get data table ranking <- scores %>% From 336b6dd6314a1fbf810dbe4d79733bc50f20f217 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 28 Nov 2022 16:25:47 +0100 Subject: [PATCH 0454/1233] fix dca method Former-commit-id: b67108156e0e9b52ffc198f29e0ad07d161ef316 --- src/denoising/api/comp_method.yaml | 35 ++++++++++---------- src/denoising/methods/dca/config.vsh.yaml | 13 +++++--- src/denoising/methods/dca/script.py | 29 ++++++++++------- src/denoising/methods/dca/test.py | 39 +++++++++++++++++++++++ src/denoising/split_dataset/script.py | 8 ++--- 5 files changed, 89 insertions(+), 35 deletions(-) create mode 100644 src/denoising/methods/dca/test.py diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index cd6c39e985..4e1a83738b 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -14,7 +14,7 @@ functionality: import subprocess from os import path - input_train_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_train.h5ad" + input_train_path = meta["resources_dir"] + "denoising/pancreas_split_data_output_train.h5ad" output_path = "output.h5ad" cmd = [ @@ -23,24 +23,27 @@ functionality: "--output", output_path ] - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) + if meta['functionality_name'] != 'dca': + - print(">> Checking whether output file exists") - assert path.exists(output_path) + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Reading h5ad files") - input_train = ad.read_h5ad(input_train_path) - output = ad.read_h5ad(output_path) - print("input_train:", input_train) - print("output:", output) + print(">> Checking whether output file exists") + assert path.exists(output_path) - print(">> Checking whether predictions were added") - assert "denoised" in output.layers - assert meta['functionality_name'] == output.uns["method_id"] + print(">> Reading h5ad files") + input_train = ad.read_h5ad(input_train_path) + output = ad.read_h5ad(output_path) + print("input_train:", input_train) + print("output:", output) - print("Checking whether data from input was copied properly to output") - assert input_train.n_obs == output.n_obs - assert input_train.uns["dataset_id"] == output.uns["dataset_id"] + print(">> Checking whether predictions were added") + assert "denoised" in output.layers + assert meta['functionality_name'] == output.uns["method_id"] + + print("Checking whether data from input was copied properly to output") + assert input_train.n_obs == output.n_obs + assert input_train.uns["dataset_id"] == output.uns["dataset_id"] print("All checks succeeded!") diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 430b407d8f..cfd5ee86e5 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -1,6 +1,5 @@ __inherits__: ../../api/comp_method.yaml functionality: - status: disabled name: "dca" namespace: "denoising/methods" description: "Deep Count Autoencoder" @@ -10,7 +9,7 @@ functionality: # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" # paper_year: 2019 - paper_doi: "0.1038/s41467-018-07931-2" + paper_doi: "10.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: /openproblems/tasks/denoising/methods/dca.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a @@ -23,12 +22,18 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - type: python_script + path: test.py platforms: - type: docker - image: "python:3.8" + image: "python:3.7" setup: - type: python packages: - - "anndata<0.8" + - anndata<0.8 - dca==0.3.4 + - keras>=2.4,<2.11 + - tensorflow==2.4.3 + - protobuf==3.20.* - type: nextflow diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index 2ac92cfde4..f6575204e5 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -1,11 +1,11 @@ import anndata as ad +import h5py +import numpy as np from dca.api import dca -# NOTE: pickup later. DCA package uses old keras imports ? - ## VIASH START par = { - 'input_train': 'output_train.h5ad', + 'input_train': 'output/denoising/pancreas_split_data_output_train.h5ad', 'output': 'output_dca.h5ad', 'epochs': 300, } @@ -15,21 +15,28 @@ ## VIASH END print("load input data") -input_train = ad.read_h5ad(par['input_train']) +# input_train = ad.read_h5ad(par['input_train']) +input_file = h5py.File(par["input_train"], 'r') +data = np.array(input_file["layers"]["counts"]) +input_train = ad.AnnData(data) print("process data") - -# make adata object with train counts # run DCA dca(input_train, epochs=par["epochs"]) -# set denoised to Xmat -output_denoised = input_train.copy -output_denoised.X = input_train.X print("Writing data") -output_denoised.uns["method_id"] = meta['functionality_name'] -output_denoised.write_h5ad(par['output'], compression="gzip") +# input_train.uns["method_id"] = meta['functionality_name'] +# input_train.write_h5ad(par['output'], compression="gzip") +with h5py.File(par['output'], "w") as output_denoised: + for key in input_file.keys(): + if key == "X": + continue + input_file.copy(input_file[key], output_denoised) + output_denoised["layers"].create_dataset('denoised', data=input_train.X) + output_denoised["uns"].create_dataset('method_id', data=meta['functionality_name']) + +input_file.close() diff --git a/src/denoising/methods/dca/test.py b/src/denoising/methods/dca/test.py new file mode 100644 index 0000000000..6662c964bf --- /dev/null +++ b/src/denoising/methods/dca/test.py @@ -0,0 +1,39 @@ +import h5py +import numpy as np +import anndata as ad +import subprocess +from os import path + +input_train_path = meta["resources_dir"] + "denoising/pancreas_split_data_output_train.h5ad" +output_path = "output.h5ad" + +cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--output", output_path +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +with h5py.File(input_train_path, 'r') as input_train: + with h5py.File(output_path, 'r') as output: + print("input_train:" , input_train.keys()) + print("input_train:", input_train.get("layers/counts")) + print("output:" , output.keys()) + print("output:", output.get("layers/counts")) + + + print(">> Checking whether predictions were added") + assert "denoised" in output["layers"].keys() + assert meta['functionality_name'] == np.string_(output["uns/method_id"]).decode('utf-8') + + print("Checking whether data from input was copied properly to output") + assert input_train.get("layers/counts").shape == output.get("layers/counts").shape + assert input_train["uns/dataset_id"] == output["uns/dataset_id"] + +print("All checks succeeded!") diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index 0e825fc9d9..01b627af96 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -6,8 +6,8 @@ ## VIASH START par = { 'input': "/home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad", - 'output_train': "output/nextflow/pancreas_split_data_output_train.h5ad", - 'output_test': "output/nextflow/pancreas_split_data_output_test.h5ad", + 'output_train': "output/denoising/pancreas_split_data_output_train.h5ad", + 'output_test': "output/denoising/pancreas_split_data_output_test.h5ad", 'train_frac': 0.9, 'seed': 0 } @@ -57,11 +57,11 @@ new_adata = adata[:, ~is_missing].copy() -output_train = ad.AnnData(scipy.sparse.csr_matrix(X_train).astype(float)) +output_train = ad.AnnData(X_train.astype(float), dtype=float) output_train.layers["counts"] = output_train.X output_train.uns["dataset_id"] = adata.uns["dataset_id"] -output_test = ad.AnnData(scipy.sparse.csr_matrix(X_test).astype(float)) +output_test = ad.AnnData(X_test.astype(float), dtype=float) output_test.layers["counts"] = output_test.X output_test.uns["dataset_id"] = adata.uns["dataset_id"] From 1bcc12d4a294cd4741d85fa2379748af3e92ffb6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 29 Nov 2022 10:09:14 +0100 Subject: [PATCH 0455/1233] add run scripts Former-commit-id: b7a643af571fc8cefadcd9557a182df0790821b9 --- .../resources_scripts/run_benchmark.sh | 82 ++++++++++++ .../resources_scripts/split_datasets.sh | 60 +++++++++ .../resources_test_scripts/pancreas.sh | 53 ++++++++ src/denoising/workflows/run/config.vsh.yaml | 4 +- src/denoising/workflows/run/main.nf | 120 ++++++++++++++++-- src/denoising/workflows/run/nextflow.config | 6 +- 6 files changed, 311 insertions(+), 14 deletions(-) create mode 100755 src/denoising/resources_scripts/run_benchmark.sh create mode 100755 src/denoising/resources_scripts/split_datasets.sh create mode 100755 src/denoising/resources_test_scripts/pancreas.sh diff --git a/src/denoising/resources_scripts/run_benchmark.sh b/src/denoising/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..e5d6bb8035 --- /dev/null +++ b/src/denoising/resources_scripts/run_benchmark.sh @@ -0,0 +1,82 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources/denoising/datasets/openproblems_v1" +OUTPUT_DIR="resources/denoising/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import yaml + +dataset_dir = "$DATASETS_DIR" +output_dir = "$OUTPUT_DIR" + +# read split datasets yaml +with open(dataset_dir + "/params.yaml", "r") as file: + split_list = yaml.safe_load(file) +datasets = split_list['param_list'] + +# figure out where train/test/solution files were stored +param_list = [] + +for dataset in datasets: + id = dataset["id"] + input_train = dataset_dir + "/" + id + ".train.h5ad" + input_test = dataset_dir + "/" + id + ".test.h5ad" + input_solution = dataset_dir + "/" + id + ".solution.h5ad" + + obj = { + 'id': id, + 'dataset_id': dataset["dataset_id"], + 'input_train': input_train, + 'input_test': input_test + } + param_list.append(obj) + +# write as output file +output = { + "param_list": param_list, +} + +with open(output_dir + "/params.yaml", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script src/denoising/workflows/run/main.nf \ + -profile docker \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" \ + -with-tower + +bin/tools/docker/nextflow/process_log/process_log \ + --output "$OUTPUT_DIR/nextflow_log.tsv" + +# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' +# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' + +# bin/nextflow run . \ +# -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ +# -profile docker \ +# --input_train resources_test/label_projection/pancreas/train.h5ad \ +# --input_test resources_test/label_projection/pancreas/test.h5ad \ +# --input_solution resources_test/label_projection/pancreas/solution.h5ad \ +# --publish_dir foo \ No newline at end of file diff --git a/src/denoising/resources_scripts/split_datasets.sh b/src/denoising/resources_scripts/split_datasets.sh new file mode 100755 index 0000000000..8ef2981b0e --- /dev/null +++ b/src/denoising/resources_scripts/split_datasets.sh @@ -0,0 +1,60 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +COMMON_DATASETS="resources/datasets/openproblems_v1" +OUTPUT_DIR="resources/denoising/datasets/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import anndata as ad +import glob +import yaml + +h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") + +param_list = [] + +for h5ad_file in h5ad_files: + print(f"Checking {h5ad_file}") + adata = ad.read_h5ad(h5ad_file, backed=True) + if "counst" in adata.layers: + dataset_id = adata.uns["dataset_id"].replace("/", ".") + id = dataset_id + obj = { + 'id': id, + 'input': h5ad_file, + 'dataset_id': dataset_id, + } + param_list.append(obj) + +output = { + "param_list": param_list, + "seed": 123, + "output_train": "\$id.train.h5ad", + "output_test": "\$id.test.h5ad" +} + +with open("$params_file", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script target/nextflow/denoising/split_dataset/main.nf \ + -profile docker \ + -resume \ + -params-file $params_file \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/denoising/resources_test_scripts/pancreas.sh b/src/denoising/resources_test_scripts/pancreas.sh new file mode 100755 index 0000000000..3e69537945 --- /dev/null +++ b/src/denoising/resources_test_scripts/pancreas.sh @@ -0,0 +1,53 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'denoising|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=output_test/denoising/pancreas + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +mkdir -p $DATASET_DIR + +# split dataset +bin/viash run src/denoising/split_dataset/config.vsh.yaml -- \ + --input $RAW_DATA \ + --output_train $DATASET_DIR/train.h5ad \ + --output_test $DATASET_DIR/test.h5ad \ + --seed 123 + +# run one method +bin/viash run src/denoising/methods/magic/config.vsh.yaml -- \ + --input_train $DATASET_DIR/train.h5ad \ + --output $DATASET_DIR/magic.h5ad + +# run one metric +bin/viash run src/denoising/metrics/poisson/config.vsh.yaml -- \ + --input_denoised $DATASET_DIR/magic.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output $DATASET_DIR/magic_poisson.h5ad + +# run benchmark +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/denoising/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --input_train $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/denoising/workflows/run/config.vsh.yaml b/src/denoising/workflows/run/config.vsh.yaml index 07960e56b1..e093719368 100644 --- a/src/denoising/workflows/run/config.vsh.yaml +++ b/src/denoising/workflows/run/config.vsh.yaml @@ -17,8 +17,8 @@ functionality: - name: "--output" direction: "output" type: file - # todo: fix inherits in nxf - # __inherits__: ../../api/anndata_raw_dataset.yaml resources: - type: nextflow_script path: main.nf +platforms: + - type: nextflow diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index e8c78197f0..74bdad3a5b 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -8,9 +8,11 @@ include { no_denoising } from "$targetDir/denoising/control_methods/no_denoising include { perfect_denoising } from "$targetDir/denoising/control_methods/perfect_denoising/main.nf" // import methods +include { alra } from "$targetDir/denoising/methods/alra/main.nf" +include { dca } from "$targetDir/denoising/methods/dca/main.nf" +include { knn_smoothing } from "$targetDir/denoising/methods/knn_smoothing/main.nf" include { magic } from "$targetDir/denoising/methods/magic/main.nf" - // import metrics include { mse } from "$targetDir/denoising/metrics/mse/main.nf" include { poisson } from "$targetDir/denoising/metrics/poisson/main.nf" @@ -24,6 +26,12 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } f config = readConfig("$projectDir/config.vsh.yaml") +// construct a map of methods (id -> method_module) +methods = [ no_denoising, perfect_denoising, alra, dca, knn_smoothing, magic] + .collectEntries{method -> + [method.config.functionality.name, method] + } + workflow { helpMessage(config) @@ -45,14 +53,16 @@ workflow run_wf { output: ["output"] ) + // multiply events by the number of method + | getWorkflowArguments(key: "preprocess") + | add_methods + + // add input_solution to data for the positive controls + | controls_can_cheat + // run methods | getWorkflowArguments(key: "method") - | ( - no_denoising & - perfect_denoising & - magic - ) - | mix + | run_methods // construct tuples for metrics | pmap{ id, file, passthrough -> @@ -64,17 +74,105 @@ workflow run_wf { } // run metrics + | getWorkflowArguments(key: "metric") + | run_metrics + + // convert to tsv + | aggregate_results + + emit: + output_ch +} + +workflow add_methods { + take: input_ch + main: + output_ch = Channel.fromList(methods.keySet()) + | combine(input_ch) + + // generate combined id for method_id and dataset_id + | pmap{method_id, dataset_id, data -> + def new_id = dataset_id + "." + method_id + def new_data = data.clone() + [method_id: method_id] + new_data.remove("id") + [new_id, new_data] + } + emit: output_ch +} + +// workflow check_filtered_normalization_id { +// take: input_ch +// main: +// output_ch = input_ch +// | pfilter{id, data -> +// data = data.clone() +// def method = methods[data.method_id] +// def preferred = method.config.functionality.info.preferred_normalization +// // if a method is just using the counts, we can use any normalization method +// if (preferred == "counts") { +// preferred = "log_cpm" +// } +// data.normalization_id == preferred +// } +// emit: output_ch +// } + +workflow controls_can_cheat { + take: input_ch + main: + output_ch = input_ch + | pmap{id, data, passthrough -> + def method = methods[data.method_id] + def method_type = method.config.functionality.info.method_type + def new_data = data.clone() + if (method_type != "method") { + new_data = new_data + [input_test: passthrough.metric.input_test] + } + [id, new_data, passthrough] + } + emit: output_ch +} + +workflow run_methods { + take: input_ch + main: + // generate one channel per method + method_chs = methods.collect { method_id, method_module -> + input_ch + | filter{it[1].method_id == method_id} + | method_module + } + // mix all results + output_ch = method_chs[0].mix(*method_chs.drop(1)) + + emit: output_ch +} + +workflow run_metrics { + take: input_ch + main: + + output_ch = input_ch | (mse & poisson) | mix - // convert to tsv + emit: output_ch +} + +workflow aggregate_results { + take: input_ch + main: + + output_ch = input_ch | toSortedList - | map{ it -> [ "combined", it.collect{ it[1] } ] + it[0].drop(2) } + | filter{ it.size() > 0 } + | map{ it -> + [ "combined", it.collect{ it[1] } ] + it[0].drop(2) + } | getWorkflowArguments(key: "output") | extract_scores.run( auto: [ publish: true ] ) - emit: - output_ch + emit: output_ch } \ No newline at end of file diff --git a/src/denoising/workflows/run/nextflow.config b/src/denoising/workflows/run/nextflow.config index 5ded7de645..b8366d5a3e 100644 --- a/src/denoising/workflows/run/nextflow.config +++ b/src/denoising/workflows/run/nextflow.config @@ -4,4 +4,8 @@ manifest { params { rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} \ No newline at end of file +} + +// include common settings +includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/nxf_utils/labels.config") \ No newline at end of file From 5e017a1c4d62e92aa1d42f706d642c49bf77124b Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 29 Nov 2022 11:01:25 +0100 Subject: [PATCH 0456/1233] removed to_array from methods Former-commit-id: 2effbc7e3f5d2b287105bd8fc4d2c7ba1cd5af85 --- output_test/denoising/pancreas/scores.tsv | 13 +++++++++++++ .../control_methods/no_denoising/script.py | 2 +- .../control_methods/perfect_denoising/script.py | 2 +- src/denoising/methods/alra/script.R | 2 +- src/denoising/methods/knn_smoothing/script.py | 2 +- src/denoising/workflows/run/main.nf | 1 - 6 files changed, 17 insertions(+), 5 deletions(-) create mode 100644 output_test/denoising/pancreas/scores.tsv diff --git a/output_test/denoising/pancreas/scores.tsv b/output_test/denoising/pancreas/scores.tsv new file mode 100644 index 0000000000..a62b8345bb --- /dev/null +++ b/output_test/denoising/pancreas/scores.tsv @@ -0,0 +1,13 @@ +dataset_id method_id metric_ids metric_values +openproblems_v1/pancreas_subsample knn_smoothing mse 4.156121253967285 +openproblems_v1/pancreas_subsample alra mse 2.5244805812835693 +openproblems_v1/pancreas_subsample knn_smoothing poisson 15.690819466648714 +openproblems_v1/pancreas_subsample dca poisson 1.7226933718037916 +openproblems_v1/pancreas_subsample alra poisson 0.23350393581391563 +openproblems_v1/pancreas_subsample magic mse 3.0098042488098145 +openproblems_v1/pancreas_subsample no_denoising poisson -0.3387860995849156 +openproblems_v1/pancreas_subsample perfect_denoising poisson 0.2872479010349084 +openproblems_v1/pancreas_subsample magic poisson 0.633910037392805 +openproblems_v1/pancreas_subsample dca mse 4.410238742828369 +openproblems_v1/pancreas_subsample perfect_denoising mse 0 +openproblems_v1/pancreas_subsample no_denoising mse 2.065342426300049 diff --git a/src/denoising/control_methods/no_denoising/script.py b/src/denoising/control_methods/no_denoising/script.py index 63c238aa06..f77fe59604 100644 --- a/src/denoising/control_methods/no_denoising/script.py +++ b/src/denoising/control_methods/no_denoising/script.py @@ -17,7 +17,7 @@ print("Process data") output_denoised = input_train.copy() -output_denoised.layers["denoised"] = input_train.layers['counts'].toarray() +output_denoised.layers["denoised"] = input_train.layers['counts'] output_denoised.uns["method_id"] = meta['functionality_name'] diff --git a/src/denoising/control_methods/perfect_denoising/script.py b/src/denoising/control_methods/perfect_denoising/script.py index 995814faf1..018ed70ea3 100644 --- a/src/denoising/control_methods/perfect_denoising/script.py +++ b/src/denoising/control_methods/perfect_denoising/script.py @@ -18,7 +18,7 @@ print("Process data") output_denoised = input_train.copy() -output_denoised.layers["denoised"] = input_test.layers['counts'].toarray() +output_denoised.layers["denoised"] = input_test.layers['counts'] output_denoised.uns["method_id"] = meta['functionality_name'] diff --git a/src/denoising/methods/alra/script.R b/src/denoising/methods/alra/script.R index 2d6f6ba06c..6072321f51 100644 --- a/src/denoising/methods/alra/script.R +++ b/src/denoising/methods/alra/script.R @@ -27,7 +27,7 @@ cat(">> Run ALRA\n") out <- alra(as.matrix(counts)) cat(">> Store output\n") -adata$layers[["denoised"]] <- as(out$A_norm_rank_k_cor_sc, "CsparseMatrix") +adata$layers[["denoised"]] <- t(out$A_norm_rank_k_cor_sc) adata$uns[["method_id"]] <- meta[["functionality_name"]] cat(">> Write output to file\n") diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py index b8b16eab03..05bf90dccf 100644 --- a/src/denoising/methods/knn_smoothing/script.py +++ b/src/denoising/methods/knn_smoothing/script.py @@ -16,7 +16,7 @@ input_train = ad.read_h5ad(par["input_train"]) print("process data") -X = input_train.layers["counts"].transpose().toarray() +X = input_train.layers["counts"].transpose() input_train.layers["denoised"] = (knn_smooth.knn_smoothing(X, k=10)).transpose() print("Writing data") diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index 74bdad3a5b..edd4cbe4a3 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -54,7 +54,6 @@ workflow run_wf { ) // multiply events by the number of method - | getWorkflowArguments(key: "preprocess") | add_methods // add input_solution to data for the positive controls From 139d1fe958d18943335fb14f3ef8f200a71036c3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 11:38:45 +0100 Subject: [PATCH 0457/1233] fix typo Former-commit-id: 9fa2bd64d3b73fdfc2db4a1803bc3d36e7eee1cf --- src/denoising/metrics/poisson/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/metrics/poisson/script.py b/src/denoising/metrics/poisson/script.py index 4a7efac1fa..62fec0bafc 100644 --- a/src/denoising/metrics/poisson/script.py +++ b/src/denoising/metrics/poisson/script.py @@ -29,7 +29,7 @@ error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) -print("Store poission value") +print("Store poisson value") input_denoised.uns["metric_ids"] = meta['functionality_name'] input_denoised.uns["metric_values"] = error From f537e94e5071c26bb35c1cf299ba1da38217c2d8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 12:57:40 +0100 Subject: [PATCH 0458/1233] remove accidentally committed file; fix script that generated it Former-commit-id: e0feea0d991a9770cacbb686da448289487d7ed0 --- output_test/denoising/pancreas/scores.tsv | 13 ------------- src/denoising/resources_test_scripts/pancreas.sh | 2 +- 2 files changed, 1 insertion(+), 14 deletions(-) delete mode 100644 output_test/denoising/pancreas/scores.tsv diff --git a/output_test/denoising/pancreas/scores.tsv b/output_test/denoising/pancreas/scores.tsv deleted file mode 100644 index a62b8345bb..0000000000 --- a/output_test/denoising/pancreas/scores.tsv +++ /dev/null @@ -1,13 +0,0 @@ -dataset_id method_id metric_ids metric_values -openproblems_v1/pancreas_subsample knn_smoothing mse 4.156121253967285 -openproblems_v1/pancreas_subsample alra mse 2.5244805812835693 -openproblems_v1/pancreas_subsample knn_smoothing poisson 15.690819466648714 -openproblems_v1/pancreas_subsample dca poisson 1.7226933718037916 -openproblems_v1/pancreas_subsample alra poisson 0.23350393581391563 -openproblems_v1/pancreas_subsample magic mse 3.0098042488098145 -openproblems_v1/pancreas_subsample no_denoising poisson -0.3387860995849156 -openproblems_v1/pancreas_subsample perfect_denoising poisson 0.2872479010349084 -openproblems_v1/pancreas_subsample magic poisson 0.633910037392805 -openproblems_v1/pancreas_subsample dca mse 4.410238742828369 -openproblems_v1/pancreas_subsample perfect_denoising mse 0 -openproblems_v1/pancreas_subsample no_denoising mse 2.065342426300049 diff --git a/src/denoising/resources_test_scripts/pancreas.sh b/src/denoising/resources_test_scripts/pancreas.sh index 3e69537945..03e2c120c0 100755 --- a/src/denoising/resources_test_scripts/pancreas.sh +++ b/src/denoising/resources_test_scripts/pancreas.sh @@ -10,7 +10,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=output_test/denoising/pancreas +DATASET_DIR=resources_test/denoising/pancreas if [ ! -f $RAW_DATA ]; then echo "Error! Could not find raw data" From 2a0492326e88a7e53585fb30c3ff107cc4539453 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 13:03:30 +0100 Subject: [PATCH 0459/1233] update nxf utils Former-commit-id: 63f26bbd2e2add81655fd7699c72d1ce302d576b --- bin/init | 2 +- src/datasets/workflows/process_openproblems_v1/main.nf | 2 +- src/nxf_utils/{DataFlowHelper.nf => DataflowHelper.nf} | 0 src/nxf_utils/WorkflowHelper.nf | 5 +++++ 4 files changed, 7 insertions(+), 2 deletions(-) rename src/nxf_utils/{DataFlowHelper.nf => DataflowHelper.nf} (100%) diff --git a/bin/init b/bin/init index 9b5ac7917c..57c31891f4 100755 --- a/bin/init +++ b/bin/init @@ -19,7 +19,7 @@ NXF_UTILS=src/nxf_utils [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf -bin/viash export resource platforms/nextflow/DataflowHelper.config > $NXF_UTILS/DataFlowHelper.config +bin/viash export resource platforms/nextflow/DataflowHelper.nf > $NXF_UTILS/DataflowHelper.nf cd bin diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 4c0506cfb6..6aa129fe43 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -11,7 +11,7 @@ include { pca } from "$targetDir/datasets/processors/pca/main.nf" include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/nxf_utils/DataFlowHelper.nf b/src/nxf_utils/DataflowHelper.nf similarity index 100% rename from src/nxf_utils/DataFlowHelper.nf rename to src/nxf_utils/DataflowHelper.nf diff --git a/src/nxf_utils/WorkflowHelper.nf b/src/nxf_utils/WorkflowHelper.nf index e86ee64cd2..de0a1d76e8 100644 --- a/src/nxf_utils/WorkflowHelper.nf +++ b/src/nxf_utils/WorkflowHelper.nf @@ -113,6 +113,11 @@ def processArgument(arg) { arg.multiple_sep = arg.multiple_sep ?: ":" arg.plainName = arg.name.replaceAll("^-*", "") + if (arg.type == "file") { + arg.must_exist = arg.must_exist ?: true + arg.create_parent = arg.create_parent ?: true + } + if (arg.type == "file" && arg.direction == "output") { def mult = arg.multiple ? "_*" : "" def extSearch = "" From e3d89e75da4eb2c6f2bcaa1b0239a8f555df9343 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 13:04:54 +0100 Subject: [PATCH 0460/1233] move nxf_utils to wf_utils Former-commit-id: c486e0cd92dfc80a647881c2d94aa1dd82712d9e --- bin/init | 2 +- src/datasets/workflows/process_openproblems_v1/main.nf | 4 ++-- .../workflows/process_openproblems_v1/nextflow.config | 4 ++-- src/denoising/workflows/run/main.nf | 4 ++-- src/denoising/workflows/run/nextflow.config | 4 ++-- src/label_projection/workflows/run/main.nf | 4 ++-- src/label_projection/workflows/run/nextflow.config | 4 ++-- src/{nxf_utils => wf_utils}/DataflowHelper.nf | 0 src/{nxf_utils => wf_utils}/ProfilesHelper.config | 0 src/{nxf_utils => wf_utils}/WorkflowHelper.nf | 0 src/{nxf_utils => wf_utils}/labels.config | 0 11 files changed, 13 insertions(+), 13 deletions(-) rename src/{nxf_utils => wf_utils}/DataflowHelper.nf (100%) rename src/{nxf_utils => wf_utils}/ProfilesHelper.config (100%) rename src/{nxf_utils => wf_utils}/WorkflowHelper.nf (100%) rename src/{nxf_utils => wf_utils}/labels.config (100%) diff --git a/bin/init b/bin/init index 57c31891f4..4f7cc768c1 100755 --- a/bin/init +++ b/bin/init @@ -15,7 +15,7 @@ curl -fsSL get.viash.io | bash -s -- \ # add --namespace_separator '/' ? # automatically export the workflow helper -NXF_UTILS=src/nxf_utils +NXF_UTILS=src/wf_utils [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 6aa129fe43..08d237a237 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -10,8 +10,8 @@ include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" include { pca } from "$targetDir/datasets/processors/pca/main.nf" include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" -include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataflowHelper.nf" +include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/datasets/workflows/process_openproblems_v1/nextflow.config b/src/datasets/workflows/process_openproblems_v1/nextflow.config index d189e3cc02..3527df50c8 100644 --- a/src/datasets/workflows/process_openproblems_v1/nextflow.config +++ b/src/datasets/workflows/process_openproblems_v1/nextflow.config @@ -10,5 +10,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/nxf_utils/labels.config") +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index edd4cbe4a3..c52905ab7c 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -21,8 +21,8 @@ include { poisson } from "$targetDir/denoising/metrics/poisson/main.nf" include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/nxf_utils/DataFlowHelper.nf" +include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/denoising/workflows/run/nextflow.config b/src/denoising/workflows/run/nextflow.config index b8366d5a3e..f390059009 100644 --- a/src/denoising/workflows/run/nextflow.config +++ b/src/denoising/workflows/run/nextflow.config @@ -7,5 +7,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/nxf_utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") \ No newline at end of file diff --git a/src/label_projection/workflows/run/main.nf b/src/label_projection/workflows/run/main.nf index 90b61d922c..ec9089d88b 100644 --- a/src/label_projection/workflows/run/main.nf +++ b/src/label_projection/workflows/run/main.nf @@ -24,8 +24,8 @@ include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/nxf_utils/DataFlowHelper.nf" +include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/wf_utils/DataflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/label_projection/workflows/run/nextflow.config b/src/label_projection/workflows/run/nextflow.config index 9a59101ea1..a2e3947b61 100644 --- a/src/label_projection/workflows/run/nextflow.config +++ b/src/label_projection/workflows/run/nextflow.config @@ -10,5 +10,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/nxf_utils/labels.config") +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") diff --git a/src/nxf_utils/DataflowHelper.nf b/src/wf_utils/DataflowHelper.nf similarity index 100% rename from src/nxf_utils/DataflowHelper.nf rename to src/wf_utils/DataflowHelper.nf diff --git a/src/nxf_utils/ProfilesHelper.config b/src/wf_utils/ProfilesHelper.config similarity index 100% rename from src/nxf_utils/ProfilesHelper.config rename to src/wf_utils/ProfilesHelper.config diff --git a/src/nxf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf similarity index 100% rename from src/nxf_utils/WorkflowHelper.nf rename to src/wf_utils/WorkflowHelper.nf diff --git a/src/nxf_utils/labels.config b/src/wf_utils/labels.config similarity index 100% rename from src/nxf_utils/labels.config rename to src/wf_utils/labels.config From c83e48383f758f41ac72923f95cf66c2fb78f48d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 13:05:26 +0100 Subject: [PATCH 0461/1233] add labels to methods Former-commit-id: 96b338dfd7b06c5eb9e6d3aeef4c30ce5caa4aed --- src/denoising/control_methods/no_denoising/config.vsh.yaml | 2 ++ src/denoising/control_methods/perfect_denoising/config.vsh.yaml | 2 ++ src/denoising/methods/alra/config.vsh.yaml | 2 ++ src/denoising/methods/dca/config.vsh.yaml | 2 ++ src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 ++ src/denoising/methods/magic/config.vsh.yaml | 2 ++ 6 files changed, 12 insertions(+) diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 6966a1366f..bebb8a51ae 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -20,3 +20,5 @@ platforms: packages: - "anndata>=0.8" - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index aef8fca288..a39582b63a 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -20,3 +20,5 @@ platforms: packages: - "anndata>=0.8" - type: nextflow + directives: + label: [ midmem, midcpu ] \ No newline at end of file diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 4bcb623681..8bf05fe52d 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -45,3 +45,5 @@ platforms: - type: docker run: git clone https://github.com/KlugerLab/ALRA.git /ALRA - type: nextflow + directives: + label: [ midmem, midcpu ] \ No newline at end of file diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index cfd5ee86e5..8155f40dc5 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -37,3 +37,5 @@ platforms: - tensorflow==2.4.3 - protobuf==3.20.* - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 050d51b19c..4a50d97ac9 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: github: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index fc79b116fb..47eb88d16c 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -38,3 +38,5 @@ platforms: - scprep - magic-impute - type: nextflow + directives: + label: [ midmem, midcpu ] From b5ce679f6b38c09a22ac2447b2c1f5260dd297be Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 13:06:50 +0100 Subject: [PATCH 0462/1233] fis scripts Former-commit-id: 1afcb8c8049df5b7b122110a42f5cdd2d5909324 --- .../resources_scripts/run_benchmark.sh | 21 +++++++++++-------- .../resources_scripts/split_datasets.sh | 18 +++++++++------- src/denoising/workflows/run/main.nf | 2 +- src/denoising/workflows/run/nextflow.config | 3 +++ 4 files changed, 27 insertions(+), 17 deletions(-) diff --git a/src/denoising/resources_scripts/run_benchmark.sh b/src/denoising/resources_scripts/run_benchmark.sh index e5d6bb8035..0068967165 100755 --- a/src/denoising/resources_scripts/run_benchmark.sh +++ b/src/denoising/resources_scripts/run_benchmark.sh @@ -22,6 +22,7 @@ params_file="$OUTPUT_DIR/params.yaml" if [ ! -f $params_file ]; then python << HERE import yaml +import os dataset_dir = "$DATASETS_DIR" output_dir = "$OUTPUT_DIR" @@ -31,22 +32,24 @@ with open(dataset_dir + "/params.yaml", "r") as file: split_list = yaml.safe_load(file) datasets = split_list['param_list'] -# figure out where train/test/solution files were stored +# figure out where train/test files were stored param_list = [] for dataset in datasets: id = dataset["id"] input_train = dataset_dir + "/" + id + ".train.h5ad" input_test = dataset_dir + "/" + id + ".test.h5ad" - input_solution = dataset_dir + "/" + id + ".solution.h5ad" - - obj = { + + if os.path.exists(input_test): + obj = { + 'id': id, 'id': id, - 'dataset_id': dataset["dataset_id"], - 'input_train': input_train, - 'input_test': input_test - } - param_list.append(obj) + 'id': id, + 'dataset_id': dataset["dataset_id"], + 'input_train': input_train, + 'input_test': input_test + } + param_list.append(obj) # write as output file output = { diff --git a/src/denoising/resources_scripts/split_datasets.sh b/src/denoising/resources_scripts/split_datasets.sh index 8ef2981b0e..ac5bbaea77 100755 --- a/src/denoising/resources_scripts/split_datasets.sh +++ b/src/denoising/resources_scripts/split_datasets.sh @@ -23,23 +23,24 @@ import yaml h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") -param_list = [] +# this task doesn't use normalizations +# +param_list = {} for h5ad_file in h5ad_files: print(f"Checking {h5ad_file}") adata = ad.read_h5ad(h5ad_file, backed=True) - if "counst" in adata.layers: + if "counts" in adata.layers: dataset_id = adata.uns["dataset_id"].replace("/", ".") - id = dataset_id obj = { - 'id': id, + 'id': dataset_id, 'input': h5ad_file, 'dataset_id': dataset_id, } - param_list.append(obj) + param_list[dataset_id] = obj output = { - "param_list": param_list, + "param_list": list(param_list.values()), "seed": 123, "output_train": "\$id.train.h5ad", "output_test": "\$id.test.h5ad" @@ -57,4 +58,7 @@ bin/nextflow \ -profile docker \ -resume \ -params-file $params_file \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" + +bin/tools/docker/nextflow/process_log/process_log \ + --output "$OUTPUT_DIR/nextflow_log.tsv" \ No newline at end of file diff --git a/src/denoising/workflows/run/main.nf b/src/denoising/workflows/run/main.nf index c52905ab7c..e596a2e707 100644 --- a/src/denoising/workflows/run/main.nf +++ b/src/denoising/workflows/run/main.nf @@ -48,7 +48,7 @@ workflow run_wf { // split params for downstream components | setWorkflowArguments( - method: ["input_train", "input_test"], + method: ["input_train"], metric: ["input_test"], output: ["output"] ) diff --git a/src/denoising/workflows/run/nextflow.config b/src/denoising/workflows/run/nextflow.config index f390059009..e5e84e82dc 100644 --- a/src/denoising/workflows/run/nextflow.config +++ b/src/denoising/workflows/run/nextflow.config @@ -1,5 +1,8 @@ manifest { + name = 'denoising/workflows/run' + mainScript = 'main.nf' nextflowVersion = '!>=22.04.5' + description = 'Denoising' } params { From 9c3d21584d08d690f5f2ccb1ebc5a7986c3f4bd1 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 14:12:47 +0100 Subject: [PATCH 0463/1233] add api file for control (baseline) methods Former-commit-id: acdaf12fc50f54539f5076f13c1e000ef90c8c49 --- src/dimensionality_reduction/api/comp_control_method.yaml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 src/dimensionality_reduction/api/comp_control_method.yaml diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml new file mode 100644 index 0000000000..1bcfdf1cdf --- /dev/null +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -0,0 +1,7 @@ +functionality: + arguments: + - name: "--input" + __inherits__: anndata_dataset.yaml + - name: "--output" + __inherits__: anndata_reduced.yaml + direction: output \ No newline at end of file From 06bd7f9d84c82fc74dee9cfb72048d078f1047de Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 14:14:06 +0100 Subject: [PATCH 0464/1233] add control method (random_features) Former-commit-id: 79c77cdbb889eb7efe9375c751b5af4971c3523a --- .../random_features/config.vsh.yaml | 28 ++++++++++++++ .../control_methods/random_features/script.py | 24 ++++++++++++ .../control_methods/random_features/test.py | 38 +++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml create mode 100644 src/dimensionality_reduction/control_methods/random_features/script.py create mode 100644 src/dimensionality_reduction/control_methods/random_features/test.py diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml new file mode 100644 index 0000000000..7f9c99c1d8 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -0,0 +1,28 @@ +__inherits__: ../../api/comp_control_method.yaml +functionality: + name: "random_features" + namespace: "dimensionality_reduction/control_methods" + description: "Negative control method which generates a random embedding " + info: + type: negative_control + label: Random features + v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + preferred_normalization: counts + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - numpy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py new file mode 100644 index 0000000000..6aad6abf8d --- /dev/null +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -0,0 +1,24 @@ +import anndata as ad +import numpy as np + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +adata = ad.read_h5ad(par['input']) + +print('Create random embedding') +adata.obsm["X_emb"] = np.random.normal(0, 1, (adata.shape[0], 2)) + +# Update .uns +adata.uns['method_id'] = 'random_features' + +print("Write output to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/test.py b/src/dimensionality_reduction/control_methods/random_features/test.py new file mode 100644 index 0000000000..19d876d230 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/random_features/test.py @@ -0,0 +1,38 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/input/dataset.h5ad" +output_path = "output.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether predictions were added") +assert "X_emb" in output.obsm +assert meta['functionality_name'] == output.uns["method_id"] + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From 879b7192f847fd84270808dee4f813b15e47195e Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 14:14:28 +0100 Subject: [PATCH 0465/1233] add control method (high_dim_pca) Former-commit-id: 5730fad5ebe3db9c1317c62a4d2e7c871f8358ad --- .../high_dim_pca/config.vsh.yaml | 33 +++++++++++++++ .../control_methods/high_dim_pca/script.py | 25 +++++++++++ .../control_methods/high_dim_pca/test.py | 41 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml create mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/script.py create mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/test.py diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml new file mode 100644 index 0000000000..c91942740b --- /dev/null +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml @@ -0,0 +1,33 @@ +__inherits__: ../../api/comp_control_method.yaml +functionality: + name: "high_dim_pca" + namespace: "dimensionality_reduction/control_methods" + description: "Positive control method which generates high-dimensional PCA embedding" + info: + type: positive_control + label: High-dimensional PCA + v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py + v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + preferred_normalization: counts + arguments: + - name: "--n_pca" + type: integer + default: 50 + description: Number of principal components of PCA to use. + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py new file mode 100644 index 0000000000..5152ed5a14 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py @@ -0,0 +1,25 @@ +import anndata as ad +import scanpy as sc + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data") +adata = ad.read_h5ad(par['input']) + +print('Create high dimensionally PCA embedding') +sc.pp.pca(adata.layers['counts'], n_comps=min(min(adata.shape), par['n_pca'])) +adata.obsm["X_emb"] = adata.obsm["X_pca"] + +# Update .uns +adata.uns['method_id'] = 'high_dim_pca' + +print("Write output to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/test.py b/src/dimensionality_reduction/control_methods/high_dim_pca/test.py new file mode 100644 index 0000000000..8ca738f5b9 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/test.py @@ -0,0 +1,41 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/input/dataset.h5ad" +output_path = "output.h5ad" +n_pca = 50 +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, + "--n_pca", str(n_pca) +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd) +# out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether predictions were added") +assert "X_emb" in output.obsm +assert meta['functionality_name'] == output.uns["method_id"] + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From dc1d9d3402676decce24e9374469f385f83ecdd1 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 14:22:27 +0100 Subject: [PATCH 0466/1233] set 500 as default n_pca and fix bug Former-commit-id: 82de54bd9f59649f2624259ad269e68f363306d2 --- .../control_methods/high_dim_pca/config.vsh.yaml | 2 +- .../control_methods/high_dim_pca/script.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml index c91942740b..eb74aebf73 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: arguments: - name: "--n_pca" type: integer - default: 50 + default: 500 description: Number of principal components of PCA to use. resources: - type: python_script diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py index 5152ed5a14..07501fcfa0 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py @@ -5,6 +5,7 @@ par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', 'output': 'output.h5ad', + 'n_pca': 500, } meta = { 'functionality_name': 'foo', @@ -15,8 +16,7 @@ adata = ad.read_h5ad(par['input']) print('Create high dimensionally PCA embedding') -sc.pp.pca(adata.layers['counts'], n_comps=min(min(adata.shape), par['n_pca'])) -adata.obsm["X_emb"] = adata.obsm["X_pca"] +adata.obsm["X_emb"] = sc.pp.pca(adata.layers['counts'], n_comps=min(min(adata.shape) - 1, par['n_pca'])) # Update .uns adata.uns['method_id'] = 'high_dim_pca' From af5c2c0dca5a214f33cb8c7d93a196a08cef543d Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 15:00:32 +0100 Subject: [PATCH 0467/1233] fix typo Former-commit-id: a0ccd9fcb836355864694083d53cacd9a5197f55 --- src/dimensionality_reduction/metrics/rmse/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index 1f28dfceb8..6aeecf1b84 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -39,7 +39,7 @@ adata.uns['metric_values'] = [] adata.uns['metric_ids'] += ['kruskal', 'rmse'] -adata.uns['metric_values'] += ['kruskal_score', 'rmse'] +adata.uns['metric_values'] += [kruskal_score, rmse] adata.obsm['kruskal'] = kruskal_matrix print("Write data to file") From 7479e32c3cdd3c5bc4829314747d12c4d52cbe15 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 15:00:55 +0100 Subject: [PATCH 0468/1233] add rmse unit test Former-commit-id: 51ab83cfc345fb4d054259b37f5d506b4a737e01 --- .../metrics/rmse/config.vsh.yaml | 5 +++ .../metrics/rmse/test.py | 45 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 src/dimensionality_reduction/metrics/rmse/test.py diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 7b32035489..f1959058e3 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -11,6 +11,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py new file mode 100644 index 0000000000..73847c815c --- /dev/null +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -0,0 +1,45 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/input/dataset.h5ad" +output_path = "output.h5ad" +n_pca = 50 +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, + "--n_pca", str(n_pca) +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd) +# out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether metrics were added") +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert meta['functionality_name'] in output.uns["metric_id"] + +print(">> Checking whether metrics are float") +assert isinstance(adata.uns['metric_values'][adata.uns['metric_ids'].index(meta['functionality_name'])], float) + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From ed314bdfbdf157cf5953e79e69f010463d62ed34 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 21:22:59 +0100 Subject: [PATCH 0469/1233] fix bug Former-commit-id: 94a812384ea51b2bcdba7fa0bc4e096b49710ee4 --- src/dimensionality_reduction/metrics/rmse/script.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index 6aeecf1b84..d0df98a4fa 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -5,8 +5,8 @@ ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'output.h5ad', + 'output': 'score.h5ad', } meta = { 'functionality_name': 'foo', @@ -36,10 +36,11 @@ print("Store metric value") if 'metric_ids' not in adata.uns.keys(): adata.uns['metric_ids'] = [] - adata.uns['metric_values'] = [] + adata.uns['metric_values'] = {} adata.uns['metric_ids'] += ['kruskal', 'rmse'] -adata.uns['metric_values'] += [kruskal_score, rmse] +adata.uns['metric_values']['rmse'] = rmse +adata.uns['metric_values']['kruskal'] = kruskal_score adata.obsm['kruskal'] = kruskal_matrix print("Write data to file") From abb030a3cea5d2bb7807208afc2425891f01defa Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 29 Nov 2022 21:23:17 +0100 Subject: [PATCH 0470/1233] add rmse unittest Former-commit-id: 258a77d47cec6867bce6405a69894980c592458d --- .../metrics/rmse/test.py | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py index 73847c815c..546460db28 100644 --- a/src/dimensionality_reduction/metrics/rmse/test.py +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -2,22 +2,27 @@ import subprocess from os import path -input_path = meta["resources_dir"] + "/input/dataset.h5ad" -output_path = "output.h5ad" +## VIASH START +meta = { + 'executable': './target/docker/dimensionality_reduction/umap', + 'resources_dir': './resources_test/common/pancreas', +} +## VIASH END + +input_path = meta["resources_dir"] + "/input/reduced.h5ad" +output_path = "score.h5ad" n_pca = 50 cmd = [ meta['executable'], "--input", input_path, "--output", output_path, - "--n_pca", str(n_pca) ] print(">> Checking whether input file exists") assert path.exists(input_path) print(">> Running script as test") -out = subprocess.run(cmd) -# out = subprocess.run(cmd, check=True, capture_output=True, text=True) +out = subprocess.run(cmd, check=True, capture_output=True, text=True) print(">> Checking whether output file exists") assert path.exists(output_path) @@ -33,10 +38,10 @@ print(">> Checking whether metrics were added") assert "metric_ids" in output.uns assert "metric_values" in output.uns -assert meta['functionality_name'] in output.uns["metric_id"] +assert meta['functionality_name'] in output.uns["metric_ids"] print(">> Checking whether metrics are float") -assert isinstance(adata.uns['metric_values'][adata.uns['metric_ids'].index(meta['functionality_name'])], float) +assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) print(">> Checking whether data from input was copied properly to output") assert input.n_obs == output.n_obs From 58589e2527fd49120dc364dce91003be06496abf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 29 Nov 2022 23:05:56 +0100 Subject: [PATCH 0471/1233] fix path Former-commit-id: 22da94f8ef3b11b27934464637884276ea6a9d28 --- src/denoising/api/comp_control_method.yaml | 2 +- src/denoising/api/comp_method.yaml | 2 +- src/denoising/api/comp_metric.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index c1cabec5f0..61d734c4db 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -8,7 +8,7 @@ functionality: __inherits__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../output/denoising + - path: ../../../../resources_test/denoising - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 4e1a83738b..4f0db2fc3a 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -6,7 +6,7 @@ functionality: __inherits__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../output/denoising + - path: ../../../../resources_test/denoising - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index a77dc789e7..07620a4675 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -8,7 +8,7 @@ functionality: __inherits__: anndata_score.yaml direction: output test_resources: - - path: ../../../../output/denoising/ + - path: ../../../../resources_test/denoising/ - type: python_script path: format_check.py text: | From 3557ec6d24ceb1993dcd30bc1c37c43fc1d82d1c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 30 Nov 2022 10:24:16 +0100 Subject: [PATCH 0472/1233] Modify input argument name Former-commit-id: 045a3a781eb1ad09355c6a8c7547325cbf20dba4 --- src/dimensionality_reduction/api/comp_metric.yaml | 2 +- src/dimensionality_reduction/metrics/rmse/test.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index d0624226f6..a589d03e72 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,6 +1,6 @@ functionality: arguments: - - name: "--input" + - name: "--input_reduced" __inherits__: anndata_reduced.yaml - name: "--output" __inherits__: anndata_score.yaml diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py index 546460db28..0ab6ef5f7a 100644 --- a/src/dimensionality_reduction/metrics/rmse/test.py +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -14,7 +14,7 @@ n_pca = 50 cmd = [ meta['executable'], - "--input", input_path, + "--input_reduced", input_path, "--output", output_path, ] From d246df7eb987c718f7ddedca1fbcd2362be7005f Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 30 Nov 2022 13:59:34 +0100 Subject: [PATCH 0473/1233] Update config and remove kruskal scores from uns Former-commit-id: d1a7e5630a746e062eb03612c189c7ae2965dafa --- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 5 +++-- src/dimensionality_reduction/metrics/rmse/script.py | 5 +++-- src/dimensionality_reduction/metrics/rmse/test.py | 2 +- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index f1959058e3..37a78ee1ea 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -4,10 +4,11 @@ functionality: namespace: "dimensionality_reduction/metrics" description: The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices info: - type: metric - label: RMSE v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + metrics: + - id: rmse + label: RMSE resources: - type: python_script path: script.py diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index d0df98a4fa..fe18b07bfa 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -38,9 +38,10 @@ adata.uns['metric_ids'] = [] adata.uns['metric_values'] = {} -adata.uns['metric_ids'] += ['kruskal', 'rmse'] +adata.uns['metric_ids'] += ['rmse'] +# adata.uns['metric_ids'] += ['kruskal', 'rmse'] adata.uns['metric_values']['rmse'] = rmse -adata.uns['metric_values']['kruskal'] = kruskal_score +# adata.uns['metric_values']['kruskal'] = kruskal_score adata.obsm['kruskal'] = kruskal_matrix print("Write data to file") diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py index 0ab6ef5f7a..546460db28 100644 --- a/src/dimensionality_reduction/metrics/rmse/test.py +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -14,7 +14,7 @@ n_pca = 50 cmd = [ meta['executable'], - "--input_reduced", input_path, + "--input", input_path, "--output", output_path, ] From d3653ced8de3f95712b29377478af27eeee5b3d5 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 30 Nov 2022 14:00:49 +0100 Subject: [PATCH 0474/1233] set input argument back to "input" Former-commit-id: faec44f85a97189f856642ea12312caf364432af --- src/dimensionality_reduction/api/comp_metric.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index a589d03e72..d0624226f6 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,6 +1,6 @@ functionality: arguments: - - name: "--input_reduced" + - name: "--input" __inherits__: anndata_reduced.yaml - name: "--output" __inherits__: anndata_score.yaml From dc20d991ff19e8d318d1e3bb0301be59787ae740 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 30 Nov 2022 14:02:01 +0100 Subject: [PATCH 0475/1233] add basic workflow Former-commit-id: 73a2bd2a831e6a26957f1f4f06a7f9c8a478eab7 --- .../workflows/run/config.vsh.yaml | 31 ++++ .../workflows/run/main.nf | 173 ++++++++++++++++++ .../workflows/run/nextflow.config | 14 ++ 3 files changed, 218 insertions(+) create mode 100644 src/dimensionality_reduction/workflows/run/config.vsh.yaml create mode 100644 src/dimensionality_reduction/workflows/run/main.nf create mode 100644 src/dimensionality_reduction/workflows/run/nextflow.config diff --git a/src/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/dimensionality_reduction/workflows/run/config.vsh.yaml new file mode 100644 index 0000000000..abd26e5c36 --- /dev/null +++ b/src/dimensionality_reduction/workflows/run/config.vsh.yaml @@ -0,0 +1,31 @@ +functionality: + name: "run_benchmark" + namespace: "dimensionality_reduction/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the normalized dataset" + required: true + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input" + type: "file" # todo: replace with includes + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + example: output.tsv + resources: + - type: nextflow_script + path: main.nf + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf new file mode 100644 index 0000000000..a226e51977 --- /dev/null +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -0,0 +1,173 @@ +nextflow.enable.dsl=2 + +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +// import control methods +include { high_dim_pca } from "$targetDir/dimensionality_reduction/control_methods/high_dim_pca/main.nf" +include { random_features } from "$targetDir/dimensionality_reduction/control_methods/random_features/main.nf" + +// import methods +include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" +include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" + +// import metrics +include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" + +// tsv generation component +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" + +// import helper functions +include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/nxf_utils/DataFlowHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +// construct a map of methods (id -> method_module) +methods = [ random_features, high_dim_pca, umap, phate ] + .collectEntries{method -> + [method.config.functionality.name, method] + } + +workflow { + helpMessage(config) + + viashChannel(params, config) + | run_wf +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + preprocess: ["dataset_id"], + method: ["input"], + metric: [], + output: ["output"] + ) + + // multiply events by the number of method + | getWorkflowArguments(key: "preprocess") + | add_methods + + // filter the normalization methods that a method actually prefers + //| check_filtered_normalization_id + + // add input_solution to data for the positive controls + | controls_can_cheat + + // run methods + | getWorkflowArguments(key: "method") + | run_methods + + // run metrics + | getWorkflowArguments(key: "metric", inputKey: "input") + | run_metrics + + // convert to tsv + | aggregate_results + + emit: + output_ch +} + +workflow add_methods { + take: input_ch + main: + output_ch = Channel.fromList(methods.keySet()) + | combine(input_ch) + + // generate combined id for method_id and dataset_id + | pmap{method_id, dataset_id, data -> + def new_id = dataset_id + "." + method_id + def new_data = data.clone() + [method_id: method_id] + new_data.remove("id") + [new_id, new_data] + } + emit: output_ch +} + +workflow check_filtered_normalization_id { + take: input_ch + main: + output_ch = input_ch + | pfilter{id, data -> + data = data.clone() + def method = methods[data.method_id] + def preferred = method.config.functionality.info.preferred_normalization + // if a method is just using the counts, we can use any normalization method + if (preferred == "counts") { + preferred = "log_cpm" + } + data.normalization_id == preferred + } + emit: output_ch +} + +workflow controls_can_cheat { + take: input_ch + main: + output_ch = input_ch + | pmap{id, data, passthrough -> + def method = methods[data.method_id] + def method_type = method.config.functionality.info.method_type + def new_data = data.clone() + // if (method_type != "method") { + // new_data = new_data + [input_solution: passthrough.metric.input_solution] + // } + [id, new_data, passthrough] + } + emit: output_ch +} + +workflow run_methods { + take: input_ch + main: + // generate one channel per method + method_chs = methods.collect { method_id, method_module -> + input_ch + | filter{it[1].method_id == method_id} + | method_module + } + // mix all results + output_ch = method_chs[0].mix(*method_chs.drop(1)) + + emit: output_ch +} + +workflow run_metrics { + take: input_ch + main: + + output_ch = input_ch + | rmse + // | mix + + emit: output_ch +} + +workflow aggregate_results { + take: input_ch + main: + + output_ch = input_ch + | toSortedList + | filter{ it.size() > 0 } + | map{ it -> + [ "combined", it.collect{ it[1] } ] + it[0].drop(2) + } + | getWorkflowArguments(key: "output") + | extract_scores.run( + auto: [ publish: true ] + ) + + emit: output_ch +} \ No newline at end of file diff --git a/src/dimensionality_reduction/workflows/run/nextflow.config b/src/dimensionality_reduction/workflows/run/nextflow.config new file mode 100644 index 0000000000..dc5390c66d --- /dev/null +++ b/src/dimensionality_reduction/workflows/run/nextflow.config @@ -0,0 +1,14 @@ +manifest { + name = 'dimensionality_reduction/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Dimensionality reduction' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/nxf_utils/labels.config") From cb1131db011cef43d82c4e7c00173404345f2567 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 14:08:23 +0100 Subject: [PATCH 0476/1233] add readme Former-commit-id: 6f86593351305d9931aef2fb1961b6fa5f98987e --- src/dimensionality_reduction/README.md | 199 +++++++++++++ src/dimensionality_reduction/README.qmd | 271 ++++++++++++++++++ .../docs/task_description.md | 2 + 3 files changed, 472 insertions(+) create mode 100644 src/dimensionality_reduction/README.md create mode 100644 src/dimensionality_reduction/README.qmd create mode 100644 src/dimensionality_reduction/docs/task_description.md diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md new file mode 100644 index 0000000000..8a3fad24a3 --- /dev/null +++ b/src/dimensionality_reduction/README.md @@ -0,0 +1,199 @@ + +- Label + Projection + - Methods + - Metrics + - Pipeline + topology + - File format API + - Dataset + - Reduced + - Score + - Component API + - Control Method + - Method + - Metric + +# Label Projection + +## Methods + +Methods for assigning labels from a reference dataset to a new dataset. + + Warning: Unknown or uninitialised column: `paper_doi`. + + Warning: Unknown or uninitialised column: `code_url`. + +| Name | Type | Description | DOI | URL | +|:----------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-----------------------------------------------------------------------|:----|:----| +| [densMAP](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | +| [PHATE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | | | | +| [t-SNE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | +| [UMAP](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | +| [Random features](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | +| [High-dimensional PCA](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./control_methods/high_dim_pca/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional PCA embedding | | | + +## Metrics + +Metrics for label projection aim to characterize how well each +classifier correctly assigns cell type labels to cells in the test set. + + Warning: Unknown or uninitialised column: `description`. + + Warning: Unknown or uninitialised column: `maximize`. + + Warning: Unknown or uninitialised column: `min`. + + Warning: Unknown or uninitialised column: `max`. + +| Name | Description | Range | +|:--------------------------------------------------------------------------------------------------------------------------|:------------|:-----------| +| [RMSE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | NA NA | \[NA, NA\] | + +## Pipeline topology + +``` mermaid +%%| column: screen-inset-shaded +flowchart LR + anndata_dataset(Dataset) + anndata_reduced(Reduced) + anndata_score(Score) + comp_control_method[/Control Method/] + comp_method[/Method/] + comp_metric[/Metric/] + anndata_dataset---comp_control_method + anndata_dataset---comp_method + anndata_reduced---comp_metric + comp_control_method-->anndata_reduced + comp_method-->anndata_reduced + comp_metric-->anndata_score +``` + +## File format API + +### `Dataset` + +A normalised data with a PCA embedding and HVG selection + +Used in: + +- [control method](#control%20method): input (as input) +- [method](#method): input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalization method, if any. | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| varm | pca_loadings | double | The PCA loadings matrix. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | pca_variance | double | The PCA variance objects. | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id', 'pca_variance' + obsm: 'X_pca' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + +### `Reduced` + +A dimensionality reduced dataset + +Used in: + +- [control method](#control%20method): output (as output) +- [method](#method): output (as output) +- [metric](#metric): input (as input) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:--------|:------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalization method, if any. | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | integer | A ranking of the features by hvg. | +| obsm | X_pca | double | The resulting PCA embedding. | +| obsm | X_emb | double | The resulting t-SNE embedding. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | +| uns | normalization_id | string | Which normalization was used | + +Example: + + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'method_id', 'normalization_id' + obsm: 'X_pca', 'X_emb' + layers: 'counts', 'normalized' + +### `Score` + +Metric score file + +Used in: + +- [metric](#metric): output (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------------|:-------|:---------------------------------------------------------------------------------------------| +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | method_id | string | A unique identifier for the method | +| uns | metric_ids | string | One or more unique metric identifiers | +| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +Example: + + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' + +## Component API + +### `Control Method` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------|:--------------------|:----------|:------------| +| `--input` | [Dataset](#dataset) | input | NA | +| `--output` | [Reduced](#reduced) | output | NA | + +### `Method` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------|:--------------------|:----------|:------------| +| `--input` | [Dataset](#dataset) | input | NA | +| `--output` | [Reduced](#reduced) | output | NA | + +### `Metric` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------|:--------------------|:----------|:------------| +| `--input` | [Reduced](#reduced) | input | NA | +| `--output` | [Score](#score) | output | Score | diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd new file mode 100644 index 0000000000..e63575720d --- /dev/null +++ b/src/dimensionality_reduction/README.qmd @@ -0,0 +1,271 @@ +--- +format: gfm +info: + v1_url: openproblems/tasks/dimensionality_reduction/README.md + v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +toc: true +--- + +```{r setup, include=FALSE} +library(tidyverse) +library(rlang) + +strip_margin <- function(text, symbol = "\\|") { + str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") +} + +dir <- "src/dimensionality_reduction" +dir <- "." +``` + +# Label Projection + +```{r description, echo=FALSE} +lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) +lines2 <- gsub("^#", "##", lines) +knitr::asis_output(lines2) +``` + +## Methods + +Methods for assigning labels from a reference dataset to a new dataset. + +```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) +method_configs <- yaml::yaml.load(method_ns_list$stdout) + +method_info <- map_df(method_configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) + info <- as_tibble(config$functionality$info) + info$comp_yaml <- config$info$config + info$name <- config$functionality$name + info$namespace <- config$functionality$namespace + info$description <- config$functionality$description + info +}) +method_info$paper_doi <- method_info$paper_doi %||% NA_character_ +method_info$code_url <- method_info$code_url %||% NA_character_ + +method_info_view <- + method_info %>% + arrange(type, label) %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Type = type, + Description = description, + DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), + URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") + ) + +cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) +``` + + +## Metrics + +Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. + +```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) +metric_configs <- yaml::yaml.load(metric_ns_list$stdout) + +metric_info <- map_df(metric_configs, function(config) { + metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) + metric_info$comp_yaml <- config$info$config + metric_info$comp_name <- config$functionality$name + metric_info$comp_namespace <- config$functionality$namespace + metric_info +}) + +metric_info$description <- metric_info$description %||% NA_character_ +metric_info$label <- metric_info$label %||% NA_character_ +metric_info$maximize <- metric_info$maximize %||% NA_character_ +metric_info$min <- metric_info$min %||% NA_character_ +metric_info$max <- metric_info$max %||% NA_character_ + +metric_info_view <- + metric_info %>% + transmute( + Name = paste0("[", label, "](", comp_yaml, ")"), + Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), + Range = paste0("[", min, ", ", max, "]") + ) + +cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) +``` + + +## Pipeline topology + +```{r data, include=FALSE} +comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) + +comp_file <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + map_df(conf$functionality$arguments, function(arg) { + tibble( + comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + arg_name = str_replace_all(arg$name, "^-*", ""), + direction = arg$direction %||% "input", + file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + ) + }) +}) + +comp_info <- map_df(comp_yamls, function(yaml_file) { + conf <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_info <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + tibble( + name = basename(yaml_file) %>% gsub("\\.yaml", "", .), + description = arg$description, + short_description = arg$info$short_description, + example = arg$example, + label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + ) +}) + +file_slot <- map_df(file_yamls, function(yaml_file) { + arg <- yaml::read_yaml(yaml_file) + + map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { + df <- map_df(slot, as.data.frame) + df$struct <- group_name + df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) + as_tibble(df) + }) +}) %>% + mutate(multiple = multiple %|% FALSE) +``` + +```{r flow, echo=FALSE,warning=FALSE,error=FALSE} +nodes <- bind_rows( + file_info %>% + transmute(id = name, label = str_to_title(label), is_comp = FALSE), + comp_info %>% + transmute(id = name, label = str_to_title(label), is_comp = TRUE) +) %>% + mutate(str = paste0( + " ", + id, + ifelse(is_comp, "[/", "("), + label, + ifelse(is_comp, "/]", ")") + )) +edges <- bind_rows( + comp_file %>% + filter(direction == "input") %>% + transmute( + from = file_name, + to = comp_name, + arrow = "---" + ), + comp_file %>% + filter(direction == "output") %>% + transmute( + from = comp_name, + to = file_name, + arrow = "-->" + ) +) %>% + mutate(str = paste0(" ", from, arrow, to)) + +# note: use ```{mermaid} instead of ```mermaid when rendering to html +out_str <- strip_margin(glue::glue(" + §```mermaid + §%%| column: screen-inset-shaded + §flowchart LR + §{paste(nodes$str, collapse = '\n')} + §{paste(edges$str, collapse = '\n')} + §``` + §"), symbol = "§") +knitr::asis_output(out_str) +``` + +## File format API + +```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +for (file_name in file_info$name) { + arg_info <- file_info %>% filter(name == file_name) + sub_out <- file_slot %>% + filter(file_name == !!file_name) %>% + select(struct, name, type, description) + + used_in <- comp_file %>% + filter(file_name == !!file_name) %>% + left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% + mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% + pull(str) + + example <- sub_out %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) + + example_str <- c(" AnnData object", paste0(" ", example$str)) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(arg_info$label)}` + § + §{arg_info$description} + § + §Used in: + § + §{paste(used_in, collapse = '\n')} + § + §Slots: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + § + §Example: + § + §{paste(example_str, collapse = '\n')} + § + §"), symbol = "§") + cat(out_str) +} +``` + + + +## Component API + +```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} +# todo: add description +# todo: add required info fields +for (comp_name in comp_info$name) { + comp <- comp_info %>% filter(name == comp_name) + sub_out <- comp_file %>% + filter(comp_name == !!comp_name) %>% + left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% + transmute( + Name = paste0("`--", arg_name, "`"), + `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), + Direction = direction, + Description = file_sdesc + ) + + out_str <- strip_margin(glue::glue(" + §### `{str_to_title(comp$label)}` + § + §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} + § + §Arguments: + § + §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} + §"), symbol = "§") + cat(out_str) +} +``` \ No newline at end of file diff --git a/src/dimensionality_reduction/docs/task_description.md b/src/dimensionality_reduction/docs/task_description.md new file mode 100644 index 0000000000..cb9bb599a0 --- /dev/null +++ b/src/dimensionality_reduction/docs/task_description.md @@ -0,0 +1,2 @@ + + \ No newline at end of file From ae60751e120ae291d0876dc5b158e6e2e7ad06ee Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 14:23:42 +0100 Subject: [PATCH 0477/1233] update task to use sparse data Former-commit-id: 0e8c776c6075a59d6c489e09d6bbe4eadc3b42c4 --- src/denoising/methods/alra/script.R | 2 +- src/denoising/methods/dca/config.vsh.yaml | 1 + src/denoising/methods/dca/script.py | 25 ++++++++++++----- .../methods/knn_smoothing/config.vsh.yaml | 1 + src/denoising/methods/knn_smoothing/script.py | 7 ++--- src/denoising/methods/magic/config.vsh.yaml | 1 + src/denoising/methods/magic/script.py | 3 ++- src/denoising/metrics/mse/script.py | 4 +-- src/denoising/metrics/poisson/script.py | 4 +-- src/denoising/split_dataset/script.py | 27 ++++++++----------- 10 files changed, 43 insertions(+), 32 deletions(-) diff --git a/src/denoising/methods/alra/script.R b/src/denoising/methods/alra/script.R index 6072321f51..10b311d296 100644 --- a/src/denoising/methods/alra/script.R +++ b/src/denoising/methods/alra/script.R @@ -27,7 +27,7 @@ cat(">> Run ALRA\n") out <- alra(as.matrix(counts)) cat(">> Store output\n") -adata$layers[["denoised"]] <- t(out$A_norm_rank_k_cor_sc) +adata$layers[["denoised"]] <- as(t(out$A_norm_rank_k_cor_sc), "CsparseMatrix") adata$uns[["method_id"]] <- meta[["functionality_name"]] cat(">> Write output to file\n") diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 8155f40dc5..afdb9cfe65 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -36,6 +36,7 @@ platforms: - keras>=2.4,<2.11 - tensorflow==2.4.3 - protobuf==3.20.* + - scipy - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index f6575204e5..318af9df40 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -2,6 +2,7 @@ import h5py import numpy as np from dca.api import dca +from scipy import sparse ## VIASH START par = { @@ -17,23 +18,33 @@ print("load input data") # input_train = ad.read_h5ad(par['input_train']) input_file = h5py.File(par["input_train"], 'r') -data = np.array(input_file["layers"]["counts"]) -input_train = ad.AnnData(data) + +# convert to csr matrix +group = input_file.get("layers/counts") +matrix = sparse.csr_matrix((group["data"], group["indices"], group["indptr"])) + +# Convert to Anndata +input_train = ad.AnnData(matrix, dtype=matrix.dtype) print("process data") # run DCA dca(input_train, epochs=par["epochs"]) +# Convert to csr matrix +output_train = sparse.csr_matrix(input_train.X) print("Writing data") -# input_train.uns["method_id"] = meta['functionality_name'] -# input_train.write_h5ad(par['output'], compression="gzip") + + with h5py.File(par['output'], "w") as output_denoised: for key in input_file.keys(): - if key == "X": - continue input_file.copy(input_file[key], output_denoised) - output_denoised["layers"].create_dataset('denoised', data=input_train.X) + denoised = output_denoised['layers'].create_group('denoised') + denoised.create_dataset('data', data=output_train.data) + denoised.create_dataset('indices', data=output_train.indices) + denoised.create_dataset('indptr', data=output_train.indptr) + for key, value in dict(input_file['layers/counts'].attrs).items(): + output_denoised['layers/denoised'].attrs[key] = value output_denoised["uns"].create_dataset('method_id', data=meta['functionality_name']) input_file.close() diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 4a50d97ac9..a28b04be08 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -24,6 +24,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - scipy github: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py index 05bf90dccf..6c88b856af 100644 --- a/src/denoising/methods/knn_smoothing/script.py +++ b/src/denoising/methods/knn_smoothing/script.py @@ -1,10 +1,11 @@ import knn_smooth import numpy as np import anndata as ad +import scipy ## VIASH START par = { - 'input_train': 'output/denoising/pancreas.split_data.output_train.h5ad', + 'input_train': 'output/denoising/pancreas_split_data_output_train.h5ad', 'output': 'output_knn.h5ad', } meta = { @@ -16,8 +17,8 @@ input_train = ad.read_h5ad(par["input_train"]) print("process data") -X = input_train.layers["counts"].transpose() -input_train.layers["denoised"] = (knn_smooth.knn_smoothing(X, k=10)).transpose() +X = input_train.layers["counts"].transpose().toarray() +input_train.layers["denoised"] = scipy.sparse.csr_matrix((knn_smooth.knn_smoothing(X, k=10)).transpose()) print("Writing data") input_train.uns["method_id"] = meta["functionality_name"] diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 47eb88d16c..22ac8cc9c9 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -37,6 +37,7 @@ platforms: - "anndata>=0.8" - scprep - magic-impute + - scipy - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/denoising/methods/magic/script.py b/src/denoising/methods/magic/script.py index 0d9174387f..7507acf094 100644 --- a/src/denoising/methods/magic/script.py +++ b/src/denoising/methods/magic/script.py @@ -2,6 +2,7 @@ import numpy as np import scprep from magic import MAGIC +import scipy ## VIASH START @@ -45,7 +46,7 @@ output_denoised = input_train.copy() output_denoised.uns["method_id"] = meta["functionality_name"] -output_denoised.layers["denoised"] = Y +output_denoised.layers["denoised"] = scipy.sparse.csr_matrix(Y) print("Writing Data") output_denoised.write_h5ad(par['output'],compression="gzip") diff --git a/src/denoising/metrics/mse/script.py b/src/denoising/metrics/mse/script.py index d3278682c6..7060380a99 100644 --- a/src/denoising/metrics/mse/script.py +++ b/src/denoising/metrics/mse/script.py @@ -20,8 +20,8 @@ input_test = ad.read_h5ad(par['input_test']) -test_data = ad.AnnData(X=input_test.layers["counts"], obs=input_test.obs, var=input_test.var, dtype="float32") -denoised_data = ad.AnnData( X=input_denoised.layers["denoised"], obs=input_denoised.obs, var=input_denoised.var, dtype="float32") +test_data = ad.AnnData(X=input_test.layers["counts"].toarray(), dtype="float") +denoised_data = ad.AnnData( X=input_denoised.layers["denoised"].toarray(), dtype="float") print("Normalize data") diff --git a/src/denoising/metrics/poisson/script.py b/src/denoising/metrics/poisson/script.py index 62fec0bafc..014539715f 100644 --- a/src/denoising/metrics/poisson/script.py +++ b/src/denoising/metrics/poisson/script.py @@ -18,8 +18,8 @@ input_test = ad.read_h5ad(par['input_test']) -test_data = input_test.layers["counts"] -denoised_data = input_denoised.layers["denoised"] +test_data = input_test.layers["counts"].toarray() +denoised_data = input_denoised.layers["denoised"].toarray() print("Compute metric value") # scaling diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index 01b627af96..ecff090b1d 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -31,31 +31,26 @@ if key != "counts": del adata.layers[key] -adata.X = adata.layers["counts"] -X = np.array(adata.X) +counts_rounded = np.array(adata.layers["counts"]).round() -# for test purposes -X = X.round() +counts = counts_rounded.astype(int) print(">> process and split data") -if scipy.sparse.issparse(X): - X = np.array(X.todense()) -if np.allclose(X, X.astype(int)): - X = X.astype(int) -else: - raise TypeError("Molecular cross-validation requires integer count data.") - -X_train, X_test = molecular_cross_validation.util.split_molecules( - X, par["train_frac"], 0.0, random_state +train_data, test_data = molecular_cross_validation.util.split_molecules( + counts.data, par["train_frac"], 0.0, random_state ) +X_train = counts.copy() +X_test = counts.copy() +X_train.data = train_data +X_test.data = test_data # Remove no cells that do not have enough reads -is_missing = X_train.sum(axis=0) == 0 -X_train, X_test = X_train[:, ~is_missing], X_test[:, ~is_missing] +is_missing = np.array(X_train.sum(axis=0) == 0) +X_train, X_test = X_train[:, ~is_missing.flatten()], X_test[:, ~is_missing.flatten()] # copy adata to train_set, test_set -new_adata = adata[:, ~is_missing].copy() +new_adata = adata[:, ~is_missing.flatten()].copy() output_train = ad.AnnData(X_train.astype(float), dtype=float) output_train.layers["counts"] = output_train.X From 5027592a8e31c70b28fa1c6843605dc4876ec343 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 14:30:55 +0100 Subject: [PATCH 0478/1233] update __inherit__ to __merge__ Former-commit-id: 414a5ea0b5dc0cd3e4d6d527310af13c8715f50b --- src/denoising/README.qmd | 2 +- src/denoising/api/comp_control_method.yaml | 6 +++--- src/denoising/api/comp_method.yaml | 4 ++-- src/denoising/api/comp_metric.yaml | 6 +++--- src/denoising/api/comp_split_dataset.yaml | 6 +++--- src/denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- .../control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 2 +- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/denoising/methods/magic/config.vsh.yaml | 2 +- src/denoising/metrics/mse/config.vsh.yaml | 2 +- src/denoising/metrics/poisson/config.vsh.yaml | 2 +- src/denoising/split_dataset/config.vsh.yaml | 2 +- 14 files changed, 21 insertions(+), 21 deletions(-) diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd index 45276f884e..a343169954 100644 --- a/src/denoising/README.qmd +++ b/src/denoising/README.qmd @@ -97,7 +97,7 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), arg_name = str_replace_all(arg$name, "^-*", ""), direction = arg$direction %||% "input", - file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) ) }) }) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 61d734c4db..42147e27da 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -1,11 +1,11 @@ functionality: arguments: - name: "--input_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml - name: "--input_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml - name: "--output" - __inherits__: anndata_denoised.yaml + __merge__: anndata_denoised.yaml direction: output test_resources: - path: ../../../../resources_test/denoising diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 4f0db2fc3a..a5546f43ce 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -1,9 +1,9 @@ functionality: arguments: - name: "--input_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml - name: "--output" - __inherits__: anndata_denoised.yaml + __merge__: anndata_denoised.yaml direction: output test_resources: - path: ../../../../resources_test/denoising diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 07620a4675..95b802825c 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -1,11 +1,11 @@ functionality: arguments: - name: "--input_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml - name: "--input_denoised" - __inherits__: anndata_denoised.yaml + __merge__: anndata_denoised.yaml - name: "--output" - __inherits__: anndata_score.yaml + __merge__: anndata_score.yaml direction: output test_resources: - path: ../../../../resources_test/denoising/ diff --git a/src/denoising/api/comp_split_dataset.yaml b/src/denoising/api/comp_split_dataset.yaml index 111e06266e..4b00eba9f0 100644 --- a/src/denoising/api/comp_split_dataset.yaml +++ b/src/denoising/api/comp_split_dataset.yaml @@ -1,12 +1,12 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_dataset.yaml + __merge__: anndata_dataset.yaml - name: "--output_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml direction: output - name: "--output_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml direction: output test_resources: - type: python_script diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index bebb8a51ae..6c06418c15 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "no_denoising" namespace: "denoising/control_methods" diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index a39582b63a..292ca830f4 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "perfect_denoising" namespace: "denoising/control_methods" diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 8bf05fe52d..c0dbc204e8 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "alra" namespace: "denoising/methods" diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index afdb9cfe65..2ed779c3bc 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "dca" namespace: "denoising/methods" diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index a28b04be08..09ed46aa1d 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "knn_smoothing" namespace: "denoising/methods" diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 22ac8cc9c9..521a602f4c 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "magic" namespace: "denoising/methods" diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index ba1eadcc12..592c1499ac 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "mse" namespace: "denoising/metrics" diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index b37712029c..4e11f2070c 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "poisson" namespace: "denoising/metrics" diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml index 478804e461..7981b38d2f 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_split_dataset.yaml functionality: name: "split_dataset" namespace: "denoising" From f8c76f8528c4abbf3bde626eef25ba3647bc259e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 14:39:34 +0100 Subject: [PATCH 0479/1233] add initial resources scripts Former-commit-id: 73d07afbd19e533c5fea5b3f7254626958c54460 --- src/dimensionality_reduction/README.qmd | 2 +- .../resources_scripts/run_benchmark.sh | 75 +++++++++++++++++++ .../resources_scripts/split_datasets.sh | 66 ++++++++++++++++ .../resources_test_scripts/pancreas.sh | 70 +++++++++++++++++ 4 files changed, 212 insertions(+), 1 deletion(-) create mode 100755 src/dimensionality_reduction/resources_scripts/run_benchmark.sh create mode 100755 src/dimensionality_reduction/resources_scripts/split_datasets.sh create mode 100755 src/dimensionality_reduction/resources_test_scripts/pancreas.sh diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd index e63575720d..9e7b7d57d3 100644 --- a/src/dimensionality_reduction/README.qmd +++ b/src/dimensionality_reduction/README.qmd @@ -109,7 +109,7 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), arg_name = str_replace_all(arg$name, "^-*", ""), direction = arg$direction %||% "input", - file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) ) }) }) diff --git a/src/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..230aa9f5e4 --- /dev/null +++ b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -0,0 +1,75 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources/dimensionality_reduction/datasets/openproblems_v1" +OUTPUT_DIR="resources/dimensionality_reduction/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import yaml + +dataset_dir = "$DATASETS_DIR" +output_dir = "$OUTPUT_DIR" + +# read split datasets yaml +with open(dataset_dir + "/params.yaml", "r") as file: + split_list = yaml.safe_load(file) +datasets = split_list['param_list'] + +# figure out where dataset/solution files were stored +param_list = [] + +for dataset in datasets: + id = dataset["id"] + # TODO: uncomment this + # input_dataset = dataset_dir + "/" + id + ".dataset.h5ad" + # input_solution = dataset_dir + "/" + id + ".solution.h5ad" + input_dataset = dataset_dir + "/" + id + ".h5ad" + + obj = { + 'id': id, + 'dataset_id': dataset["dataset_id"], + 'normalization_id': dataset["normalization_id"], + # TODO: uncomment this when the file exists + # 'input_dataset': input_dataset, + # 'input_solution': input_solution + 'input': input_dataset + } + param_list.append(obj) + +# write as output file +output = { + "param_list": param_list, +} + +with open(output_dir + "/params.yaml", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script src/dimensionality_reduction/workflows/run/main.nf \ + -profile docker \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" \ + -with-tower + +bin/tools/docker/nextflow/process_log/process_log \ + --output "$OUTPUT_DIR/nextflow_log.tsv" diff --git a/src/dimensionality_reduction/resources_scripts/split_datasets.sh b/src/dimensionality_reduction/resources_scripts/split_datasets.sh new file mode 100755 index 0000000000..857339e2e5 --- /dev/null +++ b/src/dimensionality_reduction/resources_scripts/split_datasets.sh @@ -0,0 +1,66 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +COMMON_DATASETS="resources/datasets/openproblems_v1" +OUTPUT_DIR="resources/dimensionality_reduction/datasets/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import anndata as ad +import glob +import yaml + +h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") + +param_list = [] + +for h5ad_file in h5ad_files: + print(f"Checking {h5ad_file}") + adata = ad.read_h5ad(h5ad_file, backed=True) + + # TODO: fix this criterion to whatever it is you need + # if "batch" in adata.obs and "celltype" in adata.obs: + dataset_id = adata.uns["dataset_id"].replace("/", ".") + normalization_id = adata.uns["normalization_id"] + id = dataset_id + "." + normalization_id + obj = { + 'id': id, + 'input': h5ad_file, + 'dataset_id': dataset_id, + 'normalization_id': normalization_id + } + param_list.append(obj) + +output = { + "param_list": param_list, + "obs_label": "celltype", + "obs_batch": "batch", + "seed": 123, + "output_dataset": "\$id.dataset.h5ad", + "output_solution": "\$id.solution.h5ad" +} + +with open("$params_file", "w") as file: + yaml.dump(output, file) +HERE +fi + +# export NXF_VER=22.04.5 +# bin/nextflow \ +# run . \ +# -main-script target/nextflow/dimensionality_reduction/split_dataset/main.nf \ +# -profile docker \ +# -resume \ +# -params-file $params_file \ +# --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh new file mode 100755 index 0000000000..59f7ef75e6 --- /dev/null +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -0,0 +1,70 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'dimensionality_reduction|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/dimensionality_reduction/pancreas + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +mkdir -p $DATASET_DIR + +# split dataset +# TODO: implement +# bin/viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ +# --input $RAW_DATA \ +# --output_dataset $DATASET_DIR/dataset.h5ad \ +# --output_solution $DATASET_DIR/solution.h5ad \ +# --seed 123 +cp $RAW_DATA $DATASET_DIR/dataset.h5ad +cp $RAW_DATA $DATASET_DIR/solution.h5ad + +# run one method +bin/viash run src/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset.h5ad \ + --output $DATASET_DIR/densmap.h5ad + +# run one metric +bin/viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ + --input_prediction $DATASET_DIR/densmap.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output $DATASET_DIR/densmap_rmse.h5ad + +# run benchmark +export NXF_VER=22.04.5 + +# after having added a split dataset component +# bin/nextflow \ +# run . \ +# -main-script src/dimensionality_reduction/workflows/run/main.nf \ +# -profile docker \ +# -resume \ +# --id pancreas \ +# --dataset_id pancreas \ +# --normalization_id log_cpm \ +# --input_dataset $DATASET_DIR/dataset.h5ad \ +# --input_solution $DATASET_DIR/solution.h5ad \ +# --output scores.tsv \ +# --publish_dir $DATASET_DIR/ + +bin/nextflow \ + run . \ + -main-script src/dimensionality_reduction/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ + --input $DATASET_DIR/dataset.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ \ No newline at end of file From 6644efe171c41639bb02bd0defc4b93ec0425d9f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 14:39:43 +0100 Subject: [PATCH 0480/1233] remove duplicate nxf imports Former-commit-id: 9fa251ac79611108a6f5d0c2540041f451ff7032 --- src/dimensionality_reduction/workflows/run/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index a226e51977..0f88798041 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -10,9 +10,9 @@ include { random_features } from "$targetDir/dimensionality_reduction/control_me // import methods include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" // import metrics include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" From c9ca3dc67802dfb2272f8299b069319a75543c1e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 14:41:06 +0100 Subject: [PATCH 0481/1233] update to viash 0.6.4 Former-commit-id: 72fa7aed4532fe5d34371b4f4f368e1c7b9b8c60 --- CONTRIBUTING.md | 12 ++++++------ CONTRIBUTING.qmd | 2 +- _viash.yaml | 2 ++ bin/init | 6 +----- src/datasets/README.qmd | 4 ++-- src/datasets/api/comp_dataset_loader.yaml | 2 +- src/datasets/api/comp_normalization.yaml | 4 ++-- src/datasets/api/comp_processor_hvg.yaml | 4 ++-- src/datasets/api/comp_processor_pca.yaml | 4 ++-- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- src/datasets/normalization/log_cpm/config.vsh.yaml | 2 +- .../normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- .../process_openproblems_v1/config.vsh.yaml | 2 +- src/label_projection/README.qmd | 2 +- src/label_projection/api/comp_control_method.yaml | 8 ++++---- src/label_projection/api/comp_method.yaml | 6 +++--- src/label_projection/api/comp_metric.yaml | 6 +++--- src/label_projection/api/comp_split_dataset.yaml | 8 ++++---- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/config.vsh.yaml | 2 +- src/label_projection/methods/scanvi/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/label_projection/methods/xgboost/config.vsh.yaml | 2 +- .../metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/label_projection/split_dataset/config.vsh.yaml | 2 +- 33 files changed, 53 insertions(+), 55 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b9a2d2dfcd..47871b35f4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -189,7 +189,7 @@ For example, to create a new Python-based method named `foo`, create a Viash config at `src/label_projection/methods/foo/config.vsh.yaml`: ``` yaml -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "foo" namespace: "label_projection/methods" @@ -264,7 +264,7 @@ with the `-h` or `--help` parameter. bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` - Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. foo Todo: fill in @@ -294,7 +294,7 @@ bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ --output resources_test/label_projection/pancreas/prediction.h5ad ``` - Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. Load data Create predictions Add method name to uns @@ -315,7 +315,7 @@ bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` - Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected.
@@ -378,7 +378,7 @@ using the **`viash test`** command. bin/viash test src/label_projection/methods/foo/config.vsh.yaml ``` - Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818' ==================================================================== +/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable/foo ---verbosity 6 ---setup cachedbuild @@ -472,7 +472,7 @@ all of the required output slots. bin/viash test src/label_projection/methods/foo/config.vsh.yaml ``` - Warning: Config inheritance (__inherits__) is an experimental feature. Changes to the API are expected. + Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789' ==================================================================== +/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable/foo ---verbosity 6 ---setup cachedbuild diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index f7616fd049..3d9aa239a4 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -163,7 +163,7 @@ You can start creating a new component by [creating a Viash component](https://v mkdir -p src/label_projection/methods/foo cat > src/label_projection/methods/foo/config.vsh.yaml << HERE -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "foo" namespace: "label_projection/methods" diff --git a/_viash.yaml b/_viash.yaml index 8b75c92cc1..1dc2cfd364 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,3 +1,5 @@ +viash_version: 0.6.4 + source: src target: target diff --git a/bin/init b/bin/init index 9b5ac7917c..1ba2ae7892 100755 --- a/bin/init +++ b/bin/init @@ -6,11 +6,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -curl -fsSL get.viash.io | bash -s -- \ - --registry ghcr.io \ - --organisation openproblems-bio \ - --target_image_source https://github.com/openproblems-bio/openproblems-v2 \ - --tag develop +curl -fsSL get.viash.io | bash -s -- --tools false # add --namespace_separator '/' ? diff --git a/src/datasets/README.qmd b/src/datasets/README.qmd index 1dd60faf7c..dc7db48fac 100644 --- a/src/datasets/README.qmd +++ b/src/datasets/README.qmd @@ -36,8 +36,8 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { direction = arg$direction %||% "input", description = arg$description ) - if ("__inherits__" %in% names(arg)) { - df$file_name <- basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + if ("__merge__" %in% names(arg)) { + df$file_name <- basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) } df }) diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 1840cab99d..1fce66c7fb 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -2,4 +2,4 @@ functionality: arguments: - name: "--output" direction: output - __inherits__: anndata_raw.yaml + __merge__: anndata_raw.yaml diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index eebb0fb7f5..77414e5001 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,10 +1,10 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_raw.yaml + __merge__: anndata_raw.yaml - name: "--output" direction: output - __inherits__: anndata_normalized.yaml + __merge__: anndata_normalized.yaml - name: "--layer_output" type: string default: "normalized" diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index c9f4cf256f..e7c45a11f2 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,14 +1,14 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_pca.yaml + __merge__: anndata_pca.yaml - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input for the PCA. - name: "--output" direction: output - __inherits__: anndata_dataset.yaml + __merge__: anndata_dataset.yaml - name: "--var_hvg" type: string default: "hvg" diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index 6276ebd305..d5f6e8d95c 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -1,14 +1,14 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_normalized.yaml + __merge__: anndata_normalized.yaml - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input for the PCA. - name: "--output" direction: output - __inherits__: anndata_pca.yaml + __merge__: anndata_pca.yaml - name: "--obsm_embedding" type: string default: "X_pca" diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 7c2ebcda1e..eb16a1ec88 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: - name: Outputs arguments: - name: "--output" - __inherits__: ../../api/anndata_raw.yaml + __merge__: ../../api/anndata_raw.yaml direction: "output" resources: - type: python_script diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 87dfa39d4c..824809bcb4 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_normalization.yaml +__merge__: ../../api/comp_normalization.yaml functionality: name: "log_cpm" namespace: "datasets/normalization" diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 4af63dba94..ae6b648739 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_normalization.yaml +__merge__: ../../api/comp_normalization.yaml functionality: name: "log_scran_pooling" namespace: "datasets/normalization" diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 4315de267c..8ceaf85bc8 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_normalization.yaml +__merge__: ../../api/comp_normalization.yaml functionality: name: "sqrt_cpm" namespace: "datasets/normalization" diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 25470f8586..a45a4dd3d2 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_processor_hvg.yaml +__merge__: ../../api/comp_processor_hvg.yaml functionality: name: "hvg" namespace: "datasets/processors" diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 1e1e569091..b6cff9bfb6 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_processor_pca.yaml +__merge__: ../../api/comp_processor_pca.yaml functionality: name: "pca" namespace: "datasets/processors" diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 55f57f212f..7d83919119 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: - name: "--output" direction: "output" # todo: fix inherits in nxf - # __inherits__: ../../api/anndata_raw.yaml + # __merge__: ../../api/anndata_raw.yaml type: file description: "A raw dataset" example: "raw_dataset.h5ad" diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index a7e5239df3..65ed05818b 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -101,7 +101,7 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), arg_name = str_replace_all(arg$name, "^-*", ""), direction = arg$direction %||% "input", - file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) ) }) }) diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index 1daacf3709..bdf3fa2b4a 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -1,13 +1,13 @@ functionality: arguments: - name: "--input_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml - name: "--input_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml - name: "--input_solution" - __inherits__: anndata_solution.yaml + __merge__: anndata_solution.yaml - name: "--output" - __inherits__: anndata_prediction.yaml + __merge__: anndata_prediction.yaml direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index d225df01a2..a685d6230e 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -1,11 +1,11 @@ functionality: arguments: - name: "--input_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml - name: "--input_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml - name: "--output" - __inherits__: anndata_prediction.yaml + __merge__: anndata_prediction.yaml direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 481d206919..148903f9db 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -1,11 +1,11 @@ functionality: arguments: - name: "--input_solution" - __inherits__: anndata_solution.yaml + __merge__: anndata_solution.yaml - name: "--input_prediction" - __inherits__: anndata_prediction.yaml + __merge__: anndata_prediction.yaml - name: "--output" - __inherits__: anndata_score.yaml + __merge__: anndata_score.yaml direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_split_dataset.yaml index 7ecd1c1e49..7092ccf19a 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_split_dataset.yaml @@ -1,15 +1,15 @@ functionality: arguments: - name: "--input" - __inherits__: ../../datasets/api/anndata_dataset.yaml + __merge__: ../../datasets/api/anndata_dataset.yaml - name: "--output_train" - __inherits__: anndata_train.yaml + __merge__: anndata_train.yaml direction: output - name: "--output_test" - __inherits__: anndata_test.yaml + __merge__: anndata_test.yaml direction: output - name: "--output_solution" - __inherits__: anndata_solution.yaml + __merge__: anndata_solution.yaml direction: output test_resources: - type: python_script diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index de17f0d032..ccdc363bf2 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "majority_vote" namespace: "label_projection/control_methods" diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 4ba8ba009c..c248b729c7 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "random_labels" namespace: "label_projection/control_methods" diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 1216e3062f..2dd81e1a7c 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "true_labels" namespace: "label_projection/control_methods" diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 4a10110638..13dad797aa 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "knn" namespace: "label_projection/methods" diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index d6c44ec918..80d31cfab8 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "logistic_regression" namespace: "label_projection/methods" diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 8fe92afca3..8b55db12aa 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "mlp" namespace: "label_projection/methods" diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 32e7840222..c6c4c24d40 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "scanvi" namespace: "label_projection/methods" diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index 8e66120b4f..bb4ba7ceb5 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "seurat_transferdata" namespace: "label_projection/methods" diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index 041f9fe96f..cd85f8fe80 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "xgboost" namespace: "label_projection/methods" diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index fe2a680dca..8cbba97e35 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "accuracy" namespace: "label_projection/metrics" diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 5d761d037f..bc59272889 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "f1" namespace: "label_projection/metrics" diff --git a/src/label_projection/split_dataset/config.vsh.yaml b/src/label_projection/split_dataset/config.vsh.yaml index 88c5ee387d..d11a48eb30 100644 --- a/src/label_projection/split_dataset/config.vsh.yaml +++ b/src/label_projection/split_dataset/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_split_dataset.yaml functionality: name: "split_dataset" namespace: "label_projection" From 2a68e778485da719b71dce14f2c3958561d72c43 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 15:25:47 +0100 Subject: [PATCH 0482/1233] update descriptions Former-commit-id: 2a294ad93ad50e9ab7973af5933c25dc7b8662c7 --- src/denoising/metrics/mse/config.vsh.yaml | 2 +- src/denoising/metrics/poisson/config.vsh.yaml | 2 +- src/denoising/split_dataset/config.vsh.yaml | 1 + 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 592c1499ac..07e0b90079 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: metrics: - id: mse label: mse - description: Mean Squared Error + description: The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio maximize: false min: 0 max: +inf diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 4e11f2070c..8645ab8415 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: metrics: - id: poisson label: poisson - description: poisson loss + description: "Poisson loss: measure the mean of the inconsistencies between predicted and target" maximize: false min: 0 max: +inf diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml index 7981b38d2f..239a13c63a 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -2,6 +2,7 @@ __merge__: ../api/comp_split_dataset.yaml functionality: name: "split_dataset" namespace: "denoising" + description: "Splits molecules into two (potentially overlapping) groups using a fraction ratio." arguments: - name: "--method" type: "string" From bec88b863636c227eb0fe7eb1b8b7464b4de704f Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 16:09:04 +0100 Subject: [PATCH 0483/1233] update l1_sqrt Former-commit-id: 3a2deb3a614e4ec7ebcf7736f32232bb53e496f4 --- .../normalization/l1_sqrt/config.vsh.yaml | 22 +++++++++++++ src/datasets/normalization/l1_sqrt/script.py | 29 +++++++++++++++++ .../normalization/sqrt_L1/config.vsh.yaml | 19 ------------ src/datasets/normalization/sqrt_L1/script.py | 31 ------------------- 4 files changed, 51 insertions(+), 50 deletions(-) create mode 100644 src/datasets/normalization/l1_sqrt/config.vsh.yaml create mode 100644 src/datasets/normalization/l1_sqrt/script.py delete mode 100644 src/datasets/normalization/sqrt_L1/config.vsh.yaml delete mode 100644 src/datasets/normalization/sqrt_L1/script.py diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml new file mode 100644 index 0000000000..07abd07995 --- /dev/null +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -0,0 +1,22 @@ +__merge__: ../../api/comp_normalization.yaml +functionality: + name: "l1_sqrt" + namespace: "common/normalization" + description: "Normalize the square rooted data with L1. + Normalizes data such that the sum of the expr values for each cell sums to 1. Returns + the median UMI count per cell scaling all cells as if they were sampled evenly." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scprep + - "anndata>=0.8" + - numpy + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/l1_sqrt/script.py b/src/datasets/normalization/l1_sqrt/script.py new file mode 100644 index 0000000000..9897ad67cc --- /dev/null +++ b/src/datasets/normalization/l1_sqrt/script.py @@ -0,0 +1,29 @@ +import anndata as ad +import scprep +import numpy as np + +## VIASH START +par = { + 'input': "output_train.h5ad", + 'output': "output_norm.h5ad" +} +meta = { + 'functionality_name': "l1_sqrt" +} +## VIASH END + +print("Load data") +adata = ad.read_h5ad(par['input']) + +print("Normalize data") +# libsize and sqrt L1 norm +sqrt_data = scprep.utils.matrix_transform(adata.layers['counts'], np.sqrt) +l1_sqrt, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) +l1_sqrt = l1_sqrt.tocsr() + +print("Store output in adata") +adata.layers["normalized"] = l1_sqrt +adata.uns["normalization_id"] = meta['functionality_name'] + +print("Write data") +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/sqrt_L1/config.vsh.yaml b/src/datasets/normalization/sqrt_L1/config.vsh.yaml deleted file mode 100644 index c815c7d491..0000000000 --- a/src/datasets/normalization/sqrt_L1/config.vsh.yaml +++ /dev/null @@ -1,19 +0,0 @@ -__inherits__: ../../api/comp_normalization.yaml -functionality: - name: "sqrt" - namespace: "common/normalization" - description: "Normalize data using sqrt L1" - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - scanpy - - scprep - - "anndata>=0.8" - - numpy - - type: nextflow diff --git a/src/datasets/normalization/sqrt_L1/script.py b/src/datasets/normalization/sqrt_L1/script.py deleted file mode 100644 index b5faf23536..0000000000 --- a/src/datasets/normalization/sqrt_L1/script.py +++ /dev/null @@ -1,31 +0,0 @@ -import anndata as ad -import scprep -import numpy as np - -## VIASH START -par = { - 'input': "output_train.h5ad", - 'output': "output_norm.h5ad" -} -meta = { - "functionality_name": "normalize_sqrt_L1" -} -## VIASH END - -print(">> Load data") -adata = ad.read_h5ad(par['input']) - -print(">> Normalize data") -# libsize and sqrt L1 norm -sqrt_data = scprep.utils.matrix_transform(adata.X, np.sqrt) -sqrt_L1, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) -sqrt_L1 = sqrt_L1.tocsr() - -print(">> Store output in adata") -adata.layers["sqrtnorm"] = sqrt_L1 -adata.uns["normalization_method"] = meta["functionality_name"].removeprefix("normalize_") - -print(adata.to_df(layer="sqrtnorm")) - -print(">> Write data") -adata.write_h5ad(par['output'], compression="gzip") From e3b68125f23eb9003efd2d8609534b95d369b42a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 16:49:48 +0100 Subject: [PATCH 0484/1233] add authors.yaml Former-commit-id: e6359671b1a6fc0a541cdb9180488283aa22e09d --- src/denoising/api/authors.yaml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 src/denoising/api/authors.yaml diff --git a/src/denoising/api/authors.yaml b/src/denoising/api/authors.yaml new file mode 100644 index 0000000000..791fafbbe7 --- /dev/null +++ b/src/denoising/api/authors.yaml @@ -0,0 +1,14 @@ +functionality: + authors: + - name: "Wesley Lewis" + roles: [ author, maintainer ] + props: { github: wes-lewis } + - name: "Scott Gigante" + roles: [ author, maintainer ] + props: { github: scottgigante } + - name: Robrecht Cannoodt + roles: [ author ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + - name: Kai Waldrant + roles: [ author ] + props: { github: KaiWaldrant } \ No newline at end of file From 46a89254e02d17f87537c52112dd07039ae0abfc Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 30 Nov 2022 16:51:08 +0100 Subject: [PATCH 0485/1233] update wf_utils Former-commit-id: 9bd503d6519d71358c4540225b772c673fdc99ed --- src/wf_utils/DataflowHelper.nf | 57 +++++++++------------------------- src/wf_utils/WorkflowHelper.nf | 19 +++++++----- 2 files changed, 27 insertions(+), 49 deletions(-) diff --git a/src/wf_utils/DataflowHelper.nf b/src/wf_utils/DataflowHelper.nf index 1057038288..e684d0b894 100644 --- a/src/wf_utils/DataflowHelper.nf +++ b/src/wf_utils/DataflowHelper.nf @@ -25,20 +25,19 @@ def setWorkflowArguments(Map args) { main: output_ = input_ | map{ tup -> - assert tup.size() : "Event should have length 2 or greater. Expected format: [id, data]." - def id = tup[0] - def data = tup[1] - def passthrough = tup.drop(2) + id = tup[0] + data = tup[1] + passthrough = tup.drop(2) // determine new data - def toRemove = args.collectMany{ _, dataKeys -> + toRemove = args.collectMany{ _, dataKeys -> // dataKeys is a map but could also be a list dataKeys instanceof List ? dataKeys : dataKeys.values() }.unique() - def newData = data.findAll{!toRemove.contains(it.key)} + newData = data.findAll{!toRemove.contains(it.key)} // determine splitargs - def splitArgs = args. + splitArgs = args. collectEntries{procKey, dataKeys -> // dataKeys is a map but could also be a list newSplitData = dataKeys @@ -77,23 +76,18 @@ def getWorkflowArguments(Map args) { main: output_ = input_ - | map{ tup -> - assert tup.size() : "Event should have length 3 or greater. Expected format: [id, data, splitArgs]." - - def id = tup[0] - def data = tup[1] - def splitArgs = tup[2].clone() + | map{ tup -> + id = tup[0] + data = tup[1] + splitArgs = tup[2].clone() - def passthrough = tup.drop(3) + passthrough = tup.drop(3) // try to infer arg name if (data !instanceof Map) { data = [[ inputKey, data ]].collectEntries() } - assert splitArgs instanceof Map: "Third element of event (id: $id) should be a map" - assert splitArgs.containsKey(args.key): "Third element of event (id: $id) should have a key ${args.key}" - - def newData = data + splitArgs.remove(args.key) + newData = data + splitArgs.remove(args.key) [ id, newData, splitArgs] + passthrough } @@ -140,7 +134,7 @@ def passthroughMap(Closure clos) { main: output_ = input_ | map{ tup -> - def out = clos(tup.take(numArgs)) + out = clos(tup.take(numArgs)) out + tup.drop(numArgs) } @@ -161,10 +155,9 @@ def passthroughFlatMap(Closure clos) { main: output_ = input_ | flatMap{ tup -> - def out = clos(tup.take(numArgs)) - def pt = tup.drop(numArgs) + out = clos(tup.take(numArgs)) for (o in out) { - o.addAll(pt) + o.addAll(tup.drop(numArgs)) } out } @@ -175,23 +168,3 @@ def passthroughFlatMap(Closure clos) { return passthroughFlatMapWf } - -def passthroughFilter(Closure clos) { - def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount - - workflow passthroughFilterWf { - take: - input_ - - main: - output_ = input_ - | filter{ tup -> - clos(tup.take(numArgs)) - } - - emit: - output_ - } - - return passthroughFilterWf -} \ No newline at end of file diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index de0a1d76e8..0fb00586e4 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -238,7 +238,7 @@ def processConfig(config) { } def readConfig(file) { - def config = readYaml(file) + def config = readYaml(file ?: "$projectDir/config.vsh.yaml") processConfig(config) } @@ -523,12 +523,17 @@ def paramsToList(params, config) { // combine params def combinedArgs = defaultArgs + paramArgs + multiParam - // check whether required arguments exist - config.functionality.allArguments - .findAll { it.required } - .forEach { par -> - assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" - } + if (workflow.stubRun) { + // if stub run, explicitly add an id if missing + combinedArgs = [id: "stub"] + combinedArgs + } else { + // else check whether required arguments exist + config.functionality.allArguments + .findAll { it.required } + .forEach { par -> + assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" + } + } // process arguments def inputs = config.functionality.allArguments From e35d13f963120efd3c9c74727e348a4d89fcde9d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 22:36:24 +0100 Subject: [PATCH 0486/1233] update readme Former-commit-id: a371c60749aa4823d76549d3479f3a443b1a012b --- src/denoising/README.md | 40 ++++++++++++---------------------------- src/denoising/README.qmd | 2 +- 2 files changed, 13 insertions(+), 29 deletions(-) diff --git a/src/denoising/README.md b/src/denoising/README.md index fb654b54be..bad196c6a9 100644 --- a/src/denoising/README.md +++ b/src/denoising/README.md @@ -88,40 +88,24 @@ edit `adata.obsm["train"]` or `adata.obsm["test"]`. Methods for assigning labels from a reference dataset to a new dataset. -| Name | Type | Description | DOI | URL | -|:-----------------------------------------------------------------------------------------------------------|:-------|:------------------------------------------------------|:----|:----| -| [ALRA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/alra/config.vsh.yaml) | method | Adaptively-thresholded Low Rank Approximation (ALRA). | | | - -ALRA is a method for imputation of missing values in single cell -RNA-sequencing data, described in the preprint, “Zero-preserving -imputation of scRNA-seq data using low-rank approximation” available -[here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a -scRNA-seq expression matrix, ALRA first computes its rank-k -approximation using randomized SVD. Next, each row (gene) is thresholded -by the magnitude of the most negative value of that gene. Finally, the -matrix is -rescaled.\|[link](https://doi.org/10.1101/397588)\|[link](https://github.com/KlugerLab/ALRA)\| -\|[knn_smooth](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/knn_smoothing/config.vsh.yaml)\|method -\|iterative K-nearest neighbor smoothing -\|[link](https://doi.org/10.1101/217737)\|[link](https://github.com/yanailab/knn-smoothing)\| -\|[magic](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/magic/config.vsh.yaml)\|method -\|MAGIC: Markov affinity-based graph imputation of cells -\|[link](https://doi.org/10.1016/j.cell.2018.05.061)\|[link](https://github.com/KrishnaswamyLab/MAGIC)\| -\|[no -denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/no_denoising/config.vsh.yaml)\|negative_control -\|negative control by copying train counts \| \| \| \|[perfect -denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/perfect_denoising/config.vsh.yaml)\|positive_control -\|Negative control by copying the train counts \| \| \| +| Name | Type | Description | DOI | URL | +|:---------------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-------------------------------------------------------|:---------------------------------------------------|:--------------------------------------------------| +| [ALRA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/alra/config.vsh.yaml) | method | Adaptively-thresholded Low Rank Approximation (ALRA). | [link](https://doi.org/10.1101/397588) | [link](https://github.com/KlugerLab/ALRA) | +| [DCA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/dca/config.vsh.yaml) | method | Deep Count Autoencoder | [link](https://doi.org/10.1038/s41467-018-07931-2) | [link](https://github.com/theislab/dca) | +| [knn_smooth](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/knn_smoothing/config.vsh.yaml) | method | iterative K-nearest neighbor smoothing | [link](https://doi.org/10.1101/217737) | [link](https://github.com/yanailab/knn-smoothing) | +| [magic](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/magic/config.vsh.yaml) | method | MAGIC: Markov affinity-based graph imputation of cells | [link](https://doi.org/10.1016/j.cell.2018.05.061) | [link](https://github.com/KrishnaswamyLab/MAGIC) | +| [no denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/no_denoising/config.vsh.yaml) | negative_control | negative control by copying train counts | | | +| [perfect denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/perfect_denoising/config.vsh.yaml) | positive_control | Negative control by copying the train counts | | | ## Metrics Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. -| Name | Description | Range | -|:-----------------------------------------------------------------------------------------------------------------|:------------------------------------|:----------------| -| [mse](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/mse/config.vsh.yaml) | Mean Squared Error Lower is better. | \[0, infinity\] | -| [poisson](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/poisson/config.vsh.yaml) | poisson loss Lower is better. | \[0, +inf\] | +| Name | Description | Range | +|:-----------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------| +| [mse](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/mse/config.vsh.yaml) | The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio Lower is better. | \[0, +inf\] | +| [poisson](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/poisson/config.vsh.yaml) | Poisson loss: measure the mean of the inconsistencies between predicted and target Lower is better. | \[0, +inf\] | ## Pipeline topology diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd index a343169954..1b09f30ab8 100644 --- a/src/denoising/README.qmd +++ b/src/denoising/README.qmd @@ -46,7 +46,7 @@ method_info_view <- transmute( Name = paste0("[", label, "](", comp_yaml, ")"), Type = type, - Description = description, + Description = gsub("\\.[ \n].*", ".", description), DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") ) From 728fb5c167196383d36bd3e911c35a71a523d4c7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 22:39:40 +0100 Subject: [PATCH 0487/1233] remove redundant sections Former-commit-id: 76e84d7fa49ba965d7ac7e2903aa3bdbb3b1e979 --- src/denoising/README.md | 28 -------------------------- src/denoising/docs/task_description.md | 24 ---------------------- 2 files changed, 52 deletions(-) diff --git a/src/denoising/README.md b/src/denoising/README.md index bad196c6a9..abfa33ff33 100644 --- a/src/denoising/README.md +++ b/src/denoising/README.md @@ -1,8 +1,6 @@ - Denoising - The task - - The metrics - - API - Methods - Metrics - Pipeline @@ -58,32 +56,6 @@ in theory and in practice, the measured denoising accuracy is representative of the accuracy that would be obtained on a ground truth dataset. -## The metrics - -Metrics for data denoising aim to assess denoising accuracy by comparing -the denoised *training* set to the randomly sampled *test* set. - -- **MSE**: The mean squared error between the denoised counts of the - training dataset and the true counts of the test dataset after - reweighting by the train/test ratio. -- **Poisson**: The Poisson log likelihood of observing the true counts - of the test dataset given the distribution given in the denoised - dataset. - -## API - -Datasets should contain the raw UMI counts in `adata.X`, subsampled to -training (`adata.obsm["train"]`) and testing (`adata.obsm["test"]`) -datasets using `openproblems.tasks.denoising.datasets.utils.split_data`. - -The task-specific data loader functions should split the provided raw -UMI counts into a training and a test dataset, as described by [Batson -et al., 2019](https://www.biorxiv.org/content/10.1101/786269v1). The -training dataset should be stored in `adata.obsm['train']`, and the test -dataset should be stored in `adata.obsm['test']`. Methods should store -the denoising result in `adata.obsm['denoised']`. Methods should not -edit `adata.obsm["train"]` or `adata.obsm["test"]`. - ## Methods Methods for assigning labels from a reference dataset to a new dataset. diff --git a/src/denoising/docs/task_description.md b/src/denoising/docs/task_description.md index 2bb88ca1b9..e689702179 100644 --- a/src/denoising/docs/task_description.md +++ b/src/denoising/docs/task_description.md @@ -27,27 +27,3 @@ dataset. Next, a denoising method is applied to the training dataset. Finally, d accuracy is measured by comparing the result to the test dataset. The authors show that both in theory and in practice, the measured denoising accuracy is representative of the accuracy that would be obtained on a ground truth dataset. - -## The metrics - -Metrics for data denoising aim to assess denoising accuracy by comparing the denoised -*training* set to the randomly sampled *test* set. - -* **MSE**: The mean squared error between the denoised counts of the training dataset - and the true counts of the test dataset after reweighting by the train/test ratio. -* **Poisson**: The Poisson log likelihood of observing the true counts of the test - dataset given the distribution given in the denoised dataset. - -## API - -Datasets should contain the raw UMI counts in `adata.X`, subsampled to training -(`adata.obsm["train"]`) and testing (`adata.obsm["test"]`) datasets using -`openproblems.tasks.denoising.datasets.utils.split_data`. - -The task-specific data loader functions should split the provided raw UMI counts into a -training and a test dataset, as described by [Batson et al., -2019](https://www.biorxiv.org/content/10.1101/786269v1). The training dataset should be -stored in `adata.obsm['train']`, and the test dataset should be stored in -`adata.obsm['test']`. Methods should store the denoising result in -`adata.obsm['denoised']`. Methods should not edit `adata.obsm["train"]` or -`adata.obsm["test"]`. \ No newline at end of file From 5757c3489f2bcafc1e149975a0a2179d7409fd5b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 22:39:53 +0100 Subject: [PATCH 0488/1233] make sync script safer Former-commit-id: 691e8badf9644ababf45cc6892a2324fe1baa057 --- src/common/resources_test_scripts/aws_sync.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/resources_test_scripts/aws_sync.sh b/src/common/resources_test_scripts/aws_sync.sh index d146cd3caf..0541df125a 100644 --- a/src/common/resources_test_scripts/aws_sync.sh +++ b/src/common/resources_test_scripts/aws_sync.sh @@ -3,5 +3,5 @@ echo "Run the command in this script manually" exit 1 -aws s3 sync "resources_test" "s3://openproblems-data/resources_test" --exclude */temp_* --delete --dryrun +aws s3 sync "resources_test" "s3://openproblems-data/resources_test" --exclude "*/temp*" --exclude "*/tmp*" --delete --dryrun aws s3 sync "resources" "s3://openproblems-data/resources" --exclude */temp_* --delete --dryrun From fcbe897ccfae18487b26f2465c578fe820877754 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Nov 2022 22:39:59 +0100 Subject: [PATCH 0489/1233] add labels to rmse and poisson Former-commit-id: 64920f170fb00d12ef6902310e7c92db9878ba15 --- src/denoising/metrics/mse/config.vsh.yaml | 2 ++ src/denoising/metrics/poisson/config.vsh.yaml | 2 ++ 2 files changed, 4 insertions(+) diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 07e0b90079..a0cb322405 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: - scanpy - scprep - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 8645ab8415..63a93011e4 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: github: - czbiohub/molecular-cross-validation - type: nextflow + directives: + label: [ midmem, midcpu ] \ No newline at end of file From 2c5abd0dc9c16e5862e377b2943592cbd95fd752 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 08:12:55 +0100 Subject: [PATCH 0490/1233] fix resource paths Former-commit-id: 83c1f30e00070f4ce00b73de4211e7c918ba3e5d --- src/denoising/api/comp_control_method.yaml | 6 +++--- src/denoising/api/comp_method.yaml | 4 ++-- src/denoising/api/comp_metric.yaml | 6 +++--- src/denoising/methods/dca/script.py | 2 +- src/denoising/methods/dca/test.py | 2 +- src/denoising/methods/knn_smoothing/script.py | 2 +- src/denoising/split_dataset/script.py | 2 +- 7 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 42147e27da..157f076452 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -8,7 +8,7 @@ functionality: __merge__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising + - path: ../../../../resources_test/denoising/pancreas - type: python_script path: generic_test.py text: | @@ -16,8 +16,8 @@ functionality: import subprocess from os import path - input_train_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_train.h5ad" - input_test_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_test.h5ad" + input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/train.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index a5546f43ce..1628eb06ea 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -6,7 +6,7 @@ functionality: __merge__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising + - path: ../../../../resources_test/denoising/pancreas - type: python_script path: generic_test.py text: | @@ -14,7 +14,7 @@ functionality: import subprocess from os import path - input_train_path = meta["resources_dir"] + "denoising/pancreas_split_data_output_train.h5ad" + input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 95b802825c..4717fc9ab1 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -8,7 +8,7 @@ functionality: __merge__: anndata_score.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising/ + - path: ../../../../resources_test/denoising/pancreas - type: python_script path: format_check.py text: | @@ -16,8 +16,8 @@ functionality: import subprocess from os import path - input_denoised_path = meta["resources_dir"] + "/denoising/output_baseline_PD.h5ad" - input_test_path = meta["resources_dir"] + "/denoising/pancreas.split_data.output_test.h5ad" + input_denoised_path = meta["resources_dir"] + "/pancreas/magic.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index 318af9df40..7e2e65f9e1 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { - 'input_train': 'output/denoising/pancreas_split_data_output_train.h5ad', + 'input_train': 'resources_test/denoising/pancreas/train.h5ad', 'output': 'output_dca.h5ad', 'epochs': 300, } diff --git a/src/denoising/methods/dca/test.py b/src/denoising/methods/dca/test.py index 6662c964bf..b426a822e1 100644 --- a/src/denoising/methods/dca/test.py +++ b/src/denoising/methods/dca/test.py @@ -4,7 +4,7 @@ import subprocess from os import path -input_train_path = meta["resources_dir"] + "denoising/pancreas_split_data_output_train.h5ad" +input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" output_path = "output.h5ad" cmd = [ diff --git a/src/denoising/methods/knn_smoothing/script.py b/src/denoising/methods/knn_smoothing/script.py index 6c88b856af..7d1fca3a0f 100644 --- a/src/denoising/methods/knn_smoothing/script.py +++ b/src/denoising/methods/knn_smoothing/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { - 'input_train': 'output/denoising/pancreas_split_data_output_train.h5ad', + 'input_train': 'resources_test/denoising/pancreas/train.h5ad', 'output': 'output_knn.h5ad', } meta = { diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index ecff090b1d..787f4670fe 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { 'input': "/home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad", - 'output_train': "output/denoising/pancreas_split_data_output_train.h5ad", + 'output_train': "resources_test/denoising/pancreas/train.h5ad", 'output_test': "output/denoising/pancreas_split_data_output_test.h5ad", 'train_frac': 0.9, 'seed': 0 From 442e78cd246746fead4ffa6312f8f835cbb8b0f7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 08:15:25 +0100 Subject: [PATCH 0491/1233] remove unneeded files Former-commit-id: 4559bf2be37178620946df902264a3b77e3d9f57 --- src/denoising/split_dataset/params.yaml | 4 ---- src/denoising/split_dataset/run_nextflow.sh | 17 ----------------- src/denoising/workflows/run/params.yaml | 4 ---- src/denoising/workflows/run/run_nextflow.sh | 16 ---------------- 4 files changed, 41 deletions(-) delete mode 100644 src/denoising/split_dataset/params.yaml delete mode 100644 src/denoising/split_dataset/run_nextflow.sh delete mode 100644 src/denoising/workflows/run/params.yaml delete mode 100644 src/denoising/workflows/run/run_nextflow.sh diff --git a/src/denoising/split_dataset/params.yaml b/src/denoising/split_dataset/params.yaml deleted file mode 100644 index d6d333fa88..0000000000 --- a/src/denoising/split_dataset/params.yaml +++ /dev/null @@ -1,4 +0,0 @@ -param_list: -- id: pancreas - input: resources_test/common/pancreas/dataset.h5ad -seed: 123 diff --git a/src/denoising/split_dataset/run_nextflow.sh b/src/denoising/split_dataset/run_nextflow.sh deleted file mode 100644 index d2b6eec0c6..0000000000 --- a/src/denoising/split_dataset/run_nextflow.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -bin/nextflow \ - run . \ - -main-script target/nextflow/denoising/split_data/main.nf \ - -profile docker \ - -resume \ - -params-file src/denoising/split_data/params.yaml \ - --publish_dir output/denoising/ \ No newline at end of file diff --git a/src/denoising/workflows/run/params.yaml b/src/denoising/workflows/run/params.yaml deleted file mode 100644 index e865650cf5..0000000000 --- a/src/denoising/workflows/run/params.yaml +++ /dev/null @@ -1,4 +0,0 @@ -param_list: -- id: pancreas - input_train: output/denoising/pancreas.split_data.output_train.h5ad - input_test: output/denoising/pancreas.split_data.output_test.h5ad diff --git a/src/denoising/workflows/run/run_nextflow.sh b/src/denoising/workflows/run/run_nextflow.sh deleted file mode 100644 index d61d3f5780..0000000000 --- a/src/denoising/workflows/run/run_nextflow.sh +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -bin/nextflow \ - run . \ - -main-script src/denoising/workflows/run/main.nf \ - -resume \ - -params-file src/denoising/workflows/run/params.yaml \ - --publish_dir output/denoising/ \ No newline at end of file From 2354d5464a786214cb7b27c3fe847e6f8a99d89a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 08:15:36 +0100 Subject: [PATCH 0492/1233] move split dataset test Former-commit-id: 5628537486f1a651866f1f018b61ff942c9d50eb --- src/denoising/api/comp_split_dataset.yaml | 44 ++++++++++++++++++++- src/denoising/split_dataset/generic_test.py | 40 ------------------- 2 files changed, 42 insertions(+), 42 deletions(-) delete mode 100644 src/denoising/split_dataset/generic_test.py diff --git a/src/denoising/api/comp_split_dataset.yaml b/src/denoising/api/comp_split_dataset.yaml index 4b00eba9f0..3752f06386 100644 --- a/src/denoising/api/comp_split_dataset.yaml +++ b/src/denoising/api/comp_split_dataset.yaml @@ -9,6 +9,46 @@ functionality: __merge__: anndata_test.yaml direction: output test_resources: + - path: ../../../resources_test/common/pancreas - type: python_script - path: generic_test.py - - path: ../../../resources_test/common/pancreas \ No newline at end of file + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + output_train_path = "output_train.h5ad" + output_test_path = "output_test.h5ad" + + cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path, + ] + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_train_path) + assert path.exists(output_test_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output_train = ad.read_h5ad(output_train_path) + output_test = ad.read_h5ad(output_test_path) + + print("input:", input) + print("output_train:", output_train) + print("output_test:", output_test) + + print(">> Checking whether data from input was copied properly to output") + assert output_train.uns["dataset_id"] == input.uns["dataset_id"] + assert output_test.uns["dataset_id"] == input.uns["dataset_id"] + + print(">> Check whether certain slots exist") + assert "counts" in output_train.layers + assert "counts" in output_test.layers + + print(">> All checks succeeded!") diff --git a/src/denoising/split_dataset/generic_test.py b/src/denoising/split_dataset/generic_test.py deleted file mode 100644 index ca7a29dbbb..0000000000 --- a/src/denoising/split_dataset/generic_test.py +++ /dev/null @@ -1,40 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -output_train_path = "output_train.h5ad" -output_test_path = "output_test.h5ad" - -cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_train_path) -assert path.exists(output_test_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output_train = ad.read_h5ad(output_train_path) -output_test = ad.read_h5ad(output_test_path) - -print("input:", input) -print("output_train:", output_train) -print("output_test:", output_test) - -print(">> Checking whether data from input was copied properly to output") -assert output_train.uns["dataset_id"] == input.uns["dataset_id"] -assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - -print(">> Check whether certain slots exist") -assert "counts" in output_train.layers -assert "counts" in output_test.layers - -print(">> All checks succeeded!") \ No newline at end of file From d1fa1f6b071671d693ed2a2ff077168d77e459ce Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 08:21:06 +0100 Subject: [PATCH 0493/1233] increase requirements Former-commit-id: 90e13c6e8ff77eaee410f9c8add3b606c9474f87 --- src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 2 +- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/denoising/methods/magic/config.vsh.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index c0dbc204e8..dbd3d0d8eb 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: run: git clone https://github.com/KlugerLab/ALRA.git /ALRA - type: nextflow directives: - label: [ midmem, midcpu ] \ No newline at end of file + label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 2ed779c3bc..f0ed0948b8 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -39,4 +39,4 @@ platforms: - scipy - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ highmem, highcpu ] diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 09ed46aa1d..42e8f55ffc 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,4 +29,4 @@ platforms: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ highmem, highcpu ] diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 521a602f4c..1137734b3a 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -40,4 +40,4 @@ platforms: - scipy - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ highmem, highcpu ] From 3ff6c215f729ff96885f01f543013daa9e153aae Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 08:21:15 +0100 Subject: [PATCH 0494/1233] has been merged into main repo Former-commit-id: 84a6d99618207c74688c1a3d95efd62ed89b6116 --- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 42e8f55ffc..3c5e6e6b2d 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -26,7 +26,7 @@ platforms: - "anndata>=0.8" - scipy github: - - scottgigante-immunai/knn-smoothing@python_package + - yanailab/knn-smoothing@python_package - type: nextflow directives: label: [ highmem, highcpu ] From 433922f3f5d53a83e512dc66eb4ef81605c50460 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 09:13:27 +0100 Subject: [PATCH 0495/1233] no need to copy input data Former-commit-id: 96c23468d0d329fd1f07f597ea8ea1ce24ee5a47 --- src/denoising/control_methods/no_denoising/script.py | 8 +++----- .../control_methods/perfect_denoising/script.py | 12 +++++------- 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/src/denoising/control_methods/no_denoising/script.py b/src/denoising/control_methods/no_denoising/script.py index f77fe59604..61fe34f3be 100644 --- a/src/denoising/control_methods/no_denoising/script.py +++ b/src/denoising/control_methods/no_denoising/script.py @@ -15,11 +15,9 @@ input_train = ad.read_h5ad(par['input_train']) print("Process data") -output_denoised = input_train.copy() +input_train.layers["denoised"] = input_train.layers['counts'] -output_denoised.layers["denoised"] = input_train.layers['counts'] - -output_denoised.uns["method_id"] = meta['functionality_name'] +input_train.uns["method_id"] = meta['functionality_name'] print("Write Data") -output_denoised.write_h5ad(par['output'],compression="gzip") +input_train.write_h5ad(par['output'],compression="gzip") diff --git a/src/denoising/control_methods/perfect_denoising/script.py b/src/denoising/control_methods/perfect_denoising/script.py index 018ed70ea3..251bf87c07 100644 --- a/src/denoising/control_methods/perfect_denoising/script.py +++ b/src/denoising/control_methods/perfect_denoising/script.py @@ -2,8 +2,8 @@ ## VIASH START par = { - 'input_train': 'output/denoising/pancreas.split_data.output_train.h5ad', - 'input_test': 'output/denoising/pancreas.split_data.output_test.h5ad', + 'input_train': 'resources_test/denoising/pancreas/train.h5ad', + 'input_test': 'resources_test/denoising/pancreas/test.h5ad', 'output': 'output_baseline_PD.h5ad', } meta = { @@ -16,11 +16,9 @@ input_test = ad.read_h5ad(par['input_test']) print("Process data") -output_denoised = input_train.copy() +input_train.layers["denoised"] = input_test.layers['counts'] -output_denoised.layers["denoised"] = input_test.layers['counts'] - -output_denoised.uns["method_id"] = meta['functionality_name'] +input_train.uns["method_id"] = meta['functionality_name'] print("Write Data") -output_denoised.write_h5ad(par['output'],compression="gzip") +input_train.write_h5ad(par['output'],compression="gzip") From f9e9e54c9404943108a59a811bf64e1dceadbca8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 10:29:18 +0100 Subject: [PATCH 0496/1233] add dump to test Former-commit-id: dd295c4e8ea1e3083ec75af8a4eef0aa69e8a512 --- src/denoising/methods/dca/test.py | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/src/denoising/methods/dca/test.py b/src/denoising/methods/dca/test.py index b426a822e1..c270b5706e 100644 --- a/src/denoising/methods/dca/test.py +++ b/src/denoising/methods/dca/test.py @@ -19,14 +19,26 @@ print(">> Checking whether output file exists") assert path.exists(output_path) +# helper functions interpreted from https://stackoverflow.com/questions/44883175/how-to-list-all-datasets-in-h5py-file +def descend_obj(obj,sep='\t'): + """ + Iterate through groups in a HDF5 file and prints the groups and datasets names and datasets attributes + """ + if type(obj) in [h5py._hl.group.Group,h5py._hl.files.File]: + for key in obj.keys(): + print(f"{sep}{key}: {obj[key]}") + descend_obj(obj[key],sep=sep+'\t') + elif type(obj)==h5py._hl.dataset.Dataset: + for key in obj.attrs.keys(): + print(f"{sep}\t{key}: {obj.attrs[key]}") + print(">> Reading h5ad files") with h5py.File(input_train_path, 'r') as input_train: with h5py.File(output_path, 'r') as output: - print("input_train:" , input_train.keys()) - print("input_train:", input_train.get("layers/counts")) - print("output:" , output.keys()) - print("output:", output.get("layers/counts")) - + print("Input:") + descend_obj(input_train) + print("Output:") + descend_obj(output) print(">> Checking whether predictions were added") assert "denoised" in output["layers"].keys() From ed93c7ba856b63084a39d8fe514320e31d094cbb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 10:32:18 +0100 Subject: [PATCH 0497/1233] add flush Former-commit-id: 992c1391d6c2ae61a2d8203d78752b0a9552f7ea --- src/denoising/methods/dca/test.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/denoising/methods/dca/test.py b/src/denoising/methods/dca/test.py index c270b5706e..866eb62d9b 100644 --- a/src/denoising/methods/dca/test.py +++ b/src/denoising/methods/dca/test.py @@ -26,21 +26,21 @@ def descend_obj(obj,sep='\t'): """ if type(obj) in [h5py._hl.group.Group,h5py._hl.files.File]: for key in obj.keys(): - print(f"{sep}{key}: {obj[key]}") + print(f"{sep}{key}: {obj[key]}", flush=True) descend_obj(obj[key],sep=sep+'\t') elif type(obj)==h5py._hl.dataset.Dataset: for key in obj.attrs.keys(): - print(f"{sep}\t{key}: {obj.attrs[key]}") + print(f"{sep}\t{key}: {obj.attrs[key]}", flush=True) print(">> Reading h5ad files") with h5py.File(input_train_path, 'r') as input_train: with h5py.File(output_path, 'r') as output: - print("Input:") + print("Input:", flush=True) descend_obj(input_train) - print("Output:") + print("Output:", flush=True) descend_obj(output) - print(">> Checking whether predictions were added") + print(">> Checking whether predictions were added", flush=True) assert "denoised" in output["layers"].keys() assert meta['functionality_name'] == np.string_(output["uns/method_id"]).decode('utf-8') From 0bdb585b734e01cc0c8055db02a13e25c115fb53 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 12:06:22 +0100 Subject: [PATCH 0498/1233] use scott's version of dca Former-commit-id: c2bbd98e3941afe894fe135221cceeb10fde38e2 --- src/denoising/api/comp_method.yaml | 33 +++++++-------- src/denoising/methods/dca/config.vsh.yaml | 16 +++---- src/denoising/methods/dca/script.py | 41 ++++-------------- src/denoising/methods/dca/test.py | 51 ----------------------- 4 files changed, 28 insertions(+), 113 deletions(-) delete mode 100644 src/denoising/methods/dca/test.py diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 1628eb06ea..0b8dabfb2c 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -23,27 +23,24 @@ functionality: "--output", output_path ] - if meta['functionality_name'] != 'dca': - + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) + print(">> Checking whether output file exists") + assert path.exists(output_path) - print(">> Checking whether output file exists") - assert path.exists(output_path) + print(">> Reading h5ad files") + input_train = ad.read_h5ad(input_train_path) + output = ad.read_h5ad(output_path) + print("input_train:", input_train) + print("output:", output) - print(">> Reading h5ad files") - input_train = ad.read_h5ad(input_train_path) - output = ad.read_h5ad(output_path) - print("input_train:", input_train) - print("output:", output) + print(">> Checking whether predictions were added") + assert "denoised" in output.layers + assert meta['functionality_name'] == output.uns["method_id"] - print(">> Checking whether predictions were added") - assert "denoised" in output.layers - assert meta['functionality_name'] == output.uns["method_id"] - - print("Checking whether data from input was copied properly to output") - assert input_train.n_obs == output.n_obs - assert input_train.uns["dataset_id"] == output.uns["dataset_id"] + print("Checking whether data from input was copied properly to output") + assert input_train.n_obs == output.n_obs + assert input_train.uns["dataset_id"] == output.uns["dataset_id"] print("All checks succeeded!") diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index f0ed0948b8..acfe9c565e 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -22,21 +22,17 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py + # test_resources: + # - type: python_script + # path: test.py platforms: - type: docker - image: "python:3.7" + image: "python:3.10" setup: - type: python packages: - - anndata<0.8 - - dca==0.3.4 - - keras>=2.4,<2.11 - - tensorflow==2.4.3 - - protobuf==3.20.* - - scipy + - anndata>=0.8 + - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index 7e2e65f9e1..9c2eca2fed 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -1,6 +1,4 @@ import anndata as ad -import h5py -import numpy as np from dca.api import dca from scipy import sparse @@ -16,39 +14,14 @@ ## VIASH END print("load input data") -# input_train = ad.read_h5ad(par['input_train']) -input_file = h5py.File(par["input_train"], 'r') +input_train = ad.read_h5ad(par['input_train']) -# convert to csr matrix -group = input_file.get("layers/counts") -matrix = sparse.csr_matrix((group["data"], group["indices"], group["indptr"])) - -# Convert to Anndata -input_train = ad.AnnData(matrix, dtype=matrix.dtype) - -print("process data") -# run DCA -dca(input_train, epochs=par["epochs"]) - -# Convert to csr matrix -output_train = sparse.csr_matrix(input_train.X) +print("running dca") +mod = dca(input_train, epochs=par["epochs"], copy=True) print("Writing data") +input_train.layers["denoised"] = mod.layers["counts"] - -with h5py.File(par['output'], "w") as output_denoised: - for key in input_file.keys(): - input_file.copy(input_file[key], output_denoised) - denoised = output_denoised['layers'].create_group('denoised') - denoised.create_dataset('data', data=output_train.data) - denoised.create_dataset('indices', data=output_train.indices) - denoised.create_dataset('indptr', data=output_train.indptr) - for key, value in dict(input_file['layers/counts'].attrs).items(): - output_denoised['layers/denoised'].attrs[key] = value - output_denoised["uns"].create_dataset('method_id', data=meta['functionality_name']) - -input_file.close() - - - - +print("Writing data") +input_train.uns["method_id"] = meta["functionality_name"] +input_train.write_h5ad(par["output"], compression="gzip") diff --git a/src/denoising/methods/dca/test.py b/src/denoising/methods/dca/test.py deleted file mode 100644 index 866eb62d9b..0000000000 --- a/src/denoising/methods/dca/test.py +++ /dev/null @@ -1,51 +0,0 @@ -import h5py -import numpy as np -import anndata as ad -import subprocess -from os import path - -input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" -output_path = "output.h5ad" - -cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--output", output_path -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -# helper functions interpreted from https://stackoverflow.com/questions/44883175/how-to-list-all-datasets-in-h5py-file -def descend_obj(obj,sep='\t'): - """ - Iterate through groups in a HDF5 file and prints the groups and datasets names and datasets attributes - """ - if type(obj) in [h5py._hl.group.Group,h5py._hl.files.File]: - for key in obj.keys(): - print(f"{sep}{key}: {obj[key]}", flush=True) - descend_obj(obj[key],sep=sep+'\t') - elif type(obj)==h5py._hl.dataset.Dataset: - for key in obj.attrs.keys(): - print(f"{sep}\t{key}: {obj.attrs[key]}", flush=True) - -print(">> Reading h5ad files") -with h5py.File(input_train_path, 'r') as input_train: - with h5py.File(output_path, 'r') as output: - print("Input:", flush=True) - descend_obj(input_train) - print("Output:", flush=True) - descend_obj(output) - - print(">> Checking whether predictions were added", flush=True) - assert "denoised" in output["layers"].keys() - assert meta['functionality_name'] == np.string_(output["uns/method_id"]).decode('utf-8') - - print("Checking whether data from input was copied properly to output") - assert input_train.get("layers/counts").shape == output.get("layers/counts").shape - assert input_train["uns/dataset_id"] == output["uns/dataset_id"] - -print("All checks succeeded!") From ab43ef1559121aac018df80e7bb5d603b9c0d01d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 12:47:31 +0100 Subject: [PATCH 0499/1233] make sure there is no X in the anndata Former-commit-id: 86dc39c80abb58a2d8077feaf5703d31fb0cc4cb --- src/denoising/split_dataset/script.py | 33 +++++++++++++++------------ 1 file changed, 19 insertions(+), 14 deletions(-) diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index 787f4670fe..01e031a2d1 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -5,9 +5,9 @@ ## VIASH START par = { - 'input': "/home/kai/Documents/openroblems/openproblems-v2/resources_test/common/pancreas/dataset.h5ad", - 'output_train': "resources_test/denoising/pancreas/train.h5ad", - 'output_test': "output/denoising/pancreas_split_data_output_test.h5ad", + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output_train': "train.h5ad", + 'output_test': "test.h5ad", 'train_frac': 0.9, 'seed': 0 } @@ -44,21 +44,26 @@ X_test = counts.copy() X_train.data = train_data X_test.data = test_data -# Remove no cells that do not have enough reads -is_missing = np.array(X_train.sum(axis=0) == 0) -X_train, X_test = X_train[:, ~is_missing.flatten()], X_test[:, ~is_missing.flatten()] # copy adata to train_set, test_set +output_train = ad.AnnData( + layers={"counts": X_train.astype(float)}, + obs=adata.obs[[]], + var=adata.var[[]], + uns={"dataset_id": adata.uns["dataset_id"]} +) +output_test = ad.AnnData( + layers={"counts": X_test.astype(float)}, + obs=adata.obs[[]], + var=adata.var[[]], + uns={"dataset_id": adata.uns["dataset_id"]} +) -new_adata = adata[:, ~is_missing.flatten()].copy() - -output_train = ad.AnnData(X_train.astype(float), dtype=float) -output_train.layers["counts"] = output_train.X -output_train.uns["dataset_id"] = adata.uns["dataset_id"] +# Remove no cells that do not have enough reads +is_missing = np.array(X_train.sum(axis=0) == 0) -output_test = ad.AnnData(X_test.astype(float), dtype=float) -output_test.layers["counts"] = output_test.X -output_test.uns["dataset_id"] = adata.uns["dataset_id"] +output_train = output_train[:, ~is_missing.flatten()] +output_test = output_test[:, ~is_missing.flatten()] # output_test = adata[:, ~is_missing].copy() # del output_test.layers["counts"] From 0faad918df2d231eb54b838537d935e30577298a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 12:48:36 +0100 Subject: [PATCH 0500/1233] make sure dca isn't using the .X accidentally Former-commit-id: 6d6358b51a2064012a4fc48f215fa33f259c50b5 --- src/denoising/methods/dca/script.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index 9c2eca2fed..b4df2677db 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -1,6 +1,5 @@ import anndata as ad from dca.api import dca -from scipy import sparse ## VIASH START par = { @@ -16,11 +15,16 @@ print("load input data") input_train = ad.read_h5ad(par['input_train']) +print("move layer to X") +input_train.X = input_train.layers["counts"] +del input_train.layers["counts"] + print("running dca") -mod = dca(input_train, epochs=par["epochs"], copy=True) +dca(input_train, epochs=par["epochs"]) -print("Writing data") -input_train.layers["denoised"] = mod.layers["counts"] +print("moving X back to layer") +input_train.layers["denoised"] = input_train.X +del input_train.X print("Writing data") input_train.uns["method_id"] = meta["functionality_name"] From 3380ac6247ee5775c3275819359cf9272ad45568 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 12:53:14 +0100 Subject: [PATCH 0501/1233] make sure output is csr Former-commit-id: a22bb125aa1515fcf49c6329c9881f05789e92a2 --- src/denoising/methods/dca/script.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index b4df2677db..c42b692d48 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -1,5 +1,6 @@ import anndata as ad from dca.api import dca +import scipy ## VIASH START par = { @@ -23,7 +24,7 @@ dca(input_train, epochs=par["epochs"]) print("moving X back to layer") -input_train.layers["denoised"] = input_train.X +input_train.layers["denoised"] = scipy.sparse.csr_matrix(input_train.X) del input_train.X print("Writing data") From 22bf7424c0221bff9cce4f982e8198238eeca0eb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Dec 2022 15:26:10 +0100 Subject: [PATCH 0502/1233] revert previous change Former-commit-id: 5c70eb361c5d2af63d74f30eecdcb391fe3c91e5 --- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 3c5e6e6b2d..42e8f55ffc 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -26,7 +26,7 @@ platforms: - "anndata>=0.8" - scipy github: - - yanailab/knn-smoothing@python_package + - scottgigante-immunai/knn-smoothing@python_package - type: nextflow directives: label: [ highmem, highcpu ] From 9df1d44a4d923c55145713b68147efb9298a765d Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:04:25 +0100 Subject: [PATCH 0503/1233] add api files for split_dataset component Former-commit-id: ee72f2367e27484fd7a1b7d1edce467f657964f9 --- .../api/anndata_test.yaml | 16 ++++++++++++ .../api/anndata_train.yaml | 25 +++++++++++++++++++ .../api/comp_split_dataset.yaml | 10 ++++++++ 3 files changed, 51 insertions(+) create mode 100644 src/dimensionality_reduction/api/anndata_test.yaml create mode 100644 src/dimensionality_reduction/api/anndata_train.yaml create mode 100644 src/dimensionality_reduction/api/comp_split_dataset.yaml diff --git a/src/dimensionality_reduction/api/anndata_test.yaml b/src/dimensionality_reduction/api/anndata_test.yaml new file mode 100644 index 0000000000..95cddc274d --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_test.yaml @@ -0,0 +1,16 @@ +type: file +description: "The test data" +example: "test.h5ad" +info: + short_description: "Test data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true diff --git a/src/dimensionality_reduction/api/anndata_train.yaml b/src/dimensionality_reduction/api/anndata_train.yaml new file mode 100644 index 0000000000..12c913966d --- /dev/null +++ b/src/dimensionality_reduction/api/anndata_train.yaml @@ -0,0 +1,25 @@ +type: file +description: "The training data" +example: "train.h5ad" +info: + short_description: "Training data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + var: + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_split_dataset.yaml new file mode 100644 index 0000000000..da0724caef --- /dev/null +++ b/src/dimensionality_reduction/api/comp_split_dataset.yaml @@ -0,0 +1,10 @@ +functionality: + arguments: + - name: "--input" + __merge__: anndata_dataset.yaml + - name: "--output_train" + __merge__: anndata_train.yaml + direction: output + - name: "--output_test" + __merge__: anndata_test.yaml + direction: output \ No newline at end of file From c0caa982380d355f8d02de66ea64c3d03b54fde5 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:04:56 +0100 Subject: [PATCH 0504/1233] add split_dataset component Former-commit-id: 132eeb8b8e6deceb2f865301a134b2f8686a25a9 --- .../split_dataset/config.vsh.yaml | 16 +++ .../split_dataset/script.py | 109 ++++++++++++++++++ 2 files changed, 125 insertions(+) create mode 100644 src/dimensionality_reduction/split_dataset/config.vsh.yaml create mode 100644 src/dimensionality_reduction/split_dataset/script.py diff --git a/src/dimensionality_reduction/split_dataset/config.vsh.yaml b/src/dimensionality_reduction/split_dataset/config.vsh.yaml new file mode 100644 index 0000000000..543482aa3e --- /dev/null +++ b/src/dimensionality_reduction/split_dataset/config.vsh.yaml @@ -0,0 +1,16 @@ +__merge__: ../api/comp_split_dataset.yaml +functionality: + name: "split_dataset" + namespace: "dimensionality_reduction" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - pyyaml + - "anndata>=0.8" + - type: nextflow diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/split_dataset/script.py new file mode 100644 index 0000000000..9988db9d7e --- /dev/null +++ b/src/dimensionality_reduction/split_dataset/script.py @@ -0,0 +1,109 @@ +import anndata as ad +import re +import yaml +import random +import pandas as pd +import numpy as np + +## VIASH START +par = { + 'input': "resources_test/common/pancreas/dataset.h5ad", + 'output_train': "train.h5ad", + 'output_test': "test.h5ad", +} +meta = { + "functionality_name": "split_data" +} +## VIASH END + +# read the .config.vsh.yaml to find out which output slots need to be copied to which output file +def read_slots(par, meta): + # read output spec from yaml + with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + + output_struct_slots = {} + + # fetch info on which slots should be copied to which file + for arg in config["functionality"]["arguments"]: + if re.match("--output_", arg["name"]): + file = re.sub("--output_", "", arg["name"]) + + struct_slots = arg['info']['slots'] + out = {} + for (struct, slots) in struct_slots.items(): + out[struct] = { slot['name'] : slot['name'] for slot in slots } + + output_struct_slots[file] = out + + return output_struct_slots + +# create new anndata objects according to api spec +def subset_anndata(adata_sub, slot_info): + structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] + kwargs = {} + + for struct in structs: + slot_mapping = slot_info.get(struct, {}) + data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} + if len(data) > 0: + if struct in ['obs', 'var']: + data = pd.concat(data, axis=1) + kwargs[struct] = data + elif struct in ['obs', 'var']: + # if no columns need to be copied, we still need an 'obs' and a 'var' + # to help determine the shape of the adata + kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] + + return ad.AnnData(**kwargs) + +print(">> Load Data") +adata = ad.read_h5ad(par["input"]) + +# print(">> Remove not required data") +# # remove all obs metadata +# del adata.obs + +# # remove all var metadata except hvg_score +# for key in adata.var.keys(): +# if key != "hvg_score": +# del adata.var[key] + +# # Remove obsm/varm matrices +# del adata.varm +# del adata.obsm + +# # remove all unstructured except dataset_id +# for key in list(adata.uns.keys()): +# if key != "dataset_id": +# del adata.uns[key] + +# # remove all unstructured except dataset_id +# for key in list(adata.layers.keys()): +# if key not in ['counts', 'normalized']: +# del adata.layers[key] + +# print(">> Create train/test data") +# output_train = adata.copy() +# output_test = adata.copy() +# del output_test.var +# del output_test.layers['normalized'] + +print(">> Figuring out which data needs to be copied to which output file") +slot_info_per_output = read_slots(par, meta) + +print(">> Creating train data") +output_train = subset_anndata( + adata_sub=adata, + slot_info=slot_info_per_output['train'] +) + +print(">> Creating test data") +output_test = subset_anndata( + adata_sub=adata, + slot_info=slot_info_per_output['test'] +) + +print(">> Writing") +output_train.write_h5ad(par["output_train"]) +output_test.write_h5ad(par["output_test"]) From 63da8b80e04610248925793e73f7ca3e6f54df6b Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:06:16 +0100 Subject: [PATCH 0505/1233] add method: trustworthiness Former-commit-id: eb64ed865b74158772f73aaefc74e5982f461bb8 --- .../metrics/trustworthiness/config.vsh.yaml | 33 ++++++++++++ .../metrics/trustworthiness/script.py | 28 +++++++++++ .../metrics/trustworthiness/test.py | 50 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/trustworthiness/script.py create mode 100644 src/dimensionality_reduction/metrics/trustworthiness/test.py diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml new file mode 100644 index 0000000000..94017a2813 --- /dev/null +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -0,0 +1,33 @@ +__inherits__: ../../api/comp_metric.yaml +functionality: + name: "trustworthiness" + namespace: "dimensionality_reduction/metrics" + description: "To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1." + info: + v1_url: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + metrics: + - id: trustworthiness + label: Trustworthiness + description: To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. + min: 0 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scikit-learn + - numpy + - "anndata>=0.8" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py new file mode 100644 index 0000000000..1646f577fe --- /dev/null +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -0,0 +1,28 @@ +import anndata as ad +import numpy as np +from sklearn import manifold + +## VIASH START +par = { + 'input': 'output.h5ad', + 'output': 'score.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load data") +adata = ad.read_h5ad(par['input']) + +print('Reduce dimensionality of raw data') +high_dim, low_dim = adata.layers['counts'], adata.obsm["X_emb"] +score = manifold.trustworthiness( + high_dim, low_dim, n_neighbors=15, metric="euclidean" +) +# for large k close to #samples, it's higher than 1.0, e.g 1.0000073552559712 +adata.uns['metric_ids'] = 'trustworthiness' +adata.uns['metric_values'] = float(np.clip(score, 0, 1)) + +print("Write data to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/test.py b/src/dimensionality_reduction/metrics/trustworthiness/test.py new file mode 100644 index 0000000000..546460db28 --- /dev/null +++ b/src/dimensionality_reduction/metrics/trustworthiness/test.py @@ -0,0 +1,50 @@ +import anndata as ad +import subprocess +from os import path + +## VIASH START +meta = { + 'executable': './target/docker/dimensionality_reduction/umap', + 'resources_dir': './resources_test/common/pancreas', +} +## VIASH END + +input_path = meta["resources_dir"] + "/input/reduced.h5ad" +output_path = "score.h5ad" +n_pca = 50 +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether metrics were added") +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert meta['functionality_name'] in output.uns["metric_ids"] + +print(">> Checking whether metrics are float") +assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From 7698749eb95a191788d5710709ff38cbca65656c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:07:03 +0100 Subject: [PATCH 0506/1233] add metric: density Former-commit-id: 9901d4d7f835a9fce15cae26463faa5b4be9e8d5 --- .../metrics/density/config.vsh.yaml | 35 ++++++++ .../metrics/density/script.py | 81 +++++++++++++++++++ .../metrics/density/test.py | 50 ++++++++++++ 3 files changed, 166 insertions(+) create mode 100644 src/dimensionality_reduction/metrics/density/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/density/script.py create mode 100644 src/dimensionality_reduction/metrics/density/test.py diff --git a/src/dimensionality_reduction/metrics/density/config.vsh.yaml b/src/dimensionality_reduction/metrics/density/config.vsh.yaml new file mode 100644 index 0000000000..71865454a5 --- /dev/null +++ b/src/dimensionality_reduction/metrics/density/config.vsh.yaml @@ -0,0 +1,35 @@ +__inherits__: ../../api/comp_metric.yaml +functionality: + name: "" + namespace: "dimensionality_reduction/metrics" + description: "" + info: + v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + metrics: + - id: + label: + description: + min: 0 + max: -1 + minimize: true + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../resources_test/common/pancreas/ + dest: input +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scipy + - numpy + - "anndata>=0.8" + - typing + - umap + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py new file mode 100644 index 0000000000..e08b4ed5cd --- /dev/null +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -0,0 +1,81 @@ +import anndata as ad +import numpy as np +from typing import Optional +from umap.umap_ import fuzzy_simplicial_set +from umap.umap_ import nearest_neighbors +from umap import UMAP +from scipy.sparse import issparse +from scipy.stats import pearsonr + +## VIASH START +par = { + 'input': 'output.h5ad', + 'output': 'score.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load data") +adata = ad.read_h5ad(par['input']) + +print('Reduce dimensionality of raw data') +_K = 30 # number of neighbors +_SEED = 42 +_, ro, _ = UMAP( + n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True +).fit_transform(adata.layers['counts']) +# in principle, we could just call _calculate_radii(high_dim, ...) +# this is made sure that the test pass (otherwise, there was .02 difference in corr) +(knn_indices, knn_dists, rp_forest,) = nearest_neighbors( + adata.obsm['X_emb'], + _K, + "euclidean", + {}, + False, + _SEED, + verbose=False, +) + +emb_graph, emb_sigmas, emb_rhos, emb_dists = fuzzy_simplicial_set( + adata.obsm['X_emb'], + _K, + _SEED, + "euclidean", + {}, + knn_indices, + knn_dists, + verbose=False, + return_dists=True, +) + +emb_graph = emb_graph.tocoo() +emb_graph.sum_duplicates() +emb_graph.eliminate_zeros() + +n_vertices = emb_graph.shape[1] + +mu_sum = np.zeros(n_vertices, dtype=np.float32) +re = np.zeros(n_vertices, dtype=np.float32) + +head = emb_graph.row +tail = emb_graph.col +for i in range(len(head)): + j = head[i] + k = tail[i] + D = emb_dists[j, k] + mu = emb_graph.data[i] + re[j] += mu * D + re[k] += mu * D + mu_sum[j] += mu + mu_sum[k] += mu + +epsilon = 1e-8 +re = np.log(epsilon + (re / mu_sum)) + +adata.uns['metric_ids'] = 'density' +adata.uns['metric_values'] = pearsonr(ro, re)[0] + +print("Write data to file") +adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/test.py b/src/dimensionality_reduction/metrics/density/test.py new file mode 100644 index 0000000000..546460db28 --- /dev/null +++ b/src/dimensionality_reduction/metrics/density/test.py @@ -0,0 +1,50 @@ +import anndata as ad +import subprocess +from os import path + +## VIASH START +meta = { + 'executable': './target/docker/dimensionality_reduction/umap', + 'resources_dir': './resources_test/common/pancreas', +} +## VIASH END + +input_path = meta["resources_dir"] + "/input/reduced.h5ad" +output_path = "score.h5ad" +n_pca = 50 +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print("input:", input) + +print("output:", output) + +print(">> Checking whether metrics were added") +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert meta['functionality_name'] in output.uns["metric_ids"] + +print(">> Checking whether metrics are float") +assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file From fe61320dc9dd23161b474f16ff19b5cd5e3af0af Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:07:49 +0100 Subject: [PATCH 0507/1233] fix bugs and modify descriptions Former-commit-id: f32de0ce16e7cba88356c94ba36e2f3da97660b9 --- .../api/anndata_dataset.yaml | 2 +- .../api/anndata_reduced.yaml | 43 ++----------------- 2 files changed, 4 insertions(+), 41 deletions(-) diff --git a/src/dimensionality_reduction/api/anndata_dataset.yaml b/src/dimensionality_reduction/api/anndata_dataset.yaml index d698890866..e5b6e29595 100644 --- a/src/dimensionality_reduction/api/anndata_dataset.yaml +++ b/src/dimensionality_reduction/api/anndata_dataset.yaml @@ -1,5 +1,5 @@ type: file -description: "A normalised data with a PCA embedding and HVG selection" +description: "A normalized data with a PCA embedding and HVG selection" example: "dataset.h5ad" info: label: "Dataset+PCA+HVG" diff --git a/src/dimensionality_reduction/api/anndata_reduced.yaml b/src/dimensionality_reduction/api/anndata_reduced.yaml index fcc7c5f83f..a806c442c9 100644 --- a/src/dimensionality_reduction/api/anndata_reduced.yaml +++ b/src/dimensionality_reduction/api/anndata_reduced.yaml @@ -1,50 +1,13 @@ type: file -description: "A dimensionality reduced dataset" +description: "A dimensionally reduced dataset" example: "reduced.h5ad" info: - label: "Dataset+HVG+X_emb" + short_description: "Training data" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalized expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalization method, if any. - required: false - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - type: double name: X_emb - description: The resulting t-SNE embedding. + description: The dimensionally reduced embedding. uns: - type: string name: dataset_id From 7266982099b37fc4b4d5bf632414c4b0b3b201ff Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:18:18 +0100 Subject: [PATCH 0508/1233] replace inherits by merge Former-commit-id: 6da507b211c1e798f31a399258b4a87562c29e06 --- src/dimensionality_reduction/api/comp_control_method.yaml | 4 ++-- src/dimensionality_reduction/api/comp_method.yaml | 4 ++-- src/dimensionality_reduction/api/comp_metric.yaml | 4 ++-- .../control_methods/high_dim_pca/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/densmap/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- src/dimensionality_reduction/metrics/density/config.vsh.yaml | 2 +- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 2 +- 11 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 1bcfdf1cdf..60d91b94bb 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_dataset.yaml + __merge__: anndata_dataset.yaml - name: "--output" - __inherits__: anndata_reduced.yaml + __merge__: anndata_reduced.yaml direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 1bcfdf1cdf..60d91b94bb 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_dataset.yaml + __merge__: anndata_dataset.yaml - name: "--output" - __inherits__: anndata_reduced.yaml + __merge__: anndata_reduced.yaml direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index d0624226f6..5e46557087 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __inherits__: anndata_reduced.yaml + __merge__: anndata_reduced.yaml - name: "--output" - __inherits__: anndata_score.yaml + __merge__: anndata_score.yaml direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml index eb74aebf73..d85ce8dd70 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "high_dim_pca" namespace: "dimensionality_reduction/control_methods" diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 7f9c99c1d8..bd81f2e1d6 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_control_method.yaml functionality: name: "random_features" namespace: "dimensionality_reduction/control_methods" diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 30852e4603..b5711e1d0d 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "densmap" namespace: "dimensionality_reduction/methods" diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 145befdae1..4168747361 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "phate" namespace: "dimensionality_reduction/methods" diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index e84ad953f0..b0be90219e 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "tsne" namespace: "dimensionality_reduction/methods" diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index c2deda27c7..21e46c89cb 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "umap" namespace: "dimensionality_reduction/methods" diff --git a/src/dimensionality_reduction/metrics/density/config.vsh.yaml b/src/dimensionality_reduction/metrics/density/config.vsh.yaml index 71865454a5..1b33a79e91 100644 --- a/src/dimensionality_reduction/metrics/density/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "" namespace: "dimensionality_reduction/metrics" diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 37a78ee1ea..4cf19edf6c 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "rmse" namespace: "dimensionality_reduction/metrics" From a71aa964a639736b9cb83da098f7158970301817 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 1 Dec 2022 20:18:39 +0100 Subject: [PATCH 0509/1233] replace inherits by merge Former-commit-id: ccb5ecbff7d33c7c02f542b0db63d5075fdab71b --- .../metrics/trustworthiness/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 94017a2813..7d139c3164 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -1,4 +1,4 @@ -__inherits__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: "trustworthiness" namespace: "dimensionality_reduction/metrics" From 165cd346216543a45a65aac552bb543b8e414881 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 1 Dec 2022 23:15:13 +0100 Subject: [PATCH 0510/1233] restore counts layer in dca denoised data Former-commit-id: 7158e0b2f7207dfb09c0726be4238e54725e55a5 --- src/denoising/methods/dca/script.py | 1 - src/denoising/split_dataset/script.py | 4 ---- 2 files changed, 5 deletions(-) diff --git a/src/denoising/methods/dca/script.py b/src/denoising/methods/dca/script.py index c42b692d48..2de2e8b236 100644 --- a/src/denoising/methods/dca/script.py +++ b/src/denoising/methods/dca/script.py @@ -18,7 +18,6 @@ print("move layer to X") input_train.X = input_train.layers["counts"] -del input_train.layers["counts"] print("running dca") dca(input_train, epochs=par["epochs"]) diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index 01e031a2d1..c7e8057bb6 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -65,10 +65,6 @@ output_train = output_train[:, ~is_missing.flatten()] output_test = output_test[:, ~is_missing.flatten()] -# output_test = adata[:, ~is_missing].copy() -# del output_test.layers["counts"] -# output_test.layers["counts"] = scipy.sparse.csr_matrix(X_test).astype(float) - print(">> Writing") output_train.write_h5ad(par["output_train"]) From 8302ec097d14e1c468ca64562305fe76a06ed64c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 06:00:41 +0100 Subject: [PATCH 0511/1233] update l1 sqrt component Former-commit-id: c71471d07f015f4d0f199eb937258e3bda3b8d73 --- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 13 ++++++++++--- src/datasets/normalization/l1_sqrt/script.py | 2 +- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 07abd07995..be227766af 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -2,9 +2,16 @@ __merge__: ../../api/comp_normalization.yaml functionality: name: "l1_sqrt" namespace: "common/normalization" - description: "Normalize the square rooted data with L1. - Normalizes data such that the sum of the expr values for each cell sums to 1. Returns - the median UMI count per cell scaling all cells as if they were sampled evenly." + description: | + Scaled L1 sqrt normalization. + + This normalization method causes all cells to have the same sum of values. + + Steps: + + * Compute the square root of the counts. + * Apply L1 normalization (rescaled such that the sum of the values of each cell sum to 1). + * Multiply by the median UMI count per cell, causing all cells to have the sum of values. resources: - type: python_script path: script.py diff --git a/src/datasets/normalization/l1_sqrt/script.py b/src/datasets/normalization/l1_sqrt/script.py index 9897ad67cc..33243e14c0 100644 --- a/src/datasets/normalization/l1_sqrt/script.py +++ b/src/datasets/normalization/l1_sqrt/script.py @@ -22,7 +22,7 @@ l1_sqrt = l1_sqrt.tocsr() print("Store output in adata") -adata.layers["normalized"] = l1_sqrt +adata.layers[par["layer_output"]] = l1_sqrt adata.uns["normalization_id"] = meta['functionality_name'] print("Write data") From 7cd7157e0099c9ecc236f8776efd0954cd31d888 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 06:34:07 +0100 Subject: [PATCH 0512/1233] workaround for viash bug Former-commit-id: 785cc09057975188771c196b9f90c4d6dff1dd1d --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 4907a485ca..1042feb350 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -85,7 +85,7 @@ jobs: run: | IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" echo "Changed files: "${changed_files[*]}"" - readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | + readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | select(.platforms[] | select(.id == "docker") | length > 0) | (.info.config | capture("^(?.*\/)").dir) as $dir | { "name": .functionality.name, "config": .info.config, From c7be2146fd57d30afdc3caf73789548b718ef2ee Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 06:46:37 +0100 Subject: [PATCH 0513/1233] add labels ci Former-commit-id: 9332bc6c5e1573b13258f9a5012d1395668c6dbe --- .github/workflows/release-build.yml | 2 +- src/wf_utils/labels_ci.config | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) create mode 100644 src/wf_utils/labels_ci.config diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index a7b38806b3..748e8b120c 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -186,7 +186,7 @@ jobs: -main-script "$script" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c workflows/utils/labels_ci.config + -c src/wf_utils/labels_ci.config ###################################3 # phase 4 diff --git a/src/wf_utils/labels_ci.config b/src/wf_utils/labels_ci.config new file mode 100644 index 0000000000..ca02bb15c8 --- /dev/null +++ b/src/wf_utils/labels_ci.config @@ -0,0 +1,8 @@ +process { + withLabel: lowmem { memory = 5.Gb } + withLabel: lowcpu { cpus = 2 } + withLabel: midmem { memory = 5.Gb } + withLabel: midcpu { cpus = 2 } + withLabel: highmem { memory = 5.Gb } + withLabel: highcpu { cpus = 2 } +} From 0b9fe7e075a7a3108e9cb0247d88e421e4afdd5f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 07:06:22 +0100 Subject: [PATCH 0514/1233] update ci Former-commit-id: 224b058698f5d4d66e0628151bb47f081a68a45a --- .github/workflows/integration-test.yml | 14 ++++---------- .github/workflows/main-build.yml | 11 +++-------- .github/workflows/release-build.yml | 19 +++++++------------ .github/workflows/viash-test.yml | 3 +-- 4 files changed, 15 insertions(+), 32 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 59a2616e7b..4cc3d3dfdc 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -47,11 +47,8 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - # build target dir - bin/viash_build -m release -t integration_build + bin/viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -94,7 +91,7 @@ jobs: - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_build -m release -t integration_build -s "$SRC_DIR" + bin/viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -106,7 +103,7 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_push -m release -t integration_build -s "$SRC_DIR" --force + bin/viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup donothing --push ################################### # phase 3 @@ -132,11 +129,8 @@ jobs: # use containers from integration_build branch, hopefully these are available - name: Build target dir run: | - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - # build target dir - bin/viash_build -m release -t integration_build + bin/viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing # use cache - name: Cache resources data diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 8ac662aee4..6086e9ce35 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -10,7 +10,6 @@ jobs: env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" steps: - uses: actions/checkout@v3 @@ -56,11 +55,8 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - # build target dir - bin/viash_build -m release -t main_build + bin/viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - name: Build nextflow schemas & params run: | @@ -99,7 +95,6 @@ jobs: needs: list_components runs-on: ubuntu-latest - if: "!contains(github.event.head_commit.message, 'ci skip')" strategy: fail-fast: false @@ -117,7 +112,7 @@ jobs: - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_build -m release -t main_build -s "$SRC_DIR" + bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -129,4 +124,4 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_push -m release -t main_build -s "$SRC_DIR" --force \ No newline at end of file + bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --push --setup donothing \ No newline at end of file diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 748e8b120c..1de61a5008 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -58,11 +58,8 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - # build target dir - bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} + bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing - name: Build nextflow schemas & params run: | @@ -122,7 +119,7 @@ jobs: - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} -s "$SRC_DIR" + bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -134,7 +131,7 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_push -m release -t ${{ github.event.inputs.version_tag }} -s "$SRC_DIR" --force + bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --push --setup donothing ###################################3 # phase 3 @@ -161,11 +158,8 @@ jobs: # use containers from release branch, hopefully these are available - name: Build target dir run: | - # force override viash build strategy to not build containers - sed -i 's#--setup "\\$setup_strat"#--setup donothing#' bin/viash_build - # build target dir - bin/viash_build -m release -t ${{ github.event.inputs.version_tag }} + bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing # use cache - name: Cache resources data @@ -220,7 +214,8 @@ jobs: timeout-minutes: 30 run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash_test -m release -t ${{ github.event.inputs.version_tag }} \ + bin/viash ns test --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ -s "$SRC_DIR" \ -c '.functionality.requirements.cpus := 2' \ - -c '.functionality.requirements.memory := "5gb"' + -c '.functionality.requirements.memory := "5gb"' \ + --setup build diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 1042feb350..8b40ea3c5b 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -7,7 +7,6 @@ on: jobs: run_ci_check_job: - if: "!contains(github.event.head_commit.message, 'ci skip')" runs-on: ubuntu-latest outputs: run_ci: ${{ steps.github_cli.outputs.check }} @@ -32,7 +31,7 @@ jobs: env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest - if: "(!contains(github.event.head_commit.message, 'ci skip')) && needs.run_ci_check_job.outputs.run_ci == 'true'" + if: "needs.run_ci_check_job.outputs.run_ci == 'true'" outputs: matrix: ${{ steps.set_matrix.outputs.matrix }} cachehash: ${{ steps.cachehash.outputs.cachehash }} From 5e3dbdaeb07b615aba0e0fae2fc58b77c2da7eee Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 07:44:26 +0100 Subject: [PATCH 0515/1233] update to viash 0.6.5 Former-commit-id: a691729303f19c6f12f9c78659e907a2e84ee1b2 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/viash-test.yml | 2 +- _viash.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 4cc3d3dfdc..6be2cadf98 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -60,7 +60,7 @@ jobs: # store component locations - id: set_matrix run: | - component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') echo "component_matrix=$component_json" >> $GITHUB_OUTPUT workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 8b40ea3c5b..2449fa56e3 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -84,7 +84,7 @@ jobs: run: | IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" echo "Changed files: "${changed_files[*]}"" - readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | select(.platforms[] | select(.id == "docker") | length > 0) | + readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | select(.platforms[] | (.info.config | capture("^(?.*\/)").dir) as $dir | { "name": .functionality.name, "config": .info.config, diff --git a/_viash.yaml b/_viash.yaml index 1dc2cfd364..64b65b5fab 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.6.4 +viash_version: 0.6.5 source: src target: target From 3de27a2bd0ee37fe2efcfb1ce6e43dc4fda4c347 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 07:59:30 +0100 Subject: [PATCH 0516/1233] fix broken ci jq command Former-commit-id: 96d0cc02d878f92b451ed26eed3cd95548c2621b --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 2449fa56e3..7bfe941f49 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -84,7 +84,7 @@ jobs: run: | IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" echo "Changed files: "${changed_files[*]}"" - readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | select(.platforms[] | + readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | (.info.config | capture("^(?.*\/)").dir) as $dir | { "name": .functionality.name, "config": .info.config, From 7366db5b41b5282314165913256e94900318882e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Dec 2022 08:23:17 +0100 Subject: [PATCH 0517/1233] update init tools Former-commit-id: 59a197d928cf35d5af0024f73909dbdf6e6adf83 --- bin/init_tools | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/init_tools b/bin/init_tools index 0f4630aea3..945ed531a9 100755 --- a/bin/init_tools +++ b/bin/init_tools @@ -12,7 +12,7 @@ function clean_up { } trap clean_up EXIT -VERSION=0.1.0 +VERSION=0.2.0 if [ $# -eq 2 ]; then git clone --depth 1 --branch $VERSION https://$1:$2@github.com/viash-io/viash_tools.git $tmpdir/ @@ -22,4 +22,4 @@ fi [ -d bin/tools ] && rm -r bin/tools -cp -r $tmpdir/target bin/tools \ No newline at end of file +cp -r $tmpdir/target bin/tools From 94badc995d26e188f9a3ac3c7e7e3adb57592e0a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 2 Dec 2022 11:15:35 +0100 Subject: [PATCH 0518/1233] update changelog with denoising Former-commit-id: a9f6d45a914766e4458910dee07ad1ec23a2ed30 --- CHANGELOG.md | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 28b2f2eb2a..c510182f2e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -60,8 +60,48 @@ * `normalization/sqrt_cpm`: A sqrt CPM normalization method. +* `normalization/l1_sqrt`: A scaled L1 sqrt normalization. extracted from Alra method in the denoising task from v1 + * `subsample`: Subsample an h5ad file. ### V1 MIGRATION * `loaders/openproblems_v1`: Fetch a dataset from OpenProblems v1 + +## denoising + +### NEW FUNCTIONALITY + +* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the split, method and metric components. + +* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. + +* `resources_test/denoising/pancreas` with `src/denoising/resources_test_scripts/pancreas.sh`. + +### V1 MIGRATION + +* `control_methods/no_denoising`: Migrated from v1. Extracted from baseline method + +* `control_methods/perfect_denoising`: Migrated from v1.Extracted from baseline method + +* `methods/alra`: Migrated from v1. Changed from python to R and uses lg_cpm normalised data instead of L1 sqrt + +* `methods/dca`: Migrated and adapted from v1. + +* `methods/knn_smoothing`: Migrated and adapted from v1. + +* `methods/magic`: Migrated from v1. + +* `metrics/mse`: Migrated from v1. + +* `metrics/poisson`: Migrated from v1. + +### Changes from V1 + +* Anndata layers are used to store data instead of obsm + +* extended the use of sparse data in methods unless it was not possible + +* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. \ No newline at end of file From 71275560e551068d3b60e2ffcc5e246da57e5fc2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 2 Dec 2022 11:18:02 +0100 Subject: [PATCH 0519/1233] update api Former-commit-id: 8c91d724d1cf51c5b26668b451d01889be4997f0 --- src/denoising/api/anndata_denoised.yaml | 4 ---- src/denoising/api/anndata_test.yaml | 4 ---- src/denoising/api/anndata_train.yaml | 4 ---- src/denoising/control_methods/no_denoising/script.py | 1 - 4 files changed, 13 deletions(-) diff --git a/src/denoising/api/anndata_denoised.yaml b/src/denoising/api/anndata_denoised.yaml index 66754b81e5..a107af982a 100644 --- a/src/denoising/api/anndata_denoised.yaml +++ b/src/denoising/api/anndata_denoised.yaml @@ -11,10 +11,6 @@ info: - type: integer name: denoised description: denoised data - obs: - - type: string - name: n_counts - description: Raw counts uns: - type: string name: dataset_id diff --git a/src/denoising/api/anndata_test.yaml b/src/denoising/api/anndata_test.yaml index 55c933409e..1bee7651db 100644 --- a/src/denoising/api/anndata_test.yaml +++ b/src/denoising/api/anndata_test.yaml @@ -8,10 +8,6 @@ info: - type: integer name: counts description: Raw counts - obs: - - type: string - name: n_counts - description: Raw counts uns: - type: string name: dataset_id diff --git a/src/denoising/api/anndata_train.yaml b/src/denoising/api/anndata_train.yaml index 803457ef73..09383b02d7 100644 --- a/src/denoising/api/anndata_train.yaml +++ b/src/denoising/api/anndata_train.yaml @@ -8,10 +8,6 @@ info: - type: integer name: counts description: Raw counts - obs: - - type: string - name: n_counts - description: Raw counts uns: - type: string name: dataset_id diff --git a/src/denoising/control_methods/no_denoising/script.py b/src/denoising/control_methods/no_denoising/script.py index 61fe34f3be..63a17750aa 100644 --- a/src/denoising/control_methods/no_denoising/script.py +++ b/src/denoising/control_methods/no_denoising/script.py @@ -3,7 +3,6 @@ ## VIASH START par = { 'input_train': 'output_train.h5ad', - 'input_test': 'output_test.h5ad', 'output': 'output_baseline_ND.h5ad', } meta = { From 5d8c489cbcd6cafbb41f47283cb7c7b3162df998 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 2 Dec 2022 12:01:20 +0100 Subject: [PATCH 0520/1233] initial commit Former-commit-id: f697820b4af2d702a6540e7321ee991ac30c0fc3 --- src/common/list_git_shas/config.vsh.yaml | 24 ++++++++++++++++++++++++ src/common/list_git_shas/script.py | 0 2 files changed, 24 insertions(+) create mode 100644 src/common/list_git_shas/config.vsh.yaml create mode 100644 src/common/list_git_shas/script.py diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml new file mode 100644 index 0000000000..f92ea5f2e2 --- /dev/null +++ b/src/common/list_git_shas/config.vsh.yaml @@ -0,0 +1,24 @@ +functionality: + name: list_git_shas + namespace: common + arguments: + - name: --input + type: file + description: Path to a git repository + required: true + example: /path/to/repo + - name: --output + type: file + description: | + A json containing a list of entries. Each entry must have the + following values: + + * "path" `string`: Path a file in the repository + * "last_modified" `string`: Date of then the file was last modified, in `yyyy-mm-dd HH:mm:ss` format. + * "sha" `string`: Sha of the commit in which the file was last modified + * "history_sha" `string` (optional): A list of SHAs during which the file was modified + required: true + example: output.json + - name: --show_history + type: boolean_true + description: Whether or not to include the full history of SHAs for each file. \ No newline at end of file diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py new file mode 100644 index 0000000000..e69de29bb2 From 4d2375c339daeff11216a65f1d317f7e6f31cd0e Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 2 Dec 2022 14:41:47 +0100 Subject: [PATCH 0521/1233] update test resource generation Former-commit-id: 3b49b11aa7b3f224df5b682ed5323fc4f957a984 --- .../subsample/utils}/g2m_genes_tirosh_hm.txt | 0 .../subsample/utils}/s_genes_tirosh_hm.txt | 0 .../resources/pancreas_mnn.h5ad | Bin 3438982 -> 0 bytes .../resources_test_scripts/pancreas.sh | 51 ++++++++++++++++++ 4 files changed, 51 insertions(+) rename src/batch_integration/{resources => datasets/subsample/utils}/g2m_genes_tirosh_hm.txt (100%) rename src/batch_integration/{resources => datasets/subsample/utils}/s_genes_tirosh_hm.txt (100%) delete mode 100644 src/batch_integration/resources/pancreas_mnn.h5ad create mode 100755 src/batch_integration/resources_test_scripts/pancreas.sh diff --git a/src/batch_integration/resources/g2m_genes_tirosh_hm.txt b/src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt similarity index 100% rename from src/batch_integration/resources/g2m_genes_tirosh_hm.txt rename to src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt diff --git a/src/batch_integration/resources/s_genes_tirosh_hm.txt b/src/batch_integration/datasets/subsample/utils/s_genes_tirosh_hm.txt 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V^BL{ZN5L>nALO>H8ir(e007sTRuBLH diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh new file mode 100755 index 0000000000..dbb11d0bf1 --- /dev/null +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -0,0 +1,51 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'batch_integration|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/batch_integration + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +mkdir -p $DATASET_DIR + +# subset data +echo subset data... +bin/viash run src/batch_integration/datasets/subsample/config.vsh.yaml -- \ + --input $RAW_DATA \ + --output $DATASET_DIR/pancreas/subsample.h5ad \ + --label celltype \ + --batch tech + +# process dataset +echo process data... +bin/viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ + --input $DATASET_DIR/pancreas/subsample.h5ad \ + --output $DATASET_DIR/pancreas/processed.h5ad \ + --label celltype \ + --batch tech \ + --hvgs 100 + +# run methods +echo run methods... +bin/viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ + --input $DATASET_DIR/pancreas/processed.h5ad \ + --output $DATASET_DIR/graph/methods/bbknn.h5ad + +bin/viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ + --input $DATASET_DIR/pancreas/processed.h5ad \ + --output $DATASET_DIR/graph/methods/combat.h5ad +# TODO: embedding method + +# run one metric +echo run metrics... \ No newline at end of file From bc9d0793b381ae8dbf93f4bbcd16e65db99809c1 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 2 Dec 2022 14:42:43 +0100 Subject: [PATCH 0522/1233] update datasets components, tests running Former-commit-id: 6617a746832b9cc411d0781ef6682e2e117a3ffa --- .../datasets/preprocessing/config.vsh.yaml | 4 ++-- src/batch_integration/datasets/preprocessing/script.py | 9 ++++++--- src/batch_integration/datasets/preprocessing/test.py | 3 ++- src/batch_integration/datasets/subsample/config.vsh.yaml | 6 +++--- src/batch_integration/datasets/subsample/script.py | 5 ++++- src/batch_integration/datasets/subsample/test.py | 4 ++-- 6 files changed, 19 insertions(+), 12 deletions(-) diff --git a/src/batch_integration/datasets/preprocessing/config.vsh.yaml b/src/batch_integration/datasets/preprocessing/config.vsh.yaml index 437c5bb26e..83bd58abf7 100644 --- a/src/batch_integration/datasets/preprocessing/config.vsh.yaml +++ b/src/batch_integration/datasets/preprocessing/config.vsh.yaml @@ -39,11 +39,11 @@ functionality: resources: - type: python_script path: script.py - - path: "../utils/_hvg_batch.py" + - path: ../utils/_hvg_batch.py test_resources: - type: python_script path: test.py - - path: '../../resources/data_loader_pancreas.h5ad' + - path: ../../../../resources_test/common/pancreas/ platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/datasets/preprocessing/script.py b/src/batch_integration/datasets/preprocessing/script.py index cf9449907e..e54904b058 100644 --- a/src/batch_integration/datasets/preprocessing/script.py +++ b/src/batch_integration/datasets/preprocessing/script.py @@ -10,7 +10,9 @@ 'output': './src/batch_integration/datasets/resources/datasets_pancreas.h5ad', 'debug': True } -resources_dir = './src/batch_integration/datasets' +meta = { + 'resources_dir': './resources_test/common/pancreas/', +} ## VIASH END print('Importing libraries') @@ -18,7 +20,8 @@ import scib from pprint import pprint import sys -sys.path.append(resources_dir) + +sys.path.append(meta['resources_dir']) from _hvg_batch import hvg_batch if par['debug']: @@ -37,7 +40,7 @@ print('Rename columns') adata.obs['label'] = adata.obs[label] adata.obs['batch'] = adata.obs[batch] -adata.layers['counts'] = adata.X.copy() +adata.X = adata.layers['counts'].copy() print('Normalise and log-transform data') sc.pp.normalize_total(adata) diff --git a/src/batch_integration/datasets/preprocessing/test.py b/src/batch_integration/datasets/preprocessing/test.py index 2e44618005..de8dacc7c6 100644 --- a/src/batch_integration/datasets/preprocessing/test.py +++ b/src/batch_integration/datasets/preprocessing/test.py @@ -1,10 +1,11 @@ +import os from os import path import subprocess import scanpy as sc import numpy as np name = 'preprocessing' -anndata_in = 'data_loader_pancreas.h5ad' +anndata_in = meta["resources_dir"] + '/pancreas/dataset.h5ad' anndata_out = 'datasets_pancreas.h5ad' print('>> Running script') diff --git a/src/batch_integration/datasets/subsample/config.vsh.yaml b/src/batch_integration/datasets/subsample/config.vsh.yaml index e48ab044aa..a74ed048b1 100644 --- a/src/batch_integration/datasets/subsample/config.vsh.yaml +++ b/src/batch_integration/datasets/subsample/config.vsh.yaml @@ -34,12 +34,12 @@ functionality: resources: - type: python_script path: script.py - - path: "../../resources/g2m_genes_tirosh_hm.txt" - - path: "../../resources/s_genes_tirosh_hm.txt" + - path: utils/g2m_genes_tirosh_hm.txt + - path: utils/s_genes_tirosh_hm.txt test_resources: - type: python_script path: test.py - - path: '../../../common/dataset_loader/download/resources/pancreas.h5ad' + - path: ../../../../resources_test/common/pancreas/dataset.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/datasets/subsample/script.py b/src/batch_integration/datasets/subsample/script.py index a12c3513d1..b1465bf2fe 100644 --- a/src/batch_integration/datasets/subsample/script.py +++ b/src/batch_integration/datasets/subsample/script.py @@ -9,7 +9,9 @@ 'output': 'src/batch_integration/resources/data_loader_pancreas.h5ad', 'debug': True } -resources_dir = './src/batch_integration/datasets' +meta = { + 'resources_dir': './src/batch_integration/datasets', +} ## VIASH END print('Importing libraries') @@ -19,6 +21,7 @@ if par['debug']: pprint(par) +resources_dir = meta['resources_dir'] adata_file = par['input'] label = par['label'] batch = par['batch'] diff --git a/src/batch_integration/datasets/subsample/test.py b/src/batch_integration/datasets/subsample/test.py index a61093382c..1ded02f287 100644 --- a/src/batch_integration/datasets/subsample/test.py +++ b/src/batch_integration/datasets/subsample/test.py @@ -4,8 +4,8 @@ import numpy as np name = 'subsample' -anndata_in = 'pancreas.h5ad' -anndata_out = 'pancreas_sub.h5ad' +anndata_in = 'dataset.h5ad' +anndata_out = 'dataset_sub.h5ad' print('>> Running script') n_hvgs = 100 From 29589a3014b7fd40b8a412038f809e4b7b5fda02 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Fri, 2 Dec 2022 15:06:46 +0100 Subject: [PATCH 0523/1233] fix tests for graph methods and metrics Former-commit-id: ac0614d152565542afd5f2caf765fdaf400ab2c2 --- src/batch_integration/graph/methods/bbknn/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/bbknn/test.py | 4 ++-- .../graph/methods/bbknn/test_scaled_hvg.py | 7 ++++--- .../graph/methods/combat/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/combat/script.py | 2 +- src/batch_integration/graph/methods/combat/test.py | 4 ++-- .../graph/methods/scanorama_embed/config.vsh.yaml | 4 ++-- .../graph/methods/scanorama_embed/test.py | 4 ++-- .../graph/methods/scanorama_feature/config.vsh.yaml | 4 ++-- .../graph/methods/scanorama_feature/script.py | 2 +- .../graph/methods/scanorama_feature/test.py | 4 ++-- src/batch_integration/graph/methods/scvi/config.vsh.yaml | 4 ++-- src/batch_integration/graph/methods/scvi/test.py | 4 ++-- src/batch_integration/graph/metrics/ari/config.vsh.yaml | 6 +++--- src/batch_integration/graph/metrics/ari/script.py | 2 +- src/batch_integration/graph/metrics/ari/test.py | 4 ++-- src/batch_integration/graph/metrics/ari/test_combat.py | 4 ++-- src/batch_integration/graph/metrics/nmi/config.vsh.yaml | 8 ++++---- src/batch_integration/graph/metrics/nmi/script.py | 2 +- src/batch_integration/graph/metrics/nmi/test.py | 4 ++-- src/batch_integration/graph/metrics/nmi/test_combat.py | 4 ++-- 21 files changed, 43 insertions(+), 42 deletions(-) diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index b1e707cf92..b2f3a55122 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -36,12 +36,12 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - type: python_script path: test_scaled_hvg.py - - path: '../../../resources/datasets_pancreas.h5ad' + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py index f53a9c90be..a1472a74ce 100644 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ b/src/batch_integration/graph/methods/bbknn/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index c47e3c6e4f..36888fe601 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'True', "--scaling", 'True', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var @@ -44,6 +44,7 @@ assert 'scaled' in adata.uns assert adata.uns['scaled'] == True assert -0.0000001 <= np.mean(adata.X) <= 0.0000001 -assert 0.8 <= np.var(adata.X) <= 1 +print(np.var(adata.X)) +assert 0.7 <= np.var(adata.X) <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml index 2244d582cb..ef2411e3f2 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -36,10 +36,10 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../datasets/resources/datasets_pancreas.h5ad' + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index fe8fac6d98..74f03f7eaa 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -35,7 +35,7 @@ adata.X = adata.layers['logcounts'] print('Integrate') -adata = combat(adata, batch='batch') +adata.X = combat(adata, batch='batch').X print('Postprocess data') sc.pp.pca( diff --git a/src/batch_integration/graph/methods/combat/test.py b/src/batch_integration/graph/methods/combat/test.py index 3549f689e6..657aad86eb 100644 --- a/src/batch_integration/graph/methods/combat/test.py +++ b/src/batch_integration/graph/methods/combat/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml index e516ab098e..2ce9abd78f 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -36,10 +36,10 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../datasets/resources/datasets_pancreas.h5ad' + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/graph/methods/scanorama_embed/test.py b/src/batch_integration/graph/methods/scanorama_embed/test.py index 682c1adaad..502e0e52bc 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/test.py +++ b/src/batch_integration/graph/methods/scanorama_embed/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index db13afd87f..f17b2ebe54 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -36,10 +36,10 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../datasets/resources/datasets_pancreas.h5ad' + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index d752fef3c9..5dd5396c98 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -35,7 +35,7 @@ adata.X = adata.layers['logcounts'] print('Integrate') -adata.X = scanorama(adata, batch='batch').X.todense() +adata.X = scanorama(adata, batch='batch').X print('Postprocess data') sc.pp.pca( diff --git a/src/batch_integration/graph/methods/scanorama_feature/test.py b/src/batch_integration/graph/methods/scanorama_feature/test.py index 404231915f..dc58cce103 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/test.py +++ b/src/batch_integration/graph/methods/scanorama_feature/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml index 14fc92cb55..37f0c89f7d 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -36,10 +36,10 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../datasets/resources/datasets_pancreas.h5ad' + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/graph/methods/scvi/test.py b/src/batch_integration/graph/methods/scvi/test.py index 700684b6fb..d1a7b35d2d 100644 --- a/src/batch_integration/graph/methods/scvi/test.py +++ b/src/batch_integration/graph/methods/scvi/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + method, - "--input", 'datasets_pancreas.h5ad', + "--input", 'processed.h5ad', "--hvg", 'False', "--scaling", 'False', "--output", output_file @@ -23,7 +23,7 @@ print('>> Checking API') adata = sc.read(output_file) -assert 'name' in adata.uns +assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns assert 'highly_variable' in adata.var diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 5b3e5d1554..5977d10dbb 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -29,11 +29,11 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/graph_pancreas_bbknn.h5ad' + - path: ../../../../../resources_test/batch_integration/graph/methods/bbknn.h5ad - type: python_script path: test_combat.py - - path: '../../../resources/graph_pancreas_combat.h5ad' + - path: ../../../../../resources_test/batch_integration/graph/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/graph/metrics/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py index 217f663031..94e47c34d1 100644 --- a/src/batch_integration/graph/metrics/ari/script.py +++ b/src/batch_integration/graph/metrics/ari/script.py @@ -23,7 +23,7 @@ print('Read adata') adata = sc.read(adata_file) -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('clustering') opt_louvain( diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index cdd69ed538..089ce4cf1e 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'graph_pancreas_bbknn.h5ad', + "--adata", 'bbknn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.2097653589001798 +assert score == 0.3995060325339174 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py index 7ce87cb116..ac1ad306f8 100644 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'graph_pancreas_combat.h5ad', + "--adata", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.5808883769609893 +assert score == 0.1439128090443822 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 7521b65424..663bda0714 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -26,14 +26,14 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../resources/graph_pancreas_bbknn.h5ad' + - path: ../../../../../resources_test/batch_integration/graph/methods/bbknn.h5ad - type: python_script path: test_combat.py - - path: '../../../resources/graph_pancreas_combat.h5ad' + - path: ../../../../../resources_test/batch_integration/graph/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:1.0.0 + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/graph/metrics/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py index 994c287378..12ae4b6b3a 100644 --- a/src/batch_integration/graph/metrics/nmi/script.py +++ b/src/batch_integration/graph/metrics/nmi/script.py @@ -23,7 +23,7 @@ print('Read adata') adata = sc.read(adata_file) -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('clustering') opt_louvain( diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index eb31d5fc8b..e676f17979 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'graph_pancreas_bbknn.h5ad', + "--adata", 'bbknn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.2179112948125749 +assert score == 0.3418185548452759 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py index 059194871f..43a78567a5 100644 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'graph_pancreas_combat.h5ad', + "--adata", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.4240058744404366 +assert score == 0.2425827787547619 print(">> All tests passed successfully") From 2081b58d6e0b52d3b45eb9fa30f7d8f2a12184d4 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 2 Dec 2022 20:56:46 +0100 Subject: [PATCH 0524/1233] add script and test Former-commit-id: ba1b2ad945bab800e54bd8df37f81b4feed9f652 --- src/common/list_git_shas/config.vsh.yaml | 13 ++++- src/common/list_git_shas/script.py | 65 ++++++++++++++++++++++++ src/common/list_git_shas/test.py | 20 ++++++++ 3 files changed, 97 insertions(+), 1 deletion(-) create mode 100644 src/common/list_git_shas/test.py diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index f92ea5f2e2..e70d8d0e0e 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -21,4 +21,15 @@ functionality: example: output.json - name: --show_history type: boolean_true - description: Whether or not to include the full history of SHAs for each file. \ No newline at end of file + description: Whether or not to include the full history of SHAs for each file. + resources: + - path: ../../../src + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + image: "python:3.10" + - type: nextflow \ No newline at end of file diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index e69de29bb2..8f60ca3228 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -0,0 +1,65 @@ +import subprocess +import os +import json + +## VIASH START + +par = { + 'input': '/home/kai/Documents/openroblems/openproblems-v2/src/denoising', + 'output': 'output/output.json', + 'show_history': True +} +meta = { + 'functionality_name': 'dca', +} + +## VIASH STOP + +print(par['show_history']) + +output = [] + +def get_git_file_info(fp, format="none", history=0): + + if history: + cmd = [ + "git", + 'log', + "--no-merges", + f"--pretty=format:%H", + "--", + fp + ] + else: + cmd = [ + "git", + 'log', + "-n", + "1", + f"--pretty=format:{format}", + "--", + fp + ] + out = subprocess.run(cmd, capture_output=True, text=True).stdout + return out + + +for root, dirs, files in os.walk(par['input']): + for file in files: + git_file= {} + fp = os.path.join(root,file) + abs_fp = fp.replace(par['input']+"/","") + git_file['path'] = abs_fp + git_file['last_modified'] = get_git_file_info(fp, "%ci") + git_file['sha'] = get_git_file_info(fp, "%H") + if "show_history" in par: + if par['show_history']: + git_file['history_sha'] = get_git_file_info(fp,history=1).split("\n") + + output.append(git_file) + +with open(par['output'], 'w') as f: + json.dump(output, f, indent=4) + + + diff --git a/src/common/list_git_shas/test.py b/src/common/list_git_shas/test.py new file mode 100644 index 0000000000..35b6417874 --- /dev/null +++ b/src/common/list_git_shas/test.py @@ -0,0 +1,20 @@ +import subprocess +from os import path + +input_path = meta["resources_dir"] + "src/common" +output_path = "output.json" + +cmd = [ + meta['executable'], + "--input_train", input_path, + "--output", output_path +] + +print(">> Running script as test") +out = subprocess.run(cmd, capture_output=True, text=True) + + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print("All checks succeeded!") \ No newline at end of file From 329da4518739bf539bc5619730982a64a61ff455 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 3 Dec 2022 20:49:15 +0100 Subject: [PATCH 0525/1233] temporarily remove nxf schemas and params Former-commit-id: 4bbfd69a7e665473dcbbb12e43850541fbe49dfa --- .github/workflows/main-build.yml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 6086e9ce35..bca12eece1 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -58,21 +58,21 @@ jobs: # build target dir bin/viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - - name: Build nextflow schemas & params - run: | - bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) - outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) - outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) - bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - - bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) - outputs_params=$(jq -r '[.[] | .info.config | capture("^(?

.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) - outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) - bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + # - name: Build nextflow schemas & params + # run: | + # bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json + # inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) + # outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) + # outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) + # bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + # bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + + # bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json + # inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) + # outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) + # outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) + # bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + # bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 From 6482e1fbe8f3e683211ef22f4930e00c6de059f1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 3 Dec 2022 21:44:48 +0100 Subject: [PATCH 0526/1233] fix command Former-commit-id: 420dde5d5ee1148b7ea17fa7738f2d3120944ae6 --- .github/workflows/main-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index bca12eece1..40ac6c44dc 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -124,4 +124,4 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --push --setup donothing \ No newline at end of file + bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup push \ No newline at end of file From 404beb770f697e95154b4e57725331a7a1529f78 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 4 Dec 2022 21:23:33 +0100 Subject: [PATCH 0527/1233] use helper script for denoising split dataset instead of separate library Former-commit-id: ae826ea14f7495d25548bd2f39ca0f0ba2546560 --- src/denoising/split_dataset/config.vsh.yaml | 9 ++-- src/denoising/split_dataset/helper.py | 55 +++++++++++++++++++++ src/denoising/split_dataset/script.py | 25 +++++----- 3 files changed, 74 insertions(+), 15 deletions(-) create mode 100644 src/denoising/split_dataset/helper.py diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml index 239a13c63a..40f1622198 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -2,7 +2,11 @@ __merge__: ../api/comp_split_dataset.yaml functionality: name: "split_dataset" namespace: "denoising" - description: "Splits molecules into two (potentially overlapping) groups using a fraction ratio." + description: | + Split data using molecular cross-validation. + + Splits molecules into two (potentially overlapping) groups using a fraction ratio. + Thise are output as two separate AnnData objects. arguments: - name: "--method" type: "string" @@ -20,6 +24,7 @@ functionality: resources: - type: python_script path: script.py + - path: helper.py platforms: - type: docker image: "python:3.10" @@ -29,6 +34,4 @@ platforms: - "anndata>=0.8" - numpy - scipy - github: - - czbiohub/molecular-cross-validation - type: nextflow diff --git a/src/denoising/split_dataset/helper.py b/src/denoising/split_dataset/helper.py new file mode 100644 index 0000000000..2044ed4c6e --- /dev/null +++ b/src/denoising/split_dataset/helper.py @@ -0,0 +1,55 @@ +# MIT License + +# Copyright (c) 2019 Chan Zuckerberg Biohub + +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: + +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. + +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. + +# Copied from https://github.com/czbiohub/molecular-cross-validation/blob/master/src/molecular_cross_validation/util.py + + +from typing import Tuple + +import numpy as np + +def split_molecules( + umis: np.ndarray, + data_split: float, + overlap_factor: float = 0.0, + random_state: np.random.RandomState = None, +) -> Tuple[np.ndarray, np.ndarray]: + """Splits molecules into two (potentially overlapping) groups. + :param umis: Array of molecules to split + :param data_split: Proportion of molecules to assign to the first group + :param overlap_factor: Overlap correction factor, if desired + :param random_state: For reproducible sampling + :return: umis_X and umis_Y, representing ``split`` and ``~(1 - split)`` counts + sampled from the input array + """ + if random_state is None: + random_state = np.random.RandomState() + + umis_X_disjoint = random_state.binomial(umis, data_split - overlap_factor) + umis_Y_disjoint = random_state.binomial( + umis - umis_X_disjoint, (1 - data_split) / (1 - data_split + overlap_factor) + ) + overlap_factor = umis - umis_X_disjoint - umis_Y_disjoint + umis_X = umis_X_disjoint + overlap_factor + umis_Y = umis_Y_disjoint + overlap_factor + + return umis_X, umis_Y \ No newline at end of file diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index c7e8057bb6..ed4520272e 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -1,7 +1,7 @@ import anndata as ad import numpy as np +import sys import scipy.sparse -import molecular_cross_validation.util ## VIASH START par = { @@ -12,31 +12,31 @@ 'seed': 0 } meta = { - "functionality_name": "split_data" + "functionality_name": "split_data", + "resources_dir": "src/denoising/split_dataset" } ## VIASH END -"""Split data using molecular cross-validation. -Stores "train" and "test" dataset in separate ad files. -""" +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from helper import split_molecules +# set random state random_state = np.random.RandomState(par['seed']) print(">> Load Data") adata = ad.read_h5ad(par["input"]) - # remove all layers except for counts for key in list(adata.layers.keys()): if key != "counts": del adata.layers[key] -counts_rounded = np.array(adata.layers["counts"]).round() - -counts = counts_rounded.astype(int) +# round counts and convert to int +counts = np.array(adata.layers["counts"]).round().astype(int) print(">> process and split data") -train_data, test_data = molecular_cross_validation.util.split_molecules( +train_data, test_data = split_molecules( counts.data, par["train_frac"], 0.0, random_state ) @@ -44,6 +44,8 @@ X_test = counts.copy() X_train.data = train_data X_test.data = test_data +X_train.eliminate_zeros() +X_test.eliminate_zeros() # copy adata to train_set, test_set output_train = ad.AnnData( @@ -65,7 +67,6 @@ output_train = output_train[:, ~is_missing.flatten()] output_test = output_test[:, ~is_missing.flatten()] - -print(">> Writing") +print(">> Writ to file") output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) From f14bf32c2d051edfc569481152112519ee928ddc Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 4 Dec 2022 13:33:56 -0800 Subject: [PATCH 0528/1233] remove unneeded dependency Former-commit-id: 18ad954eb8e816781ba4ce035d4d1207cf406050 --- src/denoising/metrics/poisson/config.vsh.yaml | 2 -- src/denoising/metrics/poisson/script.py | 8 ++++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 63a93011e4..488463e828 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -24,8 +24,6 @@ platforms: packages: - "anndata>=0.8" - scprep - github: - - czbiohub/molecular-cross-validation - type: nextflow directives: label: [ midmem, midcpu ] \ No newline at end of file diff --git a/src/denoising/metrics/poisson/script.py b/src/denoising/metrics/poisson/script.py index 014539715f..8e65f080eb 100644 --- a/src/denoising/metrics/poisson/script.py +++ b/src/denoising/metrics/poisson/script.py @@ -1,6 +1,6 @@ import anndata as ad import scprep -from molecular_cross_validation.mcv_sweep import poisson_nll_loss +import numpy as np ## VIASH START par = { @@ -17,7 +17,6 @@ input_denoised = ad.read_h5ad(par['input_denoised']) input_test = ad.read_h5ad(par['input_test']) - test_data = input_test.layers["counts"].toarray() denoised_data = input_denoised.layers["denoised"].toarray() @@ -27,6 +26,11 @@ target_sum = test_data.sum() denoised_data = denoised_data * target_sum / initial_sum +# from molecular_cross_validation.mcv_sweep import poisson_nll_loss +# copied from: https://github.com/czbiohub/molecular-cross-validation/blob/master/src/molecular_cross_validation/mcv_sweep.py +def poisson_nll_loss(y_pred: np.ndarray, y_true: np.ndarray) -> float: + return (y_pred - y_true * np.log(y_pred + 1e-6)).mean() + error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) print("Store poisson value") From de7de87cdd94a346c7206624e782ce357f332dd0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 5 Dec 2022 08:08:27 +0100 Subject: [PATCH 0529/1233] small fixes to git sha Former-commit-id: a2a58850a90fb3c5326d5e691d396cd68bf2625d --- src/common/list_git_shas/config.vsh.yaml | 4 +- src/common/list_git_shas/script.py | 79 ++++++++++++------------ 2 files changed, 42 insertions(+), 41 deletions(-) diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index e70d8d0e0e..67dc667e09 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -9,12 +9,13 @@ functionality: example: /path/to/repo - name: --output type: file + direction: output description: | A json containing a list of entries. Each entry must have the following values: * "path" `string`: Path a file in the repository - * "last_modified" `string`: Date of then the file was last modified, in `yyyy-mm-dd HH:mm:ss` format. + * "last_modified" `string`: Date of when the file was last modified, in `yyyy-mm-dd HH:mm:ss` format. * "sha" `string`: Sha of the commit in which the file was last modified * "history_sha" `string` (optional): A list of SHAs during which the file was modified required: true @@ -23,7 +24,6 @@ functionality: type: boolean_true description: Whether or not to include the full history of SHAs for each file. resources: - - path: ../../../src - type: python_script path: script.py test_resources: diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 8f60ca3228..0c7c617116 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -3,60 +3,61 @@ import json ## VIASH START - par = { - 'input': '/home/kai/Documents/openroblems/openproblems-v2/src/denoising', + 'input': '.', 'output': 'output/output.json', 'show_history': True } meta = { 'functionality_name': 'dca', } - ## VIASH STOP -print(par['show_history']) +# to do: what to do with untracked files? output = [] -def get_git_file_info(fp, format="none", history=0): - - if history: - cmd = [ - "git", - 'log', - "--no-merges", - f"--pretty=format:%H", - "--", - fp - ] - else: - cmd = [ - "git", - 'log', - "-n", - "1", - f"--pretty=format:{format}", - "--", - fp - ] - out = subprocess.run(cmd, capture_output=True, text=True).stdout +def git_ls_files(directory): + cmd = ["git", "ls-files"] + cmd_out = subprocess.run(cmd, capture_output=True, text=True, cwd=directory).stdout + out = [ line for line in cmd_out.split("\n") if line != "" ] return out + +def get_git_file_info(file, full_history=False): + # construct command + cmd = ["git", "log", "--no-merges", "--pretty=%H\t%ci"] + + if not full_history: + cmd.extend(["-n", "1"]) + + cmd.extend(["--", file]) + # run command + out = subprocess.run(cmd, capture_output=True, text=True).stdout + + # split output + split = [line.split("\t") for line in out.split("\n") if "\t" in line] + + return split + + + +for relative_path in git_ls_files(par['input']): + # construct path + path = os.path.join(par["input"], relative_path) + + # get git file info + git_file_info = get_git_file_info(path, full_history=par["show_history"]) + last = git_file_info[len(git_file_info)-1] + out = { + "path": relative_path, + "last_modified": last[1], + "sha": last[0] + } + if par['show_history']: + out['history_sha'] = [info[0] for info in git_file_info] -for root, dirs, files in os.walk(par['input']): - for file in files: - git_file= {} - fp = os.path.join(root,file) - abs_fp = fp.replace(par['input']+"/","") - git_file['path'] = abs_fp - git_file['last_modified'] = get_git_file_info(fp, "%ci") - git_file['sha'] = get_git_file_info(fp, "%H") - if "show_history" in par: - if par['show_history']: - git_file['history_sha'] = get_git_file_info(fp,history=1).split("\n") - - output.append(git_file) + output.append(out) with open(par['output'], 'w') as f: json.dump(output, f, indent=4) From 547e091ed8a5bc801eb2444c0a9e6d13c6007f04 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 5 Dec 2022 08:11:45 +0100 Subject: [PATCH 0530/1233] fix viash codeblock Former-commit-id: ac396a0f5c3d89528433a1602f267417d0326511 --- src/common/list_git_shas/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 0c7c617116..da5d37497a 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -11,7 +11,7 @@ meta = { 'functionality_name': 'dca', } -## VIASH STOP +## VIASH END # to do: what to do with untracked files? From 5a169e53e7a80eeb6ff0f25e9d4364cefe06068a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 5 Dec 2022 08:49:14 +0100 Subject: [PATCH 0531/1233] fix last variable Former-commit-id: 6cc4290b7e31b95d33a402b319e379e4a808457f --- src/common/list_git_shas/script.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index da5d37497a..31ae24470e 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -9,7 +9,7 @@ 'show_history': True } meta = { - 'functionality_name': 'dca', + 'functionality_name': 'foo', } ## VIASH END @@ -48,7 +48,7 @@ def get_git_file_info(file, full_history=False): # get git file info git_file_info = get_git_file_info(path, full_history=par["show_history"]) - last = git_file_info[len(git_file_info)-1] + last = git_file_info[0] out = { "path": relative_path, "last_modified": last[1], From f13bcbfdffabe1ba1741230bc681d50b5cbb435a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 5 Dec 2022 11:37:05 +0100 Subject: [PATCH 0532/1233] add cwd to get_git_file_info Former-commit-id: 041f515acba6a0f8fed76af987962c05b1c58379 --- src/common/list_git_shas/script.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 31ae24470e..4e739bb47c 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -33,21 +33,17 @@ def get_git_file_info(file, full_history=False): cmd.extend(["--", file]) # run command - out = subprocess.run(cmd, capture_output=True, text=True).stdout + out = subprocess.run(cmd, capture_output=True, text=True, cwd=par["input"]).stdout # split output split = [line.split("\t") for line in out.split("\n") if "\t" in line] return split - - for relative_path in git_ls_files(par['input']): - # construct path - path = os.path.join(par["input"], relative_path) # get git file info - git_file_info = get_git_file_info(path, full_history=par["show_history"]) + git_file_info = get_git_file_info(relative_path, full_history=par["show_history"]) last = git_file_info[0] out = { "path": relative_path, From 0c46e8112f6036703a7179355b16f26edc0bb6be Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 5 Dec 2022 11:38:20 +0100 Subject: [PATCH 0533/1233] update test Former-commit-id: eb97a5cd1f091a6eae10c2c8e4e03326d7e89995 --- src/common/list_git_shas/config.vsh.yaml | 1 + src/common/list_git_shas/test.py | 12 +++++++++--- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index 67dc667e09..d1e44450d8 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -27,6 +27,7 @@ functionality: - type: python_script path: script.py test_resources: + - path: ../../../../openproblems-v2 - type: python_script path: test.py platforms: diff --git a/src/common/list_git_shas/test.py b/src/common/list_git_shas/test.py index 35b6417874..ef937e8d7a 100644 --- a/src/common/list_git_shas/test.py +++ b/src/common/list_git_shas/test.py @@ -1,20 +1,26 @@ import subprocess from os import path +import json -input_path = meta["resources_dir"] + "src/common" +input_path = meta["resources_dir"] + "/openproblems-v2" output_path = "output.json" cmd = [ meta['executable'], - "--input_train", input_path, + "--input", input_path, "--output", output_path ] print(">> Running script as test") -out = subprocess.run(cmd, capture_output=True, text=True) +out = subprocess.run(cmd, check=True, capture_output=True, text=True) print(">> Checking whether output file exists") assert path.exists(output_path) +print(">> Reading json file") +with open(output_path) as f: + out = json.load(f) + print(out[0]) + print("All checks succeeded!") \ No newline at end of file From 9c1008ad4567f4a0ab20172b1cba14ff69af326d Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 5 Dec 2022 14:47:58 +0100 Subject: [PATCH 0534/1233] update unit test to work Former-commit-id: 38f9c90b459163d5ceb1f51153e82b6fc29e2f21 --- src/common/list_git_shas/config.vsh.yaml | 4 +++- src/common/list_git_shas/test.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index d1e44450d8..8c29f3df88 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -27,10 +27,12 @@ functionality: - type: python_script path: script.py test_resources: - - path: ../../../../openproblems-v2 - type: python_script path: test.py platforms: - type: docker image: "python:3.10" + test_setup: + - type: docker + run: [git clone https://github.com/openproblems-bio/openproblems-v2.git] - type: nextflow \ No newline at end of file diff --git a/src/common/list_git_shas/test.py b/src/common/list_git_shas/test.py index ef937e8d7a..23a02ed233 100644 --- a/src/common/list_git_shas/test.py +++ b/src/common/list_git_shas/test.py @@ -2,7 +2,7 @@ from os import path import json -input_path = meta["resources_dir"] + "/openproblems-v2" +input_path = "/openproblems-v2" output_path = "output.json" cmd = [ From 1cb00ebadcea716c953ecfad8699ee2d3d295cba Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 5 Dec 2022 14:51:04 +0100 Subject: [PATCH 0535/1233] update changelog common Former-commit-id: 813d55f2d04887ae027b09818edc37dfd92ef549 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 28b2f2eb2a..8f36c2125f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. +* `list_git_shas`: create list of latest commit hashes of all files in repo. + ## label_projection From c0839dd307123d46132e3e59b62f3f114624c6d1 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 6 Dec 2022 10:02:50 +0100 Subject: [PATCH 0536/1233] fix typo #ae826ea Former-commit-id: 694dcaef20eb906aa293c3f283c11c938e6093da --- src/denoising/split_dataset/config.vsh.yaml | 2 +- src/denoising/split_dataset/script.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/split_dataset/config.vsh.yaml index 40f1622198..bd80df46d2 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/split_dataset/config.vsh.yaml @@ -6,7 +6,7 @@ functionality: Split data using molecular cross-validation. Splits molecules into two (potentially overlapping) groups using a fraction ratio. - Thise are output as two separate AnnData objects. + These are output as two separate AnnData objects. arguments: - name: "--method" type: "string" diff --git a/src/denoising/split_dataset/script.py b/src/denoising/split_dataset/script.py index ed4520272e..95fcd0544d 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/split_dataset/script.py @@ -67,6 +67,6 @@ output_train = output_train[:, ~is_missing.flatten()] output_test = output_test[:, ~is_missing.flatten()] -print(">> Writ to file") +print(">> Write to file") output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) From 3f94f9e5873e1c884b25fdf791eaeb4b7d60ff62 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 6 Dec 2022 12:33:18 +0100 Subject: [PATCH 0537/1233] create new anndata object for metrics Former-commit-id: 2f04bc4699dd4fc6505abc787ec0723aa17fe22e --- src/denoising/metrics/mse/script.py | 22 ++++++++++++++++------ src/denoising/metrics/poisson/script.py | 16 +++++++++++++--- 2 files changed, 29 insertions(+), 9 deletions(-) diff --git a/src/denoising/metrics/mse/script.py b/src/denoising/metrics/mse/script.py index 7060380a99..4f217ff305 100644 --- a/src/denoising/metrics/mse/script.py +++ b/src/denoising/metrics/mse/script.py @@ -6,8 +6,8 @@ ## VIASH START par = { - 'input_test': 'output_test.h5ad', - 'input_denoised': 'output_magic.h5ad', + 'input_test': 'resources_test/denoising/pancreas/test.h5ad', + 'input_denoised': 'resources_test/denoising/pancreas/magic.h5ad', 'output': 'output_mse.h5ad' } meta = { @@ -39,10 +39,20 @@ scprep.utils.toarray(test_data.X), denoised_data.X ) -print("Store metric value") -input_denoised.uns["metric_ids"] = meta['functionality_name'] -input_denoised.uns["metric_values"] = error +print("Store mse value") +output_metric = ad.AnnData( + layers={}, + obs=input_denoised.obs[[]], + var=input_denoised.var[[]], + uns={} +) + +for key in input_denoised.uns_keys(): + output_metric.uns[key] = input_denoised.uns[key] + +output_metric.uns["metric_ids"] = meta['functionality_name'] +output_metric.uns["metric_values"] = error print("Write adata to file") -input_denoised.write_h5ad(par['output'], compression="gzip") +output_metric.write_h5ad(par['output'], compression="gzip") diff --git a/src/denoising/metrics/poisson/script.py b/src/denoising/metrics/poisson/script.py index 8e65f080eb..f85c1d751b 100644 --- a/src/denoising/metrics/poisson/script.py +++ b/src/denoising/metrics/poisson/script.py @@ -34,8 +34,18 @@ def poisson_nll_loss(y_pred: np.ndarray, y_true: np.ndarray) -> float: error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) print("Store poisson value") -input_denoised.uns["metric_ids"] = meta['functionality_name'] -input_denoised.uns["metric_values"] = error +output_metric = ad.AnnData( + layers={}, + obs=input_denoised.obs[[]], + var=input_denoised.var[[]], + uns={} +) + +for key in input_denoised.uns_keys(): + output_metric.uns[key] = input_denoised.uns[key] + +output_metric.uns["metric_ids"] = meta['functionality_name'] +output_metric.uns["metric_values"] = error print("Write adata to file") -input_denoised.write_h5ad(par['output'], compression="gzip") +output_metric.write_h5ad(par['output'], compression="gzip") From 5f2086201aa46c265c87a945b9e827e4e5e42bb5 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 6 Dec 2022 15:08:50 +0100 Subject: [PATCH 0538/1233] Rename variables and add/read metadata in methods Former-commit-id: 77bafd547a9744cdd0ea1157b1bdeb4726fef141 --- .../methods/densmap/config.vsh.yaml | 1 + .../methods/densmap/script.py | 33 ++++++++------ .../methods/phate/config.vsh.yaml | 5 ++- .../methods/phate/script.py | 43 ++++++++++--------- .../methods/tsne/config.vsh.yaml | 1 + .../methods/tsne/script.py | 40 +++++++++-------- .../methods/umap/config.vsh.yaml | 1 + .../methods/umap/script.py | 34 +++++++++------ 8 files changed, 91 insertions(+), 67 deletions(-) diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index b5711e1d0d..1cbad1a90d 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -24,4 +24,5 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index b9d4212260..4bd2efc009 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -1,39 +1,46 @@ import anndata as ad from umap import UMAP import scanpy as sc +import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/train.h5ad', + 'output': 'reduced.h5ad', 'no_pca': False, } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'densmap', + 'config': 'src/dimensionality_reduction/methods/densmap/config.vsh.yaml' } ## VIASH END print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) print('Select top 1000 high variable genes') n_genes = 1000 -idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] print("Run UMAP...") if par['no_pca']: print('... using logCPM data') - adata.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(adata.layers['normalized'][:, idx]) + input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.layers['normalized'][:, idx]) else: print('... after applying PCA with 50 dimensions to logCPM data') - adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack") - adata.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(adata.obsm['X_pca_hvg']) + input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack") + input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) -print(adata.obsm['X_emb'][:10,:]) +print("Delete layers and var") +del input.layers +del input.var -# Update .uns -adata.uns['method_id'] = 'densmap' -adata.uns['normalization_id'] = 'log_cpm' +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 4168747361..7d6d768126 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -8,9 +8,9 @@ functionality: label: PHATE v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 - preferred_normalization: log_cpm + preferred_normalization: sqrt_cpm arguments: - - name: '--hvg' + - name: '--log_cpm' type: boolean_true description: Use logCPM of 1000 HVGs instead of the square-root CPM transformed expression matrix. - name: '--n_pca' @@ -32,4 +32,5 @@ platforms: - "anndata>=0.8" - phate - scprep + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 7642d8b3a5..df00c1891f 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -1,49 +1,50 @@ import anndata as ad from phate import PHATE import scprep as sc -# import yaml +import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/train.h5ad', + 'output': 'reduced.h5ad', 'n_pca': 50, 'g0': False, - 'hvg': False + 'log_cpm': False } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'phate', 'config': 'src/dimensionality_reduction/methods/phate/config.vsh.yaml' } ## VIASH END -# with open(meta['config'], 'r') as config_file: -# config = yaml.safe_load(config_file) - -# config['functionality']['info']['preferred_normalization'] -# print(meta) print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) print("Run PHATE...") gamma = 0 if par['g0'] else 1 print('... with gamma=' + str(gamma) + ' and...') phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=gamma) -if par['hvg']: +if par['log_cpm']: print('... using logCPM data') n_genes = 1000 - idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] - adata.obsm["X_emb"] = phate_op.fit_transform(adata.layers['normalized'][:, idx]) - adata.uns['normalization_id'] = 'log_cpm' + idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized'][:, idx]) + input.uns['normalization_id'] = 'log_cpm' else: print('... using sqrt-CPM data') - adata.layers['sqrt_cpm'] = sc.transform.sqrt(adata.layers['normalized'].expm1()) - adata.obsm["X_emb"] = phate_op.fit_transform(adata.layers['sqrt_cpm']) - adata.uns['normalization_id'] = 'sqrt_cpm' + input.layers['sqrt_cpm'] = sc.transform.sqrt(input.layers['normalized'].expm1()) + input.obsm["X_emb"] = phate_op.fit_transform(input.layers['sqrt_cpm']) + with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] + +print("Delete layers and var") +del input.layers +del input.var -# Update .uns -adata.uns['method_id'] = 'phate' +print('Add method') +input.uns['method_id'] = meta['functionality_name'] print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index b0be90219e..aedfb43ad1 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -25,4 +25,5 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index cc0a0ea1b6..874ca47301 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -1,39 +1,43 @@ import anndata as ad import scanpy as sc +import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/train.h5ad', + 'output': 'reduced.h5ad', 'n_pca': 50, } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'tsne', + 'config': 'src/dimensionality_reduction/methods/tsne/config.vsh.yaml' } ## VIASH END print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) print('Select top 1000 high variable genes') n_genes = 1000 -idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] print('Apply PCA with 50 dimensions') -adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") +input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") print('Run t-SNE') -sc.tl.tsne(adata, use_rep="X_pca_hvg", n_pcs=par['n_pca']) -adata.obsm["X_emb"] = adata.obsm["X_tsne"].copy() - -# Update .uns -adata.uns['method_id'] = 'tsne' -adata.uns['normalization_id'] = 'log_cpm' -#del(adata.uns["pca_variance"]) -#del(adata.uns["tsne"]) -# Update .obsm/.varm -#del(adata.obsm["X_tsne"]) -#del(adata.varm["pca_loadings"]) +sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) +input.obsm["X_emb"] = input.obsm["X_tsne"].copy() + +print("Delete layers and var") +del input.layers +del input.var + +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 21e46c89cb..aed655cc17 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -30,4 +30,5 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index ad8181b1ad..dd715fd5b6 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -1,38 +1,46 @@ import anndata as ad import scanpy as sc +import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/train.h5ad', + 'output': 'reduced.h5ad', 'n_pca': 50, } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'umap', + 'config': 'src/dimensionality_reduction/methods/umap/config.vsh.yaml' } ## VIASH END print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) print('Select top 1000 high variable genes') n_genes = 1000 -idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] print('Apply PCA with 50 dimensions') -adata.obsm['X_pca_hvg'] = sc.tl.pca(adata.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") +input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") print('Calculate a nearest-neighbour graph') -sc.pp.neighbors(adata, use_rep="X_pca_hvg", n_pcs=par['n_pca']) +sc.pp.neighbors(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) print("Run UMAP") -sc.tl.umap(adata) +sc.tl.umap(input) +input.obsm["X_emb"] = input.obsm["X_umap"].copy() -adata.obsm["X_emb"] = adata.obsm["X_umap"].copy() +print("Delete layers and var") +del input.layers +del input.var -# Update .uns -adata.uns['method_id'] = 'umap' -adata.uns['normalization_id'] = 'log_cpm' +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 6a68231fee2a7dd9efdba795e159ae2b0ab56b54 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 6 Dec 2022 15:59:22 +0100 Subject: [PATCH 0539/1233] Rename variables and add/read metadata in metrics Former-commit-id: 40a6d6f06eb0de46119c0bcf52ee033f92025065 --- .../metrics/density/script.py | 24 ++++++++++------ .../metrics/rmse/script.py | 28 +++++++++---------- .../metrics/trustworthiness/script.py | 20 ++++++++----- 3 files changed, 41 insertions(+), 31 deletions(-) diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py index e08b4ed5cd..7a389789a3 100644 --- a/src/dimensionality_reduction/metrics/density/script.py +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -9,27 +9,29 @@ ## VIASH START par = { - 'input': 'output.h5ad', + 'input_reduced': 'reduced.h5ad', + 'input_test': 'test.h5ad', 'output': 'score.h5ad', } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'density', } ## VIASH END print("Load data") -adata = ad.read_h5ad(par['input']) +input_reduced = ad.read_h5ad(par['input_reduced']) +input_test = ad.read_h5ad(par['input_test']) print('Reduce dimensionality of raw data') _K = 30 # number of neighbors _SEED = 42 _, ro, _ = UMAP( n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True -).fit_transform(adata.layers['counts']) +).fit_transform(input_test.layers['counts']) # in principle, we could just call _calculate_radii(high_dim, ...) # this is made sure that the test pass (otherwise, there was .02 difference in corr) (knn_indices, knn_dists, rp_forest,) = nearest_neighbors( - adata.obsm['X_emb'], + input_reduced.obsm['X_emb'], _K, "euclidean", {}, @@ -39,7 +41,7 @@ ) emb_graph, emb_sigmas, emb_rhos, emb_dists = fuzzy_simplicial_set( - adata.obsm['X_emb'], + input_reduced.obsm['X_emb'], _K, _SEED, "euclidean", @@ -74,8 +76,12 @@ epsilon = 1e-8 re = np.log(epsilon + (re / mu_sum)) -adata.uns['metric_ids'] = 'density' -adata.uns['metric_values'] = pearsonr(ro, re)[0] +print("Store metric value") +input_reduced.uns['metric_ids'] = meta['functionality_name'] +input_reduced.uns['metric_values'] = pearsonr(ro, re)[0] + +print("Delete obs matrix") +del input_reduced.obsm print("Write data to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index fe18b07bfa..6b9aff0a89 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -5,23 +5,25 @@ ## VIASH START par = { - 'input': 'output.h5ad', + 'input_reduced': 'reduced.h5ad', + 'input_test': 'test.h5ad', 'output': 'score.h5ad', } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'rmse', } ## VIASH END print("Load data") -adata = ad.read_h5ad(par['input']) +input_reduced = ad.read_h5ad(par['input_reduced']) +input_test = ad.read_h5ad(par['input_test']) print('Reduce dimensionality of raw data') -adata.obsm['svd'] = decomposition.TruncatedSVD(n_components = 200).fit_transform(adata.layers['counts']) +input_reduced.obsm['svd'] = decomposition.TruncatedSVD(n_components = 200).fit_transform(input_test.layers['counts']) print('Compute pairwise distance between points in a matrix and format it into a squared-form vector.') -high_dim_dist_matrix = dist.squareform(dist.pdist(adata.obsm['svd'])) -low_dim_dist_matrix = dist.squareform(dist.pdist(adata.obsm["X_emb"])) +high_dim_dist_matrix = dist.squareform(dist.pdist(input_reduced.obsm['svd'])) +low_dim_dist_matrix = dist.squareform(dist.pdist(input_reduced.obsm["X_emb"])) print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix') y_actual = high_dim_dist_matrix @@ -34,15 +36,11 @@ kruskal_score = np.sqrt(sum(diff**2) / sum(low_dim_dist_matrix**2)) print("Store metric value") -if 'metric_ids' not in adata.uns.keys(): - adata.uns['metric_ids'] = [] - adata.uns['metric_values'] = {} +input_reduced.uns['metric_ids'] = meta['functionality_name'] +input_reduced.uns['metric_values'] = rmse -adata.uns['metric_ids'] += ['rmse'] -# adata.uns['metric_ids'] += ['kruskal', 'rmse'] -adata.uns['metric_values']['rmse'] = rmse -# adata.uns['metric_values']['kruskal'] = kruskal_score -adata.obsm['kruskal'] = kruskal_matrix +print("Delete obs matrix") +del input_reduced.obsm print("Write data to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py index 1646f577fe..b33881c34d 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -4,25 +4,31 @@ ## VIASH START par = { - 'input': 'output.h5ad', + 'input_reduced': 'reduced.h5ad', + 'input_test': 'test.h5ad', 'output': 'score.h5ad', } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'trustworthiness', } ## VIASH END print("Load data") -adata = ad.read_h5ad(par['input']) +input_reduced = ad.read_h5ad(par['input_reduced']) +input_test = ad.read_h5ad(par['input_test']) print('Reduce dimensionality of raw data') -high_dim, low_dim = adata.layers['counts'], adata.obsm["X_emb"] +high_dim, low_dim = input_test.layers['counts'], input_reduced.obsm["X_emb"] score = manifold.trustworthiness( high_dim, low_dim, n_neighbors=15, metric="euclidean" ) # for large k close to #samples, it's higher than 1.0, e.g 1.0000073552559712 -adata.uns['metric_ids'] = 'trustworthiness' -adata.uns['metric_values'] = float(np.clip(score, 0, 1)) +print("Store metric value") +input_reduced.uns['metric_ids'] = meta['functionality_name'] +input_reduced.uns['metric_values'] = float(np.clip(score, 0, 1)) + +print("Delete obs matrix") +del input_reduced.obsm print("Write data to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From dd07e50e29d183b727e926f30e3cd1b0d961a23c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 6 Dec 2022 16:00:17 +0100 Subject: [PATCH 0540/1233] Add test to split_dataset component Former-commit-id: 433eddc2a383e2a29aa8b07f2d5d200a33886d52 --- .../split_dataset/config.vsh.yaml | 5 ++ .../split_dataset/script.py | 29 ---------- .../split_dataset/test.py | 54 +++++++++++++++++++ 3 files changed, 59 insertions(+), 29 deletions(-) create mode 100644 src/dimensionality_reduction/split_dataset/test.py diff --git a/src/dimensionality_reduction/split_dataset/config.vsh.yaml b/src/dimensionality_reduction/split_dataset/config.vsh.yaml index 543482aa3e..ee547f30b1 100644 --- a/src/dimensionality_reduction/split_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/split_dataset/config.vsh.yaml @@ -5,6 +5,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../resources_test/common/pancreas/ + dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/split_dataset/script.py index 9988db9d7e..eb917de836 100644 --- a/src/dimensionality_reduction/split_dataset/script.py +++ b/src/dimensionality_reduction/split_dataset/script.py @@ -60,35 +60,6 @@ def subset_anndata(adata_sub, slot_info): print(">> Load Data") adata = ad.read_h5ad(par["input"]) -# print(">> Remove not required data") -# # remove all obs metadata -# del adata.obs - -# # remove all var metadata except hvg_score -# for key in adata.var.keys(): -# if key != "hvg_score": -# del adata.var[key] - -# # Remove obsm/varm matrices -# del adata.varm -# del adata.obsm - -# # remove all unstructured except dataset_id -# for key in list(adata.uns.keys()): -# if key != "dataset_id": -# del adata.uns[key] - -# # remove all unstructured except dataset_id -# for key in list(adata.layers.keys()): -# if key not in ['counts', 'normalized']: -# del adata.layers[key] - -# print(">> Create train/test data") -# output_train = adata.copy() -# output_test = adata.copy() -# del output_test.var -# del output_test.layers['normalized'] - print(">> Figuring out which data needs to be copied to which output file") slot_info_per_output = read_slots(par, meta) diff --git a/src/dimensionality_reduction/split_dataset/test.py b/src/dimensionality_reduction/split_dataset/test.py new file mode 100644 index 0000000000..ddf8e3f608 --- /dev/null +++ b/src/dimensionality_reduction/split_dataset/test.py @@ -0,0 +1,54 @@ +import anndata as ad +import subprocess +from os import path + +## VIASH START +meta = { + 'executable': './target/docker/dimensionality_reduction/', + 'resources_dir': './resources_test/common/', +} +## VIASH END + +input_path = meta["resources_dir"] + "/input/dataset.h5ad" +output_train_path = "train.h5ad" +output_test_path = "test.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path +] + +print(">> Checking whether input file exists") +assert path.exists(input_path) + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output files exist") +assert path.exists(output_train_path) +assert path.exists(output_test_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output_train = ad.read_h5ad(output_train_path) +output_test = ad.read_h5ad(output_test_path) + +print("input:", input) +print("output_train:", output_train) +print("output_test:", output_test) + +print(">> Checking whether data from input was copied properly to output") +assert input.n_obs == output_train.n_obs +assert input.n_obs == output_test.n_obs +assert input.uns["dataset_id"] == output_train.uns["dataset_id"] +assert input.uns["dataset_id"] == output_test.uns["dataset_id"] + + +print(">> Check whether certain slots exist") +assert "counts" in output_train.layers +assert "normalized" in output_train.layers +assert 'hvg_score' in output_train.var +assert "counts" in output_test.layers + +print("All checks succeeded!") \ No newline at end of file From 774f16041a96f9ba4b81896e1f594f3f8df4d525 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 6 Dec 2022 16:01:14 +0100 Subject: [PATCH 0541/1233] Adapt api files to changes given by split_dataset Former-commit-id: 7a6c63b3926090fd95fdcdb913149c9426a1b543 --- .../api/anndata_dataset.yaml | 2 +- .../api/comp_method.yaml | 2 +- .../api/comp_metric.yaml | 4 ++- .../metrics/rmse/test.py | 25 +++++++++++-------- 4 files changed, 20 insertions(+), 13 deletions(-) diff --git a/src/dimensionality_reduction/api/anndata_dataset.yaml b/src/dimensionality_reduction/api/anndata_dataset.yaml index e5b6e29595..27002e8f19 100644 --- a/src/dimensionality_reduction/api/anndata_dataset.yaml +++ b/src/dimensionality_reduction/api/anndata_dataset.yaml @@ -2,7 +2,7 @@ type: file description: "A normalized data with a PCA embedding and HVG selection" example: "dataset.h5ad" info: - label: "Dataset+PCA+HVG" + short_description: "Dataset+PCA+HVG" slots: layers: - type: integer diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 60d91b94bb..478759e12a 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -1,7 +1,7 @@ functionality: arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: anndata_train.yaml - name: "--output" __merge__: anndata_reduced.yaml direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 5e46557087..d9112334cf 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,7 +1,9 @@ functionality: arguments: - - name: "--input" + - name: "--input_reduced" __merge__: anndata_reduced.yaml + - name: "--input_test" + __merge__: anndata_test.yaml - name: "--output" __merge__: anndata_score.yaml direction: output \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py index 546460db28..fe676b98f0 100644 --- a/src/dimensionality_reduction/metrics/rmse/test.py +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -9,17 +9,19 @@ } ## VIASH END -input_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_test_path = meta["resources_dir"] + "/input/test.h5ad" output_path = "score.h5ad" -n_pca = 50 cmd = [ meta['executable'], - "--input", input_path, + "--input_reduced", input_reduced_path, + "--input_test", input_reduced_path, "--output", output_path, ] -print(">> Checking whether input file exists") -assert path.exists(input_path) +print(">> Checking whether input files exist") +assert path.exists(input_reduced_path) +assert path.exists(input_test_path) print(">> Running script as test") out = subprocess.run(cmd, check=True, capture_output=True, text=True) @@ -28,11 +30,12 @@ assert path.exists(output_path) print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) +input_reduced = ad.read_h5ad(input_reduced_path) +input_test = ad.read_h5ad(input_test_path) output = ad.read_h5ad(output_path) -print("input:", input) - +print("input reduced:", input_reduced) +print("input test:", input_test) print("output:", output) print(">> Checking whether metrics were added") @@ -44,7 +47,9 @@ assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] +assert input_reduced.uns["method_id"] == output.uns["method_id"] + print("All checks succeeded!") \ No newline at end of file From d205f1d302c1c7ad8bfa923ffea4fcd04d69bf74 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 6 Dec 2022 16:01:32 +0100 Subject: [PATCH 0542/1233] Rename variables Former-commit-id: b92375e052746d8a2a033a979dfb2e8e61d24fc0 --- src/dimensionality_reduction/methods/umap/test.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/methods/umap/test.py b/src/dimensionality_reduction/methods/umap/test.py index 962fde2cc6..2d1de511e1 100644 --- a/src/dimensionality_reduction/methods/umap/test.py +++ b/src/dimensionality_reduction/methods/umap/test.py @@ -6,12 +6,11 @@ meta = { 'executable': './target/docker/dimensionality_reduction/umap', 'resources_dir': './resources_test/common/', - 'cpus': 2 } ## VIASH END input_path = meta["resources_dir"] + "/input/dataset.h5ad" -output_path = "output.h5ad" +output_path = "reduced.h5ad" cmd = [ meta['executable'], "--input", input_path, @@ -32,7 +31,6 @@ output = ad.read_h5ad(output_path) print("input:", input) - print("output:", output) print(">> Checking whether predictions were added") From e40eb1c5dd8274bc44386fcc21c6b63717eb050e Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 6 Dec 2022 17:11:11 +0100 Subject: [PATCH 0543/1233] add check migration_status component Former-commit-id: bab6983412ec81b82e4773a9120abb599298ceca --- _viash.yaml | 2 +- .../check_migration_status/config.vsh.yaml | 25 ++++++++++++ src/common/check_migration_status/script.py | 40 +++++++++++++++++++ src/common/get_method_info/config.vsh.yaml | 12 +++--- src/common/get_method_info/script.R | 6 ++- 5 files changed, 75 insertions(+), 10 deletions(-) create mode 100644 src/common/check_migration_status/config.vsh.yaml create mode 100644 src/common/check_migration_status/script.py diff --git a/_viash.yaml b/_viash.yaml index 64b65b5fab..d1653a0e9c 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.6.5 +viash_version: 0.6.6 source: src target: target diff --git a/src/common/check_migration_status/config.vsh.yaml b/src/common/check_migration_status/config.vsh.yaml new file mode 100644 index 0000000000..01efd3ac02 --- /dev/null +++ b/src/common/check_migration_status/config.vsh.yaml @@ -0,0 +1,25 @@ +functionality: + name: "check_migration_status" + namespace: "common" + description: "Check migration status" + arguments: + - name: "--git_sha" + type: "file" + example: git_sha.json + description: "a json with git sha info" + - name: "--comp_info" + type: "file" + example: comp_info.json + description: "a json with component info" + - name: "--output" + type: "file" + direction: "output" + default: "output.csv" + description: "Output csv" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.10 + - type: nextflow diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py new file mode 100644 index 0000000000..0a3e8ba01f --- /dev/null +++ b/src/common/check_migration_status/script.py @@ -0,0 +1,40 @@ +import json +import csv + +## VIASH START + +par = { + 'git_sha': 'temp/openproblems-v1.json', + 'comp_info': 'temp/method_info.json', + 'output': 'temp/migration_status.csv' +} + +## VIASH END + +output = {} + +with open(par['git_sha'], 'r') as f1: + git = json.load(f1) + + with open(par['comp_info'], 'r') as f2: + comp = json.load(f2) + for comp_item in comp: + if comp_item['v1_url']: + for obj in git: + if obj['path'] in comp_item['v1_url']: + if obj['sha'] != comp_item['v1_commit']: + output[comp_item['namespace'] + "/" + comp_item['id']] = "not latest commit" + else: + output[comp_item['namespace'] + "/" + comp_item['id']] = "v1_url missing" + + +with open(par['output'], 'w') as outf: + csv_writer = csv.writer(outf) + for k, v in output.items(): + csv_writer.writerow([k, v]) + + + + + + diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index e596f764a4..cb22fc19af 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -11,8 +11,8 @@ functionality: - name: "--output" type: "file" direction: "output" - default: "output.yaml" - description: "Output yaml" + default: "output.json" + description: "Output json" resources: - type: r_script path: script.R @@ -21,9 +21,7 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata, tidyverse ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata>=0.8 ] + cran: [ tidyverse ] + - type: docker + run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin" - type: nextflow diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index da1abedc78..b31bb47cc5 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -4,7 +4,7 @@ library(rlang) ## VIASH START par <- list( input = "src/label_projection", - output = "resources/label_projection/output/method_info.yaml" + output = "temp/method_info.json" ) ## VIASH END @@ -26,5 +26,7 @@ df <- map_df(configs, function(config) { }) %>% select(id, type, label, everything()) -yaml::write_yaml(purrr::transpose(df), par$output) +# yaml::write_yaml(purrr::transpose(df), par$output) + +jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) From 0009367adb9658ba001a5aad30618365187661fd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 6 Dec 2022 21:16:48 +0000 Subject: [PATCH 0544/1233] Bump tj-actions/changed-files from 34.5.0 to 34.5.1 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.5.0 to 34.5.1. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.5.0...v34.5.1) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: 9697d768ed85a9b4b329c327f8903cc3afc2f1e3 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 7bfe941f49..052e71856d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.5.0 + uses: tj-actions/changed-files@v34.5.1 with: separator: ";" diff_relative: true From 1e94a7cebe6d12f2e79b1400bfe395fe0ed2a159 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 7 Dec 2022 09:09:38 +0100 Subject: [PATCH 0545/1233] Adapt control methods to changes in split_dataset Former-commit-id: c30a99c772a096c7bc237e3267de5a1a2c1f7805 --- .../high_dim_pca/config.vsh.yaml | 1 + .../control_methods/high_dim_pca/script.py | 23 +++++++++++-------- .../control_methods/high_dim_pca/test.py | 5 ++-- .../random_features/config.vsh.yaml | 1 + .../control_methods/random_features/script.py | 22 ++++++++++-------- .../control_methods/random_features/test.py | 4 ++-- 6 files changed, 33 insertions(+), 23 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml index d85ce8dd70..3bc0c99065 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml @@ -30,4 +30,5 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py index 07501fcfa0..155fd4d5cc 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py @@ -1,25 +1,30 @@ import anndata as ad import scanpy as sc +import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/test.h5ad', + 'output': 'reduced.h5ad', 'n_pca': 500, } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'high_dim_pca', } ## VIASH END print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) -print('Create high dimensionally PCA embedding') -adata.obsm["X_emb"] = sc.pp.pca(adata.layers['counts'], n_comps=min(min(adata.shape) - 1, par['n_pca'])) +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -# Update .uns -adata.uns['method_id'] = 'high_dim_pca' +print('Create high dimensionally PCA embedding') +input.obsm["X_emb"] = sc.pp.pca(input.layers[input.uns['normalization_id']], n_comps=min(min(input.shape) - 1, par['n_pca'])) print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/test.py b/src/dimensionality_reduction/control_methods/high_dim_pca/test.py index 8ca738f5b9..b38bafe527 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/test.py +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/test.py @@ -2,8 +2,8 @@ import subprocess from os import path -input_path = meta["resources_dir"] + "/input/dataset.h5ad" -output_path = "output.h5ad" +input_path = meta["resources_dir"] + "/input/train.h5ad" +output_path = "reduced.h5ad" n_pca = 50 cmd = [ meta['executable'], @@ -27,7 +27,6 @@ output = ad.read_h5ad(output_path) print("input:", input) - print("output:", output) print(">> Checking whether predictions were added") diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index bd81f2e1d6..36ae9f30b8 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -25,4 +25,5 @@ platforms: packages: - numpy - "anndata>=0.8" + - pyyaml - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index 6aad6abf8d..9b3e41e735 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -3,22 +3,26 @@ ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'output': 'output.h5ad', + 'input': 'resources_test/common/pancreas/test.h5ad', + 'output': 'reduced.h5ad', } meta = { - 'functionality_name': 'foo', + 'functionality_name': 'random_features', } ## VIASH END print("Load input data") -adata = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input']) -print('Create random embedding') -adata.obsm["X_emb"] = np.random.normal(0, 1, (adata.shape[0], 2)) +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -# Update .uns -adata.uns['method_id'] = 'random_features' +print('Create random embedding') +input.obsm["X_emb"] = np.random.normal(0, 1, (input.shape[0], 2)) print("Write output to file") -adata.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/test.py b/src/dimensionality_reduction/control_methods/random_features/test.py index 19d876d230..778cd32194 100644 --- a/src/dimensionality_reduction/control_methods/random_features/test.py +++ b/src/dimensionality_reduction/control_methods/random_features/test.py @@ -14,7 +14,8 @@ assert path.exists(input_path) print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) +out = subprocess.run(cmd) +# out = subprocess.run(cmd, check=True, capture_output=True, text=True) print(">> Checking whether output file exists") assert path.exists(output_path) @@ -24,7 +25,6 @@ output = ad.read_h5ad(output_path) print("input:", input) - print("output:", output) print(">> Checking whether predictions were added") From fa4039b77a66cbaf8fea715513850ffc063fc84e Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 7 Dec 2022 10:59:46 +0100 Subject: [PATCH 0546/1233] fix phate arguments/preferred_normalization key Former-commit-id: 3cb053b6e9d82313f61c3cbc1b5f6b47e2a42bcc --- .../methods/phate/config.vsh.yaml | 3 --- .../methods/phate/script.py | 17 ++++++++--------- 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 7d6d768126..8094dbd413 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -10,9 +10,6 @@ functionality: v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 preferred_normalization: sqrt_cpm arguments: - - name: '--log_cpm' - type: boolean_true - description: Use logCPM of 1000 HVGs instead of the square-root CPM transformed expression matrix. - name: '--n_pca' type: integer default: 50 diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index df00c1891f..7f41823c6a 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -25,19 +25,18 @@ print('... with gamma=' + str(gamma) + ' and...') phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=gamma) -if par['log_cpm']: +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] + +if input.uns['normalization_id'] == 'sqrt_cpm': + print('... using sqrt-CPM data') + input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) +elif input.uns['normalization_id'] == 'log_cpm': print('... using logCPM data') n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized'][:, idx]) - input.uns['normalization_id'] = 'log_cpm' -else: - print('... using sqrt-CPM data') - input.layers['sqrt_cpm'] = sc.transform.sqrt(input.layers['normalized'].expm1()) - input.obsm["X_emb"] = phate_op.fit_transform(input.layers['sqrt_cpm']) - with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print("Delete layers and var") del input.layers From 1039c95460494fa87a4b515b2f74661916341ff1 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 7 Dec 2022 11:27:30 +0100 Subject: [PATCH 0547/1233] revert wf_utils to previous commit c486e0c Former-commit-id: b21a821107cac5f58d9750912d9b24b6e1a11cbb --- src/wf_utils/DataflowHelper.nf | 57 +++++++++++++++++++++++++--------- 1 file changed, 42 insertions(+), 15 deletions(-) diff --git a/src/wf_utils/DataflowHelper.nf b/src/wf_utils/DataflowHelper.nf index e684d0b894..1057038288 100644 --- a/src/wf_utils/DataflowHelper.nf +++ b/src/wf_utils/DataflowHelper.nf @@ -25,19 +25,20 @@ def setWorkflowArguments(Map args) { main: output_ = input_ | map{ tup -> - id = tup[0] - data = tup[1] - passthrough = tup.drop(2) + assert tup.size() : "Event should have length 2 or greater. Expected format: [id, data]." + def id = tup[0] + def data = tup[1] + def passthrough = tup.drop(2) // determine new data - toRemove = args.collectMany{ _, dataKeys -> + def toRemove = args.collectMany{ _, dataKeys -> // dataKeys is a map but could also be a list dataKeys instanceof List ? dataKeys : dataKeys.values() }.unique() - newData = data.findAll{!toRemove.contains(it.key)} + def newData = data.findAll{!toRemove.contains(it.key)} // determine splitargs - splitArgs = args. + def splitArgs = args. collectEntries{procKey, dataKeys -> // dataKeys is a map but could also be a list newSplitData = dataKeys @@ -76,18 +77,23 @@ def getWorkflowArguments(Map args) { main: output_ = input_ - | map{ tup -> - id = tup[0] - data = tup[1] - splitArgs = tup[2].clone() + | map{ tup -> + assert tup.size() : "Event should have length 3 or greater. Expected format: [id, data, splitArgs]." + + def id = tup[0] + def data = tup[1] + def splitArgs = tup[2].clone() - passthrough = tup.drop(3) + def passthrough = tup.drop(3) // try to infer arg name if (data !instanceof Map) { data = [[ inputKey, data ]].collectEntries() } - newData = data + splitArgs.remove(args.key) + assert splitArgs instanceof Map: "Third element of event (id: $id) should be a map" + assert splitArgs.containsKey(args.key): "Third element of event (id: $id) should have a key ${args.key}" + + def newData = data + splitArgs.remove(args.key) [ id, newData, splitArgs] + passthrough } @@ -134,7 +140,7 @@ def passthroughMap(Closure clos) { main: output_ = input_ | map{ tup -> - out = clos(tup.take(numArgs)) + def out = clos(tup.take(numArgs)) out + tup.drop(numArgs) } @@ -155,9 +161,10 @@ def passthroughFlatMap(Closure clos) { main: output_ = input_ | flatMap{ tup -> - out = clos(tup.take(numArgs)) + def out = clos(tup.take(numArgs)) + def pt = tup.drop(numArgs) for (o in out) { - o.addAll(tup.drop(numArgs)) + o.addAll(pt) } out } @@ -168,3 +175,23 @@ def passthroughFlatMap(Closure clos) { return passthroughFlatMapWf } + +def passthroughFilter(Closure clos) { + def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount + + workflow passthroughFilterWf { + take: + input_ + + main: + output_ = input_ + | filter{ tup -> + clos(tup.take(numArgs)) + } + + emit: + output_ + } + + return passthroughFilterWf +} \ No newline at end of file From e0dd8668c6d80dfc5dc3614db29a009f36ca200a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 7 Dec 2022 16:20:19 +0100 Subject: [PATCH 0548/1233] fix get_method_info to work with docker Former-commit-id: 0b7402eb06c35b2a24f6f0aaabd322a958d9cf96 --- src/common/get_method_info/config.vsh.yaml | 4 +++- src/common/list_git_shas/test.py | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index cb22fc19af..db1f31b211 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -22,6 +22,8 @@ platforms: setup: - type: r cran: [ tidyverse ] + - type: apt + packages: [ curl, default-jdk ] - type: docker - run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin" + run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" - type: nextflow diff --git a/src/common/list_git_shas/test.py b/src/common/list_git_shas/test.py index 23a02ed233..2bf49c70b0 100644 --- a/src/common/list_git_shas/test.py +++ b/src/common/list_git_shas/test.py @@ -19,7 +19,7 @@ assert path.exists(output_path) print(">> Reading json file") -with open(output_path) as f: +with open(output_path, 'r') as f: out = json.load(f) print(out[0]) From 978472ae90f2602159ca510de5a71362171cdbe2 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 7 Dec 2022 17:36:21 +0100 Subject: [PATCH 0549/1233] fix bug: add yaml package Former-commit-id: 46a89e226cfa1708c0ccbb96a3badde24e6d730c --- .../control_methods/random_features/script.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index 9b3e41e735..5a87d33b88 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -1,5 +1,6 @@ import anndata as ad import numpy as np +import yaml ## VIASH START par = { From 944593e2e7a17482688916a5778c6457a2686d85 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 7 Dec 2022 17:37:08 +0100 Subject: [PATCH 0550/1233] fix bugs to run pipeline Former-commit-id: 001be4cdcc475b2e94ab6da2dc75baefefa3be76 --- .../resources_test_scripts/pancreas.sh | 25 +++++++-------- .../workflows/run/config.vsh.yaml | 9 +++++- .../workflows/run/main.nf | 32 +++++++++++-------- .../workflows/run/nextflow.config | 4 +-- 4 files changed, 40 insertions(+), 30 deletions(-) diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index 59f7ef75e6..96c87d8a32 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -21,24 +21,22 @@ mkdir -p $DATASET_DIR # split dataset # TODO: implement -# bin/viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ -# --input $RAW_DATA \ -# --output_dataset $DATASET_DIR/dataset.h5ad \ -# --output_solution $DATASET_DIR/solution.h5ad \ -# --seed 123 -cp $RAW_DATA $DATASET_DIR/dataset.h5ad -cp $RAW_DATA $DATASET_DIR/solution.h5ad +bin/viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ + --input $RAW_DATA \ + --output_train $DATASET_DIR/train.h5ad \ + --output_test $DATASET_DIR/test.h5ad + # run one method bin/viash run src/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/densmap.h5ad + --input $DATASET_DIR/train.h5ad \ + --output $DATASET_DIR/reduced.h5ad # run one metric bin/viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/densmap.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output $DATASET_DIR/densmap_rmse.h5ad + --input_reduced $DATASET_DIR/reduced.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output $DATASET_DIR/score.h5ad # run benchmark export NXF_VER=22.04.5 @@ -61,10 +59,9 @@ bin/nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ - -resume \ --id pancreas \ --dataset_id pancreas \ --normalization_id log_cpm \ - --input $DATASET_DIR/dataset.h5ad \ + --input $DATASET_DIR/train.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/dimensionality_reduction/workflows/run/config.vsh.yaml index abd26e5c36..d8cfb4d74a 100644 --- a/src/dimensionality_reduction/workflows/run/config.vsh.yaml +++ b/src/dimensionality_reduction/workflows/run/config.vsh.yaml @@ -13,13 +13,20 @@ functionality: description: "The ID of the dataset" required: true - name: "--input" - type: "file" # todo: replace with includes + type: "file" + required: true + - name: "--input_test" + type: "file" + required: true + - name: "--normalization_id" + type: "string" - name: Outputs arguments: - name: "--output" direction: "output" type: file example: output.tsv + required: true resources: - type: nextflow_script path: main.nf diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index 0f88798041..7030250156 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -9,25 +9,26 @@ include { random_features } from "$targetDir/dimensionality_reduction/control_me // import methods include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" +include { densmap } from "$targetDir/dimensionality_reduction/methods/densmap/main.nf" include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -// include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" +include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" // import metrics include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" +include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" +include { density } from "$targetDir/dimensionality_reduction/metrics/density/main.nf" // tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/nxf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/nxf_utils/DataFlowHelper.nf" +include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/wf_utils/DataflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // construct a map of methods (id -> method_module) -methods = [ random_features, high_dim_pca, umap, phate ] +methods = [ random_features, high_dim_pca, umap, densmap, phate ] .collectEntries{method -> [method.config.functionality.name, method] } @@ -47,29 +48,34 @@ workflow run_wf { output_ch = input_ch // split params for downstream components + | view{"step 0: $it"} | setWorkflowArguments( - preprocess: ["dataset_id"], + preprocess: ["dataset_id", "normalization_id"], method: ["input"], - metric: [], + metric: ["input_test"], output: ["output"] ) - // multiply events by the number of method | getWorkflowArguments(key: "preprocess") | add_methods + | view{"step 1: $it"} // filter the normalization methods that a method actually prefers - //| check_filtered_normalization_id + | check_filtered_normalization_id + | view{"step 2: $it"} // add input_solution to data for the positive controls | controls_can_cheat + | view{"step 3: $it"} // run methods | getWorkflowArguments(key: "method") | run_methods + | view{"step 4: $it"} // run metrics - | getWorkflowArguments(key: "metric", inputKey: "input") + | getWorkflowArguments(key: "metric", inputKey: "input_reduced") + | view{"step 5: $it"} | run_metrics // convert to tsv @@ -148,8 +154,8 @@ workflow run_metrics { main: output_ch = input_ch - | rmse - // | mix + | (rmse & trustworthiness) + | mix emit: output_ch } diff --git a/src/dimensionality_reduction/workflows/run/nextflow.config b/src/dimensionality_reduction/workflows/run/nextflow.config index dc5390c66d..ed0d87ccd0 100644 --- a/src/dimensionality_reduction/workflows/run/nextflow.config +++ b/src/dimensionality_reduction/workflows/run/nextflow.config @@ -10,5 +10,5 @@ params { } // include common settings -includeConfig("${params.rootDir}/src/nxf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/nxf_utils/labels.config") +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") From 33811ed25f00e5cd2ed0e54a0da61cd236f525d2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 8 Dec 2022 10:18:24 +0100 Subject: [PATCH 0551/1233] add test get_method_info Former-commit-id: c8e352a4c440062e541523f24d0557807ae18f42 --- src/common/get_method_info/config.vsh.yaml | 4 ++++ src/common/get_method_info/test.py | 25 ++++++++++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 src/common/get_method_info/test.py diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index db1f31b211..238d91d27b 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -16,6 +16,10 @@ functionality: resources: - type: r_script path: script.R + test_resources: + - path: ../../../src/label_projection + - type: python_script + path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 diff --git a/src/common/get_method_info/test.py b/src/common/get_method_info/test.py new file mode 100644 index 0000000000..993e07f7c4 --- /dev/null +++ b/src/common/get_method_info/test.py @@ -0,0 +1,25 @@ +import subprocess +from os import path +import json + +input_path = meta["resources_dir"] + "/label_projection" +output_path = "output.json" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading json file") +with open(output_path, 'r') as f: + out = json.load(f) + print(out[0]) + +print("All checks succeeded!") From 18f5f44010839d9b6d995b608a09019118c5a567 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Dec 2022 10:39:41 +0100 Subject: [PATCH 0552/1233] move v1_url to right location Former-commit-id: 000300ab746b109efa8a7444f6433e927e069c3a --- src/label_projection/README.md | 38 +++++++++---------- src/label_projection/README.qmd | 10 +---- ...sk_description.md => task_description.qmd} | 6 ++- 3 files changed, 26 insertions(+), 28 deletions(-) rename src/label_projection/docs/{task_description.md => task_description.qmd} (91%) diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 5f7e8fbc7e..7b5c4ea384 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -55,31 +55,31 @@ labels onto the test set. Methods for assigning labels from a reference dataset to a new dataset. -| Name | Type | Description | DOI | URL | -|:---------------------------------------------------------------------|:--------------------------------------------------|:-----------------------------------------------------------|:-----------------------------------------------------|:-----------------------------------------------------| -| [KNN](./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://github.com/scikit-learn/scikit-learn) | -| [Logistic Regression](./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://github.com/scikit-learn/scikit-learn) | -| [Multilayer perceptron](./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://github.com/scikit-learn/scikit-learn) | -| [SCANVI](./methods/scanvi/config.vsh.yaml) | method | Probabilistic harmonization and annotation of single-cell | | | -| transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | | | -| [Seurat TransferData](./methods/seurat_transferdata/config.vsh.yaml) | method | The Seurat v3 anchoring procedure is designed to integrate | | | -| diverse single-cell datasets across technologies and modalities. | [link](https://doi.org/10.1101/460147) | [link](https://github.com/satijalab/seurat) | | | -| [XGBoost](./methods/xgboost/config.vsh.yaml) | method | XGBoost: A Scalable Tree Boosting System | [link](https://doi.org/10.1145/2939672.2939785) | [link](https://github.com/dmlc/xgboost) | -| [Majority Vote](./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | -| [Random Labels](./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | -| [True labels](./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | +| Name | Type | Description | DOI | URL | +|:------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|:-----------------------------------------------------------|:-----------------------------------------------------|:-----------------------------------------------------| +| [KNN](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://github.com/scikit-learn/scikit-learn) | +| [Logistic Regression](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://github.com/scikit-learn/scikit-learn) | +| [Multilayer perceptron](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://github.com/scikit-learn/scikit-learn) | +| [SCANVI](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/scanvi/config.vsh.yaml) | method | Probabilistic harmonization and annotation of single-cell | | | +| transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | | | +| [Seurat TransferData](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/seurat_transferdata/config.vsh.yaml) | method | The Seurat v3 anchoring procedure is designed to integrate | | | +| diverse single-cell datasets across technologies and modalities. | [link](https://doi.org/10.1101/460147) | [link](https://github.com/satijalab/seurat) | | | +| [XGBoost](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/xgboost/config.vsh.yaml) | method | XGBoost: A Scalable Tree Boosting System | [link](https://doi.org/10.1145/2939672.2939785) | [link](https://github.com/dmlc/xgboost) | +| [Majority Vote](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | +| [Random Labels](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | +| [True labels](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | ## Metrics Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. -| Name | Description | Range | -|:-----------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------| -| [Accuracy](./metrics/accuracy/config.vsh.yaml) | The percentage of correctly predicted labels. Higher is better. | \[0, 1\] | -| [F1 weighted](./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. Higher is better. | \[0, 1\] | -| [F1 macro](./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. Higher is better. | \[0, 1\] | -| [F1 micro](./metrics/f1/config.vsh.yaml) | Calculates the F1 score globally by counting the total true positives, false negatives and false positives. Higher is better. | \[0, 1\] | +| Name | Description | Range | +|:--------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------| +| [Accuracy](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/accuracy/config.vsh.yaml) | The percentage of correctly predicted labels. Higher is better. | \[0, 1\] | +| [F1 weighted](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. Higher is better. | \[0, 1\] | +| [F1 macro](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. Higher is better. | \[0, 1\] | +| [F1 micro](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score globally by counting the total true positives, false negatives and false positives. Higher is better. | \[0, 1\] | ## Pipeline topology diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd index 65ed05818b..053cd2f7a8 100644 --- a/src/label_projection/README.qmd +++ b/src/label_projection/README.qmd @@ -1,8 +1,5 @@ --- format: gfm -info: - v1_url: openproblems/tasks/label_projection/README.md - v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 toc: true --- @@ -20,11 +17,8 @@ dir <- "." # Label Projection -```{r description, echo=FALSE} -lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) -lines2 <- gsub("^#", "##", lines) -knitr::asis_output(lines2) -``` +## Task description +{{< include docs/task_description.qmd >}} ## Methods diff --git a/src/label_projection/docs/task_description.md b/src/label_projection/docs/task_description.qmd similarity index 91% rename from src/label_projection/docs/task_description.md rename to src/label_projection/docs/task_description.qmd index be120e2b88..41b181bbd0 100644 --- a/src/label_projection/docs/task_description.md +++ b/src/label_projection/docs/task_description.qmd @@ -1,4 +1,8 @@ -# Task description +--- +info: + v1_url: openproblems/tasks/label_projection/README.md + v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +--- A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) whereby cells are aggregated into clusters based on feature similarity and then manually characterized based on differential gene expression or previously identified marker genes. Recently, methods have emerged to build on this strategy and annotate cells using [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. From 7dd9551483ccfcf328176103973fc171f4e2f57f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Dec 2022 10:39:49 +0100 Subject: [PATCH 0553/1233] Update to viash 0.6.6 Former-commit-id: 3795ac1cfec908230ed0fbe33486682a92648a81 --- _viash.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 64b65b5fab..d1653a0e9c 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.6.5 +viash_version: 0.6.6 source: src target: target From 3377d8f6e3cc06d01ebd24ad4faf1809eca3dbf1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Dec 2022 10:57:41 +0100 Subject: [PATCH 0554/1233] disable exporting resources for now Former-commit-id: bf3c3dfcda5a6daf89043eded4c59d7ad61013dc --- bin/init | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/bin/init b/bin/init index b26b1afd0d..8d2bf830d9 100755 --- a/bin/init +++ b/bin/init @@ -10,12 +10,12 @@ curl -fsSL get.viash.io | bash -s -- --tools false # add --namespace_separator '/' ? -# automatically export the workflow helper -NXF_UTILS=src/wf_utils -[[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS -bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config -bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf -bin/viash export resource platforms/nextflow/DataflowHelper.nf > $NXF_UTILS/DataflowHelper.nf +# # automatically export the workflow helper +# NXF_UTILS=src/wf_utils +# [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS +# bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config +# bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf +# bin/viash export resource platforms/nextflow/DataflowHelper.nf > $NXF_UTILS/DataflowHelper.nf cd bin From 1f0d403fc96915a90d69b2b2d0ef48d284ea6b56 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 15:46:22 +0100 Subject: [PATCH 0555/1233] Move unit tests to api files Former-commit-id: 38003b835ab5c3e85ef811420cd935fe06c8fdc5 --- .../api/comp_control_method.yaml | 47 +++++++++++++++- .../api/comp_method.yaml | 45 +++++++++++++++- .../api/comp_metric.yaml | 54 ++++++++++++++++++- .../api/comp_split_dataset.yaml | 54 ++++++++++++++++++- .../high_dim_pca/config.vsh.yaml | 5 -- .../random_features/config.vsh.yaml | 5 -- .../methods/densmap/config.vsh.yaml | 1 + .../methods/umap/config.vsh.yaml | 5 -- .../metrics/density/config.vsh.yaml | 19 +++---- .../metrics/rmse/config.vsh.yaml | 9 ++-- .../metrics/trustworthiness/config.vsh.yaml | 5 -- .../split_dataset/config.vsh.yaml | 5 -- 12 files changed, 208 insertions(+), 46 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 60d91b94bb..8fe94c0247 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -4,4 +4,49 @@ functionality: __merge__: anndata_dataset.yaml - name: "--output" __merge__: anndata_reduced.yaml - direction: output \ No newline at end of file + direction: output + test_resources: + - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/train.h5ad" + output_path = "reduced.h5ad" + n_pca = 50 + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, + "--n_pca", str(n_pca) + ] + + print(">> Checking whether input file exists") + assert path.exists(input_path) + + print(">> Running script as test") + out = subprocess.run(cmd) + # out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + + print("input:", input) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "X_emb" in output.obsm + assert meta['functionality_name'] == output.uns["method_id"] + + print(">> Checking whether data from input was copied properly to output") + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 478759e12a..01074e08c9 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -4,4 +4,47 @@ functionality: __merge__: anndata_train.yaml - name: "--output" __merge__: anndata_reduced.yaml - direction: output \ No newline at end of file + direction: output + test_resources: + - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/train.h5ad" + output_path = "reduced.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] + + print(">> Checking whether input file exists") + assert path.exists(input_path) + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + + print("input:", input) + print("output:", output) + + print(">> Checking whether predictions were added") + assert "X_emb" in output.obsm + assert meta['functionality_name'] == output.uns["method_id"] + assert 'normalization_id' in output.uns + + print(">> Checking whether data from input was copied properly to output") + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index d9112334cf..0a2eb1b126 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -6,4 +6,56 @@ functionality: __merge__: anndata_test.yaml - name: "--output" __merge__: anndata_score.yaml - direction: output \ No newline at end of file + direction: output + test_resources: + - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_reduced_path = meta["resources_dir"] + "/pancreas/reduced.h5ad" + input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" + output_path = "score.h5ad" + cmd = [ + meta['executable'], + "--input_reduced", input_reduced_path, + "--input_test", input_test_path, + "--output", output_path, + ] + + print(">> Checking whether input files exist") + assert path.exists(input_reduced_path) + assert path.exists(input_test_path) + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input_reduced = ad.read_h5ad(input_reduced_path) + input_test = ad.read_h5ad(input_test_path) + output = ad.read_h5ad(output_path) + + print("input reduced:", input_reduced) + print("input test:", input_test) + print("output:", output) + + print(">> Checking whether metrics were added") + assert "metric_ids" in output.uns + assert "metric_values" in output.uns + assert meta['functionality_name'] in output.uns["metric_ids"] + + print(">> Checking whether metrics are float") + assert isinstance(output.uns['metric_values'], float) + + print(">> Checking whether data from input was copied properly to output") + assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] + assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] + assert input_reduced.uns["method_id"] == output.uns["method_id"] + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_split_dataset.yaml index da0724caef..856dc411fe 100644 --- a/src/dimensionality_reduction/api/comp_split_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_split_dataset.yaml @@ -7,4 +7,56 @@ functionality: direction: output - name: "--output_test" __merge__: anndata_test.yaml - direction: output \ No newline at end of file + direction: output + test_resources: + - path: ../../../resources_test/common/pancreas/ + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + output_train_path = "train.h5ad" + output_test_path = "test.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path + ] + + print(">> Checking whether input file exists") + assert path.exists(input_path) + + print(">> Running script as test") + out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + print(">> Checking whether output files exist") + assert path.exists(output_train_path) + assert path.exists(output_test_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output_train = ad.read_h5ad(output_train_path) + output_test = ad.read_h5ad(output_test_path) + + print("input:", input) + print("output_train:", output_train) + print("output_test:", output_test) + + print(">> Checking whether data from input was copied properly to output") + assert input.n_obs == output_train.n_obs + assert input.n_obs == output_test.n_obs + assert input.uns["dataset_id"] == output_train.uns["dataset_id"] + assert input.uns["dataset_id"] == output_test.uns["dataset_id"] + + + print(">> Check whether certain slots exist") + assert "counts" in output_train.layers + assert "normalized" in output_train.layers + assert 'hvg_score' in output_train.var + assert "counts" in output_test.layers + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml index 3bc0c99065..219051c863 100644 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml @@ -17,11 +17,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 36ae9f30b8..07da98d7a3 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -12,11 +12,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 1cbad1a90d..f50800d670 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -25,4 +25,5 @@ platforms: - scanpy - "anndata>=0.8" - pyyaml + - umap-learn - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index aed655cc17..8fd84c8285 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -17,11 +17,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/metrics/density/config.vsh.yaml b/src/dimensionality_reduction/metrics/density/config.vsh.yaml index 1b33a79e91..990dec3d66 100644 --- a/src/dimensionality_reduction/metrics/density/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density/config.vsh.yaml @@ -1,26 +1,21 @@ __merge__: ../../api/comp_metric.yaml functionality: - name: "" + name: "density" namespace: "dimensionality_reduction/metrics" - description: "" + description: "density preservation: correlation of local radius with the local radii in the original data space" info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a metrics: - - id: - label: - description: + - id: density + label: Density + description: "density preservation: correlation of local radius with the local radii in the original data space" min: 0 max: -1 - minimize: true + maximize: true resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" @@ -31,5 +26,5 @@ platforms: - numpy - "anndata>=0.8" - typing - - umap + - umap-learn - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 4cf19edf6c..80bc319dec 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -9,14 +9,13 @@ functionality: metrics: - id: rmse label: RMSE + description: "The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices" + min: 0 + max: Inf + maximize: true resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 7d139c3164..fa483564bb 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -16,11 +16,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" diff --git a/src/dimensionality_reduction/split_dataset/config.vsh.yaml b/src/dimensionality_reduction/split_dataset/config.vsh.yaml index ee547f30b1..543482aa3e 100644 --- a/src/dimensionality_reduction/split_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/split_dataset/config.vsh.yaml @@ -5,11 +5,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../resources_test/common/pancreas/ - dest: input platforms: - type: docker image: "python:3.10" From 8fb362c13a4a0489fd896d97af2121493a6d5788 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 15:47:16 +0100 Subject: [PATCH 0556/1233] Rename variables to fix some bugs Former-commit-id: 234580ae1eaf2b2b4e861369745e1350be373d7f --- .../methods/umap/test.py | 2 +- .../metrics/density/script.py | 118 ++++++++++-------- .../metrics/density/test.py | 31 +++-- .../metrics/rmse/test.py | 4 +- .../metrics/trustworthiness/test.py | 27 ++-- 5 files changed, 102 insertions(+), 80 deletions(-) diff --git a/src/dimensionality_reduction/methods/umap/test.py b/src/dimensionality_reduction/methods/umap/test.py index 2d1de511e1..d986a1aa0f 100644 --- a/src/dimensionality_reduction/methods/umap/test.py +++ b/src/dimensionality_reduction/methods/umap/test.py @@ -9,7 +9,7 @@ } ## VIASH END -input_path = meta["resources_dir"] + "/input/dataset.h5ad" +input_path = meta["resources_dir"] + "/input/train.h5ad" output_path = "reduced.h5ad" cmd = [ meta['executable'], diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py index 7a389789a3..8ddba9f76a 100644 --- a/src/dimensionality_reduction/metrics/density/script.py +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -1,8 +1,6 @@ import anndata as ad import numpy as np from typing import Optional -from umap.umap_ import fuzzy_simplicial_set -from umap.umap_ import nearest_neighbors from umap import UMAP from scipy.sparse import issparse from scipy.stats import pearsonr @@ -17,68 +15,82 @@ 'functionality_name': 'density', } ## VIASH END +def _calculate_radii( + X: np.ndarray, n_neighbors: int = 30, random_state: Optional[int] = None +) -> np.ndarray: + from umap.umap_ import fuzzy_simplicial_set + from umap.umap_ import nearest_neighbors -print("Load data") -input_reduced = ad.read_h5ad(par['input_reduced']) -input_test = ad.read_h5ad(par['input_test']) + # directly taken from: https://github.com/lmcinnes/umap/blob/ + # 317ce81dc64aec9e279aa1374ac809d9ced236f6/umap/umap_.py#L1190-L1243 + (knn_indices, knn_dists, rp_forest,) = nearest_neighbors( + X, + n_neighbors, + "euclidean", + {}, + False, + random_state, + verbose=False, + ) + + emb_graph, emb_sigmas, emb_rhos, emb_dists = fuzzy_simplicial_set( + X, + n_neighbors, + random_state, + "euclidean", + {}, + knn_indices, + knn_dists, + verbose=False, + return_dists=True, + ) -print('Reduce dimensionality of raw data') -_K = 30 # number of neighbors -_SEED = 42 -_, ro, _ = UMAP( - n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True -).fit_transform(input_test.layers['counts']) -# in principle, we could just call _calculate_radii(high_dim, ...) -# this is made sure that the test pass (otherwise, there was .02 difference in corr) -(knn_indices, knn_dists, rp_forest,) = nearest_neighbors( - input_reduced.obsm['X_emb'], - _K, - "euclidean", - {}, - False, - _SEED, - verbose=False, -) + emb_graph = emb_graph.tocoo() + emb_graph.sum_duplicates() + emb_graph.eliminate_zeros() -emb_graph, emb_sigmas, emb_rhos, emb_dists = fuzzy_simplicial_set( - input_reduced.obsm['X_emb'], - _K, - _SEED, - "euclidean", - {}, - knn_indices, - knn_dists, - verbose=False, - return_dists=True, -) + n_vertices = emb_graph.shape[1] -emb_graph = emb_graph.tocoo() -emb_graph.sum_duplicates() -emb_graph.eliminate_zeros() + mu_sum = np.zeros(n_vertices, dtype=np.float32) + re = np.zeros(n_vertices, dtype=np.float32) -n_vertices = emb_graph.shape[1] + head = emb_graph.row + tail = emb_graph.col + for i in range(len(head)): + j = head[i] + k = tail[i] + D = emb_dists[j, k] + mu = emb_graph.data[i] + re[j] += mu * D + re[k] += mu * D + mu_sum[j] += mu + mu_sum[k] += mu -mu_sum = np.zeros(n_vertices, dtype=np.float32) -re = np.zeros(n_vertices, dtype=np.float32) + epsilon = 1e-8 + return np.log(epsilon + (re / mu_sum)) -head = emb_graph.row -tail = emb_graph.col -for i in range(len(head)): - j = head[i] - k = tail[i] - D = emb_dists[j, k] - mu = emb_graph.data[i] - re[j] += mu * D - re[k] += mu * D - mu_sum[j] += mu - mu_sum[k] += mu +print("Load data") +input_reduced = ad.read_h5ad(par['input_reduced']) +input_test = ad.read_h5ad(par['input_test']) -epsilon = 1e-8 -re = np.log(epsilon + (re / mu_sum)) +if np.any(np.isnan(input_reduced.obsm['X_emb'])): + density = 0.0 +else: + _K = 30 # number of neighbors + _SEED = 42 + + print('Reduce dimensionality of raw data') + _, ro, _ = UMAP( + n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True + ).fit_transform(input_test.layers['counts']) + re = _calculate_radii(input_reduced.obsm['X_emb'], n_neighbors=_K, random_state=_SEED) + + print('Compute Density between the full (or processed) data matrix and a dimensionally-reduced matrix') + density = pearsonr(ro, re)[0] print("Store metric value") input_reduced.uns['metric_ids'] = meta['functionality_name'] -input_reduced.uns['metric_values'] = pearsonr(ro, re)[0] +input_reduced.uns['metric_values'] = density print("Delete obs matrix") del input_reduced.obsm diff --git a/src/dimensionality_reduction/metrics/density/test.py b/src/dimensionality_reduction/metrics/density/test.py index 546460db28..f34fbf5b1e 100644 --- a/src/dimensionality_reduction/metrics/density/test.py +++ b/src/dimensionality_reduction/metrics/density/test.py @@ -4,22 +4,24 @@ ## VIASH START meta = { - 'executable': './target/docker/dimensionality_reduction/umap', - 'resources_dir': './resources_test/common/pancreas', + 'executable': './target/docker/dimensionality_reduction/density', + 'resources_dir': './resources_test/dimensionality_reduction/pancreas', } ## VIASH END -input_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_test_path = meta["resources_dir"] + "/input/test.h5ad" output_path = "score.h5ad" -n_pca = 50 cmd = [ meta['executable'], - "--input", input_path, + "--input_reduced", input_reduced_path, + "--input_test", input_test_path, "--output", output_path, ] -print(">> Checking whether input file exists") -assert path.exists(input_path) +print(">> Checking whether input files exist") +assert path.exists(input_reduced_path) +assert path.exists(input_test_path) print(">> Running script as test") out = subprocess.run(cmd, check=True, capture_output=True, text=True) @@ -28,11 +30,12 @@ assert path.exists(output_path) print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) +input_reduced = ad.read_h5ad(input_reduced_path) +input_test = ad.read_h5ad(input_test_path) output = ad.read_h5ad(output_path) -print("input:", input) - +print("input reduced:", input_reduced) +print("input test:", input_test) print("output:", output) print(">> Checking whether metrics were added") @@ -41,10 +44,12 @@ assert meta['functionality_name'] in output.uns["metric_ids"] print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) +assert isinstance(output.uns['metric_values'], float) print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] +assert input_reduced.uns["method_id"] == output.uns["method_id"] + print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/test.py b/src/dimensionality_reduction/metrics/rmse/test.py index fe676b98f0..eeb84c998a 100644 --- a/src/dimensionality_reduction/metrics/rmse/test.py +++ b/src/dimensionality_reduction/metrics/rmse/test.py @@ -15,7 +15,7 @@ cmd = [ meta['executable'], "--input_reduced", input_reduced_path, - "--input_test", input_reduced_path, + "--input_test", input_test_path, "--output", output_path, ] @@ -44,7 +44,7 @@ assert meta['functionality_name'] in output.uns["metric_ids"] print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) +assert isinstance(output.uns['metric_values'], float) print(">> Checking whether data from input was copied properly to output") assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] diff --git a/src/dimensionality_reduction/metrics/trustworthiness/test.py b/src/dimensionality_reduction/metrics/trustworthiness/test.py index 546460db28..eeb84c998a 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/test.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/test.py @@ -9,17 +9,19 @@ } ## VIASH END -input_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" +input_test_path = meta["resources_dir"] + "/input/test.h5ad" output_path = "score.h5ad" -n_pca = 50 cmd = [ meta['executable'], - "--input", input_path, + "--input_reduced", input_reduced_path, + "--input_test", input_test_path, "--output", output_path, ] -print(">> Checking whether input file exists") -assert path.exists(input_path) +print(">> Checking whether input files exist") +assert path.exists(input_reduced_path) +assert path.exists(input_test_path) print(">> Running script as test") out = subprocess.run(cmd, check=True, capture_output=True, text=True) @@ -28,11 +30,12 @@ assert path.exists(output_path) print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) +input_reduced = ad.read_h5ad(input_reduced_path) +input_test = ad.read_h5ad(input_test_path) output = ad.read_h5ad(output_path) -print("input:", input) - +print("input reduced:", input_reduced) +print("input test:", input_test) print("output:", output) print(">> Checking whether metrics were added") @@ -41,10 +44,12 @@ assert meta['functionality_name'] in output.uns["metric_ids"] print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'][meta['functionality_name']], float) +assert isinstance(output.uns['metric_values'], float) print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] +assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] +assert input_reduced.uns["method_id"] == output.uns["method_id"] + print("All checks succeeded!") \ No newline at end of file From b79d7001bb1113a2f1b7bdf00748f120af296966 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 15:48:01 +0100 Subject: [PATCH 0557/1233] Fix pipeline bugs Former-commit-id: 41b1919364d8ee923717e249a33a1061a1489843 --- .../resources_test_scripts/pancreas.sh | 16 +--------------- .../workflows/run/main.nf | 10 ++-------- 2 files changed, 3 insertions(+), 23 deletions(-) diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index 96c87d8a32..c196f99367 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -1,5 +1,4 @@ #!/bin/bash -# #make sure the following command has been executed #bin/viash_build -q 'dimensionality_reduction|common' @@ -20,7 +19,6 @@ fi mkdir -p $DATASET_DIR # split dataset -# TODO: implement bin/viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ @@ -42,19 +40,6 @@ bin/viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ export NXF_VER=22.04.5 # after having added a split dataset component -# bin/nextflow \ -# run . \ -# -main-script src/dimensionality_reduction/workflows/run/main.nf \ -# -profile docker \ -# -resume \ -# --id pancreas \ -# --dataset_id pancreas \ -# --normalization_id log_cpm \ -# --input_dataset $DATASET_DIR/dataset.h5ad \ -# --input_solution $DATASET_DIR/solution.h5ad \ -# --output scores.tsv \ -# --publish_dir $DATASET_DIR/ - bin/nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ @@ -63,5 +48,6 @@ bin/nextflow \ --dataset_id pancreas \ --normalization_id log_cpm \ --input $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index 7030250156..3574a37593 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -28,7 +28,7 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; pa config = readConfig("$projectDir/config.vsh.yaml") // construct a map of methods (id -> method_module) -methods = [ random_features, high_dim_pca, umap, densmap, phate ] +methods = [ random_features, high_dim_pca, umap, densmap, phate, tsne ] .collectEntries{method -> [method.config.functionality.name, method] } @@ -58,24 +58,18 @@ workflow run_wf { // multiply events by the number of method | getWorkflowArguments(key: "preprocess") | add_methods - | view{"step 1: $it"} // filter the normalization methods that a method actually prefers | check_filtered_normalization_id - | view{"step 2: $it"} - // add input_solution to data for the positive controls | controls_can_cheat - | view{"step 3: $it"} // run methods | getWorkflowArguments(key: "method") | run_methods - | view{"step 4: $it"} // run metrics | getWorkflowArguments(key: "metric", inputKey: "input_reduced") - | view{"step 5: $it"} | run_metrics // convert to tsv @@ -154,7 +148,7 @@ workflow run_metrics { main: output_ch = input_ch - | (rmse & trustworthiness) + | (rmse & trustworthiness & density) | mix emit: output_ch From 566379d5b7b1325f0610ef847698c56b834dc468 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 16:19:50 +0100 Subject: [PATCH 0558/1233] Add description for PHATE method Former-commit-id: 211ac343a8fc15e23d09c3d1e34f0230b781eb58 --- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 8094dbd413..4ce72d4425 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "phate" namespace: "dimensionality_reduction/methods" - description: "" + description: "Potential of heat-diffusion for affinity-based transition embedding" info: type: method label: PHATE From b246eb26675dcd7107fd1bde75170915ebc7bb72 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 16:20:13 +0100 Subject: [PATCH 0559/1233] Add task description Former-commit-id: 6b663e1be1b037819e35f2b955c3f8dc47455a6f --- .../docs/task_description.md | 26 +++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/docs/task_description.md b/src/dimensionality_reduction/docs/task_description.md index cb9bb599a0..497350c21d 100644 --- a/src/dimensionality_reduction/docs/task_description.md +++ b/src/dimensionality_reduction/docs/task_description.md @@ -1,2 +1,24 @@ - - \ No newline at end of file +--- +info: + v1_url: openproblems/tasks/dimensionality_reduction/README.md + v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b +--- + +Dimensionality reduction is one of the key challenges in single-cell data +representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells +in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also +other functional elements encoded in mRNA such as lncRNAs). Since its inception, +scRNA-seq experiments have been growing in terms of the number of cells measured. +Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. +Now, it is not uncommon to see experiments that yield over [100,000 +cells]() or even [> 1 million +cells.](https://doi.org/10.1126/science.aba7721) + +Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 +dimensions measured in each cell contribute to an underlying data structure, the overall +structure of the data is challenging to display in few dimensions due to data sparsity +and the [*"curse of +dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in +high dimensional data don’t distinguish data points well). Thus, we need to find a way +to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the +data for visualization and interpretation. \ No newline at end of file From 954f1167d058ea945e72e33342bcd386518bc659 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 16:20:28 +0100 Subject: [PATCH 0560/1233] Add changes Former-commit-id: c2df3e3c7e1bdfb0cfc996c234f7b8456e7082fa --- CHANGELOG.md | 35 ++++++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e4f1c3ff9d..9c0f0509cf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -100,10 +100,43 @@ * `metrics/poisson`: Migrated from v1. +## Dimensionality reduction +### New functionality +* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the split, control method, method and metric components. + +* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. + +* `control_methods`: Added a component for baseline methods specifically. + +* `resources_test/dimensionality_reduction/pancreas` with `src/dimensionality_reduction/resources_test_scripts/pancreas.sh`. + +### V1 migration +* `control_methods/high_dim_pca`: Migrated from v1. Extracted from baseline method `High-dimensional PCA`. + +* `control_methods/random_features`: Migrated from v1. Extracted from baseline method `Random Features`. + +* `methods/umap`: Migrated from v1. + +* `methods/tsne`: Migrated and adapted from v1. + +* `methods/densmap`: Migrated and adapted from v1. + +* `methods/phate`: Migrated from v1. + +* `metrics/rmse`: Migrated from v1. + +* `metrics/trustworthiness`: Migrated from v1. + +* `metrics/density`: Migrated from v1. + ### Changes from V1 * Anndata layers are used to store data instead of obsm * extended the use of sparse data in methods unless it was not possible -* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. \ No newline at end of file +* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. + + From 1714a6cb483c0398d13d1b541847687344eb65aa Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 16:28:58 +0100 Subject: [PATCH 0561/1233] Add info to readme Former-commit-id: 9c966c21c6d93d53cc2a158b89b8a98386a3b2e0 --- src/dimensionality_reduction/README.qmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd index 9e7b7d57d3..ac90e41c42 100644 --- a/src/dimensionality_reduction/README.qmd +++ b/src/dimensionality_reduction/README.qmd @@ -18,7 +18,7 @@ dir <- "src/dimensionality_reduction" dir <- "." ``` -# Label Projection +# Dimensionality reduction ```{r description, echo=FALSE} lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) @@ -28,7 +28,7 @@ knitr::asis_output(lines2) ## Methods -Methods for assigning labels from a reference dataset to a new dataset. +Methods to assign dimensionally-reduced 2D embedding coordinates to adata.obsm['X_emb']. ```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) @@ -63,7 +63,7 @@ cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) ## Metrics -Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. +Metrics for dimensionality reduction aim to compare the dimensionality reduced dataset (the embedding) with a whole or a higher dimensional dataset. The more similar they are, the better the reduction is. ```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) From cd0b6c14ceb003083298ac897f9dd870c14ca03e Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 18:41:16 +0100 Subject: [PATCH 0562/1233] remove max key Former-commit-id: 2019aa82e0860b0713e3be1a9294ede7efe76dd4 --- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 80bc319dec..b1ab75442a 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: label: RMSE description: "The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices" min: 0 - max: Inf + # max: maximize: true resources: - type: python_script From 1e3c5dfd3ff793afc7623d243f291dd699823a4c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 18:41:35 +0100 Subject: [PATCH 0563/1233] generate readme Former-commit-id: 9416a66d3997fb86a0fda7bcc4b597ca6276e286 --- src/dimensionality_reduction/README.md | 222 ++++++++++++++++++------- 1 file changed, 161 insertions(+), 61 deletions(-) diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 8a3fad24a3..3a7ee2a124 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -1,6 +1,6 @@ -- Label - Projection +- Dimensionality reduction - Methods - Metrics - Pipeline @@ -9,47 +9,94 @@ - Dataset - Reduced - Score + - Test + - Train - Component API - Control Method - Method - Metric + - Split Dataset -# Label Projection +# Dimensionality reduction -## Methods +Dimensionality reduction is one of the key challenges in single-cell +data -Methods for assigning labels from a reference dataset to a new dataset. +representation. Routine single-cell RNA sequencing (scRNA-seq) +experiments measure cells - Warning: Unknown or uninitialised column: `paper_doi`. +in roughly 20,000-30,000 dimensions (i.e., features - mostly gene +transcripts but also - Warning: Unknown or uninitialised column: `code_url`. +other functional elements encoded in mRNA such as lncRNAs). Since its +inception, -| Name | Type | Description | DOI | URL | -|:----------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-----------------------------------------------------------------------|:----|:----| -| [densMAP](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | -| [PHATE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | | | | -| [t-SNE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | -| [UMAP](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | -| [Random features](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | -| [High-dimensional PCA](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./control_methods/high_dim_pca/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional PCA embedding | | | +scRNA-seq experiments have been growing in terms of the number of cells +measured. -## Metrics +Originally, cutting-edge SmartSeq experiments would yield a few hundred +cells, at best. + +Now, it is not uncommon to see experiments that yield over \[100,000 + +cells\]() or even +\[\> 1 million + +cells.\](https://doi.org/10.1126/science.aba7721) + +Each *feature* in a dataset functions as a single dimension. While each +of the \~30,000 + +dimensions measured in each cell contribute to an underlying data +structure, the overall + +structure of the data is challenging to display in few dimensions due to +data sparsity + +and the \[\*“curse of + +dimensionality”\*\](https://en.wikipedia.org/wiki/Curse_of_dimensionality) +(distances in + +high dimensional data don’t distinguish data points well). Thus, we need +to find a way + +to [dimensionally +reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the + +data for visualization and interpretation. + +## Methods -Metrics for label projection aim to characterize how well each -classifier correctly assigns cell type labels to cells in the test set. +Methods to assign dimensionally-reduced 2D embedding coordinates to +adata.obsm\[‘X_emb’\]. - Warning: Unknown or uninitialised column: `description`. + Warning: Unknown or uninitialised column: `paper_doi`. - Warning: Unknown or uninitialised column: `maximize`. + Warning: Unknown or uninitialised column: `code_url`. - Warning: Unknown or uninitialised column: `min`. +| Name | Type | Description | DOI | URL | +|:--------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-----------------------------------------------------------------------|:----|:----| +| [densMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | +| [PHATE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | Potential of heat-diffusion for affinity-based transition embedding | | | +| [t-SNE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | +| [UMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | +| [Random features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | +| [High-dimensional PCA](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/high_dim_pca/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional PCA embedding | | | - Warning: Unknown or uninitialised column: `max`. +## Metrics -| Name | Description | Range | -|:--------------------------------------------------------------------------------------------------------------------------|:------------|:-----------| -| [RMSE](/home/rcannood/workspace/openproblems/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | NA NA | \[NA, NA\] | +Metrics for dimensionality reduction aim to compare the dimensionality +reduced dataset (the embedding) with a whole or a higher dimensional +dataset. The more similar they are, the better the reduction is. + +| Name | Description | Range | +|:----------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------|:----------| +| [RMSE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices Higher is better. | \[0, NA\] | +| [Density](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/density/config.vsh.yaml) | density preservation: correlation of local radius with the local radii in the original data space Higher is better. | \[0, -1\] | +| [Trustworthiness](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/trustworthiness/config.vsh.yaml) | To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. Higher is better. | \[0, 1\] | ## Pipeline topology @@ -59,27 +106,34 @@ flowchart LR anndata_dataset(Dataset) anndata_reduced(Reduced) anndata_score(Score) + anndata_test(Test) + anndata_train(Train) comp_control_method[/Control Method/] comp_method[/Method/] comp_metric[/Metric/] + comp_split_dataset[/Split Dataset/] anndata_dataset---comp_control_method - anndata_dataset---comp_method + anndata_train---comp_method anndata_reduced---comp_metric + anndata_test---comp_metric + anndata_dataset---comp_split_dataset comp_control_method-->anndata_reduced comp_method-->anndata_reduced comp_metric-->anndata_score + comp_split_dataset-->anndata_train + comp_split_dataset-->anndata_test ``` ## File format API ### `Dataset` -A normalised data with a PCA embedding and HVG selection +A normalized data with a PCA embedding and HVG selection Used in: - [control method](#control%20method): input (as input) -- [method](#method): input (as input) +- [split dataset](#split%20dataset): input (as input) Slots: @@ -111,40 +165,28 @@ Example: ### `Reduced` -A dimensionality reduced dataset +A dimensionally reduced dataset Used in: - [control method](#control%20method): output (as output) - [method](#method): output (as output) -- [metric](#metric): input (as input) +- [metric](#metric): input_reduced (as input) Slots: -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| obs | celltype | string | Cell type information | -| obs | batch | string | Batch information | -| obs | tissue | string | Tissue information | -| obs | size_factors | double | The size factors created by the normalization method, if any. | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| obsm | X_emb | double | The resulting t-SNE embedding. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | -| uns | normalization_id | string | Which normalization was used | +| struct | name | type | description | +|:-------|:-----------------|:-------|:-------------------------------------| +| obsm | X_emb | double | The dimensionally reduced embedding. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | method_id | string | A unique identifier for the method | +| uns | normalization_id | string | Which normalization was used | Example: AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' uns: 'dataset_id', 'method_id', 'normalization_id' - obsm: 'X_pca', 'X_emb' - layers: 'counts', 'normalized' + obsm: 'X_emb' ### `Score` @@ -169,31 +211,89 @@ Example: AnnData object uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' +### `Test` + +The test data + +Used in: + +- [metric](#metric): input_test (as input) +- [split dataset](#split%20dataset): output_test (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + uns: 'dataset_id' + layers: 'counts' + +### `Train` + +The training data + +Used in: + +- [method](#method): input (as input) +- [split dataset](#split%20dataset): output_train (as output) + +Slots: + +| struct | name | type | description | +|:-------|:-----------|:--------|:------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| var | hvg_score | integer | A ranking of the features by hvg. | +| uns | dataset_id | string | A unique identifier for the dataset | + +Example: + + AnnData object + var: 'hvg_score' + uns: 'dataset_id' + layers: 'counts', 'normalized' + ## Component API ### `Control Method` Arguments: -| Name | File format | Direction | Description | -|:-----------|:--------------------|:----------|:------------| -| `--input` | [Dataset](#dataset) | input | NA | -| `--output` | [Reduced](#reduced) | output | NA | +| Name | File format | Direction | Description | +|:-----------|:--------------------|:----------|:----------------| +| `--input` | [Dataset](#dataset) | input | Dataset+PCA+HVG | +| `--output` | [Reduced](#reduced) | output | Training data | ### `Method` Arguments: -| Name | File format | Direction | Description | -|:-----------|:--------------------|:----------|:------------| -| `--input` | [Dataset](#dataset) | input | NA | -| `--output` | [Reduced](#reduced) | output | NA | +| Name | File format | Direction | Description | +|:-----------|:--------------------|:----------|:--------------| +| `--input` | [Train](#train) | input | Training data | +| `--output` | [Reduced](#reduced) | output | Training data | ### `Metric` Arguments: -| Name | File format | Direction | Description | -|:-----------|:--------------------|:----------|:------------| -| `--input` | [Reduced](#reduced) | input | NA | -| `--output` | [Score](#score) | output | Score | +| Name | File format | Direction | Description | +|:------------------|:--------------------|:----------|:--------------| +| `--input_reduced` | [Reduced](#reduced) | input | Training data | +| `--input_test` | [Test](#test) | input | Test data | +| `--output` | [Score](#score) | output | Score | + +### `Split Dataset` + +Arguments: + +| Name | File format | Direction | Description | +|:-----------------|:--------------------|:----------|:----------------| +| `--input` | [Dataset](#dataset) | input | Dataset+PCA+HVG | +| `--output_train` | [Train](#train) | output | Training data | +| `--output_test` | [Test](#test) | output | Test data | From d830fc3220e7ae942faf75ce1bf2cdd498a1f340 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 8 Dec 2022 18:57:52 +0100 Subject: [PATCH 0564/1233] Update changelog Former-commit-id: f968f57770e4db7aa732c87e35b5bcf25b933b68 --- CHANGELOG.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9c0f0509cf..226bb42c07 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -100,6 +100,14 @@ * `metrics/poisson`: Migrated from v1. +### Changes from V1 + +* Anndata layers are used to store data instead of obsm + +* extended the use of sparse data in methods unless it was not possible + +* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. + ## Dimensionality reduction ### New functionality * `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. @@ -133,10 +141,12 @@ ### Changes from V1 -* Anndata layers are used to store data instead of obsm - -* extended the use of sparse data in methods unless it was not possible +* Anndata layers are used to store normalized and raw counts instead of `.X`. -* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. +* Metrics are stored in `.uns` data. + +* `split_dataset` removes nonessential data from train and test datasets for the methods and metrics. +* Higher dimensional data used to obtain the metrics is calculated from test data instead of the whole dataset. So far test and train data contain the same counts values, but this may change eventually. +* Test data is used instead of the whole dataset in control (baseline) methods. From cf1a0f90dbe28c86537e804bc026fd11e5aade1e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Dec 2022 19:02:12 +0100 Subject: [PATCH 0565/1233] fix api and metric info components Former-commit-id: 5f1f23cf73ecbd74daf914ab183cb08d7170c337 --- src/common/get_api_info/script.R | 2 +- src/common/get_metric_info/script.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index dce054cfde..d55a28ed44 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -20,7 +20,7 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), arg_name = str_replace_all(arg$name, "^-*", ""), direction = arg$direction %||% "input", - file_name = basename(arg$`__inherits__`) %>% gsub("\\.yaml", "", .) + file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) ) }) }) diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index ede6d7b0cc..f7c5a42137 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -18,7 +18,7 @@ configs <- yaml::yaml.load(ns_list$stdout) df <- map_df(configs, function(config) { info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) info$config_path <- gsub(".*\\./", "", config$info$config) - info$id <- config$functionality$name + info$component_id <- config$functionality$name info$namespace <- config$functionality$namespace info$description <- config$functionality$description info From 65e5386fb04fce431b1c36dd2d437fcc99892647 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 12 Dec 2022 11:15:00 +0100 Subject: [PATCH 0566/1233] update check migration with yaml Former-commit-id: d459b3d15a88c9b87899482dd892f1c6138d3820 --- .../check_migration_status/config.vsh.yaml | 12 +++++++-- src/common/check_migration_status/script.py | 20 +++++++------- src/common/check_migration_status/test.py | 27 +++++++++++++++++++ 3 files changed, 48 insertions(+), 11 deletions(-) create mode 100644 src/common/check_migration_status/test.py diff --git a/src/common/check_migration_status/config.vsh.yaml b/src/common/check_migration_status/config.vsh.yaml index 01efd3ac02..0e719cb603 100644 --- a/src/common/check_migration_status/config.vsh.yaml +++ b/src/common/check_migration_status/config.vsh.yaml @@ -14,12 +14,20 @@ functionality: - name: "--output" type: "file" direction: "output" - default: "output.csv" - description: "Output csv" + default: "output.yaml" + description: "Output yaml file with migration status" resources: - type: python_script path: script.py + test_resources: + - path: ../../../temp + - type: python_script + path: test.py platforms: - type: docker image: python:3.10 + setup: + - type: python + pip: + - pyyaml - type: nextflow diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py index 0a3e8ba01f..2bb5d78ccd 100644 --- a/src/common/check_migration_status/script.py +++ b/src/common/check_migration_status/script.py @@ -1,12 +1,12 @@ import json -import csv +from yaml import load, CSafeLoader, dump ## VIASH START par = { 'git_sha': 'temp/openproblems-v1.json', - 'comp_info': 'temp/method_info.json', - 'output': 'temp/migration_status.csv' + 'comp_info': 'temp/denoising_metrics.yaml', + 'output': 'temp/migration_status.yaml' } ## VIASH END @@ -17,21 +17,23 @@ git = json.load(f1) with open(par['comp_info'], 'r') as f2: - comp = json.load(f2) + comp = load(f2, Loader = CSafeLoader) for comp_item in comp: + if comp_item['namespace'] not in output: + output[comp_item['namespace']] = {} if comp_item['v1_url']: for obj in git: if obj['path'] in comp_item['v1_url']: if obj['sha'] != comp_item['v1_commit']: - output[comp_item['namespace'] + "/" + comp_item['id']] = "not latest commit" + output[comp_item['namespace']][comp_item['id']] = {'v1_url': comp_item['v1_url'], 'status': "not latest commit"} + else : + output[comp_item['namespace']][comp_item['id']] = {'v1_url': comp_item['v1_url'],'status': "up to date"} else: - output[comp_item['namespace'] + "/" + comp_item['id']] = "v1_url missing" + output[comp_item['namespace']][comp_item['id']] ={'v1_url': "v1_url missing"} with open(par['output'], 'w') as outf: - csv_writer = csv.writer(outf) - for k, v in output.items(): - csv_writer.writerow([k, v]) + dump(output, outf) diff --git a/src/common/check_migration_status/test.py b/src/common/check_migration_status/test.py new file mode 100644 index 0000000000..4ce5fd1353 --- /dev/null +++ b/src/common/check_migration_status/test.py @@ -0,0 +1,27 @@ +import subprocess +from os import path +from yaml import load, CSafeLoader + +input_sha = meta["resources_dir"] + "temp/openproblems-v1.json" +input_method_info = meta["resources_dir"] + "temp/method_info.json" +output_path = "output.csv" + +cmd = [ + meta['executable'], + "--git_sha", input_sha, + "--comp_info", input_method_info, + "--output", output_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading yaml file") +with open(output_path, 'r') as f: + out = load(f, Loader=CSafeLoader) + print(out) + +print("All checks succeeded!") From 250befb3c132fa8de9ae6a0459743c20723eeaa4 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 12 Dec 2022 11:48:59 +0100 Subject: [PATCH 0567/1233] revert back to yaml output Former-commit-id: a4294ff37f764bb912a9966d5ced88d0612d3c68 --- src/common/get_method_info/config.vsh.yaml | 7 +++++- src/common/get_method_info/script.R | 7 ++---- src/common/get_method_info/test.py | 10 ++++----- src/common/get_metric_info/config.vsh.yaml | 15 ++++++++++--- src/common/get_metric_info/script.R | 18 ++++++++++------ src/common/get_metric_info/test.py | 25 ++++++++++++++++++++++ src/common/list_git_shas/script.py | 1 - src/common/list_git_shas/test.py | 1 - 8 files changed, 61 insertions(+), 23 deletions(-) create mode 100644 src/common/get_metric_info/test.py diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 238d91d27b..156433cedc 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: - type: r_script path: script.R test_resources: - - path: ../../../src/label_projection + - path: ../../../src - type: python_script path: test.py platforms: @@ -30,4 +30,9 @@ platforms: packages: [ curl, default-jdk ] - type: docker run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" + test_setup: + - type: apt + packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] + - type: python + pip: [pyyaml] - type: nextflow diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index b31bb47cc5..436c22a301 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -4,7 +4,7 @@ library(rlang) ## VIASH START par <- list( input = "src/label_projection", - output = "temp/method_info.json" + output = "temp/method_info.yaml" ) ## VIASH END @@ -26,7 +26,4 @@ df <- map_df(configs, function(config) { }) %>% select(id, type, label, everything()) -# yaml::write_yaml(purrr::transpose(df), par$output) - -jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) - +yaml::write_yaml(purrr::transpose(df), par$output) \ No newline at end of file diff --git a/src/common/get_method_info/test.py b/src/common/get_method_info/test.py index 993e07f7c4..6617c5ebc2 100644 --- a/src/common/get_method_info/test.py +++ b/src/common/get_method_info/test.py @@ -1,9 +1,9 @@ import subprocess from os import path -import json +from yaml import load, CSafeLoader -input_path = meta["resources_dir"] + "/label_projection" -output_path = "output.json" +input_path = meta["resources_dir"] + "src/label_projection" +output_path = "output.yaml" cmd = [ meta['executable'], @@ -17,9 +17,9 @@ print(">> Checking whether output file exists") assert path.exists(output_path) -print(">> Reading json file") +print(">> Reading yaml file") with open(output_path, 'r') as f: - out = json.load(f) + out = load(f, Loader= CSafeLoader) print(out[0]) print("All checks succeeded!") diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index bb709f31f5..99195eb9c0 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -16,14 +16,23 @@ functionality: resources: - type: r_script path: script.R + test_resources: + - path: ../../../src + - type: python_script + path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata, tidyverse ] + cran: [ tidyverse ] - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + packages: [ curl, default-jdk ] + - type: docker + run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" + test_setup: + - type: apt + packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - type: python - pip: [ anndata>=0.8 ] + pip: [ pyyaml ] - type: nextflow diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index ede6d7b0cc..44b1f93f0e 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -3,8 +3,8 @@ library(rlang) ## VIASH START par <- list( - input = "src/label_projection", - output = "resources/label_projection/output/metric_info.yaml" + input = "src/denoising", + output = "temp/denoising_metrics.yaml" ) ## VIASH END @@ -16,13 +16,17 @@ ns_list <- processx::run( configs <- yaml::yaml.load(ns_list$stdout) df <- map_df(configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) + colnames(info) <- paste0("metrics_", colnames(info)) info$config_path <- gsub(".*\\./", "", config$info$config) - info$id <- config$functionality$name + info$id <- config$functionality$name # overwrites metrics id first add the Id to metrics _id ? info$namespace <- config$functionality$namespace - info$description <- config$functionality$description + info$description <- config$functionality$description # same as id + info$v1_url <- config$functionality$info$v1_url + info$v1_commit <- config$functionality$info$v1_commit info -}) - -yaml::write_yaml(purrr::transpose(df), par$output) +}) %>% + select(id, everything()) +yaml::write_yaml(purrr::transpose(df), par$output) \ No newline at end of file diff --git a/src/common/get_metric_info/test.py b/src/common/get_metric_info/test.py new file mode 100644 index 0000000000..6617c5ebc2 --- /dev/null +++ b/src/common/get_metric_info/test.py @@ -0,0 +1,25 @@ +import subprocess +from os import path +from yaml import load, CSafeLoader + +input_path = meta["resources_dir"] + "src/label_projection" +output_path = "output.yaml" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading yaml file") +with open(output_path, 'r') as f: + out = load(f, Loader= CSafeLoader) + print(out[0]) + +print("All checks succeeded!") diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 4e739bb47c..5a6e0b7636 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -1,5 +1,4 @@ import subprocess -import os import json ## VIASH START diff --git a/src/common/list_git_shas/test.py b/src/common/list_git_shas/test.py index 2bf49c70b0..d9db07ede6 100644 --- a/src/common/list_git_shas/test.py +++ b/src/common/list_git_shas/test.py @@ -14,7 +14,6 @@ print(">> Running script as test") out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Checking whether output file exists") assert path.exists(output_path) From c12b515bf14089c8cdfdbc8a4f0e1f941b317ae8 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 12 Dec 2022 16:07:07 +0100 Subject: [PATCH 0568/1233] add component_id/description Former-commit-id: ceeddf3c0a8930d7ccd85ddf4845bece3c02918e --- src/common/get_metric_info/script.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 44b1f93f0e..61c757725f 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -18,11 +18,10 @@ configs <- yaml::yaml.load(ns_list$stdout) df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - colnames(info) <- paste0("metrics_", colnames(info)) info$config_path <- gsub(".*\\./", "", config$info$config) - info$id <- config$functionality$name # overwrites metrics id first add the Id to metrics _id ? + info$component_id <- config$functionality$name info$namespace <- config$functionality$namespace - info$description <- config$functionality$description # same as id + info$component_description <- config$functionality$description info$v1_url <- config$functionality$info$v1_url info$v1_commit <- config$functionality$info$v1_commit info From 008026b1e9f2a3325b7cdbea6237157c6ecd08a4 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 12 Dec 2022 17:10:06 +0100 Subject: [PATCH 0569/1233] add v1_comp_id to config.vsh Former-commit-id: c9caf432de9202906b6464f3cbb7d422323ad842 --- src/denoising/control_methods/no_denoising/config.vsh.yaml | 1 + src/denoising/control_methods/perfect_denoising/config.vsh.yaml | 1 + src/denoising/methods/alra/config.vsh.yaml | 1 + src/denoising/methods/dca/config.vsh.yaml | 1 + src/denoising/methods/knn_smoothing/config.vsh.yaml | 1 + src/denoising/methods/magic/config.vsh.yaml | 1 + .../control_methods/majority_vote/config.vsh.yaml | 1 + .../control_methods/random_labels/config.vsh.yaml | 1 + src/label_projection/control_methods/true_labels/config.vsh.yaml | 1 + src/label_projection/methods/knn/config.vsh.yaml | 1 + src/label_projection/methods/logistic_regression/config.vsh.yaml | 1 + src/label_projection/methods/mlp/config.vsh.yaml | 1 + src/label_projection/methods/scanvi/config.vsh.yaml | 1 + src/label_projection/methods/seurat_transferdata/config.vsh.yaml | 1 + src/label_projection/methods/xgboost/config.vsh.yaml | 1 + 15 files changed, 15 insertions(+) diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 6c06418c15..c4b23f3638 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: label: no denoising v1_url: /openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_comp_id: no_denoising preferred_normalization: counts resources: - type: python_script diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index 292ca830f4..de14b2b360 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: label: perfect denoising v1_url: /openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_comp_id: perfect_denoising preferred_normalization: counts resources: - type: python_script diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index dbd3d0d8eb..5f79048e7d 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -19,6 +19,7 @@ functionality: doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md v1_url: /openproblems/tasks/denoising/methods/alra.py v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + v1_comp_id: "alra" preferred_normalization: counts arguments: - name: "--layer_input" diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index acfe9c565e..c29edfb36f 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: code_url: "https://github.com/theislab/dca" v1_url: /openproblems/tasks/denoising/methods/dca.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_comp_id: "dca" preferred_normalization: counts arguments: - name: "--epochs" diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 42e8f55ffc..263a92c5c2 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: code_url: "https://github.com/yanailab/knn-smoothing" v1_url: /openproblems/tasks/denoising/methods/knn_smoothing.py v1_commit: bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1 + v1_comp_id: "knn_smoothing" preferred_normalization: counts resources: - type: python_script diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 1137734b3a..5131d80a99 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: code_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: /openproblems/tasks/denoising/methods/magic.py v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e + v1_comp_id: "magic" preferred_normalization: counts arguments: - name: "--solver" diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index ccdc363bf2..d02f178465 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_comp_id: majority_vote preferred_normalization: counts resources: - type: python_script diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index c248b729c7..68a14bf3d3 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: label: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_comp_id: random_labels preferred_normalization: counts resources: - type: python_script diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 2dd81e1a7c..6f21416029 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: label: True labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_comp_id: true_labels preferred_normalization: counts resources: - type: python_script diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 13dad797aa..20605bfc8a 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -14,6 +14,7 @@ functionality: doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d + v1_comp_id: knn_classifier_log_cpm preferred_normalization: log_cpm resources: - type: python_script diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 80d31cfab8..60e2498e08 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d + v1_comp_id: logistic_regression_log_cpm preferred_normalization: log_cpm resources: - type: python_script diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 8b55db12aa..623be8e793 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -14,6 +14,7 @@ functionality: doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1_url: openproblems/tasks/label_projection/methods/mlp.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_comp_id: mlp_log_cpm preferred_normalization: log_cpm arguments: - name: "--hidden_layer_sizes" diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index c6c4c24d40..8bb5b20ead 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + v1_comp_id: scarches_scanvi_hvg preferred_normalization: log_cpm arguments: - name: "--hvg" diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index bb4ba7ceb5..cd39529cf8 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -13,6 +13,7 @@ functionality: doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" v1_url: openproblems/tasks/label_projection/methods/seurat.py v1_commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 + v1_comp_id: seurat preferred_normalization: log_cpm resources: - type: r_script diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index cd85f8fe80..b475c4ce9c 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -11,6 +11,7 @@ functionality: doc_url: "https://xgboost.readthedocs.io/en/stable/index.html" v1_url: openproblems/tasks/label_projection/methods/xgboost.py v1_commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c + v1_comp_id: xgboost_log_cpm preferred_normalization: log_cpm resources: - type: python_script From 9b41452bd977e2bd6d098d2f08d9006fd1a15df1 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 13 Dec 2022 14:57:33 +0100 Subject: [PATCH 0570/1233] change yaml output to json Former-commit-id: 2a8fe2f3360c9a1237a7488ed6055fbf5f6f4c5b --- .../check_migration_status/config.vsh.yaml | 2 +- src/common/check_migration_status/script.py | 5 ++-- src/common/check_migration_status/test.py | 12 ++++----- src/common/get_api_info/config.vsh.yaml | 13 ++++++---- src/common/get_api_info/script.R | 4 +-- src/common/get_api_info/test.py | 25 +++++++++++++++++++ src/common/get_method_info/config.vsh.yaml | 2 -- src/common/get_method_info/script.R | 4 +-- src/common/get_method_info/test.py | 10 ++++---- src/common/get_metric_info/config.vsh.yaml | 6 ++--- src/common/get_metric_info/script.R | 4 +-- src/common/get_metric_info/test.py | 8 +++--- src/common/get_results/config.vsh.yaml | 9 +++---- src/common/get_results/script.R | 3 +-- src/common/list_git_shas/config.vsh.yaml | 3 ++- src/common/list_git_shas/script.py | 6 ++--- 16 files changed, 69 insertions(+), 47 deletions(-) create mode 100644 src/common/get_api_info/test.py diff --git a/src/common/check_migration_status/config.vsh.yaml b/src/common/check_migration_status/config.vsh.yaml index 0e719cb603..a89e338fad 100644 --- a/src/common/check_migration_status/config.vsh.yaml +++ b/src/common/check_migration_status/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: - type: python_script path: script.py test_resources: - - path: ../../../temp + - path: ../../../resources_test - type: python_script path: test.py platforms: diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py index 2bb5d78ccd..502ff03dcb 100644 --- a/src/common/check_migration_status/script.py +++ b/src/common/check_migration_status/script.py @@ -1,5 +1,4 @@ import json -from yaml import load, CSafeLoader, dump ## VIASH START @@ -17,7 +16,7 @@ git = json.load(f1) with open(par['comp_info'], 'r') as f2: - comp = load(f2, Loader = CSafeLoader) + comp = json.load(f2) for comp_item in comp: if comp_item['namespace'] not in output: output[comp_item['namespace']] = {} @@ -33,7 +32,7 @@ with open(par['output'], 'w') as outf: - dump(output, outf) + json.dump(output, outf) diff --git a/src/common/check_migration_status/test.py b/src/common/check_migration_status/test.py index 4ce5fd1353..8864e1339b 100644 --- a/src/common/check_migration_status/test.py +++ b/src/common/check_migration_status/test.py @@ -1,10 +1,10 @@ import subprocess from os import path -from yaml import load, CSafeLoader +import json -input_sha = meta["resources_dir"] + "temp/openproblems-v1.json" -input_method_info = meta["resources_dir"] + "temp/method_info.json" -output_path = "output.csv" +input_sha = meta["resources_dir"] + "resources_test/common/input_git_sha.json" +input_method_info = meta["resources_dir"] + "resources_test/common/method_info.json" +output_path = "output.json" cmd = [ meta['executable'], @@ -19,9 +19,9 @@ print(">> Checking whether output file exists") assert path.exists(output_path) -print(">> Reading yaml file") +print(">> Reading json file") with open(output_path, 'r') as f: - out = load(f, Loader=CSafeLoader) + out = json.load(f) print(out) print("All checks succeeded!") diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index fa6c91d34a..ad343bec05 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -11,19 +11,22 @@ functionality: - name: "--output" type: "file" direction: "output" - default: "output.yaml" - description: "Output yaml" + default: "output.json" + description: "Output json" resources: - type: r_script path: script.R + test_resources: + - path: ../../../src + - type: python_script + path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata, tidyverse ] + cran: [ tidyverse ] + test_setup: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata>=0.8 ] - type: nextflow diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index d55a28ed44..7bacbf010c 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -4,7 +4,7 @@ library(rlang) ## VIASH START par <- list( input = "src/label_projection", - output = "resources/label_projection/output/api.yaml" + output = "resources/label_projection/output/api.json" ) ## VIASH END @@ -68,4 +68,4 @@ out <- list( file_schema = purrr::transpose(file_slot) ) -yaml::write_yaml(out, par$output) +jsonlite::write_json(purrr::transpose(out), par$output, auto_unbox = TRUE) diff --git a/src/common/get_api_info/test.py b/src/common/get_api_info/test.py new file mode 100644 index 0000000000..2bdc232d30 --- /dev/null +++ b/src/common/get_api_info/test.py @@ -0,0 +1,25 @@ +import subprocess +from os import path +import json + +input_path = meta["resources_dir"] + "src/label_projection" +output_path = "output.json" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading json file") +with open(output_path, 'r') as f: + out = json.load(f) + print(out[0]) + +print("All checks succeeded!") \ No newline at end of file diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 156433cedc..4ea7fbb405 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -33,6 +33,4 @@ platforms: test_setup: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - - type: python - pip: [pyyaml] - type: nextflow diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 436c22a301..0909f5e566 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -4,7 +4,7 @@ library(rlang) ## VIASH START par <- list( input = "src/label_projection", - output = "temp/method_info.yaml" + output = "resources_test/common/method_info.json" ) ## VIASH END @@ -26,4 +26,4 @@ df <- map_df(configs, function(config) { }) %>% select(id, type, label, everything()) -yaml::write_yaml(purrr::transpose(df), par$output) \ No newline at end of file +jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file diff --git a/src/common/get_method_info/test.py b/src/common/get_method_info/test.py index 6617c5ebc2..2bdc232d30 100644 --- a/src/common/get_method_info/test.py +++ b/src/common/get_method_info/test.py @@ -1,9 +1,9 @@ import subprocess from os import path -from yaml import load, CSafeLoader +import json input_path = meta["resources_dir"] + "src/label_projection" -output_path = "output.yaml" +output_path = "output.json" cmd = [ meta['executable'], @@ -17,9 +17,9 @@ print(">> Checking whether output file exists") assert path.exists(output_path) -print(">> Reading yaml file") +print(">> Reading json file") with open(output_path, 'r') as f: - out = load(f, Loader= CSafeLoader) + out = json.load(f) print(out[0]) -print("All checks succeeded!") +print("All checks succeeded!") \ No newline at end of file diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 99195eb9c0..695cb715a1 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -11,8 +11,8 @@ functionality: - name: "--output" type: "file" direction: "output" - default: "output.yaml" - description: "Output yaml" + default: "output.json" + description: "Output json" resources: - type: r_script path: script.R @@ -33,6 +33,4 @@ platforms: test_setup: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - - type: python - pip: [ pyyaml ] - type: nextflow diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 61c757725f..659def459b 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -4,7 +4,7 @@ library(rlang) ## VIASH START par <- list( input = "src/denoising", - output = "temp/denoising_metrics.yaml" + output = "temp/denoising_metrics.json" ) ## VIASH END @@ -28,4 +28,4 @@ df <- map_df(configs, function(config) { }) %>% select(id, everything()) -yaml::write_yaml(purrr::transpose(df), par$output) \ No newline at end of file +jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file diff --git a/src/common/get_metric_info/test.py b/src/common/get_metric_info/test.py index 6617c5ebc2..0756fbd034 100644 --- a/src/common/get_metric_info/test.py +++ b/src/common/get_metric_info/test.py @@ -1,9 +1,9 @@ import subprocess from os import path -from yaml import load, CSafeLoader +import json input_path = meta["resources_dir"] + "src/label_projection" -output_path = "output.yaml" +output_path = "output.json" cmd = [ meta['executable'], @@ -17,9 +17,9 @@ print(">> Checking whether output file exists") assert path.exists(output_path) -print(">> Reading yaml file") +print(">> Reading json file") with open(output_path, 'r') as f: - out = load(f, Loader= CSafeLoader) + out = json.load(f) print(out[0]) print("All checks succeeded!") diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 83a031f21b..155fcffe24 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -16,8 +16,8 @@ functionality: - name: "--output" type: "file" direction: "output" - default: "output.yaml" - description: "Output yaml" + default: "output.json" + description: "Output json" resources: - type: r_script path: script.R @@ -26,9 +26,8 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata, tidyverse ] + cran: [ tidyverse ] + test_setup: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata>=0.8 ] - type: nextflow diff --git a/src/common/get_results/script.R b/src/common/get_results/script.R index 6abe4ab034..87547acee9 100644 --- a/src/common/get_results/script.R +++ b/src/common/get_results/script.R @@ -38,5 +38,4 @@ execution_info <- nxf_log %>% df <- full_join(raw_scores, execution_info, by = c("method_id", "dataset_id")) -yaml::write_yaml(purrr::transpose(df), par$output) - +jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index 8c29f3df88..5b2a7aaec6 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -1,6 +1,7 @@ functionality: name: list_git_shas namespace: common + description: "Extract git file info from a git repo" arguments: - name: --input type: file @@ -34,5 +35,5 @@ platforms: image: "python:3.10" test_setup: - type: docker - run: [git clone https://github.com/openproblems-bio/openproblems-v2.git] + run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow \ No newline at end of file diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 5a6e0b7636..28c7c0d4ef 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { 'input': '.', - 'output': 'output/output.json', + 'output': 'resources_test/input_git_sha.json', 'show_history': True } meta = { @@ -12,7 +12,7 @@ } ## VIASH END -# to do: what to do with untracked files? +#? to do: what to do with untracked files? output = [] @@ -55,7 +55,7 @@ def get_git_file_info(file, full_history=False): output.append(out) with open(par['output'], 'w') as f: - json.dump(output, f, indent=4) + json.dump(output, f) From af23a70ae0545d9fbda09e88221cbcf996a17484 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 13 Dec 2022 15:10:44 +0100 Subject: [PATCH 0571/1233] update changelog Former-commit-id: 6b6ccf72be1d86ce17d097fa31de78989ab94281 --- CHANGELOG.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e4f1c3ff9d..eaf3a49a7a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,19 @@ * `list_git_shas`: create list of latest commit hashes of all files in repo. +* `get_api_info`: extract api info from tasks + +* `get_method_info`: extract method info vrom config yaml + +* `get_metric_info`: extract metric info vrom config yaml + +* `check_migration_status`: compare git shas from methods with v1 + +* `get_results`: extract benchmark scores + + + + ## label_projection From 8ce2889a9494c212e178cf884ed6c48b4018e69c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 13 Dec 2022 16:24:32 +0100 Subject: [PATCH 0572/1233] Add methods: pca and neuralee Former-commit-id: 10b8b6b0a5b451f0b194cebf4468e78e9e3432ee --- .../methods/neuralee/config.vsh.yaml | 31 ++++++++++ .../methods/neuralee/script.py | 56 +++++++++++++++++++ .../methods/pca/config.vsh.yaml | 24 ++++++++ .../methods/pca/script.py | 38 +++++++++++++ 4 files changed, 149 insertions(+) create mode 100644 src/dimensionality_reduction/methods/neuralee/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/neuralee/script.py create mode 100644 src/dimensionality_reduction/methods/pca/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/pca/script.py diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml new file mode 100644 index 0000000000..9c36d95294 --- /dev/null +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -0,0 +1,31 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "neuralee" + namespace: "dimensionality_reduction/methods" + description: "A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/)." + info: + type: method + label: NeuralEE + v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py + v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 + preferred_normalization: counts + arguments: + - name: "--maxit" + type: integer + default: 100 + description: "max number of iterations for NeuralEE." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - pyyaml + - torch + - "git+https://github.com/michalk8/neuralee@8946abf" + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py new file mode 100644 index 0000000000..19143068e8 --- /dev/null +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -0,0 +1,56 @@ +import anndata as ad +import scanpy as sc +import yaml +import torch +from neuralee.embedding import NeuralEE +from neuralee.dataset import GeneExpressionDataset + +## VIASH START +par = { + 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', + 'output': 'reduced.h5ad', + 'no_pca': False, +} +meta = { + 'functionality_name': 'neuralee', + 'config': 'src/dimensionality_reduction/methods/neuralee/config.vsh.yaml' +} +## VIASH END + +print("Load input data") +input = ad.read_h5ad(par['input']) + +print('Add method and normalization ID') +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +input.uns['method_id'] = meta['functionality_name'] + +if input.uns['normalization_id'] == 'counts': + print('Select top 500 high variable genes') + idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:500] + dataset = GeneExpressionDataset(input.layers['counts'][:, idx]) + dataset.log_shift() + dataset.standardscale() +elif input.uns['normalization_id'] == 'log_cpm': + print('Select top 1000 high variable genes') + idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:1000] + dataset = GeneExpressionDataset(input.layers['normalized'][:, idx]) + +# 1000 cells as a batch to estimate the affinity matrix +dataset.affinity_split(N_small=min(1000, input.n_obs)) +NEE = NeuralEE(dataset, d=2, device=torch.device("cpu")) +fine_tune_kwargs = dict(verbose=False) +fine_tune_kwargs["maxit"] = par['maxit'] +fine_tune_kwargs["maxit"] = 10 +res = NEE.fine_tune(**fine_tune_kwargs) + +input.obsm["X_emb"] = res["X"].detach().cpu().numpy() + +print("Delete layers and var") +del input.layers +del input.var + +print("Write output to file") +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml new file mode 100644 index 0000000000..f5d04ee3c6 --- /dev/null +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -0,0 +1,24 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "pca" + namespace: "dimensionality_reduction/methods" + description: "Principal component analysis" + info: + type: method + label: PCA + v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + preferred_normalization: log_cpm + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - pyyaml + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py new file mode 100644 index 0000000000..0c1b241c85 --- /dev/null +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -0,0 +1,38 @@ +import anndata as ad +import scanpy as sc +import yaml + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/train.h5ad', + 'output': 'reduced.h5ad', +} +meta = { + 'functionality_name': 'umap', + 'config': 'src/dimensionality_reduction/methods/PCA/config.vsh.yaml' +} +## VIASH END + +print("Load input data") +input = ad.read_h5ad(par['input']) + +print('Select top 1000 high variable genes') +n_genes = 1000 +idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] + +print('Apply PCA with 50 dimensions') +input.obsm["X_emb"] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack")[:, :2] + +print("Delete layers and var") +del input.layers +del input.var + +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] + +print("Write output to file") +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 6da5cbd117ad6cb732a18b1f242b6e69e0e2a247 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 13 Dec 2022 21:11:16 +0100 Subject: [PATCH 0573/1233] test data must contain hvg_score in .var Former-commit-id: 6296ff81df5189a245067b24b6ddf862c65e99a6 --- src/dimensionality_reduction/api/anndata_test.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/dimensionality_reduction/api/anndata_test.yaml b/src/dimensionality_reduction/api/anndata_test.yaml index 95cddc274d..16f2b31276 100644 --- a/src/dimensionality_reduction/api/anndata_test.yaml +++ b/src/dimensionality_reduction/api/anndata_test.yaml @@ -9,6 +9,11 @@ info: name: counts description: Raw counts required: true + var: + - type: float + name: hvg_score + description: high variability gene score. The greater, the more variable. + required: true uns: - type: string name: dataset_id From 4731c47ce06c64bd79d2d22aca3aff4fb9b7afe4 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 15:57:07 +0100 Subject: [PATCH 0574/1233] change description and type of hvg_score Former-commit-id: df299111da02beadb6073119b62f58ea5c1e9bfa --- src/dimensionality_reduction/api/anndata_dataset.yaml | 4 ++-- src/dimensionality_reduction/api/anndata_test.yaml | 8 ++++++-- src/dimensionality_reduction/api/anndata_train.yaml | 4 ++-- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/src/dimensionality_reduction/api/anndata_dataset.yaml b/src/dimensionality_reduction/api/anndata_dataset.yaml index 27002e8f19..774179aa5c 100644 --- a/src/dimensionality_reduction/api/anndata_dataset.yaml +++ b/src/dimensionality_reduction/api/anndata_dataset.yaml @@ -34,9 +34,9 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score - description: A ranking of the features by hvg. + description: High variability gene score (normalized dispersion). The greater, the more variable. required: true obsm: - type: double diff --git a/src/dimensionality_reduction/api/anndata_test.yaml b/src/dimensionality_reduction/api/anndata_test.yaml index 16f2b31276..e6f2e4b3d1 100644 --- a/src/dimensionality_reduction/api/anndata_test.yaml +++ b/src/dimensionality_reduction/api/anndata_test.yaml @@ -9,10 +9,14 @@ info: name: counts description: Raw counts required: true + - type: double + name: normalized + description: Normalized expression values + required: true var: - - type: float + - type: double name: hvg_score - description: high variability gene score. The greater, the more variable. + description: High variability gene score (normalized dispersion). The greater, the more variable. required: true uns: - type: string diff --git a/src/dimensionality_reduction/api/anndata_train.yaml b/src/dimensionality_reduction/api/anndata_train.yaml index 12c913966d..458eaef906 100644 --- a/src/dimensionality_reduction/api/anndata_train.yaml +++ b/src/dimensionality_reduction/api/anndata_train.yaml @@ -14,9 +14,9 @@ info: description: Normalized expression values required: true var: - - type: integer + - type: double name: hvg_score - description: A ranking of the features by hvg. + description: High variability gene score (normalized dispersion). The greater, the more variable. required: true uns: - type: string From ed5ada904e4a1474a7b1638ec375de8af40df07f Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 15:57:55 +0100 Subject: [PATCH 0575/1233] add metric: nn_ranking Former-commit-id: 5ffb4c42b3c9e56cc735df86bc44ffa4d0e5f4fc --- .../metrics/nn_ranking/config.vsh.yaml | 28 +++ .../metrics/nn_ranking/script.py | 171 ++++++++++++++++++ 2 files changed, 199 insertions(+) create mode 100644 src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/nn_ranking/script.py diff --git a/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml new file mode 100644 index 0000000000..3bc415a845 --- /dev/null +++ b/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml @@ -0,0 +1,28 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: "nn_ranking" + namespace: "dimensionality_reduction/metrics" + description: A set of metrics from the pyDRMetrics package. + info: + v1_url: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + metrics: + - id: nn_ranking + label: NN_Ranking + description: "A set of metrics from the pyDRMetrics package." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - numba + - numpy + - typing + - "anndata>=0.8" + - scipy + - scikit-learn + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/nn_ranking/script.py b/src/dimensionality_reduction/metrics/nn_ranking/script.py new file mode 100644 index 0000000000..3a3fd90391 --- /dev/null +++ b/src/dimensionality_reduction/metrics/nn_ranking/script.py @@ -0,0 +1,171 @@ +import anndata as ad +from numba import njit +from typing import Tuple +import numpy as np +from sklearn.metrics import pairwise_distances +from scipy.sparse import issparse + + +_K = 30 + +@njit(cache=True, fastmath=True) +def _ranking_matrix(D: np.ndarray) -> np.ndarray: # pragma: no cover + assert D.shape[0] == D.shape[1] + R = np.zeros(D.shape) + m = len(R) + ks = np.arange(m) + + for i in range(m): + for j in range(m): + R[i, j] = np.sum( + (D[i, :] < D[i, j]) | ((ks < j) & (np.abs(D[i, :] - D[i, j]) <= 1e-12)) + ) + + return R + + +@njit(cache=True, fastmath=True) +def _coranking_matrix(R1: np.ndarray, R2: np.ndarray) -> np.ndarray: # pragma: no cover + assert R1.shape == R2.shape + Q = np.zeros(R1.shape, dtype=np.int32) + m = len(Q) + for i in range(m): + for j in range(m): + k = int(R1[i, j]) + l = int(R2[i, j]) # noqa: E741 + Q[k, l] += 1 + + return Q + + +@njit(cache=True, fastmath=True) +def _trustworthiness(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover + + T = np.zeros(m - 1) # trustworthiness + + for k in range(m - 1): + Qs = Q[k:, :k] + # a column vector of weights. weight = rank error = actual_rank - k + W = np.arange(Qs.shape[0]).reshape(-1, 1) + # 1 - normalized hard-k-intrusions. lower-left region. + # weighted by rank error (rank - k) + T[k] = 1 - np.sum(Qs * W) / ((k + 1) * m * (m - 1 - k)) + + return T + + +@njit(cache=True, fastmath=True) +def _continuity(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover + + C = np.zeros(m - 1) # continuity + + for k in range(m - 1): + Qs = Q[:k, k:] + # a row vector of weights. weight = rank error = actual_rank - k + W = np.arange(Qs.shape[1]).reshape(1, -1) + # 1 - normalized hard-k-extrusions. upper-right region + C[k] = 1 - np.sum(Qs * W) / ((k + 1) * m * (m - 1 - k)) + + return C + + +@njit(cache=True, fastmath=True) +def _qnn(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover + + QNN = np.zeros(m) # Co-k-nearest neighbor size + + for k in range(m): + # Q[0,0] is always m. 0-th nearest neighbor is always the point itself. + # Exclude Q[0,0] + QNN[k] = np.sum(Q[: k + 1, : k + 1]) / ((k + 1) * m) + + return QNN + + +def _lcmc(QNN: np.ndarray, m: int) -> np.ndarray: + LCMC = QNN - (np.arange(m) + 1) / (m - 1) + return LCMC + + +def _kmax(LCMC: np.ndarray) -> int: + kmax = np.argmax(LCMC) + return kmax # type: ignore + + +def _q_local(QNN: np.ndarray, kmax: int) -> float: + Qlocal = np.sum(QNN[: kmax + 1]) / (kmax + 1) + return Qlocal + + +def _q_global(QNN: np.ndarray, kmax: int, m: int) -> float: + # skip the last. The last is (m-1)-nearest neighbor, including all samples. + Qglobal = np.sum(QNN[kmax:-1]) / (m - kmax - 1) + return Qglobal + + +def _qnn_auc(QNN: np.ndarray) -> float: + AUC = np.mean(QNN) + return AUC # type: ignore + +def _metrics( + Q: np.ndarray, +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray, int, float, float]: + Q = Q[1:, 1:] + m = len(Q) + + T = _trustworthiness(Q, m) + C = _continuity(Q, m) + QNN = _qnn(Q, m) + LCMC = _lcmc(QNN, m) + kmax = _kmax(LCMC) + Qlocal = _q_local(QNN, kmax) + Qglobal = _q_global(QNN, kmax, m) + AUC = _qnn_auc(QNN) + + return T, C, QNN, AUC, LCMC, kmax, Qlocal, Qglobal + + +## VIASH START +par = { + 'input_reduced': 'resources_test/dimensionality_reduction/pancreas/reduced.h5ad', + 'input_test': 'resources_test/dimensionality_reduction/pancreas/test.h5ad', + 'output': 'score.h5ad', +} +meta = { + 'functionality_name': 'nn_ranking', +} +## VIASH END + +print("Load data") +input_reduced = ad.read_h5ad(par['input_reduced']) +input_test = ad.read_h5ad(par['input_test']) + +# Select 1000 most variable genes +idx = input_test.var['hvg_score'].to_numpy().argsort()[-1000:] +input_test = input_test[:, idx] + +# Compute pairwise distances +if issparse(input_test): + Dx = pairwise_distances(input_test.layers['normalized'].A) +else: + Dx = pairwise_distances(input_test.layers['normalized']) + +De = pairwise_distances(input_reduced.obsm["X_emb"]) +Rx, Re = _ranking_matrix(Dx), _ranking_matrix(De) +Q = _coranking_matrix(Rx, Re) + +T, C, QNN, AUC, LCMC, _kmax, Qlocal, Qglobal = _metrics(Q) + +print("Store metric value") +input_reduced.uns['metric_ids'] = {meta['functionality_name']: ['continuity', 'co-KNN size', 'co-KNN AUC', 'local continuity meta criterion', 'local property', 'global property']} +if np.any(np.isnan(input_reduced.obsm["X_emb"])): + input_reduced.uns['metric_values'] = [0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf] +else: + input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] + + +print("Delete obs matrix") +del input_reduced.obsm + +print("Write data to file") +input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 3fd534b3ae7c5d507b0ddccbad1a2439c1fbede9 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 15:59:31 +0100 Subject: [PATCH 0576/1233] use original hvg selection instead of scanpy Former-commit-id: 8d1427ee1d471c002dce74aa1dea7a8d4035ab76 --- .../methods/neuralee/script.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 19143068e8..06dd6b5dbd 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -29,14 +29,19 @@ if input.uns['normalization_id'] == 'counts': print('Select top 500 high variable genes') - idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:500] - dataset = GeneExpressionDataset(input.layers['counts'][:, idx]) + # idx = input.var['hvg_score'].to_numpy().argsort()[-500:] + # dataset = GeneExpressionDataset(input.layers['counts'][:, idx]) + dataset = GeneExpressionDataset(input.layers['counts']) dataset.log_shift() + dataset.subsample_genes(500) dataset.standardscale() elif input.uns['normalization_id'] == 'log_cpm': print('Select top 1000 high variable genes') - idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:1000] - dataset = GeneExpressionDataset(input.layers['normalized'][:, idx]) + # idx = input.var['hvg_score'].to_numpy().argsort()[-1000:] + # dataset = GeneExpressionDataset(input.layers['normalized'][:, idx]) + dataset = GeneExpressionDataset(input.layers['normalized']) + dataset.subsample_genes(500) + # 1000 cells as a batch to estimate the affinity matrix dataset.affinity_split(N_small=min(1000, input.n_obs)) From 3293eb103f93bb8a4a7af4a04b477441b67e9fab Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 15:59:52 +0100 Subject: [PATCH 0577/1233] fix bugs in tests Former-commit-id: e423ef250d00f3f5137140856dfb57323c4cb5d3 --- src/dimensionality_reduction/api/comp_metric.yaml | 3 --- src/dimensionality_reduction/api/comp_split_dataset.yaml | 2 ++ 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 0a2eb1b126..c9bb22b5fe 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -50,9 +50,6 @@ functionality: assert "metric_values" in output.uns assert meta['functionality_name'] in output.uns["metric_ids"] - print(">> Checking whether metrics are float") - assert isinstance(output.uns['metric_values'], float) - print(">> Checking whether data from input was copied properly to output") assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_split_dataset.yaml index 856dc411fe..8488762e94 100644 --- a/src/dimensionality_reduction/api/comp_split_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_split_dataset.yaml @@ -58,5 +58,7 @@ functionality: assert "normalized" in output_train.layers assert 'hvg_score' in output_train.var assert "counts" in output_test.layers + assert "normalized" in output_test.layers + assert 'hvg_score' in output_test.var print("All checks succeeded!") \ No newline at end of file From c8a69c0e72f6e42d786c1b3c5ade545d8b3d6722 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 16:31:16 +0100 Subject: [PATCH 0578/1233] store normalized dispersion in hvg_score Former-commit-id: 8bb701a435f612ec185f0ace660d177d99c53241 --- src/datasets/api/comp_processor_hvg.yaml | 39 +++++++++++++++++++++++- src/datasets/processors/hvg/script.py | 2 +- 2 files changed, 39 insertions(+), 2 deletions(-) diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index e7c45a11f2..dbbe1b02e3 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -16,8 +16,45 @@ functionality: - name: "--var_hvg_score" type: string default: "hvg_score" - description: "In which .var slot to store whether a ranking of the features by variance." + description: "In which .var slot to store the gene variance score (normalized dispersion)." - name: "--num_features" type: integer default: 1000 description: "The number of HVG to select" + test_resources: + - type: python_script + path: generic_test.py + text: | + import scanpy as sc + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + output_path = "output.h5ad" + + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path, + ] + + print(">> Running script as test") + out = subprocess.check_output(cmd).decode("utf-8") + + print(">> Checking whether output file exists") + assert path.exists(output_path) + + print(">> Reading h5ad files") + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + print("input:", input) + print("output:", output) + + print(">> Checking whether output data structures were added") + assert par["var_hvg"] in output.var + + print("Checking whether data from input was copied properly to output") + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print("All checks succeeded!") \ No newline at end of file diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index 0f97161529..ac8e757dc3 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -29,7 +29,7 @@ print(">> Storing output") adata.var[par["var_hvg"]] = out['highly_variable'].values -adata.var[par["var_hvg_score"]] = out['dispersions'].values +adata.var[par["var_hvg_score"]] = out['dispersions_norm'].values print(">> Writing data") adata.write_h5ad(par['output']) From f0c728e19146da9db4fe3501544e305834fbea71 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 14 Dec 2022 19:50:14 +0100 Subject: [PATCH 0579/1233] fix unit tests for datasets/processors/hvg Former-commit-id: 0166aa910425fbcb877fda32ee63bbe46a676452 --- src/datasets/api/comp_processor_hvg.yaml | 24 ++++++++++++++++++--- src/datasets/processors/hvg/config.vsh.yaml | 3 ++- 2 files changed, 23 insertions(+), 4 deletions(-) diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index dbbe1b02e3..fd0a49ecfc 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -22,12 +22,14 @@ functionality: default: 1000 description: "The number of HVG to select" test_resources: + - path: ../../../../resources_test/common/pancreas - type: python_script path: generic_test.py text: | - import scanpy as sc + import anndata as ad import subprocess from os import path + import yaml input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" output_path = "output.h5ad" @@ -38,8 +40,22 @@ functionality: "--output", output_path, ] + with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + + for arg in config["functionality"]["arguments"]: + if arg['name'] == '--layer_input': + layer_input = arg['default'][0] + cmd += ['--layer_input', layer_input] + elif arg['name'] == '--var_hvg': + var_hvg = arg['default'][0] + cmd += ['--var_hvg', var_hvg] + elif arg['name'] == '--var_hvg_score': + var_hvg_score = arg['default'][0] + cmd += ['--var_hvg_score', var_hvg_score] + print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") + out = subprocess.check_output(cmd) print(">> Checking whether output file exists") assert path.exists(output_path) @@ -51,7 +67,9 @@ functionality: print("output:", output) print(">> Checking whether output data structures were added") - assert par["var_hvg"] in output.var + assert layer_input in output.layers + assert var_hvg in output.var + assert var_hvg_score in output.var print("Checking whether data from input was copied properly to output") assert input.n_obs == output.n_obs diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index a45a4dd3d2..ce49676631 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -17,5 +17,6 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata>=0.8" + - pyyaml - type: nextflow From c70eed34093b461e415934408f5e47f7eda7ea61 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 14 Dec 2022 21:46:23 +0000 Subject: [PATCH 0580/1233] Bump tj-actions/changed-files from 34.5.1 to 34.6.1 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.5.1 to 34.6.1. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.5.1...v34.6.1) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: 6299bac1df05f012c5b7a0dd58dfd38400e2e0e8 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 052e71856d..cfdc7e369f 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.5.1 + uses: tj-actions/changed-files@v34.6.1 with: separator: ";" diff_relative: true From c4b255465349b6d5677de1e121f5aa408880e0e1 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 09:27:23 +0100 Subject: [PATCH 0581/1233] Fix bug: phate dependencies Former-commit-id: 611f4f6ea09599b9e57351f67b06bfe2f70c898f --- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 3 ++- src/dimensionality_reduction/methods/phate/script.py | 1 - 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 4ce72d4425..ec547b3383 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -27,7 +27,8 @@ platforms: - type: python packages: - "anndata>=0.8" - - phate + - phate==1.0.* - scprep - pyyaml + - "scikit-learn<1.2" - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 7f41823c6a..2805dbc9a9 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -9,7 +9,6 @@ 'output': 'reduced.h5ad', 'n_pca': 50, 'g0': False, - 'log_cpm': False } meta = { 'functionality_name': 'phate', From 031c5c22bc0648180acf8c280586dc2032291240 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 12:23:31 +0100 Subject: [PATCH 0582/1233] adapt script to viash 0.6.6 Former-commit-id: 0ada0889c5a1a0f8371b81000105c8a0951d2e42 --- .../resources_test_scripts/pancreas.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index c196f99367..81d97ba004 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -1,6 +1,6 @@ #!/bin/bash #make sure the following command has been executed -#bin/viash_build -q 'dimensionality_reduction|common' +#viash ns build -q 'dimensionality_reduction|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -19,19 +19,19 @@ fi mkdir -p $DATASET_DIR # split dataset -bin/viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ +viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad # run one method -bin/viash run src/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ +viash run src/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ --input $DATASET_DIR/train.h5ad \ --output $DATASET_DIR/reduced.h5ad # run one metric -bin/viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ +viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ --input_reduced $DATASET_DIR/reduced.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/score.h5ad From 6f53ba2ca26ab2c572a5a1984684b5f61ca97829 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 12:23:46 +0100 Subject: [PATCH 0583/1233] Add remaining methods and metrics Former-commit-id: 88e7f83519e7e20a67cafbcd6714c19a88bee223 --- src/dimensionality_reduction/workflows/run/main.nf | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index 3574a37593..e21e4ea950 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -12,11 +12,14 @@ include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" include { densmap } from "$targetDir/dimensionality_reduction/methods/densmap/main.nf" include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" +include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" +include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" // import metrics include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" include { density } from "$targetDir/dimensionality_reduction/metrics/density/main.nf" +include { nn_ranking } from "$targetDir/dimensionality_reduction/metrics/nn_ranking/main.nf" // tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" @@ -28,7 +31,7 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; pa config = readConfig("$projectDir/config.vsh.yaml") // construct a map of methods (id -> method_module) -methods = [ random_features, high_dim_pca, umap, densmap, phate, tsne ] +methods = [ random_features, high_dim_pca, umap, densmap, phate, tsne, pca, neuralee ] .collectEntries{method -> [method.config.functionality.name, method] } From 8c2b5b11f2cefcc1148efa58e43c263cef4c2500 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 14:30:51 +0100 Subject: [PATCH 0584/1233] Add spectral rmse calculation Former-commit-id: d26314d84c25af66aabfcb82653a790219b85050 --- .../metrics/rmse/config.vsh.yaml | 7 ++-- .../metrics/rmse/script.py | 36 +++++++++++-------- 2 files changed, 26 insertions(+), 17 deletions(-) diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index b1ab75442a..bdbcf18bc0 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -11,8 +11,10 @@ functionality: label: RMSE description: "The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices" min: 0 - # max: - maximize: true + arguments: + - name: "--spectral" + type: boolean_true + description: Calculate the spectral root mean squared error. resources: - type: python_script path: script.py @@ -22,6 +24,7 @@ platforms: setup: - type: python packages: + - umap-learn - scikit-learn - numpy - scipy diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index 6b9aff0a89..10ae5b49e4 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -1,5 +1,7 @@ import anndata as ad +from umap import UMAP, spectral import scipy.spatial.distance as dist +from scipy.optimize import nnls import numpy as np from sklearn import decomposition, metrics @@ -19,21 +21,25 @@ input_test = ad.read_h5ad(par['input_test']) print('Reduce dimensionality of raw data') -input_reduced.obsm['svd'] = decomposition.TruncatedSVD(n_components = 200).fit_transform(input_test.layers['counts']) - -print('Compute pairwise distance between points in a matrix and format it into a squared-form vector.') -high_dim_dist_matrix = dist.squareform(dist.pdist(input_reduced.obsm['svd'])) -low_dim_dist_matrix = dist.squareform(dist.pdist(input_reduced.obsm["X_emb"])) - -print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix') -y_actual = high_dim_dist_matrix -y_predict = low_dim_dist_matrix -rmse = np.sqrt(metrics.mean_squared_error(y_actual, y_predict)) - -print('Compute Kruskal stress between the full (or processed) data matrix and a dimensionally-reduced matrix') -diff = high_dim_dist_matrix - low_dim_dist_matrix -kruskal_matrix = np.sqrt(diff**2 / sum(low_dim_dist_matrix**2)) -kruskal_score = np.sqrt(sum(diff**2) / sum(low_dim_dist_matrix**2)) +n_comps = 200 +if not par['spectral']: + input_reduced.obsm['high_dim'] = decomposition.TruncatedSVD(n_components = n_comps).fit_transform(input_test.layers['counts']) + print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix, invariant to scalar multiplication') +else: + n_comps = min(n_comps, min(input_test.shape) - 2) + graph = UMAP(transform_mode="graph").fit_transform(input_test.layers['counts']) + input_reduced.obsm['high_dim'] = spectral.spectral_layout( + input_test.layers['counts'], graph, n_comps, random_state=np.random.default_rng() + ) + meta['functionality_name'] += ' spectral' + print('Computes (RMSE) between high-dimensional Laplacian eigenmaps on the full (or processed) data matrix and the dimensionally-reduced matrix, invariant to scalar multiplication') + +high_dim_dist = dist.pdist(input_reduced.obsm['high_dim']) +low_dim_dist = dist.pdist(input_reduced.obsm["X_emb"]) + +scale, rmse = nnls( + low_dim_dist[:, None], high_dim_dist + ) print("Store metric value") input_reduced.uns['metric_ids'] = meta['functionality_name'] From 3be83d9410d7bdd12d2f148dea08ff0e4f544c4e Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 14:31:08 +0100 Subject: [PATCH 0585/1233] Update readme Former-commit-id: 6b552a73ba246e8ba8d75841a4d763ffdd4e0c59 --- .../docs/task_description.md | 22 +++++-------------- 1 file changed, 5 insertions(+), 17 deletions(-) diff --git a/src/dimensionality_reduction/docs/task_description.md b/src/dimensionality_reduction/docs/task_description.md index 497350c21d..843fa52849 100644 --- a/src/dimensionality_reduction/docs/task_description.md +++ b/src/dimensionality_reduction/docs/task_description.md @@ -4,21 +4,9 @@ info: v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b --- -Dimensionality reduction is one of the key challenges in single-cell data -representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells -in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also -other functional elements encoded in mRNA such as lncRNAs). Since its inception, -scRNA-seq experiments have been growing in terms of the number of cells measured. -Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. -Now, it is not uncommon to see experiments that yield over [100,000 -cells]() or even [> 1 million -cells.](https://doi.org/10.1126/science.aba7721) +Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also +other functional elements encoded in mRNA such as lncRNAs). Since its inception, scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. +Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells.](https://doi.org/10.1126/science.aba7721). -Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 -dimensions measured in each cell contribute to an underlying data structure, the overall -structure of the data is challenging to display in few dimensions due to data sparsity -and the [*"curse of -dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in -high dimensional data don’t distinguish data points well). Thus, we need to find a way -to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the -data for visualization and interpretation. \ No newline at end of file +Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity +and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file From 69539059af5fb0f4e2acc42d4a3ee41f27d7883a Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 15:10:15 +0100 Subject: [PATCH 0586/1233] update v1 commit Former-commit-id: 52ad1b7661035664a8ccf3d015158046a1a0d33f --- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index bdbcf18bc0..0339965413 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b metrics: - id: rmse label: RMSE From 6695676798660010ae48f47cd9d1fcaee63b138d Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 15:12:58 +0100 Subject: [PATCH 0587/1233] Update high_dim_pca to true_features Former-commit-id: d1680079a1a1fbf186a6b55cb93af404b14072cc --- .../true_features/config.vsh.yaml | 29 ++++++++++++++++++ .../control_methods/true_features/script.py | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml create mode 100644 src/dimensionality_reduction/control_methods/true_features/script.py diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml new file mode 100644 index 0000000000..726505ce44 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -0,0 +1,29 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: "true_features" + namespace: "dimensionality_reduction/control_methods" + description: "Positive control method which generates high-dimensional (full data) embedding" + info: + type: positive_control + label: True Features + v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py + v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 + preferred_normalization: counts + arguments: + - name: "--n_comps" + type: integer + default: 100 + description: Number of principal components to use. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - pyyaml + - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/script.py b/src/dimensionality_reduction/control_methods/true_features/script.py new file mode 100644 index 0000000000..f3805ccf90 --- /dev/null +++ b/src/dimensionality_reduction/control_methods/true_features/script.py @@ -0,0 +1,30 @@ +import anndata as ad +import scanpy as sc +import yaml + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/test.h5ad', + 'output': 'reduced.h5ad', + 'n_comps': 100, +} +meta = { + 'functionality_name': 'true_features', +} +## VIASH END + +print("Load input data") +input = ad.read_h5ad(par['input']) + +print('Add method and normalization ID') +input.uns['method_id'] = meta['functionality_name'] +with open(meta['config'], 'r') as config_file: + config = yaml.safe_load(config_file) + +input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] + +print('Create high dimensionally embedding with all features') +input.obsm["X_emb"] = input.layers['counts'][:, :par['n_comps']].toarray() + +print("Write output to file") +input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From a7c9a7e597345466e179a420cd3ea72be65f15b7 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 18:01:23 +0100 Subject: [PATCH 0588/1233] update readme Former-commit-id: 9f7483228de3581abf62936334d8cc981b455aaa --- src/dimensionality_reduction/README.md | 141 +++++++++++-------------- 1 file changed, 63 insertions(+), 78 deletions(-) diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 3a7ee2a124..4276939607 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -22,51 +22,30 @@ # Dimensionality reduction Dimensionality reduction is one of the key challenges in single-cell -data - -representation. Routine single-cell RNA sequencing (scRNA-seq) -experiments measure cells - -in roughly 20,000-30,000 dimensions (i.e., features - mostly gene -transcripts but also +data representation. Routine single-cell RNA sequencing (scRNA-seq) +experiments measure cells in roughly 20,000-30,000 dimensions (i.e., +features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its -inception, - -scRNA-seq experiments have been growing in terms of the number of cells -measured. - -Originally, cutting-edge SmartSeq experiments would yield a few hundred -cells, at best. +inception, scRNA-seq experiments have been growing in terms of the +number of cells measured. Originally, cutting-edge SmartSeq experiments +would yield a few hundred cells, at best. -Now, it is not uncommon to see experiments that yield over \[100,000 - -cells\]() or even -\[\> 1 million - -cells.\](https://doi.org/10.1126/science.aba7721) +Now, it is not uncommon to see experiments that yield over [100,000 +cells](https://www.nature.com/articles/s41586-018-0590-4) or even [\> 1 +million cells.](https://doi.org/10.1126/science.aba7721). Each *feature* in a dataset functions as a single dimension. While each -of the \~30,000 - -dimensions measured in each cell contribute to an underlying data -structure, the overall +of the \~30,000 dimensions measured in each cell contribute to an +underlying data structure, the overall structure of the data is +challenging to display in few dimensions due to data sparsity -structure of the data is challenging to display in few dimensions due to -data sparsity - -and the \[\*“curse of - -dimensionality”\*\](https://en.wikipedia.org/wiki/Curse_of_dimensionality) -(distances in - -high dimensional data don’t distinguish data points well). Thus, we need -to find a way - -to [dimensionally -reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the - -data for visualization and interpretation. +and the [*“curse of +dimensionality”*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) +(distances in high dimensional data don’t distinguish data points well). +Thus, we need to find a way to [dimensionally +reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data +for visualization and interpretation. ## Methods @@ -77,14 +56,16 @@ adata.obsm\[‘X_emb’\]. Warning: Unknown or uninitialised column: `code_url`. -| Name | Type | Description | DOI | URL | -|:--------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-----------------------------------------------------------------------|:----|:----| -| [densMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | -| [PHATE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | Potential of heat-diffusion for affinity-based transition embedding | | | -| [t-SNE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | -| [UMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | -| [Random features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | -| [High-dimensional PCA](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/high_dim_pca/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional PCA embedding | | | +| Name | Type | Description | DOI | URL | +|:------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:----------------------------------------------------------------------------------------------------------------------------------------|:----|:----| +| [densMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | +| [NeuralEE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/neuralee/config.vsh.yaml) | method | A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/). | | | +| [PCA](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/pca/config.vsh.yaml) | method | Principal component analysis | | | +| [PHATE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | Potential of heat-diffusion for affinity-based transition embedding | | | +| [t-SNE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | +| [UMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | +| [Random features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | +| [True Features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/true_features/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional (full data) embedding | | | ## Metrics @@ -92,11 +73,12 @@ Metrics for dimensionality reduction aim to compare the dimensionality reduced dataset (the embedding) with a whole or a higher dimensional dataset. The more similar they are, the better the reduction is. -| Name | Description | Range | -|:----------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------|:----------| -| [RMSE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices Higher is better. | \[0, NA\] | -| [Density](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/density/config.vsh.yaml) | density preservation: correlation of local radius with the local radii in the original data space Higher is better. | \[0, -1\] | -| [Trustworthiness](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/trustworthiness/config.vsh.yaml) | To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. Higher is better. | \[0, 1\] | +| Name | Description | Range | +|:----------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------|:-----------| +| [RMSE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices NA | \[0, NA\] | +| [NN_Ranking](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/nn_ranking/config.vsh.yaml) | A set of metrics from the pyDRMetrics package. NA | \[NA, NA\] | +| [Density](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/density/config.vsh.yaml) | density preservation: correlation of local radius with the local radii in the original data space Higher is better. | \[0, -1\] | +| [Trustworthiness](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/trustworthiness/config.vsh.yaml) | To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. Higher is better. | \[0, 1\] | ## Pipeline topology @@ -137,21 +119,21 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| obs | celltype | string | Cell type information | -| obs | batch | string | Batch information | -| obs | tissue | string | Tissue information | -| obs | size_factors | double | The size factors created by the normalization method, if any. | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| varm | pca_loadings | double | The PCA loadings matrix. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | pca_variance | double | The PCA variance objects. | +| struct | name | type | description | +|:-------|:-----------------|:--------|:-------------------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| obs | celltype | string | Cell type information | +| obs | batch | string | Batch information | +| obs | tissue | string | Tissue information | +| obs | size_factors | double | The size factors created by the normalization method, if any. | +| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | +| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | +| obsm | X_pca | double | The resulting PCA embedding. | +| varm | pca_loadings | double | The PCA loadings matrix. | +| uns | dataset_id | string | A unique identifier for the dataset | +| uns | normalization_id | string | Which normalization was used | +| uns | pca_variance | double | The PCA variance objects. | Example: @@ -222,16 +204,19 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------|:--------|:-------------------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | +| uns | dataset_id | string | A unique identifier for the dataset | Example: AnnData object + var: 'hvg_score' uns: 'dataset_id' - layers: 'counts' + layers: 'counts', 'normalized' ### `Train` @@ -244,12 +229,12 @@ Used in: Slots: -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| var | hvg_score | integer | A ranking of the features by hvg. | -| uns | dataset_id | string | A unique identifier for the dataset | +| struct | name | type | description | +|:-------|:-----------|:--------|:-------------------------------------------------------------------------------------| +| layers | counts | integer | Raw counts | +| layers | normalized | double | Normalized expression values | +| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | +| uns | dataset_id | string | A unique identifier for the dataset | Example: From b1a15abfc3138ff4aa8b4c669a89d8f52c753e36 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 18:03:19 +0100 Subject: [PATCH 0589/1233] update readme Former-commit-id: ddd7315c2204847125f3419efd08ebf059c62c1e --- src/dimensionality_reduction/README.md | 22 +++++++++------------- 1 file changed, 9 insertions(+), 13 deletions(-) diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 4276939607..6fea822031 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -24,23 +24,19 @@ Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., -features - mostly gene transcripts but also - -other functional elements encoded in mRNA such as lncRNAs). Since its -inception, scRNA-seq experiments have been growing in terms of the -number of cells measured. Originally, cutting-edge SmartSeq experiments -would yield a few hundred cells, at best. - -Now, it is not uncommon to see experiments that yield over [100,000 -cells](https://www.nature.com/articles/s41586-018-0590-4) or even [\> 1 -million cells.](https://doi.org/10.1126/science.aba7721). +features - mostly gene transcripts but also other functional elements +encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq +experiments have been growing in terms of the number of cells measured. +Originally, cutting-edge SmartSeq experiments would yield a few hundred +cells, at best. Now, it is not uncommon to see experiments that yield +over [100,000 cells](https://www.nature.com/articles/s41586-018-0590-4) +or even [\> 1 million cells.](https://doi.org/10.1126/science.aba7721). Each *feature* in a dataset functions as a single dimension. While each of the \~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is -challenging to display in few dimensions due to data sparsity - -and the [*“curse of +challenging to display in few dimensions due to data sparsity and the +[*“curse of dimensionality”*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally From bc7507ccfb361797450458ed08a0ffb1dbfb5f88 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 18:04:24 +0100 Subject: [PATCH 0590/1233] update readme Former-commit-id: 5314991f0b991bf1e82d5c9a2d34185570c07388 --- src/dimensionality_reduction/README.md | 2 +- src/dimensionality_reduction/docs/task_description.md | 7 ++----- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 6fea822031..40409b5594 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -30,7 +30,7 @@ experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells](https://www.nature.com/articles/s41586-018-0590-4) -or even [\> 1 million cells.](https://doi.org/10.1126/science.aba7721). +or even [\> 1 million cells](https://doi.org/10.1126/science.aba7721). Each *feature* in a dataset functions as a single dimension. While each of the \~30,000 dimensions measured in each cell contribute to an diff --git a/src/dimensionality_reduction/docs/task_description.md b/src/dimensionality_reduction/docs/task_description.md index 843fa52849..9e16fc1d17 100644 --- a/src/dimensionality_reduction/docs/task_description.md +++ b/src/dimensionality_reduction/docs/task_description.md @@ -4,9 +4,6 @@ info: v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b --- -Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also -other functional elements encoded in mRNA such as lncRNAs). Since its inception, scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. -Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells.](https://doi.org/10.1126/science.aba7721). +Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). -Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity -and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file +Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file From 7cdffbaed993404b2ce3e61f6eaacf1ec30860a3 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 15 Dec 2022 18:09:03 +0100 Subject: [PATCH 0591/1233] rename high_dim_pca to true_features Former-commit-id: 8fd62b0c599e7ad74ac993d361905189771f3054 --- .../high_dim_pca/config.vsh.yaml | 29 -------------- .../control_methods/high_dim_pca/script.py | 30 -------------- .../control_methods/high_dim_pca/test.py | 40 ------------------- 3 files changed, 99 deletions(-) delete mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml delete mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/script.py delete mode 100644 src/dimensionality_reduction/control_methods/high_dim_pca/test.py diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml b/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml deleted file mode 100644 index 219051c863..0000000000 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/config.vsh.yaml +++ /dev/null @@ -1,29 +0,0 @@ -__merge__: ../../api/comp_control_method.yaml -functionality: - name: "high_dim_pca" - namespace: "dimensionality_reduction/control_methods" - description: "Positive control method which generates high-dimensional PCA embedding" - info: - type: positive_control - label: High-dimensional PCA - v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - preferred_normalization: counts - arguments: - - name: "--n_pca" - type: integer - default: 500 - description: Number of principal components of PCA to use. - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - scanpy - - "anndata>=0.8" - - pyyaml - - type: nextflow \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py b/src/dimensionality_reduction/control_methods/high_dim_pca/script.py deleted file mode 100644 index 155fd4d5cc..0000000000 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/script.py +++ /dev/null @@ -1,30 +0,0 @@ -import anndata as ad -import scanpy as sc -import yaml - -## VIASH START -par = { - 'input': 'resources_test/common/pancreas/test.h5ad', - 'output': 'reduced.h5ad', - 'n_pca': 500, -} -meta = { - 'functionality_name': 'high_dim_pca', -} -## VIASH END - -print("Load input data") -input = ad.read_h5ad(par['input']) - -print('Add method and normalization ID') -input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] - -print('Create high dimensionally PCA embedding') -input.obsm["X_emb"] = sc.pp.pca(input.layers[input.uns['normalization_id']], n_comps=min(min(input.shape) - 1, par['n_pca'])) - -print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/high_dim_pca/test.py b/src/dimensionality_reduction/control_methods/high_dim_pca/test.py deleted file mode 100644 index b38bafe527..0000000000 --- a/src/dimensionality_reduction/control_methods/high_dim_pca/test.py +++ /dev/null @@ -1,40 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/input/train.h5ad" -output_path = "reduced.h5ad" -n_pca = 50 -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path, - "--n_pca", str(n_pca) -] - -print(">> Checking whether input file exists") -assert path.exists(input_path) - -print(">> Running script as test") -out = subprocess.run(cmd) -# out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) - -print("input:", input) -print("output:", output) - -print(">> Checking whether predictions were added") -assert "X_emb" in output.obsm -assert meta['functionality_name'] == output.uns["method_id"] - -print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -print("All checks succeeded!") \ No newline at end of file From 8cff89609d2c2f45b6a61b72ae5d3622a763a630 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Dec 2022 07:16:20 +0100 Subject: [PATCH 0592/1233] refactor check migration status script Former-commit-id: e900f0d6fb0cbb44035aebca807c6c35458a2b24 --- src/common/check_migration_status/script.py | 61 ++++++++++++--------- 1 file changed, 36 insertions(+), 25 deletions(-) diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py index 502ff03dcb..eef9aab8f7 100644 --- a/src/common/check_migration_status/script.py +++ b/src/common/check_migration_status/script.py @@ -1,41 +1,52 @@ import json +from typing import Dict, List ## VIASH START - par = { 'git_sha': 'temp/openproblems-v1.json', 'comp_info': 'temp/denoising_metrics.yaml', 'output': 'temp/migration_status.yaml' } - ## VIASH END -output = {} +def check_status(comp_item: Dict[str, str], git_objects: List[Dict[str, str]]) -> str: + """Looks for the comp_item's matching git_object + based on the comp_item["v1_url"] and git_object["path"]. + If found, checks whether the comp_item["v1_commit"] equals + git_object["sha"].""" + + v1_url = comp_item.get("v1_url") + if not v1_url: + return "v1_url missing" + + v1_commit = comp_item.get("v1_commit") + if not v1_commit: + return "v1_commit missing" + + git_object = [ obj for obj in git_objects if obj["path"] == v1_url ] + if not git_object: + return "v1_url does not exist in git repo" + + git_sha = git_object[0]["sha"] + if git_sha == comp_item["v1_commit"]: + return "up to date" + else: + return f"out of date (sha: {git_sha})" with open(par['git_sha'], 'r') as f1: - git = json.load(f1) - - with open(par['comp_info'], 'r') as f2: - comp = json.load(f2) - for comp_item in comp: - if comp_item['namespace'] not in output: - output[comp_item['namespace']] = {} - if comp_item['v1_url']: - for obj in git: - if obj['path'] in comp_item['v1_url']: - if obj['sha'] != comp_item['v1_commit']: - output[comp_item['namespace']][comp_item['id']] = {'v1_url': comp_item['v1_url'], 'status': "not latest commit"} - else : - output[comp_item['namespace']][comp_item['id']] = {'v1_url': comp_item['v1_url'],'status': "up to date"} - else: - output[comp_item['namespace']][comp_item['id']] ={'v1_url': "v1_url missing"} - - -with open(par['output'], 'w') as outf: - json.dump(output, outf) - - + git_objects = json.load(f1) +with open(par['comp_info'], 'r') as f2: + comp_items = json.load(f2) +output = [] +for comp_item in comp_items: + # get status + status = check_status(comp_item, git_objects) + # store results + output.append(comp_item | {"status": status}) +# write to file +with open(par['output'], 'w') as outf: + json.dump(output, outf) From 150b439f4949d67a1c52839edbf6a11ac8a75ede Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 16 Dec 2022 15:01:00 +0100 Subject: [PATCH 0593/1233] fix viash build issue #41 Former-commit-id: 8a4877920fc79009dcb1e4bb16674b3b441c75ab --- CONTRIBUTING.md | 2 +- CONTRIBUTING.qmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 47871b35f4..d730339a1e 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -83,7 +83,7 @@ executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. ``` bash -bin/viash_build -q 'label_projection|common' +bin/viash nas build -q 'label_projection|common' --parallel ``` In development mode with 'dev'. diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 3d9aa239a4..ef04dd6158 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -58,7 +58,7 @@ bin/viash run src/common/sync_test_resources/config.vsh.yaml **Step 2, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. ```bash -bin/viash_build -q 'label_projection|common' +bin/viash ns build -q 'label_projection|common' --parallel ``` In development mode with 'dev'. From 6323730938b5aceda4b6a7fabf96b5e115b5b2d9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 16 Dec 2022 21:50:24 +0000 Subject: [PATCH 0594/1233] Bump tj-actions/changed-files from 34.6.1 to 34.6.2 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.6.1 to 34.6.2. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.6.1...v34.6.2) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: 6ecf5b42aa2b40a46b81891d070736252c59a215 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index cfdc7e369f..f474abf8b2 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.6.1 + uses: tj-actions/changed-files@v34.6.2 with: separator: ";" diff_relative: true From f9470685888402c662ba07a286e936545d48419e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Dec 2022 23:22:55 +0100 Subject: [PATCH 0595/1233] add mem/cpu specs Former-commit-id: 15776c5553f5a00ed88220f3fa584fff714cbc87 --- .../control_methods/random_features/config.vsh.yaml | 4 +++- .../control_methods/true_features/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/densmap/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/neuralee/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/pca/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 4 +++- src/dimensionality_reduction/metrics/density/config.vsh.yaml | 4 +++- .../metrics/nn_ranking/config.vsh.yaml | 4 +++- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 4 +++- .../metrics/trustworthiness/config.vsh.yaml | 4 +++- src/dimensionality_reduction/split_dataset/config.vsh.yaml | 2 ++ 13 files changed, 38 insertions(+), 12 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 07da98d7a3..2e29240797 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -21,4 +21,6 @@ platforms: - numpy - "anndata>=0.8" - pyyaml - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 726505ce44..2885f05972 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -26,4 +26,6 @@ platforms: - scanpy - "anndata>=0.8" - pyyaml - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index f50800d670..0a92568bb7 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -26,4 +26,6 @@ platforms: - "anndata>=0.8" - pyyaml - umap-learn - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 9c36d95294..a50d0b9ebe 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -28,4 +28,6 @@ platforms: - pyyaml - torch - "git+https://github.com/michalk8/neuralee@8946abf" - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index f5d04ee3c6..e9ff24ce40 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -21,4 +21,6 @@ platforms: - scanpy - "anndata>=0.8" - pyyaml - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index ec547b3383..06e87e6516 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -31,4 +31,6 @@ platforms: - scprep - pyyaml - "scikit-learn<1.2" - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index aedfb43ad1..f2615f751e 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -26,4 +26,6 @@ platforms: - scanpy - "anndata>=0.8" - pyyaml - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 8fd84c8285..11f9a68ea2 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -26,4 +26,6 @@ platforms: - scanpy - "anndata>=0.8" - pyyaml - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/metrics/density/config.vsh.yaml b/src/dimensionality_reduction/metrics/density/config.vsh.yaml index 990dec3d66..c0b63a8905 100644 --- a/src/dimensionality_reduction/metrics/density/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density/config.vsh.yaml @@ -27,4 +27,6 @@ platforms: - "anndata>=0.8" - typing - umap-learn - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ lowmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml index 3bc415a845..289a498850 100644 --- a/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml @@ -25,4 +25,6 @@ platforms: - "anndata>=0.8" - scipy - scikit-learn - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 0339965413..5c7b8f6926 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -29,4 +29,6 @@ platforms: - numpy - scipy - "anndata>=0.8" - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index fa483564bb..58b9cc1862 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -25,4 +25,6 @@ platforms: - scikit-learn - numpy - "anndata>=0.8" - - type: nextflow \ No newline at end of file + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/dimensionality_reduction/split_dataset/config.vsh.yaml b/src/dimensionality_reduction/split_dataset/config.vsh.yaml index 543482aa3e..7fb8cd56d2 100644 --- a/src/dimensionality_reduction/split_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/split_dataset/config.vsh.yaml @@ -14,3 +14,5 @@ platforms: - pyyaml - "anndata>=0.8" - type: nextflow + directives: + label: [ highmem, highcpu ] From 49055478c2a043f6763863a15469773282707753 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Dec 2022 23:23:03 +0100 Subject: [PATCH 0596/1233] fix scripts Former-commit-id: 5cc62d115fad057ca5ed1c65850980fbc15ebb07 --- .../resources_scripts/run_benchmark.sh | 13 +++++------- .../resources_scripts/split_datasets.sh | 20 +++++++++---------- 2 files changed, 15 insertions(+), 18 deletions(-) diff --git a/src/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh index 230aa9f5e4..620341604d 100755 --- a/src/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -36,19 +36,15 @@ param_list = [] for dataset in datasets: id = dataset["id"] - # TODO: uncomment this - # input_dataset = dataset_dir + "/" + id + ".dataset.h5ad" - # input_solution = dataset_dir + "/" + id + ".solution.h5ad" - input_dataset = dataset_dir + "/" + id + ".h5ad" + input_train = dataset_dir + "/" + id + ".train.h5ad" + input_test = dataset_dir + "/" + id + ".test.h5ad" obj = { 'id': id, 'dataset_id': dataset["dataset_id"], 'normalization_id': dataset["normalization_id"], - # TODO: uncomment this when the file exists - # 'input_dataset': input_dataset, - # 'input_solution': input_solution - 'input': input_dataset + 'input': input_train, + 'input_test': input_test } param_list.append(obj) @@ -67,6 +63,7 @@ bin/nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ + -resume \ -params-file "$params_file" \ --publish_dir "$OUTPUT_DIR" \ -with-tower diff --git a/src/dimensionality_reduction/resources_scripts/split_datasets.sh b/src/dimensionality_reduction/resources_scripts/split_datasets.sh index 857339e2e5..ee97aff0d4 100755 --- a/src/dimensionality_reduction/resources_scripts/split_datasets.sh +++ b/src/dimensionality_reduction/resources_scripts/split_datasets.sh @@ -47,8 +47,8 @@ output = { "obs_label": "celltype", "obs_batch": "batch", "seed": 123, - "output_dataset": "\$id.dataset.h5ad", - "output_solution": "\$id.solution.h5ad" + "output_train": "\$id.train.h5ad", + "output_test": "\$id.test.h5ad" } with open("$params_file", "w") as file: @@ -56,11 +56,11 @@ with open("$params_file", "w") as file: HERE fi -# export NXF_VER=22.04.5 -# bin/nextflow \ -# run . \ -# -main-script target/nextflow/dimensionality_reduction/split_dataset/main.nf \ -# -profile docker \ -# -resume \ -# -params-file $params_file \ -# --publish_dir "$OUTPUT_DIR" \ No newline at end of file +export NXF_VER=22.04.5 +bin/nextflow \ + run . \ + -main-script target/nextflow/dimensionality_reduction/split_dataset/main.nf \ + -profile docker \ + -resume \ + -params-file $params_file \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file From 72a76a83bb586da0f715506d82f48ccece11511a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 17 Dec 2022 08:48:48 +0100 Subject: [PATCH 0597/1233] update contributing instructions Former-commit-id: f03dd72ab5cf04988695694e05a5648ced109deb --- CONTRIBUTING.md | 330 ++++++++++++++++++++++++----------------------- CONTRIBUTING.qmd | 121 ++++++++--------- 2 files changed, 223 insertions(+), 228 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d730339a1e..510c8af643 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -52,23 +52,29 @@ To use this repository, please install the following dependencies: The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. -**Step 0, fetch viash and nextflow:** run the `bin/init` executable. +**Step 0, fetch Viash and Nextflow** ``` bash -bin/init +mkdir $HOME/bin +curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false +curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin ``` - > Using tag develop - > Cleanup - > Downloading Viash source code @develop - > Building Viash from source - > Building Viash helper scripts from source - > Done, happy viash-ing! +Make sure that Viash and Nextflow are on the \$PATH by checking whether +the following commands work: + +``` bash +viash -v +nextflow -v +``` + + viash 0.6.6 (c) 2020 Data Intuitive + nextflow version 22.10.4.5836 **Step 1, download test resources:** by running the following command. ``` bash -bin/viash run src/common/sync_test_resources/config.vsh.yaml +viash run src/common/sync_test_resources/config.vsh.yaml ``` Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining @@ -83,7 +89,7 @@ executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. ``` bash -bin/viash nas build -q 'label_projection|common' --parallel +viash ns build --query 'label_projection|common' --parallel --setup cachedbuild ``` In development mode with 'dev'. @@ -95,10 +101,16 @@ bin/viash nas build -q 'label_projection|common' --parallel [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile ... -These standalone executables you can give to somebody else, and they -will be able to run it, provided that they have Bash and Docker -installed. The command might take a while to run, since it is building a -docker container for each of the components. +Viash will build a whole namespace (`ns`) into executables and Nextflow +pipelines into the `target/docker` and `target/nextflow` folders +respectively. By adding the `-q/--query` flag, you can filter which +components to build using a regex. By adding the `--parallel` flag, +these components are built in parallel (otherwise it will take a really +long time). The flag `--setup cachedbuild` will automatically start +building Docker containers for each of these methods. + +The command might take a while to run, since it is building a docker +container for each of the components. **Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/label_projection/workflows/run_nextflow.sh`: @@ -108,73 +120,58 @@ src/label_projection/workflows/run/run_test.sh ``` N E X T F L O W ~ version 22.04.5 - Launching `src/label_projection/workflows/run/main.nf` [small_becquerel] DSL2 - revision: ece87259df - executor > local (19) - [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ - [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ - [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ - [fd/92edc7] process > run_wf:knn:knn_process (1) [100%] 1 of 1 ✔ - [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ - [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ - [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ - [72/5076e8] process > run_wf:f1:f1_process (6) [100%] 6 of 6 ✔ - [cf/eccd48] process > run_wf:extract_scores:extract_scores_process [100%] 1 of 1 ✔ + Launching `src/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 + executor > local (28) + [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ + [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ + [15/f0a427] process > run_wf:run_methods:random_labels:random_labels_process (pancreas.random_labels) [100%] 1 of 1 ✔ + [02/969d05] process > run_wf:run_methods:knn:knn_process (pancreas.knn) [100%] 1 of 1 ✔ + [90/5fdf9a] process > run_wf:run_methods:mlp:mlp_process (pancreas.mlp) [100%] 1 of 1 ✔ + [c7/dee2e5] process > run_wf:run_methods:logistic_regression:logistic_regression_process (pancreas.logistic_regression) [100%] 1 of 1 ✔ + [83/3ba0c9] process > run_wf:run_methods:scanvi:scanvi_process (pancreas.scanvi) [100%] 1 of 1 ✔ + [e3/2c298e] process > run_wf:run_methods:seurat_transferdata:seurat_transferdata_process (pancreas.seurat_transferdata) [100%] 1 of 1 ✔ + [d6/7212ab] process > run_wf:run_methods:xgboost:xgboost_process (pancreas.xgboost) [100%] 1 of 1 ✔ + [b6/7dc1a7] process > run_wf:run_metrics:accuracy:accuracy_process (pancreas.scanvi) [100%] 9 of 9 ✔ + [be/7d4da4] process > run_wf:run_metrics:f1:f1_process (pancreas.scanvi) [100%] 9 of 9 ✔ + [89/dcd77a] process > run_wf:aggregate_results:extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ ## Project structure - . - ├── bin Helper scripts for building the project and developing a new component. - ├── resources_test Datasets for testing components. If you don't have this folder, run **Step 1** above. - ├── src Source files for each component in the pipeline. - │ ├── common Common processing components. - │ ├── datasets Components for ingesting datasets from a source. - │ ├── label_projection Source files related to the 'Label projection' task. - │ └── ... Other tasks. - └── target Executables generated by viash based on the components listed under `src/`. - ├── docker Bash executables which can be used from a terminal. - └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. - - - bin/ Helper scripts for building the project and developing a new component. - resources_test/ Datasets for testing components. - src/ Source files for each component in the pipeline. - common/ Common processing components. - datasets/ Components related to ingesting datasets into OpenProblems v2. - api/ Specs for the data loaders and normalisation methods. - loaders/ Components for ingesting datasets from a source. - normalization/ Common normalization methods. - label_projection/ Source files related to the 'Label projection' task. - datasets/ Dataset downloader components. - methods/ Modality alignment method components. - metrics/ Modality alignment metric components. - utils/ Utils functions. - workflow/ The pipeline workflow for this task. - target/ Executables generated by viash based on the components listed under `src/`. - docker/ Bash executables which can be used from a terminal. - nextflow/ Nextflow modules which can be used in a Nextflow pipeline. - work/ A working directory used by Nextflow. - output/ Output generated by the pipeline. - -The `src/datasets` folder - -src/datasets/ ├── api Specs for the data loaders and normalisation -methods. ├── loaders Components for ingesting datasets from a source. -├── normalization Common normalization methods. ├── -resource_test_scripts Scripts for generating the objects in the -`resources_test` folder. └── workflows A set of Nextflow workflows which -tie together various components. - -The `src/label_projection` folder - -src/label_projection/ ├── api Specs for the split_dataset, methods and -metrics in this task. ├── control_methods Positive and negative control -methods for quality control. ├── methods Method components. ├── metrics -Metric components. ├── [README.md](src/label_projection/) More -information on how this task works. ├── resources_test_scripts Scripts -for generating the objects in the `resources_test` folder. ├── -split_dataset A component for splitting a common dataset into a `train`, -`test` and `solution` object. └── workflows A set of Nextflow workflows -which tie together various components. +High level overview: . ├── bin Helper scripts for building the project +and developing a new component. ├── resources_test Datasets for testing +components. If you don’t have this folder, run **Step 1** above. ├── src +Source files for each component in the pipeline. │ ├── common Common +processing components. │ ├── datasets Components and pipelines for +building the ‘Common datasets’ │ ├── label_projection Source files +related to the ‘Label projection’ task. │ └── … Other tasks. └── target +Executables generated by viash based on the components listed under +`src/`. ├── docker Bash executables which can be used from a terminal. +└── nextflow Nextflow modules which can be used as a standalone pipeline +or as part of a bigger pipeline. + +Detailed overview of a task folder (e.g. `src/label_projection`): + + src/label_projection/ + ├── api Specs for the components in this task. + ├── control_methods Control methods which serve as quality control checks for the benchmark. + ├── docs Task documentation + ├── methods Label projection method components. + ├── metrics Label projection metric components. + ├── resources_scripts The scripts needed to run the benchmark. + ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). + ├── split_dataset A component that masks a common dataset for use in the benchmark + └── workflows The benchmarking workflow. + +Detailed overview of the `src/datasets` folder: + + src/datasets/ + ├── api Specs for the data loaders and normalisation methods. + ├── loaders Components for ingesting datasets from a source. + ├── normalization Normalization method components. + ├── processors Other preprocessing components (e.g. HVG and PCA). + ├── resource_scripts The scripts needed to generate the common datasets. + ├── resource_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). + └── workflows The workflow which generates the common datasets. ## Adding a Viash component @@ -264,24 +261,23 @@ with the `-h` or `--help` parameter. bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` - Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. - foo + foo dev Todo: fill in Arguments: --input_train - type: file + type: file, file must exist example: training.h5ad The training data --input_test - type: file + type: file, file must exist example: test.h5ad The test data (without labels) --output - type: file, output + type: file, output, file must exist example: prediction.h5ad The prediction file @@ -294,7 +290,9 @@ bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ --output resources_test/label_projection/pancreas/prediction.h5ad ``` - Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. + [notice] Checking if Docker image is available at 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev' + [warning] Could not pull from 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev'. Docker image doesn't exist or is not accessible. + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev' with Dockerfile Load data Create predictions Add method name to uns @@ -315,8 +313,6 @@ bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` - Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. -
> **Note** @@ -333,23 +329,23 @@ executable with the `-h` parameter. target/docker/label_projection/methods/foo/foo -h ``` - foo + foo dev Todo: fill in Arguments: --input_train - type: file + type: file, file must exist example: training.h5ad The training data --input_test - type: file + type: file, file must exist example: test.h5ad The test data (without labels) --output - type: file, output + type: file, output, file must exist example: prediction.h5ad The prediction file @@ -378,53 +374,56 @@ using the **`viash test`** command. bin/viash test src/label_projection/methods/foo/config.vsh.yaml ``` - Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'label_projection/methods_foo:test_rIrBSI' with Dockerfile - [info] Running 'docker build -t label_projection/methods_foo:test_rIrBSI /home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/build_executable/tmp/dockerbuild-foo-y7Hdos/Dockerfile' - Sending build context to Docker daemon 37.89kB + +/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE' with Dockerfile + [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE /home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable/tmp/dockerbuild-foo-C7VuUU/Dockerfile' + Sending build context to Docker daemon 39.94kB Step 1/7 : FROM python:3.10 - ---> ecbdd6bafdb5 + ---> 465483cdaa4e Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" ---> Using cache - ---> f1fbd09c8ccd + ---> 91f658ec0590 Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" ---> Using cache - ---> 063049300b14 - Step 4/7 : LABEL org.opencontainers.image.created="2022-11-17T07:37:39+01:00" - ---> Running in 5d3bda2ec79c - Removing intermediate container 5d3bda2ec79c - ---> e77cbb1b5502 - Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" - ---> Running in fed5d3371cea - Removing intermediate container fed5d3371cea - ---> 9db7959fd7af - Step 6/7 : LABEL org.opencontainers.image.revision="8f9371ddfa5f5c20df01612342040a2003274da3" - ---> Running in 9a2f654aedb9 - Removing intermediate container 9a2f654aedb9 - ---> 912628903c90 - Step 7/7 : LABEL org.opencontainers.image.version="test_rIrBSI" - ---> Running in 82b6f860d949 - Removing intermediate container 82b6f860d949 - ---> e0720a8407a9 - Successfully built e0720a8407a9 - Successfully tagged label_projection/methods_foo:test_rIrBSI + ---> f1ace85a71b0 + Step 4/7 : LABEL org.opencontainers.image.created="2022-12-17T08:47:34+01:00" + ---> Running in 299ea3924905 + Removing intermediate container 299ea3924905 + ---> 6fc97da56de8 + Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2" + ---> Running in bf60068c5fe8 + Removing intermediate container bf60068c5fe8 + ---> 20ff545ec27a + Step 6/7 : LABEL org.opencontainers.image.revision="8a4877920fc79009dcb1e4bb16674b3b441c75ab" + ---> Running in c4410d3a7c78 + Removing intermediate container c4410d3a7c78 + ---> 1a57a0d9a7e5 + Step 7/7 : LABEL org.opencontainers.image.version="test_nGvjdE" + ---> Running in 81d7a66aa40a + Removing intermediate container 81d7a66aa40a + ---> 9d84592b1c1e + Successfully built 9d84592b1c1e + Successfully tagged ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo7865291233056269818/test_generic_test/test_executable + +/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/test_generic_test/test_executable >> Running script as test >> Checking whether output file exists >> Reading h5ad files - input_test: AnnData object with n_obs × n_vars = 307 × 443 + input_test: AnnData object with n_obs × n_vars = 130 × 443 obs: 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling' - output: AnnData object with n_obs × n_vars = 307 × 443 + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' + output: AnnData object with n_obs × n_vars = 130 × 443 obs: 'batch', 'label_pred' - uns: 'dataset_id', 'method_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'method_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' >> Checking whether predictions were added Checking whether data from input was copied properly to output All checks succeeded! @@ -472,57 +471,60 @@ all of the required output slots. bin/viash test src/label_projection/methods/foo/config.vsh.yaml ``` - Warning: Config inheritance (__merge__) is an experimental feature. Changes to the API are expected. - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789' + Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128' ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'label_projection/methods_foo:test_5q5NGA' with Dockerfile - [info] Running 'docker build -t label_projection/methods_foo:test_5q5NGA /home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/build_executable/tmp/dockerbuild-foo-GRvLt9/Dockerfile' - Sending build context to Docker daemon 37.89kB + +/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh' with Dockerfile + [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh /home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable/tmp/dockerbuild-foo-VUcsWQ/Dockerfile' + Sending build context to Docker daemon 39.94kB Step 1/7 : FROM python:3.10 - ---> ecbdd6bafdb5 + ---> 465483cdaa4e Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" ---> Using cache - ---> f1fbd09c8ccd + ---> 91f658ec0590 Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" ---> Using cache - ---> 063049300b14 - Step 4/7 : LABEL org.opencontainers.image.created="2022-11-17T07:38:03+01:00" - ---> Running in 2211c2f3d253 - Removing intermediate container 2211c2f3d253 - ---> 4a7607ecb7b4 - Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2.git" - ---> Running in 21c85f7d64bc - Removing intermediate container 21c85f7d64bc - ---> ad15f8b03066 - Step 6/7 : LABEL org.opencontainers.image.revision="8f9371ddfa5f5c20df01612342040a2003274da3" - ---> Running in 94c15d5c9736 - Removing intermediate container 94c15d5c9736 - ---> 423d9a6d04e2 - Step 7/7 : LABEL org.opencontainers.image.version="test_5q5NGA" - ---> Running in d31d99d449ef - Removing intermediate container d31d99d449ef - ---> 7f9635195fe8 - Successfully built 7f9635195fe8 - Successfully tagged label_projection/methods_foo:test_5q5NGA + ---> f1ace85a71b0 + Step 4/7 : LABEL org.opencontainers.image.created="2022-12-17T08:47:52+01:00" + ---> Running in ae1e366b6410 + Removing intermediate container ae1e366b6410 + ---> 458c1b49e8b4 + Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2" + ---> Running in 06a244e7be1e + Removing intermediate container 06a244e7be1e + ---> cc48147df9e8 + Step 6/7 : LABEL org.opencontainers.image.revision="8a4877920fc79009dcb1e4bb16674b3b441c75ab" + ---> Running in 2372d2bddd3d + Removing intermediate container 2372d2bddd3d + ---> 7bcad47b5d1b + Step 7/7 : LABEL org.opencontainers.image.version="test_lnevgh" + ---> Running in 6499fcfa63af + Removing intermediate container 6499fcfa63af + ---> 2213de86e5bc + Successfully built 2213de86e5bc + Successfully tagged ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/test_generic_test/test_executable + +/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/test_generic_test/test_executable Traceback (most recent call last): >> Running script as test - File "/viash_automount/home/rcannood/workspace/viash_temp/viash_test_foo15779522933199950789/test_generic_test/tmp//viash-run-foo-j6Jfba", line 56, in >> Checking whether output file exists - assert "label_pred" in output.obs + File "/viash_automount/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/test_generic_test/tmp//viash-run-foo-BVsf0m.py", line 57, in >> Reading h5ad files + assert "label_pred" in output.obs + input_test: AnnData object with n_obs × n_vars = 130 × 443 AssertionError - input_test: AnnData object with n_obs × n_vars = 307 × 443 obs: 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling' - output: AnnData object with n_obs × n_vars = 307 × 443 + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' + output: AnnData object with n_obs × n_vars = 130 × 443 obs: 'batch' - uns: 'dataset_id' - layers: 'counts', 'log_cpm', 'log_scran_pooling' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' >> Checking whether predictions were added ==================================================================== ERROR! Only 0 out of 1 test scripts succeeded! @@ -530,12 +532,12 @@ bin/viash test src/label_projection/methods/foo/config.vsh.yaml create an issue at https://github.com/viash-io/viash/issues containing a reproducible example and the stack trace below. - viash - 0.6.3 + viash - 0.6.6 Stacktrace: java.lang.RuntimeException: Only 0 out of 1 test scripts succeeded! - at io.viash.ViashTest$.apply(ViashTest.scala:110) - at io.viash.Main$.internalMain(Main.scala:99) - at io.viash.Main$.main(Main.scala:39) + at io.viash.ViashTest$.apply(ViashTest.scala:111) + at io.viash.Main$.internalMain(Main.scala:185) + at io.viash.Main$.main(Main.scala:77) at io.viash.Main.main(Main.scala) ## More information diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index ef04dd6158..c543f4732c 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -29,23 +29,25 @@ To use this repository, please install the following dependencies: The `src/` folder contains modular software components for running a modality alignment benchmark. Running the full pipeline is quite easy. -**Step 0, fetch viash and nextflow:** run the `bin/init` executable. +**Step 0, fetch Viash and Nextflow** ```bash -bin/init +mkdir $HOME/bin +curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false +curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin ``` - > Using tag develop - > Cleanup - > Downloading Viash source code @develop - > Building Viash from source - > Building Viash helper scripts from source - > Done, happy viash-ing! +Make sure that Viash and Nextflow are on the $PATH by checking whether the following commands work: + +```{bash} +viash -v +nextflow -v +``` **Step 1, download test resources:** by running the following command. ```bash -bin/viash run src/common/sync_test_resources/config.vsh.yaml +viash run src/common/sync_test_resources/config.vsh.yaml ``` Completed 256.0 KiB/7.2 MiB (302.6 KiB/s) with 6 file(s) remaining @@ -58,7 +60,7 @@ bin/viash run src/common/sync_test_resources/config.vsh.yaml **Step 2, build all the components:** in the `src/` folder as standalone executables in the `target/` folder. Use the `-q 'xxx'` parameter to build a subset of components in the repository. ```bash -bin/viash ns build -q 'label_projection|common' --parallel +viash ns build --query 'label_projection|common' --parallel --setup cachedbuild ``` In development mode with 'dev'. @@ -70,7 +72,11 @@ bin/viash ns build -q 'label_projection|common' --parallel [notice] Building container 'label_projection/metrics_accuracy:dev' with Dockerfile ... -These standalone executables you can give to somebody else, and they will be able to run it, provided that they have Bash and Docker installed. +Viash will build a whole namespace (`ns`) into executables and Nextflow pipelines into the `target/docker` and `target/nextflow` folders respectively. +By adding the `-q/--query` flag, you can filter which components to build using a regex. +By adding the `--parallel` flag, these components are built in parallel (otherwise it will take a really long time). +The flag `--setup cachedbuild` will automatically start building Docker containers for each of these methods. + The command might take a while to run, since it is building a docker container for each of the components. **Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/label_projection/workflows/run_nextflow.sh`: @@ -80,73 +86,60 @@ src/label_projection/workflows/run/run_test.sh ``` N E X T F L O W ~ version 22.04.5 - Launching `src/label_projection/workflows/run/main.nf` [small_becquerel] DSL2 - revision: ece87259df - executor > local (19) - [39/e1bb01] process > run_wf:true_labels:true_labels_process (1) [100%] 1 of 1 ✔ - [3b/d41f8a] process > run_wf:random_labels:random_labels_process (1) [100%] 1 of 1 ✔ - [c2/0398dd] process > run_wf:majority_vote:majority_vote_process (1) [100%] 1 of 1 ✔ - [fd/92edc7] process > run_wf:knn:knn_process (1) [100%] 1 of 1 ✔ - [f7/7cdb34] process > run_wf:logistic_regression:logistic_regression_process (1) [100%] 1 of 1 ✔ - [4f/6a67e4] process > run_wf:mlp:mlp_process (1) [100%] 1 of 1 ✔ - [a5/ae6341] process > run_wf:accuracy:accuracy_process (6) [100%] 6 of 6 ✔ - [72/5076e8] process > run_wf:f1:f1_process (6) [100%] 6 of 6 ✔ - [cf/eccd48] process > run_wf:extract_scores:extract_scores_process [100%] 1 of 1 ✔ + Launching `src/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 + executor > local (28) + [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ + [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ + [15/f0a427] process > run_wf:run_methods:random_labels:random_labels_process (pancreas.random_labels) [100%] 1 of 1 ✔ + [02/969d05] process > run_wf:run_methods:knn:knn_process (pancreas.knn) [100%] 1 of 1 ✔ + [90/5fdf9a] process > run_wf:run_methods:mlp:mlp_process (pancreas.mlp) [100%] 1 of 1 ✔ + [c7/dee2e5] process > run_wf:run_methods:logistic_regression:logistic_regression_process (pancreas.logistic_regression) [100%] 1 of 1 ✔ + [83/3ba0c9] process > run_wf:run_methods:scanvi:scanvi_process (pancreas.scanvi) [100%] 1 of 1 ✔ + [e3/2c298e] process > run_wf:run_methods:seurat_transferdata:seurat_transferdata_process (pancreas.seurat_transferdata) [100%] 1 of 1 ✔ + [d6/7212ab] process > run_wf:run_methods:xgboost:xgboost_process (pancreas.xgboost) [100%] 1 of 1 ✔ + [b6/7dc1a7] process > run_wf:run_metrics:accuracy:accuracy_process (pancreas.scanvi) [100%] 9 of 9 ✔ + [be/7d4da4] process > run_wf:run_metrics:f1:f1_process (pancreas.scanvi) [100%] 9 of 9 ✔ + [89/dcd77a] process > run_wf:aggregate_results:extract_scores:extract_scores_process (combined) [100%] 1 of 1 ✔ ## Project structure +High level overview: . ├── bin Helper scripts for building the project and developing a new component. ├── resources_test Datasets for testing components. If you don't have this folder, run **Step 1** above. ├── src Source files for each component in the pipeline. │ ├── common Common processing components. - │ ├── datasets Components for ingesting datasets from a source. + │ ├── datasets Components and pipelines for building the 'Common datasets' │ ├── label_projection Source files related to the 'Label projection' task. │ └── ... Other tasks. └── target Executables generated by viash based on the components listed under `src/`. ├── docker Bash executables which can be used from a terminal. └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. - - bin/ Helper scripts for building the project and developing a new component. - resources_test/ Datasets for testing components. - src/ Source files for each component in the pipeline. - common/ Common processing components. - datasets/ Components related to ingesting datasets into OpenProblems v2. - api/ Specs for the data loaders and normalisation methods. - loaders/ Components for ingesting datasets from a source. - normalization/ Common normalization methods. - label_projection/ Source files related to the 'Label projection' task. - datasets/ Dataset downloader components. - methods/ Modality alignment method components. - metrics/ Modality alignment metric components. - utils/ Utils functions. - workflow/ The pipeline workflow for this task. - target/ Executables generated by viash based on the components listed under `src/`. - docker/ Bash executables which can be used from a terminal. - nextflow/ Nextflow modules which can be used in a Nextflow pipeline. - work/ A working directory used by Nextflow. - output/ Output generated by the pipeline. - -The `src/datasets` folder - -src/datasets/ -├── api Specs for the data loaders and normalisation methods. -├── loaders Components for ingesting datasets from a source. -├── normalization Common normalization methods. -├── resource_test_scripts Scripts for generating the objects in the `resources_test` folder. -└── workflows A set of Nextflow workflows which tie together various components. - -The `src/label_projection` folder - -src/label_projection/ -├── api Specs for the split_dataset, methods and metrics in this task. -├── control_methods Positive and negative control methods for quality control. -├── methods Method components. -├── metrics Metric components. -├── [README.md](src/label_projection/) More information on how this task works. -├── resources_test_scripts Scripts for generating the objects in the `resources_test` folder. -├── split_dataset A component for splitting a common dataset into a `train`, `test` and `solution` object. -└── workflows A set of Nextflow workflows which tie together various components. +Detailed overview of a task folder (e.g. `src/label_projection`): + + src/label_projection/ + ├── api Specs for the components in this task. + ├── control_methods Control methods which serve as quality control checks for the benchmark. + ├── docs Task documentation + ├── methods Label projection method components. + ├── metrics Label projection metric components. + ├── resources_scripts The scripts needed to run the benchmark. + ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). + ├── split_dataset A component that masks a common dataset for use in the benchmark + └── workflows The benchmarking workflow. + + +Detailed overview of the `src/datasets` folder: + + src/datasets/ + ├── api Specs for the data loaders and normalisation methods. + ├── loaders Components for ingesting datasets from a source. + ├── normalization Normalization method components. + ├── processors Other preprocessing components (e.g. HVG and PCA). + ├── resource_scripts The scripts needed to generate the common datasets. + ├── resource_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). + └── workflows The workflow which generates the common datasets. ## Adding a Viash component From ad8299e18af9d58c0b5ea4303a82b2905b90a0bd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 17 Dec 2022 08:49:01 +0100 Subject: [PATCH 0598/1233] add back run_test script Former-commit-id: b1f57c49b7bf8596ccb574712f64c13eb5ae7f85 --- .../workflows/run/run_test.sh | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100755 src/label_projection/workflows/run/run_test.sh diff --git a/src/label_projection/workflows/run/run_test.sh b/src/label_projection/workflows/run/run_test.sh new file mode 100755 index 0000000000..9b022e62b3 --- /dev/null +++ b/src/label_projection/workflows/run/run_test.sh @@ -0,0 +1,35 @@ +#!/bin/bash +# +#make sure the following command has been executed +#bin/viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/label_projection/pancreas + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +# run benchmark +export NXF_VER=22.04.5 + +bin/nextflow \ + run . \ + -main-script src/label_projection/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ + --input_train $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output scores.tsv \ + --publish_dir output/ \ No newline at end of file From 1d1e34ae4ad2381d31f902cf3eaf66e63873fafb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 15:59:59 +0100 Subject: [PATCH 0599/1233] print pretty json Former-commit-id: 00d25ea74a3e3705b3264726f7796db421495dc4 --- src/common/get_api_info/script.R | 7 ++++++- src/common/get_method_info/script.R | 7 ++++++- src/common/get_metric_info/script.R | 7 ++++++- src/common/get_results/script.R | 7 ++++++- 4 files changed, 24 insertions(+), 4 deletions(-) diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index 7bacbf010c..da5535c260 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -68,4 +68,9 @@ out <- list( file_schema = purrr::transpose(file_slot) ) -jsonlite::write_json(purrr::transpose(out), par$output, auto_unbox = TRUE) +jsonlite::write_json( + out, + par$output, + auto_unbox = TRUE, + pretty = TRUE +) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 0909f5e566..ffdc3f6bf8 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -26,4 +26,9 @@ df <- map_df(configs, function(config) { }) %>% select(id, type, label, everything()) -jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file +jsonlite::write_json( + purrr::transpose(df), + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 659def459b..6271d3a43f 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -28,4 +28,9 @@ df <- map_df(configs, function(config) { }) %>% select(id, everything()) -jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file +jsonlite::write_json( + purrr::transpose(df), + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file diff --git a/src/common/get_results/script.R b/src/common/get_results/script.R index 87547acee9..5e8c253834 100644 --- a/src/common/get_results/script.R +++ b/src/common/get_results/script.R @@ -38,4 +38,9 @@ execution_info <- nxf_log %>% df <- full_join(raw_scores, execution_info, by = c("method_id", "dataset_id")) -jsonlite::write_json(purrr::transpose(df), par$output, auto_unbox = TRUE) \ No newline at end of file +jsonlite::write_json( + purrr::transpose(df), + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file From f16f2f7e549d419841f3231b7ce60ca82ad1591a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 16:01:44 +0100 Subject: [PATCH 0600/1233] temporarily add native platforms Former-commit-id: 833aa241397e44a39a4e22fc17abdf239a3be6e7 --- src/common/check_migration_status/config.vsh.yaml | 1 + src/common/get_api_info/config.vsh.yaml | 1 + src/common/get_method_info/config.vsh.yaml | 1 + src/common/get_metric_info/config.vsh.yaml | 1 + src/common/get_results/config.vsh.yaml | 1 + src/common/list_git_shas/config.vsh.yaml | 3 ++- 6 files changed, 7 insertions(+), 1 deletion(-) diff --git a/src/common/check_migration_status/config.vsh.yaml b/src/common/check_migration_status/config.vsh.yaml index a89e338fad..93cbb77097 100644 --- a/src/common/check_migration_status/config.vsh.yaml +++ b/src/common/check_migration_status/config.vsh.yaml @@ -31,3 +31,4 @@ platforms: pip: - pyyaml - type: nextflow + - type: native diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index ad343bec05..4e65b2ffd9 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -30,3 +30,4 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: nextflow + - type: native diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 4ea7fbb405..ba1a940ce8 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -34,3 +34,4 @@ platforms: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - type: nextflow + - type: native diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 695cb715a1..6f6796aa6b 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -34,3 +34,4 @@ platforms: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - type: nextflow + - type: native diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 155fcffe24..46838779ba 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -31,3 +31,4 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: nextflow + - type: native diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/common/list_git_shas/config.vsh.yaml index 5b2a7aaec6..233c8099f4 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/common/list_git_shas/config.vsh.yaml @@ -36,4 +36,5 @@ platforms: test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - - type: nextflow \ No newline at end of file + - type: nextflow + - type: native \ No newline at end of file From 3a0824a2fa7312ad05779d9fa583195fa37c6177 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 16:02:22 +0100 Subject: [PATCH 0601/1233] add temporary helper script Former-commit-id: 3f944322fe47835377a2497edeac3d00bd4aa1ac --- src/common/collect_data/script.sh | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100755 src/common/collect_data/script.sh diff --git a/src/common/collect_data/script.sh b/src/common/collect_data/script.sh new file mode 100755 index 0000000000..28fc46b1d6 --- /dev/null +++ b/src/common/collect_data/script.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +# task_id="label_projection" +# task_id="dimensionality_reduction" +# task_id="denoising" + +# run a couple of components to generate experimental website view + +for task_id in label_projection dimensionality_reduction denoising; do + out_dir="../website-experimental/results_v2/$task_id/data" + + mkdir -p $out_dir + + viash run src/common/get_method_info/config.vsh.yaml -p native -- \ + --input "src/$task_id" \ + --output "$out_dir/method_info.json" + viash run src/common/get_metric_info/config.vsh.yaml -p native -- \ + --input "src/$task_id" \ + --output "$out_dir/metric_info.json" + viash run src/common/get_results/config.vsh.yaml -p native -- \ + --input_scores "resources/$task_id/benchmarks/openproblems_v1/combined.extract_scores.output.tsv" \ + --input_execution "resources/$task_id/benchmarks/openproblems_v1/nextflow_log.tsv" \ + --output "$out_dir/results.json" + viash run src/common/get_api_info/config.vsh.yaml -p native -- \ + --input "src/$task_id" \ + --output "$out_dir/api.json" +done \ No newline at end of file From ef43f1c106b7f8085f40f9da4439d6a2ddd78605 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 20:42:21 +0100 Subject: [PATCH 0602/1233] add indents Former-commit-id: b4784d422d374d439c95e5b7edf701efe7f46d5d --- src/common/check_migration_status/script.py | 2 +- src/common/list_git_shas/script.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py index eef9aab8f7..532f48ecb2 100644 --- a/src/common/check_migration_status/script.py +++ b/src/common/check_migration_status/script.py @@ -49,4 +49,4 @@ def check_status(comp_item: Dict[str, str], git_objects: List[Dict[str, str]]) - # write to file with open(par['output'], 'w') as outf: - json.dump(output, outf) + json.dump(output, outf, indent=2) diff --git a/src/common/list_git_shas/script.py b/src/common/list_git_shas/script.py index 28c7c0d4ef..46c56990e8 100644 --- a/src/common/list_git_shas/script.py +++ b/src/common/list_git_shas/script.py @@ -55,7 +55,7 @@ def get_git_file_info(file, full_history=False): output.append(out) with open(par['output'], 'w') as f: - json.dump(output, f) + json.dump(output, f, indent=2) From 8ce31b6f4ffc8019508fd77b80f7ffa1dc3223ee Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 20:43:00 +0100 Subject: [PATCH 0603/1233] remove extra / Former-commit-id: e5274e3dd523c2e9ad35eb8cc9846a884f872497 --- src/denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- src/denoising/control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 2 +- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/denoising/methods/magic/config.vsh.yaml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index c4b23f3638..91374fa5d3 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -6,7 +6,7 @@ functionality: info: type: negative_control label: no denoising - v1_url: /openproblems/tasks/denoising/methods/baseline.py + v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c v1_comp_id: no_denoising preferred_normalization: counts diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index de14b2b360..9673d97737 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -6,7 +6,7 @@ functionality: info: type: positive_control label: perfect denoising - v1_url: /openproblems/tasks/denoising/methods/baseline.py + v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c v1_comp_id: perfect_denoising preferred_normalization: counts diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 5f79048e7d..bbded04a44 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: paper_doi: "10.1101/397588" code_url: "https://github.com/KlugerLab/ALRA" doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md - v1_url: /openproblems/tasks/denoising/methods/alra.py + v1_url: openproblems/tasks/denoising/methods/alra.py v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa v1_comp_id: "alra" preferred_normalization: counts diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index c29edfb36f..b580521254 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # paper_year: 2019 paper_doi: "10.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" - v1_url: /openproblems/tasks/denoising/methods/dca.py + v1_url: openproblems/tasks/denoising/methods/dca.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a v1_comp_id: "dca" preferred_normalization: counts diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 263a92c5c2..58643f86b9 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # paper_year: 2018 paper_doi: "10.1101/217737" code_url: "https://github.com/yanailab/knn-smoothing" - v1_url: /openproblems/tasks/denoising/methods/knn_smoothing.py + v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py v1_commit: bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1 v1_comp_id: "knn_smoothing" preferred_normalization: counts diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 5131d80a99..ce2a97cd3b 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # paper_year: 2018 paper_doi: "10.1016/j.cell.2018.05.061" code_url: "https://github.com/KrishnaswamyLab/MAGIC" - v1_url: /openproblems/tasks/denoising/methods/magic.py + v1_url: openproblems/tasks/denoising/methods/magic.py v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e v1_comp_id: "magic" preferred_normalization: counts From dee4cb92a69eb70f17899636266bad6c72ea024e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 19 Dec 2022 20:43:08 +0100 Subject: [PATCH 0604/1233] update script Former-commit-id: a1b91154fc7cf0a6f218d3b2890cdb2f29bf9613 --- src/common/collect_data/script.sh | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/src/common/collect_data/script.sh b/src/common/collect_data/script.sh index 28fc46b1d6..85554b743c 100755 --- a/src/common/collect_data/script.sh +++ b/src/common/collect_data/script.sh @@ -1,26 +1,48 @@ #!/bin/bash -# task_id="label_projection" -# task_id="dimensionality_reduction" -# task_id="denoising" + # run a couple of components to generate experimental website view +viash run src/common/list_git_shas/config.vsh.yaml -p native -- \ + --input "../openproblems/" \ + --output "openproblems_git.json" + +# task_id="label_projection" +# task_id="dimensionality_reduction" +# task_id="denoising" for task_id in label_projection dimensionality_reduction denoising; do out_dir="../website-experimental/results_v2/$task_id/data" mkdir -p $out_dir + # generate method info viash run src/common/get_method_info/config.vsh.yaml -p native -- \ --input "src/$task_id" \ + --output "$out_dir/temp_method_info.json" + viash run src/common/check_migration_status/config.vsh.yaml -p native -- \ + --git_sha "openproblems_git.json" \ + --comp_info "$out_dir/temp_method_info.json" \ --output "$out_dir/method_info.json" + rm "$out_dir/temp_method_info.json" + + # generate metric info viash run src/common/get_metric_info/config.vsh.yaml -p native -- \ --input "src/$task_id" \ + --output "$out_dir/temp_metric_info.json" + viash run src/common/check_migration_status/config.vsh.yaml -p native -- \ + --git_sha "openproblems_git.json" \ + --comp_info "$out_dir/temp_metric_info.json" \ --output "$out_dir/metric_info.json" + rm "$out_dir/temp_metric_info.json" + + # generate results viash run src/common/get_results/config.vsh.yaml -p native -- \ --input_scores "resources/$task_id/benchmarks/openproblems_v1/combined.extract_scores.output.tsv" \ --input_execution "resources/$task_id/benchmarks/openproblems_v1/nextflow_log.tsv" \ --output "$out_dir/results.json" + + # generate api info viash run src/common/get_api_info/config.vsh.yaml -p native -- \ --input "src/$task_id" \ --output "$out_dir/api.json" From e44a0ca22ad8fbfac26a8ae2b7a78fd65399afe1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Dec 2022 21:29:08 +0000 Subject: [PATCH 0605/1233] Bump tj-actions/changed-files from 34.6.2 to 35.1.0 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 34.6.2 to 35.1.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v34.6.2...v35.1.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Former-commit-id: 0b5097287279baaf3352d300966e19aaa60186d6 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f474abf8b2..98d4119535 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v34.6.2 + uses: tj-actions/changed-files@v35.1.0 with: separator: ";" diff_relative: true From 37b99aae8915dc17c06dc20ef46706fa03778439 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 20 Dec 2022 16:22:07 +0100 Subject: [PATCH 0606/1233] add task_meta resource script Former-commit-id: bab22d4dac915aeaa671adaf944fb36ba7eb503a --- src/common/check_migration_status/script.py | 6 +- src/common/check_migration_status/test.py | 4 +- .../resources_test_scripts/task_metadata.sh | 118 ++++++++++++++++++ 3 files changed, 123 insertions(+), 5 deletions(-) create mode 100644 src/common/resources_test_scripts/task_metadata.sh diff --git a/src/common/check_migration_status/script.py b/src/common/check_migration_status/script.py index 532f48ecb2..30118d7fdd 100644 --- a/src/common/check_migration_status/script.py +++ b/src/common/check_migration_status/script.py @@ -4,12 +4,12 @@ ## VIASH START par = { 'git_sha': 'temp/openproblems-v1.json', - 'comp_info': 'temp/denoising_metrics.yaml', - 'output': 'temp/migration_status.yaml' + 'comp_info': 'temp/denoising_metrics.json', + 'output': 'temp/migration_status.json' } ## VIASH END -def check_status(comp_item: Dict[str, str], git_objects: List[Dict[str, str]]) -> str: +def check_status(comp_item: List[Dict[str, str]], git_objects: List[Dict[str, str]]) -> str: """Looks for the comp_item's matching git_object based on the comp_item["v1_url"] and git_object["path"]. If found, checks whether the comp_item["v1_commit"] equals diff --git a/src/common/check_migration_status/test.py b/src/common/check_migration_status/test.py index 8864e1339b..8ea161324e 100644 --- a/src/common/check_migration_status/test.py +++ b/src/common/check_migration_status/test.py @@ -2,8 +2,8 @@ from os import path import json -input_sha = meta["resources_dir"] + "resources_test/common/input_git_sha.json" -input_method_info = meta["resources_dir"] + "resources_test/common/method_info.json" +input_sha = meta["resources_dir"] + "resources_test/common/task_metadata/input_git_sha.json" +input_method_info = meta["resources_dir"] + "resources_test/common/task_metadata/method_info.json" output_path = "output.json" cmd = [ diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh new file mode 100644 index 0000000000..4a148ab1d3 --- /dev/null +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -0,0 +1,118 @@ +#!/bin/bash + +# make sure folloewing command has been executed +# viash ns build -q 'common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +OUTPUT_DIR="resources_test/common/task_metadata" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +sha_file="$OUTPUT_DIR/input_git_sha.json" + +cat < $sha_file +[ + { + "path": "tasks/denoising/README.md", + "last_modified": "2022-09-20 14:26:51 -0400", + "sha": "3fe9251ba906061b6769eed2ac9da0db5f8e26bb" + }, + { + "path": "tasks/denoising/__init__.py", + "last_modified": "2022-09-30 14:49:17 +0200", + "sha": "c97decf07adb2e3050561d6fa9ae46132be07bef" + }, + { + "path": "tasks/denoising/api.py", + "last_modified": "2022-10-21 13:56:15 -0400", + "sha": "b460ecb183328c857cbbf653488f522a4034a61c" + }, + { + "path": "tasks/denoising/datasets/__init__.py", + "last_modified": "2022-11-23 10:32:02 -0500", + "sha": "725ff0c46140aaa6bbded68646256f64bc63df6d" + }, + { + "path": "tasks/denoising/datasets/pancreas.py", + "last_modified": "2022-12-04 12:06:43 -0500", + "sha": "4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4" + }, + { + "path": "tasks/denoising/datasets/pbmc.py", + "last_modified": "2022-12-04 12:06:43 -0500", + "sha": "4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4" + }, + { + "path": "tasks/denoising/datasets/tabula_muris_senis.py", + "last_modified": "2022-12-04 12:06:43 -0500", + "sha": "4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4" + }, + { + "path": "tasks/denoising/datasets/utils.py", + "last_modified": "2022-11-15 17:19:16 -0500", + "sha": "c2470ce02e6f196267cec1c554ba7ae389c0956a" + }, + { + "path": "tasks/denoising/methods/__init__.py", + "last_modified": "2022-10-21 13:56:15 -0400", + "sha": "b460ecb183328c857cbbf653488f522a4034a61c" + }, + { + "path": "tasks/denoising/methods/alra.R", + "last_modified": "2022-05-16 15:10:42 -0400", + "sha": "ba06cf71b564eb23823a662341055dc5ac2be231" + }, + { + "path": "tasks/denoising/methods/alra.py", + "last_modified": "2022-07-25 12:29:34 -0400", + "sha": "411a416150ecabce25e1f59bde422a029d0a8baa" + }, + { + "path": "tasks/denoising/methods/baseline.py", + "last_modified": "2022-10-21 13:56:15 -0400", + "sha": "b460ecb183328c857cbbf653488f522a4034a61c" + }, + { + "path": "tasks/denoising/methods/dca.py", + "last_modified": "2022-12-01 15:38:21 -0500", + "sha": "aa2253779e9aa9cd178f54ac0f3b6ba521ecd59f" + }, + { + "path": "tasks/denoising/methods/knn_smoothing.py", + "last_modified": "2022-11-14 11:54:15 -0500", + "sha": "bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1" + }, + { + "path": "tasks/denoising/methods/magic.py", + "last_modified": "2022-11-14 11:57:35 -0500", + "sha": "2af9a4918ed3370859f71774558068961f6d22c6" + }, + { + "path": "tasks/denoising/metrics/__init__.py", + "last_modified": "2021-01-19 13:31:20 -0500", + "sha": "8e0600c516c392fa747137415b6a93b8af0f61d8" + }, + { + "path": "tasks/denoising/metrics/mse.py", + "last_modified": "2022-11-15 17:19:16 -0500", + "sha": "c2470ce02e6f196267cec1c554ba7ae389c0956a" + }, + { + "path": "tasks/denoising/metrics/poisson.py", + "last_modified": "2022-12-04 12:06:43 -0500", + "sha": "4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4" + } +] +EOT + + +bin/viash run src/common/get_method_info/config.vsh.yaml -- \ + --input "src/denoising" \ + --output $OUTPUT_DIR/"method_info.json" \ No newline at end of file From d209930f124f1989d4555a11df45abdf8aed168d Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 20 Dec 2022 16:34:22 +0100 Subject: [PATCH 0607/1233] fix get_api_info test Former-commit-id: e2b29a740af23fd827c56a9875156f121261366f --- src/common/get_api_info/test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/get_api_info/test.py b/src/common/get_api_info/test.py index 2bdc232d30..02309e7246 100644 --- a/src/common/get_api_info/test.py +++ b/src/common/get_api_info/test.py @@ -20,6 +20,6 @@ print(">> Reading json file") with open(output_path, 'r') as f: out = json.load(f) - print(out[0]) + print(out) print("All checks succeeded!") \ No newline at end of file From 0ac5733d92751e798122cf8fc1cf61a223ed6ecc Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 20 Dec 2022 16:35:00 +0100 Subject: [PATCH 0608/1233] add comments task_metadata Former-commit-id: 6cecd18761a3a78af7ee5bd6ab9d2337b15f02c5 --- src/common/resources_test_scripts/task_metadata.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index 4a148ab1d3..c1fca5185e 100644 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -15,6 +15,7 @@ if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi +# Create small git sha input file sha_file="$OUTPUT_DIR/input_git_sha.json" cat < $sha_file @@ -112,7 +113,7 @@ cat < $sha_file ] EOT - +# Create a method info json bin/viash run src/common/get_method_info/config.vsh.yaml -- \ --input "src/denoising" \ --output $OUTPUT_DIR/"method_info.json" \ No newline at end of file From 6215212db7fdebf4571383a7af684e560936cd13 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 20 Dec 2022 21:00:49 +0100 Subject: [PATCH 0609/1233] update input parameters Former-commit-id: 4af90f8a055328eba9432e03066eab0552c10f3b --- src/common/get_api_info/config.vsh.yaml | 6 +++++- src/common/get_api_info/script.R | 9 +++++---- src/common/get_method_info/config.vsh.yaml | 6 ++++-- src/common/get_method_info/script.R | 7 ++++--- src/common/get_metric_info/config.vsh.yaml | 7 +++++-- src/common/get_metric_info/script.R | 7 ++++--- 6 files changed, 27 insertions(+), 15 deletions(-) diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 4e65b2ffd9..54cb950a47 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -6,8 +6,12 @@ functionality: - name: "--input" type: "file" multiple: true - example: src/label_projection + example: src + description: "A source dir" + - name: "--query" + type: "file" description: "A task dir" + example: label_projection - name: "--output" type: "file" direction: "output" diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index da5535c260..1c3c0acda1 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -3,13 +3,14 @@ library(rlang) ## VIASH START par <- list( - input = "src/label_projection", - output = "resources/label_projection/output/api.json" + input = "src", + query = "label_projection", + output = "output/api.json" ) ## VIASH END -comp_yamls <- list.files(paste0(par$input, "/api"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste0(par$input, "/api"), pattern = "anndata_", full.names = TRUE) +comp_yamls <- list.files(paste(par$input, par$query, "api", sep = "/"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste(par$input, par$query, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) # list component - file args links comp_file <- map_df(comp_yamls, function(yaml_file) { diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index ba1a940ce8..b10334837f 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -5,9 +5,11 @@ functionality: arguments: - name: "--input" type: "file" - multiple: true - example: src/label_projection + example: src + - name: "--query" + type: "file" description: "A task dir" + example: label_projection - name: "--output" type: "file" direction: "output" diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index ffdc3f6bf8..28eb250cbb 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -3,14 +3,15 @@ library(rlang) ## VIASH START par <- list( - input = "src/label_projection", - output = "resources_test/common/method_info.json" + input = "src", + query = "label_projection", + output = "output/method_info.json" ) ## VIASH END ns_list <- processx::run( "viash", - c("ns", "list", "-q", "methods", "--src", "."), + c("ns", "list", "-q", "methods", "--src", par$query), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 6f6796aa6b..19fc6979ac 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -5,9 +5,12 @@ functionality: arguments: - name: "--input" type: "file" - multiple: true - example: src/label_projection + example: src + description: "A source dir" + - name: "--query" + type: "file" description: "A task dir" + example: label_projection - name: "--output" type: "file" direction: "output" diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 6271d3a43f..17cd07dc48 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -3,14 +3,15 @@ library(rlang) ## VIASH START par <- list( - input = "src/denoising", - output = "temp/denoising_metrics.json" + input = "src", + query = "label_projection", + output = "output/metrics.json" ) ## VIASH END ns_list <- processx::run( "viash", - c("ns", "list", "-q", "metrics", "--src", "."), + c("ns", "list", "-q", "metrics", "--src", par$query), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) From 715745282ffa5ffec50c1626197c76646be0ff55 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 21 Dec 2022 11:07:48 +0100 Subject: [PATCH 0610/1233] update tests Former-commit-id: 17d0ade956318529a5d34362ad3713cd5504d18e --- src/common/get_api_info/config.vsh.yaml | 2 +- src/common/get_api_info/test.py | 4 +++- src/common/get_method_info/config.vsh.yaml | 2 +- src/common/get_method_info/test.py | 4 +++- src/common/get_metric_info/config.vsh.yaml | 2 +- src/common/get_metric_info/test.py | 4 +++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 54cb950a47..819cbf7b47 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: example: src description: "A source dir" - name: "--query" - type: "file" + type: "string" description: "A task dir" example: label_projection - name: "--output" diff --git a/src/common/get_api_info/test.py b/src/common/get_api_info/test.py index 02309e7246..e0f8ee6305 100644 --- a/src/common/get_api_info/test.py +++ b/src/common/get_api_info/test.py @@ -2,12 +2,14 @@ from os import path import json -input_path = meta["resources_dir"] + "src/label_projection" +input_path = meta["resources_dir"] + "src" +query = "denoising" output_path = "output.json" cmd = [ meta['executable'], "--input", input_path, + "--query", query, "--output", output_path, ] diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index b10334837f..83c10c4253 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: type: "file" example: src - name: "--query" - type: "file" + type: "string" description: "A task dir" example: label_projection - name: "--output" diff --git a/src/common/get_method_info/test.py b/src/common/get_method_info/test.py index 2bdc232d30..58ac7e462c 100644 --- a/src/common/get_method_info/test.py +++ b/src/common/get_method_info/test.py @@ -2,12 +2,14 @@ from os import path import json -input_path = meta["resources_dir"] + "src/label_projection" +input_path = meta["resources_dir"] + "src" +query = "label_projection" output_path = "output.json" cmd = [ meta['executable'], "--input", input_path, + "--query", query, "--output", output_path, ] diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 19fc6979ac..ac481e3964 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: example: src description: "A source dir" - name: "--query" - type: "file" + type: "string" description: "A task dir" example: label_projection - name: "--output" diff --git a/src/common/get_metric_info/test.py b/src/common/get_metric_info/test.py index 0756fbd034..55fc7d72c1 100644 --- a/src/common/get_metric_info/test.py +++ b/src/common/get_metric_info/test.py @@ -2,12 +2,14 @@ from os import path import json -input_path = meta["resources_dir"] + "src/label_projection" +input_path = meta["resources_dir"] + "src" +query = "label_projection" output_path = "output.json" cmd = [ meta['executable'], "--input", input_path, + "--query", query, "--output", output_path, ] From fdd6cdfef32b422afd1e1c6b937449191b914480 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 21 Dec 2022 15:01:40 +0100 Subject: [PATCH 0611/1233] add get_task_info component Former-commit-id: 0bbd335bb2a43368ac6316a17da69eb798d5af94 --- src/common/get_task_info/config.vsh.yaml | 33 +++++++++++++++++++++++ src/common/get_task_info/script.py | 24 +++++++++++++++++ src/common/get_task_info/test.py | 27 +++++++++++++++++++ src/denoising/README.qmd | 3 --- src/denoising/docs/task_description.md | 29 -------------------- src/denoising/docs/task_description.yaml | 34 ++++++++++++++++++++++++ 6 files changed, 118 insertions(+), 32 deletions(-) create mode 100644 src/common/get_task_info/config.vsh.yaml create mode 100644 src/common/get_task_info/script.py create mode 100644 src/common/get_task_info/test.py delete mode 100644 src/denoising/docs/task_description.md create mode 100644 src/denoising/docs/task_description.yaml diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml new file mode 100644 index 0000000000..feb0858d80 --- /dev/null +++ b/src/common/get_task_info/config.vsh.yaml @@ -0,0 +1,33 @@ +functionality: + name: "get_task_info" + namespace: "common" + description: "Extract task info" + arguments: + - name: "--input" + type: "file" + example: src + description: "A s dir" + - name: "--query" + type: "string" + description: "A task dir" + example: label_projection + - name: "--output" + type: "file" + direction: "output" + default: "output.json" + description: "Output json" + resources: + - type: python_script + path: script.py + test_resources: + - path: ../../../src + - type: python_script + path: test.py +platforms: + - type: docker + image: python:3.10 + setup: + - type: python + pip: [ pyyaml ] + - type: nextflow + - type: native diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py new file mode 100644 index 0000000000..7cda3324cb --- /dev/null +++ b/src/common/get_task_info/script.py @@ -0,0 +1,24 @@ +from os import path +from yaml import load, CSafeLoader +import json + +## VIASH START +par = { + "input" : "src", + "query" : "denoising", + "output": "output/task.json", + +} +meta = { "functionality" : "foo" } + +## VIASH END + +task_info_path = path.join(par['input'], par['query'], "docs", "task_description.yaml") + + + +with open(task_info_path, 'r') as f: + task_info = load(f, Loader=CSafeLoader ) + +with open(par["output"], 'w') as out: + json.dump(task_info, out, indent=2) \ No newline at end of file diff --git a/src/common/get_task_info/test.py b/src/common/get_task_info/test.py new file mode 100644 index 0000000000..dc9cbfa0b4 --- /dev/null +++ b/src/common/get_task_info/test.py @@ -0,0 +1,27 @@ +import subprocess +from os import path +import json + +input_path = meta["resources_dir"] + "src" +query = "denoising" +output_path = "output.json" + +cmd = [ + meta['executable'], + "--input", input_path, + "--query", query, + "--output", output_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading json file") +with open(output_path, 'r') as f: + out = json.load(f) + print(out) + +print("All checks succeeded!") diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd index 1b09f30ab8..6f6a01297f 100644 --- a/src/denoising/README.qmd +++ b/src/denoising/README.qmd @@ -1,8 +1,5 @@ --- format: gfm -info: - v1_url: openproblems/tasks/denoising/README.md - v1_commit: null # todo: fill in toc: true --- diff --git a/src/denoising/docs/task_description.md b/src/denoising/docs/task_description.md deleted file mode 100644 index e689702179..0000000000 --- a/src/denoising/docs/task_description.md +++ /dev/null @@ -1,29 +0,0 @@ -## The task - -Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present -in each cell. As a result, the measurements (UMI counts) observed for each gene and each -cell are associated with generally high levels of technical noise ([Grün et al., -2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes the task of -estimating the true expression level of each gene in each cell. In the single-cell -literature, this task is also referred to as *imputation*, a term which is typically -used for missing data problems in statistics. Similar to the use of the terms "dropout", -"missing data", and "technical zeros", this terminology can create confusion about the -underlying measurement process ([Sarkar and Stephens, -2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). - -A key challenge in evaluating denoising methods is the general lack of a ground truth. A -recent benchmark study ([Hou et al., -2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) -relied on flow-sorted datasets, mixture control experiments ([Tian et al., -2019](https://www.nature.com/articles/s41592-019-0425-8)), and comparisons with bulk -RNA-Seq data. Since each of these approaches suffers from specific limitations, it is -difficult to combine these different approaches into a single quantitative measure of -denoising accuracy. Here, we instead rely on an approach termed molecular -cross-validation (MCV), which was specifically developed to quantify denoising accuracy -in the absence of a ground truth ([Batson et al., -2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the observed molecules -in a given scRNA-Seq dataset are first partitioned between a *training* and a *test* -dataset. Next, a denoising method is applied to the training dataset. Finally, denoising -accuracy is measured by comparing the result to the test dataset. The authors show that -both in theory and in practice, the measured denoising accuracy is representative of the -accuracy that would be obtained on a ground truth dataset. diff --git a/src/denoising/docs/task_description.yaml b/src/denoising/docs/task_description.yaml new file mode 100644 index 0000000000..06ac023fb4 --- /dev/null +++ b/src/denoising/docs/task_description.yaml @@ -0,0 +1,34 @@ +info: + id: denoising + name: Denoising + v1_url: openproblems/tasks/denoising/README.md + v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb + short_description: Denoising describes the task of estimating the true expression level of each gene in each cell. + description: | + Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present + in each cell. As a result, the measurements (UMI counts) observed for each gene and each + cell are associated with generally high levels of technical noise ([Grün et al., + 2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes the task of + estimating the true expression level of each gene in each cell. In the single-cell + literature, this task is also referred to as *imputation*, a term which is typically + used for missing data problems in statistics. Similar to the use of the terms "dropout", + "missing data", and "technical zeros", this terminology can create confusion about the + underlying measurement process ([Sarkar and Stephens, + 2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). + + A key challenge in evaluating denoising methods is the general lack of a ground truth. A + recent benchmark study ([Hou et al., + 2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) + relied on flow-sorted datasets, mixture control experiments ([Tian et al., + 2019](https://www.nature.com/articles/s41592-019-0425-8)), and comparisons with bulk + RNA-Seq data. Since each of these approaches suffers from specific limitations, it is + difficult to combine these different approaches into a single quantitative measure of + denoising accuracy. Here, we instead rely on an approach termed molecular + cross-validation (MCV), which was specifically developed to quantify denoising accuracy + in the absence of a ground truth ([Batson et al., + 2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the observed molecules + in a given scRNA-Seq dataset are first partitioned between a *training* and a *test* + dataset. Next, a denoising method is applied to the training dataset. Finally, denoising + accuracy is measured by comparing the result to the test dataset. The authors show that + both in theory and in practice, the measured denoising accuracy is representative of the + accuracy that would be obtained on a ground truth dataset. From db162102c3375cfbd9da45a54f1cf6f0505741a7 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 21 Dec 2022 15:21:36 +0100 Subject: [PATCH 0612/1233] update collect_data script Former-commit-id: 945492aea7e8823a1428c8bc454c3ead3bf3df3f --- src/common/collect_data/script.sh | 29 ++++++++++++++++-------- src/denoising/docs/task_description.yaml | 4 ++-- 2 files changed, 21 insertions(+), 12 deletions(-) diff --git a/src/common/collect_data/script.sh b/src/common/collect_data/script.sh index 85554b743c..94d31e6555 100755 --- a/src/common/collect_data/script.sh +++ b/src/common/collect_data/script.sh @@ -4,7 +4,7 @@ # run a couple of components to generate experimental website view -viash run src/common/list_git_shas/config.vsh.yaml -p native -- \ +viash run src/common/list_git_shas/config.vsh.yaml -- \ --input "../openproblems/" \ --output "openproblems_git.json" @@ -16,34 +16,43 @@ for task_id in label_projection dimensionality_reduction denoising; do mkdir -p $out_dir + # generate task info + viash run src/common/get_task_info/config.vsh.yaml -- \ + --input "src" \ + --query $task_id \ + --output "$out_dir/task_info.json" + # generate method info - viash run src/common/get_method_info/config.vsh.yaml -p native -- \ - --input "src/$task_id" \ + viash run src/common/get_method_info/config.vsh.yaml -- \ + --input "src" \ + --query $task_id \ --output "$out_dir/temp_method_info.json" - viash run src/common/check_migration_status/config.vsh.yaml -p native -- \ + viash run src/common/check_migration_status/config.vsh.yaml -- \ --git_sha "openproblems_git.json" \ --comp_info "$out_dir/temp_method_info.json" \ --output "$out_dir/method_info.json" rm "$out_dir/temp_method_info.json" # generate metric info - viash run src/common/get_metric_info/config.vsh.yaml -p native -- \ - --input "src/$task_id" \ + viash run src/common/get_metric_info/config.vsh.yaml -- \ + --input "src" \ + --query $task_id \ --output "$out_dir/temp_metric_info.json" - viash run src/common/check_migration_status/config.vsh.yaml -p native -- \ + viash run src/common/check_migration_status/config.vsh.yaml -- \ --git_sha "openproblems_git.json" \ --comp_info "$out_dir/temp_metric_info.json" \ --output "$out_dir/metric_info.json" rm "$out_dir/temp_metric_info.json" # generate results - viash run src/common/get_results/config.vsh.yaml -p native -- \ + viash run src/common/get_results/config.vsh.yaml -- \ --input_scores "resources/$task_id/benchmarks/openproblems_v1/combined.extract_scores.output.tsv" \ --input_execution "resources/$task_id/benchmarks/openproblems_v1/nextflow_log.tsv" \ --output "$out_dir/results.json" # generate api info - viash run src/common/get_api_info/config.vsh.yaml -p native -- \ - --input "src/$task_id" \ + viash run src/common/get_api_info/config.vsh.yaml -- \ + --input "src" \ + --query $task_id \ --output "$out_dir/api.json" done \ No newline at end of file diff --git a/src/denoising/docs/task_description.yaml b/src/denoising/docs/task_description.yaml index 06ac023fb4..fe8caef82c 100644 --- a/src/denoising/docs/task_description.yaml +++ b/src/denoising/docs/task_description.yaml @@ -3,8 +3,8 @@ info: name: Denoising v1_url: openproblems/tasks/denoising/README.md v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb - short_description: Denoising describes the task of estimating the true expression level of each gene in each cell. - description: | + description: "Removing noise in sparse single-cell RNA-sequencing count data" + full_description: | Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present in each cell. As a result, the measurements (UMI counts) observed for each gene and each cell are associated with generally high levels of technical noise ([Grün et al., From 8872090648dec76c9d527549c7894cda12c45435 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 21 Dec 2022 15:31:54 +0100 Subject: [PATCH 0613/1233] update changelog Former-commit-id: 6b1d095f331155360e10310e65b97e06863ba775 --- CHANGELOG.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a55a57a969..d03456e7c6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,16 +15,15 @@ * `get_api_info`: extract api info from tasks -* `get_method_info`: extract method info vrom config yaml +* `get_method_info`: extract method info from config yaml -* `get_metric_info`: extract metric info vrom config yaml +* `get_metric_info`: extract metric info from config yaml * `check_migration_status`: compare git shas from methods with v1 * `get_results`: extract benchmark scores - - +* `get_task_info`: extract task info ## label_projection From 3d11e5fa22237a423c161b1cf8cbea0ba6d28443 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 21 Dec 2022 17:52:21 +0100 Subject: [PATCH 0614/1233] Add methods metadata (paper_doi, code_url, etc.) Former-commit-id: 0e42b68bed65167ec77721a2cdfa465cd4a254b9 --- .../control_methods/random_features/config.vsh.yaml | 4 ++++ .../control_methods/true_features/config.vsh.yaml | 4 ++++ .../methods/densmap/config.vsh.yaml | 2 ++ .../methods/neuralee/config.vsh.yaml | 2 ++ src/dimensionality_reduction/methods/pca/config.vsh.yaml | 4 +++- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 2 ++ src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 6 +++++- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 4 +++- 8 files changed, 25 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 2e29240797..c4d8bc766a 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -6,6 +6,10 @@ functionality: info: type: negative_control label: Random features + paper_name: "Random Features (baseline)" + paper_url: "https://openproblems.bio" + paper_year: 2022 + code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 2885f05972..96ce8fe1c2 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -6,6 +6,10 @@ functionality: info: type: positive_control label: True Features + paper_name: "True Features (baseline)" + paper_url: "https://openproblems.bio" + paper_year: 2022 + code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 0a92568bb7..54be143b64 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -6,6 +6,8 @@ functionality: info: type: method label: densMAP + paper_doi: "10.1038/s41587-020-00801-7" + code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index a50d0b9ebe..8116b4d92e 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -6,6 +6,8 @@ functionality: info: type: method label: NeuralEE + paper_doi: "10.3389/fgene.2020.00786" + code_url: https://github.com/HiBearME/NeuralEE v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 preferred_normalization: counts diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index e9ff24ce40..20b6722f9d 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -2,10 +2,12 @@ __merge__: ../../api/comp_method.yaml functionality: name: "pca" namespace: "dimensionality_reduction/methods" - description: "Principal component analysis" + description: "Principal component analysis (PCA)" info: type: method label: PCA + paper_doi: "10.1080/14786440109462720" + code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 06e87e6516..94d8c9965f 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -6,6 +6,8 @@ functionality: info: type: method label: PHATE + paper_doi: "10.1038/s41587-019-0336-3" + code_url: https://github.com/KrishnaswamyLab/PHATE/ v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 preferred_normalization: sqrt_cpm diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index f2615f751e..73518585d5 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -2,10 +2,14 @@ __merge__: ../../api/comp_method.yaml functionality: name: "tsne" namespace: "dimensionality_reduction/methods" - description: "t-distributed stochastic neighbor embedding" + description: "t-Distributed Stochastic Neighbor Embedding (t-SNE)" info: type: method label: t-SNE + paper_name: "Visualizing Data using t-SNE" + paper_url: "https://www.jmlr.org/papers/v9/vandermaaten08a.html" + paper_year: 2008 + code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 11f9a68ea2..2c68f8efe6 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -2,10 +2,12 @@ __merge__: ../../api/comp_method.yaml functionality: name: "umap" namespace: "dimensionality_reduction/methods" - description: "Uniform manifold approximation and projection" + description: "Uniform Manifold Approximation and Projection (UMAP) as implemented by scanpy" info: type: method label: UMAP + paper_doi: "10.21105/joss.00861" + code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm From eae48de1e12f3f91ae41ec70d8839a302d709776 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 22 Dec 2022 09:56:17 +0100 Subject: [PATCH 0615/1233] delete .obsm['X_umap'] Former-commit-id: 1942b49c8c5a2dd1c008523cdd8868132035b30c --- src/dimensionality_reduction/methods/umap/script.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index dd715fd5b6..8d2d63d0b4 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', + 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', 'output': 'reduced.h5ad', 'n_pca': 50, } @@ -30,6 +30,7 @@ print("Run UMAP") sc.tl.umap(input) input.obsm["X_emb"] = input.obsm["X_umap"].copy() +del input.obsm["X_umap"] print("Delete layers and var") del input.layers From 197eae8cf3e6c691ef954cb6dc3bd066b837f414 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 22 Dec 2022 11:31:27 +0100 Subject: [PATCH 0616/1233] Add v1_comp_id to all methods Former-commit-id: 89e1ae076d7177b31bfc9e3ee48426730762bba5 --- .../control_methods/random_features/config.vsh.yaml | 1 + .../control_methods/true_features/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/densmap/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/neuralee/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/pca/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/phate/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/umap/config.vsh.yaml | 1 + 8 files changed, 8 insertions(+) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index c4d8bc766a..9a65664c96 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -11,6 +11,7 @@ functionality: paper_year: 2022 code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py + v1_comp_id: "Random Features" v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts resources: diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 96ce8fe1c2..2e1d55fdca 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -11,6 +11,7 @@ functionality: paper_year: 2022 code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py + v1_comp_id: "True Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts arguments: diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 54be143b64..705be94bc1 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -9,6 +9,7 @@ functionality: paper_doi: "10.1038/s41587-020-00801-7" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py + v1_comp_id: "densMAP PCA (logCPM, 1kHVG)" v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm arguments: diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 8116b4d92e..91852abf6c 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -9,6 +9,7 @@ functionality: paper_doi: "10.3389/fgene.2020.00786" code_url: https://github.com/HiBearME/NeuralEE v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py + v1_comp_id: "NeuralEE (CPU) (Default)" v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 preferred_normalization: counts arguments: diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 20b6722f9d..1a16e28fef 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -9,6 +9,7 @@ functionality: paper_doi: "10.1080/14786440109462720" code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py + v1_comp_id: pca_logCPM_1kHVG v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm resources: diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 94d8c9965f..73a3ea3be9 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -9,6 +9,7 @@ functionality: paper_doi: "10.1038/s41587-019-0336-3" code_url: https://github.com/KrishnaswamyLab/PHATE/ v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py + v1_comp_id: "PHATE (default)" v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 preferred_normalization: sqrt_cpm arguments: diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 73518585d5..1e69dd6f0d 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -11,6 +11,7 @@ functionality: paper_year: 2008 code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py + v1_comp_id: tsne_logCPM_1kHVG v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm arguments: diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 2c68f8efe6..2cc564bd1c 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -9,6 +9,7 @@ functionality: paper_doi: "10.21105/joss.00861" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py + v1_comp_id: umap_logCPM_1kHVG v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm arguments: From 12726edac383b1e371b50f12847c17a6c7894b22 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 22 Dec 2022 11:32:08 +0100 Subject: [PATCH 0617/1233] Add task_description.yaml file instead of md Former-commit-id: 32759a19f32ab82ef621a485ea6b864bd64c9967 --- .../docs/task_description.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 src/dimensionality_reduction/docs/task_description.yaml diff --git a/src/dimensionality_reduction/docs/task_description.yaml b/src/dimensionality_reduction/docs/task_description.yaml new file mode 100644 index 0000000000..df074e1854 --- /dev/null +++ b/src/dimensionality_reduction/docs/task_description.yaml @@ -0,0 +1,10 @@ +info: + id: dimensionality_reduction + name: "Dimensionality reduction" + v1_url: openproblems/tasks/dimensionality_reduction/README.md + v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b + description: "Reduction of high-dimensional datasets to 2D for visualization &interpretation" + full_description: | + Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). + + Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file From fc1460bf11a376801603a18dcae16cceadf5c306 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 22 Dec 2022 11:40:37 +0100 Subject: [PATCH 0618/1233] fix magic method Former-commit-id: ee47b4d7f70d6e0e85250ee19c025b8a7a1ae4a1 --- src/denoising/methods/magic/config.vsh.yaml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index ce2a97cd3b..192c94c319 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -34,11 +34,7 @@ platforms: image: "python:3.10" setup: - type: python - packages: - - "anndata>=0.8" - - scprep - - magic-impute - - scipy + pip: [ "anndata>=0.8", scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: label: [ highmem, highcpu ] From decfd31d194287a90271c763429504308353af82 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 13:57:24 +0100 Subject: [PATCH 0619/1233] Add missing normalization_id to the api Former-commit-id: c3817ddcb0aca2e0852d5e9d6361e96e087549d0 --- src/dimensionality_reduction/api/anndata_test.yaml | 4 ++++ src/dimensionality_reduction/api/anndata_train.yaml | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/src/dimensionality_reduction/api/anndata_test.yaml b/src/dimensionality_reduction/api/anndata_test.yaml index e6f2e4b3d1..3454b7d87e 100644 --- a/src/dimensionality_reduction/api/anndata_test.yaml +++ b/src/dimensionality_reduction/api/anndata_test.yaml @@ -23,3 +23,7 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/dimensionality_reduction/api/anndata_train.yaml b/src/dimensionality_reduction/api/anndata_train.yaml index 458eaef906..7387d03ee0 100644 --- a/src/dimensionality_reduction/api/anndata_train.yaml +++ b/src/dimensionality_reduction/api/anndata_train.yaml @@ -23,3 +23,7 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true From b292382e829cee26c068deadbe19345919e46149 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 13:57:50 +0100 Subject: [PATCH 0620/1233] update viash start codeblock for debugging purposes Former-commit-id: 55a971cb0b0404370dcc0006aa28e0e3514fb1ab --- src/dimensionality_reduction/split_dataset/script.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/split_dataset/script.py index eb917de836..85ee6f5896 100644 --- a/src/dimensionality_reduction/split_dataset/script.py +++ b/src/dimensionality_reduction/split_dataset/script.py @@ -12,7 +12,8 @@ 'output_test': "test.h5ad", } meta = { - "functionality_name": "split_data" + "functionality_name": "split_data", + "config": "src/dimensionality_reduction/split_dataset/.config.vsh.yaml" } ## VIASH END From 11fb44ee7bd094542d06b45f441e580e5b560c43 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 14:07:37 +0100 Subject: [PATCH 0621/1233] add variants to phate Former-commit-id: 11475877bae6e421be8ec24962437969e88f4ac7 --- .../methods/phate/config.vsh.yaml | 19 ++++++-- .../methods/phate/script.py | 46 ++++++++----------- 2 files changed, 36 insertions(+), 29 deletions(-) diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 06e87e6516..666d62cc9e 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -9,14 +9,27 @@ functionality: v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 preferred_normalization: sqrt_cpm + variants: + phate: + phate_sqrt: + gamma: 0 + phate_logCPM_1kHVG: + num_hvg_genes: 1000 + preferred_normalization: log_cpm arguments: - name: '--n_pca' type: integer default: 50 description: Number of principal components of PCA to use. - - name: '--g0' - type: boolean_true - description: Set informational distance constant to 0. + - name: '--gamma' + type: double + description: Gamma value + default: 1 + - name: '--num_hvg_genes' + type: integer + description: | + Subset to the highly variable genes as specified + by the .var['hvg_score'] column. resources: - type: python_script path: script.py diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 2805dbc9a9..d6186b93da 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -1,14 +1,13 @@ import anndata as ad from phate import PHATE -import scprep as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', + 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', 'output': 'reduced.h5ad', 'n_pca': 50, - 'g0': False, + 'gamma': 1, + 'num_hvg_genes': None } meta = { 'functionality_name': 'phate', @@ -16,33 +15,28 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print("Run PHATE...") -gamma = 0 if par['g0'] else 1 -print('... with gamma=' + str(gamma) + ' and...') -phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=gamma) - -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] - -if input.uns['normalization_id'] == 'sqrt_cpm': - print('... using sqrt-CPM data') - input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) -elif input.uns['normalization_id'] == 'log_cpm': - print('... using logCPM data') - n_genes = 1000 - idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] - input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized'][:, idx]) - -print("Delete layers and var") +print("Run PHATE", flush=True) +phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=par['gamma']) +X_mat = input.layers['normalized'] + +if par["num_hvg_genes"]: + print("Subsetting to hvg genes", flush=True) + num_features = par["num_hvg_genes"] + hvg_idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:num_features] + X_mat = X_mat[:, hvg_idx] + +# store embedding +input.obsm["X_emb"] = phate_op.fit_transform(X_mat) + +print("Delete layers and var", flush=True) del input.layers del input.var -print('Add method') +print('Add method', flush=True) input.uns['method_id'] = meta['functionality_name'] -print("Write output to file") +print("Write output to file", flush=True) input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From aaea9c8bacfc947708a87d0d3fb5339bb105aff4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 14:37:03 +0100 Subject: [PATCH 0622/1233] add v2 variants Former-commit-id: 0ae87bd53bb883ba6a1a3ddedcdd7c2ab81bd245 --- .../control_methods/majority_vote/config.vsh.yaml | 3 ++- .../control_methods/random_labels/config.vsh.yaml | 3 ++- .../control_methods/true_labels/config.vsh.yaml | 3 ++- src/label_projection/methods/knn/config.vsh.yaml | 7 +++++-- .../methods/logistic_regression/config.vsh.yaml | 7 +++++-- src/label_projection/methods/mlp/config.vsh.yaml | 5 ++++- src/label_projection/methods/scanvi/config.vsh.yaml | 13 ++++++++----- src/label_projection/methods/scanvi/script.py | 9 +++++---- .../methods/seurat_transferdata/config.vsh.yaml | 3 ++- .../methods/xgboost/config.vsh.yaml | 5 ++++- 10 files changed, 39 insertions(+), 19 deletions(-) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index d02f178465..a3c5c9fbd8 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -8,7 +8,8 @@ functionality: label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - v1_comp_id: majority_vote + variants: + majority_vote: preferred_normalization: counts resources: - type: python_script diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 68a14bf3d3..b602fc6137 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -8,8 +8,9 @@ functionality: label: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - v1_comp_id: random_labels preferred_normalization: counts + variants: + random_labels: resources: - type: python_script path: script.py diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 6f21416029..4576b54483 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -8,8 +8,9 @@ functionality: label: True labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - v1_comp_id: true_labels preferred_normalization: counts + variants: + true_labels: resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 20605bfc8a..f73583c5de 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -13,9 +13,12 @@ functionality: code_url: https://github.com/scikit-learn/scikit-learn doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py - v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d - v1_comp_id: knn_classifier_log_cpm + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm + variants: + knn_classifier_log_cpm: + knn_classifier_scran: + preferred_normalization: log_scran_pooling resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 60e2498e08..6ec8d66bdd 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -12,9 +12,12 @@ functionality: code_url: https://github.com/scikit-learn/scikit-learn doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py - v1_commit: 2097bbb3e996f66e98128c9ac95bc9640a496e0d - v1_comp_id: logistic_regression_log_cpm + v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm + variants: + logistic_regression_log_cpm: + logistic_regression_scran: + preferred_normalization: log_scran_pooling resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 623be8e793..df5eab7516 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -14,8 +14,11 @@ functionality: doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1_url: openproblems/tasks/label_projection/methods/mlp.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - v1_comp_id: mlp_log_cpm preferred_normalization: log_cpm + variants: + mlp_log_cpm: + mlp_scran: + preferred_normalization: log_scran_pooling arguments: - name: "--hidden_layer_sizes" type: "integer" diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 8bb5b20ead..f09dc9fe04 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -12,14 +12,17 @@ functionality: code_url: "https://github.com/YosefLab/scvi-tools" doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py - v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 v1_comp_id: scarches_scanvi_hvg preferred_normalization: log_cpm + variants: + scanvi_all_genes: + scanvi_hvg: + num_hvg: 2000 arguments: - - name: "--hvg" - type: boolean - default: true - description: "Whether or not to reduce the input matrix to the set of HVG genes before training the model." + - name: "--num_hvg" + type: integer + description: "The number of HVG genes to subset to." resources: - type: python_script path: script.py diff --git a/src/label_projection/methods/scanvi/script.py b/src/label_projection/methods/scanvi/script.py index fef2366a9c..d9834bdca6 100644 --- a/src/label_projection/methods/scanvi/script.py +++ b/src/label_projection/methods/scanvi/script.py @@ -9,7 +9,7 @@ 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', 'output': 'output.h5ad', - 'hvg': True + 'num_hvg': 2000 } meta = { 'functionality_name': 'scanvi' @@ -20,10 +20,11 @@ input_train_orig = ad.read_h5ad(par['input_train']) input_test_orig = ad.read_h5ad(par['input_test']) -if par["hvg"]: +if par["num_hvg"]: print("Subsetting to HVG", flush=True) - input_train = input_train_orig[:,input_train_orig.var['hvg']] - input_test = input_test_orig[:,input_test_orig.var['hvg']] + hvg_idx = input_train_orig.var['hvg_score'].to_numpy().argsort()[:par["num_hvg"]] + input_train = input_train_orig[:,hvg_idx] + input_test = input_test_orig[:,hvg_idx] else: input_train = input_train_orig input_test = input_test_orig diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index cd39529cf8..c6cb19baf3 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -13,8 +13,9 @@ functionality: doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" v1_url: openproblems/tasks/label_projection/methods/seurat.py v1_commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 - v1_comp_id: seurat preferred_normalization: log_cpm + variants: + seurat: resources: - type: r_script path: script.R diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index b475c4ce9c..caeb1395c1 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -11,8 +11,11 @@ functionality: doc_url: "https://xgboost.readthedocs.io/en/stable/index.html" v1_url: openproblems/tasks/label_projection/methods/xgboost.py v1_commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c - v1_comp_id: xgboost_log_cpm preferred_normalization: log_cpm + variants: + xgboost_log_cpm: + xgboost_scran: + preferred_normalization: log_scran_pooling resources: - type: python_script path: script.py From 680cfe2a8560f56131ffa488c158771772efd5d0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 14:43:54 +0100 Subject: [PATCH 0623/1233] add task info Former-commit-id: 6bd297d70358cbde958e7aa424bdf0456f6855a9 --- src/label_projection/task_info.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 src/label_projection/task_info.yaml diff --git a/src/label_projection/task_info.yaml b/src/label_projection/task_info.yaml new file mode 100644 index 0000000000..b1a0568418 --- /dev/null +++ b/src/label_projection/task_info.yaml @@ -0,0 +1,29 @@ +task_id: label_projection +task_name: Label projection +v1_url: openproblems/tasks/label_projection/README.md +v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +short_description: Automated cell type annotation from rich, labeled reference data +description: | + A major challenge for integrating single cell datasets is creating matching + cell type annotations for each cell. One of the most common strategies for + annotating cell types is referred to as + ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) + whereby cells are aggregated into clusters based on feature similarity and + then manually characterized based on differential gene expression or previously + identified marker genes. Recently, methods have emerged to build on this + strategy and annotate cells using + [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). + However, these strategies pose a difficulty for integrating atlas-scale + datasets as the particular annotations may not match. + + To ensure that the cell type labels in newly generated datasets match + existing reference datasets, some methods align cells to a previously + annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) + and then _project_ labels from the reference to the new dataset. + + Here, we compare methods for annotation based on a reference dataset. + The datasets consist of two or more samples of single cell profiles that + have been manually annotated with matching labels. These datasets are then + split into training and test batches, and the task of each method is to + train a cell type classifer on the training set and project those labels + onto the test set. \ No newline at end of file From de97ebe284764b772f68b2f376c2c87bf9d2fa07 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 14:46:22 +0100 Subject: [PATCH 0624/1233] move and refactor task info Former-commit-id: cc1a1c1c5fcc2092b6e5bacdcf027a8081fab15e --- .../api/task_info.yaml | 22 +++++++++++++++++++ .../docs/task_description.md | 9 -------- .../docs/task_description.yaml | 10 --------- 3 files changed, 22 insertions(+), 19 deletions(-) create mode 100644 src/dimensionality_reduction/api/task_info.yaml delete mode 100644 src/dimensionality_reduction/docs/task_description.md delete mode 100644 src/dimensionality_reduction/docs/task_description.yaml diff --git a/src/dimensionality_reduction/api/task_info.yaml b/src/dimensionality_reduction/api/task_info.yaml new file mode 100644 index 0000000000..99f65af393 --- /dev/null +++ b/src/dimensionality_reduction/api/task_info.yaml @@ -0,0 +1,22 @@ +task_id: dimensionality_reduction +task_name: "Dimensionality reduction" +v1_url: openproblems/tasks/dimensionality_reduction/README.md +v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b +short_description: Reduction of high-dimensional datasets to 2D for visualization & interpretation +description: | + Dimensionality reduction is one of the key challenges in single-cell data representation. + Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly + 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional + elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have + been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq + experiments would yield a few hundred cells, at best. Now, it is not uncommon to see + experiments that yield over [100,000 cells]() + or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). + + Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 + dimensions measured in each cell contribute to an underlying data structure, the overall + structure of the data is challenging to display in few dimensions due to data sparsity + and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) + (distances in high dimensional data don't distinguish data points well). Thus, we need to find + a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) + the data for visualization and interpretation. \ No newline at end of file diff --git a/src/dimensionality_reduction/docs/task_description.md b/src/dimensionality_reduction/docs/task_description.md deleted file mode 100644 index 9e16fc1d17..0000000000 --- a/src/dimensionality_reduction/docs/task_description.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -info: - v1_url: openproblems/tasks/dimensionality_reduction/README.md - v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b ---- - -Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). - -Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file diff --git a/src/dimensionality_reduction/docs/task_description.yaml b/src/dimensionality_reduction/docs/task_description.yaml deleted file mode 100644 index df074e1854..0000000000 --- a/src/dimensionality_reduction/docs/task_description.yaml +++ /dev/null @@ -1,10 +0,0 @@ -info: - id: dimensionality_reduction - name: "Dimensionality reduction" - v1_url: openproblems/tasks/dimensionality_reduction/README.md - v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b - description: "Reduction of high-dimensional datasets to 2D for visualization &interpretation" - full_description: | - Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). - - Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file From 2cb287edb2a76ae6b74453b6d7b6a36af5f62318 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Dec 2022 14:46:53 +0100 Subject: [PATCH 0625/1233] move and remove task metadata Former-commit-id: 7ebb7c041cba7e98f51c41795c3b38f05d6c3509 --- src/label_projection/{ => api}/task_info.yaml | 0 src/label_projection/docs/task_description.qmd | 11 ----------- 2 files changed, 11 deletions(-) rename src/label_projection/{ => api}/task_info.yaml (100%) delete mode 100644 src/label_projection/docs/task_description.qmd diff --git a/src/label_projection/task_info.yaml b/src/label_projection/api/task_info.yaml similarity index 100% rename from src/label_projection/task_info.yaml rename to src/label_projection/api/task_info.yaml diff --git a/src/label_projection/docs/task_description.qmd b/src/label_projection/docs/task_description.qmd deleted file mode 100644 index 41b181bbd0..0000000000 --- a/src/label_projection/docs/task_description.qmd +++ /dev/null @@ -1,11 +0,0 @@ ---- -info: - v1_url: openproblems/tasks/label_projection/README.md - v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 ---- - -A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as ["cluster-then-annotate"](https://www.nature.com/articles/s41576-018-0088-9) whereby cells are aggregated into clusters based on feature similarity and then manually characterized based on differential gene expression or previously identified marker genes. Recently, methods have emerged to build on this strategy and annotate cells using [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. - -To ensure that the cell type labels in newly generated datasets match existing reference datasets, some methods align cells to a previously annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) and then _project_ labels from the reference to the new dataset. - -Here, we compare methods for annotation based on a reference dataset. The datasets consist of two or more samples of single cell profiles that have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels onto the test set. \ No newline at end of file From ec176dfdd7e726a81929eb078001aa6911da90c2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 22 Dec 2022 15:02:01 +0100 Subject: [PATCH 0626/1233] update methods to include v1 variants Former-commit-id: ea76a06c0593bef35edde90ad72bdcc019e88695 --- .../no_denoising/config.vsh.yaml | 3 ++- .../perfect_denoising/config.vsh.yaml | 5 ++-- src/denoising/methods/alra/config.vsh.yaml | 5 ++-- src/denoising/methods/dca/config.vsh.yaml | 12 ++++------ .../methods/knn_smoothing/config.vsh.yaml | 9 ++++---- src/denoising/methods/magic/config.vsh.yaml | 23 +++++++++++++++---- src/denoising/methods/magic/script.py | 6 +++-- 7 files changed, 41 insertions(+), 22 deletions(-) diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 91374fa5d3..964ef54197 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -8,7 +8,8 @@ functionality: label: no denoising v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - v1_comp_id: no_denoising + variants: + no_denoising: preferred_normalization: counts resources: - type: python_script diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index 9673d97737..36d1a057f8 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -8,7 +8,8 @@ functionality: label: perfect denoising v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c - v1_comp_id: perfect_denoising + variants: + perfect_denoising: preferred_normalization: counts resources: - type: python_script @@ -22,4 +23,4 @@ platforms: - "anndata>=0.8" - type: nextflow directives: - label: [ midmem, midcpu ] \ No newline at end of file + label: [ midmem, midcpu ] diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index bbded04a44..ff4c8aae43 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -19,7 +19,8 @@ functionality: doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md v1_url: openproblems/tasks/denoising/methods/alra.py v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa - v1_comp_id: "alra" + variants: + alra: preferred_normalization: counts arguments: - name: "--layer_input" @@ -47,4 +48,4 @@ platforms: run: git clone https://github.com/KlugerLab/ALRA.git /ALRA - type: nextflow directives: - label: [ highmem, highcpu ] \ No newline at end of file + label: [ highmem, highcpu ] diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index b580521254..5a79391ed2 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -6,14 +6,15 @@ functionality: info: type: method label: DCA - # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" - # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" - # paper_year: 2019 + paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder" + paper_url: "https://www.nature.com/articles/s41467-018-07931-2" + paper_year: 2019 paper_doi: "10.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: openproblems/tasks/denoising/methods/dca.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - v1_comp_id: "dca" + variants: + dca: preferred_normalization: counts arguments: - name: "--epochs" @@ -23,9 +24,6 @@ functionality: resources: - type: python_script path: script.py - # test_resources: - # - type: python_script - # path: test.py platforms: - type: docker image: "python:3.10" diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 58643f86b9..101225d421 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -6,14 +6,15 @@ functionality: info: type: method label: knn_smooth - # paper_name: "K-nearest neighbor smoothing for high-throughput" - # paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" - # paper_year: 2018 + paper_name: "K-nearest neighbor smoothing for high-throughput" + paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" + paper_year: 2018 paper_doi: "10.1101/217737" code_url: "https://github.com/yanailab/knn-smoothing" v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py v1_commit: bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1 - v1_comp_id: "knn_smoothing" + variants: + knn_smoothing: preferred_normalization: counts resources: - type: python_script diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 192c94c319..4d65c1c751 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -6,14 +6,21 @@ functionality: info: type: method label: magic - # paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" - # paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" - # paper_year: 2018 + paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" + paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" + paper_year: 2018 paper_doi: "10.1016/j.cell.2018.05.061" code_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: openproblems/tasks/denoising/methods/magic.py v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e - v1_comp_id: "magic" + variants: + magic: + magic_approx: + solver: approximate + knn_naive: + norm: log + decay: none + t: 1 preferred_normalization: counts arguments: - name: "--solver" @@ -26,6 +33,14 @@ functionality: choices: ["sqrt", "log"] default: "sqrt" description: Normalization method + - name: "--decay" + type: "double" + default: 1 + description: sets decay rate of kernel tails + - name: "--t" + type: "double" + default: 3 + description: power to which the diffusion operator is powered resources: - type: python_script path: script.py diff --git a/src/denoising/methods/magic/script.py b/src/denoising/methods/magic/script.py index 7507acf094..059f5fe4a5 100644 --- a/src/denoising/methods/magic/script.py +++ b/src/denoising/methods/magic/script.py @@ -10,7 +10,9 @@ 'input_train': 'output_train.h5ad', 'output': 'output_magic.h5ad', 'solver': 'exact', - 'norm': 'sqrt' + 'norm': 'sqrt', + 'decay': 1, + 't': 3, } meta = { 'functionality_name': 'foo', @@ -37,7 +39,7 @@ ) X = scprep.utils.matrix_transform(X, norm_fn) -Y = MAGIC(solver=par['solver'], verbose=False).fit_transform( +Y = MAGIC(solver=par['solver'], verbose=False, decay=par['decay'], t=par['t']).fit_transform( X, genes="all_genes" ) From 5a4f71b8b236d3e8d555bc1012865f25e711ea3a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 22 Dec 2022 16:07:00 +0100 Subject: [PATCH 0627/1233] comment paper parameters Former-commit-id: 3fa61fba08e9d33aef431101e686eac14a890afb --- src/denoising/methods/dca/config.vsh.yaml | 6 +++--- src/denoising/methods/knn_smoothing/config.vsh.yaml | 6 +++--- src/denoising/methods/magic/config.vsh.yaml | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 5a79391ed2..6f5c600358 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -6,9 +6,9 @@ functionality: info: type: method label: DCA - paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder" - paper_url: "https://www.nature.com/articles/s41467-018-07931-2" - paper_year: 2019 + # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder" + # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" + # paper_year: 2019 paper_doi: "10.1038/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: openproblems/tasks/denoising/methods/dca.py diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 101225d421..153c518bb4 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -6,9 +6,9 @@ functionality: info: type: method label: knn_smooth - paper_name: "K-nearest neighbor smoothing for high-throughput" - paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" - paper_year: 2018 + # paper_name: "K-nearest neighbor smoothing for high-throughput" + # paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" + # paper_year: 2018 paper_doi: "10.1101/217737" code_url: "https://github.com/yanailab/knn-smoothing" v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 4d65c1c751..34e6bc3a08 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -6,9 +6,9 @@ functionality: info: type: method label: magic - paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" - paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" - paper_year: 2018 + # paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" + # paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" + # paper_year: 2018 paper_doi: "10.1016/j.cell.2018.05.061" code_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: openproblems/tasks/denoising/methods/magic.py From 9f389e28faaf3104b6c1d38039bb6ed7dc2cff97 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 22 Dec 2022 16:27:20 +0100 Subject: [PATCH 0628/1233] fix magic Former-commit-id: 6fe56d3ad2192d6afb590832d37781f156819f8e --- src/denoising/methods/magic/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 34e6bc3a08..60e3a8392f 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -34,11 +34,11 @@ functionality: default: "sqrt" description: Normalization method - name: "--decay" - type: "double" + type: integer default: 1 description: sets decay rate of kernel tails - name: "--t" - type: "double" + type: integer default: 3 description: power to which the diffusion operator is powered resources: From 4fa79f1b1ada2a909a7fd779a18f437cd9812e93 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 23 Dec 2022 16:55:10 +0100 Subject: [PATCH 0629/1233] propose changes to v2 metadata Former-commit-id: de774246930d21391600f0b86cb51ba735fdae00 --- src/common/get_method_info/script.R | 9 +++++++-- src/common/get_metric_info/script.R | 3 ++- src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 8 ++++++-- src/denoising/metrics/mse/config.vsh.yaml | 6 +++--- 5 files changed, 19 insertions(+), 9 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index ffdc3f6bf8..9a9136291d 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -19,12 +19,17 @@ df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(config$functionality$info) info$config_path <- gsub(".*\\./", "", config$info$config) - info$id <- config$functionality$name + info$task_id <- par$query + info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace info$description <- config$functionality$description + info$is_baseline <- FALSE + if (grepl("control", info$type)) { + info$is_baseline <- TRUE + } info }) %>% - select(id, type, label, everything()) + select(method_id, type, method_name, everything()) jsonlite::write_json( purrr::transpose(df), diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 6271d3a43f..58693c9d0f 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -19,6 +19,7 @@ df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) info$config_path <- gsub(".*\\./", "", config$info$config) + info$task_id <- par$query info$component_id <- config$functionality$name info$namespace <- config$functionality$namespace info$component_description <- config$functionality$description @@ -26,7 +27,7 @@ df <- map_df(configs, function(config) { info$v1_commit <- config$functionality$info$v1_commit info }) %>% - select(id, everything()) + select(metric_id, everything()) jsonlite::write_json( purrr::transpose(df), diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index bbded04a44..c73f25ccd9 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: Finally, the matrix is rescaled. info: type: method - label: ALRA + method_name: ALRA paper_doi: "10.1101/397588" code_url: "https://github.com/KlugerLab/ALRA" doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index b580521254..c71a858e56 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -2,10 +2,14 @@ __merge__: ../../api/comp_method.yaml functionality: name: "dca" namespace: "denoising/methods" - description: "Deep Count Autoencoder" + description: | + Deep Count Autoencoder + + Removes the dropout effect by taking the count structure, overdispersed nature and sparsity of the data into account + using a deep autoencoder with zero-inflated negative binomial (ZINB) loss function. info: type: method - label: DCA + method_name: DCA # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder"" # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" # paper_year: 2019 diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index a0cb322405..623e03b130 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -7,9 +7,9 @@ functionality: v1_url: openproblems/tasks/denoising/metrics/mse.py v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 metrics: - - id: mse - label: mse - description: The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio + - metric_id: mse + metric_name: Mean-squared error + metric_description: The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio maximize: false min: 0 max: +inf From 38e23531b7ce571af665eddae961743828f03e4c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 06:37:27 +0100 Subject: [PATCH 0630/1233] Update methods to V1 changes according to commits Former-commit-id: eb0de4525f514092ea60a61b267608a00474bf16 --- .../control_methods/random_features/config.vsh.yaml | 2 +- .../methods/densmap/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/densmap/script.py | 5 +++-- src/dimensionality_reduction/methods/neuralee/script.py | 6 +++--- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/phate/script.py | 5 +++-- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/tsne/script.py | 4 ++-- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/umap/script.py | 3 ++- 10 files changed, 18 insertions(+), 15 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 9a65664c96..4315fe0e96 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_comp_id: "Random Features" - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts resources: - type: python_script diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 705be94bc1..d5442fe3a0 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py v1_comp_id: "densMAP PCA (logCPM, 1kHVG)" - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm arguments: - name: "--no_pca" diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index 4bd2efc009..75ce33f7d8 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -21,14 +21,15 @@ print('Select top 1000 high variable genes') n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +input = input[:, idx].copy() print("Run UMAP...") if par['no_pca']: print('... using logCPM data') - input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.layers['normalized'][:, idx]) + input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.layers['normalized']) else: print('... after applying PCA with 50 dimensions to logCPM data') - input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack") + input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=50, svd_solver="arpack") input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) print("Delete layers and var") diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 06dd6b5dbd..0487833bb3 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -36,11 +36,11 @@ dataset.subsample_genes(500) dataset.standardscale() elif input.uns['normalization_id'] == 'log_cpm': + n_genes = 1000 print('Select top 1000 high variable genes') - # idx = input.var['hvg_score'].to_numpy().argsort()[-1000:] - # dataset = GeneExpressionDataset(input.layers['normalized'][:, idx]) + idx = input.var['hvg_score'].to_numpy().argsort()[-n_genes:] + input = input[:, idx].copy() dataset = GeneExpressionDataset(input.layers['normalized']) - dataset.subsample_genes(500) # 1000 cells as a batch to estimate the affinity matrix diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 73a3ea3be9..895532bd02 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: code_url: https://github.com/KrishnaswamyLab/PHATE/ v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py v1_comp_id: "PHATE (default)" - v1_commit: 4baa8619e232fec2e3bcb3fb73d2f991d16c6f69 + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: sqrt_cpm arguments: - name: '--n_pca' diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 2805dbc9a9..dc0d5e96d5 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', + 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', 'output': 'reduced.h5ad', 'n_pca': 50, 'g0': False, @@ -35,7 +35,8 @@ print('... using logCPM data') n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] - input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized'][:, idx]) + input = input[:, idx].copy() + input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) print("Delete layers and var") del input.layers diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 1e69dd6f0d..8de701ec52 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py v1_comp_id: tsne_logCPM_1kHVG - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm arguments: - name: "--n_pca" diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index 874ca47301..a2fd1077c9 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -20,9 +20,9 @@ print('Select top 1000 high variable genes') n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] - +input = input[:, idx].copy() print('Apply PCA with 50 dimensions') -input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") +input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") print('Run t-SNE') sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 2cc564bd1c..8ae62cffe4 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py v1_comp_id: umap_logCPM_1kHVG - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm arguments: - name: "--n_pca" diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index 8d2d63d0b4..15ed00083d 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -20,9 +20,10 @@ print('Select top 1000 high variable genes') n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +input = input[:, idx].copy() print('Apply PCA with 50 dimensions') -input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=par['n_pca'], svd_solver="arpack") +input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") print('Calculate a nearest-neighbour graph') sc.pp.neighbors(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) From 9f8aaf0fcd7770c4ac1e0f71adaaf747afd76236 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 07:36:00 +0100 Subject: [PATCH 0631/1233] Add v2 variants Former-commit-id: f1fade5274951aad80ddbce72f4e9aa622e2fd95 --- .../control_methods/random_features/config.vsh.yaml | 3 ++- .../control_methods/true_features/config.vsh.yaml | 3 ++- .../methods/densmap/config.vsh.yaml | 4 +++- .../methods/neuralee/config.vsh.yaml | 7 ++++++- src/dimensionality_reduction/methods/pca/config.vsh.yaml | 3 ++- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 7 ++++++- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 3 ++- 7 files changed, 23 insertions(+), 7 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 4315fe0e96..67f2b9611f 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -11,9 +11,10 @@ functionality: paper_year: 2022 code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_comp_id: "Random Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts + variants: + random_features: resources: - type: python_script path: script.py diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 2e1d55fdca..c6532550fb 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -11,9 +11,10 @@ functionality: paper_year: 2022 code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_comp_id: "True Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts + variants: + true_features: arguments: - name: "--n_comps" type: integer diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index d5442fe3a0..91d781f161 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -9,9 +9,11 @@ functionality: paper_doi: "10.1038/s41587-020-00801-7" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py - v1_comp_id: "densMAP PCA (logCPM, 1kHVG)" v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm + variants: + densmap_logCPM_1kHVG: + densmap_pca_logCPM_1kHVG: arguments: - name: "--no_pca" type: boolean_true diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 91852abf6c..5b8835b294 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -9,9 +9,14 @@ functionality: paper_doi: "10.3389/fgene.2020.00786" code_url: https://github.com/HiBearME/NeuralEE v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py - v1_comp_id: "NeuralEE (CPU) (Default)" v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 preferred_normalization: counts + variants: + neuralee_default: + neuralee_logCPM_1kHVG: + normalize: False + subsample_genes: None + preferred_normalization: log_cpm arguments: - name: "--maxit" type: integer diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 1a16e28fef..9c3c8611a0 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -9,9 +9,10 @@ functionality: paper_doi: "10.1080/14786440109462720" code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py - v1_comp_id: pca_logCPM_1kHVG v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm + variants: + pca_logCPM_1kHVG: resources: - type: python_script path: script.py diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 895532bd02..6d7ea3edb2 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -9,9 +9,14 @@ functionality: paper_doi: "10.1038/s41587-019-0336-3" code_url: https://github.com/KrishnaswamyLab/PHATE/ v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py - v1_comp_id: "PHATE (default)" v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: sqrt_cpm + variants: + phate_default: + phate_sqrt: + gamma: 0 + phate_logCPM_1kHVG: + preferred_normalization: log_cpm arguments: - name: '--n_pca' type: integer diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 8ae62cffe4..a38534a4b3 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -9,9 +9,10 @@ functionality: paper_doi: "10.21105/joss.00861" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py - v1_comp_id: umap_logCPM_1kHVG v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm + variants: + umap_logCPM_1kHVG: arguments: - name: "--n_pca" type: integer From dd12e0752233c43fa4fa9c0211e576d3143301a6 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 07:36:27 +0100 Subject: [PATCH 0632/1233] Add v2 variants Former-commit-id: 5091827de3a61cd1daa40ee0bbb2c5a8f598b7b2 --- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 8de701ec52..319498a035 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -11,9 +11,10 @@ functionality: paper_year: 2008 code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py - v1_comp_id: tsne_logCPM_1kHVG v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm + variants: + tsne_logCPM_1kHVG: arguments: - name: "--n_pca" type: integer From 1cbf332dc8456b9486aa8d7cbf8bf69b97afdc3a Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 12:35:15 +0100 Subject: [PATCH 0633/1233] Copy required data to a new anndata object Former-commit-id: f0ceafa6376b65ffb106730b98661b2ea2658bc2 --- .../methods/densmap/script.py | 16 +++++++++++----- .../methods/neuralee/script.py | 14 ++++++++++---- .../methods/pca/script.py | 16 +++++++++++----- .../methods/phate/script.py | 16 +++++++++++----- .../methods/tsne/script.py | 16 +++++++++++----- .../methods/umap/script.py | 17 +++++++++++------ .../metrics/density/script.py | 13 ++++++++++--- .../metrics/nn_ranking/script.py | 13 ++++++++++--- .../metrics/trustworthiness/script.py | 13 ++++++++++--- 9 files changed, 95 insertions(+), 39 deletions(-) diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index 75ce33f7d8..1e738551c7 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -32,10 +32,6 @@ input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=50, svd_solver="arpack") input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) -print("Delete layers and var") -del input.layers -del input.var - print('Add method and normalization ID') input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: @@ -43,5 +39,15 @@ input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 0487833bb3..ef83882330 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -53,9 +53,15 @@ input.obsm["X_emb"] = res["X"].detach().cpu().numpy() -print("Delete layers and var") -del input.layers -del input.var +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index 0c1b241c85..fc5525e73a 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -23,10 +23,6 @@ print('Apply PCA with 50 dimensions') input.obsm["X_emb"] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack")[:, :2] -print("Delete layers and var") -del input.layers -del input.var - print('Add method and normalization ID') input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: @@ -34,5 +30,15 @@ input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index dc0d5e96d5..fb9fb9a0c6 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -38,12 +38,18 @@ input = input[:, idx].copy() input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) -print("Delete layers and var") -del input.layers -del input.var - print('Add method') input.uns['method_id'] = meta['functionality_name'] +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index a2fd1077c9..73c6f5ae04 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -28,10 +28,6 @@ sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) input.obsm["X_emb"] = input.obsm["X_tsne"].copy() -print("Delete layers and var") -del input.layers -del input.var - print('Add method and normalization ID') input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: @@ -39,5 +35,15 @@ input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index 15ed00083d..f95a3ff166 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -31,11 +31,6 @@ print("Run UMAP") sc.tl.umap(input) input.obsm["X_emb"] = input.obsm["X_umap"].copy() -del input.obsm["X_umap"] - -print("Delete layers and var") -del input.layers -del input.var print('Add method and normalization ID') input.uns['method_id'] = meta['functionality_name'] @@ -44,5 +39,15 @@ input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py index 8ddba9f76a..9b63ceddd8 100644 --- a/src/dimensionality_reduction/metrics/density/script.py +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -92,8 +92,15 @@ def _calculate_radii( input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = density -print("Delete obs matrix") -del input_reduced.obsm +print("Copy data to new AnnData object") +output = ad.AnnData( + uns={} +) +output.uns['normalization_id'] = input_reduced.uns['normalization_id'] +output.uns['method_id'] = input_reduced.uns['method_id'] +output.uns['dataset_id'] = input_reduced.uns['dataset_id'] +output.uns['metric_ids'] = input_reduced.uns['metric_ids'] +output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file") -input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/nn_ranking/script.py b/src/dimensionality_reduction/metrics/nn_ranking/script.py index 3a3fd90391..78689318da 100644 --- a/src/dimensionality_reduction/metrics/nn_ranking/script.py +++ b/src/dimensionality_reduction/metrics/nn_ranking/script.py @@ -164,8 +164,15 @@ def _metrics( input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] -print("Delete obs matrix") -del input_reduced.obsm +print("Copy data to new AnnData object") +output = ad.AnnData( + uns={} +) +output.uns['normalization_id'] = input_reduced.uns['normalization_id'] +output.uns['method_id'] = input_reduced.uns['method_id'] +output.uns['dataset_id'] = input_reduced.uns['dataset_id'] +output.uns['metric_ids'] = input_reduced.uns['metric_ids'] +output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file") -input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py index b33881c34d..5513fb71f9 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -27,8 +27,15 @@ input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = float(np.clip(score, 0, 1)) -print("Delete obs matrix") -del input_reduced.obsm +print("Copy data to new AnnData object") +output = ad.AnnData( + uns={} +) +output.uns['normalization_id'] = input_reduced.uns['normalization_id'] +output.uns['method_id'] = input_reduced.uns['method_id'] +output.uns['dataset_id'] = input_reduced.uns['dataset_id'] +output.uns['metric_ids'] = input_reduced.uns['metric_ids'] +output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file") -input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 75e09da163d2c0b1d6c3debafb7b6b2ef12565eb Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 12:46:39 +0100 Subject: [PATCH 0634/1233] Copy required data to a new anndata object Former-commit-id: 59bfa0c64809960d4c84282e27ff661a2736d567 --- src/dimensionality_reduction/metrics/rmse/script.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index 10ae5b49e4..efb88d8626 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -45,8 +45,15 @@ input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = rmse -print("Delete obs matrix") -del input_reduced.obsm +print("Copy data to new AnnData object") +output = ad.AnnData( + uns={} +) +output.uns['normalization_id'] = input_reduced.uns['normalization_id'] +output.uns['method_id'] = input_reduced.uns['method_id'] +output.uns['dataset_id'] = input_reduced.uns['dataset_id'] +output.uns['metric_ids'] = input_reduced.uns['metric_ids'] +output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file") -input_reduced.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 0379e50c02e7fc1b973751718f3b13f490b1700e Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 14:01:34 +0100 Subject: [PATCH 0635/1233] Copy required data to a new anndata object Former-commit-id: c21f659759eba6cb584994f4a6ce0c22eb10cda6 --- .../control_methods/random_features/script.py | 12 +++++++++++- .../control_methods/true_features/script.py | 12 +++++++++++- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index 5a87d33b88..316c573587 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -25,5 +25,15 @@ print('Create random embedding') input.obsm["X_emb"] = np.random.normal(0, 1, (input.shape[0], 2)) +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/script.py b/src/dimensionality_reduction/control_methods/true_features/script.py index f3805ccf90..ca6760af02 100644 --- a/src/dimensionality_reduction/control_methods/true_features/script.py +++ b/src/dimensionality_reduction/control_methods/true_features/script.py @@ -26,5 +26,15 @@ print('Create high dimensionally embedding with all features') input.obsm["X_emb"] = input.layers['counts'][:, :par['n_comps']].toarray() +print('Copy data to new AnnData object') +output = ad.AnnData( + obs=input.obs[[]], + uns={} +) +output.obsm['X_emb'] = input.obsm['X_emb'] +output.uns['dataset_id'] = input.uns['dataset_id'] +output.uns['normalization_id'] = input.uns['normalization_id'] +output.uns['method_id'] = input.uns['method_id'] + print("Write output to file") -input.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From ce4fde28825a7c141aa5f454d71c29300bca1abb Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 14:13:31 +0100 Subject: [PATCH 0636/1233] Add comment about unittests-specific parameters Former-commit-id: cde525086126edd47610637f9acd9e5a3962dd30 --- src/dimensionality_reduction/README.qmd | 5 +++-- .../methods/neuralee/config.vsh.yaml | 1 + 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd index ac90e41c42..d72d5b598a 100644 --- a/src/dimensionality_reduction/README.qmd +++ b/src/dimensionality_reduction/README.qmd @@ -28,7 +28,7 @@ knitr::asis_output(lines2) ## Methods -Methods to assign dimensionally-reduced 2D embedding coordinates to adata.obsm['X_emb']. +Methods to assign dimensionally-reduced 2D embedding coordinates to `adata.obsm['X_emb']`. ```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) @@ -60,7 +60,8 @@ method_info_view <- cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) ``` - +To-do list: + - Add specific options for unit tests only (such as `--max-iter` in *NeuralEE*). ## Metrics Metrics for dimensionality reduction aim to compare the dimensionality reduced dataset (the embedding) with a whole or a higher dimensional dataset. The more similar they are, the better the reduction is. diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 5b8835b294..07e9eaba9e 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -17,6 +17,7 @@ functionality: normalize: False subsample_genes: None preferred_normalization: log_cpm + # To-do: add specific options for unit tests such as --maxit arguments: - name: "--maxit" type: integer From 96b5e433e99c872a93238d2e44cd1c336c837d34 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 14:24:41 +0100 Subject: [PATCH 0637/1233] Update changelog Former-commit-id: 0169c1388c872b3834633374b25f620a6bf55570 --- CHANGELOG.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a55a57a969..191a108ff4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -133,8 +133,10 @@ * `resources_test/dimensionality_reduction/pancreas` with `src/dimensionality_reduction/resources_test_scripts/pancreas.sh`. +* Added `variant` key to config files to store variants (different input parameters) of every component. + ### V1 migration -* `control_methods/high_dim_pca`: Migrated from v1. Extracted from baseline method `High-dimensional PCA`. +* `control_methods/true_features`: Migrated from v1. Extracted from baseline method `True Features`. * `control_methods/random_features`: Migrated from v1. Extracted from baseline method `Random Features`. @@ -146,6 +148,10 @@ * `methods/phate`: Migrated from v1. +* `methods/pca`: Migrated from v1. + +* `methods/neuralee`: Migrated from v1. + * `metrics/rmse`: Migrated from v1. * `metrics/trustworthiness`: Migrated from v1. From 9fc4e0f8bf305be87ce60c81070d840aa99689a8 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Tue, 3 Jan 2023 14:38:16 +0100 Subject: [PATCH 0638/1233] Set flush to true in all prints Former-commit-id: 866e0f61e7084892364e3a308f673702d75ee85a --- .../api/comp_control_method.yaml | 18 ++++++++--------- .../api/comp_method.yaml | 18 ++++++++--------- .../api/comp_metric.yaml | 20 +++++++++---------- .../api/comp_split_dataset.yaml | 20 +++++++++---------- .../control_methods/random_features/script.py | 10 +++++----- .../control_methods/true_features/script.py | 10 +++++----- .../methods/densmap/script.py | 16 +++++++-------- .../methods/neuralee/script.py | 12 +++++------ .../methods/pca/script.py | 12 +++++------ .../methods/phate/script.py | 16 +++++++-------- .../methods/tsne/script.py | 14 ++++++------- .../methods/umap/script.py | 16 +++++++-------- .../metrics/density/script.py | 10 +++++----- .../metrics/nn_ranking/script.py | 8 ++++---- .../metrics/rmse/script.py | 14 ++++++------- .../metrics/trustworthiness/script.py | 10 +++++----- .../split_dataset/script.py | 10 +++++----- 17 files changed, 117 insertions(+), 117 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 8fe94c0247..6918aba03e 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -24,29 +24,29 @@ functionality: "--n_pca", str(n_pca) ] - print(">> Checking whether input file exists") + print(">> Checking whether input file exists", flush=True) assert path.exists(input_path) - print(">> Running script as test") + print(">> Running script as test", flush=True) out = subprocess.run(cmd) # out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Checking whether output file exists") + print(">> Checking whether output file exists", flush=True) assert path.exists(output_path) - print(">> Reading h5ad files") + print(">> Reading h5ad files", flush=True) input = ad.read_h5ad(input_path) output = ad.read_h5ad(output_path) - print("input:", input) - print("output:", output) + print("input:", input, flush=True) + print("output:", output, flush=True) - print(">> Checking whether predictions were added") + print(">> Checking whether predictions were added", flush=True) assert "X_emb" in output.obsm assert meta['functionality_name'] == output.uns["method_id"] - print(">> Checking whether data from input was copied properly to output") + print(">> Checking whether data from input was copied properly to output", flush=True) assert input.n_obs == output.n_obs assert input.uns["dataset_id"] == output.uns["dataset_id"] - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 01074e08c9..708e2faf7a 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -22,29 +22,29 @@ functionality: "--output", output_path ] - print(">> Checking whether input file exists") + print(">> Checking whether input file exists", flush=True) assert path.exists(input_path) - print(">> Running script as test") + print(">> Running script as test", flush=True) out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Checking whether output file exists") + print(">> Checking whether output file exists", flush=True) assert path.exists(output_path) - print(">> Reading h5ad files") + print(">> Reading h5ad files", flush=True) input = ad.read_h5ad(input_path) output = ad.read_h5ad(output_path) - print("input:", input) - print("output:", output) + print("input:", input, flush=True) + print("output:", output, flush=True) - print(">> Checking whether predictions were added") + print(">> Checking whether predictions were added", flush=True) assert "X_emb" in output.obsm assert meta['functionality_name'] == output.uns["method_id"] assert 'normalization_id' in output.uns - print(">> Checking whether data from input was copied properly to output") + print(">> Checking whether data from input was copied properly to output", flush=True) assert input.n_obs == output.n_obs assert input.uns["dataset_id"] == output.uns["dataset_id"] - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index c9bb22b5fe..2587d5c4aa 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -26,33 +26,33 @@ functionality: "--output", output_path, ] - print(">> Checking whether input files exist") + print(">> Checking whether input files exist", flush=True) assert path.exists(input_reduced_path) assert path.exists(input_test_path) - print(">> Running script as test") + print(">> Running script as test", flush=True) out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Checking whether output file exists") + print(">> Checking whether output file exists", flush=True) assert path.exists(output_path) - print(">> Reading h5ad files") + print(">> Reading h5ad files", flush=True) input_reduced = ad.read_h5ad(input_reduced_path) input_test = ad.read_h5ad(input_test_path) output = ad.read_h5ad(output_path) - print("input reduced:", input_reduced) - print("input test:", input_test) - print("output:", output) + print("input reduced:", input_reduced, flush=True) + print("input test:", input_test, flush=True) + print("output:", output, flush=True) - print(">> Checking whether metrics were added") + print(">> Checking whether metrics were added", flush=True) assert "metric_ids" in output.uns assert "metric_values" in output.uns assert meta['functionality_name'] in output.uns["metric_ids"] - print(">> Checking whether data from input was copied properly to output") + print(">> Checking whether data from input was copied properly to output", flush=True) assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] assert input_reduced.uns["method_id"] == output.uns["method_id"] - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_split_dataset.yaml index 8488762e94..6a2bc619fb 100644 --- a/src/dimensionality_reduction/api/comp_split_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_split_dataset.yaml @@ -27,33 +27,33 @@ functionality: "--output_test", output_test_path ] - print(">> Checking whether input file exists") + print(">> Checking whether input file exists", flush=True) assert path.exists(input_path) - print(">> Running script as test") + print(">> Running script as test", flush=True) out = subprocess.run(cmd, check=True, capture_output=True, text=True) - print(">> Checking whether output files exist") + print(">> Checking whether output files exist", flush=True) assert path.exists(output_train_path) assert path.exists(output_test_path) - print(">> Reading h5ad files") + print(">> Reading h5ad files", flush=True) input = ad.read_h5ad(input_path) output_train = ad.read_h5ad(output_train_path) output_test = ad.read_h5ad(output_test_path) - print("input:", input) - print("output_train:", output_train) - print("output_test:", output_test) + print("input:", input, flush=True) + print("output_train:", output_train, flush=True) + print("output_test:", output_test, flush=True) - print(">> Checking whether data from input was copied properly to output") + print(">> Checking whether data from input was copied properly to output", flush=True) assert input.n_obs == output_train.n_obs assert input.n_obs == output_test.n_obs assert input.uns["dataset_id"] == output_train.uns["dataset_id"] assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - print(">> Check whether certain slots exist") + print(">> Check whether certain slots exist", flush=True) assert "counts" in output_train.layers assert "normalized" in output_train.layers assert 'hvg_score' in output_train.var @@ -61,4 +61,4 @@ functionality: assert "normalized" in output_test.layers assert 'hvg_score' in output_test.var - print("All checks succeeded!") \ No newline at end of file + print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index 316c573587..a988884359 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -12,20 +12,20 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Create random embedding') +print('Create random embedding', flush=True) input.obsm["X_emb"] = np.random.normal(0, 1, (input.shape[0], 2)) -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -35,5 +35,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/script.py b/src/dimensionality_reduction/control_methods/true_features/script.py index ca6760af02..9381808fb8 100644 --- a/src/dimensionality_reduction/control_methods/true_features/script.py +++ b/src/dimensionality_reduction/control_methods/true_features/script.py @@ -13,20 +13,20 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Create high dimensionally embedding with all features') +print('Create high dimensionally embedding with all features', flush=True) input.obsm["X_emb"] = input.layers['counts'][:, :par['n_comps']].toarray() -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -36,5 +36,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index 1e738551c7..33dd910bbb 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -15,31 +15,31 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Select top 1000 high variable genes') +print('Select top 1000 high variable genes', flush=True) n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] input = input[:, idx].copy() -print("Run UMAP...") +print("Run UMAP...", flush=True) if par['no_pca']: - print('... using logCPM data') + print('... using logCPM data', flush=True) input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.layers['normalized']) else: - print('... after applying PCA with 50 dimensions to logCPM data') + print('... after applying PCA with 50 dimensions to logCPM data', flush=True) input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=50, svd_solver="arpack") input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -49,5 +49,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index ef83882330..6a42006c1b 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -17,10 +17,10 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) @@ -28,7 +28,7 @@ input.uns['method_id'] = meta['functionality_name'] if input.uns['normalization_id'] == 'counts': - print('Select top 500 high variable genes') + print('Select top 500 high variable genes', flush=True) # idx = input.var['hvg_score'].to_numpy().argsort()[-500:] # dataset = GeneExpressionDataset(input.layers['counts'][:, idx]) dataset = GeneExpressionDataset(input.layers['counts']) @@ -37,7 +37,7 @@ dataset.standardscale() elif input.uns['normalization_id'] == 'log_cpm': n_genes = 1000 - print('Select top 1000 high variable genes') + print('Select top 1000 high variable genes', flush=True) idx = input.var['hvg_score'].to_numpy().argsort()[-n_genes:] input = input[:, idx].copy() dataset = GeneExpressionDataset(input.layers['normalized']) @@ -53,7 +53,7 @@ input.obsm["X_emb"] = res["X"].detach().cpu().numpy() -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -63,5 +63,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index fc5525e73a..eb5ba55e7c 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -13,24 +13,24 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Select top 1000 high variable genes') +print('Select top 1000 high variable genes', flush=True) n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] -print('Apply PCA with 50 dimensions') +print('Apply PCA with 50 dimensions', flush=True) input.obsm["X_emb"] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack")[:, :2] -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -40,5 +40,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index fb9fb9a0c6..a4fd0da923 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -16,12 +16,12 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print("Run PHATE...") +print("Run PHATE...", flush=True) gamma = 0 if par['g0'] else 1 -print('... with gamma=' + str(gamma) + ' and...') +print('... with gamma=' + str(gamma) + ' and...', flush=True) phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=gamma) with open(meta['config'], 'r') as config_file: @@ -29,19 +29,19 @@ input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] if input.uns['normalization_id'] == 'sqrt_cpm': - print('... using sqrt-CPM data') + print('... using sqrt-CPM data', flush=True) input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) elif input.uns['normalization_id'] == 'log_cpm': - print('... using logCPM data') + print('... using logCPM data', flush=True) n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] input = input[:, idx].copy() input.obsm["X_emb"] = phate_op.fit_transform(input.layers['normalized']) -print('Add method') +print('Add method', flush=True) input.uns['method_id'] = meta['functionality_name'] -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -51,5 +51,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index 73c6f5ae04..41bf3a0d36 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -14,28 +14,28 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Select top 1000 high variable genes') +print('Select top 1000 high variable genes', flush=True) n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] input = input[:, idx].copy() -print('Apply PCA with 50 dimensions') +print('Apply PCA with 50 dimensions', flush=True) input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") -print('Run t-SNE') +print('Run t-SNE', flush=True) sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) input.obsm["X_emb"] = input.obsm["X_tsne"].copy() -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -45,5 +45,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index f95a3ff166..8c11be64b7 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -14,32 +14,32 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Select top 1000 high variable genes') +print('Select top 1000 high variable genes', flush=True) n_genes = 1000 idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] input = input[:, idx].copy() -print('Apply PCA with 50 dimensions') +print('Apply PCA with 50 dimensions', flush=True) input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") -print('Calculate a nearest-neighbour graph') +print('Calculate a nearest-neighbour graph', flush=True) sc.pp.neighbors(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) -print("Run UMAP") +print("Run UMAP", flush=True) sc.tl.umap(input) input.obsm["X_emb"] = input.obsm["X_umap"].copy() -print('Add method and normalization ID') +print('Add method and normalization ID', flush=True) input.uns['method_id'] = meta['functionality_name'] with open(meta['config'], 'r') as config_file: config = yaml.safe_load(config_file) input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] -print('Copy data to new AnnData object') +print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], uns={} @@ -49,5 +49,5 @@ output.uns['normalization_id'] = input.uns['normalization_id'] output.uns['method_id'] = input.uns['method_id'] -print("Write output to file") +print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py index 9b63ceddd8..9edc308979 100644 --- a/src/dimensionality_reduction/metrics/density/script.py +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -79,20 +79,20 @@ def _calculate_radii( _K = 30 # number of neighbors _SEED = 42 - print('Reduce dimensionality of raw data') + print('Reduce dimensionality of raw data', flush=True) _, ro, _ = UMAP( n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True ).fit_transform(input_test.layers['counts']) re = _calculate_radii(input_reduced.obsm['X_emb'], n_neighbors=_K, random_state=_SEED) - print('Compute Density between the full (or processed) data matrix and a dimensionally-reduced matrix') + print('Compute Density between the full (or processed) data matrix and a dimensionally-reduced matrix', flush=True) density = pearsonr(ro, re)[0] -print("Store metric value") +print("Store metric value", flush=True) input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = density -print("Copy data to new AnnData object") +print("Copy data to new AnnData object", flush=True) output = ad.AnnData( uns={} ) @@ -102,5 +102,5 @@ def _calculate_radii( output.uns['metric_ids'] = input_reduced.uns['metric_ids'] output.uns['metric_values'] = input_reduced.uns['metric_values'] -print("Write data to file") +print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/nn_ranking/script.py b/src/dimensionality_reduction/metrics/nn_ranking/script.py index 78689318da..3920c82095 100644 --- a/src/dimensionality_reduction/metrics/nn_ranking/script.py +++ b/src/dimensionality_reduction/metrics/nn_ranking/script.py @@ -136,7 +136,7 @@ def _metrics( } ## VIASH END -print("Load data") +print("Load data", flush=True) input_reduced = ad.read_h5ad(par['input_reduced']) input_test = ad.read_h5ad(par['input_test']) @@ -156,7 +156,7 @@ def _metrics( T, C, QNN, AUC, LCMC, _kmax, Qlocal, Qglobal = _metrics(Q) -print("Store metric value") +print("Store metric value", flush=True) input_reduced.uns['metric_ids'] = {meta['functionality_name']: ['continuity', 'co-KNN size', 'co-KNN AUC', 'local continuity meta criterion', 'local property', 'global property']} if np.any(np.isnan(input_reduced.obsm["X_emb"])): input_reduced.uns['metric_values'] = [0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf] @@ -164,7 +164,7 @@ def _metrics( input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] -print("Copy data to new AnnData object") +print("Copy data to new AnnData object", flush=True) output = ad.AnnData( uns={} ) @@ -174,5 +174,5 @@ def _metrics( output.uns['metric_ids'] = input_reduced.uns['metric_ids'] output.uns['metric_values'] = input_reduced.uns['metric_values'] -print("Write data to file") +print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index efb88d8626..debd18c86c 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -16,15 +16,15 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_reduced = ad.read_h5ad(par['input_reduced']) input_test = ad.read_h5ad(par['input_test']) -print('Reduce dimensionality of raw data') +print('Reduce dimensionality of raw data', flush=True) n_comps = 200 if not par['spectral']: input_reduced.obsm['high_dim'] = decomposition.TruncatedSVD(n_components = n_comps).fit_transform(input_test.layers['counts']) - print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix, invariant to scalar multiplication') + print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix, invariant to scalar multiplication', flush=True) else: n_comps = min(n_comps, min(input_test.shape) - 2) graph = UMAP(transform_mode="graph").fit_transform(input_test.layers['counts']) @@ -32,7 +32,7 @@ input_test.layers['counts'], graph, n_comps, random_state=np.random.default_rng() ) meta['functionality_name'] += ' spectral' - print('Computes (RMSE) between high-dimensional Laplacian eigenmaps on the full (or processed) data matrix and the dimensionally-reduced matrix, invariant to scalar multiplication') + print('Computes (RMSE) between high-dimensional Laplacian eigenmaps on the full (or processed) data matrix and the dimensionally-reduced matrix, invariant to scalar multiplication', flush=True) high_dim_dist = dist.pdist(input_reduced.obsm['high_dim']) low_dim_dist = dist.pdist(input_reduced.obsm["X_emb"]) @@ -41,11 +41,11 @@ low_dim_dist[:, None], high_dim_dist ) -print("Store metric value") +print("Store metric value", flush=True) input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = rmse -print("Copy data to new AnnData object") +print("Copy data to new AnnData object", flush=True) output = ad.AnnData( uns={} ) @@ -55,5 +55,5 @@ output.uns['metric_ids'] = input_reduced.uns['metric_ids'] output.uns['metric_values'] = input_reduced.uns['metric_values'] -print("Write data to file") +print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py index 5513fb71f9..6e554d3853 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -13,21 +13,21 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_reduced = ad.read_h5ad(par['input_reduced']) input_test = ad.read_h5ad(par['input_test']) -print('Reduce dimensionality of raw data') +print('Reduce dimensionality of raw data', flush=True) high_dim, low_dim = input_test.layers['counts'], input_reduced.obsm["X_emb"] score = manifold.trustworthiness( high_dim, low_dim, n_neighbors=15, metric="euclidean" ) # for large k close to #samples, it's higher than 1.0, e.g 1.0000073552559712 -print("Store metric value") +print("Store metric value", flush=True) input_reduced.uns['metric_ids'] = meta['functionality_name'] input_reduced.uns['metric_values'] = float(np.clip(score, 0, 1)) -print("Copy data to new AnnData object") +print("Copy data to new AnnData object", flush=True) output = ad.AnnData( uns={} ) @@ -37,5 +37,5 @@ output.uns['metric_ids'] = input_reduced.uns['metric_ids'] output.uns['metric_values'] = input_reduced.uns['metric_values'] -print("Write data to file") +print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/split_dataset/script.py index eb917de836..508c53e547 100644 --- a/src/dimensionality_reduction/split_dataset/script.py +++ b/src/dimensionality_reduction/split_dataset/script.py @@ -57,24 +57,24 @@ def subset_anndata(adata_sub, slot_info): return ad.AnnData(**kwargs) -print(">> Load Data") +print(">> Load Data", flush=True) adata = ad.read_h5ad(par["input"]) -print(">> Figuring out which data needs to be copied to which output file") +print(">> Figuring out which data needs to be copied to which output file", flush=True) slot_info_per_output = read_slots(par, meta) -print(">> Creating train data") +print(">> Creating train data", flush=True) output_train = subset_anndata( adata_sub=adata, slot_info=slot_info_per_output['train'] ) -print(">> Creating test data") +print(">> Creating test data", flush=True) output_test = subset_anndata( adata_sub=adata, slot_info=slot_info_per_output['test'] ) -print(">> Writing") +print(">> Writing", flush=True) output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) From acaae19413b0bb488003519955db53b44e5ae169 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 3 Jan 2023 20:28:04 +0100 Subject: [PATCH 0639/1233] add dataset metadata yaml structure Former-commit-id: f46dbc744272454d9dcca2f75ae6fc33fbc79b8f --- .../loaders/openproblems_v1/metadata.yaml | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 src/datasets/loaders/openproblems_v1/metadata.yaml diff --git a/src/datasets/loaders/openproblems_v1/metadata.yaml b/src/datasets/loaders/openproblems_v1/metadata.yaml new file mode 100644 index 0000000000..dd676703e2 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1/metadata.yaml @@ -0,0 +1,67 @@ +allen_brain_atlas: + dataset_id: 'allen_brain_atlas' + dataset_name: + data_url: + data_reference: + dataset_summary: +cengen: + dataset_id: 'cengen' + dataset_name: + data_url: + data_reference: + dataset_summary: +immune_cells: + dataset_id: 'immune_cells' + dataset_name: + data_url: + data_reference: + dataset_summary: +mouse_blood_olssen_labelled: + dataset_id: 'mouse_blood_olssen_labelled' + dataset_name: + data_url: + data_reference: + dataset_summary: +pancreas: + dataset_id: 'pancreas' + dataset_name: + data_url: + data_reference: + dataset_summary: +mouse_hspc_nestorowa2016: + dataset_id: 'mouse_hspc_nestorowa2016' + dataset_name: + data_url: + data_reference: + dataset_summary: +tabula_muris_senis_droplet_lung: + dataset_id: 'tabula_muris_senis_droplet_lung' + dataset_name: + data_url: + data_reference: + dataset_summary: +tenx_1k_pbmc: + dataset_id: 'tenx_1k_pbmc' + dataset_name: + data_url: + data_reference: + dataset_summary: +tenx_5k_pbmc: + dataset_id: 'tenx_5k_pbmc' + dataset_name: + data_url: + data_reference: + dataset_summary: +tnbc_wu2021: + dataset_id: 'tnbc_wu2021' + dataset_name: + data_url: + data_reference: + dataset_summary: +zebrafish: + dataset_id: 'zebrafish' + dataset_name: + data_url: + data_reference: + dataset_summary: + From 49675fb51330d87edb5c64048557a00a8c59411f Mon Sep 17 00:00:00 2001 From: jacorvar Date: Wed, 4 Jan 2023 09:55:04 +0100 Subject: [PATCH 0640/1233] inherit normalization id from input dataset Former-commit-id: 11a4142b02a0a0486ec0f9cab2833ca950fe5c08 --- .../control_methods/random_features/script.py | 6 +----- .../control_methods/true_features/script.py | 6 +----- src/dimensionality_reduction/methods/densmap/script.py | 6 +----- src/dimensionality_reduction/methods/neuralee/script.py | 6 +----- src/dimensionality_reduction/methods/pca/script.py | 6 +----- src/dimensionality_reduction/methods/tsne/script.py | 6 +----- src/dimensionality_reduction/methods/umap/script.py | 6 +----- 7 files changed, 7 insertions(+), 35 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index a988884359..d4abbdb274 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -15,12 +15,8 @@ print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Create random embedding', flush=True) input.obsm["X_emb"] = np.random.normal(0, 1, (input.shape[0], 2)) diff --git a/src/dimensionality_reduction/control_methods/true_features/script.py b/src/dimensionality_reduction/control_methods/true_features/script.py index 9381808fb8..20f42f688e 100644 --- a/src/dimensionality_reduction/control_methods/true_features/script.py +++ b/src/dimensionality_reduction/control_methods/true_features/script.py @@ -16,12 +16,8 @@ print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Create high dimensionally embedding with all features', flush=True) input.obsm["X_emb"] = input.layers['counts'][:, :par['n_comps']].toarray() diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index 33dd910bbb..bf8b4abee1 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -32,12 +32,8 @@ input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=50, svd_solver="arpack") input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Copy data to new AnnData object', flush=True) output = ad.AnnData( diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 6a42006c1b..99bcc53a7e 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -20,11 +20,7 @@ print("Load input data", flush=True) input = ad.read_h5ad(par['input']) -print('Add method and normalization ID', flush=True) -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] if input.uns['normalization_id'] == 'counts': diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index eb5ba55e7c..5f8fb12a03 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -23,12 +23,8 @@ print('Apply PCA with 50 dimensions', flush=True) input.obsm["X_emb"] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack")[:, :2] -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Copy data to new AnnData object', flush=True) output = ad.AnnData( diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index 41bf3a0d36..cc74845101 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -28,12 +28,8 @@ sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) input.obsm["X_emb"] = input.obsm["X_tsne"].copy() -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Copy data to new AnnData object', flush=True) output = ad.AnnData( diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index 7df37ee964..b787b66328 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -33,12 +33,8 @@ input.obsm["X_emb"] = input.obsm["X_umap"].copy() del input.obsm["X_umap"] -print('Add method and normalization ID', flush=True) +print('Add method ID', flush=True) input.uns['method_id'] = meta['functionality_name'] -with open(meta['config'], 'r') as config_file: - config = yaml.safe_load(config_file) - -input.uns['normalization_id'] = config['functionality']['info']['preferred_normalization'] print('Copy data to new AnnData object', flush=True) output = ad.AnnData( From 1aa95f349c75cdcd50811edc29ed362468e2101c Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 5 Jan 2023 13:06:35 +0100 Subject: [PATCH 0641/1233] remove paper info and code url in control methods Former-commit-id: 4bfaa527bb2cac006ca7bcd64d6ae17a259314a4 --- .../control_methods/random_features/config.vsh.yaml | 4 ---- .../control_methods/true_features/config.vsh.yaml | 4 ---- 2 files changed, 8 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 67f2b9611f..dfb03b9e7e 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -6,10 +6,6 @@ functionality: info: type: negative_control label: Random features - paper_name: "Random Features (baseline)" - paper_url: "https://openproblems.bio" - paper_year: 2022 - code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 292b89c907..c79735d1a1 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -6,10 +6,6 @@ functionality: info: type: positive_control label: True Features - paper_name: "True Features (baseline)" - paper_url: "https://openproblems.bio" - paper_year: 2022 - code_url: "https://github.com/openproblems-bio/openproblems" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_comp_id: "True Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 From f2b58372459c42b20a53aa99e668dcf2bfa7b9f1 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 5 Jan 2023 13:14:25 +0100 Subject: [PATCH 0642/1233] Create AnnData with just one function call Former-commit-id: f2169c36f050067c940272be3242f22e1458be4f --- src/dimensionality_reduction/methods/densmap/script.py | 7 ++----- src/dimensionality_reduction/methods/neuralee/script.py | 7 ++----- src/dimensionality_reduction/methods/pca/script.py | 7 ++----- src/dimensionality_reduction/methods/phate/script.py | 7 ++----- src/dimensionality_reduction/methods/tsne/script.py | 7 ++----- src/dimensionality_reduction/methods/umap/script.py | 7 ++----- src/dimensionality_reduction/metrics/density/script.py | 7 +------ src/dimensionality_reduction/metrics/nn_ranking/script.py | 7 +------ src/dimensionality_reduction/metrics/rmse/script.py | 7 +------ .../metrics/trustworthiness/script.py | 7 +------ 10 files changed, 16 insertions(+), 54 deletions(-) diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index bf8b4abee1..44e71c4262 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -38,12 +38,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 99bcc53a7e..80a4178a77 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -52,12 +52,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index 5f8fb12a03..7de656b2ec 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -29,12 +29,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index eedeacee5c..4b6b31b80a 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -37,12 +37,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index cc74845101..a214b31b0c 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -34,12 +34,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index b787b66328..f89e8cd5e6 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -39,12 +39,9 @@ print('Copy data to new AnnData object', flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={"X_emb": input.obsm["X_emb"]}, + uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py index 9edc308979..ed37a28298 100644 --- a/src/dimensionality_reduction/metrics/density/script.py +++ b/src/dimensionality_reduction/metrics/density/script.py @@ -94,13 +94,8 @@ def _calculate_radii( print("Copy data to new AnnData object", flush=True) output = ad.AnnData( - uns={} + uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} ) -output.uns['normalization_id'] = input_reduced.uns['normalization_id'] -output.uns['method_id'] = input_reduced.uns['method_id'] -output.uns['dataset_id'] = input_reduced.uns['dataset_id'] -output.uns['metric_ids'] = input_reduced.uns['metric_ids'] -output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/nn_ranking/script.py b/src/dimensionality_reduction/metrics/nn_ranking/script.py index 3920c82095..e082793e35 100644 --- a/src/dimensionality_reduction/metrics/nn_ranking/script.py +++ b/src/dimensionality_reduction/metrics/nn_ranking/script.py @@ -166,13 +166,8 @@ def _metrics( print("Copy data to new AnnData object", flush=True) output = ad.AnnData( - uns={} + uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} ) -output.uns['normalization_id'] = input_reduced.uns['normalization_id'] -output.uns['method_id'] = input_reduced.uns['method_id'] -output.uns['dataset_id'] = input_reduced.uns['dataset_id'] -output.uns['metric_ids'] = input_reduced.uns['metric_ids'] -output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index debd18c86c..b0b8f0608c 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -47,13 +47,8 @@ print("Copy data to new AnnData object", flush=True) output = ad.AnnData( - uns={} + uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} ) -output.uns['normalization_id'] = input_reduced.uns['normalization_id'] -output.uns['method_id'] = input_reduced.uns['method_id'] -output.uns['dataset_id'] = input_reduced.uns['dataset_id'] -output.uns['metric_ids'] = input_reduced.uns['metric_ids'] -output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py index 6e554d3853..35637d3c55 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -29,13 +29,8 @@ print("Copy data to new AnnData object", flush=True) output = ad.AnnData( - uns={} + uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} ) -output.uns['normalization_id'] = input_reduced.uns['normalization_id'] -output.uns['method_id'] = input_reduced.uns['method_id'] -output.uns['dataset_id'] = input_reduced.uns['dataset_id'] -output.uns['metric_ids'] = input_reduced.uns['metric_ids'] -output.uns['metric_values'] = input_reduced.uns['metric_values'] print("Write data to file", flush=True) output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 41bb833d5ac5c8b1e37a1389874d73fc49b85fc4 Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 5 Jan 2023 13:14:47 +0100 Subject: [PATCH 0643/1233] Remove task_description.yaml file Former-commit-id: 3c41960ec9fbaa4919aef137e0447b1df40ac5d7 --- .../docs/task_description.yaml | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 src/dimensionality_reduction/docs/task_description.yaml diff --git a/src/dimensionality_reduction/docs/task_description.yaml b/src/dimensionality_reduction/docs/task_description.yaml deleted file mode 100644 index df074e1854..0000000000 --- a/src/dimensionality_reduction/docs/task_description.yaml +++ /dev/null @@ -1,10 +0,0 @@ -info: - id: dimensionality_reduction - name: "Dimensionality reduction" - v1_url: openproblems/tasks/dimensionality_reduction/README.md - v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b - description: "Reduction of high-dimensional datasets to 2D for visualization &interpretation" - full_description: | - Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). - - Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don’t distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. \ No newline at end of file From d3193265b02fda74b25f1f366b2ef7fdfa9ea2bf Mon Sep 17 00:00:00 2001 From: jacorvar Date: Thu, 5 Jan 2023 13:51:45 +0100 Subject: [PATCH 0644/1233] Remove v1_comp_id Former-commit-id: 1fdcf4242a6a270b0709cafca6b45653f5e7e4cf --- src/dimensionality_reduction/methods/neuralee/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/pca/config.vsh.yaml | 1 - 2 files changed, 2 deletions(-) diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 8685e8d82b..07e9eaba9e 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -9,7 +9,6 @@ functionality: paper_doi: "10.3389/fgene.2020.00786" code_url: https://github.com/HiBearME/NeuralEE v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py - v1_comp_id: "NeuralEE (CPU) (Default)" v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 preferred_normalization: counts variants: diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 7db0b9df83..9c3c8611a0 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -9,7 +9,6 @@ functionality: paper_doi: "10.1080/14786440109462720" code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py - v1_comp_id: pca_logCPM_1kHVG v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 preferred_normalization: log_cpm variants: From 85dfa8663f6de8e84283bd0058f4207807315965 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 14:57:03 +0100 Subject: [PATCH 0645/1233] update task_info Former-commit-id: 4c6444b988e5b188f49623c0dbf80ed5453138a9 --- src/denoising/docs/task_description.yaml | 34 ------------------------ src/denoising/docs/task_info.yaml | 33 +++++++++++++++++++++++ 2 files changed, 33 insertions(+), 34 deletions(-) delete mode 100644 src/denoising/docs/task_description.yaml create mode 100644 src/denoising/docs/task_info.yaml diff --git a/src/denoising/docs/task_description.yaml b/src/denoising/docs/task_description.yaml deleted file mode 100644 index fe8caef82c..0000000000 --- a/src/denoising/docs/task_description.yaml +++ /dev/null @@ -1,34 +0,0 @@ -info: - id: denoising - name: Denoising - v1_url: openproblems/tasks/denoising/README.md - v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb - description: "Removing noise in sparse single-cell RNA-sequencing count data" - full_description: | - Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present - in each cell. As a result, the measurements (UMI counts) observed for each gene and each - cell are associated with generally high levels of technical noise ([Grün et al., - 2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes the task of - estimating the true expression level of each gene in each cell. In the single-cell - literature, this task is also referred to as *imputation*, a term which is typically - used for missing data problems in statistics. Similar to the use of the terms "dropout", - "missing data", and "technical zeros", this terminology can create confusion about the - underlying measurement process ([Sarkar and Stephens, - 2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). - - A key challenge in evaluating denoising methods is the general lack of a ground truth. A - recent benchmark study ([Hou et al., - 2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) - relied on flow-sorted datasets, mixture control experiments ([Tian et al., - 2019](https://www.nature.com/articles/s41592-019-0425-8)), and comparisons with bulk - RNA-Seq data. Since each of these approaches suffers from specific limitations, it is - difficult to combine these different approaches into a single quantitative measure of - denoising accuracy. Here, we instead rely on an approach termed molecular - cross-validation (MCV), which was specifically developed to quantify denoising accuracy - in the absence of a ground truth ([Batson et al., - 2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the observed molecules - in a given scRNA-Seq dataset are first partitioned between a *training* and a *test* - dataset. Next, a denoising method is applied to the training dataset. Finally, denoising - accuracy is measured by comparing the result to the test dataset. The authors show that - both in theory and in practice, the measured denoising accuracy is representative of the - accuracy that would be obtained on a ground truth dataset. diff --git a/src/denoising/docs/task_info.yaml b/src/denoising/docs/task_info.yaml new file mode 100644 index 0000000000..a5e77d59ef --- /dev/null +++ b/src/denoising/docs/task_info.yaml @@ -0,0 +1,33 @@ +task_id: denoising +task_name: Denoising +v1_url: openproblems/tasks/denoising/README.md +v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb +short_description: "Removing noise in sparse single-cell RNA-sequencing count data" +description: | + Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present + in each cell. As a result, the measurements (UMI counts) observed for each gene and each + cell are associated with generally high levels of technical noise ([Grün et al., + 2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes the task of + estimating the true expression level of each gene in each cell. In the single-cell + literature, this task is also referred to as *imputation*, a term which is typically + used for missing data problems in statistics. Similar to the use of the terms "dropout", + "missing data", and "technical zeros", this terminology can create confusion about the + underlying measurement process ([Sarkar and Stephens, + 2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). + + A key challenge in evaluating denoising methods is the general lack of a ground truth. A + recent benchmark study ([Hou et al., + 2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) + relied on flow-sorted datasets, mixture control experiments ([Tian et al., + 2019](https://www.nature.com/articles/s41592-019-0425-8)), and comparisons with bulk + RNA-Seq data. Since each of these approaches suffers from specific limitations, it is + difficult to combine these different approaches into a single quantitative measure of + denoising accuracy. Here, we instead rely on an approach termed molecular + cross-validation (MCV), which was specifically developed to quantify denoising accuracy + in the absence of a ground truth ([Batson et al., + 2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the observed molecules + in a given scRNA-Seq dataset are first partitioned between a *training* and a *test* + dataset. Next, a denoising method is applied to the training dataset. Finally, denoising + accuracy is measured by comparing the result to the test dataset. The authors show that + both in theory and in practice, the measured denoising accuracy is representative of the + accuracy that would be obtained on a ground truth dataset. From e6b3b0753e2e262b1c73ddddbad1b897bb6c92ea Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 20:40:59 +0100 Subject: [PATCH 0646/1233] create api for common get_info scripts Former-commit-id: 2d0db4310cd36d37a25937dc44f770c28a63daae --- src/common/api/get_info.yaml | 48 ++++++++++++++++++++++ src/common/get_api_info/config.vsh.yaml | 24 ++--------- src/common/get_api_info/script.R | 6 +-- src/common/get_api_info/test.py | 27 ------------ src/common/get_method_info/config.vsh.yaml | 20 ++------- src/common/get_method_info/script.R | 4 +- src/common/get_method_info/test.py | 27 ------------ src/common/get_metric_info/config.vsh.yaml | 21 ++-------- src/common/get_metric_info/script.R | 4 +- src/common/get_metric_info/test.py | 27 ------------ src/common/get_task_info/config.vsh.yaml | 22 ++-------- src/common/get_task_info/script.py | 4 +- src/common/get_task_info/test.py | 27 ------------ 13 files changed, 71 insertions(+), 190 deletions(-) create mode 100644 src/common/api/get_info.yaml delete mode 100644 src/common/get_api_info/test.py delete mode 100644 src/common/get_method_info/test.py delete mode 100644 src/common/get_metric_info/test.py delete mode 100644 src/common/get_task_info/test.py diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml new file mode 100644 index 0000000000..bffa3bde92 --- /dev/null +++ b/src/common/api/get_info.yaml @@ -0,0 +1,48 @@ +functionality: + arguments: + - name: "--input" + type: "file" + multiple: false + example: ../openproblems-v2 + description: "the root repo" + - name: "--task_id" + type: "string" + description: "A task dir" + example: label_projection + - name: "--output" + type: "file" + direction: "output" + default: "output.json" + description: "Output json" + test_resources: + - type: python_script + path: generic_test.py + text: | + import subprocess + from os import path + import json + + input_path = "/openproblems-v2" + task_id = "denoising" + output_path = "output.json" + + cmd = [ + meta['executable'], + "--input", input_path, + "--task_id", task_id, + "--output", output_path, + ] + + print(">> Running script as test", flush=True) + out = subprocess.run(cmd, capture_output=True, text=True) + print(out.stderr) + + print(">> Checking whether output file exists", flush=True) + assert path.exists(output_path) + + print(">> Reading json file", flush=True) + with open(output_path, 'r') as f: + out = json.load(f) + print(out) + + print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 819cbf7b47..1152da6e53 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -1,29 +1,11 @@ +__merge__: ../api/get_info.yaml functionality: name: "get_api_info" namespace: "common" description: "Extract api info" - arguments: - - name: "--input" - type: "file" - multiple: true - example: src - description: "A source dir" - - name: "--query" - type: "string" - description: "A task dir" - example: label_projection - - name: "--output" - type: "file" - direction: "output" - default: "output.json" - description: "Output json" resources: - type: r_script path: script.R - test_resources: - - path: ../../../src - - type: python_script - path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 @@ -32,6 +14,8 @@ platforms: cran: [ tidyverse ] test_setup: - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] + - type: docker + run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow - type: native diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index 1c3c0acda1..2913db6455 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -4,13 +4,13 @@ library(rlang) ## VIASH START par <- list( input = "src", - query = "label_projection", + task_id = "label_projection", output = "output/api.json" ) ## VIASH END -comp_yamls <- list.files(paste(par$input, par$query, "api", sep = "/"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste(par$input, par$query, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) +comp_yamls <- list.files(paste(par$input, 'src', par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste(par$input, 'src', par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) # list component - file args links comp_file <- map_df(comp_yamls, function(yaml_file) { diff --git a/src/common/get_api_info/test.py b/src/common/get_api_info/test.py deleted file mode 100644 index e0f8ee6305..0000000000 --- a/src/common/get_api_info/test.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -from os import path -import json - -input_path = meta["resources_dir"] + "src" -query = "denoising" -output_path = "output.json" - -cmd = [ - meta['executable'], - "--input", input_path, - "--query", query, - "--output", output_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading json file") -with open(output_path, 'r') as f: - out = json.load(f) - print(out) - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 83c10c4253..c36388e56f 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -1,27 +1,11 @@ +__merge__: ../api/get_info.yaml functionality: name: "get_method_info" namespace: "common" description: "Extract method info" - arguments: - - name: "--input" - type: "file" - example: src - - name: "--query" - type: "string" - description: "A task dir" - example: label_projection - - name: "--output" - type: "file" - direction: "output" - default: "output.json" - description: "Output json" resources: - type: r_script path: script.R - test_resources: - - path: ../../../src - - type: python_script - path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 @@ -35,5 +19,7 @@ platforms: test_setup: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] + - type: docker + run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow - type: native diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 28eb250cbb..0a758dbe87 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -4,14 +4,14 @@ library(rlang) ## VIASH START par <- list( input = "src", - query = "label_projection", + task_id = "label_projection", output = "output/method_info.json" ) ## VIASH END ns_list <- processx::run( "viash", - c("ns", "list", "-q", "methods", "--src", par$query), + c("ns", "list", "-q", "methods", "--src", paste("src", par$task_id, sep = "/")), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) diff --git a/src/common/get_method_info/test.py b/src/common/get_method_info/test.py deleted file mode 100644 index 58ac7e462c..0000000000 --- a/src/common/get_method_info/test.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -from os import path -import json - -input_path = meta["resources_dir"] + "src" -query = "label_projection" -output_path = "output.json" - -cmd = [ - meta['executable'], - "--input", input_path, - "--query", query, - "--output", output_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading json file") -with open(output_path, 'r') as f: - out = json.load(f) - print(out[0]) - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index ac481e3964..37dbb29a4c 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -1,28 +1,11 @@ +__merge__: ../api/get_info.yaml functionality: name: "get_metric_info" namespace: "common" description: "Extract metric info" - arguments: - - name: "--input" - type: "file" - example: src - description: "A source dir" - - name: "--query" - type: "string" - description: "A task dir" - example: label_projection - - name: "--output" - type: "file" - direction: "output" - default: "output.json" - description: "Output json" resources: - type: r_script path: script.R - test_resources: - - path: ../../../src - - type: python_script - path: test.py platforms: - type: docker image: eddelbuettel/r2u:22.04 @@ -36,5 +19,7 @@ platforms: test_setup: - type: apt packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] + - type: docker + run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow - type: native diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 17cd07dc48..3650e139be 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -4,14 +4,14 @@ library(rlang) ## VIASH START par <- list( input = "src", - query = "label_projection", + task_id = "label_projection", output = "output/metrics.json" ) ## VIASH END ns_list <- processx::run( "viash", - c("ns", "list", "-q", "metrics", "--src", par$query), + c("ns", "list", "-q", "metrics", "--src", paste("src", par$task_id, sep = "/")), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) diff --git a/src/common/get_metric_info/test.py b/src/common/get_metric_info/test.py deleted file mode 100644 index 55fc7d72c1..0000000000 --- a/src/common/get_metric_info/test.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -from os import path -import json - -input_path = meta["resources_dir"] + "src" -query = "label_projection" -output_path = "output.json" - -cmd = [ - meta['executable'], - "--input", input_path, - "--query", query, - "--output", output_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading json file") -with open(output_path, 'r') as f: - out = json.load(f) - print(out[0]) - -print("All checks succeeded!") diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index feb0858d80..5812adc95b 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -1,33 +1,19 @@ +__merge__: ../api/get_info.yaml functionality: name: "get_task_info" namespace: "common" description: "Extract task info" - arguments: - - name: "--input" - type: "file" - example: src - description: "A s dir" - - name: "--query" - type: "string" - description: "A task dir" - example: label_projection - - name: "--output" - type: "file" - direction: "output" - default: "output.json" - description: "Output json" resources: - type: python_script path: script.py - test_resources: - - path: ../../../src - - type: python_script - path: test.py platforms: - type: docker image: python:3.10 setup: - type: python pip: [ pyyaml ] + test_setup: + - type: docker + run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow - type: native diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py index 7cda3324cb..0d529a1e36 100644 --- a/src/common/get_task_info/script.py +++ b/src/common/get_task_info/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { "input" : "src", - "query" : "denoising", + "task_id" : "denoising", "output": "output/task.json", } @@ -13,7 +13,7 @@ ## VIASH END -task_info_path = path.join(par['input'], par['query'], "docs", "task_description.yaml") +task_info_path = path.join(par['input'], 'src', par['task_id'], "docs", "task_info.yaml") diff --git a/src/common/get_task_info/test.py b/src/common/get_task_info/test.py deleted file mode 100644 index dc9cbfa0b4..0000000000 --- a/src/common/get_task_info/test.py +++ /dev/null @@ -1,27 +0,0 @@ -import subprocess -from os import path -import json - -input_path = meta["resources_dir"] + "src" -query = "denoising" -output_path = "output.json" - -cmd = [ - meta['executable'], - "--input", input_path, - "--query", query, - "--output", output_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading json file") -with open(output_path, 'r') as f: - out = json.load(f) - print(out) - -print("All checks succeeded!") From 8c57241a6f39f1a14c5fbf9558f2fb755ae8bc5a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 20:52:53 +0100 Subject: [PATCH 0647/1233] update collect_data script Former-commit-id: 6910147cc4ac167e67d7afc97bfc7f53b2cd8d89 --- src/common/collect_data/script.sh | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/common/collect_data/script.sh b/src/common/collect_data/script.sh index 94d31e6555..70d2cd1e17 100755 --- a/src/common/collect_data/script.sh +++ b/src/common/collect_data/script.sh @@ -18,14 +18,14 @@ for task_id in label_projection dimensionality_reduction denoising; do # generate task info viash run src/common/get_task_info/config.vsh.yaml -- \ - --input "src" \ - --query $task_id \ + --input "../openproblems-v2" \ + --task_id $task_id \ --output "$out_dir/task_info.json" # generate method info viash run src/common/get_method_info/config.vsh.yaml -- \ - --input "src" \ - --query $task_id \ + --input "../openproblems-v2" \ + --task_id $task_id \ --output "$out_dir/temp_method_info.json" viash run src/common/check_migration_status/config.vsh.yaml -- \ --git_sha "openproblems_git.json" \ @@ -35,8 +35,8 @@ for task_id in label_projection dimensionality_reduction denoising; do # generate metric info viash run src/common/get_metric_info/config.vsh.yaml -- \ - --input "src" \ - --query $task_id \ + --input "../openproblems-v2" \ + --task_id $task_id \ --output "$out_dir/temp_metric_info.json" viash run src/common/check_migration_status/config.vsh.yaml -- \ --git_sha "openproblems_git.json" \ @@ -52,7 +52,7 @@ for task_id in label_projection dimensionality_reduction denoising; do # generate api info viash run src/common/get_api_info/config.vsh.yaml -- \ - --input "src" \ - --query $task_id \ + --input "../openproblems-v2" \ + --task_id $task_id \ --output "$out_dir/api.json" done \ No newline at end of file From 573c4e83f43b390a2849c5d50c1698f7e278fc0d Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 20:58:43 +0100 Subject: [PATCH 0648/1233] improve get_method_info Former-commit-id: 5dc36c57a74d5a4ec22c44e51a4370880587f55f --- src/common/get_method_info/script.R | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 9a9136291d..19c7173934 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -23,10 +23,7 @@ df <- map_df(configs, function(config) { info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace info$description <- config$functionality$description - info$is_baseline <- FALSE - if (grepl("control", info$type)) { - info$is_baseline <- TRUE - } + info$is_baseline <- grepl("control", info$type) info }) %>% select(method_id, type, method_name, everything()) From f134b40e5e7a274602193f3b538a1d2ab6fb178c Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 21:17:05 +0100 Subject: [PATCH 0649/1233] add task_info.yaml Former-commit-id: dd0f8a48ffc38af3364c8da13cfaa80a8bce4c1c --- src/joint_embedding/docs/task_info.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 src/joint_embedding/docs/task_info.yaml diff --git a/src/joint_embedding/docs/task_info.yaml b/src/joint_embedding/docs/task_info.yaml new file mode 100644 index 0000000000..6565c0c292 --- /dev/null +++ b/src/joint_embedding/docs/task_info.yaml @@ -0,0 +1,16 @@ +task_id: joint_embedding +task_name: Joint Embedding +v1_url: neurips2021_multimodal_viash/src/joint_embedding/readme.md +v1_commit: 0f8eae583444ba3f71c3083b860cc34b9ecb2fa2 +short_description: Learning of an embedded space that leverages the information of multiple modalities (e.g. for improved cell type annotation). +description: | + The functioning of organs, tissues, and whole organisms is determined by the interplay of cells. + Cells are characterised into broad types, which in turn can take on different states. Here, a cell + state is made up of the sum of all processes that are occurring within the cell. We can gain insight + into the state of a cell by different types of measurements: e.g., RNA expression, protein abundance, + or chromatin conformation. Combining this information to describe cellular heterogeneity requires the + formation of joint embeddings generated from this multimodal data. These embeddings must account for + and remove possible batch effects between different measurement batches. The reward for methods that + can achieve this is great: a highly resolved description of the underlying biological state of a cell + that determines its function, how it interacts with other cells, and thus the cell’s role in the f + unctioning of the whole tissue. \ No newline at end of file From 26308e944166c2ea25529249605a140236cddc56 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 5 Jan 2023 21:22:10 +0100 Subject: [PATCH 0650/1233] Revert "add task_info.yaml" This reverts commit f134b40e5e7a274602193f3b538a1d2ab6fb178c [formerly dd0f8a48ffc38af3364c8da13cfaa80a8bce4c1c]. Former-commit-id: e47e67542998b1a5d3810bd4422989f912e4e915 --- src/joint_embedding/docs/task_info.yaml | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 src/joint_embedding/docs/task_info.yaml diff --git a/src/joint_embedding/docs/task_info.yaml b/src/joint_embedding/docs/task_info.yaml deleted file mode 100644 index 6565c0c292..0000000000 --- a/src/joint_embedding/docs/task_info.yaml +++ /dev/null @@ -1,16 +0,0 @@ -task_id: joint_embedding -task_name: Joint Embedding -v1_url: neurips2021_multimodal_viash/src/joint_embedding/readme.md -v1_commit: 0f8eae583444ba3f71c3083b860cc34b9ecb2fa2 -short_description: Learning of an embedded space that leverages the information of multiple modalities (e.g. for improved cell type annotation). -description: | - The functioning of organs, tissues, and whole organisms is determined by the interplay of cells. - Cells are characterised into broad types, which in turn can take on different states. Here, a cell - state is made up of the sum of all processes that are occurring within the cell. We can gain insight - into the state of a cell by different types of measurements: e.g., RNA expression, protein abundance, - or chromatin conformation. Combining this information to describe cellular heterogeneity requires the - formation of joint embeddings generated from this multimodal data. These embeddings must account for - and remove possible batch effects between different measurement batches. The reward for methods that - can achieve this is great: a highly resolved description of the underlying biological state of a cell - that determines its function, how it interacts with other cells, and thus the cell’s role in the f - unctioning of the whole tissue. \ No newline at end of file From 4dca50f6bc669cd2eb4d570e73d81cca2bf7d0d2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 5 Jan 2023 21:24:12 +0000 Subject: [PATCH 0651/1233] Bump tj-actions/changed-files from 35.1.0 to 35.4.0 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.1.0 to 35.4.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.1.0...v35.4.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: 6a90f03d878ea36a4c702e64fea22c9c905b2cbf --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 98d4119535..1edc56fb55 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.1.0 + uses: tj-actions/changed-files@v35.4.0 with: separator: ";" diff_relative: true From c3195c6b014f0d6ed2d04b1ac95b2d70c90e1e9b Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 6 Jan 2023 13:51:08 +0100 Subject: [PATCH 0652/1233] add datset metadata to anndata Former-commit-id: b82f22d7ae7352c661d7f2cd52d79edb1058acbd --- .../loaders/openproblems_v1/config.vsh.yaml | 3 ++ .../loaders/openproblems_v1/script.py | 11 +++++-- src/datasets/loaders/openproblems_v1/test.py | 31 +++++++++---------- 3 files changed, 25 insertions(+), 20 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index eb16a1ec88..29f3f02d9e 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -34,6 +34,8 @@ functionality: resources: - type: python_script path: script.py + - type: file + path: metadata.yaml test_resources: - type: python_script path: test.py @@ -45,4 +47,5 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 2a5b958427..fec313c8b0 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -2,6 +2,7 @@ import openproblems as op import scanpy as sc import scipy +import yaml ## VIASH START par = { @@ -11,7 +12,6 @@ "obs_tissue": "tissue", "layer_counts": "counts", "output": "test_data.h5ad", - "layer_counts_output": "counts" } ## VIASH END @@ -36,8 +36,13 @@ adata = dataset_funs[par['id']]() -print("Setting .uns['dataset_id']") -adata.uns["dataset_id"] = "openproblems_v1/" + par["id"] +print("Setting .uns metadata") + +with open( "metadata.yaml") as md: + metadata = yaml.safe_load(md) + +for key in metadata[par["id"]]: + adata.uns[key] = metadata[par["id"]][key] print("Setting .obs['celltype']") if par["obs_celltype"]: diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index 274cf8510b..69ad280d24 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -7,38 +7,35 @@ obs_celltype = "celltype" obs_batch = "tech" -layer_counts_output = "foobar" - -print(">> Running script") -out = subprocess.check_output([ +print(">> Running script", flush=True) +out = subprocess.run([ meta["executable"], "--id", name, "--obs_celltype", obs_celltype, "--obs_batch", obs_batch, "--layer_counts", "counts", - "--layer_counts_output", layer_counts_output, - "--output", output -]).decode("utf-8") + "--output", output], + capture_output=True, + text=True +) + +print(out.stdout) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists(output) -print(">> Read output anndata") +print(">> Read output anndata", flush=True) adata = sc.read_h5ad(output) print(adata) -print(">> Check that output fits expected API") -if layer_counts_output is not None: - assert adata.X is None - assert layer_counts_output in adata.layers -else: - assert adata.X is not None - assert layer_counts_output not in adata.layers +print(">> Check that output fits expected API", flush=True) +assert adata.X is None +assert "counts" in adata.layers assert adata.uns["dataset_id"] == name if obs_celltype: assert "celltype" in adata.obs.columns if obs_batch: assert "batch" in adata.obs.columns -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) From 3405e7c7a100a51a15d701193aaa3eacd9a5dd10 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 6 Jan 2023 13:59:07 +0100 Subject: [PATCH 0653/1233] update dataloader script Former-commit-id: a8aca6cee1383fe1bb6adf01f144551137f9847d --- src/datasets/loaders/openproblems_v1/script.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index fec313c8b0..bb6816bdfc 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -37,12 +37,11 @@ adata = dataset_funs[par['id']]() print("Setting .uns metadata") - -with open( "metadata.yaml") as md: +with open( "src/datasets/loaders/openproblems_v1/metadata.yaml") as md: metadata = yaml.safe_load(md) - -for key in metadata[par["id"]]: - adata.uns[key] = metadata[par["id"]][key] + +for key, value in metadata[par["id"]].items(): + adata.uns[key] = value print("Setting .obs['celltype']") if par["obs_celltype"]: From bd70a6eed6e1f343e5937fa607f4b3b62ed6c929 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 6 Jan 2023 14:06:43 +0100 Subject: [PATCH 0654/1233] fix metadata.yaml path Former-commit-id: 5449152165a5fe9b8a8b2e00cfec1427f49aea8e --- src/datasets/loaders/openproblems_v1/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index bb6816bdfc..7e8ff46c6c 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -37,7 +37,7 @@ adata = dataset_funs[par['id']]() print("Setting .uns metadata") -with open( "src/datasets/loaders/openproblems_v1/metadata.yaml") as md: +with open( "metadata.yaml") as md: metadata = yaml.safe_load(md) for key, value in metadata[par["id"]].items(): From 4979d63ab1314dc7e819fd1c1f2e3800f4c68efa Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 6 Jan 2023 14:14:43 +0100 Subject: [PATCH 0655/1233] update metadata.yaml Former-commit-id: e6f652ac76139f21d11d688890d170429f1caa44 --- .../loaders/openproblems_v1/metadata.yaml | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/metadata.yaml b/src/datasets/loaders/openproblems_v1/metadata.yaml index dd676703e2..6369bb89bd 100644 --- a/src/datasets/loaders/openproblems_v1/metadata.yaml +++ b/src/datasets/loaders/openproblems_v1/metadata.yaml @@ -1,65 +1,65 @@ allen_brain_atlas: - dataset_id: 'allen_brain_atlas' + dataset_id: 'openproblems_v1/allen_brain_atlas' dataset_name: data_url: data_reference: dataset_summary: cengen: - dataset_id: 'cengen' + dataset_id: 'openproblems_v1/cengen' dataset_name: data_url: data_reference: dataset_summary: immune_cells: - dataset_id: 'immune_cells' + dataset_id: 'openproblems_v1/immune_cells' dataset_name: data_url: data_reference: dataset_summary: mouse_blood_olssen_labelled: - dataset_id: 'mouse_blood_olssen_labelled' + dataset_id: 'openproblems_v1/mouse_blood_olssen_labelled' dataset_name: data_url: data_reference: dataset_summary: pancreas: - dataset_id: 'pancreas' + dataset_id: 'openproblems_v1/pancreas' dataset_name: data_url: data_reference: dataset_summary: mouse_hspc_nestorowa2016: - dataset_id: 'mouse_hspc_nestorowa2016' + dataset_id: 'openproblems_v1/mouse_hspc_nestorowa2016' dataset_name: data_url: data_reference: dataset_summary: tabula_muris_senis_droplet_lung: - dataset_id: 'tabula_muris_senis_droplet_lung' + dataset_id: 'openproblems_v1/tabula_muris_senis_droplet_lung' dataset_name: data_url: data_reference: dataset_summary: tenx_1k_pbmc: - dataset_id: 'tenx_1k_pbmc' + dataset_id: 'openproblems_v1/tenx_1k_pbmc' dataset_name: data_url: data_reference: dataset_summary: tenx_5k_pbmc: - dataset_id: 'tenx_5k_pbmc' + dataset_id: 'openproblems_v1/tenx_5k_pbmc' dataset_name: data_url: data_reference: dataset_summary: tnbc_wu2021: - dataset_id: 'tnbc_wu2021' + dataset_id: 'openproblems_v1/tnbc_wu2021' dataset_name: data_url: data_reference: dataset_summary: zebrafish: - dataset_id: 'zebrafish' + dataset_id: 'openproblems_v1/zebrafish' dataset_name: data_url: data_reference: From ef94a4eab54356ebf37e9be14fd32ff03cf589ab Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Jan 2023 15:31:51 +0100 Subject: [PATCH 0656/1233] use resource instead of git clone to pass openproblems-v2 Former-commit-id: ca5979ffff3414a6c8a0f093eb1f526e789bcb1b --- src/common/api/get_info.yaml | 6 +++++- src/common/get_api_info/config.vsh.yaml | 4 +--- src/common/get_method_info/config.vsh.yaml | 4 +--- src/common/get_metric_info/config.vsh.yaml | 4 +--- src/common/get_results/config.vsh.yaml | 3 --- src/common/get_task_info/config.vsh.yaml | 3 --- 6 files changed, 8 insertions(+), 16 deletions(-) diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml index bffa3bde92..e0545712bf 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/api/get_info.yaml @@ -15,6 +15,10 @@ functionality: default: "output.json" description: "Output json" test_resources: + - path: ../../../src + dest: openproblems-v2/src + - path: ../../../_viash.yaml + dest: openproblems-v2/_viash.yaml - type: python_script path: generic_test.py text: | @@ -22,7 +26,7 @@ functionality: from os import path import json - input_path = "/openproblems-v2" + input_path = meta["resources_dir"] + "/openproblems-v2" task_id = "denoising" output_path = "output.json" diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 1152da6e53..a0528d2ad6 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -14,8 +14,6 @@ platforms: cran: [ tidyverse ] test_setup: - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] - - type: docker - run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" + packages: [ python3, python3-pip, python3-dev, python-is-python3 ] - type: nextflow - type: native diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index c36388e56f..81e54bf45f 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -18,8 +18,6 @@ platforms: run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" test_setup: - type: apt - packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - - type: docker - run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" + packages: [python3, python3-pip, python3-dev, python-is-python3] - type: nextflow - type: native diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 37dbb29a4c..419cd6c140 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -18,8 +18,6 @@ platforms: run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" test_setup: - type: apt - packages: [libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git] - - type: docker - run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" + packages: [python3, python3-pip, python3-dev, python-is-python3, git] - type: nextflow - type: native diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 46838779ba..97d5344348 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -27,8 +27,5 @@ platforms: setup: - type: r cran: [ tidyverse ] - test_setup: - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: nextflow - type: native diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index 5812adc95b..595665948e 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -12,8 +12,5 @@ platforms: setup: - type: python pip: [ pyyaml ] - test_setup: - - type: docker - run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - type: nextflow - type: native From 7595c4d62b061c1c073e6696397763e69514e231 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Jan 2023 15:37:55 +0100 Subject: [PATCH 0657/1233] fix quotes Former-commit-id: 3d80cc3c9f310f3fa0bee58ff3d2444fcfd4f9da --- src/common/get_api_info/script.R | 4 ++-- src/common/get_task_info/script.py | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index 2913db6455..9252a94a4b 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -9,8 +9,8 @@ par <- list( ) ## VIASH END -comp_yamls <- list.files(paste(par$input, 'src', par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste(par$input, 'src', par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) +comp_yamls <- list.files(paste(par$input, "src", par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste(par$input, "src", par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) # list component - file args links comp_file <- map_df(comp_yamls, function(yaml_file) { diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py index 0d529a1e36..3db738c217 100644 --- a/src/common/get_task_info/script.py +++ b/src/common/get_task_info/script.py @@ -13,12 +13,12 @@ ## VIASH END -task_info_path = path.join(par['input'], 'src', par['task_id'], "docs", "task_info.yaml") +task_info_path = path.join(par["input"], "src", par["task_id"], "docs", "task_info.yaml") -with open(task_info_path, 'r') as f: +with open(task_info_path, "r") as f: task_info = load(f, Loader=CSafeLoader ) -with open(par["output"], 'w') as out: +with open(par["output"], "w") as out: json.dump(task_info, out, indent=2) \ No newline at end of file From d20142f5d0e8ea9f41cc62aec10516ae449fedaa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Jan 2023 15:45:56 +0100 Subject: [PATCH 0658/1233] query was renamed to task_id Former-commit-id: 498955faa9eeff8393f12a55996f1156bda07f74 --- src/common/get_method_info/script.R | 2 +- src/common/get_metric_info/script.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 800565891f..6999adfdc2 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -20,7 +20,7 @@ df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(config$functionality$info) info$config_path <- gsub(".*\\./", "", config$info$config) - info$task_id <- par$query + info$task_id <- par$task_id info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace info$description <- config$functionality$description diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index dfe9e3d968..2c2913f737 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -20,7 +20,7 @@ df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) info$config_path <- gsub(".*\\./", "", config$info$config) - info$task_id <- par$query + info$task_id <- par$task_id info$component_id <- config$functionality$name info$namespace <- config$functionality$namespace info$component_description <- config$functionality$description From 90c0694030bcff53a2958fc9580a2cb35ef928fb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Jan 2023 15:52:42 +0100 Subject: [PATCH 0659/1233] throw warning if method_name does not exist (instead of an error) Former-commit-id: 980950cbde79ab68f39a198b52170fa781539f7c --- src/common/get_method_info/script.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 6999adfdc2..97150f7d1b 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -3,7 +3,7 @@ library(rlang) ## VIASH START par <- list( - input = "src", + input = ".", task_id = "label_projection", output = "output/method_info.json" ) @@ -27,7 +27,7 @@ df <- map_df(configs, function(config) { info$is_baseline <- grepl("control", info$type) info }) %>% - select(method_id, type, method_name, everything()) + select(method_id, type, one_of("method_name"), everything()) jsonlite::write_json( purrr::transpose(df), From e46b72bf3ab80b6322f325c11f3ce73ffc280142 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Jan 2023 15:52:53 +0100 Subject: [PATCH 0660/1233] fix similar issues as previous commit Former-commit-id: b29f0b4ca337845b1fc7c932e18998584ee5fc52 --- src/common/get_api_info/script.R | 2 +- src/common/get_metric_info/script.R | 2 +- src/common/get_task_info/script.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index 9252a94a4b..623684225d 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -3,7 +3,7 @@ library(rlang) ## VIASH START par <- list( - input = "src", + input = ".", task_id = "label_projection", output = "output/api.json" ) diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 2c2913f737..1872f90872 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -3,7 +3,7 @@ library(rlang) ## VIASH START par <- list( - input = "src", + input = ".", task_id = "label_projection", output = "output/metrics.json" ) diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py index 3db738c217..239b8e1750 100644 --- a/src/common/get_task_info/script.py +++ b/src/common/get_task_info/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - "input" : "src", + "input" : ".", "task_id" : "denoising", "output": "output/task.json", From af8085a25d9a453ef3f32dc3bbacb54f4e6b1332 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 10 Jan 2023 11:03:23 +0100 Subject: [PATCH 0661/1233] refactor the way the dataset loader component fetches metadata from v1 Former-commit-id: 49fa871e77fdd6ed6b5d7834174b601149a7431c --- .../loaders/openproblems_v1/config.vsh.yaml | 3 - .../loaders/openproblems_v1/metadata.yaml | 67 ---------------- .../loaders/openproblems_v1/script.py | 80 +++++++++++-------- src/datasets/loaders/openproblems_v1/test.py | 25 +++--- 4 files changed, 57 insertions(+), 118 deletions(-) delete mode 100644 src/datasets/loaders/openproblems_v1/metadata.yaml diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 29f3f02d9e..eb16a1ec88 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -34,8 +34,6 @@ functionality: resources: - type: python_script path: script.py - - type: file - path: metadata.yaml test_resources: - type: python_script path: test.py @@ -47,5 +45,4 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/metadata.yaml b/src/datasets/loaders/openproblems_v1/metadata.yaml deleted file mode 100644 index 6369bb89bd..0000000000 --- a/src/datasets/loaders/openproblems_v1/metadata.yaml +++ /dev/null @@ -1,67 +0,0 @@ -allen_brain_atlas: - dataset_id: 'openproblems_v1/allen_brain_atlas' - dataset_name: - data_url: - data_reference: - dataset_summary: -cengen: - dataset_id: 'openproblems_v1/cengen' - dataset_name: - data_url: - data_reference: - dataset_summary: -immune_cells: - dataset_id: 'openproblems_v1/immune_cells' - dataset_name: - data_url: - data_reference: - dataset_summary: -mouse_blood_olssen_labelled: - dataset_id: 'openproblems_v1/mouse_blood_olssen_labelled' - dataset_name: - data_url: - data_reference: - dataset_summary: -pancreas: - dataset_id: 'openproblems_v1/pancreas' - dataset_name: - data_url: - data_reference: - dataset_summary: -mouse_hspc_nestorowa2016: - dataset_id: 'openproblems_v1/mouse_hspc_nestorowa2016' - dataset_name: - data_url: - data_reference: - dataset_summary: -tabula_muris_senis_droplet_lung: - dataset_id: 'openproblems_v1/tabula_muris_senis_droplet_lung' - dataset_name: - data_url: - data_reference: - dataset_summary: -tenx_1k_pbmc: - dataset_id: 'openproblems_v1/tenx_1k_pbmc' - dataset_name: - data_url: - data_reference: - dataset_summary: -tenx_5k_pbmc: - dataset_id: 'openproblems_v1/tenx_5k_pbmc' - dataset_name: - data_url: - data_reference: - dataset_summary: -tnbc_wu2021: - dataset_id: 'openproblems_v1/tnbc_wu2021' - dataset_name: - data_url: - data_reference: - dataset_summary: -zebrafish: - dataset_id: 'openproblems_v1/zebrafish' - dataset_name: - data_url: - data_reference: - dataset_summary: - diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 7e8ff46c6c..1dccba8ecb 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -1,8 +1,7 @@ -print("Importing libraries") +from typing import Any, Callable, Dict, Tuple import openproblems as op import scanpy as sc import scipy -import yaml ## VIASH START par = { @@ -13,75 +12,86 @@ "layer_counts": "counts", "output": "test_data.h5ad", } +meta = { + "resources_dir": "src/datasets/loaders/openproblems_v1/" +} ## VIASH END -dataset_funs = { - 'allen_brain_atlas': op.data.allen_brain_atlas.load_mouse_brain_atlas, - 'cengen': op.data.cengen.load_cengen, - 'immune_cells': op.data.immune_cells.load_immune, - 'mouse_blood_olssen_labelled': op.data.mouse_blood_olssen_labelled.load_olsson_2016_mouse_blood, - 'mouse_hspc_nestorowa2016': op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, - 'pancreas': op.data.pancreas.load_pancreas, - # 'tabula_muris_senis': op.data.tabula_muris_senis.load_tabula_muris_senis, - 'tabula_muris_senis_droplet_lung': lambda : op.data.tabula_muris_senis.load_tabula_muris_senis( - organ_list=["lung"], - method_list=["droplet"] +# make dataset lookup table +# If need be, this could be stored in a separate yaml file +dataset_funs: Dict[str, Tuple[Callable, Dict[str, Any]]] = { + "allen_brain_atlas": (op.data.allen_brain_atlas.load_mouse_brain_atlas, {}), + "cengen": (op.data.cengen.load_cengen, {}), + "immune_cells": (op.data.immune_cells.load_immune, {}), + "mouse_blood_olssen_labelled": (op.data.mouse_blood_olssen_labelled.load_olsson_2016_mouse_blood, {}), + "mouse_hspc_nestorowa2016": (op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, {}), + "pancreas": (op.data.pancreas.load_pancreas, {}), + # "tabula_muris_senis": op.data.tabula_muris_senis.load_tabula_muris_senis, + "tabula_muris_senis_droplet_lung": ( + op.data.tabula_muris_senis.load_tabula_muris_senis, + {"organ_list": ["lung"], "method_list": ["droplet"]} ), - 'tenx_1k_pbmc': op.data.tenx.load_tenx_1k_pbmc, - 'tenx_5k_pbmc': op.data.tenx.load_tenx_5k_pbmc, - 'tnbc_wu2021': op.data.tnbc_wu2021.load_tnbc_data, - # 'Wagner_2018_zebrafish_embryo_CRISPR': op.data.Wagner_2018_zebrafish_embryo_CRISPR.load_zebrafish_chd_tyr, - 'zebrafish': op.data.zebrafish.load_zebrafish + "tenx_1k_pbmc": (op.data.tenx.load_tenx_1k_pbmc, {}), + "tenx_5k_pbmc": (op.data.tenx.load_tenx_5k_pbmc, {}), + "tnbc_wu2021": (op.data.tnbc_wu2021.load_tnbc_data, {}), + # "Wagner_2018_zebrafish_embryo_CRISPR": op.data.Wagner_2018_zebrafish_embryo_CRISPR.load_zebrafish_chd_tyr, + "zebrafish": (op.data.zebrafish.load_zebrafish, {}) } -adata = dataset_funs[par['id']]() +# fetch dataset +dataset_fun, kwargs = dataset_funs[par["id"]] + +print("Fetch dataset", flush=True) +adata = dataset_fun(**kwargs) -print("Setting .uns metadata") -with open( "metadata.yaml") as md: - metadata = yaml.safe_load(md) +print("Setting .uns['dataset_id']", flush=True) +adata.uns["dataset_id"] = par["id"] -for key, value in metadata[par["id"]].items(): +# override values one by one because adata.uns and +# metadata are two different classes. +for key, value in dataset_fun.metadata.items(): + print(f"Setting .uns['{key}']", flush=True) adata.uns[key] = value -print("Setting .obs['celltype']") +print("Setting .obs['celltype']", flush=True) if par["obs_celltype"]: if par["obs_celltype"] in adata.obs: adata.obs["celltype"] = adata.obs[par["obs_celltype"]] else: - print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.") + print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.", flush=True) -print("Setting .obs['batch']") +print("Setting .obs['batch']", flush=True) if par["obs_batch"]: if par["obs_batch"] in adata.obs: adata.obs["batch"] = adata.obs[par["obs_batch"]] else: - print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.") + print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.", flush=True) -print("Setting .obs['tissue']") +print("Setting .obs['tissue']", flush=True) if par["obs_tissue"]: if par["obs_tissue"] in adata.obs: adata.obs["tissue"] = adata.obs[par["obs_tissue"]] else: - print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") + print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.", flush=True) if par["layer_counts"] and par["layer_counts"] in adata.layers: - print(f" Temporarily moving .layers['{par['layer_counts']}'] to .X") + print(f"Temporarily moving .layers['{par['layer_counts']}'] to .X", flush=True) adata.X = adata.layers[par["layer_counts"]] del adata.layers[par["layer_counts"]] if par["sparse"] and not scipy.sparse.issparse(adata.X): - print(" Make counts sparse") + print("Make counts sparse", flush=True) adata.X = scipy.sparse.csr_matrix(adata.X) -print(" Removing empty genes") +print("Removing empty genes", flush=True) sc.pp.filter_genes(adata, min_cells=1) -print(" Removing empty cells") +print("Removing empty cells", flush=True) sc.pp.filter_cells(adata, min_counts=2) -print(f" Moving .X to .layers['counts']") +print("Moving .X to .layers['counts']", flush=True) adata.layers["counts"] = adata.X del adata.X -print("Writing adata to file") +print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index 69ad280d24..6606bc47d8 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -1,6 +1,6 @@ from os import path import subprocess -import scanpy as sc +import anndata as ad name = "pancreas" output = "dataset.h5ad" @@ -8,24 +8,23 @@ obs_batch = "tech" print(">> Running script", flush=True) -out = subprocess.run([ - meta["executable"], - "--id", name, - "--obs_celltype", obs_celltype, - "--obs_batch", obs_batch, - "--layer_counts", "counts", - "--output", output], - capture_output=True, - text=True +out = subprocess.run( + [ + meta["executable"], + "--id", name, + "--obs_celltype", obs_celltype, + "--obs_batch", obs_batch, + "--layer_counts", "counts", + "--output", output + ], + check=True ) -print(out.stdout) - print(">> Checking whether file exists", flush=True) assert path.exists(output) print(">> Read output anndata", flush=True) -adata = sc.read_h5ad(output) +adata = ad.read_h5ad(output) print(adata) From 04ba70311b8ef037b56dde00e95cbe4eb653b863 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 10 Jan 2023 15:30:29 +0100 Subject: [PATCH 0662/1233] clean up methods Former-commit-id: fbcc7089b09ed15d71c5c2758c576fb70fcc961b --- .../api/comp_method.yaml | 2 +- .../random_features/config.vsh.yaml | 8 +- .../control_methods/random_features/script.py | 33 ++++---- .../control_methods/random_features/test.py | 38 --------- .../true_features/config.vsh.yaml | 18 +++- .../control_methods/true_features/script.py | 43 ++++++---- .../methods/densmap/config.vsh.yaml | 26 ++++-- .../methods/densmap/script.py | 57 +++++++------ .../methods/neuralee/config.vsh.yaml | 30 ++++--- .../methods/neuralee/script.py | 84 +++++++++++-------- .../methods/pca/config.vsh.yaml | 12 ++- .../methods/pca/script.py | 40 +++++---- .../methods/phate/config.vsh.yaml | 19 ++--- .../methods/phate/script.py | 50 +++++------ .../methods/tsne/config.vsh.yaml | 23 +++-- .../methods/tsne/script.py | 50 ++++++----- .../methods/umap/config.vsh.yaml | 24 ++++-- .../methods/umap/script.py | 63 +++++++------- .../methods/umap/test.py | 45 ---------- 19 files changed, 338 insertions(+), 327 deletions(-) delete mode 100644 src/dimensionality_reduction/control_methods/random_features/test.py delete mode 100644 src/dimensionality_reduction/methods/umap/test.py diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 708e2faf7a..e9c6776d3a 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -26,7 +26,7 @@ functionality: assert path.exists(input_path) print(">> Running script as test", flush=True) - out = subprocess.run(cmd, check=True, capture_output=True, text=True) + subprocess.run(cmd, check=True) print(">> Checking whether output file exists", flush=True) assert path.exists(output_path) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index dfb03b9e7e..d4224281b5 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_features" namespace: "dimensionality_reduction/control_methods" - description: "Negative control method which generates a random embedding " + description: "Uses a normal distribution to generate random embeddings." info: type: negative_control - label: Random features + method_name: Random Features v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: counts variants: random_features: @@ -20,9 +20,7 @@ platforms: setup: - type: python packages: - - numpy - "anndata>=0.8" - - pyyaml - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/control_methods/random_features/script.py b/src/dimensionality_reduction/control_methods/random_features/script.py index d4abbdb274..7908207bda 100644 --- a/src/dimensionality_reduction/control_methods/random_features/script.py +++ b/src/dimensionality_reduction/control_methods/random_features/script.py @@ -1,35 +1,34 @@ import anndata as ad import numpy as np -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/test.h5ad', - 'output': 'reduced.h5ad', + "input": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "reduced.h5ad", } meta = { - 'functionality_name': 'random_features', + "functionality_name": "random_features", } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +print("Create random embedding", flush=True) +X_emb = np.random.normal(0, 1, (input.shape[0], 2)) -print('Create random embedding', flush=True) -input.obsm["X_emb"] = np.random.normal(0, 1, (input.shape[0], 2)) - -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/test.py b/src/dimensionality_reduction/control_methods/random_features/test.py deleted file mode 100644 index 778cd32194..0000000000 --- a/src/dimensionality_reduction/control_methods/random_features/test.py +++ /dev/null @@ -1,38 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/input/dataset.h5ad" -output_path = "output.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] - -print(">> Checking whether input file exists") -assert path.exists(input_path) - -print(">> Running script as test") -out = subprocess.run(cmd) -# out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) - -print("input:", input) -print("output:", output) - -print(">> Checking whether predictions were added") -assert "X_emb" in output.obsm -assert meta['functionality_name'] == output.uns["method_id"] - -print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index c79735d1a1..92fb2cae71 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -12,11 +12,22 @@ functionality: preferred_normalization: counts variants: true_features: + true_features_log_cpm: + preferred_normalization: log_cpm + use_normalized_layer: true + true_features_log_cpm_hvg: + preferred_normalization: log_cpm + use_normalized_layer: true + n_hvg: 1000 arguments: - - name: "--n_comps" + - name: "--use_normalized_layer" + type: boolean + default: false + description: Whether to work with the raw counts or the normalized counts. + - name: "--n_hvg" type: integer - default: 100 - description: Number of principal components to use. + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + default: 1000 resources: - type: python_script path: script.py @@ -28,7 +39,6 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/control_methods/true_features/script.py b/src/dimensionality_reduction/control_methods/true_features/script.py index 20f42f688e..aa8469051c 100644 --- a/src/dimensionality_reduction/control_methods/true_features/script.py +++ b/src/dimensionality_reduction/control_methods/true_features/script.py @@ -1,36 +1,43 @@ import anndata as ad -import scanpy as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/test.h5ad', - 'output': 'reduced.h5ad', - 'n_comps': 100, + "input": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "reduced.h5ad", + "n_hvg": 100, + "use_normalized_layer": False } meta = { - 'functionality_name': 'true_features', + "functionality_name": "true_features", } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +print("Create high dimensionally embedding with all features", flush=True) +if par["use_normalized_layer"]: + X_emb = input.layers["counts"].toarray() +else: + X_emb = input.layers["normalized"].toarray() -print('Create high dimensionally embedding with all features', flush=True) -input.obsm["X_emb"] = input.layers['counts'][:, :par['n_comps']].toarray() +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_emb = X_emb[:, idx] -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - uns={} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) -output.obsm['X_emb'] = input.obsm['X_emb'] -output.uns['dataset_id'] = input.uns['dataset_id'] -output.uns['normalization_id'] = input.uns['normalization_id'] -output.uns['method_id'] = input.uns['method_id'] print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 91d781f161..eb6695275c 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -2,22 +2,31 @@ __merge__: ../../api/comp_method.yaml functionality: name: "densmap" namespace: "dimensionality_reduction/methods" - description: "density-preserving based on UMAP" + description: "Density-preserving UMAP" info: type: method - label: densMAP - paper_doi: "10.1038/s41587-020-00801-7" + method_name: densMAP + paper_reference: "narayan2021assessing" code_url: https://github.com/lmcinnes/umap - v1_url: openproblems/tasks/dimensionality_reduction/methods/densmap.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: + densmap_logCPM: + densmap_pca_logCPM: + n_pca_dims: 50 densmap_logCPM_1kHVG: + n_hvg: 1000 densmap_pca_logCPM_1kHVG: + n_pca_dims: 50 + n_hvg: 1000 arguments: - - name: "--no_pca" - type: boolean_true - description: Do not apply PCA with 50 dimensions before running UMAP. + - name: "--n_hvg" + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + - name: "--n_pca_dims" + type: integer + description: Number of PCA dimensions to use. If not specified, no PCA will be performed. resources: - type: python_script path: script.py @@ -29,7 +38,6 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index 44e71c4262..e02386010d 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -1,46 +1,55 @@ import anndata as ad from umap import UMAP import scanpy as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', - 'output': 'reduced.h5ad', - 'no_pca': False, + "input": "resources_test/common/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_pca_dims": False, + "n_hvg": 1000 } meta = { - 'functionality_name': 'densmap', - 'config': 'src/dimensionality_reduction/methods/densmap/config.vsh.yaml' + "functionality_name": "densmap", + "config": "src/dimensionality_reduction/methods/densmap/config.vsh.yaml" } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) +X_mat = input.layers["normalized"] -print('Select top 1000 high variable genes', flush=True) -n_genes = 1000 -idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] -input = input[:, idx].copy() +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] -print("Run UMAP...", flush=True) -if par['no_pca']: - print('... using logCPM data', flush=True) - input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.layers['normalized']) +if par["n_pca_dims"]: + print("Apply PCA to normalized data", flush=True) + umap_input = sc.tl.pca( + X_mat, + n_comps=par["n_pca_dims"], + svd_solver="arpack" + ) else: - print('... after applying PCA with 50 dimensions to logCPM data', flush=True) - input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=50, svd_solver="arpack") - input.obsm["X_emb"] = UMAP(densmap=True, random_state=42).fit_transform(input.obsm['X_pca_hvg']) + print("Use normalized data as input for UMAP", flush=True) + umap_input = X_mat -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +print("Run densMAP", flush=True) +X_emb = UMAP(densmap=True, random_state=42).fit_transform(umap_input) -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 07e9eaba9e..6b083bd880 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -5,24 +5,31 @@ functionality: description: "A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/)." info: type: method - label: NeuralEE - paper_doi: "10.3389/fgene.2020.00786" + method_name: NeuralEE + paper_reference: "xiong2020neuralee" code_url: https://github.com/HiBearME/NeuralEE v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py - v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 - preferred_normalization: counts + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + preferred_normalization: log_cpm variants: neuralee_default: + normalize: true + n_hvg: 500 neuralee_logCPM_1kHVG: - normalize: False - subsample_genes: None - preferred_normalization: log_cpm - # To-do: add specific options for unit tests such as --maxit + normalize: false + n_hvg: 1000 arguments: - - name: "--maxit" + - name: "--n_iter" type: integer - default: 100 - description: "max number of iterations for NeuralEE." + description: Number of iterations. + - name: "--n_hvg" + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + default: 1000 + - name: "--normalize" + type: boolean + default: false + description: Whether to perform own normalization resources: - type: python_script path: script.py @@ -34,7 +41,6 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml - torch - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index 80a4178a77..d66d41e522 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -1,60 +1,78 @@ import anndata as ad -import scanpy as sc -import yaml import torch from neuralee.embedding import NeuralEE from neuralee.dataset import GeneExpressionDataset +# todo: allow gpu +device = torch.device("cpu") + ## VIASH START par = { - 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', - 'output': 'reduced.h5ad', - 'no_pca': False, + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_hvg": 1000, + "normalize": False, + "n_iter": None } meta = { - 'functionality_name': 'neuralee', - 'config': 'src/dimensionality_reduction/methods/neuralee/config.vsh.yaml' + "functionality_name": "neuralee", } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) - -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +input = ad.read_h5ad(par["input"]) -if input.uns['normalization_id'] == 'counts': - print('Select top 500 high variable genes', flush=True) - # idx = input.var['hvg_score'].to_numpy().argsort()[-500:] - # dataset = GeneExpressionDataset(input.layers['counts'][:, idx]) - dataset = GeneExpressionDataset(input.layers['counts']) +if par["normalize"]: + print("Performing own normalization", flush=True) + # perform own normalization based on the "recommended" preprocessing taken from example notebooks, e.g.: + # https://github.com/HiBearME/NeuralEE/blob/master/tests/notebooks/retina_dataset.ipynb + dataset = GeneExpressionDataset(input.layers["counts"]) dataset.log_shift() - dataset.subsample_genes(500) + if par["n_hvg"]: + dataset.subsample_genes(par["n_hvg"]) dataset.standardscale() -elif input.uns['normalization_id'] == 'log_cpm': - n_genes = 1000 - print('Select top 1000 high variable genes', flush=True) - idx = input.var['hvg_score'].to_numpy().argsort()[-n_genes:] - input = input[:, idx].copy() - dataset = GeneExpressionDataset(input.layers['normalized']) + +else: + X_mat = input.layers["normalized"] + + if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[-par["n_hvg"]:] + X_mat = X_mat[:, idx] + + print("Using pre-normalized data", flush=True) + dataset = GeneExpressionDataset(X_mat) -# 1000 cells as a batch to estimate the affinity matrix -dataset.affinity_split(N_small=min(1000, input.n_obs)) -NEE = NeuralEE(dataset, d=2, device=torch.device("cpu")) +# estimate the affinity matrix +batch_size = min(1000, input.n_obs) +print(f"Use {batch_size} cells as batch to estimate the affinity matrix", flush=True) +dataset.affinity_split(N_small=batch_size) + +print("Create NeuralEE object", flush=True) +NEE = NeuralEE(dataset, d=2, device=device) fine_tune_kwargs = dict(verbose=False) -fine_tune_kwargs["maxit"] = par['maxit'] -fine_tune_kwargs["maxit"] = 10 + +if par["n_iter"]: + fine_tune_kwargs["maxit"] = par["n_iter"] + +print("Run NeuralEE", flush=True) res = NEE.fine_tune(**fine_tune_kwargs) -input.obsm["X_emb"] = res["X"].detach().cpu().numpy() +X_emb = res["X"].detach().cpu().numpy() -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 9c3c8611a0..b78c33a723 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -5,14 +5,20 @@ functionality: description: "Principal component analysis (PCA)" info: type: method - label: PCA - paper_doi: "10.1080/14786440109462720" + method_name: "PCA" + paper_reference: pearson1901pca code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: + pca_logCPM: pca_logCPM_1kHVG: + n_hvg: 1000 + arguments: + - name: "--n_hvg" + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. resources: - type: python_script path: script.py diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index 7de656b2ec..760d9bc360 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -1,37 +1,41 @@ import anndata as ad import scanpy as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', - 'output': 'reduced.h5ad', + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_hvg": 1000, } meta = { - 'functionality_name': 'umap', - 'config': 'src/dimensionality_reduction/methods/PCA/config.vsh.yaml' + "functionality_name": "pca", } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) +X_mat = input.layers["normalized"] -print('Select top 1000 high variable genes', flush=True) -n_genes = 1000 -idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] -print('Apply PCA with 50 dimensions', flush=True) -input.obsm["X_emb"] = sc.tl.pca(input.layers['normalized'][:, idx], n_comps=50, svd_solver="arpack")[:, :2] +print(f"Running PCA", flush=True) +X_emb = sc.tl.pca(X_mat, n_comps=2, svd_solver="arpack")[:, :2] -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] - -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 92e8d19eaf..28e90b8525 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -5,33 +5,33 @@ functionality: description: "Potential of heat-diffusion for affinity-based transition embedding" info: type: method - label: PHATE - paper_doi: "10.1038/s41587-019-0336-3" + method_name: PHATE + paper_reference: "moon2019visualizing" code_url: https://github.com/KrishnaswamyLab/PHATE/ v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: sqrt_cpm variants: phate_default: phate_sqrt: gamma: 0 + phate_logCPM: + preferred_normalization: log_cpm phate_logCPM_1kHVG: num_hvg_genes: 1000 preferred_normalization: log_cpm arguments: - - name: '--n_pca' + - name: '--n_pca_dims' type: integer default: 50 description: Number of principal components of PCA to use. + - name: "--n_hvg" + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. - name: '--gamma' type: double description: Gamma value default: 1 - - name: '--num_hvg_genes' - type: integer - description: | - Subset to the highly variable genes as specified - by the .var['hvg_score'] column. resources: - type: python_script path: script.py @@ -44,7 +44,6 @@ platforms: - "anndata>=0.8" - phate==1.0.* - scprep - - pyyaml - "scikit-learn<1.2" - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 4b6b31b80a..279c93c11e 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -3,43 +3,43 @@ ## VIASH START par = { - 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', - 'output': 'reduced.h5ad', - 'n_pca': 50, - 'gamma': 1, - 'num_hvg_genes': None + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_pca_dims": 50, + "gamma": 1, + "n_hvg": None } meta = { - 'functionality_name': 'phate', - 'config': 'src/dimensionality_reduction/methods/phate/config.vsh.yaml' + "functionality_name": "phate", } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) -print("Run PHATE", flush=True) -phate_op = PHATE(n_pca=par['n_pca'], verbose=False, n_jobs=-1, gamma=par['gamma']) -X_mat = input.layers['normalized'] - -if par["num_hvg_genes"] and input.uns['normalization_id'] == 'log_cpm': - print("Subsetting to hvg genes", flush=True) - num_features = par["num_hvg_genes"] - hvg_idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:num_features] - X_mat = X_mat[:, hvg_idx] +X_mat = input.layers["normalized"] -# store embedding -input.obsm["X_emb"] = phate_op.fit_transform(X_mat) +if par["n_hvg"]: + print(f"Subsetting to {par['n_hvg']} HVG", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] -print('Add method', flush=True) -input.uns['method_id'] = meta['functionality_name'] +print("Run PHATE", flush=True) +phate_op = PHATE(n_pca=par["n_pca_dims"], verbose=False, n_jobs=-1, gamma=par["gamma"]) +X_emb = phate_op.fit_transform(X_mat) -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 319498a035..9f67413462 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -5,21 +5,24 @@ functionality: description: "t-Distributed Stochastic Neighbor Embedding (t-SNE)" info: type: method - label: t-SNE - paper_name: "Visualizing Data using t-SNE" - paper_url: "https://www.jmlr.org/papers/v9/vandermaaten08a.html" - paper_year: 2008 + method_name: t-SNE + paper_reference: vandermaaten2008visualizing code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: + tsne_logCPM: tsne_logCPM_1kHVG: + n_hvg: 1000 arguments: - - name: "--n_pca" + - name: "--n_hvg" type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + - name: "--n_pca_dims" + type: integer + description: Number of PCA dimensions to use. If not specified, no PCA will be performed. default: 50 - description: Number of principal components of PCA to use. resources: - type: python_script path: script.py @@ -27,11 +30,15 @@ platforms: - type: docker image: "python:3.10" setup: + - type: apt + packages: + - cmake + - gcc - type: python packages: - scanpy - "anndata>=0.8" - - pyyaml + - MulticoreTSNE - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index a214b31b0c..b90a177b15 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -1,42 +1,48 @@ import anndata as ad import scanpy as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/common/pancreas/train.h5ad', - 'output': 'reduced.h5ad', - 'n_pca': 50, + "input": "resources_test/common/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_pca_dims": 50, + "n_hvg": 1000 } meta = { - 'functionality_name': 'tsne', - 'config': 'src/dimensionality_reduction/methods/tsne/config.vsh.yaml' + "functionality_name": "tsne", + "config": "src/dimensionality_reduction/methods/tsne/config.vsh.yaml" } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par["input"]) -print('Select top 1000 high variable genes', flush=True) -n_genes = 1000 -idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] -input = input[:, idx].copy() -print('Apply PCA with 50 dimensions', flush=True) -input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") +X_mat = input.layers["normalized"] -print('Run t-SNE', flush=True) -sc.tl.tsne(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) -input.obsm["X_emb"] = input.obsm["X_tsne"].copy() +if par["n_hvg"]: + print(f"Subsetting to {par['n_hvg']} HVG", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +print("Computing PCA", flush=True) +input.obsm["X_pca"] = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack") -print('Copy data to new AnnData object', flush=True) +print("Run t-SNE", flush=True) +sc.tl.tsne(input, use_rep="X_pca", n_pcs=par["n_pca_dims"]) +X_emb = input.obsm["X_tsne"].copy() + +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index a38534a4b3..0d21b52625 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -2,22 +2,32 @@ __merge__: ../../api/comp_method.yaml functionality: name: "umap" namespace: "dimensionality_reduction/methods" - description: "Uniform Manifold Approximation and Projection (UMAP) as implemented by scanpy" + description: "Uniform Manifold Approximation and Projection for Dimension Reduction" info: type: method label: UMAP - paper_doi: "10.21105/joss.00861" + paper_doi: "10.1038/s41587-020-00801-7" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: + umap_logCPM: + umap_pca_logCPM: + n_pca_dims: 50 umap_logCPM_1kHVG: + n_hvg: 1000 + umap_pca_logCPM_1kHVG: + n_pca_dims: 50 + n_hvg: 1000 arguments: - - name: "--n_pca" + - name: "--n_hvg" type: integer - default: 50 - description: Number of principal components of PCA to use. + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + default: 1000 + - name: "--n_pca_dims" + type: integer + description: Number of PCA dimensions to use. If not specified, no PCA will be performed. resources: - type: python_script path: script.py @@ -29,7 +39,7 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml + - umap-learn - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index f89e8cd5e6..c3b7058269 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -1,47 +1,54 @@ import anndata as ad +from umap import UMAP import scanpy as sc -import yaml ## VIASH START par = { - 'input': 'resources_test/dimensionality_reduction/pancreas/train.h5ad', - 'output': 'reduced.h5ad', - 'n_pca': 50, + "input": "resources_test/common/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_pca_dims": False, } meta = { - 'functionality_name': 'umap', - 'config': 'src/dimensionality_reduction/methods/umap/config.vsh.yaml' + "functionality_name": "densmap", + "config": "src/dimensionality_reduction/methods/densmap/config.vsh.yaml" } ## VIASH END print("Load input data", flush=True) -input = ad.read_h5ad(par['input']) - -print('Select top 1000 high variable genes', flush=True) -n_genes = 1000 -idx = input.var['hvg_score'].to_numpy().argsort()[::-1][:n_genes] -input = input[:, idx].copy() - -print('Apply PCA with 50 dimensions', flush=True) -input.obsm['X_pca_hvg'] = sc.tl.pca(input.layers['normalized'], n_comps=par['n_pca'], svd_solver="arpack") - -print('Calculate a nearest-neighbour graph', flush=True) -sc.pp.neighbors(input, use_rep="X_pca_hvg", n_pcs=par['n_pca']) +input = ad.read_h5ad(par["input"]) +X_mat = input.layers["normalized"] + +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] + +if par["n_pca_dims"]: + print("Apply PCA to normalized data", flush=True) + umap_input = sc.tl.pca( + X_mat, + n_comps=par["n_pca_dims"], + svd_solver="arpack" + ) +else: + print("Use normalized data as input for UMAP", flush=True) + umap_input = X_mat print("Run UMAP", flush=True) -sc.tl.umap(input) -input.obsm["X_emb"] = input.obsm["X_umap"].copy() -del input.obsm["X_umap"] - -print('Add method ID', flush=True) -input.uns['method_id'] = meta['functionality_name'] +X_emb = UMAP(densmap=False, random_state=42).fit_transform(umap_input) -print('Copy data to new AnnData object', flush=True) +print("Create output AnnData", flush=True) output = ad.AnnData( obs=input.obs[[]], - obsm={"X_emb": input.obsm["X_emb"]}, - uns={key: input.uns[key] for key in ["dataset_id", "normalization_id", "method_id"]} + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } ) print("Write output to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/umap/test.py b/src/dimensionality_reduction/methods/umap/test.py deleted file mode 100644 index d986a1aa0f..0000000000 --- a/src/dimensionality_reduction/methods/umap/test.py +++ /dev/null @@ -1,45 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -## VIASH START -meta = { - 'executable': './target/docker/dimensionality_reduction/umap', - 'resources_dir': './resources_test/common/', -} -## VIASH END - -input_path = meta["resources_dir"] + "/input/train.h5ad" -output_path = "reduced.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] - -print(">> Checking whether input file exists") -assert path.exists(input_path) - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) - -print("input:", input) -print("output:", output) - -print(">> Checking whether predictions were added") -assert "X_emb" in output.obsm -assert meta['functionality_name'] == output.uns["method_id"] -assert 'normalization_id' in output.uns - -print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -print("All checks succeeded!") \ No newline at end of file From b1c7e0c2dd07cc0651f84a1a10cf19c0f3032064 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 11 Jan 2023 10:21:12 +0100 Subject: [PATCH 0663/1233] use updated test objects Former-commit-id: 494021d5ee805034782ab9f7b954beb2ab67748a --- .../embedding/methods/combat/config.vsh.yaml | 46 ++++++++++++++++ .../embedding/methods/combat/run_example.sh | 14 +++++ .../embedding/methods/combat/script.py | 53 +++++++++++++++++++ .../embedding/methods/combat/test.py | 47 ++++++++++++++++ .../metrics/asw_batch/config.vsh.yaml | 9 ++-- .../embedding/metrics/asw_batch/script.py | 8 ++- .../embedding/metrics/asw_batch/test.py | 2 +- .../metrics/asw_label/config.vsh.yaml | 7 ++- .../embedding/metrics/asw_label/script.py | 4 +- .../embedding/metrics/asw_label/test.py | 4 +- .../cell_cycle_conservation/config.vsh.yaml | 7 ++- .../metrics/cell_cycle_conservation/script.py | 4 +- .../metrics/cell_cycle_conservation/test.py | 2 +- .../embedding/metrics/pcr/config.vsh.yaml | 7 ++- .../embedding/metrics/pcr/script.py | 4 +- .../embedding/metrics/pcr/test.py | 5 +- 16 files changed, 188 insertions(+), 35 deletions(-) create mode 100644 src/batch_integration/embedding/methods/combat/config.vsh.yaml create mode 100644 src/batch_integration/embedding/methods/combat/run_example.sh create mode 100644 src/batch_integration/embedding/methods/combat/script.py create mode 100644 src/batch_integration/embedding/methods/combat/test.py diff --git a/src/batch_integration/embedding/methods/combat/config.vsh.yaml b/src/batch_integration/embedding/methods/combat/config.vsh.yaml new file mode 100644 index 0000000000..403a113571 --- /dev/null +++ b/src/batch_integration/embedding/methods/combat/config.vsh.yaml @@ -0,0 +1,46 @@ +functionality: + name: combat + namespace: batch_integration/embedding/methods + version: dev + description: Run Combat + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + arguments: + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] + required: true + - name: --input + type: file + description: Unintegrated anndata HDF5 file + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: true + required: false + - name: --scaling + type: boolean + description: Whether to scale the data or not + default: false + required: false + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + - type: nextflow diff --git a/src/batch_integration/embedding/methods/combat/run_example.sh b/src/batch_integration/embedding/methods/combat/run_example.sh new file mode 100644 index 0000000000..ce00a91fac --- /dev/null +++ b/src/batch_integration/embedding/methods/combat/run_example.sh @@ -0,0 +1,14 @@ +set -e +SCRIPTPATH="$( + cd "$(dirname "$0")" >/dev/null 2>&1 || exit + pwd -P +)" + +bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ + --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ + --label celltype \ + --batch batch \ + --hvg true \ + --scaling true \ + --output src/batch_integration/resources/graph_pancreas_combat.h5ad \ + --debug true diff --git a/src/batch_integration/embedding/methods/combat/script.py b/src/batch_integration/embedding/methods/combat/script.py new file mode 100644 index 0000000000..50a2c2d486 --- /dev/null +++ b/src/batch_integration/embedding/methods/combat/script.py @@ -0,0 +1,53 @@ +## VIASH START +par = { + 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', + 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'hvg': True, + 'scaling': True, + 'debug': True +} +## VIASH END + +print('Importing libraries') +from pprint import pprint +import scanpy as sc +from scipy.sparse import csr_matrix + +if par['debug']: + pprint(par) + +adata_file = par['input'] +output = par['output'] +hvg = par['hvg'] +scaling = par['scaling'] + +print('Read adata') +adata = sc.read_h5ad(adata_file) + +if hvg: + print('Select HVGs') + adata = adata[:, adata.var['highly_variable']] + +if scaling: + print('Scale') + adata.X = adata.layers['logcounts_scaled'] +else: + adata.X = adata.layers['logcounts'] + +print('Integrate') +adata.X = csr_matrix(sc.pp.combat(adata, key='batch', inplace=False)) + +print('Postprocess data') +adata.obsm['X_emb'] = sc.pp.pca( + adata.X, + n_comps=50, + use_highly_variable=False, + svd_solver='arpack', + return_info=False +) + +print('Save HDF5') +adata.uns['hvg'] = hvg +adata.uns['scaled'] = scaling + +adata.write(output, compression='gzip') diff --git a/src/batch_integration/embedding/methods/combat/test.py b/src/batch_integration/embedding/methods/combat/test.py new file mode 100644 index 0000000000..7f4179db31 --- /dev/null +++ b/src/batch_integration/embedding/methods/combat/test.py @@ -0,0 +1,47 @@ +from os import path +import subprocess +import numpy as np +import scanpy as sc + +np.random.seed(42) + +method = 'combat' +output_file = method + '.h5ad' + +print(">> Running script") +out = subprocess.check_output([ + "./" + method, + "--input", 'processed.h5ad', + "--hvg", 'False', + "--scaling", 'False', + "--output", output_file +]).decode("utf-8") + +print(">> Checking whether file exists") +assert path.exists(output_file) + +print('>> Checking API') +adata = sc.read(output_file) + +assert 'dataset_id' in adata.uns +assert 'label' in adata.obs.columns +assert 'batch' in adata.obs.columns +assert 'highly_variable' in adata.var +assert 'counts' in adata.layers +assert 'logcounts' in adata.layers +assert 'logcounts_scaled' in adata.layers +assert 'X_pca' in adata.obsm +assert 'X_emb' in adata.obsm +assert 'X_uni' in adata.obsm +assert 'uni' in adata.uns + +assert 'hvg' in adata.uns +assert adata.uns['hvg'] == False +assert 'scaled' in adata.uns +assert adata.uns['scaled'] == False + +unintegrated = sc.read('processed.h5ad') +assert len(unintegrated.X.data) != len(adata.X.data) +assert not np.any(np.not_equal(unintegrated.obsm['X_pca'], adata.obsm['X_pca'])) + +print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index 91fd23a4dc..2658b10e91 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: asw_batch - namespace: batch_integration/graph/metrics + namespace: batch_integration/embedding/metrics version: dev description: Average silhouette of batches per label authors: @@ -26,12 +26,11 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:0.1 - - type: native + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/embedding/metrics/asw_batch/script.py b/src/batch_integration/embedding/metrics/asw_batch/script.py index 8ab202df57..b798354f01 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/script.py +++ b/src/batch_integration/embedding/metrics/asw_batch/script.py @@ -9,7 +9,7 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.metrics import silhouette_batch +from scib.metrics import silhouette_batch if par['debug']: pprint.pprint(par) @@ -23,17 +23,15 @@ print('Read adata') adata = sc.read(adata_file) -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('compute score') -_, sil_clus = silhouette_batch( +score = silhouette_batch( adata, batch_key='batch', group_key='label', embed=EMBEDDING, - verbose=False ) -score = sil_clus['silhouette_score'].mean() with open(output, 'w') as file: header = ['dataset', 'output_type', 'metric', 'value'] diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py index 0fe5bb4c4e..45d57db43f 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ b/src/batch_integration/embedding/metrics/asw_batch/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml index 7b8df766f8..8be1d3037e 100644 --- a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml @@ -26,12 +26,11 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:0.1 - - type: native + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/embedding/metrics/asw_label/script.py index 2c878a7c6c..cffd0a9eb0 100644 --- a/src/batch_integration/embedding/metrics/asw_label/script.py +++ b/src/batch_integration/embedding/metrics/asw_label/script.py @@ -9,7 +9,7 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.metrics import silhouette +from scib.metrics import silhouette if par['debug']: pprint.pprint(par) @@ -22,7 +22,7 @@ print('Read adata') adata = sc.read(adata_file) -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('compute score') score = silhouette(adata, group_key='label', embed='X_emb') diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py index 4fc1ee63b5..9f2e4e02e6 100644 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.6171182170510292 +assert score == 0.49921771598747 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml index bd11ba8461..5d1866ddc0 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml @@ -30,12 +30,11 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:0.1 - - type: native + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py index 498e24863b..c267279a63 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py @@ -10,7 +10,7 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.metrics import cell_cycle +from scib.metrics import cell_cycle if par['debug']: pprint.pprint(par) @@ -25,7 +25,7 @@ print('Read adata') adata = sc.read(adata_file) adata_int = adata.copy() -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('compute score') score = cell_cycle( diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py index 7962d6fb13..e370bc85bd 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'combat.h5ad', "--organism", "human", "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml index 60265425e8..43ea41f5d0 100644 --- a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml @@ -26,12 +26,11 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - - path: '../../../resources/pancreas_mnn.h5ad' + - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker - image: mumichae/scib-base:0.1 - - type: native + image: mumichae/scib-base:1.0.2 - type: nextflow diff --git a/src/batch_integration/embedding/metrics/pcr/script.py b/src/batch_integration/embedding/metrics/pcr/script.py index 5d2e0da2c7..22e6521ea6 100644 --- a/src/batch_integration/embedding/metrics/pcr/script.py +++ b/src/batch_integration/embedding/metrics/pcr/script.py @@ -9,7 +9,7 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.metrics import pcr_comparison +from scib.metrics import pcr_comparison if par['debug']: pprint.pprint(par) @@ -23,7 +23,7 @@ print('Read adata') adata = sc.read(adata_file) adata_int = adata.copy() -name = adata.uns['name'] +name = adata.uns['dataset_id'] print('compute score') score = pcr_comparison( diff --git a/src/batch_integration/embedding/metrics/pcr/test.py b/src/batch_integration/embedding/metrics/pcr/test.py index d900fae98c..4fc0c5a890 100644 --- a/src/batch_integration/embedding/metrics/pcr/test.py +++ b/src/batch_integration/embedding/metrics/pcr/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'pancreas_mnn.h5ad', + "--adata", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.0356482252608894 +assert 0 <= score <= 1 print(">> All tests passed successfully") From 68994e457889e9731eca673490cc218cac2670a9 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 11 Jan 2023 10:22:08 +0100 Subject: [PATCH 0664/1233] subset from full pancreas instead of test object Former-commit-id: 4ae1fc18845ec150eb6a2eb707ebeb3cf2d3618f --- .../datasets/subsample/script.py | 5 -- .../resources_test_scripts/pancreas.sh | 54 ++++++++++++------- 2 files changed, 36 insertions(+), 23 deletions(-) diff --git a/src/batch_integration/datasets/subsample/script.py b/src/batch_integration/datasets/subsample/script.py index b1465bf2fe..ca06541e55 100644 --- a/src/batch_integration/datasets/subsample/script.py +++ b/src/batch_integration/datasets/subsample/script.py @@ -29,11 +29,6 @@ g2m_file = f'{resources_dir}/g2m_genes_tirosh_hm.txt' s_file = f'{resources_dir}/s_genes_tirosh_hm.txt' -print(g2m_file) -import os -print(os.getcwd()) -print(os.listdir()) - print('Read adata') adata = sc.read_h5ad(adata_file) diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index dbb11d0bf1..e1ae707eed 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -1,4 +1,5 @@ #!/bin/bash +set -xe # #make sure the following command has been executed #bin/viash_build -q 'batch_integration|common' @@ -9,43 +10,60 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/batch_integration if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 + echo "Error! Could not find raw data" + exit 1 fi mkdir -p $DATASET_DIR +# build components +bin/viash_build -q batch + +# load data +echo load data... +bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ + --output $DATASET_DIR/pancreas/download.h5ad \ + --url https://ndownloader.figshare.com/files/24539828 \ + --name pancreas \ + --obs_cell_type celltype \ + --obs_batch tech + # subset data echo subset data... bin/viash run src/batch_integration/datasets/subsample/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output $DATASET_DIR/pancreas/subsample.h5ad \ - --label celltype \ - --batch tech + --input $DATASET_DIR/pancreas/download.h5ad \ + --output $DATASET_DIR/pancreas/subsample.h5ad \ + --label celltype \ + --batch tech # process dataset echo process data... bin/viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/subsample.h5ad \ - --output $DATASET_DIR/pancreas/processed.h5ad \ - --label celltype \ - --batch tech \ - --hvgs 100 + --input $DATASET_DIR/pancreas/subsample.h5ad \ + --output $DATASET_DIR/pancreas/processed.h5ad \ + --label celltype \ + --batch tech \ + --hvgs 100 # run methods echo run methods... + +# Graph methods bin/viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/processed.h5ad \ - --output $DATASET_DIR/graph/methods/bbknn.h5ad + --input $DATASET_DIR/pancreas/processed.h5ad \ + --output $DATASET_DIR/graph/methods/bbknn.h5ad bin/viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/processed.h5ad \ - --output $DATASET_DIR/graph/methods/combat.h5ad -# TODO: embedding method + --input $DATASET_DIR/pancreas/processed.h5ad \ + --output $DATASET_DIR/graph/methods/combat.h5ad + +# Embedding method +bin/viash run src/batch_integration/embedding/methods/combat/config.vsh.yaml -- \ + --input $DATASET_DIR/pancreas/processed.h5ad \ + --output $DATASET_DIR/embedding/methods/combat.h5ad # run one metric -echo run metrics... \ No newline at end of file +echo run metrics... From f17d598a165f9bcd76543024d46c9c8ef9e714c0 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 11 Jan 2023 10:24:37 +0100 Subject: [PATCH 0665/1233] update combat calling Former-commit-id: 74a71f22f427b3422d9b7e18cfee96873fcf5e46 --- .../graph/methods/combat/script.py | 14 +++++++------- src/batch_integration/graph/methods/combat/test.py | 6 +++++- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index 74f03f7eaa..8aafc18149 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -11,7 +11,7 @@ print('Importing libraries') from pprint import pprint import scanpy as sc -from scib.integration import combat +from scipy.sparse import csr_matrix if par['debug']: pprint(par) @@ -35,17 +35,17 @@ adata.X = adata.layers['logcounts'] print('Integrate') -adata.X = combat(adata, batch='batch').X +adata.X = sc.pp.combat(adata, key='batch', inplace=False) print('Postprocess data') -sc.pp.pca( - adata, +adata.obsm['X_emb'] = sc.pp.pca( + adata.X, n_comps=50, - use_highly_variable=True, + use_highly_variable=False, svd_solver='arpack', - return_info=True + return_info=False ) -sc.pp.neighbors(adata, use_rep='X_pca') +sc.pp.neighbors(adata, use_rep='X_emb') print('Save HDF5') adata.uns['hvg'] = hvg diff --git a/src/batch_integration/graph/methods/combat/test.py b/src/batch_integration/graph/methods/combat/test.py index 657aad86eb..bb5d279b4c 100644 --- a/src/batch_integration/graph/methods/combat/test.py +++ b/src/batch_integration/graph/methods/combat/test.py @@ -21,7 +21,7 @@ assert path.exists(output_file) print('>> Checking API') -adata = sc.read(output_file) +adata = sc.read(output_file, as_sparse='X') assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns @@ -43,4 +43,8 @@ assert 'scaled' in adata.uns assert adata.uns['scaled'] == False +unintegrated = sc.read('processed.h5ad', as_sparse='X') +assert len(unintegrated.X.data) != len(adata.X.data) +assert not np.any(np.not_equal(unintegrated.obsm['X_pca'], adata.obsm['X_pca'])) + print(">> All tests passed successfully") From 813fe6dde4e7a50b1c3976c538f5742504c51138 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 11:23:06 +0100 Subject: [PATCH 0666/1233] Allow keeping certain features when running the subsample component Former-commit-id: ca64c86861e5ec14e10668f756216728a9e78910 --- CHANGELOG.md | 3 +- .../resource_test_scripts/pancreas.sh | 17 ++- src/datasets/subsample/config.vsh.yaml | 4 + src/datasets/subsample/script.py | 121 ++++++++++++------ src/datasets/subsample/test_script.py | 4 + 5 files changed, 104 insertions(+), 45 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d03456e7c6..451a96cdb0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,7 +76,8 @@ * `normalization/l1_sqrt`: A scaled L1 sqrt normalization. extracted from Alra method in the denoising task from v1 -* `subsample`: Subsample an h5ad file. +* `subsample`: Subsample an h5ad file. Allows keeping observations from specific batches and celltypes, + also allows keeping certain features. ### V1 MIGRATION diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index e48a845a24..399c02f763 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -11,36 +11,43 @@ cd "$REPO_ROOT" DATASET_DIR=resources_test/common/pancreas +set -e + mkdir -p $DATASET_DIR # download dataset -bin/viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ +viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ --id "pancreas" \ --obs_celltype "celltype" \ --obs_batch "tech" \ --layer_counts "counts" \ --output $DATASET_DIR/temp_dataset_full.h5ad +wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/g2m_genes_tirosh_hm.txt -O $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt +wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/s_genes_tirosh_hm.txt -O $DATASET_DIR/temp_s_genes_tirosh_hm.txt +KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s_genes_tirosh_hm.txt | paste -sd ":" -` + # subsample -bin/viash run src/datasets/subsample/config.vsh.yaml -- \ +viash run src/datasets/subsample/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset_full.h5ad \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ + --keep_features "$KEEP_FEATURES" \ --output $DATASET_DIR/temp_dataset0.h5ad \ --seed 123 # run log cpm normalisation -bin/viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ +viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset0.h5ad \ --output $DATASET_DIR/temp_dataset1.h5ad # run pca -bin/viash run src/datasets/processors/pca/config.vsh.yaml -- \ +viash run src/datasets/processors/pca/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset1.h5ad \ --output $DATASET_DIR/temp_dataset2.h5ad # run log cpm normalisation -bin/viash run src/datasets/processors/hvg/config.vsh.yaml -- \ +viash run src/datasets/processors/hvg/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset2.h5ad \ --output $DATASET_DIR/dataset.h5ad diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index 7616039183..82585a60c1 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -8,6 +8,10 @@ functionality: description: "Input data to be resized" required: true example: input.h5ad + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. - name: "--keep_celltype_categories" type: "string" multiple: true diff --git a/src/datasets/subsample/script.py b/src/datasets/subsample/script.py index b3b19cff30..be94c0e6a7 100644 --- a/src/datasets/subsample/script.py +++ b/src/datasets/subsample/script.py @@ -1,11 +1,14 @@ import scanpy as sc import random +import anndata as ad +import numpy as np ### VIASH START par = { - "input": "resources_test/common/pancreas/dataset.h5ad", + "input": "resources_test/common/pancreas/temp_dataset_full.h5ad", "keep_celltype_categories": None, "keep_batch_categories": None, + "keep_features": ["HMGB2", "CDK1", "NUSAP1", "UBE2C"], # "keep_celltype_categories": ["acinar", "beta"], # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], "even": True, @@ -14,58 +17,98 @@ } ### VIASH END -if par["seed"]: - print(f">> Setting seed to {par['seed']}") - random.seed(par["seed"]) - def filter_genes_cells(adata): """Remove empty cells and genes.""" sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) - return adata -print(">> Load data") -adata = sc.read(par['input']) -# copy counts to .X because otherwise filter_genes and filter_cells won't work -adata.X = adata.layers["counts"] - -if par.get('even'): - keep_batch_categories = adata.obs["batch"].unique() - adata_out = None - n_batch_obs_per_value = 500 // len(keep_batch_categories) - for t in keep_batch_categories: - batch_idx = adata.obs["batch"] == t - adata_subset = adata[batch_idx].copy() - sc.pp.subsample(adata_subset, n_obs=min(n_batch_obs_per_value, adata_subset.shape[0])) - if adata_out is None: - adata_out = adata_subset - else: - adata_out = adata_out.concatenate(adata_subset, batch_key="_obs_batch") +def subsample_even(adata, n_obs, even_obs): + """Subsample a dataset evenly across an obs. + Parameters + ---------- + adata : AnnData + n_obs : int + Total number of cells to retain + even_obs : str + `adata.obs[even_obs]` to be subsampled evenly across partitions. + Returns + ------- + adata : AnnData + Subsampled AnnData object + """ + import scanpy as sc + + values = adata.obs[even_obs].unique() + adatas = [] + n_obs_per_value = n_obs // len(values) + for v in values: + adata_subset = adata[adata.obs[even_obs] == v].copy() + sc.pp.subsample(adata_subset, n_obs=min(n_obs_per_value, adata_subset.shape[0])) + adatas.append(adata_subset) + + adata_out = ad.concat(adatas, label="_obs_batch") + adata_out.uns = adata.uns adata_out.varm = adata.varm adata_out.varp = adata.varp - adata = adata_out[:, :500].copy() + return adata_out + + +if par["seed"]: + print(f">> Setting seed to {par['seed']}", flush=True) + random.seed(par["seed"]) + +print(">> Load data", flush=True) +adata_input = sc.read_h5ad(par["input"]) + +# copy counts to .X because otherwise filter_genes and filter_cells won't work +adata_input.X = adata_input.layers["counts"] + +# filter by celltype +if par.get("keep_celltype_categories"): + print(f">> Selecting celltype_categories {par['keep_celltype_categories']}") + idx = adata_input.obs["celltype"].isin(par["keep_celltype_categories"]) + adata_input = adata_input[idx] + +# filter by batch +if par.get("keep_batch_categories"): + print(f">> Selecting celltype_categories {par['keep_batch_categories']}") + idx = adata_input.obs["batch"].isin(par["keep_batch_categories"]) + adata_input = adata_input[idx] + +print(">> Remove empty observations and features", flush=True) +filter_genes_cells(adata_input) + +print(">> Subsampling the observations", flush=True) +n_obs = min(500, adata_input.shape[0]) +n_vars = min(500, adata_input.shape[1]) +if par.get("even"): + adata_output = subsample_even(adata_input, n_obs, "batch") else: - adata = adata[:, :500].copy() + adata_output = sc.pp.subsample(adata_input, n_obs=n_obs, copy=True) -filter_genes_cells(adata) -if par.get('keep_celltype_categories') and par.get('keep_batch_categories'): - print(">> Selecting celltype_categories {categories}".format(categories=par.get('keep_celltype_categories'))) - print(">> Selecting batch_categories {categories}".format(categories=par.get('keep_batch_categories'))) - keep_batch_idx = adata.obs["batch"].isin(par['keep_batch_categories']) - keep_celltype_idx = adata.obs["celltype"].isin(par['keep_celltype_categories']) - adata = adata[keep_celltype_idx & keep_batch_idx].copy() +print(">> Subsampling the features", flush=True) +if par.get("keep_features"): + initial_filt = adata_output.var_names.isin(par["keep_features"]) + initial_idx, *_ = initial_filt.nonzero() + remaining_idx, *_ = (~initial_filt).nonzero() + rest_idx = remaining_idx[np.random.choice(len(remaining_idx), n_vars - len(initial_idx), replace=False)] + feature_ix = np.concatenate([initial_idx, rest_idx]) + adata_output = adata_output[:, feature_ix] +else: + feature_ix = np.random.choice(adata_input.shape[1], n_vars, replace=False) + adata_output = adata_output[:, feature_ix] + +print(">> Remove empty observations and features", flush=True) +filter_genes_cells(adata_output) -# Note: could also use 200-500 HVGs rather than 200 random genes -# Ensure there are no cells or genes with 0 counts -sc.pp.subsample(adata, n_obs=min(500, adata.shape[0])) -filter_genes_cells(adata) -adata.uns["dataset_id"] = adata.uns["dataset_id"] + "_subsample" +print(">> Update dataset_id", flush=True) +adata_output.uns["dataset_id"] = adata_output.uns["dataset_id"] + "_subsample" # remove previously copied .X -del adata.X +del adata_output.X print(">> Writing data") -adata.write_h5ad(par['output']) +adata_output.write_h5ad(par["output"]) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index 2cf9b791e3..840ce77928 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -34,11 +34,14 @@ print(">> Runing script as test for specific batch and celltype categories") output2_path = "output.h5ad" + +keep_features = ["HMGB2", "CDK1", "NUSAP1", "UBE2C"] out = subprocess.check_output([ meta["executable"], "--input", input_path, "--keep_celltype_categories", "acinar:beta", "--keep_batch_categories", "celseq:inDrop4:smarter", + "--keep_features", ":".join(keep_features), "--output", output_path, "--seed", "123" ]).decode("utf-8") @@ -50,3 +53,4 @@ assert input.n_obs >= output2.n_obs assert input.n_vars == output2.n_vars +assert set(keep_features).issubset(output2.var_names) From ca161bb4011e501612dd9917a0d55c03db97f29d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 15:12:49 +0100 Subject: [PATCH 0667/1233] fix viash codeblocks Former-commit-id: 638b593003cbed23897a48abf0be6a05cb26330d --- src/dimensionality_reduction/methods/densmap/script.py | 7 +++---- src/dimensionality_reduction/methods/neuralee/script.py | 6 +++--- src/dimensionality_reduction/methods/pca/script.py | 4 ++-- .../methods/phate/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/phate/script.py | 6 +++--- src/dimensionality_reduction/methods/tsne/script.py | 5 ++--- src/dimensionality_reduction/methods/umap/script.py | 8 ++++---- 7 files changed, 18 insertions(+), 20 deletions(-) diff --git a/src/dimensionality_reduction/methods/densmap/script.py b/src/dimensionality_reduction/methods/densmap/script.py index e02386010d..985c95d78a 100644 --- a/src/dimensionality_reduction/methods/densmap/script.py +++ b/src/dimensionality_reduction/methods/densmap/script.py @@ -4,14 +4,13 @@ ## VIASH START par = { - "input": "resources_test/common/pancreas/train.h5ad", + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", - "n_pca_dims": False, + "n_pca_dims": 50, "n_hvg": 1000 } meta = { - "functionality_name": "densmap", - "config": "src/dimensionality_reduction/methods/densmap/config.vsh.yaml" + "functionality_name": "foo", } ## VIASH END diff --git a/src/dimensionality_reduction/methods/neuralee/script.py b/src/dimensionality_reduction/methods/neuralee/script.py index d66d41e522..bd13a2f34d 100644 --- a/src/dimensionality_reduction/methods/neuralee/script.py +++ b/src/dimensionality_reduction/methods/neuralee/script.py @@ -11,11 +11,11 @@ "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", "n_hvg": 1000, - "normalize": False, - "n_iter": None + "n_iter": 10, + "normalize": True } meta = { - "functionality_name": "neuralee", + "functionality_name": "foo", } ## VIASH END diff --git a/src/dimensionality_reduction/methods/pca/script.py b/src/dimensionality_reduction/methods/pca/script.py index 760d9bc360..81cff3441f 100644 --- a/src/dimensionality_reduction/methods/pca/script.py +++ b/src/dimensionality_reduction/methods/pca/script.py @@ -5,10 +5,10 @@ par = { "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", - "n_hvg": 1000, + "n_hvg": 1000 } meta = { - "functionality_name": "pca", + "functionality_name": "foo", } ## VIASH END diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 28e90b8525..cdc43b3be9 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: phate_logCPM: preferred_normalization: log_cpm phate_logCPM_1kHVG: - num_hvg_genes: 1000 + n_hvg: 1000 preferred_normalization: log_cpm arguments: - name: '--n_pca_dims' diff --git a/src/dimensionality_reduction/methods/phate/script.py b/src/dimensionality_reduction/methods/phate/script.py index 279c93c11e..a21d9e0d87 100644 --- a/src/dimensionality_reduction/methods/phate/script.py +++ b/src/dimensionality_reduction/methods/phate/script.py @@ -6,11 +6,11 @@ "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", "n_pca_dims": 50, - "gamma": 1, - "n_hvg": None + "n_hvg": 1000, + "gamma": 1 } meta = { - "functionality_name": "phate", + "functionality_name": "foo", } ## VIASH END diff --git a/src/dimensionality_reduction/methods/tsne/script.py b/src/dimensionality_reduction/methods/tsne/script.py index b90a177b15..171e17bded 100644 --- a/src/dimensionality_reduction/methods/tsne/script.py +++ b/src/dimensionality_reduction/methods/tsne/script.py @@ -3,14 +3,13 @@ ## VIASH START par = { - "input": "resources_test/common/pancreas/train.h5ad", + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", "n_pca_dims": 50, "n_hvg": 1000 } meta = { - "functionality_name": "tsne", - "config": "src/dimensionality_reduction/methods/tsne/config.vsh.yaml" + "functionality_name": "foo", } ## VIASH END diff --git a/src/dimensionality_reduction/methods/umap/script.py b/src/dimensionality_reduction/methods/umap/script.py index c3b7058269..800e65328c 100644 --- a/src/dimensionality_reduction/methods/umap/script.py +++ b/src/dimensionality_reduction/methods/umap/script.py @@ -4,13 +4,13 @@ ## VIASH START par = { - "input": "resources_test/common/pancreas/train.h5ad", + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", "output": "reduced.h5ad", - "n_pca_dims": False, + "n_pca_dims": 50, + "n_hvg": 1000 } meta = { - "functionality_name": "densmap", - "config": "src/dimensionality_reduction/methods/densmap/config.vsh.yaml" + "functionality_name": "foo", } ## VIASH END From 9513d1b9978d290e1b02318d06024e1893c2a59e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 15:13:06 +0100 Subject: [PATCH 0668/1233] clean up coranking and density metrics Former-commit-id: 563f554f08f993ccffb3f69cedcfc659fed20770 --- .../api/comp_metric.yaml | 2 +- .../metrics/coranking/config.vsh.yaml | 77 +++++++ .../metrics/coranking/library.bib | 62 ++++++ .../metrics/coranking/script.R | 99 +++++++++ .../{nn_ranking => coranking}/script.py | 200 ++++++++++-------- .../metrics/density/config.vsh.yaml | 32 --- .../metrics/density/script.py | 101 --------- .../metrics/density/test.py | 55 ----- .../density_preservation/config.vsh.yaml | 36 ++++ .../metrics/density_preservation/script.py | 135 ++++++++++++ .../metrics/nn_ranking/config.vsh.yaml | 30 --- 11 files changed, 521 insertions(+), 308 deletions(-) create mode 100644 src/dimensionality_reduction/metrics/coranking/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/coranking/library.bib create mode 100644 src/dimensionality_reduction/metrics/coranking/script.R rename src/dimensionality_reduction/metrics/{nn_ranking => coranking}/script.py (59%) delete mode 100644 src/dimensionality_reduction/metrics/density/config.vsh.yaml delete mode 100644 src/dimensionality_reduction/metrics/density/script.py delete mode 100644 src/dimensionality_reduction/metrics/density/test.py create mode 100644 src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml create mode 100644 src/dimensionality_reduction/metrics/density_preservation/script.py delete mode 100644 src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 2587d5c4aa..84abd00ad6 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -31,7 +31,7 @@ functionality: assert path.exists(input_test_path) print(">> Running script as test", flush=True) - out = subprocess.run(cmd, check=True, capture_output=True, text=True) + subprocess.run(cmd, check=True) print(">> Checking whether output file exists", flush=True) assert path.exists(output_path) diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml new file mode 100644 index 0000000000..9492eb59a3 --- /dev/null +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -0,0 +1,77 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: "coranking" + namespace: "dimensionality_reduction/metrics" + description: | + This is a set of metrics which all use a co-ranking matrix as the basis of the metric. + info: + v1_url: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1_note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. + paper_reference: kraemer2018dimred + metrics: + - id: continuity_at_k30 + name: Continuity at k=30 + paper_reference: venna2006local + min: 0 + max: 1 + maximize: true + - id: trustworthiness_at_k30 + name: Trustworthiness at k=30 + paper_reference: venna2006local + min: 0 + max: 1 + maximize: true + - id: qnx_at_k30 + name: The value for QNX at k=30 + paper_reference: lee2009quality + min: 0 + max: 1 + maximize: true + - id: lcmc_at_k30 + name: The value for LCMC at k=30 + paper_reference: chen2009local + min: 0 + max: 1 + maximize: true + - id: qnx_auc + name: Area under the QNX curve + paper_reference: lueks2011evaluate + min: 0 + max: 1 + maximize: true + - id: qlocal + name: Local quality measure + paper_reference: lueks2011evaluate + min: 0 + max: 1 + maximize: true + - id: qglobal + name: Global quality measure + paper_reference: lueks2011evaluate + min: 0 + max: 1 + maximize: true + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: eddelbuettel/r2u:22.04 + setup: + - type: r + cran: [ anndata, coRanking ] + - type: apt + packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + - type: python + pip: [ anndata>=0.8 ] + - type: nextflow + directives: + label: [ highmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/coranking/library.bib b/src/dimensionality_reduction/metrics/coranking/library.bib new file mode 100644 index 0000000000..5ecdb67e51 --- /dev/null +++ b/src/dimensionality_reduction/metrics/coranking/library.bib @@ -0,0 +1,62 @@ + +@misc{lueks2011evaluate, + doi = {10.48550/ARXIV.1110.3917}, + url = {https://arxiv.org/abs/1110.3917}, + author = {Lueks, Wouter and Mokbel, Bassam and Biehl, Michael and Hammer, Barbara}, + keywords = {Machine Learning (cs.LG), Information Retrieval (cs.IR), FOS: Computer and information sciences, FOS: Computer and information sciences}, + title = {How to Evaluate Dimensionality Reduction? - Improving the Co-ranking Matrix}, + publisher = {arXiv}, + year = {2011}, + copyright = {arXiv.org perpetual, non-exclusive license} +} +@article{kraemer2018dimred, + doi = {10.32614/rj-2018-039}, + url = {https://doi.org/10.32614/rj-2018-039}, + year = {2018}, + publisher = {The R Foundation}, + volume = {10}, + number = {1}, + pages = {342}, + author = {Guido Kraemer and Markus Reichstein and Miguel, D. Mahecha}, + title = {{dimRed} and {coRanking} - Unifying Dimensionality Reduction in R}, + journal = {The R Journal} +} +@article{chen2009local, + doi = {10.1198/jasa.2009.0111}, + url = {https://doi.org/10.1198/jasa.2009.0111}, + year = {2009}, + month = mar, + publisher = {Informa {UK} Limited}, + volume = {104}, + number = {485}, + pages = {209--219}, + author = {Lisha Chen and Andreas Buja}, + title = {Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis}, + journal = {Journal of the American Statistical Association} +} +@article{lee2009quality, + doi = {10.1016/j.neucom.2008.12.017}, + url = {https://doi.org/10.1016/j.neucom.2008.12.017}, + year = {2009}, + month = mar, + publisher = {Elsevier {BV}}, + volume = {72}, + number = {7-9}, + pages = {1431--1443}, + author = {John A. Lee and Michel Verleysen}, + title = {Quality assessment of dimensionality reduction: Rank-based criteria}, + journal = {Neurocomputing} +} +@article{venna2006local, + doi = {10.1016/j.neunet.2006.05.014}, + url = {https://doi.org/10.1016/j.neunet.2006.05.014}, + year = {2006}, + month = jul, + publisher = {Elsevier {BV}}, + volume = {19}, + number = {6-7}, + pages = {889--899}, + author = {Jarkko Venna and Samuel Kaski}, + title = {Local multidimensional scaling}, + journal = {Neural Networks} +} \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/coranking/script.R b/src/dimensionality_reduction/metrics/coranking/script.R new file mode 100644 index 0000000000..5878b9e3f5 --- /dev/null +++ b/src/dimensionality_reduction/metrics/coranking/script.R @@ -0,0 +1,99 @@ +library(anndata) +library(coRanking) + +## VIASH START +par <- list( + "input_reduced" = "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_test" = "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output" = "score.h5ad" +) +## VIASH END + +cat("Read anndata objects") +input_test <- anndata::read_h5ad(par[["input_test"]]) +input_reduced <- anndata::read_h5ad(par[["input_reduced"]]) + +# get datasets +high_dim <- input_test$layers[["normalized"]] +X_emb <- input_reduced$obsm[["X_emb"]] + +if (any(is.na(X_emb))) { + continuity_at_k30 <- + trustworthiness_at_k30 <- + qnx_at_k30 <- + lcmc_at_k30 <- + qnx_auc <- + qlocal <- + qglobal <- + 0 +} else { + cat("Compute pairwise distances\n") + # TODO: this is problematic for large datasets! + dist_highdim <- coRanking:::euclidean(as.matrix(high_dim)) + dist_emb <- coRanking:::euclidean(as.matrix(X_emb)) + + cat("Compute ranking matrices\n") + rmat_highdim <- rankmatrix(dist_highdim, input = "dist") + rmat_emb <- rankmatrix(dist_emb, input = "dist") + + cat("Compute coranking matrix\n") + corank <- coranking(rmat_highdim, rmat_emb, "rank") + + cat("Compute metrics\n") + # Compute QNX. This is a curve indicating the percentage of points + # that are mild in- and extrusions or keep their rank. + qnx <- Q_NX(corank) + + # Calculate the local continuity meta-criterion from a co-ranking matrix. + lcmc <- LCMC(corank) + + # the values of qnx are split into local and global values by kmax + kmax <- which.max(lcmc) + + # check certain quality values at k=30 + k30 <- 30 + trustworthiness_at_k30 <- coRanking:::cm.M_T(corank, k30) + continuity_at_k30 <- coRanking:::cm.M_C(corank, k30) + qnx_at_k30 <- qnx[[k30]] + lcmc_at_k30 <- lcmc[[k30]] + + # area under the QNX curve + qnx_auc <- mean(qnx) + + # local quality measure + qlocal <- mean(qnx[seq_len(kmax)]) + + # global quality measure + qglobal <- mean(qnx[-seq_len(kmax)]) +} + +cat("construct output AnnData\n") +output <- AnnData( + shape = c(0L, 0L), + uns = list( + dataset_id = input_test$uns[["dataset_id"]], + normalization_id = input_test$uns[["normalization_id"]], + method_id = input_reduced$uns[["method_id"]], + metric_ids = c( + "continuity_at_k30", + "trustworthiness_at_k30", + "qnx_at_k30", + "lcmc_at_k30", + "qnx_auc", + "qlocal", + "qglobal" + ), + metric_values = c( + continuity_at_k30, + trustworthiness_at_k30, + qnx_at_k30, + lcmc_at_k30, + qnx_auc, + qlocal, + qglobal + ) + ) +) + +cat("Write to file\n") +output$write_h5ad(par$output) diff --git a/src/dimensionality_reduction/metrics/nn_ranking/script.py b/src/dimensionality_reduction/metrics/coranking/script.py similarity index 59% rename from src/dimensionality_reduction/metrics/nn_ranking/script.py rename to src/dimensionality_reduction/metrics/coranking/script.py index e082793e35..76a7cbbf6e 100644 --- a/src/dimensionality_reduction/metrics/nn_ranking/script.py +++ b/src/dimensionality_reduction/metrics/coranking/script.py @@ -1,3 +1,19 @@ +""" +This file is uses slightly modified code from pyDRMetrics [1]_, see: + + - https://doi.org/10.1016/j.heliyon.2021.e06199 - the article. + - https://data.mendeley.com/datasets/jbjd5fmggh/1 - the supplementary files. + +The following changes have been made: + + - :mod:`numba` JIT for performance reasons + - use broadcasting instead of a 3rd loop in :func:`_ranking_matrix` + +[1] Zhang, Yinsheng (2021), + “Source code, sample data, and case study report for pyDRMetrics”, + Mendeley Data, V1, doi: 10.17632/jbjd5fmggh.1 +""" + import anndata as ad from numba import njit from typing import Tuple @@ -8,37 +24,110 @@ _K = 30 -@njit(cache=True, fastmath=True) -def _ranking_matrix(D: np.ndarray) -> np.ndarray: # pragma: no cover - assert D.shape[0] == D.shape[1] - R = np.zeros(D.shape) - m = len(R) - ks = np.arange(m) +## VIASH START +par = { + "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "score.h5ad", +} +## VIASH END +print("Load data", flush=True) +input_reduced = ad.read_h5ad(par["input_reduced"]) +input_test = ad.read_h5ad(par["input_test"]) + +X_emb = input_reduced.obsm["X_emb"] +high_dim = input_test.layers["normalized"] + +def _ranking_matrix(pdist_mat: np.ndarray) -> np.ndarray: + """The pairwise distance matrix is ranked using argsort.""" + assert pdist_mat.shape[0] == pdist_mat.shape[1] + return np.argsort(np.argsort(pdist_mat)) + +def _coranking_matrix(rmat1: np.ndarray, rmat2: np.ndarray) -> np.ndarray: + """Compute the coranking matrix from two ranking matrices.""" + assert rmat1.shape == rmat2.shape + m = rmat1.shape[0] + corank_mat = np.zeros((m - 1, m - 1), dtype=np.int32) for i in range(m): for j in range(m): - R[i, j] = np.sum( - (D[i, :] < D[i, j]) | ((ks < j) & (np.abs(D[i, :] - D[i, j]) <= 1e-12)) - ) + if i != j: + k = rmat1[i, j] - 1 + l = rmat2[i, j] - 1 + corank_mat[k, l] += 1 + return corank_mat + +def _metrics( + Q: np.ndarray, +) -> Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray, int, float, float]: + Q = Q[1:, 1:] + m = len(Q) + + T = _trustworthiness(Q, m) + C = _continuity(Q, m) + QNN = _qnn(Q, m) + LCMC = _lcmc(QNN, m) + kmax = _kmax(LCMC) + Qlocal = _q_local(QNN, kmax) + Qglobal = _q_global(QNN, kmax, m) + AUC = _qnn_auc(QNN) + + return T, C, QNN, AUC, LCMC, kmax, Qlocal, Qglobal + +def _fit( + original: np.ndarray, embedding: np.ndarray +) -> Tuple[float, float, float, float, float, float, float]: + from sklearn.metrics import pairwise_distances + + if np.any(np.isnan(E)): + return 0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf + + pdist_original = pairwise_distances(original) + pdist_embedding = pairwise_distances(embedding) + rmat_original = _ranking_matrix(pdist_original) + rmat_embedding = _ranking_matrix(pdist_embedding) + corank = _coranking_matrix(rmat_original, rmat_embedding) + + T, C, QNN, AUC, LCMC, _kmax, Qlocal, Qglobal = _metrics(corank) + + return T[_K], C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal + + +print("Store metric value", flush=True) +input_reduced.uns['metric_ids'] = {meta['functionality_name']: ['continuity', 'co-KNN size', 'co-KNN AUC', 'local continuity meta criterion', 'local property', 'global property']} +if np.any(np.isnan(input_reduced.obsm["X_emb"])): + input_reduced.uns['metric_values'] = [0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf] +else: + input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] + + +print("Copy data to new AnnData object", flush=True) +output = ad.AnnData( + uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} +) + +print("Write data to file", flush=True) +output.write_h5ad(par['output'], compression="gzip") + + + + + + + + + + + + + + - return R -@njit(cache=True, fastmath=True) -def _coranking_matrix(R1: np.ndarray, R2: np.ndarray) -> np.ndarray: # pragma: no cover - assert R1.shape == R2.shape - Q = np.zeros(R1.shape, dtype=np.int32) - m = len(Q) - for i in range(m): - for j in range(m): - k = int(R1[i, j]) - l = int(R2[i, j]) # noqa: E741 - Q[k, l] += 1 - return Q -@njit(cache=True, fastmath=True) def _trustworthiness(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover T = np.zeros(m - 1) # trustworthiness @@ -54,7 +143,6 @@ def _trustworthiness(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover return T -@njit(cache=True, fastmath=True) def _continuity(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover C = np.zeros(m - 1) # continuity @@ -69,7 +157,6 @@ def _continuity(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover return C -@njit(cache=True, fastmath=True) def _qnn(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover QNN = np.zeros(m) # Co-k-nearest neighbor size @@ -106,68 +193,3 @@ def _q_global(QNN: np.ndarray, kmax: int, m: int) -> float: def _qnn_auc(QNN: np.ndarray) -> float: AUC = np.mean(QNN) return AUC # type: ignore - -def _metrics( - Q: np.ndarray, -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray, int, float, float]: - Q = Q[1:, 1:] - m = len(Q) - - T = _trustworthiness(Q, m) - C = _continuity(Q, m) - QNN = _qnn(Q, m) - LCMC = _lcmc(QNN, m) - kmax = _kmax(LCMC) - Qlocal = _q_local(QNN, kmax) - Qglobal = _q_global(QNN, kmax, m) - AUC = _qnn_auc(QNN) - - return T, C, QNN, AUC, LCMC, kmax, Qlocal, Qglobal - - -## VIASH START -par = { - 'input_reduced': 'resources_test/dimensionality_reduction/pancreas/reduced.h5ad', - 'input_test': 'resources_test/dimensionality_reduction/pancreas/test.h5ad', - 'output': 'score.h5ad', -} -meta = { - 'functionality_name': 'nn_ranking', -} -## VIASH END - -print("Load data", flush=True) -input_reduced = ad.read_h5ad(par['input_reduced']) -input_test = ad.read_h5ad(par['input_test']) - -# Select 1000 most variable genes -idx = input_test.var['hvg_score'].to_numpy().argsort()[-1000:] -input_test = input_test[:, idx] - -# Compute pairwise distances -if issparse(input_test): - Dx = pairwise_distances(input_test.layers['normalized'].A) -else: - Dx = pairwise_distances(input_test.layers['normalized']) - -De = pairwise_distances(input_reduced.obsm["X_emb"]) -Rx, Re = _ranking_matrix(Dx), _ranking_matrix(De) -Q = _coranking_matrix(Rx, Re) - -T, C, QNN, AUC, LCMC, _kmax, Qlocal, Qglobal = _metrics(Q) - -print("Store metric value", flush=True) -input_reduced.uns['metric_ids'] = {meta['functionality_name']: ['continuity', 'co-KNN size', 'co-KNN AUC', 'local continuity meta criterion', 'local property', 'global property']} -if np.any(np.isnan(input_reduced.obsm["X_emb"])): - input_reduced.uns['metric_values'] = [0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf] -else: - input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] - - -print("Copy data to new AnnData object", flush=True) -output = ad.AnnData( - uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} -) - -print("Write data to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/config.vsh.yaml b/src/dimensionality_reduction/metrics/density/config.vsh.yaml deleted file mode 100644 index c0b63a8905..0000000000 --- a/src/dimensionality_reduction/metrics/density/config.vsh.yaml +++ /dev/null @@ -1,32 +0,0 @@ -__merge__: ../../api/comp_metric.yaml -functionality: - name: "density" - namespace: "dimensionality_reduction/metrics" - description: "density preservation: correlation of local radius with the local radii in the original data space" - info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - metrics: - - id: density - label: Density - description: "density preservation: correlation of local radius with the local radii in the original data space" - min: 0 - max: -1 - maximize: true - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - scipy - - numpy - - "anndata>=0.8" - - typing - - umap-learn - - type: nextflow - directives: - label: [ lowmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/density/script.py b/src/dimensionality_reduction/metrics/density/script.py deleted file mode 100644 index ed37a28298..0000000000 --- a/src/dimensionality_reduction/metrics/density/script.py +++ /dev/null @@ -1,101 +0,0 @@ -import anndata as ad -import numpy as np -from typing import Optional -from umap import UMAP -from scipy.sparse import issparse -from scipy.stats import pearsonr - -## VIASH START -par = { - 'input_reduced': 'reduced.h5ad', - 'input_test': 'test.h5ad', - 'output': 'score.h5ad', -} -meta = { - 'functionality_name': 'density', -} -## VIASH END -def _calculate_radii( - X: np.ndarray, n_neighbors: int = 30, random_state: Optional[int] = None -) -> np.ndarray: - from umap.umap_ import fuzzy_simplicial_set - from umap.umap_ import nearest_neighbors - - # directly taken from: https://github.com/lmcinnes/umap/blob/ - # 317ce81dc64aec9e279aa1374ac809d9ced236f6/umap/umap_.py#L1190-L1243 - (knn_indices, knn_dists, rp_forest,) = nearest_neighbors( - X, - n_neighbors, - "euclidean", - {}, - False, - random_state, - verbose=False, - ) - - emb_graph, emb_sigmas, emb_rhos, emb_dists = fuzzy_simplicial_set( - X, - n_neighbors, - random_state, - "euclidean", - {}, - knn_indices, - knn_dists, - verbose=False, - return_dists=True, - ) - - emb_graph = emb_graph.tocoo() - emb_graph.sum_duplicates() - emb_graph.eliminate_zeros() - - n_vertices = emb_graph.shape[1] - - mu_sum = np.zeros(n_vertices, dtype=np.float32) - re = np.zeros(n_vertices, dtype=np.float32) - - head = emb_graph.row - tail = emb_graph.col - for i in range(len(head)): - j = head[i] - k = tail[i] - D = emb_dists[j, k] - mu = emb_graph.data[i] - re[j] += mu * D - re[k] += mu * D - mu_sum[j] += mu - mu_sum[k] += mu - - epsilon = 1e-8 - return np.log(epsilon + (re / mu_sum)) - -print("Load data") -input_reduced = ad.read_h5ad(par['input_reduced']) -input_test = ad.read_h5ad(par['input_test']) - -if np.any(np.isnan(input_reduced.obsm['X_emb'])): - density = 0.0 -else: - _K = 30 # number of neighbors - _SEED = 42 - - print('Reduce dimensionality of raw data', flush=True) - _, ro, _ = UMAP( - n_neighbors=_K, random_state=_SEED, densmap=True, output_dens=True - ).fit_transform(input_test.layers['counts']) - re = _calculate_radii(input_reduced.obsm['X_emb'], n_neighbors=_K, random_state=_SEED) - - print('Compute Density between the full (or processed) data matrix and a dimensionally-reduced matrix', flush=True) - density = pearsonr(ro, re)[0] - -print("Store metric value", flush=True) -input_reduced.uns['metric_ids'] = meta['functionality_name'] -input_reduced.uns['metric_values'] = density - -print("Copy data to new AnnData object", flush=True) -output = ad.AnnData( - uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} -) - -print("Write data to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density/test.py b/src/dimensionality_reduction/metrics/density/test.py deleted file mode 100644 index f34fbf5b1e..0000000000 --- a/src/dimensionality_reduction/metrics/density/test.py +++ /dev/null @@ -1,55 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -## VIASH START -meta = { - 'executable': './target/docker/dimensionality_reduction/density', - 'resources_dir': './resources_test/dimensionality_reduction/pancreas', -} -## VIASH END - -input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" -input_test_path = meta["resources_dir"] + "/input/test.h5ad" -output_path = "score.h5ad" -cmd = [ - meta['executable'], - "--input_reduced", input_reduced_path, - "--input_test", input_test_path, - "--output", output_path, -] - -print(">> Checking whether input files exist") -assert path.exists(input_reduced_path) -assert path.exists(input_test_path) - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input_reduced = ad.read_h5ad(input_reduced_path) -input_test = ad.read_h5ad(input_test_path) -output = ad.read_h5ad(output_path) - -print("input reduced:", input_reduced) -print("input test:", input_test) -print("output:", output) - -print(">> Checking whether metrics were added") -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert meta['functionality_name'] in output.uns["metric_ids"] - -print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'], float) - -print(">> Checking whether data from input was copied properly to output") -assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] -assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] -assert input_reduced.uns["method_id"] == output.uns["method_id"] - - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml new file mode 100644 index 0000000000..c03ebe56c0 --- /dev/null +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -0,0 +1,36 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: "density_preservation" + namespace: "dimensionality_reduction/metrics" + description: | + Similarity between local densities in the high-dimensional data and the reduced data. + info: + v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + metrics: + - id: density_preservation + label: Density preservation + description: | + Similarity between local densities in the high-dimensional data and the reduced data. + + This is computed as the pearson correlation of local radii with the local radii in the original data space. + paper_reference: narayan2021assessing + min: -1 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scipy + - numpy + - "anndata>=0.8" + - umap-learn + - type: nextflow + directives: + label: [ lowmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/density_preservation/script.py b/src/dimensionality_reduction/metrics/density_preservation/script.py new file mode 100644 index 0000000000..f4a31d3caf --- /dev/null +++ b/src/dimensionality_reduction/metrics/density_preservation/script.py @@ -0,0 +1,135 @@ + + +import anndata as ad +import numpy as np +from typing import Optional +from umap import UMAP +from scipy.stats import pearsonr + +## VIASH START +par = { + "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "score.h5ad", +} +## VIASH END + +# Interpreted from: +# https://github.com/lmcinnes/umap/blob/317ce81dc64aec9e279aa1374ac809d9ced236f6/umap/umap_.py#L1190-L1243 +# +# Author: Leland McInnes +# +# License: BSD 3 clause +def _calculate_radii( + X: np.ndarray, + n_neighbors: int = 30, + random_state: Optional[int] = None +) -> np.ndarray: + from umap.umap_ import fuzzy_simplicial_set + from umap.umap_ import nearest_neighbors + + (knn_indices, knn_dists, _) = nearest_neighbors( + X, + n_neighbors, + "euclidean", + {}, + False, + random_state, + verbose=False, + ) + + emb_graph, _, _, emb_dists = fuzzy_simplicial_set( + X, + n_neighbors, + random_state, + "euclidean", + {}, + knn_indices, + knn_dists, + verbose=False, + return_dists=True, + ) + + emb_graph = emb_graph.tocoo() + emb_graph.sum_duplicates() + emb_graph.eliminate_zeros() + + n_vertices = emb_graph.shape[1] + + mu_sum = np.zeros(n_vertices, dtype=np.float32) + re = np.zeros(n_vertices, dtype=np.float32) + + head = emb_graph.row + tail = emb_graph.col + for i in range(len(head)): + j = head[i] + k = tail[i] + D = emb_dists[j, k] + mu = emb_graph.data[i] + re[j] += mu * D + re[k] += mu * D + mu_sum[j] += mu + mu_sum[k] += mu + + epsilon = 1e-8 + return np.log(epsilon + (re / mu_sum)) + +def compute_density_preservation( + X_emb: np.ndarray, + high_dim: np.ndarray, + n_neighbors: int = 30, + random_state: Optional[int] = None +) -> float: + if np.any(np.isnan(X_emb)): + return 0.0 + + print("Compute local radii in original data", flush=True) + _, ro, _ = UMAP( + n_neighbors=_K, + random_state=_SEED, + densmap=True, + output_dens=True + ).fit_transform(high_dim) + + print("Compute local radii of embedding", flush=True) + re = _calculate_radii( + X_emb, + n_neighbors=_K, + random_state=_SEED + ) + + print("Compute pearson correlation", flush=True) + return pearsonr(ro, re)[0] + +# number of neighbors +_K = 30 +# Fix seed +_SEED = 42 + +print("Load data", flush=True) +input_test = ad.read_h5ad(par["input_test"]) +input_reduced = ad.read_h5ad(par["input_reduced"]) + +high_dim = input_test.layers["normalized"] +X_emb = input_reduced.obsm["X_emb"] + +density_preservation = compute_density_preservation( + X_emb=X_emb, + high_dim=high_dim, + n_neighbors=_K, + random_state=_SEED +) + +print("Create output AnnData object", flush=True) +output = ad.AnnData( + uns={ + "dataset_id": input_test.uns["dataset_id"], + "normalization_id": input_test.uns["normalization_id"], + "method_id": input_reduced.uns["method_id"], + "metric_ids": [ "density_preservation" ], + "metric_values": [ density_preservation ] + } +) + +print("Write data to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml deleted file mode 100644 index 289a498850..0000000000 --- a/src/dimensionality_reduction/metrics/nn_ranking/config.vsh.yaml +++ /dev/null @@ -1,30 +0,0 @@ -__merge__: ../../api/comp_metric.yaml -functionality: - name: "nn_ranking" - namespace: "dimensionality_reduction/metrics" - description: A set of metrics from the pyDRMetrics package. - info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - v1_commit: a796e02e13a43e8861b124edbb9d287f162d4a14 - metrics: - - id: nn_ranking - label: NN_Ranking - description: "A set of metrics from the pyDRMetrics package." - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - numba - - numpy - - typing - - "anndata>=0.8" - - scipy - - scikit-learn - - type: nextflow - directives: - label: [ lowmem, lowcpu ] From 77b0e8100b68f90509098ab0c7ba1cd6201dff25 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 15:14:37 +0100 Subject: [PATCH 0669/1233] remove unused script Former-commit-id: 454ea61269bdc0c2e80acf15615b7dba2152b799 --- .../metrics/coranking/script.py | 195 ------------------ 1 file changed, 195 deletions(-) delete mode 100644 src/dimensionality_reduction/metrics/coranking/script.py diff --git a/src/dimensionality_reduction/metrics/coranking/script.py b/src/dimensionality_reduction/metrics/coranking/script.py deleted file mode 100644 index 76a7cbbf6e..0000000000 --- a/src/dimensionality_reduction/metrics/coranking/script.py +++ /dev/null @@ -1,195 +0,0 @@ -""" -This file is uses slightly modified code from pyDRMetrics [1]_, see: - - - https://doi.org/10.1016/j.heliyon.2021.e06199 - the article. - - https://data.mendeley.com/datasets/jbjd5fmggh/1 - the supplementary files. - -The following changes have been made: - - - :mod:`numba` JIT for performance reasons - - use broadcasting instead of a 3rd loop in :func:`_ranking_matrix` - -[1] Zhang, Yinsheng (2021), - “Source code, sample data, and case study report for pyDRMetrics”, - Mendeley Data, V1, doi: 10.17632/jbjd5fmggh.1 -""" - -import anndata as ad -from numba import njit -from typing import Tuple -import numpy as np -from sklearn.metrics import pairwise_distances -from scipy.sparse import issparse - - -_K = 30 - -## VIASH START -par = { - "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", - "output": "score.h5ad", -} -## VIASH END - -print("Load data", flush=True) -input_reduced = ad.read_h5ad(par["input_reduced"]) -input_test = ad.read_h5ad(par["input_test"]) - -X_emb = input_reduced.obsm["X_emb"] -high_dim = input_test.layers["normalized"] - -def _ranking_matrix(pdist_mat: np.ndarray) -> np.ndarray: - """The pairwise distance matrix is ranked using argsort.""" - assert pdist_mat.shape[0] == pdist_mat.shape[1] - return np.argsort(np.argsort(pdist_mat)) - -def _coranking_matrix(rmat1: np.ndarray, rmat2: np.ndarray) -> np.ndarray: - """Compute the coranking matrix from two ranking matrices.""" - assert rmat1.shape == rmat2.shape - m = rmat1.shape[0] - corank_mat = np.zeros((m - 1, m - 1), dtype=np.int32) - for i in range(m): - for j in range(m): - if i != j: - k = rmat1[i, j] - 1 - l = rmat2[i, j] - 1 - corank_mat[k, l] += 1 - return corank_mat - -def _metrics( - Q: np.ndarray, -) -> Tuple[np.ndarray, np.ndarray, np.ndarray, float, np.ndarray, int, float, float]: - Q = Q[1:, 1:] - m = len(Q) - - T = _trustworthiness(Q, m) - C = _continuity(Q, m) - QNN = _qnn(Q, m) - LCMC = _lcmc(QNN, m) - kmax = _kmax(LCMC) - Qlocal = _q_local(QNN, kmax) - Qglobal = _q_global(QNN, kmax, m) - AUC = _qnn_auc(QNN) - - return T, C, QNN, AUC, LCMC, kmax, Qlocal, Qglobal - -def _fit( - original: np.ndarray, embedding: np.ndarray -) -> Tuple[float, float, float, float, float, float, float]: - from sklearn.metrics import pairwise_distances - - if np.any(np.isnan(E)): - return 0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf - - pdist_original = pairwise_distances(original) - pdist_embedding = pairwise_distances(embedding) - rmat_original = _ranking_matrix(pdist_original) - rmat_embedding = _ranking_matrix(pdist_embedding) - corank = _coranking_matrix(rmat_original, rmat_embedding) - - T, C, QNN, AUC, LCMC, _kmax, Qlocal, Qglobal = _metrics(corank) - - return T[_K], C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal - - -print("Store metric value", flush=True) -input_reduced.uns['metric_ids'] = {meta['functionality_name']: ['continuity', 'co-KNN size', 'co-KNN AUC', 'local continuity meta criterion', 'local property', 'global property']} -if np.any(np.isnan(input_reduced.obsm["X_emb"])): - input_reduced.uns['metric_values'] = [0.0, 0.0, 0.0, 0.5, -np.inf, -np.inf, -np.inf] -else: - input_reduced.uns['metric_values'] = [C[_K], QNN[_K], AUC, LCMC[_K], Qlocal, Qglobal] - - -print("Copy data to new AnnData object", flush=True) -output = ad.AnnData( - uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} -) - -print("Write data to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") - - - - - - - - - - - - - - - - - - - - -def _trustworthiness(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover - - T = np.zeros(m - 1) # trustworthiness - - for k in range(m - 1): - Qs = Q[k:, :k] - # a column vector of weights. weight = rank error = actual_rank - k - W = np.arange(Qs.shape[0]).reshape(-1, 1) - # 1 - normalized hard-k-intrusions. lower-left region. - # weighted by rank error (rank - k) - T[k] = 1 - np.sum(Qs * W) / ((k + 1) * m * (m - 1 - k)) - - return T - - -def _continuity(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover - - C = np.zeros(m - 1) # continuity - - for k in range(m - 1): - Qs = Q[:k, k:] - # a row vector of weights. weight = rank error = actual_rank - k - W = np.arange(Qs.shape[1]).reshape(1, -1) - # 1 - normalized hard-k-extrusions. upper-right region - C[k] = 1 - np.sum(Qs * W) / ((k + 1) * m * (m - 1 - k)) - - return C - - -def _qnn(Q: np.ndarray, m: int) -> np.ndarray: # pragma: no cover - - QNN = np.zeros(m) # Co-k-nearest neighbor size - - for k in range(m): - # Q[0,0] is always m. 0-th nearest neighbor is always the point itself. - # Exclude Q[0,0] - QNN[k] = np.sum(Q[: k + 1, : k + 1]) / ((k + 1) * m) - - return QNN - - -def _lcmc(QNN: np.ndarray, m: int) -> np.ndarray: - LCMC = QNN - (np.arange(m) + 1) / (m - 1) - return LCMC - - -def _kmax(LCMC: np.ndarray) -> int: - kmax = np.argmax(LCMC) - return kmax # type: ignore - - -def _q_local(QNN: np.ndarray, kmax: int) -> float: - Qlocal = np.sum(QNN[: kmax + 1]) / (kmax + 1) - return Qlocal - - -def _q_global(QNN: np.ndarray, kmax: int, m: int) -> float: - # skip the last. The last is (m-1)-nearest neighbor, including all samples. - Qglobal = np.sum(QNN[kmax:-1]) / (m - kmax - 1) - return Qglobal - - -def _qnn_auc(QNN: np.ndarray) -> float: - AUC = np.mean(QNN) - return AUC # type: ignore From c9f3044be22e494aac16d2239e42e3d564452722 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 15:32:41 +0100 Subject: [PATCH 0670/1233] update authorship Former-commit-id: edc195c45e081a6849e08c1cf00c9969e0761f89 --- src/dimensionality_reduction/api/authors.yaml | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/api/authors.yaml b/src/dimensionality_reduction/api/authors.yaml index d5a676935d..d1a6fd6eee 100644 --- a/src/dimensionality_reduction/api/authors.yaml +++ b/src/dimensionality_reduction/api/authors.yaml @@ -1,9 +1,20 @@ functionality: authors: + - name: Luke Zappia + roles: [ maintainer, author ] + props: { github: lazappi } + - name: Michal Klein + roles: [ author ] + props: { github: michalk8 } + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: Ben DeMeo + roles: [ author ] + props: { github: bendemeo } - name: "Juan A. Cordero Varela" roles: [ contributor ] props: { github: jacorvar, orcid: 0000-0002-7373-5433} - name: Robrecht Cannoodt - roles: [ author ] + roles: [ contributor ] props: { github: rcannood, orcid: "0000-0003-3641-729X" } - From 0be40feca2baa66f6531c814266c139020edb2a5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 15:47:46 +0100 Subject: [PATCH 0671/1233] add back ivis Former-commit-id: 3132fc3fb7761cab3eeeb7f71a7bf9c2af9ad815 --- .../methods/ivis/config.vsh.yaml | 44 ++++++++++++++ .../methods/ivis/script.py | 57 +++++++++++++++++++ .../methods/pca/config.vsh.yaml | 1 - 3 files changed, 101 insertions(+), 1 deletion(-) create mode 100644 src/dimensionality_reduction/methods/ivis/config.vsh.yaml create mode 100644 src/dimensionality_reduction/methods/ivis/script.py diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml new file mode 100644 index 0000000000..b397c0a0f4 --- /dev/null +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -0,0 +1,44 @@ +# see https://github.com/openproblems-bio/openproblems/blob/9ebb777b3b76337e731a3b99f4bf39462a15c4cc/openproblems/tasks/dimensionality_reduction/methods/ivis.py + +__merge__: ../../api/comp_method.yaml +functionality: + name: "ivis" + namespace: "dimensionality_reduction/methods" + description: | + ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. + ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using + a parametric mapping function, and scales linearly to millions of observations. + info: + type: method + method_name: "ivis" + paper_reference: szubert2019structurepreserving + code_url: https://github.com/beringresearch/ivis + v1_url: openproblems/tasks/dimensionality_reduction/methods/ivis.py + v1_commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc + preferred_normalization: log_cpm + variants: + ivis_logCPM_1kHVG: + arguments: + - name: '--n_pca_dims' + type: integer + default: 50 + description: Number of principal components of PCA to use. + - name: "--n_hvg" + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + default: 1000 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.10" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - ivis[cpu] + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/ivis/script.py b/src/dimensionality_reduction/methods/ivis/script.py new file mode 100644 index 0000000000..8af3b8e242 --- /dev/null +++ b/src/dimensionality_reduction/methods/ivis/script.py @@ -0,0 +1,57 @@ +import anndata as ad +import scanpy as sc +from ivis import Ivis + +# todo: allow using gpus instead! + +## VIASH START +par = { + "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", + "output": "reduced.h5ad", + "n_hvg": 1000, + "n_pca_dims": 50 +} +meta = { + "functionality_name": "foo", +} +## VIASH END + +print("Load input data", flush=True) +input = ad.read_h5ad(par["input"]) +X_mat = input.layers["normalized"] + +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] + +print(f"Running PCA with {par['n_pca_dims']} dimensions", flush=True) +X_pca = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack")[:, :2] + +print("Run ivis") +# parameters taken from: +# https://bering-ivis.readthedocs.io/en/latest/scanpy_singlecell.html#reducing-dimensionality-using-ivis +ivis = Ivis( + k=15, + model="maaten", + n_epochs_without_progress=5, + verbose=0, + embedding_dims=2, +) +X_emb = ivis.fit_transform(X_pca) + +print("Create output AnnData", flush=True) +output = ad.AnnData( + obs=input.obs[[]], + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index b78c33a723..c066a90b9f 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -30,7 +30,6 @@ platforms: packages: - scanpy - "anndata>=0.8" - - pyyaml - type: nextflow directives: label: [ highmem, highcpu ] From 5049bc7bca6b7b7e39a9b90961b05292dcc35ae2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Jan 2023 16:24:16 +0100 Subject: [PATCH 0672/1233] fix unit test and coranking Former-commit-id: f57fe3cf2e61c4d533c1e3923287a748a61ffe28 --- src/dimensionality_reduction/api/comp_metric.yaml | 3 ++- src/dimensionality_reduction/metrics/coranking/config.vsh.yaml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 84abd00ad6..48d07e06bc 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -48,7 +48,8 @@ functionality: print(">> Checking whether metrics were added", flush=True) assert "metric_ids" in output.uns assert "metric_values" in output.uns - assert meta['functionality_name'] in output.uns["metric_ids"] + # assert meta['functionality_name'] in output.uns["metric_ids"] + # todo: look at config to check whether all metric ids are available print(">> Checking whether data from input was copied properly to output", flush=True) assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 9492eb59a3..72b77cb501 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -67,7 +67,7 @@ platforms: image: eddelbuettel/r2u:22.04 setup: - type: r - cran: [ anndata, coRanking ] + cran: [ anndata, coRanking, bit64 ] - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python From 9226432e64e158c65e05ba6346f13e9a6b0c4179 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 11 Jan 2023 17:04:58 +0100 Subject: [PATCH 0673/1233] update graph metrics assertion values Former-commit-id: 47c3581de6a38f71feae55680a237fc1a78cd3b1 --- src/batch_integration/graph/methods/combat/script.py | 3 ++- src/batch_integration/graph/metrics/ari/test.py | 2 +- src/batch_integration/graph/metrics/ari/test_combat.py | 2 +- src/batch_integration/graph/metrics/nmi/test.py | 2 +- src/batch_integration/graph/metrics/nmi/test_combat.py | 2 +- 5 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index 8aafc18149..161b7df9a2 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -26,7 +26,7 @@ if hvg: print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] + adata = adata[:, adata.var['highly_variable']].copy() if scaling: print('Scale') @@ -36,6 +36,7 @@ print('Integrate') adata.X = sc.pp.combat(adata, key='batch', inplace=False) +adata.X = csr_matrix(adata.X) print('Postprocess data') adata.obsm['X_emb'] = sc.pp.pca( diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index 089ce4cf1e..18e3fc30eb 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.3995060325339174 +assert score == 0.937800663971526 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py index ac1ad306f8..2faa6aae80 100644 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.1439128090443822 +assert score == 0.9372504013586168 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index e676f17979..d82a050c3a 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.3418185548452759 +assert score == 0.8705271595688995 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py index 43a78567a5..f6a57e724b 100644 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.2425827787547619 +assert score == 0.8849932681650504 print(">> All tests passed successfully") From 064f022058ec81b975d430e03a3dc08269d45485 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 11 Jan 2023 18:20:52 +0100 Subject: [PATCH 0674/1233] update embedding metrics assertion values Former-commit-id: 9a8ab08c452e868e844d1beca3de735423616be8 --- src/batch_integration/embedding/methods/combat/script.py | 5 +++-- src/batch_integration/embedding/metrics/asw_batch/test.py | 2 +- src/batch_integration/embedding/metrics/asw_label/test.py | 2 +- .../embedding/metrics/cell_cycle_conservation/script.py | 3 +++ .../embedding/metrics/cell_cycle_conservation/test.py | 6 +++++- 5 files changed, 13 insertions(+), 5 deletions(-) diff --git a/src/batch_integration/embedding/methods/combat/script.py b/src/batch_integration/embedding/methods/combat/script.py index 50a2c2d486..67fa809148 100644 --- a/src/batch_integration/embedding/methods/combat/script.py +++ b/src/batch_integration/embedding/methods/combat/script.py @@ -26,7 +26,7 @@ if hvg: print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] + adata = adata[:, adata.var['highly_variable']].copy() if scaling: print('Scale') @@ -35,7 +35,8 @@ adata.X = adata.layers['logcounts'] print('Integrate') -adata.X = csr_matrix(sc.pp.combat(adata, key='batch', inplace=False)) +adata.X = sc.pp.combat(adata, key='batch', inplace=False) +adata.X = csr_matrix(adata.X) print('Postprocess data') adata.obsm['X_emb'] = sc.pp.pca( diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py index 45d57db43f..e3534d13d8 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ b/src/batch_integration/embedding/metrics/asw_batch/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.9035066414882263 +assert score == 0.9698405638892912 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py index 9f2e4e02e6..ef380bac7a 100644 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.49921771598747 +assert score == 0.5758476480841637 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py index c267279a63..764264fed4 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py @@ -11,6 +11,7 @@ import pprint import scanpy as sc from scib.metrics import cell_cycle +from scipy.sparse import csr_matrix if par['debug']: pprint.pprint(par) @@ -27,6 +28,8 @@ adata_int = adata.copy() name = adata.uns['dataset_id'] +adata.X = adata.layers['logcounts'] + print('compute score') score = cell_cycle( adata, diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py index e370bc85bd..b8a7767916 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -2,12 +2,15 @@ import subprocess import pandas as pd import numpy as np +import scanpy as sc np.random.seed(42) metric = 'cell_cycle_conservation' metric_file = metric + '.tsv' +print(sc.read('combat.h5ad')) + print(">> Running script") out = subprocess.check_output([ "./" + metric, @@ -26,6 +29,7 @@ print(score) assert 0 < score < 1 -assert 0.9380807 <= score <= 0.938081 + +assert score == 0.9495255717047036 print(">> All tests passed successfully") From 14aec291e5f291e4005ad7cc5d32fb0ba19a1c23 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 12 Jan 2023 21:47:41 +0100 Subject: [PATCH 0675/1233] remove bin/ from nexflow cmd from bash scripts CONTRIBUTING.md instructions not working #41 Former-commit-id: b898fb5d794ee4902259bcc5957aff254510141d --- src/datasets/loaders/openproblems_v1/run.sh | 2 +- src/datasets/resource_scripts/openproblems_v1.sh | 2 +- src/denoising/resources_scripts/run_benchmark.sh | 8 ++++---- src/denoising/resources_scripts/split_datasets.sh | 2 +- src/denoising/resources_test_scripts/pancreas.sh | 2 +- .../resources_scripts/run_benchmark.sh | 2 +- .../resources_scripts/split_datasets.sh | 2 +- .../resources_test_scripts/pancreas.sh | 2 +- src/label_projection/resources_scripts/run_benchmark.sh | 8 ++++---- src/label_projection/resources_scripts/split_datasets.sh | 2 +- src/label_projection/resources_test_scripts/pancreas.sh | 2 +- src/label_projection/workflows/run/run_test.sh | 2 +- src/modality_alignment/workflows/run/run_nextflow.sh | 2 +- 13 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/run.sh b/src/datasets/loaders/openproblems_v1/run.sh index db158b7521..1edd5e5efb 100755 --- a/src/datasets/loaders/openproblems_v1/run.sh +++ b/src/datasets/loaders/openproblems_v1/run.sh @@ -8,7 +8,7 @@ cd "$REPO_ROOT" export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script target/nextflow/datasets/loaders/openproblems_v1/main.nf \ -resume \ diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index fced1e226c..420da43210 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -73,7 +73,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ -profile docker \ diff --git a/src/denoising/resources_scripts/run_benchmark.sh b/src/denoising/resources_scripts/run_benchmark.sh index 0068967165..2e53d2b6dd 100755 --- a/src/denoising/resources_scripts/run_benchmark.sh +++ b/src/denoising/resources_scripts/run_benchmark.sh @@ -62,7 +62,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/denoising/workflows/run/main.nf \ -profile docker \ @@ -73,10 +73,10 @@ bin/nextflow \ bin/tools/docker/nextflow/process_log/process_log \ --output "$OUTPUT_DIR/nextflow_log.tsv" -# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' -# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' +# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' +# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' -# bin/nextflow run . \ +# nextflow run . \ # -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ # -profile docker \ # --input_train resources_test/label_projection/pancreas/train.h5ad \ diff --git a/src/denoising/resources_scripts/split_datasets.sh b/src/denoising/resources_scripts/split_datasets.sh index ac5bbaea77..0e0333a825 100755 --- a/src/denoising/resources_scripts/split_datasets.sh +++ b/src/denoising/resources_scripts/split_datasets.sh @@ -52,7 +52,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script target/nextflow/denoising/split_dataset/main.nf \ -profile docker \ diff --git a/src/denoising/resources_test_scripts/pancreas.sh b/src/denoising/resources_test_scripts/pancreas.sh index 03e2c120c0..0a42dc5e8c 100755 --- a/src/denoising/resources_test_scripts/pancreas.sh +++ b/src/denoising/resources_test_scripts/pancreas.sh @@ -40,7 +40,7 @@ bin/viash run src/denoising/metrics/poisson/config.vsh.yaml -- \ # run benchmark export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/denoising/workflows/run/main.nf \ -profile docker \ diff --git a/src/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh index 620341604d..7ffc4d7995 100755 --- a/src/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -59,7 +59,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ diff --git a/src/dimensionality_reduction/resources_scripts/split_datasets.sh b/src/dimensionality_reduction/resources_scripts/split_datasets.sh index ee97aff0d4..c447076c02 100755 --- a/src/dimensionality_reduction/resources_scripts/split_datasets.sh +++ b/src/dimensionality_reduction/resources_scripts/split_datasets.sh @@ -57,7 +57,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script target/nextflow/dimensionality_reduction/split_dataset/main.nf \ -profile docker \ diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index 81d97ba004..e1a455b88b 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -40,7 +40,7 @@ viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ export NXF_VER=22.04.5 # after having added a split dataset component -bin/nextflow \ +nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ diff --git a/src/label_projection/resources_scripts/run_benchmark.sh b/src/label_projection/resources_scripts/run_benchmark.sh index 9aac51109d..389c15ab4d 100755 --- a/src/label_projection/resources_scripts/run_benchmark.sh +++ b/src/label_projection/resources_scripts/run_benchmark.sh @@ -61,7 +61,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ -profile docker \ @@ -72,10 +72,10 @@ bin/nextflow \ bin/tools/docker/nextflow/process_log/process_log \ --output "$OUTPUT_DIR/nextflow_log.tsv" -# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' -# bin/viash_build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' +# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' +# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' -# bin/nextflow run . \ +# nextflow run . \ # -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ # -profile docker \ # --input_train resources_test/label_projection/pancreas/train.h5ad \ diff --git a/src/label_projection/resources_scripts/split_datasets.sh b/src/label_projection/resources_scripts/split_datasets.sh index 8cc4217555..d561760373 100755 --- a/src/label_projection/resources_scripts/split_datasets.sh +++ b/src/label_projection/resources_scripts/split_datasets.sh @@ -56,7 +56,7 @@ HERE fi export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script target/nextflow/label_projection/split_dataset/main.nf \ -profile docker \ diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index e8b4064022..19a3ae652b 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -42,7 +42,7 @@ bin/viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ # run benchmark export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ -profile docker \ diff --git a/src/label_projection/workflows/run/run_test.sh b/src/label_projection/workflows/run/run_test.sh index 9b022e62b3..cfd3fa9fac 100755 --- a/src/label_projection/workflows/run/run_test.sh +++ b/src/label_projection/workflows/run/run_test.sh @@ -20,7 +20,7 @@ fi # run benchmark export NXF_VER=22.04.5 -bin/nextflow \ +nextflow \ run . \ -main-script src/label_projection/workflows/run/main.nf \ -profile docker \ diff --git a/src/modality_alignment/workflows/run/run_nextflow.sh b/src/modality_alignment/workflows/run/run_nextflow.sh index e0b946aa54..2294a9b50f 100755 --- a/src/modality_alignment/workflows/run/run_nextflow.sh +++ b/src/modality_alignment/workflows/run/run_nextflow.sh @@ -12,7 +12,7 @@ cd "$REPO_ROOT" # choose a particular version of nextflow export NXF_VER=21.10.6 -bin/nextflow \ +nextflow \ run . \ -main-script src/modality_alignment/workflows/run/main.nf \ --publish_dir output/modality_alignment \ From 10d0d9c0206fe86e3533c6b9690a4247d90b2f4c Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 12 Jan 2023 21:53:14 +0100 Subject: [PATCH 0676/1233] remove remaining `bin/` from contributing Former-commit-id: 83074d1d6ca1c5c432d495ef8e8fc23ac9adbe60 --- CONTRIBUTING.qmd | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index c543f4732c..7f52701b1b 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -151,7 +151,6 @@ You can start creating a new component by [creating a Viash component](https://v ```{bash, include=FALSE} -# bin/viash_skeleton --name foo --namespace "label_projection/methods" --language python mkdir -p src/label_projection/methods/foo @@ -239,13 +238,13 @@ src/label_projection/methods/foo/script.py You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. ```{bash} -bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help +viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` You can **run the component** as follows: ```{bash} -bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ +viash run src/label_projection/methods/foo/config.vsh.yaml -- \ --input_train resources_test/label_projection/pancreas/train.h5ad \ --input_test resources_test/label_projection/pancreas/test.h5ad \ --output resources_test/label_projection/pancreas/prediction.h5ad @@ -260,12 +259,12 @@ This standalone executable you can give to somebody else, and they will be able run it, provided that they have Bash and Docker installed. ```{bash} -bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ +viash build src/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` :::{.callout-note} -The `bin/viash_build` component does a much better job of setting up +The `viash ns build` component does a much better job of setting up a collection of components. ::: @@ -291,7 +290,7 @@ The [method API specifications](src/label_projection/api/comp_method.yaml) comes This means you can unit test your component using the **`viash test`** command. ```{bash} -bin/viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/label_projection/methods/foo/config.vsh.yaml ``` ```{bash include=FALSE} @@ -335,7 +334,7 @@ src/label_projection/methods/foo/script.py If we now run the test, we should get an error since we didn't create all of the required output slots. ```{bash error=TRUE} -bin/viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/label_projection/methods/foo/config.vsh.yaml ``` From 27e4aa22ecb573810fcf694ad98f0d2f50761c68 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 12 Jan 2023 22:27:30 +0100 Subject: [PATCH 0677/1233] update denoising to latest OP -v1 and OP-v2 format Former-commit-id: c121b04e633df681a5fab4a334f13c1f934ddb10 --- .../control_methods/no_denoising/config.vsh.yaml | 4 ++-- .../control_methods/perfect_denoising/config.vsh.yaml | 4 ++-- src/denoising/methods/alra/config.vsh.yaml | 4 ++-- src/denoising/methods/dca/config.vsh.yaml | 7 ++----- src/denoising/methods/knn_smoothing/config.vsh.yaml | 9 +++------ src/denoising/methods/magic/config.vsh.yaml | 9 +++------ src/denoising/metrics/mse/config.vsh.yaml | 3 ++- src/denoising/metrics/poisson/config.vsh.yaml | 11 ++++++----- 8 files changed, 22 insertions(+), 29 deletions(-) diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 964ef54197..64e601f7ab 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -5,9 +5,9 @@ functionality: description: "negative control by copying train counts" info: type: negative_control - label: no denoising + method_name: No Denoising v1_url: openproblems/tasks/denoising/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: no_denoising: preferred_normalization: counts diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index 36d1a057f8..e24fb9cf9c 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -5,9 +5,9 @@ functionality: description: "Negative control by copying the train counts" info: type: positive_control - label: perfect denoising + method_name: Perfect Denoising v1_url: openproblems/tasks/denoising/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: perfect_denoising: preferred_normalization: counts diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index de2d249a07..394193e458 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -14,11 +14,11 @@ functionality: info: type: method method_name: ALRA - paper_doi: "10.1101/397588" + paper_reference: "linderman2018zero" code_url: "https://github.com/KlugerLab/ALRA" doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md v1_url: openproblems/tasks/denoising/methods/alra.py - v1_commit: 411a416150ecabce25e1f59bde422a029d0a8baa + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: alra: preferred_normalization: counts diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index afac47d528..0ce04986bd 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -10,13 +10,10 @@ functionality: info: type: method method_name: DCA - # paper_name: "Single-cell RNA-seq denoising using a deep count autoencoder" - # paper_url: "https://www.nature.com/articles/s41467-018-07931-2" - # paper_year: 2019 - paper_doi: "10.1038/s41467-018-07931-2" + paper_reference: "https://www.nature.com/articles/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" v1_url: openproblems/tasks/denoising/methods/dca.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: dca: preferred_normalization: counts diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 153c518bb4..2fd5c0ed6e 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -5,14 +5,11 @@ functionality: description: "iterative K-nearest neighbor smoothing" info: type: method - label: knn_smooth - # paper_name: "K-nearest neighbor smoothing for high-throughput" - # paper_url: "https://www.biorxiv.org/content/10.1101/217737v3" - # paper_year: 2018 - paper_doi: "10.1101/217737" + method_name: KNN Smoothing + paper_reference: "wagner2018knearest" code_url: "https://github.com/yanailab/knn-smoothing" v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py - v1_commit: bbecf4e9ad90007c2711394e7fbd8e49cbd3e4a1 + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: knn_smoothing: preferred_normalization: counts diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 60e3a8392f..d9b820ed07 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -5,14 +5,11 @@ functionality: description: "MAGIC: Markov affinity-based graph imputation of cells" info: type: method - label: magic - # paper_name: "Recovering Gene Interactions from Single-Cell Data using Data Diffusion" - # paper_url: "https://doi.org/10.1016/j.cell.2018.05.061" - # paper_year: 2018 - paper_doi: "10.1016/j.cell.2018.05.061" + method_name: MAGIC + paper_reference: "https://doi.org/10.1016/j.cell.2018.05.061" code_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: openproblems/tasks/denoising/methods/magic.py - v1_commit: 2fbc2d4c8d3ff955ea948fc082635cf779b1927e + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: magic: magic_approx: diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 623e03b130..4f795e34ea 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -4,8 +4,9 @@ functionality: namespace: "denoising/metrics" description: "Mean Squared Error." info: + paper_reference: "batson2019molecular" v1_url: openproblems/tasks/denoising/metrics/mse.py - v1_commit: f24fb718b1115ca85130a45f2e56fddb00075d22 + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - metric_id: mse metric_name: Mean-squared error diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 488463e828..06f96b4f0c 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -4,12 +4,13 @@ functionality: namespace: "denoising/metrics" description: "Poisson loss" info: + paper_reference: "batson2019molecular" v1_url: openproblems/tasks/denoising/metrics/poisson.py - v1_commit: 4524f7bbcc4ea94cfb4acf1bd7f7c93c1ba7d0c9 + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - - id: poisson - label: poisson - description: "Poisson loss: measure the mean of the inconsistencies between predicted and target" + - metric_id: poisson + metric_name: Poisson Loss + metric_description: "Poisson loss: measure the mean of the inconsistencies between predicted and target" maximize: false min: 0 max: +inf @@ -21,7 +22,7 @@ platforms: image: "python:3.10" setup: - type: python - packages: + pip: - "anndata>=0.8" - scprep - type: nextflow From 34b61d8a75c9197786e73eec450150ee5cbc2c18 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 13 Jan 2023 15:00:14 +0100 Subject: [PATCH 0678/1233] update metrics Former-commit-id: 2d4515bc9cb635e73b9bc231c20a4a6dd06da429 --- .../metrics/coranking/config.vsh.yaml | 28 +++---- .../metrics/coranking/script.R | 4 +- .../density_preservation/config.vsh.yaml | 6 +- .../metrics/rmse/config.vsh.yaml | 17 +++- .../metrics/rmse/script.py | 82 ++++++++++--------- .../metrics/trustworthiness/config.vsh.yaml | 7 +- .../metrics/trustworthiness/script.py | 39 ++++----- .../split_dataset/script.py | 20 ++--- .../workflows/run/main.nf | 6 +- 9 files changed, 114 insertions(+), 95 deletions(-) diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 72b77cb501..2485507175 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -17,44 +17,44 @@ functionality: properly attribute the original authors of each of the metrics. paper_reference: kraemer2018dimred metrics: - - id: continuity_at_k30 - name: Continuity at k=30 + - metric_id: continuity_at_k30 + metric_name: Continuity at k=30 paper_reference: venna2006local min: 0 max: 1 maximize: true - - id: trustworthiness_at_k30 - name: Trustworthiness at k=30 + - metric_id: trustworthiness_at_k30 + metric_name: Trustworthiness at k=30 paper_reference: venna2006local min: 0 max: 1 maximize: true - - id: qnx_at_k30 - name: The value for QNX at k=30 + - metric_id: qnx_at_k30 + metric_name: The value for QNX at k=30 paper_reference: lee2009quality min: 0 max: 1 maximize: true - - id: lcmc_at_k30 - name: The value for LCMC at k=30 + - metric_id: lcmc_at_k30 + metric_name: The value for LCMC at k=30 paper_reference: chen2009local min: 0 max: 1 maximize: true - - id: qnx_auc - name: Area under the QNX curve + - metric_id: qnx_auc + metric_name: Area under the QNX curve paper_reference: lueks2011evaluate min: 0 max: 1 maximize: true - - id: qlocal - name: Local quality measure + - metric_id: qlocal + metric_name: Local quality measure paper_reference: lueks2011evaluate min: 0 max: 1 maximize: true - - id: qglobal - name: Global quality measure + - metric_id: qglobal + metric_name: Global quality measure paper_reference: lueks2011evaluate min: 0 max: 1 diff --git a/src/dimensionality_reduction/metrics/coranking/script.R b/src/dimensionality_reduction/metrics/coranking/script.R index 5878b9e3f5..63a6b68769 100644 --- a/src/dimensionality_reduction/metrics/coranking/script.R +++ b/src/dimensionality_reduction/metrics/coranking/script.R @@ -28,7 +28,9 @@ if (any(is.na(X_emb))) { 0 } else { cat("Compute pairwise distances\n") - # TODO: this is problematic for large datasets! + # TODO: computing a square distance matrix is problematic for large datasets! + # TODO: should we use a different distance metric for the high_dim? + # TODO: or should we subset to the HVG? dist_highdim <- coRanking:::euclidean(as.matrix(high_dim)) dist_emb <- coRanking:::euclidean(as.matrix(X_emb)) diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index c03ebe56c0..474e035f71 100644 --- a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -8,9 +8,9 @@ functionality: v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - - id: density_preservation - label: Density preservation - description: | + - metric_id: density_preservation + metric_name: Density preservation + metric_description: | Similarity between local densities in the high-dimensional data and the reduced data. This is computed as the pearson correlation of local radii with the local radii in the original data space. diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 5c7b8f6926..f67ae5a06d 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -6,11 +6,22 @@ functionality: info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b + v1_note: This metric was ported but will probably be removed soon. metrics: - - id: rmse - label: RMSE - description: "The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices" + - metric_id: rmse + metric_name: RMSE + metric_description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." + paper_reference: kruskal1964mds min: 0 + max: +inf + maximize: false + - metric_id: rmse_spectral + metric_name: RMSE Spectral + metric_description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." + paper_reference: coifman2006diffusion + min: 0 + max: +inf + maximize: false arguments: - name: "--spectral" type: boolean_true diff --git a/src/dimensionality_reduction/metrics/rmse/script.py b/src/dimensionality_reduction/metrics/rmse/script.py index b0b8f0608c..d738c95c47 100644 --- a/src/dimensionality_reduction/metrics/rmse/script.py +++ b/src/dimensionality_reduction/metrics/rmse/script.py @@ -1,54 +1,58 @@ import anndata as ad -from umap import UMAP, spectral -import scipy.spatial.distance as dist -from scipy.optimize import nnls import numpy as np -from sklearn import decomposition, metrics +import sklearn.decomposition +import scipy.optimize +import scipy.spatial +from sklearn.metrics import pairwise_distances +import umap +import umap.spectral ## VIASH START par = { - 'input_reduced': 'reduced.h5ad', - 'input_test': 'test.h5ad', - 'output': 'score.h5ad', -} -meta = { - 'functionality_name': 'rmse', + "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "score.h5ad", } ## VIASH END -print("Load data", flush=True) -input_reduced = ad.read_h5ad(par['input_reduced']) -input_test = ad.read_h5ad(par['input_test']) - -print('Reduce dimensionality of raw data', flush=True) -n_comps = 200 -if not par['spectral']: - input_reduced.obsm['high_dim'] = decomposition.TruncatedSVD(n_components = n_comps).fit_transform(input_test.layers['counts']) - print('Compute RMSE between the full (or processed) data matrix and a dimensionally-reduced matrix, invariant to scalar multiplication', flush=True) -else: - n_comps = min(n_comps, min(input_test.shape) - 2) - graph = UMAP(transform_mode="graph").fit_transform(input_test.layers['counts']) - input_reduced.obsm['high_dim'] = spectral.spectral_layout( - input_test.layers['counts'], graph, n_comps, random_state=np.random.default_rng() +def _rmse(X, X_emb): + high_dimensional_distance_vector = scipy.spatial.distance.pdist(X) + low_dimensional_distance_vector = scipy.spatial.distance.pdist(X_emb) + _, rmse = scipy.optimize.nnls( + low_dimensional_distance_vector[:, None], high_dimensional_distance_vector ) - meta['functionality_name'] += ' spectral' - print('Computes (RMSE) between high-dimensional Laplacian eigenmaps on the full (or processed) data matrix and the dimensionally-reduced matrix, invariant to scalar multiplication', flush=True) - -high_dim_dist = dist.pdist(input_reduced.obsm['high_dim']) -low_dim_dist = dist.pdist(input_reduced.obsm["X_emb"]) + return rmse -scale, rmse = nnls( - low_dim_dist[:, None], high_dim_dist - ) - -print("Store metric value", flush=True) -input_reduced.uns['metric_ids'] = meta['functionality_name'] -input_reduced.uns['metric_values'] = rmse +print("Load data", flush=True) +input_test = ad.read_h5ad(par["input_test"]) +input_reduced = ad.read_h5ad(par["input_reduced"]) + +high_dim = input_test.layers["normalized"] +X_emb = input_reduced.obsm["X_emb"] + +print("Compute NNLS residual after SVD", flush=True) +n_svd = 200 +svd_emb = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(high_dim) +rmse = _rmse(svd_emb, X_emb) + +print("Compute NLSS residual after spectral embedding", flush=True) +n_comps = min(200, min(input_test.shape) - 2) +umap_graph = umap.UMAP(transform_mode="graph").fit_transform(high_dim) +spectral_emb = umap.spectral.spectral_layout( + high_dim, umap_graph, n_comps, random_state=np.random.default_rng() +) +rmse_spectral = _rmse(spectral_emb, X_emb) -print("Copy data to new AnnData object", flush=True) +print("Create output AnnData object", flush=True) output = ad.AnnData( - uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} + uns={ + "dataset_id": input_test.uns["dataset_id"], + "normalization_id": input_test.uns["normalization_id"], + "method_id": input_reduced.uns["method_id"], + "metric_ids": [ "rmse", "rmse_spectral" ], + "metric_values": [ rmse, rmse_spectral ] + } ) print("Write data to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 58b9cc1862..ee5c3b3899 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -6,10 +6,11 @@ functionality: info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1_note: This metric is already included in the 'coranking' component and can be removed. metrics: - - id: trustworthiness - label: Trustworthiness - description: To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. + - method_id: trustworthiness + metric_name: Trustworthiness at k=15 + paper_reference: venna2006local min: 0 max: 1 maximize: true diff --git a/src/dimensionality_reduction/metrics/trustworthiness/script.py b/src/dimensionality_reduction/metrics/trustworthiness/script.py index 35637d3c55..9f76a7f8ed 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/dimensionality_reduction/metrics/trustworthiness/script.py @@ -4,33 +4,34 @@ ## VIASH START par = { - 'input_reduced': 'reduced.h5ad', - 'input_test': 'test.h5ad', - 'output': 'score.h5ad', -} -meta = { - 'functionality_name': 'trustworthiness', + "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "score.h5ad", } ## VIASH END print("Load data", flush=True) -input_reduced = ad.read_h5ad(par['input_reduced']) -input_test = ad.read_h5ad(par['input_test']) +input_test = ad.read_h5ad(par["input_test"]) +input_reduced = ad.read_h5ad(par["input_reduced"]) + +high_dim = input_test.layers["normalized"] +X_emb = input_reduced.obsm["X_emb"] -print('Reduce dimensionality of raw data', flush=True) -high_dim, low_dim = input_test.layers['counts'], input_reduced.obsm["X_emb"] -score = manifold.trustworthiness( - high_dim, low_dim, n_neighbors=15, metric="euclidean" +print("Reduce dimensionality of raw data", flush=True) +trustworthiness = manifold.trustworthiness( + high_dim, X_emb, n_neighbors=15, metric="euclidean" ) -# for large k close to #samples, it's higher than 1.0, e.g 1.0000073552559712 -print("Store metric value", flush=True) -input_reduced.uns['metric_ids'] = meta['functionality_name'] -input_reduced.uns['metric_values'] = float(np.clip(score, 0, 1)) -print("Copy data to new AnnData object", flush=True) +print("Create output AnnData object", flush=True) output = ad.AnnData( - uns={key: input_reduced.uns[key] for key in ["dataset_id", "normalization_id", "method_id", 'metric_ids', 'metric_values']} + uns={ + "dataset_id": input_test.uns["dataset_id"], + "normalization_id": input_test.uns["normalization_id"], + "method_id": input_reduced.uns["method_id"], + "metric_ids": [ "trustworthiness" ], + "metric_values": [ trustworthiness ] + } ) print("Write data to file", flush=True) -output.write_h5ad(par['output'], compression="gzip") \ No newline at end of file +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/split_dataset/script.py index 86889424f1..d51e7471a0 100644 --- a/src/dimensionality_reduction/split_dataset/script.py +++ b/src/dimensionality_reduction/split_dataset/script.py @@ -7,9 +7,9 @@ ## VIASH START par = { - 'input': "resources_test/common/pancreas/dataset.h5ad", - 'output_train': "train.h5ad", - 'output_test': "test.h5ad", + "input": "resources_test/common/pancreas/dataset.h5ad", + "output_train": "train.h5ad", + "output_test": "test.h5ad", } meta = { "functionality_name": "split_data", @@ -30,10 +30,10 @@ def read_slots(par, meta): if re.match("--output_", arg["name"]): file = re.sub("--output_", "", arg["name"]) - struct_slots = arg['info']['slots'] + struct_slots = arg["info"]["slots"] out = {} for (struct, slots) in struct_slots.items(): - out[struct] = { slot['name'] : slot['name'] for slot in slots } + out[struct] = { slot["name"] : slot["name"] for slot in slots } output_struct_slots[file] = out @@ -48,11 +48,11 @@ def subset_anndata(adata_sub, slot_info): slot_mapping = slot_info.get(struct, {}) data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} if len(data) > 0: - if struct in ['obs', 'var']: + if struct in ["obs", "var"]: data = pd.concat(data, axis=1) kwargs[struct] = data - elif struct in ['obs', 'var']: - # if no columns need to be copied, we still need an 'obs' and a 'var' + elif struct in ["obs", "var"]: + # if no columns need to be copied, we still need an "obs" and a "var" # to help determine the shape of the adata kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] @@ -67,13 +67,13 @@ def subset_anndata(adata_sub, slot_info): print(">> Creating train data", flush=True) output_train = subset_anndata( adata_sub=adata, - slot_info=slot_info_per_output['train'] + slot_info=slot_info_per_output["train"] ) print(">> Creating test data", flush=True) output_test = subset_anndata( adata_sub=adata, - slot_info=slot_info_per_output['test'] + slot_info=slot_info_per_output["test"] ) print(">> Writing", flush=True) diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index e21e4ea950..92a70a1434 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -16,10 +16,10 @@ include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" // import metrics +include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" +include { coranking } from "$targetDir/dimensionality_reduction/metrics/coranking/main.nf" include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" -include { density } from "$targetDir/dimensionality_reduction/metrics/density/main.nf" -include { nn_ranking } from "$targetDir/dimensionality_reduction/metrics/nn_ranking/main.nf" // tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" @@ -151,7 +151,7 @@ workflow run_metrics { main: output_ch = input_ch - | (rmse & trustworthiness & density) + | (density_preservation & coranking & rmse & trustworthiness) | mix emit: output_ch From 3b4d4e563158478b2b0d1f6485dae48731919487 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 13 Jan 2023 15:09:10 +0100 Subject: [PATCH 0679/1233] update readme Former-commit-id: 993473604fc6547cb0d70241fd5ac387a54a0b25 --- src/dimensionality_reduction/README.md | 263 +---------------- src/dimensionality_reduction/README.qmd | 265 +----------------- .../api/task_info.yaml | 4 +- 3 files changed, 21 insertions(+), 511 deletions(-) diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 40409b5594..4538aab017 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -1,25 +1,10 @@ -- Dimensionality reduction - - Methods - - Metrics - - Pipeline - topology - - File format API - - Dataset - - Reduced - - Score - - Test - - Train - - Component API - - Control Method - - Method - - Metric - - Split Dataset +# Dimensionality reduction for visualization -# Dimensionality reduction +Reduction of high-dimensional datasets to 2D for visualization & +interpretation + +## Task description Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) @@ -43,238 +28,8 @@ Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. -## Methods - -Methods to assign dimensionally-reduced 2D embedding coordinates to -adata.obsm\[‘X_emb’\]. - - Warning: Unknown or uninitialised column: `paper_doi`. - - Warning: Unknown or uninitialised column: `code_url`. - -| Name | Type | Description | DOI | URL | -|:------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:----------------------------------------------------------------------------------------------------------------------------------------|:----|:----| -| [densMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/densmap/config.vsh.yaml) | method | density-preserving based on UMAP | | | -| [NeuralEE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/neuralee/config.vsh.yaml) | method | A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/). | | | -| [PCA](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/pca/config.vsh.yaml) | method | Principal component analysis | | | -| [PHATE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/phate/config.vsh.yaml) | method | Potential of heat-diffusion for affinity-based transition embedding | | | -| [t-SNE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/tsne/config.vsh.yaml) | method | t-distributed stochastic neighbor embedding | | | -| [UMAP](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./methods/umap/config.vsh.yaml) | method | Uniform manifold approximation and projection | | | -| [Random features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/random_features/config.vsh.yaml) | negative_control | Negative control method which generates a random embedding | | | -| [True Features](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./control_methods/true_features/config.vsh.yaml) | positive_control | Positive control method which generates high-dimensional (full data) embedding | | | - -## Metrics - -Metrics for dimensionality reduction aim to compare the dimensionality -reduced dataset (the embedding) with a whole or a higher dimensional -dataset. The more similar they are, the better the reduction is. - -| Name | Description | Range | -|:----------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------|:-----------| -| [RMSE](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/rmse/config.vsh.yaml) | The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices NA | \[0, NA\] | -| [NN_Ranking](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/nn_ranking/config.vsh.yaml) | A set of metrics from the pyDRMetrics package. NA | \[NA, NA\] | -| [Density](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/density/config.vsh.yaml) | density preservation: correlation of local radius with the local radii in the original data space Higher is better. | \[0, -1\] | -| [Trustworthiness](/home/jacorvar/DI/openproblems-v2/src/dimensionality_reduction/./metrics/trustworthiness/config.vsh.yaml) | To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1. Higher is better. | \[0, 1\] | - -## Pipeline topology - -``` mermaid -%%| column: screen-inset-shaded -flowchart LR - anndata_dataset(Dataset) - anndata_reduced(Reduced) - anndata_score(Score) - anndata_test(Test) - anndata_train(Train) - comp_control_method[/Control Method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_split_dataset[/Split Dataset/] - anndata_dataset---comp_control_method - anndata_train---comp_method - anndata_reduced---comp_metric - anndata_test---comp_metric - anndata_dataset---comp_split_dataset - comp_control_method-->anndata_reduced - comp_method-->anndata_reduced - comp_metric-->anndata_score - comp_split_dataset-->anndata_train - comp_split_dataset-->anndata_test -``` - -## File format API - -### `Dataset` - -A normalized data with a PCA embedding and HVG selection - -Used in: - -- [control method](#control%20method): input (as input) -- [split dataset](#split%20dataset): input (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:--------|:-------------------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| obs | celltype | string | Cell type information | -| obs | batch | string | Batch information | -| obs | tissue | string | Tissue information | -| obs | size_factors | double | The size factors created by the normalization method, if any. | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | -| obsm | X_pca | double | The resulting PCA embedding. | -| varm | pca_loadings | double | The PCA loadings matrix. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | pca_variance | double | The PCA variance objects. | - -Example: - - AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id', 'pca_variance' - obsm: 'X_pca' - varm: 'pca_loadings' - layers: 'counts', 'normalized' - -### `Reduced` - -A dimensionally reduced dataset - -Used in: - -- [control method](#control%20method): output (as output) -- [method](#method): output (as output) -- [metric](#metric): input_reduced (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:-------|:-------------------------------------| -| obsm | X_emb | double | The dimensionally reduced embedding. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | -| uns | normalization_id | string | Which normalization was used | - -Example: - - AnnData object - uns: 'dataset_id', 'method_id', 'normalization_id' - obsm: 'X_emb' - -### `Score` - -Metric score file - -Used in: - -- [metric](#metric): output (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - -Example: - - AnnData object - uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' - -### `Test` - -The test data - -Used in: - -- [metric](#metric): input_test (as input) -- [split dataset](#split%20dataset): output_test (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:-------------------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | -| uns | dataset_id | string | A unique identifier for the dataset | - -Example: - - AnnData object - var: 'hvg_score' - uns: 'dataset_id' - layers: 'counts', 'normalized' - -### `Train` - -The training data - -Used in: - -- [method](#method): input (as input) -- [split dataset](#split%20dataset): output_train (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:-------------------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized expression values | -| var | hvg_score | double | High variability gene score (normalized dispersion). The greater, the more variable. | -| uns | dataset_id | string | A unique identifier for the dataset | - -Example: - - AnnData object - var: 'hvg_score' - uns: 'dataset_id' - layers: 'counts', 'normalized' - -## Component API - -### `Control Method` - -Arguments: - -| Name | File format | Direction | Description | -|:-----------|:--------------------|:----------|:----------------| -| `--input` | [Dataset](#dataset) | input | Dataset+PCA+HVG | -| `--output` | [Reduced](#reduced) | output | Training data | - -### `Method` - -Arguments: - -| Name | File format | Direction | Description | -|:-----------|:--------------------|:----------|:--------------| -| `--input` | [Train](#train) | input | Training data | -| `--output` | [Reduced](#reduced) | output | Training data | - -### `Metric` - -Arguments: - -| Name | File format | Direction | Description | -|:------------------|:--------------------|:----------|:--------------| -| `--input_reduced` | [Reduced](#reduced) | input | Training data | -| `--input_test` | [Test](#test) | input | Test data | -| `--output` | [Score](#score) | output | Score | - -### `Split Dataset` - -Arguments: +## More information -| Name | File format | Direction | Description | -|:-----------------|:--------------------|:----------|:----------------| -| `--input` | [Dataset](#dataset) | input | Dataset+PCA+HVG | -| `--output_train` | [Train](#train) | output | Training data | -| `--output_test` | [Test](#test) | output | Test data | +- [Benchmarking + results](https://openproblems-experimental.netlify.app/results_v2/dimensionality_reduction/) +- [Documentation](https://openproblems-experimental.netlify.app/results_v2/dimensionality_reduction/documentation) diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd index d72d5b598a..526abd9044 100644 --- a/src/dimensionality_reduction/README.qmd +++ b/src/dimensionality_reduction/README.qmd @@ -1,272 +1,27 @@ --- format: gfm -info: - v1_url: openproblems/tasks/dimensionality_reduction/README.md - v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 -toc: true --- ```{r setup, include=FALSE} -library(tidyverse) -library(rlang) - -strip_margin <- function(text, symbol = "\\|") { - str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") -} - dir <- "src/dimensionality_reduction" dir <- "." -``` -# Dimensionality reduction - -```{r description, echo=FALSE} -lines <- readr::read_lines(paste0(dir, "/docs/task_description.md")) -lines2 <- gsub("^#", "##", lines) -knitr::asis_output(lines2) +task_info <- yaml::read_yaml(paste0(dir, "/api/task_info.yaml")) ``` -## Methods - -Methods to assign dimensionally-reduced 2D embedding coordinates to `adata.obsm['X_emb']`. +# `r task_info$task_name` -```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) -method_configs <- yaml::yaml.load(method_ns_list$stdout) - -method_info <- map_df(method_configs, function(config) { - if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) - info <- as_tibble(config$functionality$info) - info$comp_yaml <- config$info$config - info$name <- config$functionality$name - info$namespace <- config$functionality$namespace - info$description <- config$functionality$description - info -}) -method_info$paper_doi <- method_info$paper_doi %||% NA_character_ -method_info$code_url <- method_info$code_url %||% NA_character_ - -method_info_view <- - method_info %>% - arrange(type, label) %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Type = type, - Description = description, - DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), - URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") - ) - -cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) +```{r echo=FALSE} +knitr::asis_output(task_info$short_description) ``` -To-do list: - - Add specific options for unit tests only (such as `--max-iter` in *NeuralEE*). -## Metrics - -Metrics for dimensionality reduction aim to compare the dimensionality reduced dataset (the embedding) with a whole or a higher dimensional dataset. The more similar they are, the better the reduction is. +## Task description -```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) -metric_configs <- yaml::yaml.load(metric_ns_list$stdout) - -metric_info <- map_df(metric_configs, function(config) { - metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - metric_info$comp_yaml <- config$info$config - metric_info$comp_name <- config$functionality$name - metric_info$comp_namespace <- config$functionality$namespace - metric_info -}) - -metric_info$description <- metric_info$description %||% NA_character_ -metric_info$label <- metric_info$label %||% NA_character_ -metric_info$maximize <- metric_info$maximize %||% NA_character_ -metric_info$min <- metric_info$min %||% NA_character_ -metric_info$max <- metric_info$max %||% NA_character_ - -metric_info_view <- - metric_info %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), - Range = paste0("[", min, ", ", max, "]") - ) - -cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) +```{r echo=FALSE} +knitr::asis_output(task_info$description) ``` +## More information -## Pipeline topology - -```{r data, include=FALSE} -comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) - -comp_file <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - map_df(conf$functionality$arguments, function(arg) { - tibble( - comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - arg_name = str_replace_all(arg$name, "^-*", ""), - direction = arg$direction %||% "input", - file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) - ) - }) -}) - -comp_info <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_info <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - description = arg$description, - short_description = arg$info$short_description, - example = arg$example, - label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_slot <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { - df <- map_df(slot, as.data.frame) - df$struct <- group_name - df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) - as_tibble(df) - }) -}) %>% - mutate(multiple = multiple %|% FALSE) -``` - -```{r flow, echo=FALSE,warning=FALSE,error=FALSE} -nodes <- bind_rows( - file_info %>% - transmute(id = name, label = str_to_title(label), is_comp = FALSE), - comp_info %>% - transmute(id = name, label = str_to_title(label), is_comp = TRUE) -) %>% - mutate(str = paste0( - " ", - id, - ifelse(is_comp, "[/", "("), - label, - ifelse(is_comp, "/]", ")") - )) -edges <- bind_rows( - comp_file %>% - filter(direction == "input") %>% - transmute( - from = file_name, - to = comp_name, - arrow = "---" - ), - comp_file %>% - filter(direction == "output") %>% - transmute( - from = comp_name, - to = file_name, - arrow = "-->" - ) -) %>% - mutate(str = paste0(" ", from, arrow, to)) - -# note: use ```{mermaid} instead of ```mermaid when rendering to html -out_str <- strip_margin(glue::glue(" - §```mermaid - §%%| column: screen-inset-shaded - §flowchart LR - §{paste(nodes$str, collapse = '\n')} - §{paste(edges$str, collapse = '\n')} - §``` - §"), symbol = "§") -knitr::asis_output(out_str) -``` - -## File format API - -```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -for (file_name in file_info$name) { - arg_info <- file_info %>% filter(name == file_name) - sub_out <- file_slot %>% - filter(file_name == !!file_name) %>% - select(struct, name, type, description) - - used_in <- comp_file %>% - filter(file_name == !!file_name) %>% - left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% - mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% - pull(str) - - example <- sub_out %>% - group_by(struct) %>% - summarise( - str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) - ) %>% - arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) - - example_str <- c(" AnnData object", paste0(" ", example$str)) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(arg_info$label)}` - § - §{arg_info$description} - § - §Used in: - § - §{paste(used_in, collapse = '\n')} - § - §Slots: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - § - §Example: - § - §{paste(example_str, collapse = '\n')} - § - §"), symbol = "§") - cat(out_str) -} -``` - - - -## Component API - -```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -# todo: add description -# todo: add required info fields -for (comp_name in comp_info$name) { - comp <- comp_info %>% filter(name == comp_name) - sub_out <- comp_file %>% - filter(comp_name == !!comp_name) %>% - left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% - transmute( - Name = paste0("`--", arg_name, "`"), - `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), - Direction = direction, - Description = file_sdesc - ) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(comp$label)}` - § - §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} - § - §Arguments: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - §"), symbol = "§") - cat(out_str) -} -``` \ No newline at end of file +* [Benchmarking results](https://openproblems-experimental.netlify.app/results_v2/`r task_info$task_id`/) +* [Documentation](https://openproblems-experimental.netlify.app/results_v2/`r task_info$task_id`/documentation) \ No newline at end of file diff --git a/src/dimensionality_reduction/api/task_info.yaml b/src/dimensionality_reduction/api/task_info.yaml index 99f65af393..ef9697c15c 100644 --- a/src/dimensionality_reduction/api/task_info.yaml +++ b/src/dimensionality_reduction/api/task_info.yaml @@ -1,5 +1,5 @@ task_id: dimensionality_reduction -task_name: "Dimensionality reduction" +task_name: "Dimensionality reduction for visualization" v1_url: openproblems/tasks/dimensionality_reduction/README.md v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b short_description: Reduction of high-dimensional datasets to 2D for visualization & interpretation @@ -19,4 +19,4 @@ description: | and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) (distances in high dimensional data don't distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) - the data for visualization and interpretation. \ No newline at end of file + the data for visualization and interpretation. From 3e8fd64fe46af539655f4e46e3acfd9d2c096e9b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 13 Jan 2023 15:48:47 +0100 Subject: [PATCH 0680/1233] fix pipeline and metadata Former-commit-id: 96dd71ee184f86007bfe1f44243012e0a00ca598 --- CHANGELOG.md | 28 +++++++++++++------ .../resources_test_scripts/pancreas.sh | 2 +- .../workflows/run/main.nf | 5 ++-- 3 files changed, 23 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 191a108ff4..66e1387b25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -122,6 +122,7 @@ * split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. ## Dimensionality reduction + ### New functionality * `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. @@ -142,6 +143,8 @@ * `methods/umap`: Migrated from v1. +* `methods/ivis`: Migrated from v1. + * `methods/tsne`: Migrated and adapted from v1. * `methods/densmap`: Migrated and adapted from v1. @@ -152,20 +155,27 @@ * `methods/neuralee`: Migrated from v1. -* `metrics/rmse`: Migrated from v1. +* `metrics/rmse`: Migrated from v1, but will likely be removed. -* `metrics/trustworthiness`: Migrated from v1. +* `metrics/trustworthiness`: Migrated from v1, but will likely be removed. -* `metrics/density`: Migrated from v1. +* `metrics/density_preservation`: Migrated from v1. -### Changes from V1 +* `metrics/coranking`: Migrated from v1. This script originally called `nn_ranking.py` and written in Python. -* Anndata layers are used to store normalized and raw counts instead of `.X`. +### Changes from V1 -* Metrics are stored in `.uns` data. +* Raw counts and normalized expression data is stored in `.layers["counts"]` and `.layers["normalized"]`, respectively, + instead of in `.X`. -* `split_dataset` removes nonessential data from train and test datasets for the methods and metrics. +* A `split_dataset` has been implemented to make a distinction between the data a method is allowed to see + (here called the train data) and what a metric is allowed to see (here called the test data). + +* `methods/ivis` had originally been removed from the v1 (temporarily) but has been added back to the v2. + +* The metrics as defined in the `nn_ranking.py` script have been documented and refactored into an R + component `metrics/coranking`. -* Higher dimensional data used to obtain the metrics is calculated from test data instead of the whole dataset. So far test and train data contain the same counts values, but this may change eventually. +* `metrics/rmse` should be removed because RMSE metrics don't really make sense here. -* Test data is used instead of the whole dataset in control (baseline) methods. +* `metrics/trustworthiness` should be removed because it is already included in `metrics/coranking`. diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index 81d97ba004..e1a455b88b 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -40,7 +40,7 @@ viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ export NXF_VER=22.04.5 # after having added a split dataset component -bin/nextflow \ +nextflow \ run . \ -main-script src/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index 92a70a1434..742695a9c7 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -4,7 +4,7 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" // import control methods -include { high_dim_pca } from "$targetDir/dimensionality_reduction/control_methods/high_dim_pca/main.nf" +include { true_features } from "$targetDir/dimensionality_reduction/control_methods/true_features/main.nf" include { random_features } from "$targetDir/dimensionality_reduction/control_methods/random_features/main.nf" // import methods @@ -14,6 +14,7 @@ include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.n include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" +include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" // import metrics include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" @@ -31,7 +32,7 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; pa config = readConfig("$projectDir/config.vsh.yaml") // construct a map of methods (id -> method_module) -methods = [ random_features, high_dim_pca, umap, densmap, phate, tsne, pca, neuralee ] +methods = [ random_features, true_features, umap, densmap, phate, tsne, pca, neuralee, ivis ] .collectEntries{method -> [method.config.functionality.name, method] } From cbf21f4e55a49d41e2677a0dfefe370dc2ebd2c4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 16 Jan 2023 10:01:41 +0100 Subject: [PATCH 0681/1233] update resource test script Former-commit-id: 98473f7dea7979e178c15aceef1ea1a54fd866c6 --- src/datasets/resource_test_scripts/pancreas.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index e48a845a24..87198790d7 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -1,7 +1,7 @@ #!/bin/bash # #make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' +#viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -14,7 +14,7 @@ DATASET_DIR=resources_test/common/pancreas mkdir -p $DATASET_DIR # download dataset -bin/viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ +viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ --id "pancreas" \ --obs_celltype "celltype" \ --obs_batch "tech" \ @@ -22,7 +22,7 @@ bin/viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ --output $DATASET_DIR/temp_dataset_full.h5ad # subsample -bin/viash run src/datasets/subsample/config.vsh.yaml -- \ +viash run src/datasets/subsample/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset_full.h5ad \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ @@ -30,17 +30,17 @@ bin/viash run src/datasets/subsample/config.vsh.yaml -- \ --seed 123 # run log cpm normalisation -bin/viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ +viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset0.h5ad \ --output $DATASET_DIR/temp_dataset1.h5ad # run pca -bin/viash run src/datasets/processors/pca/config.vsh.yaml -- \ +viash run src/datasets/processors/pca/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset1.h5ad \ --output $DATASET_DIR/temp_dataset2.h5ad # run log cpm normalisation -bin/viash run src/datasets/processors/hvg/config.vsh.yaml -- \ +viash run src/datasets/processors/hvg/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset2.h5ad \ --output $DATASET_DIR/dataset.h5ad From e1fdb78bf88da78536d333ccf7d4d299b728687e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 18 Jan 2023 12:52:22 +0100 Subject: [PATCH 0682/1233] refactor code so subsample only happens once Former-commit-id: 748213202b88e4ddd29b928b614d71ee4cad1c2a --- src/datasets/subsample/config.vsh.yaml | 8 +++ src/datasets/subsample/script.py | 92 +++++++++----------------- src/datasets/subsample/test_script.py | 16 +++-- 3 files changed, 48 insertions(+), 68 deletions(-) diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index 82585a60c1..9971e34d3c 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -8,6 +8,14 @@ functionality: description: "Input data to be resized" required: true example: input.h5ad + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 - name: "--keep_features" type: string multiple: true diff --git a/src/datasets/subsample/script.py b/src/datasets/subsample/script.py index be94c0e6a7..60d238581d 100644 --- a/src/datasets/subsample/script.py +++ b/src/datasets/subsample/script.py @@ -9,52 +9,14 @@ "keep_celltype_categories": None, "keep_batch_categories": None, "keep_features": ["HMGB2", "CDK1", "NUSAP1", "UBE2C"], - # "keep_celltype_categories": ["acinar", "beta"], - # "keep_batch_categories": ["celseq", "inDrop4", "smarter"], + "keep_celltype_categories": ["acinar", "beta"], + "keep_batch_categories": ["celseq", "inDrop4", "smarter"], "even": True, "output": "toy_data.h5ad", "seed": 123 } ### VIASH END -def filter_genes_cells(adata): - """Remove empty cells and genes.""" - sc.pp.filter_genes(adata, min_cells=1) - sc.pp.filter_cells(adata, min_counts=2) - - -def subsample_even(adata, n_obs, even_obs): - """Subsample a dataset evenly across an obs. - Parameters - ---------- - adata : AnnData - n_obs : int - Total number of cells to retain - even_obs : str - `adata.obs[even_obs]` to be subsampled evenly across partitions. - Returns - ------- - adata : AnnData - Subsampled AnnData object - """ - import scanpy as sc - - values = adata.obs[even_obs].unique() - adatas = [] - n_obs_per_value = n_obs // len(values) - for v in values: - adata_subset = adata[adata.obs[even_obs] == v].copy() - sc.pp.subsample(adata_subset, n_obs=min(n_obs_per_value, adata_subset.shape[0])) - adatas.append(adata_subset) - - adata_out = ad.concat(adatas, label="_obs_batch") - - adata_out.uns = adata.uns - adata_out.varm = adata.varm - adata_out.varp = adata.varp - return adata_out - - if par["seed"]: print(f">> Setting seed to {par['seed']}", flush=True) random.seed(par["seed"]) @@ -65,44 +27,52 @@ def subsample_even(adata, n_obs, even_obs): # copy counts to .X because otherwise filter_genes and filter_cells won't work adata_input.X = adata_input.layers["counts"] -# filter by celltype +print(">> Determining output shape", flush=True) +n_obs = min(par["n_obs"], adata_input.shape[0]) +n_vars = min(par["n_vars"], adata_input.shape[1]) + +print(">> Subsampling the observations", flush=True) +obs_filt = np.ones(dtype=np.bool_, shape=adata_input.n_obs) + +# subset by celltype if par.get("keep_celltype_categories"): print(f">> Selecting celltype_categories {par['keep_celltype_categories']}") - idx = adata_input.obs["celltype"].isin(par["keep_celltype_categories"]) - adata_input = adata_input[idx] + obs_filt = obs_filt & adata_input.obs["celltype"].isin(par["keep_celltype_categories"]) -# filter by batch +# subset by batch if par.get("keep_batch_categories"): print(f">> Selecting celltype_categories {par['keep_batch_categories']}") - idx = adata_input.obs["batch"].isin(par["keep_batch_categories"]) - adata_input = adata_input[idx] + obs_filt = obs_filt & adata_input.obs["batch"].isin(par["keep_batch_categories"]) -print(">> Remove empty observations and features", flush=True) -filter_genes_cells(adata_input) - -print(">> Subsampling the observations", flush=True) -n_obs = min(500, adata_input.shape[0]) -n_vars = min(500, adata_input.shape[1]) +# subsample evenly across batches or not if par.get("even"): - adata_output = subsample_even(adata_input, n_obs, "batch") + obs_evenly = "batch" + choice_ix = np.where(obs_filt)[0] + choice_batch = adata_input[choice_ix].obs[obs_evenly] + names, counts = np.unique(choice_batch, return_counts=True) + probs = dict(zip(names, 1 / counts / len(names))) + + choice_probs = [ probs[batch] for batch in choice_batch ] + obs_index = np.random.choice(choice_ix, size=n_obs, replace=False, p=choice_probs) else: - adata_output = sc.pp.subsample(adata_input, n_obs=n_obs, copy=True) - + obs_index = np.random.choice(np.where(obs_filt)[0], n_vars, replace=False) print(">> Subsampling the features", flush=True) if par.get("keep_features"): - initial_filt = adata_output.var_names.isin(par["keep_features"]) + initial_filt = adata_input.var_names.isin(par["keep_features"]) initial_idx, *_ = initial_filt.nonzero() remaining_idx, *_ = (~initial_filt).nonzero() rest_idx = remaining_idx[np.random.choice(len(remaining_idx), n_vars - len(initial_idx), replace=False)] - feature_ix = np.concatenate([initial_idx, rest_idx]) - adata_output = adata_output[:, feature_ix] + var_ix = np.concatenate([initial_idx, rest_idx]) else: - feature_ix = np.random.choice(adata_input.shape[1], n_vars, replace=False) - adata_output = adata_output[:, feature_ix] + var_ix = np.random.choice(adata_input.shape[1], n_vars, replace=False) + + +adata_output = adata_input[obs_index, var_ix].copy() print(">> Remove empty observations and features", flush=True) -filter_genes_cells(adata_output) +sc.pp.filter_genes(adata_output, min_cells=1) +sc.pp.filter_cells(adata_output, min_counts=2) print(">> Update dataset_id", flush=True) adata_output.uns["dataset_id"] = adata_output.uns["dataset_id"] + "_subsample" diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index 840ce77928..be631b2bbf 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -4,7 +4,7 @@ ### VIASH START meta = { - "resources_dir": "resources_test/label_projection" + "resources_dir": "resources_test/common" } ### VIASH END @@ -18,7 +18,9 @@ "--input", input_path, "--output", output_path, "--even", - "--seed", "123" + "--seed", "123", + "--n_obs", "100", + "--n_vars", "120" ]).decode("utf-8") print(">> Checking whether file exists") @@ -27,15 +29,15 @@ print(">> Check that test output fits expected API") output = sc.read_h5ad(output_path) -assert input.n_obs >= output.n_obs -assert input.n_vars == output.n_vars +assert output.n_obs <= 100 +assert output.n_vars <= 120 print(">> Runing script as test for specific batch and celltype categories") output2_path = "output.h5ad" -keep_features = ["HMGB2", "CDK1", "NUSAP1", "UBE2C"] +keep_features = list(input.var_names[:10]) out = subprocess.check_output([ meta["executable"], "--input", input_path, @@ -51,6 +53,6 @@ print(">> Check that test output fits expected API") output2 = sc.read_h5ad(output2_path) -assert input.n_obs >= output2.n_obs -assert input.n_vars == output2.n_vars +assert output2.n_obs <= 500 +assert output2.n_vars <= 500 assert set(keep_features).issubset(output2.var_names) From 65c5d20ba78ce0af12a6f22b41a2364c211677eb Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 18 Jan 2023 22:19:55 +0100 Subject: [PATCH 0683/1233] update scores to latest pancreas subset Former-commit-id: 44dd3c55f99ed94a5d5baf0d4ce2f596bbf58df1 --- .../embedding/metrics/asw_label/test.py | 2 +- .../metrics/cell_cycle_conservation/test.py | 2 +- .../graph/methods/bbknn/test_scaled_hvg.py | 5 +++-- .../graph/metrics/ari/test.py | 2 +- .../graph/metrics/ari/test_combat.py | 2 +- .../graph/metrics/nmi/test.py | 2 +- .../graph/metrics/nmi/test_combat.py | 2 +- .../resources_test_scripts/pancreas.sh | 20 ++----------------- 8 files changed, 11 insertions(+), 26 deletions(-) diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py index ef380bac7a..5fdb7fd732 100644 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.5758476480841637 +assert score == 0.4942782782018184 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py index b8a7767916..e8867d0925 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -30,6 +30,6 @@ assert 0 < score < 1 -assert score == 0.9495255717047036 +assert score == 0.932432887041937 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py index 36888fe601..51106111a7 100644 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py @@ -23,6 +23,8 @@ print('>> Checking API') adata = sc.read(output_file) +adata.X = adata.X.todense() + assert 'dataset_id' in adata.uns assert 'label' in adata.obs.columns assert 'batch' in adata.obs.columns @@ -44,7 +46,6 @@ assert 'scaled' in adata.uns assert adata.uns['scaled'] == True assert -0.0000001 <= np.mean(adata.X) <= 0.0000001 -print(np.var(adata.X)) -assert 0.7 <= np.var(adata.X) <= 1 +assert 0.8 <= np.var(adata.X) <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index 18e3fc30eb..eab8938e96 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.937800663971526 +assert score == 0.2450740201875055 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py index 2faa6aae80..21520b8e8b 100644 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.9372504013586168 +assert score == 0.3416195872819286 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index d82a050c3a..848b466a4e 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.8705271595688995 +assert score == 0.3558236928210666 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py index f6a57e724b..a2edd89727 100644 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -25,6 +25,6 @@ print(score) assert 0 < score < 1 -assert score == 0.8849932681650504 +assert score == 0.1909856215679946 print(">> All tests passed successfully") diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index e1ae707eed..cf233fc306 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -10,6 +10,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/batch_integration if [ ! -f $RAW_DATA ]; then @@ -22,27 +23,10 @@ mkdir -p $DATASET_DIR # build components bin/viash_build -q batch -# load data -echo load data... -bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ - --output $DATASET_DIR/pancreas/download.h5ad \ - --url https://ndownloader.figshare.com/files/24539828 \ - --name pancreas \ - --obs_cell_type celltype \ - --obs_batch tech - -# subset data -echo subset data... -bin/viash run src/batch_integration/datasets/subsample/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/download.h5ad \ - --output $DATASET_DIR/pancreas/subsample.h5ad \ - --label celltype \ - --batch tech - # process dataset echo process data... bin/viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/subsample.h5ad \ + --input $RAW_DATA \ --output $DATASET_DIR/pancreas/processed.h5ad \ --label celltype \ --batch tech \ From f7c157e76c206cde569c8d71ceeb8da51602dc59 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 19 Jan 2023 21:24:16 +0000 Subject: [PATCH 0684/1233] Bump tj-actions/changed-files from 35.4.0 to 35.4.4 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.4.0 to 35.4.4. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.4.0...v35.4.4) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: 27870a8035d128ee4bb376a1410ecaa8ced680cb --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 1edc56fb55..9d8d9072aa 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.4.0 + uses: tj-actions/changed-files@v35.4.4 with: separator: ";" diff_relative: true From 186801aea0af8dfcf0ba7940613b0a35f3e81c15 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 20 Jan 2023 11:58:21 +0100 Subject: [PATCH 0685/1233] manually setting viash_temp environment variable Former-commit-id: 2b38b39953c6cd891799665e0e8051879bced875 --- .github/workflows/viash-test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 9d8d9072aa..d63953304e 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -141,6 +141,8 @@ jobs: - name: Run test timeout-minutes: 30 run: | + export VIASH_TEMP="$HOME/tmp" + mkdir -p "$VIASH_TEMP" bin/viash test -p docker ${{ matrix.component.config }} \ -c '.functionality.requirements.cpus := 2' \ -c '.functionality.requirements.memory := "5gb"' From 19d0e1859c5dbbbd0d615dc217d9efe5bd9eda53 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 20 Jan 2023 13:32:26 +0100 Subject: [PATCH 0686/1233] try viash 0.6.7 Former-commit-id: 639fcf2aca7776e5b5fc2b76086f537e34ee7093 --- .github/workflows/viash-test.yml | 2 -- _viash.yaml | 2 +- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index d63953304e..9d8d9072aa 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -141,8 +141,6 @@ jobs: - name: Run test timeout-minutes: 30 run: | - export VIASH_TEMP="$HOME/tmp" - mkdir -p "$VIASH_TEMP" bin/viash test -p docker ${{ matrix.component.config }} \ -c '.functionality.requirements.cpus := 2' \ -c '.functionality.requirements.memory := "5gb"' diff --git a/_viash.yaml b/_viash.yaml index d1653a0e9c..200ea0ed73 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.6.6 +viash_version: 0.6.7 source: src target: target From 114305d6a730f606b30cace3688a600964938f1e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 09:04:56 +0100 Subject: [PATCH 0687/1233] remove bin folder Former-commit-id: 085c3a019f857d2f9829f87d756627457324fad2 --- .github/workflows/integration-test.yml | 32 +++----- .github/workflows/main-build.yml | 68 ++++++++--------- .github/workflows/release-build.yml | 73 ++++++++----------- .github/workflows/viash-test.yml | 28 +++---- CONTRIBUTING.md | 12 +-- bin/.gitignore | 4 - bin/README.md | 10 --- bin/init | 22 ------ bin/init_tools | 25 ------- .../resources_test_scripts/task_metadata.sh | 2 +- .../resources_test_scripts/pancreas.sh | 8 +- .../resources_test_scripts/pancreas.sh | 8 +- .../workflows/run/run_test.sh | 2 +- .../workflows/run/run_nextflow.sh | 2 +- 14 files changed, 98 insertions(+), 198 deletions(-) delete mode 100644 bin/.gitignore delete mode 100644 bin/README.md delete mode 100755 bin/init delete mode 100755 bin/init_tools diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 6be2cadf98..19a2b67bce 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -12,10 +12,7 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Fetch viash - run: | - bin/init - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 # create cachehash key - name: Create hash key @@ -35,7 +32,7 @@ jobs: # sync if need be - name: Sync test resources run: | - bin/viash run \ + viash run \ -p native \ src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ @@ -48,7 +45,7 @@ jobs: sed -i '/^target.*/d' .gitignore # build target dir - bin/viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing + viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -60,9 +57,9 @@ jobs: # store component locations - id: set_matrix run: | - component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') echo "component_matrix=$component_json" >> $GITHUB_OUTPUT - workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') + workflow_json=$(viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT outputs: component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} @@ -83,15 +80,12 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Fetch viash - run: | - bin/init - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup build + viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -103,7 +97,7 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup donothing --push + viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup push ################################### # phase 3 @@ -120,17 +114,15 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Fetch viash - run: | - bin/init - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: nf-core/setup-nextflow@v1.2.0 # build target dir # use containers from integration_build branch, hopefully these are available - name: Build target dir run: | # build target dir - bin/viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing + viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing # use cache - name: Cache resources data @@ -147,7 +139,7 @@ jobs: config_dir=`dirname ${{ matrix.component.config }}` script="$config_dir/${{ matrix.component.test_script }}" export NXF_VER=22.04.5 - bin/nextflow run . \ + nextflow run . \ -main-script "$script" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 40ac6c44dc..406ebb19cf 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -13,17 +13,14 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init - bin/viash -h - + - uses: viash-io/viash-actions/setup@v1.0.0 - name: Fetch viash tools - run: | - - bin/init_tools ${{ secrets.GTHB_USER }} ${{ secrets.GTHB_PAT }} - tree bin/tools + uses: actions/checkout@v3 + with: + repository: "viash-io/viash_tools" + token: ${{ secrets.GTHB_PAT }} + ref: "main_build" + path: "../viash_tools" # create cachehash key - name: Create hash key @@ -43,7 +40,7 @@ jobs: # sync if need be - name: Sync test resources run: | - bin/viash run \ + viash run \ -p native \ src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ @@ -56,23 +53,23 @@ jobs: sed -i '/^target.*/d' .gitignore # build target dir - bin/viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - - # - name: Build nextflow schemas & params - # run: | - # bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json - # inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) - # outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) - # outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) - # bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - # bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - - # bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json - # inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) - # outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) - # outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) - # bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - # bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing + + - name: Build nextflow schemas & params + run: | + viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) + outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) + outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) + ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + + viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json + inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) + outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) + outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) + ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -84,8 +81,9 @@ jobs: # store component locations - id: set_matrix run: | - component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "namespace": .functionality.namespace, "config": .info.config } ]') + component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "namespace": .functionality.namespace, "config": .info.config } ]') echo "component_matrix=$component_json" >> $GITHUB_OUTPUT + outputs: component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} cachehash: ${{ steps.cachehash.outputs.cachehash }} @@ -103,16 +101,11 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init - bin/viash -h - + - uses: viash-io/viash-actions/setup@v1.0.0 - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build + viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -123,5 +116,4 @@ jobs: - name: Push containers run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup push \ No newline at end of file + viash build ${{ matrix.component.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 1de61a5008..cb1ed921eb 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -17,16 +17,15 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Fetch viash - run: | - bin/init - bin/viash -h - + - uses: viash-io/viash-actions/setup@v1.0.0 + - name: Fetch viash tools - run: | - - bin/init_tools ${{ secrets.GTHB_USER }} ${{ secrets.GTHB_PAT }} - tree bin/tools + uses: actions/checkout@v3 + with: + repository: "viash-io/viash_tools" + token: ${{ secrets.GTHB_PAT }} + ref: "main_build" + path: "../viash_tools" # create cachehash key - name: Create hash key @@ -46,7 +45,7 @@ jobs: # sync if need be - name: Sync test resources run: | - bin/viash run \ + viash run \ -p native \ src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ @@ -59,23 +58,23 @@ jobs: sed -i '/^target.*/d' .gitignore # build target dir - bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing + viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing - name: Build nextflow schemas & params run: | - bin/viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json + viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) - bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - bin/viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json + viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) - bin/tools/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - bin/tools/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" + ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -88,9 +87,9 @@ jobs: # store component locations - id: set_matrix run: | - component_json=$(bin/viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') + component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') echo "component_matrix=$component_json" >> $GITHUB_OUTPUT - workflow_json=$(bin/viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') + workflow_json=$(viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT outputs: component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} @@ -110,16 +109,11 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init - bin/viash -h - + - uses: viash-io/viash-actions/setup@v1.0.0 - name: Build container run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup build + viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 @@ -131,7 +125,7 @@ jobs: - name: Push containers run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --push --setup donothing + viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup push ###################################3 # phase 3 @@ -148,18 +142,14 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 # build target dir # use containers from release branch, hopefully these are available - name: Build target dir run: | # build target dir - bin/viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing + viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing # use cache - name: Cache resources data @@ -176,11 +166,11 @@ jobs: config_dir=`dirname ${{ matrix.component.config }}` script="$config_dir/${{ matrix.component.test_script }}" export NXF_VER=22.04.5 - bin/nextflow run . \ + nextflow run . \ -main-script "$script" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ - -c src/wf_utils/labels_ci.config + -c workflows/utils/labels_ci.config ###################################3 # phase 4 @@ -196,11 +186,7 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 # use cache - name: Cache resources data @@ -214,8 +200,7 @@ jobs: timeout-minutes: 30 run: | SRC_DIR=`dirname ${{ matrix.component.config }}` - bin/viash ns test --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ + viash ns test --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ -s "$SRC_DIR" \ - -c '.functionality.requirements.cpus := 2' \ - -c '.functionality.requirements.memory := "5gb"' \ - --setup build + --cpus 2 \ + --memory "5gb" \ No newline at end of file diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 9d8d9072aa..5e7a0032e7 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -16,7 +16,7 @@ jobs: run: | pull_request=$(gh pr list -R ${{ github.repository }} -H ${{ github.ref_name }} --json url --state open --limit 1 | jq '.[0].url') # If the branch has a PR and this run was triggered by a push event, do not run - if [[ "$pull_request" != "null" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then + if [[ "$pull_request" != "null" && "$GITHUB_REF_NAME" != "main" && "${{ github.event_name == 'push' }}" == "true" && "${{ !contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then echo "check=false" >> $GITHUB_OUTPUT else echo "check=true" >> $GITHUB_OUTPUT @@ -40,11 +40,7 @@ jobs: with: fetch-depth: 0 - - name: Fetch viash - run: | - bin/init -n - tree . - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 # create cachehash key - name: Create hash key @@ -64,7 +60,7 @@ jobs: # sync if need be - name: Sync test resources run: | - bin/viash run \ + viash run \ -p native \ src/common/sync_test_resources/config.vsh.yaml -- \ --input $s3_bucket \ @@ -73,7 +69,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.4.4 + uses: tj-actions/changed-files@v35.4.1 with: separator: ";" diff_relative: true @@ -84,7 +80,7 @@ jobs: run: | IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" echo "Changed files: "${changed_files[*]}"" - readarray -t components < <(bin/viash ns list -p docker --format json | jq -c '[ .[] | + readarray -t components < <(viash ns list -p docker --format json | jq -c '[ .[] | (.info.config | capture("^(?.*\/)").dir) as $dir | { "name": .functionality.name, "config": .info.config, @@ -124,16 +120,12 @@ jobs: steps: - uses: actions/checkout@v3 - - - name: Fetch viash - run: | - bin/init -n - bin/viash -h + - uses: viash-io/viash-actions/setup@v1.0.0 # use cache - name: Cache resources data uses: actions/cache@v3 - timeout-minutes: 5 + timeout-minutes: 10 with: path: resources_test key: ${{ needs.list_components.outputs.cachehash }} @@ -141,7 +133,7 @@ jobs: - name: Run test timeout-minutes: 30 run: | - bin/viash test -p docker ${{ matrix.component.config }} \ - -c '.functionality.requirements.cpus := 2' \ - -c '.functionality.requirements.memory := "5gb"' + viash test -p docker ${{ matrix.component.config }} \ + --cpus 2 \ + --memory "5gb" diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 510c8af643..c1ce7fa2e2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -258,7 +258,7 @@ You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. ``` bash -bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help +viash run src/label_projection/methods/foo/config.vsh.yaml -- --help ``` foo dev @@ -284,7 +284,7 @@ bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- --help You can **run the component** as follows: ``` bash -bin/viash run src/label_projection/methods/foo/config.vsh.yaml -- \ +viash run src/label_projection/methods/foo/config.vsh.yaml -- \ --input_train resources_test/label_projection/pancreas/train.h5ad \ --input_test resources_test/label_projection/pancreas/test.h5ad \ --output resources_test/label_projection/pancreas/prediction.h5ad @@ -309,7 +309,7 @@ and they will be able to run it, provided that they have Bash and Docker installed. ``` bash -bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ +viash build src/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` @@ -317,7 +317,7 @@ bin/viash build src/label_projection/methods/foo/config.vsh.yaml \ > **Note** > -> The `bin/viash_build` component does a much better job of setting up a +> The `viash_build` component does a much better job of setting up a > collection of components.
@@ -371,7 +371,7 @@ generic unit test for free. This means you can unit test your component using the **`viash test`** command. ``` bash -bin/viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/label_projection/methods/foo/config.vsh.yaml ``` Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011' @@ -468,7 +468,7 @@ If we now run the test, we should get an error since we didn’t create all of the required output slots. ``` bash -bin/viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/label_projection/methods/foo/config.vsh.yaml ``` Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128' diff --git a/bin/.gitignore b/bin/.gitignore deleted file mode 100644 index 042da6f70d..0000000000 --- a/bin/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -fetch -viash* -nextflow -tools \ No newline at end of file diff --git a/bin/README.md b/bin/README.md deleted file mode 100644 index 35f41588de..0000000000 --- a/bin/README.md +++ /dev/null @@ -1,10 +0,0 @@ -These executables were generated by running the `bin/init` executable. - -``` -$ bin/init -curl -fsSL get.viash.io | bash -s -- --registry openpipeline --tag 0.5.0-rc3 --log check_results/results.tsv - -cd bin - -curl -s https://get.nextflow.io | bash -``` diff --git a/bin/init b/bin/init deleted file mode 100755 index 8d2bf830d9..0000000000 --- a/bin/init +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -curl -fsSL get.viash.io | bash -s -- --tools false - -# add --namespace_separator '/' ? - -# # automatically export the workflow helper -# NXF_UTILS=src/wf_utils -# [[ -d $NXF_UTILS ]] || mkdir -p $NXF_UTILS -# bin/viash export resource platforms/nextflow/ProfilesHelper.config > $NXF_UTILS/ProfilesHelper.config -# bin/viash export resource platforms/nextflow/WorkflowHelper.nf > $NXF_UTILS/WorkflowHelper.nf -# bin/viash export resource platforms/nextflow/DataflowHelper.nf > $NXF_UTILS/DataflowHelper.nf - -cd bin - -curl -s https://get.nextflow.io | bash diff --git a/bin/init_tools b/bin/init_tools deleted file mode 100755 index 945ed531a9..0000000000 --- a/bin/init_tools +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -tmpdir=$(mktemp -d) -function clean_up { - rm -rf "$tmpdir" -} -trap clean_up EXIT - -VERSION=0.2.0 - -if [ $# -eq 2 ]; then - git clone --depth 1 --branch $VERSION https://$1:$2@github.com/viash-io/viash_tools.git $tmpdir/ -else - git clone --depth 1 --branch $VERSION git@github.com:viash-io/viash_tools.git $tmpdir/ -fi - -[ -d bin/tools ] && rm -r bin/tools - -cp -r $tmpdir/target bin/tools diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index c1fca5185e..880e03e9df 100644 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -114,6 +114,6 @@ cat < $sha_file EOT # Create a method info json -bin/viash run src/common/get_method_info/config.vsh.yaml -- \ +viash run src/common/get_method_info/config.vsh.yaml -- \ --input "src/denoising" \ --output $OUTPUT_DIR/"method_info.json" \ No newline at end of file diff --git a/src/denoising/resources_test_scripts/pancreas.sh b/src/denoising/resources_test_scripts/pancreas.sh index 0a42dc5e8c..9fa4796e15 100755 --- a/src/denoising/resources_test_scripts/pancreas.sh +++ b/src/denoising/resources_test_scripts/pancreas.sh @@ -1,7 +1,7 @@ #!/bin/bash # #make sure the following command has been executed -#bin/viash_build -q 'denoising|common' +#viash_build -q 'denoising|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -20,19 +20,19 @@ fi mkdir -p $DATASET_DIR # split dataset -bin/viash run src/denoising/split_dataset/config.vsh.yaml -- \ +viash run src/denoising/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ --seed 123 # run one method -bin/viash run src/denoising/methods/magic/config.vsh.yaml -- \ +viash run src/denoising/methods/magic/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --output $DATASET_DIR/magic.h5ad # run one metric -bin/viash run src/denoising/metrics/poisson/config.vsh.yaml -- \ +viash run src/denoising/metrics/poisson/config.vsh.yaml -- \ --input_denoised $DATASET_DIR/magic.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/magic_poisson.h5ad diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index 19a3ae652b..d0040dca43 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -1,7 +1,7 @@ #!/bin/bash # #make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' +#viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -20,7 +20,7 @@ fi mkdir -p $DATASET_DIR # split dataset -bin/viash run src/label_projection/split_dataset/config.vsh.yaml -- \ +viash run src/label_projection/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ @@ -28,13 +28,13 @@ bin/viash run src/label_projection/split_dataset/config.vsh.yaml -- \ --seed 123 # run one method -bin/viash run src/label_projection/methods/knn/config.vsh.yaml -- \ +viash run src/label_projection/methods/knn/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/knn.h5ad # run one metric -bin/viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ +viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ --input_prediction $DATASET_DIR/knn.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/knn_accuracy.h5ad diff --git a/src/label_projection/workflows/run/run_test.sh b/src/label_projection/workflows/run/run_test.sh index cfd3fa9fac..cece1a44e7 100755 --- a/src/label_projection/workflows/run/run_test.sh +++ b/src/label_projection/workflows/run/run_test.sh @@ -1,7 +1,7 @@ #!/bin/bash # #make sure the following command has been executed -#bin/viash_build -q 'label_projection|common' +#viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) diff --git a/src/modality_alignment/workflows/run/run_nextflow.sh b/src/modality_alignment/workflows/run/run_nextflow.sh index 2294a9b50f..c47d633f2a 100755 --- a/src/modality_alignment/workflows/run/run_nextflow.sh +++ b/src/modality_alignment/workflows/run/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# bin/viash_build -q 'modality_alignment|utils' +# viash_build -q 'modality_alignment|utils' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) From 0ae0dce9cdaf2b56cfdceb8b8acba5f392e2ae8b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 10:17:20 +0100 Subject: [PATCH 0688/1233] rename task Former-commit-id: 634343accc98f8151f3ea77ecce340ab1d44d151 --- src/multimodal_data_integration/README.md | 23 ++++++++++++++++++ .../datasets/datasets_scprep_csv.tsv | 0 .../datasets/sample_dataset/config.vsh.yaml | 2 +- .../datasets/sample_dataset/script.py | 0 .../datasets/sample_dataset/test.py | 0 .../datasets/scprep_csv/config.vsh.yaml | 2 +- .../datasets/scprep_csv/script.py | 0 .../datasets/scprep_csv/test.py | 0 .../harmonic_alignment/config.vsh.yaml | 2 +- .../methods/harmonic_alignment/script.py | 0 .../methods/harmonic_alignment/test.py | 0 .../methods/mnn/config.vsh.yaml | 2 +- .../methods/mnn/script.R | 0 .../methods/mnn/test.py | 0 .../methods/sample_method/config.vsh.yaml | 2 +- .../methods/sample_method/script.py | 0 .../methods/sample_method/test.py | 0 .../methods/scot/config.vsh.yaml | 2 +- .../methods/scot/script.py | 0 .../methods/scot/test.py | 0 .../metrics/knn_auc/config.vsh.yaml | 2 +- .../metrics/knn_auc/script.py | 4 +-- .../metrics/knn_auc/test.py | 0 .../metrics/mse/config.vsh.yaml | 2 +- .../metrics/mse/script.py | 4 +-- .../metrics/mse/test.py | 0 .../resources/sample_dataset.h5ad | Bin .../resources/sample_output.h5ad | Bin .../utils/preprocessing.py | 0 .../utils/utils.py | 0 .../workflows/run/main.nf | 18 +++++++------- .../workflows/run/nextflow.config | 0 .../workflows/run/run_nextflow.sh | 6 ++--- 33 files changed, 47 insertions(+), 24 deletions(-) create mode 100644 src/multimodal_data_integration/README.md rename src/{modality_alignment => multimodal_data_integration}/datasets/datasets_scprep_csv.tsv (100%) rename src/{modality_alignment => multimodal_data_integration}/datasets/sample_dataset/config.vsh.yaml (95%) rename src/{modality_alignment => multimodal_data_integration}/datasets/sample_dataset/script.py (100%) rename src/{modality_alignment => multimodal_data_integration}/datasets/sample_dataset/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/datasets/scprep_csv/config.vsh.yaml (97%) rename src/{modality_alignment => multimodal_data_integration}/datasets/scprep_csv/script.py (100%) rename src/{modality_alignment => multimodal_data_integration}/datasets/scprep_csv/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/harmonic_alignment/config.vsh.yaml (97%) rename src/{modality_alignment => multimodal_data_integration}/methods/harmonic_alignment/script.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/harmonic_alignment/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/mnn/config.vsh.yaml (96%) rename src/{modality_alignment => multimodal_data_integration}/methods/mnn/script.R (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/mnn/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/sample_method/config.vsh.yaml (95%) rename src/{modality_alignment => multimodal_data_integration}/methods/sample_method/script.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/sample_method/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/scot/config.vsh.yaml (97%) rename src/{modality_alignment => multimodal_data_integration}/methods/scot/script.py (100%) rename src/{modality_alignment => multimodal_data_integration}/methods/scot/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/metrics/knn_auc/config.vsh.yaml (96%) rename src/{modality_alignment => multimodal_data_integration}/metrics/knn_auc/script.py (91%) rename src/{modality_alignment => multimodal_data_integration}/metrics/knn_auc/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/metrics/mse/config.vsh.yaml (95%) rename src/{modality_alignment => multimodal_data_integration}/metrics/mse/script.py (85%) rename src/{modality_alignment => multimodal_data_integration}/metrics/mse/test.py (100%) rename src/{modality_alignment => multimodal_data_integration}/resources/sample_dataset.h5ad (100%) rename src/{modality_alignment => multimodal_data_integration}/resources/sample_output.h5ad (100%) rename src/{modality_alignment => multimodal_data_integration}/utils/preprocessing.py (100%) rename src/{modality_alignment => multimodal_data_integration}/utils/utils.py (100%) rename src/{modality_alignment => multimodal_data_integration}/workflows/run/main.nf (63%) rename src/{modality_alignment => multimodal_data_integration}/workflows/run/nextflow.config (100%) rename src/{modality_alignment => multimodal_data_integration}/workflows/run/run_nextflow.sh (65%) diff --git a/src/multimodal_data_integration/README.md b/src/multimodal_data_integration/README.md new file mode 100644 index 0000000000..d8d0d58cc5 --- /dev/null +++ b/src/multimodal_data_integration/README.md @@ -0,0 +1,23 @@ +# Multimodal data integration + +Structure of this task: + + src/multimodal_data_integration + ├── api Interface specifications for components and datasets in this task + ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── methods Methods to be benchmarked + ├── metrics Metrics used to quantify performance of methods + ├── README.md This file + ├── resources_scripts Scripts to process the datasets + ├── resources_test_scripts Scripts to process the test resources + ├── split_dataset Component to prepare common datasets + └── workflows Pipelines to run the full benchmark + +Relevant links: + +* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/multimodal_data_integration/) + +* [Experimental results](https://openproblems-experimental.netlify.app/results/multimodal_data_integration/) + + +* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) diff --git a/src/modality_alignment/datasets/datasets_scprep_csv.tsv b/src/multimodal_data_integration/datasets/datasets_scprep_csv.tsv similarity index 100% rename from src/modality_alignment/datasets/datasets_scprep_csv.tsv rename to src/multimodal_data_integration/datasets/datasets_scprep_csv.tsv diff --git a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml b/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml similarity index 95% rename from src/modality_alignment/datasets/sample_dataset/config.vsh.yaml rename to src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml index 04d9c26a80..9d40c2ed70 100644 --- a/src/modality_alignment/datasets/sample_dataset/config.vsh.yaml +++ b/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "sample_dataset" - namespace: "modality_alignment/datasets" + namespace: "multimodal_data_integration/datasets" version: "dev" description: "Sample dataset for testing purposes" authors: diff --git a/src/modality_alignment/datasets/sample_dataset/script.py b/src/multimodal_data_integration/datasets/sample_dataset/script.py similarity index 100% rename from src/modality_alignment/datasets/sample_dataset/script.py rename to src/multimodal_data_integration/datasets/sample_dataset/script.py diff --git a/src/modality_alignment/datasets/sample_dataset/test.py b/src/multimodal_data_integration/datasets/sample_dataset/test.py similarity index 100% rename from src/modality_alignment/datasets/sample_dataset/test.py rename to src/multimodal_data_integration/datasets/sample_dataset/test.py diff --git a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml b/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml similarity index 97% rename from src/modality_alignment/datasets/scprep_csv/config.vsh.yaml rename to src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml index 799336bbf9..c82069822a 100644 --- a/src/modality_alignment/datasets/scprep_csv/config.vsh.yaml +++ b/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "scprep_csv" - namespace: "modality_alignment/datasets" + namespace: "multimodal_data_integration/datasets" version: "dev" description: "Create a modality alignment dataset from CSV using scprep." authors: diff --git a/src/modality_alignment/datasets/scprep_csv/script.py b/src/multimodal_data_integration/datasets/scprep_csv/script.py similarity index 100% rename from src/modality_alignment/datasets/scprep_csv/script.py rename to src/multimodal_data_integration/datasets/scprep_csv/script.py diff --git a/src/modality_alignment/datasets/scprep_csv/test.py b/src/multimodal_data_integration/datasets/scprep_csv/test.py similarity index 100% rename from src/modality_alignment/datasets/scprep_csv/test.py rename to src/multimodal_data_integration/datasets/scprep_csv/test.py diff --git a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml b/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml similarity index 97% rename from src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml rename to src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml index 025ec3d2f9..5be7dbb60a 100644 --- a/src/modality_alignment/methods/harmonic_alignment/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "harmonic_alignment" - namespace: "modality_alignment/methods" + namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Harmonic Alignment" authors: diff --git a/src/modality_alignment/methods/harmonic_alignment/script.py b/src/multimodal_data_integration/methods/harmonic_alignment/script.py similarity index 100% rename from src/modality_alignment/methods/harmonic_alignment/script.py rename to src/multimodal_data_integration/methods/harmonic_alignment/script.py diff --git a/src/modality_alignment/methods/harmonic_alignment/test.py b/src/multimodal_data_integration/methods/harmonic_alignment/test.py similarity index 100% rename from src/modality_alignment/methods/harmonic_alignment/test.py rename to src/multimodal_data_integration/methods/harmonic_alignment/test.py diff --git a/src/modality_alignment/methods/mnn/config.vsh.yaml b/src/multimodal_data_integration/methods/mnn/config.vsh.yaml similarity index 96% rename from src/modality_alignment/methods/mnn/config.vsh.yaml rename to src/multimodal_data_integration/methods/mnn/config.vsh.yaml index 98598cbb3b..7ca9ac5690 100644 --- a/src/modality_alignment/methods/mnn/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/mnn/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "mnn" - namespace: "modality_alignment/methods" + namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Mutual Nearest Neighbours" authors: diff --git a/src/modality_alignment/methods/mnn/script.R b/src/multimodal_data_integration/methods/mnn/script.R similarity index 100% rename from src/modality_alignment/methods/mnn/script.R rename to src/multimodal_data_integration/methods/mnn/script.R diff --git a/src/modality_alignment/methods/mnn/test.py b/src/multimodal_data_integration/methods/mnn/test.py similarity index 100% rename from src/modality_alignment/methods/mnn/test.py rename to src/multimodal_data_integration/methods/mnn/test.py diff --git a/src/modality_alignment/methods/sample_method/config.vsh.yaml b/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml similarity index 95% rename from src/modality_alignment/methods/sample_method/config.vsh.yaml rename to src/multimodal_data_integration/methods/sample_method/config.vsh.yaml index f83d4a16ba..30baa7d77d 100644 --- a/src/modality_alignment/methods/sample_method/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "sample_method" - namespace: "modality_alignment/methods" + namespace: "multimodal_data_integration/methods" version: "dev" description: "Sample method" authors: diff --git a/src/modality_alignment/methods/sample_method/script.py b/src/multimodal_data_integration/methods/sample_method/script.py similarity index 100% rename from src/modality_alignment/methods/sample_method/script.py rename to src/multimodal_data_integration/methods/sample_method/script.py diff --git a/src/modality_alignment/methods/sample_method/test.py b/src/multimodal_data_integration/methods/sample_method/test.py similarity index 100% rename from src/modality_alignment/methods/sample_method/test.py rename to src/multimodal_data_integration/methods/sample_method/test.py diff --git a/src/modality_alignment/methods/scot/config.vsh.yaml b/src/multimodal_data_integration/methods/scot/config.vsh.yaml similarity index 97% rename from src/modality_alignment/methods/scot/config.vsh.yaml rename to src/multimodal_data_integration/methods/scot/config.vsh.yaml index 2bb4f829f5..99e205bad5 100644 --- a/src/modality_alignment/methods/scot/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/scot/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "scot" - namespace: "modality_alignment/methods" + namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Single Cell Optimal Transport" authors: diff --git a/src/modality_alignment/methods/scot/script.py b/src/multimodal_data_integration/methods/scot/script.py similarity index 100% rename from src/modality_alignment/methods/scot/script.py rename to src/multimodal_data_integration/methods/scot/script.py diff --git a/src/modality_alignment/methods/scot/test.py b/src/multimodal_data_integration/methods/scot/test.py similarity index 100% rename from src/modality_alignment/methods/scot/test.py rename to src/multimodal_data_integration/methods/scot/test.py diff --git a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml b/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml similarity index 96% rename from src/modality_alignment/metrics/knn_auc/config.vsh.yaml rename to src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml index 51f8de3f03..17c614be2d 100644 --- a/src/modality_alignment/metrics/knn_auc/config.vsh.yaml +++ b/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "knn_auc" - namespace: "modality_alignment/metrics" + namespace: "multimodal_data_integration/metrics" version: "dev" description: "Compute the kNN Area Under the Curve" authors: diff --git a/src/modality_alignment/metrics/knn_auc/script.py b/src/multimodal_data_integration/metrics/knn_auc/script.py similarity index 91% rename from src/modality_alignment/metrics/knn_auc/script.py rename to src/multimodal_data_integration/metrics/knn_auc/script.py index 48569c0e9e..8625d9ae1b 100644 --- a/src/modality_alignment/metrics/knn_auc/script.py +++ b/src/multimodal_data_integration/metrics/knn_auc/script.py @@ -2,8 +2,8 @@ # The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. par = { - "input": "out_bash/modality_alignment/methods/citeseq_cbmc_mnn.h5ad", - "output": "out_bash/modality_alignment/metrics/citeseq_cbmc_mnn_knn_auc.h5ad", + "input": "out_bash/multimodal_data_integration/methods/citeseq_cbmc_mnn.h5ad", + "output": "out_bash/multimodal_data_integration/metrics/citeseq_cbmc_mnn_knn_auc.h5ad", "proportion_neighbors": 0.1, "n_svd": 100 } diff --git a/src/modality_alignment/metrics/knn_auc/test.py b/src/multimodal_data_integration/metrics/knn_auc/test.py similarity index 100% rename from src/modality_alignment/metrics/knn_auc/test.py rename to src/multimodal_data_integration/metrics/knn_auc/test.py diff --git a/src/modality_alignment/metrics/mse/config.vsh.yaml b/src/multimodal_data_integration/metrics/mse/config.vsh.yaml similarity index 95% rename from src/modality_alignment/metrics/mse/config.vsh.yaml rename to src/multimodal_data_integration/metrics/mse/config.vsh.yaml index 97da63adac..3e754ce3e4 100644 --- a/src/modality_alignment/metrics/mse/config.vsh.yaml +++ b/src/multimodal_data_integration/metrics/mse/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "mse" - namespace: "modality_alignment/metrics" + namespace: "multimodal_data_integration/metrics" version: "dev" description: "Compute the mean squared error" authors: diff --git a/src/modality_alignment/metrics/mse/script.py b/src/multimodal_data_integration/metrics/mse/script.py similarity index 85% rename from src/modality_alignment/metrics/mse/script.py rename to src/multimodal_data_integration/metrics/mse/script.py index 740b49cdc6..c17058f6f0 100644 --- a/src/modality_alignment/metrics/mse/script.py +++ b/src/multimodal_data_integration/metrics/mse/script.py @@ -2,8 +2,8 @@ # The code between the the comments above and below gets stripped away before # execution. Here you can put anything that helps the prototyping of your script. par = { - "input": "out_bash/modality_alignment/methods/citeseq_cbmc_mnn.h5ad", - "output": "out_bash/modality_alignment/metrics/citeseq_cbmc_mnn_knn_auc.h5ad" + "input": "out_bash/multimodal_data_integration/methods/citeseq_cbmc_mnn.h5ad", + "output": "out_bash/multimodal_data_integration/metrics/citeseq_cbmc_mnn_knn_auc.h5ad" } ## VIASH END diff --git a/src/modality_alignment/metrics/mse/test.py b/src/multimodal_data_integration/metrics/mse/test.py similarity index 100% rename from src/modality_alignment/metrics/mse/test.py rename to src/multimodal_data_integration/metrics/mse/test.py diff --git a/src/modality_alignment/resources/sample_dataset.h5ad b/src/multimodal_data_integration/resources/sample_dataset.h5ad similarity index 100% rename from src/modality_alignment/resources/sample_dataset.h5ad rename to src/multimodal_data_integration/resources/sample_dataset.h5ad diff --git a/src/modality_alignment/resources/sample_output.h5ad b/src/multimodal_data_integration/resources/sample_output.h5ad similarity index 100% rename from src/modality_alignment/resources/sample_output.h5ad rename to src/multimodal_data_integration/resources/sample_output.h5ad diff --git a/src/modality_alignment/utils/preprocessing.py b/src/multimodal_data_integration/utils/preprocessing.py similarity index 100% rename from src/modality_alignment/utils/preprocessing.py rename to src/multimodal_data_integration/utils/preprocessing.py diff --git a/src/modality_alignment/utils/utils.py b/src/multimodal_data_integration/utils/utils.py similarity index 100% rename from src/modality_alignment/utils/utils.py rename to src/multimodal_data_integration/utils/utils.py diff --git a/src/modality_alignment/workflows/run/main.nf b/src/multimodal_data_integration/workflows/run/main.nf similarity index 63% rename from src/modality_alignment/workflows/run/main.nf rename to src/multimodal_data_integration/workflows/run/main.nf index 4c1cb68cf8..ae06b48bd3 100644 --- a/src/modality_alignment/workflows/run/main.nf +++ b/src/multimodal_data_integration/workflows/run/main.nf @@ -8,18 +8,18 @@ nextflow.enable.dsl=2 targetDir = "${params.rootDir}/target/nextflow" // import dataset loaders -include { sample_dataset } from "$targetDir/modality_alignment/datasets/sample_dataset/main.nf" params(params) -include { scprep_csv } from "$targetDir/modality_alignment/datasets/scprep_csv/main.nf" params(params) +include { sample_dataset } from "$targetDir/multimodal_data_integration/datasets/sample_dataset/main.nf" params(params) +include { scprep_csv } from "$targetDir/multimodal_data_integration/datasets/scprep_csv/main.nf" params(params) // import methods -include { sample_method } from "$targetDir/modality_alignment/methods/sample_method/main.nf" params(params) -include { mnn } from "$targetDir/modality_alignment/methods/mnn/main.nf" params(params) -include { scot } from "$targetDir/modality_alignment/methods/scot/main.nf" params(params) -include { harmonic_alignment } from "$targetDir/modality_alignment/methods/harmonic_alignment/main.nf" params(params) +include { sample_method } from "$targetDir/multimodal_data_integration/methods/sample_method/main.nf" params(params) +include { mnn } from "$targetDir/multimodal_data_integration/methods/mnn/main.nf" params(params) +include { scot } from "$targetDir/multimodal_data_integration/methods/scot/main.nf" params(params) +include { harmonic_alignment } from "$targetDir/multimodal_data_integration/methods/harmonic_alignment/main.nf" params(params) // import metrics -include { knn_auc } from "$targetDir/modality_alignment/metrics/knn_auc/main.nf" params(params) -include { mse } from "$targetDir/modality_alignment/metrics/mse/main.nf" params(params) +include { knn_auc } from "$targetDir/multimodal_data_integration/metrics/knn_auc/main.nf" params(params) +include { mse } from "$targetDir/multimodal_data_integration/metrics/mse/main.nf" params(params) // import helper functions include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) @@ -37,7 +37,7 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" workflow get_scprep_csv_datasets { main: - output_ = Channel.fromPath("$launchDir/src/modality_alignment/datasets/datasets_scprep_csv.tsv") + output_ = Channel.fromPath("$launchDir/src/multimodal_data_integration/datasets/datasets_scprep_csv.tsv") | splitCsv(header: true, sep: "\t") | map { row -> [ row.id, [ "input1": file(row.input1), "input2": file(row.input2), "id": row.id ]] diff --git a/src/modality_alignment/workflows/run/nextflow.config b/src/multimodal_data_integration/workflows/run/nextflow.config similarity index 100% rename from src/modality_alignment/workflows/run/nextflow.config rename to src/multimodal_data_integration/workflows/run/nextflow.config diff --git a/src/modality_alignment/workflows/run/run_nextflow.sh b/src/multimodal_data_integration/workflows/run/run_nextflow.sh similarity index 65% rename from src/modality_alignment/workflows/run/run_nextflow.sh rename to src/multimodal_data_integration/workflows/run/run_nextflow.sh index c47d633f2a..84cc18c3b2 100755 --- a/src/modality_alignment/workflows/run/run_nextflow.sh +++ b/src/multimodal_data_integration/workflows/run/run_nextflow.sh @@ -1,7 +1,7 @@ #!/bin/bash # Run this prior to executing this script: -# viash_build -q 'modality_alignment|utils' +# viash_build -q 'multimodal_data_integration|utils' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -14,8 +14,8 @@ export NXF_VER=21.10.6 nextflow \ run . \ - -main-script src/modality_alignment/workflows/run/main.nf \ - --publish_dir output/modality_alignment \ + -main-script src/multimodal_data_integration/workflows/run/main.nf \ + --publish_dir output/multimodal_data_integration \ -resume \ -with-docker From 14dc261f3df9cef3ef57854767bb3ff198770a8c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 10:17:32 +0100 Subject: [PATCH 0689/1233] update readmes and task info Former-commit-id: 1286eb5c3d9a4b00f885fd6bfa25f1bab29b2cb8 --- src/denoising/README.md | 279 +------------- src/denoising/README.qmd | 256 ------------- src/denoising/{docs => api}/task_info.yaml | 2 +- src/dimensionality_reduction/README.md | 46 +-- src/dimensionality_reduction/README.qmd | 27 -- .../api/task_info.yaml | 2 +- src/label_projection/README.md | 352 +----------------- src/label_projection/README.qmd | 257 ------------- src/label_projection/api/task_info.yaml | 2 +- src/modality_alignment/README.md | 55 --- src/modality_alignment/README.qmd | 30 -- 11 files changed, 53 insertions(+), 1255 deletions(-) delete mode 100644 src/denoising/README.qmd rename src/denoising/{docs => api}/task_info.yaml (96%) delete mode 100644 src/dimensionality_reduction/README.qmd delete mode 100644 src/label_projection/README.qmd delete mode 100644 src/modality_alignment/README.md delete mode 100644 src/modality_alignment/README.qmd diff --git a/src/denoising/README.md b/src/denoising/README.md index abfa33ff33..84038fdbb6 100644 --- a/src/denoising/README.md +++ b/src/denoising/README.md @@ -1,270 +1,23 @@ - -- Denoising - - The task - - Methods - - Metrics - - Pipeline - topology - - File format API - - Dataset - - Denoised - - Score - - Test - - Train - - Component API - - Control Method - - Method - - Metric - - Split Dataset - # Denoising -## The task - -Single-cell RNA-Seq protocols only detect a fraction of the mRNA -molecules present in each cell. As a result, the measurements (UMI -counts) observed for each gene and each cell are associated with -generally high levels of technical noise ([Grün et al., -2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes -the task of estimating the true expression level of each gene in each -cell. In the single-cell literature, this task is also referred to as -*imputation*, a term which is typically used for missing data problems -in statistics. Similar to the use of the terms “dropout”, “missing -data”, and “technical zeros”, this terminology can create confusion -about the underlying measurement process ([Sarkar and Stephens, -2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). - -A key challenge in evaluating denoising methods is the general lack of a -ground truth. A recent benchmark study ([Hou et al., -2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) -relied on flow-sorted datasets, mixture control experiments ([Tian et -al., 2019](https://www.nature.com/articles/s41592-019-0425-8)), and -comparisons with bulk RNA-Seq data. Since each of these approaches -suffers from specific limitations, it is difficult to combine these -different approaches into a single quantitative measure of denoising -accuracy. Here, we instead rely on an approach termed molecular -cross-validation (MCV), which was specifically developed to quantify -denoising accuracy in the absence of a ground truth ([Batson et al., -2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the -observed molecules in a given scRNA-Seq dataset are first partitioned -between a *training* and a *test* dataset. Next, a denoising method is -applied to the training dataset. Finally, denoising accuracy is measured -by comparing the result to the test dataset. The authors show that both -in theory and in practice, the measured denoising accuracy is -representative of the accuracy that would be obtained on a ground truth -dataset. - -## Methods - -Methods for assigning labels from a reference dataset to a new dataset. - -| Name | Type | Description | DOI | URL | -|:---------------------------------------------------------------------------------------------------------------------------------------------|:-----------------|:-------------------------------------------------------|:---------------------------------------------------|:--------------------------------------------------| -| [ALRA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/alra/config.vsh.yaml) | method | Adaptively-thresholded Low Rank Approximation (ALRA). | [link](https://doi.org/10.1101/397588) | [link](https://github.com/KlugerLab/ALRA) | -| [DCA](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/dca/config.vsh.yaml) | method | Deep Count Autoencoder | [link](https://doi.org/10.1038/s41467-018-07931-2) | [link](https://github.com/theislab/dca) | -| [knn_smooth](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/knn_smoothing/config.vsh.yaml) | method | iterative K-nearest neighbor smoothing | [link](https://doi.org/10.1101/217737) | [link](https://github.com/yanailab/knn-smoothing) | -| [magic](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./methods/magic/config.vsh.yaml) | method | MAGIC: Markov affinity-based graph imputation of cells | [link](https://doi.org/10.1016/j.cell.2018.05.061) | [link](https://github.com/KrishnaswamyLab/MAGIC) | -| [no denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/no_denoising/config.vsh.yaml) | negative_control | negative control by copying train counts | | | -| [perfect denoising](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./control_methods/perfect_denoising/config.vsh.yaml) | positive_control | Negative control by copying the train counts | | | - -## Metrics - -Metrics for label projection aim to characterize how well each -classifier correctly assigns cell type labels to cells in the test set. - -| Name | Description | Range | -|:-----------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:------------| -| [mse](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/mse/config.vsh.yaml) | The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio Lower is better. | \[0, +inf\] | -| [poisson](/home/rcannood/workspace/openproblems/openproblems-v2/src/denoising/./metrics/poisson/config.vsh.yaml) | Poisson loss: measure the mean of the inconsistencies between predicted and target Lower is better. | \[0, +inf\] | - -## Pipeline topology - -``` mermaid -%%| column: screen-inset-shaded -flowchart LR - anndata_dataset(Dataset) - anndata_denoised(Denoised) - anndata_score(Score) - anndata_test(Test) - anndata_train(Train) - comp_control_method[/Control Method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_split_dataset[/Split Dataset/] - anndata_train---comp_control_method - anndata_test---comp_control_method - anndata_train---comp_method - anndata_test---comp_metric - anndata_denoised---comp_metric - anndata_dataset---comp_split_dataset - comp_control_method-->anndata_denoised - comp_method-->anndata_denoised - comp_metric-->anndata_score - comp_split_dataset-->anndata_train - comp_split_dataset-->anndata_test -``` - -## File format API - -### `Dataset` - -A preprocessed dataset - -Used in: - -- [split dataset](#split%20dataset): input (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| uns | dataset_id | string | A unique identifier for the dataset | - -Example: - - AnnData object - uns: 'dataset_id' - layers: 'counts' - -### `Denoised` - -The denoised data - -Used in: - -- [control method](#control%20method): output (as output) -- [method](#method): output (as output) -- [metric](#metric): input_denoised (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| layers | denoised | integer | denoised data | -| obs | n_counts | string | Raw counts | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | - -Example: - - AnnData object - obs: 'n_counts' - uns: 'dataset_id', 'method_id' - layers: 'counts', 'denoised' - -### `Score` - -Metric score file - -Used in: - -- [metric](#metric): output (as output) - -Slots: - -| struct | name | type | description | -|:-------|:--------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - -Example: - - AnnData object - uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' - -### `Test` - -The test data - -Used in: - -- [control method](#control%20method): input_test (as input) -- [metric](#metric): input_test (as input) -- [split dataset](#split%20dataset): output_test (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| obs | n_counts | string | Raw counts | -| uns | dataset_id | string | A unique identifier for the dataset | - -Example: - - AnnData object - obs: 'n_counts' - uns: 'dataset_id' - layers: 'counts' - -### `Train` - -The training data - -Used in: - -- [control method](#control%20method): input_train (as input) -- [method](#method): input_train (as input) -- [split dataset](#split%20dataset): output_train (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------|:--------|:------------------------------------| -| layers | counts | integer | Raw counts | -| obs | n_counts | string | Raw counts | -| uns | dataset_id | string | A unique identifier for the dataset | - -Example: - - AnnData object - obs: 'n_counts' - uns: 'dataset_id' - layers: 'counts' - -## Component API - -### `Control Method` - -Arguments: - -| Name | File format | Direction | Description | -|:----------------|:----------------------|:----------|:--------------| -| `--input_train` | [Train](#train) | input | Training data | -| `--input_test` | [Test](#test) | input | Test data | -| `--output` | [Denoised](#denoised) | output | Denoised data | - -### `Method` - -Arguments: - -| Name | File format | Direction | Description | -|:----------------|:----------------------|:----------|:--------------| -| `--input_train` | [Train](#train) | input | Training data | -| `--output` | [Denoised](#denoised) | output | Denoised data | - -### `Metric` +Structure of this task: -Arguments: + src/denoising + ├── api Interface specifications for components and datasets in this task + ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── methods Methods to be benchmarked + ├── metrics Metrics used to quantify performance of methods + ├── README.md This file + ├── resources_scripts Scripts to process the datasets + ├── resources_test_scripts Scripts to process the test resources + ├── split_dataset Component to prepare common datasets + └── workflows Pipelines to run the full benchmark -| Name | File format | Direction | Description | -|:-------------------|:----------------------|:----------|:--------------| -| `--input_test` | [Test](#test) | input | Test data | -| `--input_denoised` | [Denoised](#denoised) | input | Denoised data | -| `--output` | [Score](#score) | output | Score | +Relevant links: -### `Split Dataset` +* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/denoising/) -Arguments: +* [Experimental results](https://openproblems-experimental.netlify.app/results/denoising/) -| Name | File format | Direction | Description | -|:-----------------|:--------------------|:----------|:---------------------| -| `--input` | [Dataset](#dataset) | input | Preprocessed dataset | -| `--output_train` | [Train](#train) | output | Training data | -| `--output_test` | [Test](#test) | output | Test data | + +* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) diff --git a/src/denoising/README.qmd b/src/denoising/README.qmd deleted file mode 100644 index 6f6a01297f..0000000000 --- a/src/denoising/README.qmd +++ /dev/null @@ -1,256 +0,0 @@ ---- -format: gfm -toc: true ---- - -```{r setup, include=FALSE} -library(tidyverse) -library(rlang) - -strip_margin <- function(text, symbol = "\\|") { - str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") -} - -dir <- "src/denoising" -dir <- "." -``` - -# Denoising - -{{< include docs/task_description.md >}} - -## Methods - -Methods for assigning labels from a reference dataset to a new dataset. - -```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) -method_configs <- yaml::yaml.load(method_ns_list$stdout) - -method_info <- map_df(method_configs, function(config) { - if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) - info <- as_tibble(config$functionality$info) - info$comp_yaml <- config$info$config - info$name <- config$functionality$name - info$namespace <- config$functionality$namespace - info$description <- config$functionality$description - info -}) - -method_info_view <- - method_info %>% - arrange(type, label) %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Type = type, - Description = gsub("\\.[ \n].*", ".", description), - DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), - URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") - ) - -cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) -``` - - -## Metrics - -Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. - -```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) -metric_configs <- yaml::yaml.load(metric_ns_list$stdout) - -metric_info <- map_df(metric_configs, function(config) { - metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - metric_info$comp_yaml <- config$info$config - metric_info$comp_name <- config$functionality$name - metric_info$comp_namespace <- config$functionality$namespace - metric_info -}) - -metric_info_view <- - metric_info %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), - Range = paste0("[", min, ", ", max, "]") - ) - -cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) -``` - - -## Pipeline topology - -```{r data, include=FALSE} -comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) - -comp_file <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - map_df(conf$functionality$arguments, function(arg) { - tibble( - comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - arg_name = str_replace_all(arg$name, "^-*", ""), - direction = arg$direction %||% "input", - file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) - ) - }) -}) - -comp_info <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_info <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - description = arg$description, - short_description = arg$info$short_description, - example = arg$example, - label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_slot <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { - df <- map_df(slot, as.data.frame) - df$struct <- group_name - df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) - as_tibble(df) - }) -}) %>% - mutate(multiple = multiple %|% FALSE) -``` - -```{r flow, echo=FALSE,warning=FALSE,error=FALSE} -nodes <- bind_rows( - file_info %>% - transmute(id = name, label = str_to_title(label), is_comp = FALSE), - comp_info %>% - transmute(id = name, label = str_to_title(label), is_comp = TRUE) -) %>% - mutate(str = paste0( - " ", - id, - ifelse(is_comp, "[/", "("), - label, - ifelse(is_comp, "/]", ")") - )) -edges <- bind_rows( - comp_file %>% - filter(direction == "input") %>% - transmute( - from = file_name, - to = comp_name, - arrow = "---" - ), - comp_file %>% - filter(direction == "output") %>% - transmute( - from = comp_name, - to = file_name, - arrow = "-->" - ) -) %>% - mutate(str = paste0(" ", from, arrow, to)) - -# note: use ```{mermaid} instead of ```mermaid when rendering to html -out_str <- strip_margin(glue::glue(" - §```mermaid - §%%| column: screen-inset-shaded - §flowchart LR - §{paste(nodes$str, collapse = '\n')} - §{paste(edges$str, collapse = '\n')} - §``` - §"), symbol = "§") -knitr::asis_output(out_str) -``` - -## File format API - -```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -for (file_name in file_info$name) { - arg_info <- file_info %>% filter(name == file_name) - sub_out <- file_slot %>% - filter(file_name == !!file_name) %>% - select(struct, name, type, description) - - used_in <- comp_file %>% - filter(file_name == !!file_name) %>% - left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% - mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% - pull(str) - - example <- sub_out %>% - group_by(struct) %>% - summarise( - str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) - ) %>% - arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) - - example_str <- c(" AnnData object", paste0(" ", example$str)) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(arg_info$label)}` - § - §{arg_info$description} - § - §Used in: - § - §{paste(used_in, collapse = '\n')} - § - §Slots: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - § - §Example: - § - §{paste(example_str, collapse = '\n')} - § - §"), symbol = "§") - cat(out_str) -} -``` - - - -## Component API - -```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -# todo: add description -# todo: add required info fields -for (comp_name in comp_info$name) { - comp <- comp_info %>% filter(name == comp_name) - sub_out <- comp_file %>% - filter(comp_name == !!comp_name) %>% - left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% - transmute( - Name = paste0("`--", arg_name, "`"), - `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), - Direction = direction, - Description = file_sdesc - ) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(comp$label)}` - § - §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} - § - §Arguments: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - §"), symbol = "§") - cat(out_str) -} -``` \ No newline at end of file diff --git a/src/denoising/docs/task_info.yaml b/src/denoising/api/task_info.yaml similarity index 96% rename from src/denoising/docs/task_info.yaml rename to src/denoising/api/task_info.yaml index a5e77d59ef..3cdd9fe60f 100644 --- a/src/denoising/docs/task_info.yaml +++ b/src/denoising/api/task_info.yaml @@ -2,7 +2,7 @@ task_id: denoising task_name: Denoising v1_url: openproblems/tasks/denoising/README.md v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb -short_description: "Removing noise in sparse single-cell RNA-sequencing count data" +summary: "Removing noise in sparse single-cell RNA-sequencing count data" description: | Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present in each cell. As a result, the measurements (UMI counts) observed for each gene and each diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 4538aab017..957b9e3b69 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -1,35 +1,23 @@ +# Dimensionality reduction -# Dimensionality reduction for visualization +Structure of this task: -Reduction of high-dimensional datasets to 2D for visualization & -interpretation + src/dimensionality_reduction + ├── api Interface specifications for components and datasets in this task + ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── methods Methods to be benchmarked + ├── metrics Metrics used to quantify performance of methods + ├── README.md This file + ├── resources_scripts Scripts to process the datasets + ├── resources_test_scripts Scripts to process the test resources + ├── split_dataset Component to prepare common datasets + └── workflows Pipelines to run the full benchmark -## Task description +Relevant links: -Dimensionality reduction is one of the key challenges in single-cell -data representation. Routine single-cell RNA sequencing (scRNA-seq) -experiments measure cells in roughly 20,000-30,000 dimensions (i.e., -features - mostly gene transcripts but also other functional elements -encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq -experiments have been growing in terms of the number of cells measured. -Originally, cutting-edge SmartSeq experiments would yield a few hundred -cells, at best. Now, it is not uncommon to see experiments that yield -over [100,000 cells](https://www.nature.com/articles/s41586-018-0590-4) -or even [\> 1 million cells](https://doi.org/10.1126/science.aba7721). +* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/dimensionality_reduction/) -Each *feature* in a dataset functions as a single dimension. While each -of the \~30,000 dimensions measured in each cell contribute to an -underlying data structure, the overall structure of the data is -challenging to display in few dimensions due to data sparsity and the -[*“curse of -dimensionality”*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) -(distances in high dimensional data don’t distinguish data points well). -Thus, we need to find a way to [dimensionally -reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data -for visualization and interpretation. +* [Experimental results](https://openproblems-experimental.netlify.app/results/dimensionality_reduction/) -## More information - -- [Benchmarking - results](https://openproblems-experimental.netlify.app/results_v2/dimensionality_reduction/) -- [Documentation](https://openproblems-experimental.netlify.app/results_v2/dimensionality_reduction/documentation) + +* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) diff --git a/src/dimensionality_reduction/README.qmd b/src/dimensionality_reduction/README.qmd deleted file mode 100644 index 526abd9044..0000000000 --- a/src/dimensionality_reduction/README.qmd +++ /dev/null @@ -1,27 +0,0 @@ ---- -format: gfm ---- - -```{r setup, include=FALSE} -dir <- "src/dimensionality_reduction" -dir <- "." - -task_info <- yaml::read_yaml(paste0(dir, "/api/task_info.yaml")) -``` - -# `r task_info$task_name` - -```{r echo=FALSE} -knitr::asis_output(task_info$short_description) -``` - -## Task description - -```{r echo=FALSE} -knitr::asis_output(task_info$description) -``` - -## More information - -* [Benchmarking results](https://openproblems-experimental.netlify.app/results_v2/`r task_info$task_id`/) -* [Documentation](https://openproblems-experimental.netlify.app/results_v2/`r task_info$task_id`/documentation) \ No newline at end of file diff --git a/src/dimensionality_reduction/api/task_info.yaml b/src/dimensionality_reduction/api/task_info.yaml index ef9697c15c..1b7c0e739e 100644 --- a/src/dimensionality_reduction/api/task_info.yaml +++ b/src/dimensionality_reduction/api/task_info.yaml @@ -2,7 +2,7 @@ task_id: dimensionality_reduction task_name: "Dimensionality reduction for visualization" v1_url: openproblems/tasks/dimensionality_reduction/README.md v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b -short_description: Reduction of high-dimensional datasets to 2D for visualization & interpretation +summary: Reduction of high-dimensional datasets to 2D for visualization & interpretation description: | Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly diff --git a/src/label_projection/README.md b/src/label_projection/README.md index 7b5c4ea384..e2c73b365e 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -1,341 +1,23 @@ +# Label projection -- Label - Projection - - Task - description - - Methods - - Metrics - - Pipeline - topology - - File format API - - Dataset - - Prediction - - Score - - Solution - - Test - - Train - - Component API - - Control Method - - Method - - Metric - - Split Dataset +Structure of this task: -# Label Projection + src/label_projection + ├── api Interface specifications for components and datasets in this task + ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── methods Methods to be benchmarked + ├── metrics Metrics used to quantify performance of methods + ├── README.md This file + ├── resources_scripts Scripts to process the datasets + ├── resources_test_scripts Scripts to process the test resources + ├── split_dataset Component to prepare common datasets + └── workflows Pipelines to run the full benchmark -## Task description +Relevant links: -A major challenge for integrating single cell datasets is creating -matching cell type annotations for each cell. One of the most common -strategies for annotating cell types is referred to as -[“cluster-then-annotate”](https://www.nature.com/articles/s41576-018-0088-9) -whereby cells are aggregated into clusters based on feature similarity -and then manually characterized based on differential gene expression or -previously identified marker genes. Recently, methods have emerged to -build on this strategy and annotate cells using [known marker -genes](https://www.nature.com/articles/s41592-019-0535-3). However, -these strategies pose a difficulty for integrating atlas-scale datasets -as the particular annotations may not match. +* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/label_projection/) -To ensure that the cell type labels in newly generated datasets match -existing reference datasets, some methods align cells to a previously -annotated [reference -dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) -and then *project* labels from the reference to the new dataset. +* [Experimental results](https://openproblems-experimental.netlify.app/results/label_projection/) -Here, we compare methods for annotation based on a reference dataset. -The datasets consist of two or more samples of single cell profiles that -have been manually annotated with matching labels. These datasets are -then split into training and test batches, and the task of each method -is to train a cell type classifer on the training set and project those -labels onto the test set. - -## Methods - -Methods for assigning labels from a reference dataset to a new dataset. - -| Name | Type | Description | DOI | URL | -|:------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------|:-----------------------------------------------------------|:-----------------------------------------------------|:-----------------------------------------------------| -| [KNN](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/knn/config.vsh.yaml) | method | K-Nearest Neighbors classifier | [link](https://doi.org/10.1109/TIT.1967.1053964) | [link](https://github.com/scikit-learn/scikit-learn) | -| [Logistic Regression](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/logistic_regression/config.vsh.yaml) | method | Logistic regression method | | [link](https://github.com/scikit-learn/scikit-learn) | -| [Multilayer perceptron](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/mlp/config.vsh.yaml) | method | Multilayer perceptron | [link](https://doi.org/10.1016/0004-3702(89)90049-0) | [link](https://github.com/scikit-learn/scikit-learn) | -| [SCANVI](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/scanvi/config.vsh.yaml) | method | Probabilistic harmonization and annotation of single-cell | | | -| transcriptomics data with deep generative models. | [link](https://doi.org/10.1101/2020.07.16.205997) | [link](https://github.com/YosefLab/scvi-tools) | | | -| [Seurat TransferData](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/seurat_transferdata/config.vsh.yaml) | method | The Seurat v3 anchoring procedure is designed to integrate | | | -| diverse single-cell datasets across technologies and modalities. | [link](https://doi.org/10.1101/460147) | [link](https://github.com/satijalab/seurat) | | | -| [XGBoost](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./methods/xgboost/config.vsh.yaml) | method | XGBoost: A Scalable Tree Boosting System | [link](https://doi.org/10.1145/2939672.2939785) | [link](https://github.com/dmlc/xgboost) | -| [Majority Vote](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/majority_vote/config.vsh.yaml) | negative_control | Baseline method using majority voting | | | -| [Random Labels](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/random_labels/config.vsh.yaml) | negative_control | Negative control method which generates random labels | | | -| [True labels](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./control_methods/true_labels/config.vsh.yaml) | positive_control | Positive control method by returning the true labels | | | - -## Metrics - -Metrics for label projection aim to characterize how well each -classifier correctly assigns cell type labels to cells in the test set. - -| Name | Description | Range | -|:--------------------------------------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------| -| [Accuracy](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/accuracy/config.vsh.yaml) | The percentage of correctly predicted labels. Higher is better. | \[0, 1\] | -| [F1 weighted](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. Higher is better. | \[0, 1\] | -| [F1 macro](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. Higher is better. | \[0, 1\] | -| [F1 micro](/home/rcannood/workspace/openproblems/openproblems-v2/src/label_projection/./metrics/f1/config.vsh.yaml) | Calculates the F1 score globally by counting the total true positives, false negatives and false positives. Higher is better. | \[0, 1\] | - -## Pipeline topology - -``` mermaid -%%| column: screen-inset-shaded -flowchart LR - anndata_dataset(Dataset) - anndata_prediction(Prediction) - anndata_score(Score) - anndata_solution(Solution) - anndata_test(Test) - anndata_train(Train) - comp_control_method[/Control Method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_split_dataset[/Split Dataset/] - anndata_train---comp_control_method - anndata_test---comp_control_method - anndata_solution---comp_control_method - anndata_train---comp_method - anndata_test---comp_method - anndata_solution---comp_metric - anndata_prediction---comp_metric - anndata_dataset---comp_split_dataset - comp_control_method-->anndata_prediction - comp_method-->anndata_prediction - comp_metric-->anndata_score - comp_split_dataset-->anndata_train - comp_split_dataset-->anndata_test - comp_split_dataset-->anndata_solution -``` - -## File format API - -### `Dataset` - -A normalised data with a PCA embedding and HVG selection - -Used in: - -- [split dataset](#split%20dataset): input (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalised expression values | -| obs | celltype | string | Cell type information | -| obs | batch | string | Batch information | -| obs | tissue | string | Tissue information | -| obs | size_factors | double | The size factors created by the normalisation method, if any. | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| varm | pca_loadings | double | The PCA loadings matrix. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | pca_variance | double | The PCA variance objects. | - -Example: - - AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id', 'pca_variance' - obsm: 'X_pca' - varm: 'pca_loadings' - layers: 'counts', 'normalized' - -### `Prediction` - -The prediction file - -Used in: - -- [control method](#control%20method): output (as output) -- [method](#method): output (as output) -- [metric](#metric): input_prediction (as input) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:-------|:-------------------------------------| -| obs | label_pred | string | Predicted labels for the test cells. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | method_id | string | A unique identifier for the method | - -Example: - - AnnData object - obs: 'label_pred' - uns: 'dataset_id', 'normalization_id', 'method_id' - -### `Score` - -Metric score file - -Used in: - -- [metric](#metric): output (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:-------|:---------------------------------------------------------------------------------------------| -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | -| uns | method_id | string | A unique identifier for the method | -| uns | metric_ids | string | One or more unique metric identifiers | -| uns | metric_values | double | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - -Example: - - AnnData object - uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' - -### `Solution` - -The solution for the test data - -Used in: - -- [control method](#control%20method): input_solution (as input) -- [metric](#metric): input_solution (as input) -- [split dataset](#split%20dataset): output_solution (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized counts | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | - -Example: - - AnnData object - obs: 'label', 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - -### `Test` - -The test data (without labels) - -Used in: - -- [control method](#control%20method): input_test (as input) -- [method](#method): input_test (as input) -- [split dataset](#split%20dataset): output_test (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized counts | -| obs | batch | string | Batch information | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | - -Example: - - AnnData object - obs: 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - -### `Train` - -The training data - -Used in: - -- [control method](#control%20method): input_train (as input) -- [method](#method): input_train (as input) -- [split dataset](#split%20dataset): output_train (as output) - -Slots: - -| struct | name | type | description | -|:-------|:-----------------|:--------|:------------------------------------------------------------------------| -| layers | counts | integer | Raw counts | -| layers | normalized | double | Normalized counts | -| obs | label | string | Ground truth cell type labels | -| obs | batch | string | Batch information | -| var | hvg | boolean | Whether or not the feature is considered to be a ‘highly variable gene’ | -| var | hvg_score | integer | A ranking of the features by hvg. | -| obsm | X_pca | double | The resulting PCA embedding. | -| uns | dataset_id | string | A unique identifier for the dataset | -| uns | normalization_id | string | Which normalization was used | - -Example: - - AnnData object - obs: 'label', 'batch' - var: 'hvg', 'hvg_score' - uns: 'dataset_id', 'normalization_id' - obsm: 'X_pca' - layers: 'counts', 'normalized' - -## Component API - -### `Control Method` - -Arguments: - -| Name | File format | Direction | Description | -|:-------------------|:--------------------------|:----------|:--------------| -| `--input_train` | [Train](#train) | input | Training data | -| `--input_test` | [Test](#test) | input | Test data | -| `--input_solution` | [Solution](#solution) | input | Solution | -| `--output` | [Prediction](#prediction) | output | Prediction | - -### `Method` - -Arguments: - -| Name | File format | Direction | Description | -|:----------------|:--------------------------|:----------|:--------------| -| `--input_train` | [Train](#train) | input | Training data | -| `--input_test` | [Test](#test) | input | Test data | -| `--output` | [Prediction](#prediction) | output | Prediction | - -### `Metric` - -Arguments: - -| Name | File format | Direction | Description | -|:---------------------|:--------------------------|:----------|:------------| -| `--input_solution` | [Solution](#solution) | input | Solution | -| `--input_prediction` | [Prediction](#prediction) | input | Prediction | -| `--output` | [Score](#score) | output | Score | - -### `Split Dataset` - -Arguments: - -| Name | File format | Direction | Description | -|:--------------------|:----------------------|:----------|:--------------| -| `--input` | [Dataset](#dataset) | input | NA | -| `--output_train` | [Train](#train) | output | Training data | -| `--output_test` | [Test](#test) | output | Test data | -| `--output_solution` | [Solution](#solution) | output | Solution | + +* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) diff --git a/src/label_projection/README.qmd b/src/label_projection/README.qmd deleted file mode 100644 index 053cd2f7a8..0000000000 --- a/src/label_projection/README.qmd +++ /dev/null @@ -1,257 +0,0 @@ ---- -format: gfm -toc: true ---- - -```{r setup, include=FALSE} -library(tidyverse) -library(rlang) - -strip_margin <- function(text, symbol = "\\|") { - str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1") -} - -dir <- "src/label_projection" -dir <- "." -``` - -# Label Projection - -## Task description -{{< include docs/task_description.qmd >}} - -## Methods - -Methods for assigning labels from a reference dataset to a new dataset. - -```{r methods, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -method_ns_list <- processx::run("viash", c("ns", "list", "-q", "methods", "--src", "."), wd = dir) -method_configs <- yaml::yaml.load(method_ns_list$stdout) - -method_info <- map_df(method_configs, function(config) { - if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) - info <- as_tibble(config$functionality$info) - info$comp_yaml <- config$info$config - info$name <- config$functionality$name - info$namespace <- config$functionality$namespace - info$description <- config$functionality$description - info -}) - -method_info_view <- - method_info %>% - arrange(type, label) %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Type = type, - Description = description, - DOI = ifelse(!is.na(paper_doi), paste0("[link](https://doi.org/", paper_doi, ")"), ""), - URL = ifelse(!is.na(code_url), paste0("[link](", code_url, ")"), "") - ) - -cat(paste(knitr::kable(method_info_view, format = 'pipe'), collapse = "\n")) -``` - - -## Metrics - -Metrics for label projection aim to characterize how well each classifier correctly assigns cell type labels to cells in the test set. - -```{r metrics, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -metric_ns_list <- processx::run("viash", c("ns", "list", "-q", "metrics", "--src", "."), wd = dir) -metric_configs <- yaml::yaml.load(metric_ns_list$stdout) - -metric_info <- map_df(metric_configs, function(config) { - metric_info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - metric_info$comp_yaml <- config$info$config - metric_info$comp_name <- config$functionality$name - metric_info$comp_namespace <- config$functionality$namespace - metric_info -}) - -metric_info_view <- - metric_info %>% - transmute( - Name = paste0("[", label, "](", comp_yaml, ")"), - Description = paste0(description, " ", ifelse(maximize, "Higher is better.", "Lower is better.")), - Range = paste0("[", min, ", ", max, "]") - ) - -cat(paste(knitr::kable(metric_info_view, format = 'pipe'), collapse = "\n")) -``` - - -## Pipeline topology - -```{r data, include=FALSE} -comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) - -comp_file <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - map_df(conf$functionality$arguments, function(arg) { - tibble( - comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - arg_name = str_replace_all(arg$name, "^-*", ""), - direction = arg$direction %||% "input", - file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) - ) - }) -}) - -comp_info <- map_df(comp_yamls, function(yaml_file) { - conf <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - label = name %>% gsub("comp_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_info <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - tibble( - name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - description = arg$description, - short_description = arg$info$short_description, - example = arg$example, - label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) - ) -}) - -file_slot <- map_df(file_yamls, function(yaml_file) { - arg <- yaml::read_yaml(yaml_file) - - map2_df(names(arg$info$slots), arg$info$slots, function(group_name, slot) { - df <- map_df(slot, as.data.frame) - df$struct <- group_name - df$file_name = basename(yaml_file) %>% gsub("\\.yaml", "", .) - as_tibble(df) - }) -}) %>% - mutate(multiple = multiple %|% FALSE) -``` - -```{r flow, echo=FALSE,warning=FALSE,error=FALSE} -nodes <- bind_rows( - file_info %>% - transmute(id = name, label = str_to_title(label), is_comp = FALSE), - comp_info %>% - transmute(id = name, label = str_to_title(label), is_comp = TRUE) -) %>% - mutate(str = paste0( - " ", - id, - ifelse(is_comp, "[/", "("), - label, - ifelse(is_comp, "/]", ")") - )) -edges <- bind_rows( - comp_file %>% - filter(direction == "input") %>% - transmute( - from = file_name, - to = comp_name, - arrow = "---" - ), - comp_file %>% - filter(direction == "output") %>% - transmute( - from = comp_name, - to = file_name, - arrow = "-->" - ) -) %>% - mutate(str = paste0(" ", from, arrow, to)) - -# note: use ```{mermaid} instead of ```mermaid when rendering to html -out_str <- strip_margin(glue::glue(" - §```mermaid - §%%| column: screen-inset-shaded - §flowchart LR - §{paste(nodes$str, collapse = '\n')} - §{paste(edges$str, collapse = '\n')} - §``` - §"), symbol = "§") -knitr::asis_output(out_str) -``` - -## File format API - -```{r file_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -for (file_name in file_info$name) { - arg_info <- file_info %>% filter(name == file_name) - sub_out <- file_slot %>% - filter(file_name == !!file_name) %>% - select(struct, name, type, description) - - used_in <- comp_file %>% - filter(file_name == !!file_name) %>% - left_join(comp_info %>% select(comp_name = name, comp_label = label), by = "comp_name") %>% - mutate(str = paste0("* [", comp_label, "](#", comp_label, "): ", arg_name, " (as ", direction, ")")) %>% - pull(str) - - example <- sub_out %>% - group_by(struct) %>% - summarise( - str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) - ) %>% - arrange(match(struct, c("obs", "var", "uns", "obsm", "obsp", "varm", "varp", "layers"))) - - example_str <- c(" AnnData object", paste0(" ", example$str)) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(arg_info$label)}` - § - §{arg_info$description} - § - §Used in: - § - §{paste(used_in, collapse = '\n')} - § - §Slots: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - § - §Example: - § - §{paste(example_str, collapse = '\n')} - § - §"), symbol = "§") - cat(out_str) -} -``` - - - -## Component API - -```{r comp_api, echo=FALSE,warning=FALSE,error=FALSE,output="asis"} -# todo: add description -# todo: add required info fields -for (comp_name in comp_info$name) { - comp <- comp_info %>% filter(name == comp_name) - sub_out <- comp_file %>% - filter(comp_name == !!comp_name) %>% - left_join(file_info %>% select(file_name = name, file_desc = description, file_sdesc = short_description, file_label = label), by = "file_name") %>% - transmute( - Name = paste0("`--", arg_name, "`"), - `File format` = paste0("[", str_to_title(file_label), "](#", file_label, ")"), - Direction = direction, - Description = file_sdesc - ) - - out_str <- strip_margin(glue::glue(" - §### `{str_to_title(comp$label)}` - § - §{ifelse(\"description\" %in% names(comp), comp$description, \"\")} - § - §Arguments: - § - §{paste(knitr::kable(sub_out, format = 'pipe'), collapse = '\n')} - §"), symbol = "§") - cat(out_str) -} -``` \ No newline at end of file diff --git a/src/label_projection/api/task_info.yaml b/src/label_projection/api/task_info.yaml index b1a0568418..97dde85074 100644 --- a/src/label_projection/api/task_info.yaml +++ b/src/label_projection/api/task_info.yaml @@ -2,7 +2,7 @@ task_id: label_projection task_name: Label projection v1_url: openproblems/tasks/label_projection/README.md v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 -short_description: Automated cell type annotation from rich, labeled reference data +summary: Automated cell type annotation from rich, labeled reference data description: | A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for diff --git a/src/modality_alignment/README.md b/src/modality_alignment/README.md deleted file mode 100644 index 1775873fec..0000000000 --- a/src/modality_alignment/README.md +++ /dev/null @@ -1,55 +0,0 @@ - -# Multimodal data integration - -## The task - -Cellular function is regulated by the complex interplay of different -types of biological molecules (DNA, RNA, proteins, etc.), which -determine the state of a cell. Several recently described technologies -allow for simultaneous measurement of different aspects of cellular -state. For example, [sci-CAR](https://doi.org/10.1126/science.aau0730) -jointly profiles RNA expression and chromatin accessibility on the same -cell and [CITE-seq](https://doi.org/10.1038/nmeth.4380) measures surface -protein abundance and RNA expression from each cell. These technologies -enable us to better understand cellular function, however datasets are -still rare and there are tradeoffs that these measurements make for to -profile multiple modalities. - -Joint methods can be more expensive or lower throughput or more noisy -than measuring a single modality at a time. Therefore it is useful to -develop methods that are capable of integrating measurements of the same -biological system but obtained using different technologies on different -cells. - -Here the goal is to learn a latent space where cells profiled by -different technologies in different modalities are matched if they have -the same state. We use jointly profiled data as ground truth so that we -can evaluate when the observations from the same cell acquired using -different modalities are similar. A perfect result has each of the -paired observations sharing the same coordinates in the latent space. - -## The metrics - -Metrics for multimodal data integration aim to characterize how well the -aligned datasets correspond to the ground truth. - -- **kNN AUC**: Let $f(i) ∈ F$ be the scRNA-seq measurement of cell $i$, - and $g(i) ∈ G$ be the scATAC- seq measurement of cell $i$. kNN-AUC - calculates the average percentage overlap of neighborhoods of $f(i)$ - in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. -- **MSE**: Mean squared error (MSE) is the average distance between each - pair of matched observations of the same cell in the learned latent - space. Lower is better. - -## API - -Datasets should include matched measurements from two modalities, which -are contained in `adata` and `adata.obsm["mode2"]`. The task is to align -these two modalities as closely as possible, without using the known -bijection between the datasets. - -Methods should create joint matrices `adata.obsm["aligned"]` and -`adata.obsm["mode2_aligned"]` which reside in a joint space. - -Metrics should evaluate how well the cells which are known to be -equivalent are aligned in the joint space. diff --git a/src/modality_alignment/README.qmd b/src/modality_alignment/README.qmd deleted file mode 100644 index 851b4469ee..0000000000 --- a/src/modality_alignment/README.qmd +++ /dev/null @@ -1,30 +0,0 @@ ---- -format: gfm -info: - migration_date: "2022-10-17 12:33:00 GMT" ---- - -# Multimodal data integration - -## The task - -Cellular function is regulated by the complex interplay of different types of biological molecules (DNA, RNA, proteins, etc.), which determine the state of a cell. Several recently described technologies allow for simultaneous measurement of different aspects of cellular state. For example, [sci-CAR](https://doi.org/10.1126/science.aau0730) jointly profiles RNA expression and chromatin accessibility on the same cell and [CITE-seq](https://doi.org/10.1038/nmeth.4380) measures surface protein abundance and RNA expression from each cell. These technologies enable us to better understand cellular function, however datasets are still rare and there are tradeoffs that these measurements make for to profile multiple modalities. - -Joint methods can be more expensive or lower throughput or more noisy than measuring a single modality at a time. Therefore it is useful to develop methods that are capable of integrating measurements of the same biological system but obtained using different technologies on different cells. - -Here the goal is to learn a latent space where cells profiled by different technologies in different modalities are matched if they have the same state. We use jointly profiled data as ground truth so that we can evaluate when the observations from the same cell acquired using different modalities are similar. A perfect result has each of the paired observations sharing the same coordinates in the latent space. - -## The metrics - -Metrics for multimodal data integration aim to characterize how well the aligned datasets correspond to the ground truth. - -* **kNN AUC**: Let $f(i) ∈ F$ be the scRNA-seq measurement of cell $i$, and $g(i) ∈ G$ be the scATAC- seq measurement of cell $i$. kNN-AUC calculates the average percentage overlap of neighborhoods of $f(i)$ in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. -* **MSE**: Mean squared error (MSE) is the average distance between each pair of matched observations of the same cell in the learned latent space. Lower is better. - -## API - -Datasets should include matched measurements from two modalities, which are contained in `adata` and `adata.obsm["mode2"]`. The task is to align these two modalities as closely as possible, without using the known bijection between the datasets. - -Methods should create joint matrices `adata.obsm["aligned"]` and `adata.obsm["mode2_aligned"]` which reside in a joint space. - -Metrics should evaluate how well the cells which are known to be equivalent are aligned in the joint space. From c1696a5e670fd20b821e421835b4613fb35a43ec Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 10:18:02 +0100 Subject: [PATCH 0690/1233] remove old script Former-commit-id: 765f73a281737438f22cb338aa211a31f22fbfa9 --- .../analysis_scripts/script.R | 80 ------------------- 1 file changed, 80 deletions(-) delete mode 100644 src/label_projection/analysis_scripts/script.R diff --git a/src/label_projection/analysis_scripts/script.R b/src/label_projection/analysis_scripts/script.R deleted file mode 100644 index 80f987e875..0000000000 --- a/src/label_projection/analysis_scripts/script.R +++ /dev/null @@ -1,80 +0,0 @@ -library(tidyverse) - -out_dir <- "resources/label_projection/benchmarks/openproblems_v1/" - -# read results -results <- map_df( - yaml::read_yaml("resources/label_projection/output/results.yaml"), - as_tibble -) - -# get method info -method_info <- map_df( - yaml::read_yaml("resources/label_projection/output/method_info.yaml"), - as_tibble -) - -# get metric info -metric_info <- map_df( - yaml::read_yaml("resources/label_projection/output/metric_info.yaml"), - as_tibble -) - - - -# get data table -ranking <- scores %>% - left_join(metric_info %>% select(metric_id = id, maximize), by = "metric_id") %>% - inner_join(method_info %>% select(method_id = id, method_label = label), by = "method_id") %>% - group_by(metric_id, dataset_id) %>% - mutate(rank = rank(ifelse(maximize, -metric_value, metric_value))) %>% - ungroup() %>% - group_by(method_id, method_label) %>% - summarise(mean_rank = mean(rank), .groups = "drop") %>% - arrange(mean_rank) - -df <- - method_info %>% - select(id, type, label) %>% - rename_all(function(x) paste0("method_", x)) %>% - inner_join(scores %>% spread(metric_id, metric_value), by = "method_id") %>% - left_join(execution_info, by = c("dataset_id", "method_id")) %>% - mutate(method_label = factor(method_label, levels = rev(ranking$method_label))) %>% - arrange(method_label) - - -# get feature info -feature_info_exec <- tribble( - ~id, ~label, ~log_x, - "realtime", "Duration (s)", FALSE, - "pcpu", "CPU usage (%)", FALSE, - "vmem_gb", "Memory usage (GB)", FALSE, - "peak_vmem_gb", "Peak memory (GB)", FALSE, - "read_bytes_mb", "Read disk (MB)", FALSE, - "write_bytes_mb", "Write disk (MB)", FALSE -) -feature_info <- bind_rows( - metric_info %>% transmute(id, label, log_x = FALSE), - feature_info_exec -) - -plots <- pmap(feature_info, function(id, label, log_x) { - g <- ggplot(df) + - geom_path(aes_string(id, "method_label", group = "dataset_id"), alpha = .2) + - geom_point(aes_string(id, "method_label", colour = "method_type")) + - theme_bw() + - theme(legend.position = "none") + - labs(x = label, y = NULL) + - expand_limits(x = 0) - if (log_x) { - g <- g + scale_x_log10() - } - g -}) -g <- patchwork::wrap_plots(plots, ncol = 2, byrow = FALSE) - - -ggsave(paste0(out_dir, "plot.pdf"), g, width = 8, height = 12) -ggsave(paste0(out_dir, "plot.png"), g, width = 8, height = 12) - - From 82ec7b5a1c88793d7a607daa3a51b867b71f9363 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 10:31:47 +0100 Subject: [PATCH 0691/1233] remove bin folder Former-commit-id: 5d286d93171fbb8dae70a0fdd188d624945e3625 --- .../resources_test_scripts/pancreas.sh | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index cf233fc306..14fb196f35 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -1,8 +1,4 @@ #!/bin/bash -set -xe -# -#make sure the following command has been executed -#bin/viash_build -q 'batch_integration|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -20,12 +16,9 @@ fi mkdir -p $DATASET_DIR -# build components -bin/viash_build -q batch - # process dataset echo process data... -bin/viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ +viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ --input $RAW_DATA \ --output $DATASET_DIR/pancreas/processed.h5ad \ --label celltype \ @@ -36,16 +29,16 @@ bin/viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ echo run methods... # Graph methods -bin/viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ +viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/processed.h5ad \ --output $DATASET_DIR/graph/methods/bbknn.h5ad -bin/viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ +viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/processed.h5ad \ --output $DATASET_DIR/graph/methods/combat.h5ad # Embedding method -bin/viash run src/batch_integration/embedding/methods/combat/config.vsh.yaml -- \ +viash run src/batch_integration/embedding/methods/combat/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/processed.h5ad \ --output $DATASET_DIR/embedding/methods/combat.h5ad From 5b34c3ccb94eb82d0cd3f325965ff527aa11f14d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 11:01:00 +0100 Subject: [PATCH 0692/1233] try with nextflow schema action Former-commit-id: ed7b610e8ea54f0887a30249d9b5865a3f164de6 --- .github/workflows/main-build.yml | 27 ++++----------------------- 1 file changed, 4 insertions(+), 23 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 406ebb19cf..c34096e835 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -14,13 +14,6 @@ jobs: steps: - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v1.0.0 - - name: Fetch viash tools - uses: actions/checkout@v3 - with: - repository: "viash-io/viash_tools" - token: ${{ secrets.GTHB_PAT }} - ref: "main_build" - path: "../viash_tools" # create cachehash key - name: Create hash key @@ -53,23 +46,11 @@ jobs: sed -i '/^target.*/d' .gitignore # build target dir - viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing + viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - - name: Build nextflow schemas & params - run: | - viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) - outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) - outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) - ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - - viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) - outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) - outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) - ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + - uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + with: + token: ${{ secrets.GTHB_PAT }} - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 From 2ce5cdd49a0c13a4e372a553699f976bb4eadb46 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 11:01:24 +0100 Subject: [PATCH 0693/1233] fix scripts Former-commit-id: 6bee2c8df5e5255e9cbbf1d3f1af261611d24527 --- src/common/resources_test_scripts/task_metadata.sh | 5 +++-- src/common/sync_test_resources/run_test.sh | 4 ++-- 2 files changed, 5 insertions(+), 4 deletions(-) mode change 100644 => 100755 src/common/resources_test_scripts/task_metadata.sh diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh old mode 100644 new mode 100755 index 880e03e9df..3acb53bd50 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -115,5 +115,6 @@ EOT # Create a method info json viash run src/common/get_method_info/config.vsh.yaml -- \ - --input "src/denoising" \ - --output $OUTPUT_DIR/"method_info.json" \ No newline at end of file + --input . \ + --task_id "denoising" \ + --output "$OUTPUT_DIR/method_info.json" \ No newline at end of file diff --git a/src/common/sync_test_resources/run_test.sh b/src/common/sync_test_resources/run_test.sh index 40b1b5e58f..67f2504531 100755 --- a/src/common/sync_test_resources/run_test.sh +++ b/src/common/sync_test_resources/run_test.sh @@ -5,11 +5,11 @@ echo ">> Run aws s3 sync" ./$meta_functionality_name \ - --input s3://openproblems-data/resources_test/label_projection/pancreas \ + --input s3://openproblems-data/resources_test/common/pancreas \ --output foo \ --quiet echo ">> Check whether the right files were copied" -[ ! -f foo/raw_data.h5ad ] && echo csv should have been copied && exit 1 +[ ! -f foo/dataset.h5ad ] && echo csv should have been copied && exit 1 echo ">> Test succeeded!" \ No newline at end of file From 061de65515bfcc6722c77ad48c81fa000a2d5722 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 11:20:02 +0100 Subject: [PATCH 0694/1233] fix get_task_info component Former-commit-id: 41b2af6d0a5c86b806d68d2f46e8664564925682 --- src/common/get_task_info/script.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py index 239b8e1750..4b906c6e5a 100644 --- a/src/common/get_task_info/script.py +++ b/src/common/get_task_info/script.py @@ -13,9 +13,7 @@ ## VIASH END -task_info_path = path.join(par["input"], "src", par["task_id"], "docs", "task_info.yaml") - - +task_info_path = path.join(par["input"], "src", par["task_id"], "api", "task_info.yaml") with open(task_info_path, "r") as f: task_info = load(f, Loader=CSafeLoader ) From bc9b344b0ece636e4e2f76c868caed75771b0993 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Jan 2023 12:48:03 +0100 Subject: [PATCH 0695/1233] temporarily disable nextflow schemas and params Former-commit-id: d4750ee282cee0aeb40d7623bcac0de034582849 --- .github/workflows/main-build.yml | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index c34096e835..5b0d5751c9 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -48,9 +48,17 @@ jobs: # build target dir viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - - uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas - with: - token: ${{ secrets.GTHB_PAT }} + # - name: Generate schemas + # uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + # with: + # token: ${{ secrets.GTHB_PAT }} + # input_dir: src + + # - name: Generate params + # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params + # with: + # token: ${{ secrets.GTHB_PAT }} + # input_dir: src - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -97,4 +105,4 @@ jobs: - name: Push containers run: | - viash build ${{ matrix.component.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file + viash build ${{ matrix.component.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file From 75be52af7ab1d6f11db23e981c92d5eb404d9945 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 24 Jan 2023 22:38:46 +0100 Subject: [PATCH 0696/1233] add general unit test for methods and metrics config files Former-commit-id: 60b662e5cc4e31c9c353ddca0821d47471df1689 --- src/common/unit_test/check_method_config.py | 31 +++++++++++++++++ src/common/unit_test/check_metric_config.py | 38 +++++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 src/common/unit_test/check_method_config.py create mode 100644 src/common/unit_test/check_metric_config.py diff --git a/src/common/unit_test/check_method_config.py b/src/common/unit_test/check_method_config.py new file mode 100644 index 0000000000..ce5b01d5ef --- /dev/null +++ b/src/common/unit_test/check_method_config.py @@ -0,0 +1,31 @@ +import yaml + + +## VIASH START + +meta = { + "config" : "foo" +} + +## VIASH END + +print("Load config data", flush=True) +with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + +info = config['functionality']['info'] + +print("Check info fields", flush=True) +assert "type" in info, "type not an info field" +info_types = ["method", "negative_control", "positive_control"] +assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" +assert "method_name" in info, "method_name not an info field" +assert "variants" in info, "variants not an info field" +assert "preferred_normalization" in info, "preferred_normalization not an info field" +if ("control" not in info["type"]): + assert "paper_reference" in info, "paper_reference not an info field" + +# TODO: check v1 fields but will not work for neurips migrated tasks + + +print("All checks succeeded!", flush=True) diff --git a/src/common/unit_test/check_metric_config.py b/src/common/unit_test/check_metric_config.py new file mode 100644 index 0000000000..1600a85ab1 --- /dev/null +++ b/src/common/unit_test/check_metric_config.py @@ -0,0 +1,38 @@ +import yaml +from typing import Dict + + +## VIASH START + +meta = { + "config" : "foo" +} + +## VIASH END + +def check_metric(metric: Dict[str, str]) -> str: + assert "metric_id" in metric, "metric_id not a field" + assert "metric_name" in metric, f"metric_name not a field in metric['metric_id']" + assert "min" in metric, f"min not a field in metric['metric_id']" + assert "max" in metric, f"max not a field in metric['metric_id']" + assert "maximize" in metric, f"maximize not a field in metric['metric_id']" + assert isinstance(metric['metric_id'], str), "not a string" + assert isinstance(metric['metric_name'], str), "not a string" + assert isinstance(metric['min'], int), "not an int" + assert isinstance(metric['max'], (int, str)), "not an int or string (+inf)" + assert isinstance(metric['maximize'], bool), "not a bool" + + +print("Load config data", flush=True) +with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + +info = config['functionality']['info'] + +print("Check info fields", flush=True) +# NOTE: also add general namespace, description and name ? +assert "metrics" in info, "metrics not an info field" +for metric in info["metrics"]: + check_metric(metric) + +print("All checks succeeded!", flush=True) From ec009ac4d1c901ab9c5ea527c3ecff3603231785 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 25 Jan 2023 08:40:40 +0100 Subject: [PATCH 0697/1233] try creating the schemas with the new viash action Former-commit-id: 748d0e7c8557dbcfd4ff2099729cabcb817e3341 --- .github/workflows/main-build.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 5b0d5751c9..8971b0d032 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -48,11 +48,11 @@ jobs: # build target dir viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - # - name: Generate schemas - # uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas - # with: - # token: ${{ secrets.GTHB_PAT }} - # input_dir: src + - name: Generate schemas + uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + with: + token: ${{ secrets.GTHB_PAT }} + input_dir: src # - name: Generate params # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params From a5b8e211a84a977edd6f0ae19cb66b48ab481d75 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 26 Jan 2023 15:24:35 +0100 Subject: [PATCH 0698/1233] add common unit tests to all tasks Former-commit-id: 028aa9073ea477a984511687b312e22d81a97aec --- src/common/unit_test/check_method_config.py | 6 ++++-- src/common/unit_test/check_metric_config.py | 5 ++++- src/denoising/api/comp_control_method.yaml | 2 ++ src/denoising/api/comp_method.yaml | 2 ++ src/denoising/api/comp_metric.yaml | 2 ++ src/denoising/control_methods/no_denoising/config.vsh.yaml | 1 + .../control_methods/perfect_denoising/config.vsh.yaml | 1 + src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 1 + src/denoising/methods/knn_smoothing/config.vsh.yaml | 1 + src/denoising/methods/magic/config.vsh.yaml | 2 +- src/denoising/metrics/mse/config.vsh.yaml | 1 + src/denoising/metrics/poisson/config.vsh.yaml | 1 + src/dimensionality_reduction/api/comp_control_method.yaml | 2 ++ src/dimensionality_reduction/api/comp_method.yaml | 2 ++ src/dimensionality_reduction/api/comp_metric.yaml | 2 ++ .../control_methods/random_features/config.vsh.yaml | 1 + .../control_methods/true_features/config.vsh.yaml | 1 + .../methods/densmap/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/ivis/config.vsh.yaml | 1 + .../methods/neuralee/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/pca/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/phate/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 1 + src/dimensionality_reduction/methods/umap/config.vsh.yaml | 1 + .../metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 1 + src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 1 + .../metrics/trustworthiness/config.vsh.yaml | 1 + src/label_projection/api/comp_control_method.yaml | 2 ++ src/label_projection/api/comp_method.yaml | 2 ++ src/label_projection/api/comp_metric.yaml | 2 ++ .../control_methods/majority_vote/config.vsh.yaml | 1 + .../control_methods/random_labels/config.vsh.yaml | 1 + .../control_methods/true_labels/config.vsh.yaml | 1 + src/label_projection/methods/knn/config.vsh.yaml | 1 + .../methods/logistic_regression/config.vsh.yaml | 1 + src/label_projection/methods/mlp/config.vsh.yaml | 1 + src/label_projection/methods/scanvi/config.vsh.yaml | 1 + .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/label_projection/methods/xgboost/config.vsh.yaml | 1 + src/label_projection/metrics/accuracy/config.vsh.yaml | 1 + src/label_projection/metrics/f1/config.vsh.yaml | 1 + 43 files changed, 58 insertions(+), 7 deletions(-) diff --git a/src/common/unit_test/check_method_config.py b/src/common/unit_test/check_method_config.py index ce5b01d5ef..ad4968642b 100644 --- a/src/common/unit_test/check_method_config.py +++ b/src/common/unit_test/check_method_config.py @@ -13,9 +13,12 @@ with open(meta["config"], "r") as file: config = yaml.safe_load(file) -info = config['functionality']['info'] + +print("check general fields", flush=True) +assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" print("Check info fields", flush=True) +info = config['functionality']['info'] assert "type" in info, "type not an info field" info_types = ["method", "negative_control", "positive_control"] assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" @@ -25,7 +28,6 @@ if ("control" not in info["type"]): assert "paper_reference" in info, "paper_reference not an info field" -# TODO: check v1 fields but will not work for neurips migrated tasks print("All checks succeeded!", flush=True) diff --git a/src/common/unit_test/check_metric_config.py b/src/common/unit_test/check_metric_config.py index 1600a85ab1..55e5ad2dbe 100644 --- a/src/common/unit_test/check_metric_config.py +++ b/src/common/unit_test/check_metric_config.py @@ -29,8 +29,11 @@ def check_metric(metric: Dict[str, str]) -> str: info = config['functionality']['info'] +print("check general fields", flush=True) +assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" + + print("Check info fields", flush=True) -# NOTE: also add general namespace, description and name ? assert "metrics" in info, "metrics not an info field" for metric in info["metrics"]: check_metric(metric) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 157f076452..9640221c6b 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -9,6 +9,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/denoising/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 0b8dabfb2c..e83f119c11 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -7,6 +7,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/denoising/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 4717fc9ab1..cb66204477 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -9,6 +9,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/denoising/pancreas + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script path: format_check.py text: | diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 64e601f7ab..2ace619c0f 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -21,6 +21,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - pyyaml - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index e24fb9cf9c..507acfa6f9 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -21,6 +21,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - pyyaml - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 394193e458..d045971b01 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -41,7 +41,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] - type: python - pip: [ anndata>=0.8 ] + pip: [ anndata>=0.8, pyyaml ] - type: r cran: [ Matrix, anndata, bit64, rsvd ] - type: docker diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 0ce04986bd..7ab3335ede 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -32,6 +32,7 @@ platforms: - type: python packages: - anndata>=0.8 + - pyyaml - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow directives: diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 2fd5c0ed6e..ca15763d4e 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -23,6 +23,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - pyyaml - scipy github: - scottgigante-immunai/knn-smoothing@python_package diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index d9b820ed07..29028b449c 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -46,7 +46,7 @@ platforms: image: "python:3.10" setup: - type: python - pip: [ "anndata>=0.8", scprep, magic-impute, scipy, scikit-learn<1.2] + pip: [ "anndata>=0.8", pyyaml, scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 4f795e34ea..0db45933d2 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -27,6 +27,7 @@ platforms: - "anndata>=0.8" - scanpy - scprep + - pyyaml - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 06f96b4f0c..e56dccebbe 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -25,6 +25,7 @@ platforms: pip: - "anndata>=0.8" - scprep + - pyyaml - type: nextflow directives: label: [ midmem, midcpu ] \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 6918aba03e..10bd9c734f 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -7,6 +7,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index e9c6776d3a..eb8ece3d6c 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -7,6 +7,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 48d07e06bc..30bb41de8e 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -9,6 +9,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index d4224281b5..2807907737 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -20,6 +20,7 @@ platforms: setup: - type: python packages: + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 92fb2cae71..63eeed2239 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -38,6 +38,7 @@ platforms: - type: python packages: - scanpy + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index eb6695275c..8144b54d9e 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -38,6 +38,7 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index b397c0a0f4..267463b0cd 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -39,6 +39,7 @@ platforms: - scanpy - "anndata>=0.8" - ivis[cpu] + - pyyaml - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 6b083bd880..81be46792a 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -41,6 +41,7 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - torch - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index c066a90b9f..02cceb017e 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -29,6 +29,7 @@ platforms: - type: python packages: - scanpy + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index cdc43b3be9..146409d76b 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -44,6 +44,7 @@ platforms: - "anndata>=0.8" - phate==1.0.* - scprep + - pyyaml - "scikit-learn<1.2" - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 9f67413462..9ca981af34 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -38,6 +38,7 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - MulticoreTSNE - type: nextflow directives: diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 0d21b52625..b7db819016 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,6 +39,7 @@ platforms: packages: - scanpy - "anndata>=0.8" + - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 2485507175..6bfc3b0ec0 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -71,7 +71,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8 ] + pip: [ anndata>=0.8, pyyaml ] - type: nextflow directives: label: [ highmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 474e035f71..3c1c9c78b5 100644 --- a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -30,6 +30,7 @@ platforms: - scipy - numpy - "anndata>=0.8" + - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index f67ae5a06d..aecfaadb1c 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -39,6 +39,7 @@ platforms: - scikit-learn - numpy - scipy + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index ee5c3b3899..a17e54cf0e 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -25,6 +25,7 @@ platforms: packages: - scikit-learn - numpy + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index bdf3fa2b4a..8fbc505651 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -11,6 +11,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index a685d6230e..dcdc7f98b7 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -9,6 +9,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 148903f9db..5d9f593214 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -9,6 +9,8 @@ functionality: direction: output test_resources: - path: ../../../../resources_test/label_projection/pancreas + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script path: format_check.py text: | diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index a3c5c9fbd8..d2b7dee39a 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -21,6 +21,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index b602fc6137..7618c49a4d 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -21,6 +21,7 @@ platforms: - type: python packages: - scanpy + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 4576b54483..6176787082 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -20,6 +20,7 @@ platforms: setup: - type: python packages: + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index f73583c5de..1bebd7d440 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -29,6 +29,7 @@ platforms: - type: python packages: - scikit-learn + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 6ec8d66bdd..e8458c69bb 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -28,6 +28,7 @@ platforms: - type: python packages: - scikit-learn + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index df5eab7516..8d70a5a280 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -39,6 +39,7 @@ platforms: - type: python packages: - scikit-learn + - pyyaml - "anndata>=0.8" - type: nextflow directives: diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index f09dc9fe04..9a841371fa 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -32,6 +32,7 @@ platforms: setup: - type: python packages: + - pyyaml - "anndata>=0.8" - scarches - type: nextflow diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index c6cb19baf3..78e6b44083 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -28,7 +28,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8 ] + pip: [ anndata>=0.8, pyyaml ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index caeb1395c1..d269671692 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -26,6 +26,7 @@ platforms: - type: python packages: - "anndata>=0.8" + - pyyaml - xgboost - type: nextflow directives: diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 8cbba97e35..c6f756b6ac 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -22,6 +22,7 @@ platforms: setup: - type: python packages: + - pyyaml - scikit-learn - "anndata>=0.8" - type: nextflow diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index bc59272889..e830c9cbc7 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -35,5 +35,6 @@ platforms: - type: python packages: - scikit-learn + - pyyaml - "anndata>=0.8" - type: nextflow From 06a2667871f4b0a4ad45c19d6bd58d5f115f4575 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 26 Jan 2023 15:29:18 +0100 Subject: [PATCH 0699/1233] update changelog Former-commit-id: 329dc1642cafbd41530ad2fe9e4c37fb765f869f --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa367f2377..1649e0c357 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,8 @@ * `get_task_info`: extract task info +* `unit_test`: Common unit test that can be used by all tasks + ## label_projection From d5dc0dea822a563a8508edfb27a7bbe0747d33a6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 26 Jan 2023 21:50:38 +0100 Subject: [PATCH 0700/1233] add initial script Former-commit-id: 3ebb550a1d3706dfdbcada3fe479d96d19f67772 --- .../check_dataset_schema/config.vsh.yaml | 45 +++++++++++++++ src/common/check_dataset_schema/script.py | 56 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 src/common/check_dataset_schema/config.vsh.yaml create mode 100644 src/common/check_dataset_schema/script.py diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml new file mode 100644 index 0000000000..25901a62f0 --- /dev/null +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -0,0 +1,45 @@ +functionality: + name: check_dataset_schema + namespace: common + description: + argument_groups: + - name: Inputs + arguments: + - name: --input + type: file + required: true + description: A h5ad file. + - name: --schema + type: file + required: true + description: A schema file for the h5ad object. + - name: Arguments + arguments: + - name: --stop_on_error + type: boolean + default: false + description: Whether or not to stop with exit code 1 if the input file does not adhere to the schema. + - name: --copy_output + type: boolean_true + description: Wether a output needs to be created for further analysis. + - name: Output + arguments: + - name: --json + type: file + required: false + description: If specified, this file will contain a structured log of which checks succeeded (or not). + - name: --output + type: file + required: false + description: If specified, the output file will be a copy of the input file. + resources: + - type: python_script + path: script.py +platform: + - type: docker + image: python:3.10 + setup: + - type: python + pip: [anndata>=0.8, pyyaml] + - type: nextflow + diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py new file mode 100644 index 0000000000..f2a37c46ed --- /dev/null +++ b/src/common/check_dataset_schema/script.py @@ -0,0 +1,56 @@ + +import anndata as ad +import yaml + + +## VIASH START +# The following code has been auto-generated by Viash. +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'schema': 'src/denoising/api/anndata_dataset.yaml', + 'stop_on_error': 'false', + 'copy_output': 'false', + # 'json': '/path/to/file', + # 'output': '/path/to/file' +} +meta = { + 'functionality_name': 'foo', + +} + +## VIASH END + +def check_structure (slot_info, adata_slot): + missing=[] + for obj in slot_info: + if obj['name'] not in adata_slot: + missing.append(obj['name']) + + return missing + + +print('Load data', flush=True) +adata = ad.read_h5ad(par['dataset']) + +with open(par['structure'], 'r') as f: + data_struct = yaml.safe_load(f) + + +def_slots = data_struct['info']['slots'] + +out={ + 'exit_code' : 0, + 'error': {} +} + +for slot in def_slots: + if slot not in out['error']: + out['error'][slot] + check = check_structure(def_slots[slot], getattr(adata, slot)) + if check is not None: + out['exit_code'] = 1 + out['error'][slot] = check + + +exit(out['exit_code']) + From 60f08e426deb80afbf5b72710b5ec0f11d9a98ff Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 27 Jan 2023 14:27:51 +0100 Subject: [PATCH 0701/1233] update script Former-commit-id: a8a48cb9c2a3e6028db2ede87b4b86228435129f --- .../check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_dataset_schema/script.py | 36 +++++++++++++------ 2 files changed, 26 insertions(+), 12 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 25901a62f0..d71569d5cc 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: check_dataset_schema namespace: common - description: + description: Checks if the dataset has the necessary slots that are predefined in a schema. argument_groups: - name: Inputs arguments: diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index f2a37c46ed..44d72c5573 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -1,6 +1,7 @@ - import anndata as ad import yaml +import shutil +import json ## VIASH START @@ -10,8 +11,8 @@ 'schema': 'src/denoising/api/anndata_dataset.yaml', 'stop_on_error': 'false', 'copy_output': 'false', - # 'json': '/path/to/file', - # 'output': '/path/to/file' + 'json': 'output/error.json', + 'output': 'output/output.h5ad' } meta = { 'functionality_name': 'foo', @@ -28,11 +29,16 @@ def check_structure (slot_info, adata_slot): return missing +def write_json(output): + if par['json'] is not None: + with open(par["json"], "w") as outf: + json.dump(output, outf, indent=2) + print('Load data', flush=True) -adata = ad.read_h5ad(par['dataset']) +adata = ad.read_h5ad(par['input']) -with open(par['structure'], 'r') as f: +with open(par['schema'], 'r') as f: data_struct = yaml.safe_load(f) @@ -40,17 +46,25 @@ def check_structure (slot_info, adata_slot): out={ 'exit_code' : 0, - 'error': {} + 'data_schema': 'ok', + 'error': { + + } } for slot in def_slots: - if slot not in out['error']: - out['error'][slot] check = check_structure(def_slots[slot], getattr(adata, slot)) - if check is not None: + if bool(check): out['exit_code'] = 1 + out['data_schema'] = 'not ok' out['error'][slot] = check +if par['stop_on_error'] == 'true': + write_json(out) + exit(out['exit_code']) -exit(out['exit_code']) - +if par['copy_output'] == 'true': + assert par['output'] is not None, 'No output defined' + write_json(out) + shutil.copyfile(par["input"], par["output"]) + From 9cde7fe040a7f5a1871b680983a9d78824c61ce3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 30 Jan 2023 15:09:37 +0100 Subject: [PATCH 0702/1233] try using latest action Former-commit-id: 3788128f505c850df158c39d86803cda6cb14168 --- .github/workflows/main-build.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 8971b0d032..6b4237b541 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -52,7 +52,8 @@ jobs: uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas with: token: ${{ secrets.GTHB_PAT }} - input_dir: src + components: src + workflows: src # - name: Generate params # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params From 676b31dc8f48bacdb3aafa9069124e6a538079bf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 30 Jan 2023 16:02:40 +0100 Subject: [PATCH 0703/1233] disable schemas for now Former-commit-id: 3e2141817dba38d9c55f349f23a044e534c73854 --- .github/workflows/main-build.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 6b4237b541..8ddd782bb8 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -48,12 +48,12 @@ jobs: # build target dir viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - - name: Generate schemas - uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas - with: - token: ${{ secrets.GTHB_PAT }} - components: src - workflows: src + # - name: Generate schemas + # uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + # with: + # token: ${{ secrets.GTHB_PAT }} + # components: src + # workflows: src # - name: Generate params # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params From 72a7857b6d82424607e45a4410ed3b95bf42e389 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 31 Jan 2023 08:40:20 +0100 Subject: [PATCH 0704/1233] try action again Former-commit-id: c4dc76e150d3914345ed17f3459e0666a938ee05 --- .github/workflows/main-build.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 8ddd782bb8..6b4237b541 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -48,12 +48,12 @@ jobs: # build target dir viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - # - name: Generate schemas - # uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas - # with: - # token: ${{ secrets.GTHB_PAT }} - # components: src - # workflows: src + - name: Generate schemas + uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + with: + token: ${{ secrets.GTHB_PAT }} + components: src + workflows: src # - name: Generate params # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params From 51bc34a0759d3b0df717582dacae8770ff1e642d Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 31 Jan 2023 11:30:29 +0100 Subject: [PATCH 0705/1233] create skeleton config yaml Former-commit-id: f6de3aa80525bd6a49224dd756a8387f5889ac69 --- src/common/create_skeleton/config.vsh.yaml | 31 +++++ src/common/create_skeleton/script.py | 134 +++++++++++++++++++++ 2 files changed, 165 insertions(+) create mode 100644 src/common/create_skeleton/config.vsh.yaml create mode 100644 src/common/create_skeleton/script.py diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml new file mode 100644 index 0000000000..aca5ea0047 --- /dev/null +++ b/src/common/create_skeleton/config.vsh.yaml @@ -0,0 +1,31 @@ +functionality: + name: create_skeleton + namespace: common + description: Create a skeleton directory containing a viash config file and python or r script file based on the task api. + arguments: + - type: string + name: --task + example: denoising + description: + - type: string + name: --comp_type + example: metric + description: + choices: ['metric', 'method', 'negative_control', 'positive_control'] + - type: string + name: --platform + example: python + description: + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.10 + setup: + - type: python + pip: + - pyyaml + - type: nextflow + + diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py new file mode 100644 index 0000000000..0be73e1ef1 --- /dev/null +++ b/src/common/create_skeleton/script.py @@ -0,0 +1,134 @@ + +import yaml + + +## VIASH START +# The following code has been auto-generated by Viash. +par = { + 'task': 'denoising', + 'comp_type': 'metric', + 'platform': 'python' +} +meta = { +} + +## VIASH END + + + + +if 'control' in par['comp_type']: + merge = 'control_method' +else: + merge = par['comp_type'] + +skeleton_config = { + '__merge__' : f'../../api/comp_{merge}.yaml', + 'functionality': { + 'name' : 'new_method_name', + 'namespace': f'{par["task"]}/{merge}s', + 'description': 'Description what this component does', + 'info' : { + 'type': par['comp_type'] + }, + 'resources': [ + { + 'type': '', + 'path': '', + } + ], + 'test_resources': [{ + 'type': '', + 'path': '' + }] + }, + 'platforms': [ + { + 'type' : 'nextflow', + 'directives': { + 'label': ['midmem', 'midcpu'] + } + } + ] +} + +# Add component specific config data + +if par['comp_type'] == 'metric': + + skeleton_config['functionality']['info']['metrics'] = [{ + 'metric_id': 'metric_id', + 'metric_name': 'Metric Name', + 'metric_description': 'metric description', + 'min': 0, + 'max': 1, + 'maximize': 'true', + } + ] + +else: + method_info = { + 'method_name': 'Method name', + 'preferred_normalization': 'log_cpm', + 'variants': { + 'method_name': '', + 'method_variant1': { + 'preferred_normalization': 'sqrt_cpm' + } + } + } + if par['comp_type'] == 'method': + method_info['paper_reference']= '' + + skeleton_config['functionality']['info'].update(method_info) + +# add elements depending on platform +if par['platform'] == 'python': + + script_outf = 'script.py' + + skeleton_config['functionality']['resources'][0]['type'] = 'python_script' + skeleton_config['functionality']['resources'][0]['path'] = script_outf + + skeleton_config['functionality']['test_resources'][0]['type'] = 'python_script' + skeleton_config['functionality']['test_resources'][0]['path'] = script_outf + + skeleton_config['platforms'].append({ + 'type': 'docker', + 'image': 'python:3.10', + 'setup': [{ + 'type': 'python', + 'pip': [ + "anndata>=0.8", + "pyyaml" + ] + }] + }) + + + + + +# Create python template +task_api = f'/src/{par["task"]}/api' +api_conf = f'{task_api}/comp_{merge}.yaml' + +with open(api_conf, 'r') as f: + api_data = yaml.safe_load(f) + +args = api_data['arguments'] + +templ_par = {} + +for arg in args: + templ_par[arg.replace('--','')] = '' + +script_templ = f''' + + +''' + + +# Write output +with open('config.vsh.yaml', 'w') as f: + yaml.safe_dump(skeleton_config, f, sort_keys=False) \ No newline at end of file From 892f6c140810d116d76a7832515e364a7b571d5a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 31 Jan 2023 17:00:52 +0100 Subject: [PATCH 0706/1233] add python template to script Former-commit-id: 27889fc996af12b01e09d85dab98d3a90469cb28 --- src/common/create_skeleton/script.py | 48 ++++++++++++++++++++++++---- 1 file changed, 42 insertions(+), 6 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 0be73e1ef1..a3401a0810 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -110,25 +110,61 @@ # Create python template -task_api = f'/src/{par["task"]}/api' +task_api = f'src/{par["task"]}/api' api_conf = f'{task_api}/comp_{merge}.yaml' with open(api_conf, 'r') as f: api_data = yaml.safe_load(f) -args = api_data['arguments'] +args = api_data['functionality']['arguments'] templ_par = {} for arg in args: - templ_par[arg.replace('--','')] = '' + templ_par[arg['name'].replace('--','')] = '' -script_templ = f''' - +script_templ = f'''import anndata as ad + +## VIASH START + +par = {templ_par} + +meta = {{ + 'functionality_name': 'foo' +}} + +## VIASH END + +print('Load input data', flush=True) +adata=ad.read_h5ad(par['{list(templ_par.keys())[0]}']) + +print('Process data', flush=True) +# insert code block here where pred is the prediction + +pred = adata + +# Create output anndata +output = ad.AnnData( + obs = {{}}, + vars = {{}}, + uns = {{ + 'dataset_id': adata.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }}, + layers = adata.layers +) + +output.layers['denoised'] = pred + +print('Write Data', flush=True) +output.write_h5ad(par['output'],compression='gzip') ''' # Write output with open('config.vsh.yaml', 'w') as f: - yaml.safe_dump(skeleton_config, f, sort_keys=False) \ No newline at end of file + yaml.safe_dump(skeleton_config, f, sort_keys=False) + +with open(script_outf, 'w') as fpy: + fpy.write(script_templ) \ No newline at end of file From 7d509b48e7edb5ba3d9f8c05b1f6371ae4f0ffe2 Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 1 Feb 2023 11:19:41 +0100 Subject: [PATCH 0707/1233] refactor pipeline Former-commit-id: 5b08463fd35fd88c5b93aedd965438201aa939b5 --- .../workflows/test/config.vsh.yaml | 22 +++ src/batch_integration/workflows/test/main.nf | 185 ++++++++++++------ .../workflows/test/run_nextflow.sh | 43 +++- 3 files changed, 184 insertions(+), 66 deletions(-) create mode 100644 src/batch_integration/workflows/test/config.vsh.yaml diff --git a/src/batch_integration/workflows/test/config.vsh.yaml b/src/batch_integration/workflows/test/config.vsh.yaml new file mode 100644 index 0000000000..ad7028f7ba --- /dev/null +++ b/src/batch_integration/workflows/test/config.vsh.yaml @@ -0,0 +1,22 @@ +functionality: + name: "run_benchmark" + namespace: "batch_integration/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input" + type: "file" # todo: replace with includes + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + resources: + - type: nextflow_script + path: main.nf +platforms: + - type: nextflow diff --git a/src/batch_integration/workflows/test/main.nf b/src/batch_integration/workflows/test/main.nf index 1559ede6b5..ad7cce333b 100644 --- a/src/batch_integration/workflows/test/main.nf +++ b/src/batch_integration/workflows/test/main.nf @@ -1,15 +1,7 @@ nextflow.enable.dsl=2 - -targetDir = "${params.rootDir}/target/nextflow" -params.download = "$launchDir/src/batch_integration/workflows/download.tsv" -params.preprocessing = "$launchDir/src/batch_integration/workflows/test/preprocessing.tsv" -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) - -// import dataset loaders -include { download } from "$targetDir/common/dataset_loader/download/main.nf" params(params) -include { subsample } from "$targetDir/batch_integration/datasets/subsample/main.nf" params(params) -include { preprocessing } from "$targetDir/batch_integration/datasets/preprocessing/main.nf" params(params) +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" // import methods include { bbknn } from "$targetDir/batch_integration/graph/methods/bbknn/main.nf" params(params) @@ -22,63 +14,66 @@ include { scvi } from "$targetDir/batch_integration/graph/methods/ include { ari } from "$targetDir/batch_integration/graph/metrics/ari/main.nf" params(params) include { nmi } from "$targetDir/batch_integration/graph/metrics/nmi/main.nf" params(params) -/******************************************************* -* Dataset processor workflows * -*******************************************************/ -// This workflow reads in a tsv containing some metadata about each dataset. -// For each entry in the metadata, a dataset is generated, usually by downloading -// and processing some files. The end result of each of these workflows -// should be simply a channel of [id, h5adfile, params] triplets. -// -// If the need arises, these workflows could be split off into a separate file. - - -workflow load_data { - main: - output_ = Channel.fromPath(params.download) - | splitCsv(header: true, sep: "\t") - | map { [ it.name, it ] } - | download - emit: - output_ -} +// tsv generation component +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) + +// import helper functions +include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +workflow { + helpMessage(config) -workflow process_data { - take: - channel_in - main: - additional_params = Channel.fromPath(params.preprocessing) - | splitCsv(header: true, sep: "\t") - | map { [ it.name, it ] } - - subset = channel_in.join(additional_params) - | map { id, data, additional -> - [ id, [ input: data ] + additional ] - } - | subsample - - output_ = subset.join(additional_params) - | map { id, data, additional -> - [ id, [ input: data ] + additional ] - } - | preprocessing - | join(additional_params) - | map { id, data, additional -> - [ id, [ input: data ] + additional ] - } - - emit: - output_ + viashChannel(params, config) + | run_wf } /******************************************************* * Main workflow * *******************************************************/ -workflow { - load_data - | process_data - | view { "integration input $it" } +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + method: ["input"], + metric: [], + output: ["output"] + ) + + // multiply events by the number of method + | add_methods + + // run methods + | getWorkflowArguments(key: "method") + | run_methods + + // construct tuples for metrics + | pmap{ id, file, passthrough -> + // derive unique ids from output filenames + def newId = file.getName().replaceAll(".output.*", "") + // combine prediction with solution + def newData = [ adata: file ] + [ newId, newData, passthrough ] + } + + // run metrics + | getWorkflowArguments(key: "metric") + | run_metrics + + // convert to tsv + | aggregate_results + + emit: + output_ch +/* | (bbknn & combat & scvi & scanorama_embed & scanorama_feature) | mix | toSortedList @@ -91,3 +86,73 @@ workflow { ) */ } + +/******************************************************* +* Sub workflows * +*******************************************************/ + +// construct a map of methods (id -> method_module) +methods = [ bbknn, combat, scanorama_embed, scanorama_feature, scvi] + .collectEntries{method -> + [method.config.functionality.name, method] + } + +workflow add_methods { + take: input_ch + main: + output_ch = Channel.fromList(methods.keySet()) + | combine(input_ch) + + // generate combined id for method_id and dataset_id + | pmap{method_id, dataset_id, data -> + def new_id = dataset_id + "." + method_id + def new_data = data.clone() + [method_id: method_id] + new_data.remove("id") + [new_id, new_data] + } + emit: output_ch +} + +workflow run_methods { + take: input_ch + main: + // generate one channel per method + method_chs = methods.collect { method_id, method_module -> + input_ch + | filter{it[1].method_id == method_id} + | method_module + } + // mix all results + output_ch = method_chs[0].mix(*method_chs.drop(1)) + + emit: output_ch +} + +workflow run_metrics { + take: input_ch + main: + + output_ch = input_ch + | (ari & nmi) + | mix + + emit: output_ch +} + +workflow aggregate_results { + take: input_ch + main: + + output_ch = input_ch + | toSortedList + | filter{ it.size() > 0 } + | map{ it -> + [ "combined", it.collect{ it[1] } ] + it[0].drop(2) + } + | getWorkflowArguments(key: "output") + | extract_scores.run( + auto: [ publish: true ] + ) + + emit: output_ch +} diff --git a/src/batch_integration/workflows/test/run_nextflow.sh b/src/batch_integration/workflows/test/run_nextflow.sh index c35e103a26..864aad59cb 100755 --- a/src/batch_integration/workflows/test/run_nextflow.sh +++ b/src/batch_integration/workflows/test/run_nextflow.sh @@ -9,13 +9,44 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -xe + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/batch_integration/pancreas + +if [ ! -d "$DATASET_DIR" ]; then + mkdir -p "$DATASET_DIR" +fi + +# viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ +# --input $RAW_DATA \ +# --output $DATASET_DIR/processed.h5ad \ +# --label celltype \ +# --batch tech \ +# --hvgs 100 + # choose a particular version of nextflow -export NXF_VER=21.10.6 +# export NXF_VER=21.10.6 -bin/nextflow \ +# bin/nextflow \ +# run . \ +# -main-script src/batch_integration/workflows/run/main.nf \ +# --publishDir output/batch_integration \ +# -resume \ +# -with-docker + + +# run benchmark +export NXF_VER=22.04.5 + + # -profile docker \ +nextflow \ run . \ - -main-script src/batch_integration/workflows/run/main.nf \ - --publishDir output/batch_integration \ + -main-script src/batch_integration/workflows/test/main.nf \ + -with-docker \ -resume \ - -with-docker - + --id pancreas \ + --dataset_id pancreas \ + --input $DATASET_DIR/processed.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ From 19e75a79b628ce728d417e76e6e2121180d14dca Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 15:40:51 +0100 Subject: [PATCH 0708/1233] try updating main build Former-commit-id: e3a19c2d616134684a81c3fa45172c45c36759a7 --- .github/workflows/main-build.yml | 36 +++++++++++++++++--------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 6b4237b541..4e560e22a2 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v2 # create cachehash key - name: Create hash key @@ -49,17 +49,18 @@ jobs: viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing - name: Generate schemas - uses: viash-io/viash-actions/build_nextflow_schemas@build_nextflow_schemas + uses: viash-io/viash-actions/build-nextflow-schemas@v2 with: token: ${{ secrets.GTHB_PAT }} components: src workflows: src - # - name: Generate params - # uses: viash-io/viash-actions/build_nextflow_params@build_nextflow_params - # with: - # token: ${{ secrets.GTHB_PAT }} - # input_dir: src + - name: Generate params + uses: viash-io/viash-actions/build-nextflow-params@v2 + with: + token: ${{ secrets.GTHB_PAT }} + components: src + workflows: src - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -68,14 +69,15 @@ jobs: publish_dir: . publish_branch: main_build - # store component locations - - id: set_matrix - run: | - component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "namespace": .functionality.namespace, "config": .info.config } ]') - echo "component_matrix=$component_json" >> $GITHUB_OUTPUT + + - id: ns_list + uses: viash-io/viash-actions/ns-list@v2 + with: + platform: docker + format: json outputs: - component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} + components_json: ${{ steps.ns_list.outputs.output }} cachehash: ${{ steps.cachehash.outputs.cachehash }} # phase 2 @@ -87,14 +89,14 @@ jobs: strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + component: ${{ fromJson(needs.list_components.outputs.components_json) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v2 - name: Build container run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` + SRC_DIR=`dirname ${{ matrix.component.info.config }}` viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build - name: Login to container registry @@ -106,4 +108,4 @@ jobs: - name: Push containers run: | - viash build ${{ matrix.component.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file + viash build ${{ matrix.component.info.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file From e27c58856d70ec4e28a408f766ff1564b28eb585 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:15:09 +0100 Subject: [PATCH 0709/1233] try fixing main build ci Former-commit-id: 3009f7ea2c0bcd73e8e1f9fb5a68a3b4d5943404 --- .github/workflows/main-build.yml | 34 ++++++++++++++++++++++++++------ 1 file changed, 28 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 4e560e22a2..33080000cf 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -69,15 +69,24 @@ jobs: publish_dir: . publish_branch: main_build - - id: ns_list uses: viash-io/viash-actions/ns-list@v2 with: platform: docker format: json + - id: set_matrix + run: | + echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output }}) '[ .[] | + { + "name": .functionality.name, + "namespace": .functionality.namespace, + "config": .info.config, + "dir": .info.config | capture("^(?.*\/)").dir + } ]'" >> $GITHUB_OUTPUT + outputs: - components_json: ${{ steps.ns_list.outputs.output }} + components_json: ${{ steps.set_matrix.outputs.matrix }} cachehash: ${{ steps.cachehash.outputs.cachehash }} # phase 2 @@ -93,10 +102,19 @@ jobs: steps: - uses: actions/checkout@v3 + - uses: viash-io/viash-actions/setup@v2 + + - name: Build container + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'main_build' + setup: build + src: ${{ matrix.dir }} + - name: Build container run: | - SRC_DIR=`dirname ${{ matrix.component.info.config }}` + SRC_DIR=`dirname ${{ matrix.config }}` viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build - name: Login to container registry @@ -106,6 +124,10 @@ jobs: username: ${{ secrets.GTHB_USER }} password: ${{ secrets.GTHB_PAT }} - - name: Push containers - run: | - viash build ${{ matrix.component.info.config }} -p docker --config_mod ".functionality.version := 'main_build'" --setup push \ No newline at end of file + - name: Push container + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'main_build' + setup: push + platform: docker + src: ${{ matrix.dir }} \ No newline at end of file From 3d21d14989aae865282a8ce3072af50c1620c598 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:15:37 +0100 Subject: [PATCH 0710/1233] remove unneeded step Former-commit-id: 67230c4a82ca2f86a4910008224ce0be93c07549 --- .github/workflows/main-build.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 33080000cf..5a09dde7dc 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -102,7 +102,7 @@ jobs: steps: - uses: actions/checkout@v3 - + - uses: viash-io/viash-actions/setup@v2 - name: Build container @@ -111,11 +111,6 @@ jobs: config_mod: .functionality.version := 'main_build' setup: build src: ${{ matrix.dir }} - - - name: Build container - run: | - SRC_DIR=`dirname ${{ matrix.config }}` - viash ns build --config_mod ".functionality.version := 'main_build'" -s "$SRC_DIR" --setup build - name: Login to container registry uses: docker/login-action@v2 From 65a8ccfbbb26d07b759413f5a2724a69e1869ae3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:19:09 +0100 Subject: [PATCH 0711/1233] fix ci Former-commit-id: ede02d2004f99eeab0e8963ed1978324bab24c80 --- .github/workflows/main-build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 5a09dde7dc..3ee51a0fd0 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -77,13 +77,13 @@ jobs: - id: set_matrix run: | - echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output }}) '[ .[] | + echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | { "name": .functionality.name, "namespace": .functionality.namespace, "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir - } ]'" >> $GITHUB_OUTPUT + } ]')" >> $GITHUB_OUTPUT outputs: components_json: ${{ steps.set_matrix.outputs.matrix }} @@ -111,7 +111,7 @@ jobs: config_mod: .functionality.version := 'main_build' setup: build src: ${{ matrix.dir }} - + - name: Login to container registry uses: docker/login-action@v2 with: From 0159b397a43c431fae247eee4d0dabce4acb0b8d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:29:29 +0100 Subject: [PATCH 0712/1233] try to fix ci once more Former-commit-id: 42f32e7aed1995d2c9cb7c399bb2ba15e1b4dea9 --- .github/workflows/main-build.yml | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 3ee51a0fd0..ae7c3f1ccb 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -77,13 +77,15 @@ jobs: - id: set_matrix run: | - echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | - { - "name": .functionality.name, - "namespace": .functionality.namespace, - "config": .info.config, - "dir": .info.config | capture("^(?.*\/)").dir - } ]')" >> $GITHUB_OUTPUT + matrix_out=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | + { + "name": .functionality.name, + "namespace": .functionality.namespace, + "config": .info.config, + "dir": .info.config | capture("^(?.*\/)").dir + } + ]') + echo "matrix=matrix_out" >> $GITHUB_OUTPUT outputs: components_json: ${{ steps.set_matrix.outputs.matrix }} From 128fabb3384fcbcf71e0b0631656b382d73090f4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:36:09 +0100 Subject: [PATCH 0713/1233] another attempt at fixing ci Former-commit-id: b4373172f200519bfc8645a69699571dec0e1177 --- .github/workflows/main-build.yml | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index ae7c3f1ccb..2a732a88e7 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -77,14 +77,7 @@ jobs: - id: set_matrix run: | - matrix_out=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | - { - "name": .functionality.name, - "namespace": .functionality.namespace, - "config": .info.config, - "dir": .info.config | capture("^(?.*\/)").dir - } - ]') + matrix_out=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name, "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } ]') echo "matrix=matrix_out" >> $GITHUB_OUTPUT outputs: From f4f79e0ba1fcbc7d31592e91dac768e03d9020aa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:40:21 +0100 Subject: [PATCH 0714/1233] fix ci... Former-commit-id: 8dd582a5d36ed583b9f8bdd39c19c684d05ffe20 --- .github/workflows/main-build.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 2a732a88e7..ecc47d2bc6 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -77,8 +77,13 @@ jobs: - id: set_matrix run: | - matrix_out=$(jq -c ${{ steps.ns_list.outputs.output }} '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name, "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } ]') - echo "matrix=matrix_out" >> $GITHUB_OUTPUT + echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output_file }} '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "config": .info.config, + "dir": .info.config | capture("^(?.*\/)").dir + } + ]')" >> $GITHUB_OUTPUT outputs: components_json: ${{ steps.set_matrix.outputs.matrix }} From eec6ff72b7b444a2fd93306bb7ee96c86be5263d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:48:03 +0100 Subject: [PATCH 0715/1233] fix ci?? Former-commit-id: 1c2d20bdffc68a35d289570504b79d3378c87cc5 --- .github/workflows/main-build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index ecc47d2bc6..e1d5f68152 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -77,13 +77,13 @@ jobs: - id: set_matrix run: | - echo "matrix=$(jq -c ${{ steps.ns_list.outputs.output_file }} '[ .[] | + echo "matrix=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } - ]')" >> $GITHUB_OUTPUT + ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT outputs: components_json: ${{ steps.set_matrix.outputs.matrix }} From d7d0cec16686cceb1b19c2e1e0ab5d675bd0ca6d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:51:02 +0100 Subject: [PATCH 0716/1233] rename jobs Former-commit-id: 2b378d3e059383715e07e0f79528e3de0a9cd81e --- .github/workflows/main-build.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index e1d5f68152..5818a0287c 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -6,7 +6,7 @@ on: jobs: # phase 1 - list_components: + list: env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest @@ -90,15 +90,15 @@ jobs: cachehash: ${{ steps.cachehash.outputs.cachehash }} # phase 2 - build_containers: - needs: list_components + build: + needs: list runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.components_json) }} + component: ${{ fromJson(needs.list.outputs.components_json) }} steps: - uses: actions/checkout@v3 From 6bf187875ac36faacaf44057dee5a7cb2666d359 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 1 Feb 2023 16:58:38 +0100 Subject: [PATCH 0717/1233] fix ci for real this time Former-commit-id: e4946657092f6d9b21e4d5bed228644153c98077 --- .github/workflows/main-build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 5818a0287c..0729185ec5 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -110,7 +110,7 @@ jobs: with: config_mod: .functionality.version := 'main_build' setup: build - src: ${{ matrix.dir }} + src: ${{ matrix.component.dir }} - name: Login to container registry uses: docker/login-action@v2 @@ -125,4 +125,4 @@ jobs: config_mod: .functionality.version := 'main_build' setup: push platform: docker - src: ${{ matrix.dir }} \ No newline at end of file + src: ${{ matrix.component.dir }} \ No newline at end of file From 1405955b15756bddfe208440301bc04c8437925c Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 2 Feb 2023 21:42:01 +0100 Subject: [PATCH 0718/1233] update skeleton script Former-commit-id: 32e115819c038b36aa3b441b271d9fea4ce3273f --- src/common/create_skeleton/config.vsh.yaml | 10 +- src/common/create_skeleton/script.py | 250 +++++++++++++-------- 2 files changed, 165 insertions(+), 95 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index aca5ea0047..d4182a744b 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -13,9 +13,13 @@ functionality: description: choices: ['metric', 'method', 'negative_control', 'positive_control'] - type: string - name: --platform + name: --language example: python - description: + description: script language + - type: string + name: --name + example: new_comp + description: name of the new method in snake case resources: - type: python_script path: script.py @@ -25,7 +29,7 @@ platforms: setup: - type: python pip: - - pyyaml + - ruamel.yaml - type: nextflow diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index a3401a0810..127567cb1f 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -1,5 +1,5 @@ - -import yaml +from ruamel.yaml import YAML +from pathlib import Path ## VIASH START @@ -7,7 +7,8 @@ par = { 'task': 'denoising', 'comp_type': 'metric', - 'platform': 'python' + 'language': 'python', + 'name': 'new_comp' } meta = { } @@ -15,48 +16,9 @@ ## VIASH END - - -if 'control' in par['comp_type']: - merge = 'control_method' -else: - merge = par['comp_type'] - -skeleton_config = { - '__merge__' : f'../../api/comp_{merge}.yaml', - 'functionality': { - 'name' : 'new_method_name', - 'namespace': f'{par["task"]}/{merge}s', - 'description': 'Description what this component does', - 'info' : { - 'type': par['comp_type'] - }, - 'resources': [ - { - 'type': '', - 'path': '', - } - ], - 'test_resources': [{ - 'type': '', - 'path': '' - }] - }, - 'platforms': [ - { - 'type' : 'nextflow', - 'directives': { - 'label': ['midmem', 'midcpu'] - } - } - ] -} - -# Add component specific config data - -if par['comp_type'] == 'metric': - - skeleton_config['functionality']['info']['metrics'] = [{ +def add_metric_config(tmpl): + + tmpl['functionality']['info']['metrics'] = [{ 'metric_id': 'metric_id', 'metric_name': 'Metric Name', 'metric_description': 'metric description', @@ -65,66 +27,67 @@ 'maximize': 'true', } ] + + return tmpl -else: - method_info = { +def add_method_config(tmpl): + + tmpl['functionality']['info'].update({ 'method_name': 'Method name', - 'preferred_normalization': 'log_cpm', + 'preferred_normalization': '', 'variants': { 'method_name': '', 'method_variant1': { - 'preferred_normalization': 'sqrt_cpm' + 'preferred_normalization': '' } } - } - if par['comp_type'] == 'method': - method_info['paper_reference']= '' - - skeleton_config['functionality']['info'].update(method_info) - -# add elements depending on platform -if par['platform'] == 'python': - - script_outf = 'script.py' - - skeleton_config['functionality']['resources'][0]['type'] = 'python_script' - skeleton_config['functionality']['resources'][0]['path'] = script_outf + }) - skeleton_config['functionality']['test_resources'][0]['type'] = 'python_script' - skeleton_config['functionality']['test_resources'][0]['path'] = script_outf + return tmpl - skeleton_config['platforms'].append({ - 'type': 'docker', - 'image': 'python:3.10', - 'setup': [{ - 'type': 'python', - 'pip': [ - "anndata>=0.8", - "pyyaml" - ] - }] - }) +def add_python_setup(conf): + conf['functionality']['resources'][0]['type'] = 'python_script' + conf['functionality']['resources'][0]['path'] = 'script.py' + conf['functionality']['test_resources'][0]['type'] = 'python_script' + conf['functionality']['test_resources'][0]['path'] = 'script.py' + for i, platform in enumerate(conf['platforms']): + if platform['type'] == 'docker': + conf['platforms'][i]['image'] = 'python:3.10' + return conf -# Create python template -task_api = f'src/{par["task"]}/api' -api_conf = f'{task_api}/comp_{merge}.yaml' +def add_r_setup(conf): -with open(api_conf, 'r') as f: - api_data = yaml.safe_load(f) + conf['functionality']['resources'][0]['type'] = 'r_script' + conf['functionality']['resources'][0]['path'] = 'script.r' -args = api_data['functionality']['arguments'] + conf['functionality']['test_resources'][0]['type'] = 'r_script' + conf['functionality']['test_resources'][0]['path'] = 'script.r' -templ_par = {} + for i, platform in enumerate(conf['platforms']): + if platform['type'] == 'docker': + pltf = conf['platforms'][i] + pltf['image'] = 'eddelbuettel/r2u:22.04' + pltf['setup'].append( + { + 'type': 'r', + 'cran': [ 'anndata'], + 'bioc': '' + }, + { + 'type': 'apt', + 'packages': ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] + } + ) -for arg in args: - templ_par[arg['name'].replace('--','')] = '' + return conf -script_templ = f'''import anndata as ad +def create_python_script(tmpl_par): + script_templ = f'''import anndata as ad ## VIASH START par = {templ_par} @@ -145,8 +108,6 @@ # Create output anndata output = ad.AnnData( - obs = {{}}, - vars = {{}}, uns = {{ 'dataset_id': adata.uns['dataset_id'], 'method_id': meta['functionality_name'] @@ -158,13 +119,118 @@ print('Write Data', flush=True) output.write_h5ad(par['output'],compression='gzip') +''' + + return script_templ + +def create_r_script(tmpl_par): + '' + +## Create config file +if 'control' in par['comp_type']: + merge = 'control_method' +else: + merge = par['comp_type'] + +config_tmpl = f''' +# points to global config e.g. parameters +__merge__: ../../api/comp_{merge}.yaml +functionality: + name: {par['name']} + namespace: {par["task"]}/{merge}s + description: # add description + info: + type: {par["comp_type"]} + + # additional parameters specific for method. always set default if required + parameters: + + # files your script needs + resources: + - type: + path: + + # resources for unit testing your component + test_resources: + - type: python_script + path: test.py + - path: sample_data + +# target platforms +platforms: + - type: docker + image: + setup: + - type: python + pip: + - pyyaml + - anndata>=0.8 + - type: nextflow + directives: + label: ['midmem', 'midcpu'] ''' +yaml = YAML() +conf_tmpl_dict = yaml.load(config_tmpl) + +# Add component specific config data + +if par['comp_type'] == 'metric': + + config_out = add_metric_config(conf_tmpl_dict) + +else: + + config_out = add_method_config(conf_tmpl_dict) + + if par['comp_type'] == 'method': + config_out['functionality']['info']['paper_reference']= '' + + +# add elements depending on language +if par['language'] == 'python': + + config_out = add_python_setup(config_out) + +if par['language'] == 'r': + + config_out = add_r_setup(config_out) + + +## Create script template +task_api = f'src/{par["task"]}/api' +api_conf = f'{task_api}/comp_{merge}.yaml' + +with open(api_conf, 'r') as f: + api_data = yaml.load(f) + +args = api_data['functionality']['arguments'] + +templ_par = {} + +for arg in args: + templ_par[arg['name'].replace('--','')] = '' + +if par['language'] == 'python': + + script_out = create_python_script(templ_par) + +if par['language'] == 'r': + + script_out = create_r_script(templ_par) + + + +## Write output +out_dir= Path(par['name']) + +out_dir.mkdir(exist_ok=True) + +with open(f'{out_dir}/config.vsh.yaml', 'w') as f: + yaml.dump(config_out, f) -# Write output -with open('config.vsh.yaml', 'w') as f: - yaml.safe_dump(skeleton_config, f, sort_keys=False) +script_f = config_out['functionality']['resources'][0]['path'] -with open(script_outf, 'w') as fpy: - fpy.write(script_templ) \ No newline at end of file +with open(f'{out_dir}/{script_f}', 'w') as fpy: + fpy.write(script_out) \ No newline at end of file From 8cc488ca41c4b975abce7b571bdf476ada445e55 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 3 Feb 2023 15:19:30 +0100 Subject: [PATCH 0719/1233] update actions Former-commit-id: bd88b1c0ab3885b61e7bf92fd96c0e5452d5cc2b --- .github/workflows/integration-test.yml | 131 +++++++++-------- .github/workflows/main-build.yml | 77 ++++------ .github/workflows/release-build.yml | 190 +++++++++++++------------ .github/workflows/viash-test.yml | 107 ++++++-------- 4 files changed, 240 insertions(+), 265 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 19a2b67bce..fd23c55152 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -4,48 +4,37 @@ on: workflow_dispatch jobs: # phase 1 - list_components: + list: env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest + outputs: + component_matrix: ${{ steps.set_matrix.outputs.components }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} + cache_key: ${{ steps.cache.outputs.cache_key }} + steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v1 - # create cachehash key - - name: Create hash key - id: cachehash - run: | - AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT - - # initialize cache - - name: Cache resources data - uses: actions/cache@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + id: cache with: - path: resources_test - key: ${{ steps.cachehash.outputs.cachehash }} - restore-keys: resources_test_ + s3_bucket: $s3_bucket + dest_path: resources_test + cache_key_prefix: resources_test__ - # sync if need be - - name: Sync test resources - run: | - viash run \ - -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ - --input $s3_bucket \ - --delete - tree resources_test/ -L 3 - - - name: Build target dir + - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # build target dir - viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing + - uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'integration_build' + parallel: true - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -54,38 +43,58 @@ jobs: publish_dir: . publish_branch: integration_build - # store component locations + - id: ns_list_components + uses: viash-io/viash-actions/ns-list@v2 + with: + platform: docker + src: src + format: json + + - id: ns_list_workflows + uses: viash-io/viash-actions/ns-list@v2 + with: + src: workflows + format: json + - id: set_matrix run: | - component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') - echo "component_matrix=$component_json" >> $GITHUB_OUTPUT - workflow_json=$(viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') - echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT - outputs: - component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} - cachehash: ${{ steps.cachehash.outputs.cachehash }} + echo "components=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "dir": .info.config | capture("^(?.*\/)").dir + } + ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT + + echo "workflows=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "main_script": (.info.config | capture("^(?.*\/)").dir + "/" + .functionality.test_resources[].path), + "entry": .functionality.test_resources[].entrypoint + } + ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT # phase 2 - build_containers: - needs: list_components + build: + needs: list runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v1 - name: Build container - run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup build + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'integration_build' + setup: build + src: ${{ matrix.component.dir }} - name: Login to container registry uses: docker/login-action@v2 @@ -94,35 +103,41 @@ jobs: username: ${{ secrets.GTHB_USER }} password: ${{ secrets.GTHB_PAT }} - - name: Push containers - run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - viash ns build --config_mod ".functionality.version := 'integration_build'" -s "$SRC_DIR" --setup push + - name: Push container + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'integration_build' + platform: docker + src: ${{ matrix.component.dir }} + setup: push ################################### # phase 3 integration_test: - needs: [ build_containers, list_components ] + needs: [ build, list ] + if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.workflow_matrix) }} + component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v1 + - uses: nf-core/setup-nextflow@v1.2.0 # build target dir # use containers from integration_build branch, hopefully these are available - name: Build target dir - run: | - # build target dir - viash ns build --config_mod ".functionality.version := 'integration_build'" --parallel --setup donothing + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: ".functionality.version := 'integration_build'" + parallel: true # use cache - name: Cache resources data @@ -130,17 +145,15 @@ jobs: timeout-minutes: 5 with: path: resources_test - key: ${{ needs.list_components.outputs.cachehash }} + key: ${{ needs.list.outputs.cache_key }} - name: Run integration test timeout-minutes: 45 run: | # todo: replace with viash test command - config_dir=`dirname ${{ matrix.component.config }}` - script="$config_dir/${{ matrix.component.test_script }}" export NXF_VER=22.04.5 nextflow run . \ - -main-script "$script" \ - -entry ${{ matrix.component.entry }} \ + -main-script "${{ matrix.component.main_script }}" \ + -entry "${{ matrix.component.entry }}" \ -profile docker,mount_temp,no_publish \ -c workflows/utils/labels_ci.config diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 0729185ec5..a8e3758c04 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -7,60 +7,42 @@ on: jobs: # phase 1 list: - env: - s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest + outputs: + component_matrix: ${{ steps.set_matrix.outputs.matrix }} + cache_key: ${{ steps.cache.outputs.cache_key }} + steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v2 - # create cachehash key - - name: Create hash key - id: cachehash - run: | - AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT - - # initialize cache - - name: Cache resources data - uses: actions/cache@v3 - with: - path: resources_test - key: ${{ steps.cachehash.outputs.cachehash }} - restore-keys: resources_test_ + - uses: viash-io/viash-actions/setup@v2 - # sync if need be - - name: Sync test resources - run: | - viash run \ - -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ - --input $s3_bucket \ - --delete - tree resources_test/ -L 3 - - - name: Build target dir + - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # build target dir - viash ns build --config_mod ".functionality.version := 'main_build'" --parallel --setup donothing + - uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'main_build' + parallel: true - - name: Generate schemas + - name: Build nextflow schemas uses: viash-io/viash-actions/build-nextflow-schemas@v2 - with: - token: ${{ secrets.GTHB_PAT }} + with: + workflows: workflows components: src - workflows: src - - - name: Generate params - uses: viash-io/viash-actions/build-nextflow-params@v2 - with: token: ${{ secrets.GTHB_PAT }} + tools_version: 'main_build' + + - name: Build parameter files + uses: viash-io/viash-actions/build-nextflow-params@v2 + with: + workflows: workflows components: src - workflows: src + token: ${{ secrets.GTHB_PAT }} + tools_version: 'main_build' - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -73,6 +55,7 @@ jobs: uses: viash-io/viash-actions/ns-list@v2 with: platform: docker + src: src format: json - id: set_matrix @@ -80,15 +63,10 @@ jobs: echo "matrix=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), - "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT - outputs: - components_json: ${{ steps.set_matrix.outputs.matrix }} - cachehash: ${{ steps.cachehash.outputs.cachehash }} - # phase 2 build: needs: list @@ -98,7 +76,7 @@ jobs: strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list.outputs.components_json) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: - uses: actions/checkout@v3 @@ -109,9 +87,10 @@ jobs: uses: viash-io/viash-actions/ns-build@v2 with: config_mod: .functionality.version := 'main_build' - setup: build + platform: docker src: ${{ matrix.component.dir }} - + setup: build + - name: Login to container registry uses: docker/login-action@v2 with: @@ -123,6 +102,6 @@ jobs: uses: viash-io/viash-actions/ns-build@v2 with: config_mod: .functionality.version := 'main_build' - setup: push platform: docker - src: ${{ matrix.component.dir }} \ No newline at end of file + src: ${{ matrix.component.dir }} + setup: push \ No newline at end of file diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index cb1ed921eb..3e21b99144 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -9,72 +9,53 @@ on: jobs: # phase 1 - list_components: + list: env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest + + outputs: + component_matrix: ${{ steps.set_matrix.outputs.components }} + workflow_matrix: ${{ steps.set_matrix.outputs.workflows }} + cache_key: ${{ steps.cache.outputs.cache_key }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 - - - name: Fetch viash tools - uses: actions/checkout@v3 - with: - repository: "viash-io/viash_tools" - token: ${{ secrets.GTHB_PAT }} - ref: "main_build" - path: "../viash_tools" + - uses: viash-io/viash-actions/setup@v1 - # create cachehash key - - name: Create hash key - id: cachehash - run: | - AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT - - # initialize cache - - name: Cache resources data - uses: actions/cache@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + id: cache with: - path: resources_test - key: ${{ steps.cachehash.outputs.cachehash }} - restore-keys: resources_test_ + s3_bucket: $s3_bucket + dest_path: resources_test + cache_key_prefix: resources_test__ - # sync if need be - - name: Sync test resources - run: | - viash run \ - -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ - --input $s3_bucket \ - --delete - tree resources_test/ -L 3 - - - name: Build target dir + - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - # build target dir - viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing + - uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" + parallel: true - - name: Build nextflow schemas & params - run: | - viash ns list -s src -p nextflow --format json 2> /dev/null > /tmp/ns_list_src.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_src.json) - outputs_params=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_src.json) - outputs_schema=$(jq -r '[.[] | "target/nextflow/" + .functionality.namespace + "/" + .functionality.name + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_src.json) - ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" - - viash ns list -s workflows --format json 2> /dev/null > /tmp/ns_list_workflow.json - inputs=$(jq -r '[.[] | .info.config] | join(";")' /tmp/ns_list_workflow.json) - outputs_params=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_params.yaml"] | join(";")' /tmp/ns_list_workflow.json) - outputs_schema=$(jq -r '[.[] | .info.config | capture("^(?.*\/)").dir + "/nextflow_schema.json"] | join(";")' /tmp/ns_list_workflow.json) - ../viash_tools/target/docker/nextflow/generate_params/generate_params --input "$inputs" --output "$outputs_params" - ../viash_tools/target/docker/nextflow/generate_schema/generate_schema --input "$inputs" --output "$outputs_schema" + - name: Build nextflow schemas + uses: viash-io/viash-actions/build-nextflow-schemas@v2 + with: + workflows: workflows + components: src + token: ${{ secrets.GTHB_PAT }} + tools_version: 'main_build' + + - name: Build parameter files + uses: viash-io/viash-actions/build-nextflow-params@v2 + with: + workflows: workflows + components: src + token: ${{ secrets.GTHB_PAT }} + tools_version: 'main_build' - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 @@ -84,36 +65,59 @@ jobs: publish_branch: release full_commit_message: "Deploy for release ${{ github.event.inputs.version_tag }} from ${{ github.sha }}" - # store component locations + - id: ns_list_components + uses: viash-io/viash-actions/ns-list@v2 + with: + platform: docker + src: src + format: json + + - id: ns_list_workflows + uses: viash-io/viash-actions/ns-list@v2 + with: + src: workflows + format: json + - id: set_matrix run: | - component_json=$(viash ns list -p docker --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config } ]') - echo "component_matrix=$component_json" >> $GITHUB_OUTPUT - workflow_json=$(viash ns list -s workflows --format json | jq -c '[ .[] | { "name": .functionality.name, "config": .info.config, "test_script": .functionality.test_resources[].path, "entry": .functionality.test_resources[].entrypoint } ]') - echo "workflow_matrix=$workflow_json" >> $GITHUB_OUTPUT - outputs: - component_matrix: ${{ steps.set_matrix.outputs.component_matrix }} - workflow_matrix: ${{ steps.set_matrix.outputs.workflow_matrix }} - cachehash: ${{ steps.cachehash.outputs.cachehash }} + echo "components=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "dir": .info.config | capture("^(?.*\/)").dir + } + ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT + + echo "workflows=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "main_script": (.info.config | capture("^(?.*\/)").dir + "/" + .functionality.test_resources[].path), + "entry": .functionality.test_resources[].entrypoint + } + ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT # phase 2 - build_containers: - needs: list_components + build: + needs: list runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + + - uses: viash-io/viash-actions/setup@v1 + - name: Build container - run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup build + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := 'main_build' + platform: docker + src: ${{ matrix.component.dir }} + setup: build - name: Login to container registry uses: docker/login-action@v2 @@ -122,34 +126,41 @@ jobs: username: ${{ secrets.GTHB_USER }} password: ${{ secrets.GTHB_PAT }} - - name: Push containers - run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" -s "$SRC_DIR" --setup push + - name: Push container + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: .functionality.version := '${{ github.event.inputs.version_tag }}' + platform: docker + src: ${{ matrix.component.dir }} + setup: push ###################################3 # phase 3 integration_test: - needs: [ build_containers, list_components ] - if: "${{ needs.list_components.outputs.workflow_matrix != '[]' }}" + needs: [ build, list ] + if: "${{ needs.list.outputs.workflow_matrix != '[]' }}" runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.workflow_matrix) }} + component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + + - uses: viash-io/viash-actions/setup@v1 + + - uses: nf-core/setup-nextflow@v1.2.0 # build target dir # use containers from release branch, hopefully these are available - name: Build target dir - run: | - # build target dir - viash ns build --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" --parallel --setup donothing + uses: viash-io/viash-actions/ns-build@v2 + with: + config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" + parallel: true # use cache - name: Cache resources data @@ -157,17 +168,15 @@ jobs: timeout-minutes: 5 with: path: resources_test - key: ${{ needs.list_components.outputs.cachehash }} + key: ${{ needs.list.outputs.cache_key }} - name: Run integration test timeout-minutes: 45 run: | # todo: replace with viash test command - config_dir=`dirname ${{ matrix.component.config }}` - script="$config_dir/${{ matrix.component.test_script }}" export NXF_VER=22.04.5 nextflow run . \ - -main-script "$script" \ + -main-script "${{ matrix.component.main_script }}" \ -entry ${{ matrix.component.entry }} \ -profile docker,mount_temp,no_publish \ -c workflows/utils/labels_ci.config @@ -175,18 +184,19 @@ jobs: ###################################3 # phase 4 component_test: - needs: [ build_containers, list_components ] - + needs: [ build, list ] + if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }} runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.component_matrix) }} + component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + + - uses: viash-io/viash-actions/setup@v1 # use cache - name: Cache resources data @@ -194,13 +204,13 @@ jobs: timeout-minutes: 5 with: path: resources_test - key: ${{ needs.list_components.outputs.cachehash }} + key: ${{ needs.list.outputs.cache_key }} - name: Test component timeout-minutes: 30 run: | - SRC_DIR=`dirname ${{ matrix.component.config }}` - viash ns test --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ - -s "$SRC_DIR" \ + viash ns test \ + --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ + -s "${{ matrix.component.dir }}" \ --cpus 2 \ --memory "5gb" \ No newline at end of file diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 5e7a0032e7..99ca6ead85 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -24,103 +24,74 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.GTHB_PAT }} - # phase 1 - list_components: + list: needs: run_ci_check_job env: s3_bucket: s3://openproblems-data/resources_test/ runs-on: ubuntu-latest if: "needs.run_ci_check_job.outputs.run_ci == 'true'" + outputs: matrix: ${{ steps.set_matrix.outputs.matrix }} - cachehash: ${{ steps.cachehash.outputs.cachehash }} + cache_key: ${{ steps.cache.outputs.cache_key }} + steps: - uses: actions/checkout@v3 with: fetch-depth: 0 - - uses: viash-io/viash-actions/setup@v1.0.0 + - uses: viash-io/viash-actions/setup@v1 - # create cachehash key - - name: Create hash key - id: cachehash - run: | - AWS_EC2_METADATA_DISABLED=true aws s3 ls $s3_bucket --recursive --no-sign-request > bucket-contents.txt - echo "cachehash=resources_test__$( md5sum bucket-contents.txt | awk '{ print $1 }' )" >> $GITHUB_OUTPUT - - # initialize cache - - name: Cache resources data - uses: actions/cache@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + id: cache with: - path: resources_test - key: ${{ steps.cachehash.outputs.cachehash }} - restore-keys: resources_test_ - - # sync if need be - - name: Sync test resources - run: | - viash run \ - -p native \ - src/common/sync_test_resources/config.vsh.yaml -- \ - --input $s3_bucket \ - --delete - tree resources_test/ -L 3 + s3_bucket: $s3_bucket + dest_path: resources_test + cache_key_prefix: resources_test__ - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.4.1 + uses: tj-actions/changed-files@v35.5.0 with: separator: ";" diff_relative: true - # store component locations - - name: Set matrix to only run tests for components that had their config or resources changed. - id: set_matrix + - id: ns_list + uses: viash-io/viash-actions/ns-list@v2 + with: + platform: docker + format: json + + - id: ns_list_filtered + uses: viash-io/viash-actions/project/detect-changed-components@restructure_and_extend + with: + input_file: "${{ steps.ns_list.outputs.output_file }}" + + - id: set_matrix run: | - IFS=$';' read -a changed_files <<< "${{ steps.changed-files.outputs.all_changed_files }}" - echo "Changed files: "${changed_files[*]}"" - readarray -t components < <(viash ns list -p docker --format json | jq -c '[ .[] | - (.info.config | capture("^(?.*\/)").dir) as $dir | - { "name": .functionality.name, - "config": .info.config, - "resources": ([.info.config] + - ([.functionality.resources[].path?, - .functionality.test_resources[].path?] | - map($dir + .) - ) - ) - } - ][]') - declare -a result_array_matrix=() - for component in "${components[@]}"; do - readarray -t resources < <(jq -cr '.resources[]' <<< "$component") - for resource_rel_path in "${resources[@]}"; do - resource_project_path=$(realpath --relative-to="$GITHUB_WORKSPACE" "$resource_rel_path") - echo "Checking path $resource_project_path" - if [[ " ${changed_files[*]} " =~ " ${resource_project_path} " || "$GITHUB_REF" == "refs/heads/main" || "${{ contains(github.event.head_commit.message, 'ci force') }}" == "true" ]]; then - result_array_matrix+="$component" - break - fi - done - done - json=$(jq -cs '.' <<< "${result_array_matrix[*]}") - echo "matrix=$json" >> $GITHUB_OUTPUT + echo "matrix=$(jq -c '[ .[] | + { + "name": (.functionality.namespace + "/" + .functionality.name), + "dir": .info.config | capture("^(?.*\/)").dir + } + ]' ${{ steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT # phase 2 viash_test: - needs: list_components - if: ${{ needs.list_components.outputs.matrix != '[]' && needs.list_components.outputs.matrix != '' }} + needs: list + if: ${{ needs.list.outputs.matrix != '[]' && needs.list.outputs.matrix != '' }} runs-on: ubuntu-latest strategy: fail-fast: false matrix: - component: ${{ fromJson(needs.list_components.outputs.matrix) }} + component: ${{ fromJson(needs.list.outputs.matrix) }} steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1.0.0 + + - uses: viash-io/viash-actions/setup@v1 # use cache - name: Cache resources data @@ -128,12 +99,14 @@ jobs: timeout-minutes: 10 with: path: resources_test - key: ${{ needs.list_components.outputs.cachehash }} + key: ${{ needs.list.outputs.cache_key }} - name: Run test timeout-minutes: 30 run: | - viash test -p docker ${{ matrix.component.config }} \ - --cpus 2 \ - --memory "5gb" + viash ns test \ + --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ + -s "${{ matrix.component.dir }}" \ + --cpus 2 \ + --memory "5gb" From 0b2e29f28552ecd83a596b100b2737e972339cfa Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 3 Feb 2023 20:26:56 +0100 Subject: [PATCH 0720/1233] update actions Former-commit-id: 011e32d98c1bc773aba4e8a78d50b51ceb070d7c --- .github/workflows/integration-test.yml | 20 ++++++++--------- .github/workflows/main-build.yml | 20 ++++++++--------- .github/workflows/release-build.yml | 30 +++++++++++++------------- .github/workflows/viash-test.yml | 10 ++++----- 4 files changed, 40 insertions(+), 40 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index fd23c55152..acc4ed9bcc 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -17,9 +17,9 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 id: cache with: s3_bucket: $s3_bucket @@ -31,7 +31,7 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v2 + - uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'integration_build' parallel: true @@ -44,14 +44,14 @@ jobs: publish_branch: integration_build - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: platform: docker src: src format: json - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: src: workflows format: json @@ -87,10 +87,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - name: Build container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'integration_build' setup: build @@ -104,7 +104,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'integration_build' platform: docker @@ -127,14 +127,14 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - uses: nf-core/setup-nextflow@v1.2.0 # build target dir # use containers from integration_build branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: ".functionality.version := 'integration_build'" parallel: true diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index a8e3758c04..a583ccadcb 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -16,32 +16,32 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v2 + - uses: viash-io/viash-actions/setup@v3 - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v2 + - uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'main_build' parallel: true - name: Build nextflow schemas - uses: viash-io/viash-actions/build-nextflow-schemas@v2 + uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 with: workflows: workflows components: src - token: ${{ secrets.GTHB_PAT }} + viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Build parameter files - uses: viash-io/viash-actions/build-nextflow-params@v2 + uses: viash-io/viash-actions/pro/build-nextflow-params@v3 with: workflows: workflows components: src - token: ${{ secrets.GTHB_PAT }} + viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Deploy to target branch @@ -52,7 +52,7 @@ jobs: publish_branch: main_build - id: ns_list - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: platform: docker src: src @@ -81,10 +81,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v2 + - uses: viash-io/viash-actions/setup@v3 - name: Build container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -99,7 +99,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'main_build' platform: docker diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 3e21b99144..ca9a52ea91 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -22,9 +22,9 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 id: cache with: s3_bucket: $s3_bucket @@ -36,25 +36,25 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v2 + - uses: viash-io/viash-actions/ns-build@v3 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true - name: Build nextflow schemas - uses: viash-io/viash-actions/build-nextflow-schemas@v2 + uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 with: workflows: workflows components: src - token: ${{ secrets.GTHB_PAT }} + viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Build parameter files - uses: viash-io/viash-actions/build-nextflow-params@v2 + uses: viash-io/viash-actions/pro/build-nextflow-params@v3 with: workflows: workflows components: src - token: ${{ secrets.GTHB_PAT }} + viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' - name: Deploy to target branch @@ -66,14 +66,14 @@ jobs: full_commit_message: "Deploy for release ${{ github.event.inputs.version_tag }} from ${{ github.sha }}" - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: platform: docker src: src format: json - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: src: workflows format: json @@ -109,10 +109,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - name: Build container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -127,7 +127,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: .functionality.version := '${{ github.event.inputs.version_tag }}' platform: docker @@ -150,14 +150,14 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - uses: nf-core/setup-nextflow@v1.2.0 # build target dir # use containers from release branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v2 + uses: viash-io/viash-actions/ns-build@v3 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true @@ -196,7 +196,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 # use cache - name: Cache resources data diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 99ca6ead85..607d7ba931 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -41,9 +41,9 @@ jobs: with: fetch-depth: 0 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@restructure_and_extend + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 id: cache with: s3_bucket: $s3_bucket @@ -58,13 +58,13 @@ jobs: diff_relative: true - id: ns_list - uses: viash-io/viash-actions/ns-list@v2 + uses: viash-io/viash-actions/ns-list@v3 with: platform: docker format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@restructure_and_extend + uses: viash-io/viash-actions/project/detect-changed-components@v3 with: input_file: "${{ steps.ns_list.outputs.output_file }}" @@ -91,7 +91,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v1 + - uses: viash-io/viash-actions/setup@v3 # use cache - name: Cache resources data From 941a302647afd9b98f0679dfd8d5c2b8b476b4dc Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 10:49:44 +0100 Subject: [PATCH 0721/1233] openproblems workflows are in `src`. Former-commit-id: 451c79d23329a91cca1308357d427992edd20e52 --- .github/workflows/main-build.yml | 4 ++-- .github/workflows/release-build.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index a583ccadcb..76768ab031 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -31,7 +31,7 @@ jobs: - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -39,7 +39,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v3 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index ca9a52ea91..3283baa537 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -44,7 +44,7 @@ jobs: - name: Build nextflow schemas uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' @@ -52,7 +52,7 @@ jobs: - name: Build parameter files uses: viash-io/viash-actions/pro/build-nextflow-params@v3 with: - workflows: workflows + workflows: src components: src viash_pro_token: ${{ secrets.GTHB_PAT }} tools_version: 'main_build' From 9342db660cbec2fa8a0dce1e7db566028501ac96 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 10:53:06 +0100 Subject: [PATCH 0722/1233] temporarily disable failing task Former-commit-id: 2cff76af4b409409340b8f8daa022f4104d36230 --- .../datasets/sample_dataset/config.vsh.yaml | 1 + .../datasets/scprep_csv/config.vsh.yaml | 1 + .../methods/harmonic_alignment/config.vsh.yaml | 1 + src/multimodal_data_integration/methods/mnn/config.vsh.yaml | 1 + .../methods/sample_method/config.vsh.yaml | 1 + src/multimodal_data_integration/methods/scot/config.vsh.yaml | 1 + src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml | 1 + src/multimodal_data_integration/metrics/mse/config.vsh.yaml | 1 + 8 files changed, 8 insertions(+) diff --git a/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml b/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml index 9d40c2ed70..524dcf0ec4 100644 --- a/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml +++ b/src/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "sample_dataset" namespace: "multimodal_data_integration/datasets" version: "dev" diff --git a/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml b/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml index c82069822a..f46ea5bf83 100644 --- a/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml +++ b/src/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scprep_csv" namespace: "multimodal_data_integration/datasets" version: "dev" diff --git a/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml b/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml index 5be7dbb60a..6364f4cd35 100644 --- a/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "harmonic_alignment" namespace: "multimodal_data_integration/methods" version: "dev" diff --git a/src/multimodal_data_integration/methods/mnn/config.vsh.yaml b/src/multimodal_data_integration/methods/mnn/config.vsh.yaml index 7ca9ac5690..1c0fb93f4c 100644 --- a/src/multimodal_data_integration/methods/mnn/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/mnn/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "mnn" namespace: "multimodal_data_integration/methods" version: "dev" diff --git a/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml b/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml index 30baa7d77d..cf367085c0 100644 --- a/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/sample_method/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "sample_method" namespace: "multimodal_data_integration/methods" version: "dev" diff --git a/src/multimodal_data_integration/methods/scot/config.vsh.yaml b/src/multimodal_data_integration/methods/scot/config.vsh.yaml index 99e205bad5..0b07e276f8 100644 --- a/src/multimodal_data_integration/methods/scot/config.vsh.yaml +++ b/src/multimodal_data_integration/methods/scot/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "scot" namespace: "multimodal_data_integration/methods" version: "dev" diff --git a/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml b/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml index 17c614be2d..02f785a343 100644 --- a/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml +++ b/src/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "knn_auc" namespace: "multimodal_data_integration/metrics" version: "dev" diff --git a/src/multimodal_data_integration/metrics/mse/config.vsh.yaml b/src/multimodal_data_integration/metrics/mse/config.vsh.yaml index 3e754ce3e4..881170462d 100644 --- a/src/multimodal_data_integration/metrics/mse/config.vsh.yaml +++ b/src/multimodal_data_integration/metrics/mse/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: "mse" namespace: "multimodal_data_integration/metrics" version: "dev" From 830302e532333738c0f6e390e1b027b797d1019e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 10:56:36 +0100 Subject: [PATCH 0723/1233] fix test ci Former-commit-id: cd6f710f10608a2b929fe0076fea4228eb266bb1 --- .github/workflows/release-build.yml | 5 +++-- .github/workflows/viash-test.yml | 6 +++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 3283baa537..2083e614ce 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -83,6 +83,7 @@ jobs: echo "components=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), + "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT @@ -209,8 +210,8 @@ jobs: - name: Test component timeout-minutes: 30 run: | - viash ns test \ + viash test \ --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ - -s "${{ matrix.component.dir }}" \ + "${{ matrix.component.config }}" \ --cpus 2 \ --memory "5gb" \ No newline at end of file diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 607d7ba931..058011a8fe 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -73,7 +73,7 @@ jobs: echo "matrix=$(jq -c '[ .[] | { "name": (.functionality.namespace + "/" + .functionality.name), - "dir": .info.config | capture("^(?.*\/)").dir + "config": .info.config } ]' ${{ steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT @@ -104,9 +104,9 @@ jobs: - name: Run test timeout-minutes: 30 run: | - viash ns test \ + viash test \ --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ - -s "${{ matrix.component.dir }}" \ + "${{ matrix.component.config }}" \ --cpus 2 \ --memory "5gb" From ce6fb335804c1f2bc667224ec62be0ff4a7160f4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 11:03:13 +0100 Subject: [PATCH 0724/1233] try to fix ci Former-commit-id: b7f6ce801b139ff93f2b712803ed9ff2c89c5786 --- .github/workflows/viash-test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 058011a8fe..4d1a29bfb5 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -105,7 +105,6 @@ jobs: timeout-minutes: 30 run: | viash test \ - --config_mod ".functionality.version := '${{ github.event.inputs.version_tag }}'" \ "${{ matrix.component.config }}" \ --cpus 2 \ --memory "5gb" From 0a2179aab8d5e48d6113a7cc6775b12aa9d392d1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 11:54:36 +0100 Subject: [PATCH 0725/1233] pin r2u to specific sha Former-commit-id: ad1b0eb785317f7d8a4f67925d78a94a7a60a3a0 --- .../normalization/log_scran_pooling/config.vsh.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index ae6b648739..6ded643aa4 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -8,10 +8,12 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + # image: eddelbuettel/r2u:22.04 + # switched to specific tag, see https://github.com/eddelbuettel/r2u/issues/29 + image: eddelbuettel/r2u@sha256:1d3a92aab5abad11787cd6b6c9479960db9f4e56dcc7f837768da2e3f3c4dfe2 setup: - type: r - cran: [ Matrix, scran, BiocParallel, rlang, anndata, bit64 ] + cran: [ Matrix, rlang, anndata, bit64, scran, BiocParallel ] - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python From f691a6db7fecc11e3ba10a4c40554fa50616aab2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 6 Feb 2023 12:43:05 +0100 Subject: [PATCH 0726/1233] try setting viash temp Former-commit-id: 18fc1baf0f691e3b9ec6a9ee51a12041a7b4be63 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 4d1a29bfb5..e8dd80c20d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -104,7 +104,7 @@ jobs: - name: Run test timeout-minutes: 30 run: | - viash test \ + VIASH_TEMP=$RUNNER_TEMP/viash viash test \ "${{ matrix.component.config }}" \ --cpus 2 \ --memory "5gb" From eeddd27353189fbb7735f053b2917dd72f27060e Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Wed, 8 Feb 2023 10:11:08 +0100 Subject: [PATCH 0727/1233] add -p to mkdir command Former-commit-id: d51be194bf0d72f3d3da1c551c29dc850c00c4d2 --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index c1ce7fa2e2..a325e89f4f 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -55,7 +55,7 @@ modality alignment benchmark. Running the full pipeline is quite easy. **Step 0, fetch Viash and Nextflow** ``` bash -mkdir $HOME/bin +mkdir -p $HOME/bin curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin ``` From 0d05e44db58a5316fdfdb3363bf19f1d00172930 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 10:34:51 +0100 Subject: [PATCH 0728/1233] Move pipeline, add includes to config Co-authored-by: Kai Waldrant Co-authored-by: Michaela Mueller Former-commit-id: 633b8818151a7bc89bca6de590c172560fc27660 --- .../workflows/{test => run}/config.vsh.yaml | 0 .../workflows/{test => run}/main.nf | 0 .../workflows/run/nextflow.config | 14 +++++ .../workflows/{test => run}/preprocessing.tsv | 0 .../workflows/run/run_nextflow.sh | 28 ++++++++++ .../workflows/test/nextflow.config | 16 ------ .../workflows/test/run_nextflow.sh | 52 ------------------- 7 files changed, 42 insertions(+), 68 deletions(-) rename src/batch_integration/workflows/{test => run}/config.vsh.yaml (100%) rename src/batch_integration/workflows/{test => run}/main.nf (100%) create mode 100644 src/batch_integration/workflows/run/nextflow.config rename src/batch_integration/workflows/{test => run}/preprocessing.tsv (100%) create mode 100755 src/batch_integration/workflows/run/run_nextflow.sh delete mode 100644 src/batch_integration/workflows/test/nextflow.config delete mode 100755 src/batch_integration/workflows/test/run_nextflow.sh diff --git a/src/batch_integration/workflows/test/config.vsh.yaml b/src/batch_integration/workflows/run/config.vsh.yaml similarity index 100% rename from src/batch_integration/workflows/test/config.vsh.yaml rename to src/batch_integration/workflows/run/config.vsh.yaml diff --git a/src/batch_integration/workflows/test/main.nf b/src/batch_integration/workflows/run/main.nf similarity index 100% rename from src/batch_integration/workflows/test/main.nf rename to src/batch_integration/workflows/run/main.nf diff --git a/src/batch_integration/workflows/run/nextflow.config b/src/batch_integration/workflows/run/nextflow.config new file mode 100644 index 0000000000..1981a33306 --- /dev/null +++ b/src/batch_integration/workflows/run/nextflow.config @@ -0,0 +1,14 @@ +manifest { + name = 'batch_integration/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Batch integration' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") diff --git a/src/batch_integration/workflows/test/preprocessing.tsv b/src/batch_integration/workflows/run/preprocessing.tsv similarity index 100% rename from src/batch_integration/workflows/test/preprocessing.tsv rename to src/batch_integration/workflows/run/preprocessing.tsv diff --git a/src/batch_integration/workflows/run/run_nextflow.sh b/src/batch_integration/workflows/run/run_nextflow.sh new file mode 100755 index 0000000000..edc9fbefd4 --- /dev/null +++ b/src/batch_integration/workflows/run/run_nextflow.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -xe + +DATASET_DIR=resources_test/batch_integration/pancreas + +# run benchmark +export NXF_VER=22.04.5 + + # -profile docker \ +nextflow run . \ + -main-script src/batch_integration/workflows/run/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + -resume \ + --id pancreas \ + --input $DATASET_DIR/processed.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ diff --git a/src/batch_integration/workflows/test/nextflow.config b/src/batch_integration/workflows/test/nextflow.config deleted file mode 100644 index 3df04f176a..0000000000 --- a/src/batch_integration/workflows/test/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} - -// set default container & default labels -process { - container = 'nextflow/bash:latest' - - withLabel: highmem { memory = 10.Gb } - withLabel: highcpu { cpus = 5 } -} diff --git a/src/batch_integration/workflows/test/run_nextflow.sh b/src/batch_integration/workflows/test/run_nextflow.sh deleted file mode 100755 index 864aad59cb..0000000000 --- a/src/batch_integration/workflows/test/run_nextflow.sh +++ /dev/null @@ -1,52 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/viash_build -q 'batch_integration' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -set -xe - -RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/batch_integration/pancreas - -if [ ! -d "$DATASET_DIR" ]; then - mkdir -p "$DATASET_DIR" -fi - -# viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ -# --input $RAW_DATA \ -# --output $DATASET_DIR/processed.h5ad \ -# --label celltype \ -# --batch tech \ -# --hvgs 100 - -# choose a particular version of nextflow -# export NXF_VER=21.10.6 - -# bin/nextflow \ -# run . \ -# -main-script src/batch_integration/workflows/run/main.nf \ -# --publishDir output/batch_integration \ -# -resume \ -# -with-docker - - -# run benchmark -export NXF_VER=22.04.5 - - # -profile docker \ -nextflow \ - run . \ - -main-script src/batch_integration/workflows/test/main.nf \ - -with-docker \ - -resume \ - --id pancreas \ - --dataset_id pancreas \ - --input $DATASET_DIR/processed.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ From 8c8eb2a8621933d24507feee405b22239778af08 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 10:35:07 +0100 Subject: [PATCH 0729/1233] Simplify score boundary testing Former-commit-id: 0244b387d00751065bcbdf8b36af2eef100fae47 --- src/batch_integration/embedding/metrics/asw_batch/test.py | 3 +-- src/batch_integration/embedding/metrics/asw_label/test.py | 3 +-- .../embedding/metrics/cell_cycle_conservation/test.py | 3 +-- src/batch_integration/graph/metrics/ari/test.py | 3 +-- src/batch_integration/graph/metrics/ari/test_combat.py | 3 +-- src/batch_integration/graph/metrics/nmi/test.py | 3 +-- src/batch_integration/graph/metrics/nmi/test_combat.py | 3 +-- 7 files changed, 7 insertions(+), 14 deletions(-) diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py index e3534d13d8..316935b609 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ b/src/batch_integration/embedding/metrics/asw_batch/test.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.9698405638892912 +assert 0 <= score <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py index 5fdb7fd732..0d62d6a4c7 100644 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.4942782782018184 +assert 0 <= score <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py index e8867d0925..39e9bc8ee0 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -28,8 +28,7 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 +assert 0 <= score <= 1 -assert score == 0.932432887041937 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index eab8938e96..22473613b3 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.2450740201875055 +assert 0 <= score <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py index 21520b8e8b..e2f85697b6 100644 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.3416195872819286 +assert 0 <= score <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index 848b466a4e..a6ddfc3f72 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.3558236928210666 +assert 0 <= score <= 1 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py index a2edd89727..b515a887f7 100644 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -24,7 +24,6 @@ score = result.loc[0, 'value'] print(score) -assert 0 < score < 1 -assert score == 0.1909856215679946 +assert 0 <= score <= 1 print(">> All tests passed successfully") From c067d7586b2595ee1c76a34ef8728639384e30b1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 10:35:24 +0100 Subject: [PATCH 0730/1233] tests is replaced by test_resources Former-commit-id: e6c6f6ae01aea8442ac30bd174598b7b937c4404 --- src/batch_integration/graph/metrics/ari/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index 5977d10dbb..f9031aed9a 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: resources: - type: python_script path: script.py - tests: + test_resources: - type: python_script path: test.py - path: ../../../../../resources_test/batch_integration/graph/methods/bbknn.h5ad From 29b868cda05657ba7c58ca215ba53e973b460e15 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 11:03:41 +0100 Subject: [PATCH 0731/1233] move arguments to api files Former-commit-id: a05e4fff5f2021e1db982a974605f04a7b33f77a --- src/batch_integration/api/comp_method.yaml | 29 +++++++++++++++++++ src/batch_integration/api/comp_metric.yaml | 19 ++++++++++++ .../embedding/methods/combat/config.vsh.yaml | 28 ++---------------- .../embedding/methods/combat/script.py | 1 + .../metrics/asw_batch/config.vsh.yaml | 18 ++---------- .../embedding/metrics/asw_batch/script.py | 4 +-- .../embedding/metrics/asw_batch/test.py | 2 +- .../metrics/asw_label/config.vsh.yaml | 18 ++---------- .../embedding/metrics/asw_label/script.py | 4 +-- .../embedding/metrics/asw_label/test.py | 2 +- .../cell_cycle_conservation/config.vsh.yaml | 17 ++--------- .../metrics/cell_cycle_conservation/script.py | 4 +-- .../metrics/cell_cycle_conservation/test.py | 2 +- .../embedding/metrics/pcr/config.vsh.yaml | 18 ++---------- .../embedding/metrics/pcr/script.py | 4 +-- .../embedding/metrics/pcr/test.py | 2 +- .../graph/methods/bbknn/config.vsh.yaml | 29 ++----------------- .../graph/methods/bbknn/script.py | 1 + .../graph/methods/combat/config.vsh.yaml | 28 ++---------------- .../graph/methods/combat/script.py | 1 + .../methods/scanorama_embed/config.vsh.yaml | 28 ++---------------- .../graph/methods/scanorama_embed/script.py | 1 + .../methods/scanorama_feature/config.vsh.yaml | 28 ++---------------- .../graph/methods/scanorama_feature/script.py | 1 + .../graph/methods/scvi/config.vsh.yaml | 28 ++---------------- .../graph/methods/scvi/script.py | 1 + .../graph/metrics/ari/config.vsh.yaml | 18 ++---------- .../graph/metrics/ari/script.py | 4 +-- .../graph/metrics/ari/test.py | 2 +- .../graph/metrics/ari/test_combat.py | 2 +- .../graph/metrics/nmi/config.vsh.yaml | 18 ++---------- .../graph/metrics/nmi/script.py | 4 +-- .../graph/metrics/nmi/test.py | 2 +- .../graph/metrics/nmi/test_combat.py | 2 +- src/batch_integration/workflows/run/main.nf | 2 +- 35 files changed, 99 insertions(+), 273 deletions(-) create mode 100644 src/batch_integration/api/comp_method.yaml create mode 100644 src/batch_integration/api/comp_metric.yaml diff --git a/src/batch_integration/api/comp_method.yaml b/src/batch_integration/api/comp_method.yaml new file mode 100644 index 0000000000..e7b682b541 --- /dev/null +++ b/src/batch_integration/api/comp_method.yaml @@ -0,0 +1,29 @@ +functionality: + arguments: + - name: --input + type: file + description: Unintegrated AnnData HDF5 file. + required: true + example: input.h5ad + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Integrated AnnData HDF5 file. + required: true + example: "output.h5ad" + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + - name: --scaling + type: boolean + description: Whether to scale the data or not + default: false + required: false + - name: --debug + type: boolean + description: Verbose output for debugging + default: false + required: false \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric.yaml b/src/batch_integration/api/comp_metric.yaml new file mode 100644 index 0000000000..40f9011ceb --- /dev/null +++ b/src/batch_integration/api/comp_metric.yaml @@ -0,0 +1,19 @@ +functionality: + arguments: + - name: --input + type: file + description: Integrated AnnData HDF5 file. + required: true + example: input.h5ad + - name: --output + alternatives: [ -o ] + type: file + direction: output + description: Output tsv file of the metric + required: true + example: output.tsv + - name: --debug + type: boolean + description: Verbose output for debugging + default: False + required: false \ No newline at end of file diff --git a/src/batch_integration/embedding/methods/combat/config.vsh.yaml b/src/batch_integration/embedding/methods/combat/config.vsh.yaml index 403a113571..0262434a74 100644 --- a/src/batch_integration/embedding/methods/combat/config.vsh.yaml +++ b/src/batch_integration/embedding/methods/combat/config.vsh.yaml @@ -1,3 +1,5 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: combat namespace: batch_integration/embedding/methods @@ -7,32 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: true - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/embedding/methods/combat/script.py b/src/batch_integration/embedding/methods/combat/script.py index 67fa809148..117a26bbe5 100644 --- a/src/batch_integration/embedding/methods/combat/script.py +++ b/src/batch_integration/embedding/methods/combat/script.py @@ -48,6 +48,7 @@ ) print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index 2658b10e91..9f803d4adc 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: asw_batch namespace: batch_integration/embedding/metrics @@ -7,22 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/embedding/metrics/asw_batch/script.py b/src/batch_integration/embedding/metrics/asw_batch/script.py index b798354f01..ba871f7a12 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/script.py +++ b/src/batch_integration/embedding/metrics/asw_batch/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/embedding/resources/asw_batch_pancreas_mnn.tsv', 'debug': True } @@ -18,7 +18,7 @@ METRIC = 'asw_batch' EMBEDDING = 'X_emb' -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] print('Read adata') diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py index 316935b609..02fa724c3c 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ b/src/batch_integration/embedding/metrics/asw_batch/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml index 8be1d3037e..43dd8f84bc 100644 --- a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: asw_label namespace: batch_integration/embedding/metrics @@ -7,22 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/embedding/metrics/asw_label/script.py index cffd0a9eb0..397bb174ba 100644 --- a/src/batch_integration/embedding/metrics/asw_label/script.py +++ b/src/batch_integration/embedding/metrics/asw_label/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/embedding/resources/asw_label_pancreas_mnn.tsv', 'debug': True } @@ -17,7 +17,7 @@ OUTPUT_TYPE = 'embedding' METRIC = 'asw_label' -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] print('Read adata') diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py index 0d62d6a4c7..faba5a1139 100644 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ b/src/batch_integration/embedding/metrics/asw_label/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml index 5d1866ddc0..edda16b343 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: cell_cycle_conservation namespace: batch_integration/embedding/metrics @@ -8,25 +10,10 @@ functionality: roles: [ maintainer, author ] props: { github: mumichae } arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] - required: true - name: --organism type: string description: Name of organism to compute cell cycle scores on required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py index 764264fed4..2431c04171 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', 'organism': 'human', 'debug': True @@ -19,7 +19,7 @@ OUTPUT_TYPE = 'embedding' METRIC = 'cell_cycle_conservation' -adata_file = par['adata'] +adata_file = par['input'] organism = par['organism'] output = par['output'] diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py index 39e9bc8ee0..af491ce150 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py @@ -14,7 +14,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--organism", "human", "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml index 43ea41f5d0..a4efdfe1eb 100644 --- a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: pcr namespace: batch_integration/embedding/metrics @@ -7,22 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with embedding in adata.obsm['X_emb'] - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/embedding/metrics/pcr/script.py b/src/batch_integration/embedding/metrics/pcr/script.py index 22e6521ea6..b975302cf3 100644 --- a/src/batch_integration/embedding/metrics/pcr/script.py +++ b/src/batch_integration/embedding/metrics/pcr/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', 'debug': True } @@ -17,7 +17,7 @@ OUTPUT_TYPE = 'embedding' METRIC = 'pcr' -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] print('Read adata') diff --git a/src/batch_integration/embedding/metrics/pcr/test.py b/src/batch_integration/embedding/metrics/pcr/test.py index 4fc0c5a890..0fc00d70b7 100644 --- a/src/batch_integration/embedding/metrics/pcr/test.py +++ b/src/batch_integration/embedding/metrics/pcr/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index b2f3a55122..01749c049d 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -1,38 +1,13 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: bbknn namespace: batch_integration/graph/methods - version: dev description: Run BBKNN on adata object authors: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 90c2aea599..7ff650afce 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -38,6 +38,7 @@ adata = bbknn(adata, batch='batch') print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml index ef2411e3f2..416520a6a6 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -1,3 +1,5 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: combat namespace: batch_integration/graph/methods @@ -7,32 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: true - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index 161b7df9a2..18abf18f82 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -49,6 +49,7 @@ sc.pp.neighbors(adata, use_rep='X_emb') print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml index 2ce9abd78f..38c0c62404 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -1,3 +1,5 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: scanorama_embed namespace: batch_integration/graph/methods @@ -7,32 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/graph/methods/scanorama_embed/script.py index f477fa1f8b..e996893608 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/script.py +++ b/src/batch_integration/graph/methods/scanorama_embed/script.py @@ -42,6 +42,7 @@ sc.pp.neighbors(adata, use_rep='X_emb') print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index f17b2ebe54..25a071db8f 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -1,3 +1,5 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: scanorama_feature namespace: batch_integration/graph/methods @@ -7,32 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index 5dd5396c98..fbf5b1962b 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -48,6 +48,7 @@ sc.pp.neighbors(adata, use_rep='X_pca') print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml index 37f0c89f7d..9b067e801d 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -1,3 +1,5 @@ +# use method api spec +__merge__: ../../../api/comp_method.yaml functionality: name: scvi namespace: batch_integration/graph/methods @@ -7,32 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Anndata HDF5 file of the integrated graph in adata.obsp['connectivities'] - required: true - - name: --input - type: file - description: Unintegrated anndata HDF5 file - required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/graph/methods/scvi/script.py index f5485db850..3e7915a9af 100644 --- a/src/batch_integration/graph/methods/scvi/script.py +++ b/src/batch_integration/graph/methods/scvi/script.py @@ -41,6 +41,7 @@ sc.pp.neighbors(adata, use_rep='X_emb') print('Save HDF5') +adata.uns['method_id'] = meta['functionality_name'] adata.uns['hvg'] = hvg adata.uns['scaled'] = scaling diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index f9031aed9a..f7e0f48e02 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: ari namespace: batch_integration/graph/metrics @@ -7,22 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with graph in adata.obsp['connectivities'] - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/metrics/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py index 94e47c34d1..8679e960a7 100644 --- a/src/batch_integration/graph/metrics/ari/script.py +++ b/src/batch_integration/graph/metrics/ari/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/graph/resources/ari_pancreas_mnn.tsv', 'debug': True } @@ -18,7 +18,7 @@ OUTPUT_TYPE = 'graph' METRIC = 'ari' -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] print('Read adata') diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index 22473613b3..4398ac8254 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'bbknn.h5ad', + "--input", 'bbknn.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py index e2f85697b6..6fc4bebbed 100644 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ b/src/batch_integration/graph/metrics/ari/test_combat.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index 663bda0714..340a69dbaa 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -1,3 +1,5 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml functionality: name: nmi namespace: batch_integration/graph/metrics @@ -7,22 +9,6 @@ functionality: - name: Michaela Mueller roles: [ maintainer, author ] props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output tsv file of the metric - required: true - - name: --adata - type: file - description: Anndata HDF5 file with graph in adata.obsp['connectivities'] - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false resources: - type: python_script path: script.py diff --git a/src/batch_integration/graph/metrics/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py index 12ae4b6b3a..19653f58ea 100644 --- a/src/batch_integration/graph/metrics/nmi/script.py +++ b/src/batch_integration/graph/metrics/nmi/script.py @@ -1,6 +1,6 @@ ## VIASH START par = { - 'adata': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', + 'input': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/graph/resources/nmi_pancreas_mnn.tsv', 'debug': True } @@ -18,7 +18,7 @@ OUTPUT_TYPE = 'graph' METRIC = 'nmi' -adata_file = par['adata'] +adata_file = par['input'] output = par['output'] print('Read adata') diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index a6ddfc3f72..bc13c152d5 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'bbknn.h5ad', + "--input", 'bbknn.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py index b515a887f7..f925918e2d 100644 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ b/src/batch_integration/graph/metrics/nmi/test_combat.py @@ -11,7 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'combat.h5ad', + "--input", 'combat.h5ad', "--output", metric_file ]).decode("utf-8") diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index ad7cce333b..e03c396010 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -60,7 +60,7 @@ workflow run_wf { // derive unique ids from output filenames def newId = file.getName().replaceAll(".output.*", "") // combine prediction with solution - def newData = [ adata: file ] + def newData = [ input: file ] [ newId, newData, passthrough ] } From d6df73beaec7232c40e6f87a23262d837c6726e5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 22:15:52 +0100 Subject: [PATCH 0732/1233] Add knn component Co-authored-by: Kai Waldrant Former-commit-id: 706f7081c0c1d5001f100625f140181d49197c47 --- src/datasets/api/anndata_dataset.yaml | 16 ++++- src/datasets/api/anndata_hvg.yaml | 63 +++++++++++++++++++ src/datasets/api/anndata_pca.yaml | 2 +- src/datasets/api/comp_processor_hvg.yaml | 4 +- src/datasets/api/comp_processor_knn.yaml | 22 +++++++ src/datasets/api/comp_processor_pca.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 4 -- src/datasets/processors/hvg/script.py | 2 +- src/datasets/processors/knn/config.vsh.yaml | 18 ++++++ src/datasets/processors/knn/script.py | 32 ++++++++++ .../resource_test_scripts/pancreas.sh | 7 ++- .../workflows/process_openproblems_v1/main.nf | 4 +- 12 files changed, 163 insertions(+), 13 deletions(-) create mode 100644 src/datasets/api/anndata_hvg.yaml create mode 100644 src/datasets/api/comp_processor_knn.yaml create mode 100644 src/datasets/processors/knn/config.vsh.yaml create mode 100644 src/datasets/processors/knn/script.py diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index 9a65630b80..8b6d47c825 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -1,8 +1,8 @@ type: file -description: "A normalised data with a PCA embedding and HVG selection" +description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" example: "dataset.h5ad" info: - label: "Dataset+PCA+HVG" + label: "Dataset+PCA+HVG+kNN" slots: layers: - type: integer @@ -43,6 +43,15 @@ info: name: X_pca description: The resulting PCA embedding. required: true + obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true varm: - type: double name: pca_loadings @@ -61,3 +70,6 @@ info: name: pca_variance description: The PCA variance objects. required: true + - type: object + name: knn + description: Neighbors data. diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_hvg.yaml new file mode 100644 index 0000000000..e770e877fd --- /dev/null +++ b/src/datasets/api/anndata_hvg.yaml @@ -0,0 +1,63 @@ +type: file +description: "A normalised dataset with a PCA embedding and HVG selection" +example: "dataset.h5ad" +info: + label: "Dataset+PCA+HVG" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalised expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: double + name: pca_variance + description: The PCA variance objects. + required: true diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/anndata_pca.yaml index fd3b19d250..41fdc680e4 100644 --- a/src/datasets/api/anndata_pca.yaml +++ b/src/datasets/api/anndata_pca.yaml @@ -1,5 +1,5 @@ type: file -description: "A normalised data with a PCA embedding" +description: "A normalised dataset with a PCA embedding" example: "dataset.h5ad" info: label: "Dataset+PCA" diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index fd0a49ecfc..db7ff6e3e6 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -5,10 +5,10 @@ functionality: - name: "--layer_input" type: string default: "normalized" - description: Which layer to use as input for the PCA. + description: Which layer to use as input. - name: "--output" direction: output - __merge__: anndata_dataset.yaml + __merge__: anndata_hvg.yaml - name: "--var_hvg" type: string default: "hvg" diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml new file mode 100644 index 0000000000..b8c7323711 --- /dev/null +++ b/src/datasets/api/comp_processor_knn.yaml @@ -0,0 +1,22 @@ +functionality: + arguments: + - name: "--input" + __merge__: anndata_hvg.yaml + - name: "--layer_input" + type: string + default: "normalized" + description: Which layer to use as input. + - name: "--output" + direction: output + __merge__: anndata_dataset.yaml + - name: "--key_added" + type: string + default: "knn" + description: | + the neighbors data is added to `.uns[key_added]`, + distances are stored in `.obsp[key_added+'_distances'] and + connectivities in `.obsp[key_added+'_connectivities']`. + - name: "--num_neighbors" + type: integer + default: 15 + description: "The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation." \ No newline at end of file diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index d5f6e8d95c..efc9202722 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -5,7 +5,7 @@ functionality: - name: "--layer_input" type: string default: "normalized" - description: Which layer to use as input for the PCA. + description: Which layer to use as input. - name: "--output" direction: output __merge__: anndata_pca.yaml diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index ce49676631..500d33f5fa 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -6,10 +6,6 @@ functionality: resources: - type: python_script path: script.py - # test_resources: - # - type: python_script - # path: test_script.py - # - path: "../../../resources_test/common/pancreas" platforms: - type: docker image: "python:3.8" diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index ac8e757dc3..1163a158db 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -13,7 +13,7 @@ ### VIASH END print(">> Load data") -adata = sc.read(par['input']) +adata = sc.read_h5ad(par['input']) print(">> Look for layer") layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml new file mode 100644 index 0000000000..7b7743df17 --- /dev/null +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -0,0 +1,18 @@ +__merge__: ../../api/comp_processor_knn.yaml +functionality: + name: "knn" + namespace: "datasets/processors" + description: "Compute KNN" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: "python:3.8" + setup: + - type: python + packages: + - scanpy + - "anndata>=0.8" + - pyyaml + - type: nextflow diff --git a/src/datasets/processors/knn/script.py b/src/datasets/processors/knn/script.py new file mode 100644 index 0000000000..d2f2f7f52b --- /dev/null +++ b/src/datasets/processors/knn/script.py @@ -0,0 +1,32 @@ + +import scanpy as sc + +### VIASH START +par = { + 'input': 'work/ca/0751ff85df6f9478cb7bda5a705cad/zebrafish.sqrt_cpm.pca.output.h5ad', + 'layer_input': 'normalized', + 'output': 'dataset.h5ad', + 'key_added': 'knn', + 'n_neighbors': 15 +} +### VIASH END + +print(">> Load data") +adata = sc.read(par['input']) + +print(">> Look for layer") +adata.X = adata.layers[par['layer_input']] + +print(">> Run kNN") +sc.pp.neighbors( + adata, + use_rep='X_pca', + key_added=par['key_added'], + n_neighbors=par['num_neighbors'] +) + +del adata.X + +print(">> Writing data") +adata.write_h5ad(par['output']) + diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index a1d440e858..81677a13bd 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -46,9 +46,14 @@ viash run src/datasets/processors/pca/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset1.h5ad \ --output $DATASET_DIR/temp_dataset2.h5ad -# run log cpm normalisation +# run hvg viash run src/datasets/processors/hvg/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset2.h5ad \ + --output $DATASET_DIR/temp_dataset3.h5ad + +# run knn +viash run src/datasets/processors/knn/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_dataset3.h5ad \ --output $DATASET_DIR/dataset.h5ad rm -r $DATASET_DIR/temp_* \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 08d237a237..5a2bd14b24 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -9,6 +9,7 @@ include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_ include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" include { pca } from "$targetDir/datasets/processors/pca/main.nf" include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" +include { knn } from "$targetDir/datasets/processors/knn/main.nf" include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" @@ -51,9 +52,10 @@ workflow run_wf { } | pca + | hvg | getWorkflowArguments(key: "output") - | hvg.run( + | knn.run( auto: [ publish: true ] ) From 2ff674934cbd1d4801a1d2a9b4b24d7f545ef298 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 8 Feb 2023 22:16:52 +0100 Subject: [PATCH 0733/1233] initial changes for batch integration refactoring Co-authored-by: Kai Waldrant Former-commit-id: 652a9a529064c57a1bf57c627206ee1d8f5824e1 --- .../api/anndata_dataset.yaml | 75 +++++++++++++ .../api/anndata_integrated_embedding.yaml | 13 +++ .../api/anndata_integrated_graph.yaml | 16 +++ .../api/anndata_solution.yaml | 52 +++++++++ .../api/anndata_unintegrated.yaml | 43 ++++++++ src/batch_integration/api/authors.yaml | 14 +++ src/batch_integration/api/comp_method.yaml | 29 ----- .../api/comp_method_embedding.yaml | 69 ++++++++++++ .../api/comp_method_graph.yaml | 57 ++++++++++ src/batch_integration/api/comp_metric.yaml | 82 +++++++++++++- .../api/comp_split_dataset.yaml | 64 +++++++++++ src/batch_integration/changes.md | 24 ++++ src/batch_integration/datasets/README.md | 6 +- .../datasets/preprocessing/config.vsh.yaml | 50 --------- .../datasets/preprocessing/run_example.sh | 12 -- .../datasets/preprocessing/script.py | 69 ------------ .../datasets/preprocessing/test.py | 45 -------- .../datasets/subsample/config.vsh.yaml | 46 -------- .../datasets/subsample/run_example.sh | 11 -- .../datasets/subsample/script.py | 55 --------- .../datasets/subsample/test.py | 27 ----- .../subsample/utils/g2m_genes_tirosh_hm.txt | 54 --------- .../subsample/utils/s_genes_tirosh_hm.txt | 43 -------- .../datasets/utils/_hvg_batch.py | 15 --- .../datasets/utils/_log_scran_pooling.py | 22 ---- .../embedding/methods/combat/config.vsh.yaml | 12 +- .../embedding/methods/combat/script.py | 56 ++++++---- .../embedding/methods/combat/test.py | 86 ++++++++------- .../metrics/asw_batch/config.vsh.yaml | 15 +-- .../embedding/metrics/asw_batch/script.py | 60 +++++----- .../embedding/metrics/asw_batch/test.py | 29 ----- .../metrics/asw_label/config.vsh.yaml | 12 +- .../embedding/metrics/asw_label/script.py | 60 ++++++---- .../embedding/metrics/asw_label/test.py | 29 ----- .../cell_cycle_conservation/config.vsh.yaml | 12 +- .../metrics/cell_cycle_conservation/script.py | 9 +- .../metrics/cell_cycle_conservation/test.py | 34 ------ .../embedding/metrics/pcr/config.vsh.yaml | 12 +- .../embedding/metrics/pcr/script.py | 9 +- .../embedding/metrics/pcr/test.py | 29 ----- src/batch_integration/graph/README.md | 6 +- .../graph/methods/bbknn/config.vsh.yaml | 26 ++--- .../graph/methods/bbknn/run_example.sh | 12 -- .../graph/methods/bbknn/script.py | 56 ++++------ .../graph/methods/bbknn/test.py | 46 -------- .../graph/methods/bbknn/test_scaled_hvg.py | 51 --------- .../graph/methods/combat/config.vsh.yaml | 27 +++-- .../graph/methods/combat/run_example.sh | 14 --- .../graph/methods/combat/script.py | 58 ++++------ .../graph/methods/combat/test.py | 50 --------- .../graph/methods/params.tsv | 10 -- .../methods/scanorama_embed/config.vsh.yaml | 26 +++-- .../methods/scanorama_embed/run_example.sh | 12 -- .../graph/methods/scanorama_embed/script.py | 56 ++++------ .../graph/methods/scanorama_embed/test.py | 46 -------- .../methods/scanorama_feature/config.vsh.yaml | 28 ++--- .../methods/scanorama_feature/run_example.sh | 12 -- .../graph/methods/scanorama_feature/script.py | 59 ++++------ .../graph/methods/scanorama_feature/test.py | 46 -------- .../graph/methods/scvi/config.vsh.yaml | 28 ++--- .../graph/methods/scvi/run_example.sh | 12 -- .../graph/methods/scvi/script.py | 54 ++++----- .../graph/methods/scvi/test.py | 46 -------- .../graph/metrics/ari/config.vsh.yaml | 25 ----- .../graph/metrics/ari/script.py | 45 -------- .../graph/metrics/ari/test.py | 29 ----- .../graph/metrics/ari/test_combat.py | 29 ----- .../clustering_overlap/config.vsh.yaml | 51 +++++++++ .../metrics/clustering_overlap/script.py | 49 +++++++++ .../graph/metrics/nmi/config.vsh.yaml | 25 ----- .../graph/metrics/nmi/script.py | 45 -------- .../graph/metrics/nmi/test.py | 29 ----- .../graph/metrics/nmi/test_combat.py | 29 ----- src/batch_integration/library.bib | 23 ++++ .../resources_test_scripts/pancreas.sh | 13 +-- .../split_dataset/config.vsh.yaml | 33 ++++++ src/batch_integration/split_dataset/script.py | 104 ++++++++++++++++++ src/batch_integration/split_dataset/test.py | 51 +++++++++ src/batch_integration/workflows/run/main.nf | 15 ++- 79 files changed, 1189 insertions(+), 1644 deletions(-) create mode 100644 src/batch_integration/api/anndata_dataset.yaml create mode 100644 src/batch_integration/api/anndata_integrated_embedding.yaml create mode 100644 src/batch_integration/api/anndata_integrated_graph.yaml create mode 100644 src/batch_integration/api/anndata_solution.yaml create mode 100644 src/batch_integration/api/anndata_unintegrated.yaml create mode 100644 src/batch_integration/api/authors.yaml delete mode 100644 src/batch_integration/api/comp_method.yaml create mode 100644 src/batch_integration/api/comp_method_embedding.yaml create mode 100644 src/batch_integration/api/comp_method_graph.yaml create mode 100644 src/batch_integration/api/comp_split_dataset.yaml create mode 100644 src/batch_integration/changes.md delete mode 100644 src/batch_integration/datasets/preprocessing/config.vsh.yaml delete mode 100644 src/batch_integration/datasets/preprocessing/run_example.sh delete mode 100644 src/batch_integration/datasets/preprocessing/script.py delete mode 100644 src/batch_integration/datasets/preprocessing/test.py delete mode 100644 src/batch_integration/datasets/subsample/config.vsh.yaml delete mode 100644 src/batch_integration/datasets/subsample/run_example.sh delete mode 100644 src/batch_integration/datasets/subsample/script.py delete mode 100644 src/batch_integration/datasets/subsample/test.py delete mode 100644 src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt delete mode 100644 src/batch_integration/datasets/subsample/utils/s_genes_tirosh_hm.txt delete mode 100644 src/batch_integration/datasets/utils/_hvg_batch.py delete mode 100644 src/batch_integration/datasets/utils/_log_scran_pooling.py delete mode 100644 src/batch_integration/embedding/metrics/asw_batch/test.py delete mode 100644 src/batch_integration/embedding/metrics/asw_label/test.py delete mode 100644 src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py delete mode 100644 src/batch_integration/embedding/metrics/pcr/test.py delete mode 100644 src/batch_integration/graph/methods/bbknn/run_example.sh delete mode 100644 src/batch_integration/graph/methods/bbknn/test.py delete mode 100644 src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py delete mode 100644 src/batch_integration/graph/methods/combat/run_example.sh delete mode 100644 src/batch_integration/graph/methods/combat/test.py delete mode 100644 src/batch_integration/graph/methods/params.tsv delete mode 100644 src/batch_integration/graph/methods/scanorama_embed/run_example.sh delete mode 100644 src/batch_integration/graph/methods/scanorama_embed/test.py delete mode 100644 src/batch_integration/graph/methods/scanorama_feature/run_example.sh delete mode 100644 src/batch_integration/graph/methods/scanorama_feature/test.py delete mode 100644 src/batch_integration/graph/methods/scvi/run_example.sh delete mode 100644 src/batch_integration/graph/methods/scvi/test.py delete mode 100644 src/batch_integration/graph/metrics/ari/config.vsh.yaml delete mode 100644 src/batch_integration/graph/metrics/ari/script.py delete mode 100644 src/batch_integration/graph/metrics/ari/test.py delete mode 100644 src/batch_integration/graph/metrics/ari/test_combat.py create mode 100644 src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml create mode 100644 src/batch_integration/graph/metrics/clustering_overlap/script.py delete mode 100644 src/batch_integration/graph/metrics/nmi/config.vsh.yaml delete mode 100644 src/batch_integration/graph/metrics/nmi/script.py delete mode 100644 src/batch_integration/graph/metrics/nmi/test.py delete mode 100644 src/batch_integration/graph/metrics/nmi/test_combat.py create mode 100644 src/batch_integration/library.bib create mode 100644 src/batch_integration/split_dataset/config.vsh.yaml create mode 100644 src/batch_integration/split_dataset/script.py create mode 100644 src/batch_integration/split_dataset/test.py diff --git a/src/batch_integration/api/anndata_dataset.yaml b/src/batch_integration/api/anndata_dataset.yaml new file mode 100644 index 0000000000..8b6d47c825 --- /dev/null +++ b/src/batch_integration/api/anndata_dataset.yaml @@ -0,0 +1,75 @@ +type: file +description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" +example: "dataset.h5ad" +info: + label: "Dataset+PCA+HVG+kNN" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalised expression values + obs: + - type: string + name: celltype + description: Cell type information + required: false + - type: string + name: batch + description: Batch information + required: false + - type: string + name: tissue + description: Tissue information + required: false + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true + varm: + - type: double + name: pca_loadings + description: The PCA loadings matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: double + name: pca_variance + description: The PCA variance objects. + required: true + - type: object + name: knn + description: Neighbors data. diff --git a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/batch_integration/api/anndata_integrated_embedding.yaml new file mode 100644 index 0000000000..0abb11e8b4 --- /dev/null +++ b/src/batch_integration/api/anndata_integrated_embedding.yaml @@ -0,0 +1,13 @@ +__merge__: "anndata_unintegrated.yaml" +type: file +description: Integrated AnnData HDF5 file. +example: input.h5ad +info: + short_description: "Integrated embedding" + slots: + obsm: + - type: double + name: X_emb + description: integration embedding prediction + required: true + diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml new file mode 100644 index 0000000000..5263417de8 --- /dev/null +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -0,0 +1,16 @@ +__merge__: "anndata_unintegrated.yaml" +type: file +description: Integrated AnnData HDF5 file. +example: input.h5ad +info: + short_description: "Integrated Graph" + slots: + obsp: + - type: double + name: integration_distances + description: Neighbors distance matrix. + required: true + - type: double + name: integration_connectivities + description: Neighbors connectivities matrix. + required: true diff --git a/src/batch_integration/api/anndata_solution.yaml b/src/batch_integration/api/anndata_solution.yaml new file mode 100644 index 0000000000..4914212565 --- /dev/null +++ b/src/batch_integration/api/anndata_solution.yaml @@ -0,0 +1,52 @@ +type: file +description: Unintegrated AnnData HDF5 file. +example: input.h5ad +info: + short_description: "Unintegrated" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: string + name: label + description: label information + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/batch_integration/api/anndata_unintegrated.yaml b/src/batch_integration/api/anndata_unintegrated.yaml new file mode 100644 index 0000000000..2ed8eadb87 --- /dev/null +++ b/src/batch_integration/api/anndata_unintegrated.yaml @@ -0,0 +1,43 @@ +type: file +description: Unintegrated AnnData HDF5 file. +example: input.h5ad +info: + short_description: "Unintegrated" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: string + name: label + description: label information + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/batch_integration/api/authors.yaml b/src/batch_integration/api/authors.yaml new file mode 100644 index 0000000000..1b36fcea59 --- /dev/null +++ b/src/batch_integration/api/authors.yaml @@ -0,0 +1,14 @@ +functionality: + authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + - name: Kai Waldrant + roles: [ contributor ] + props: { github: KaiWaldrant } + - name: Robrecht Cannoodt + roles: [ contributor ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + - name: Daniel Strobl + roles: [ author ] + props: { github: danielStrobl } diff --git a/src/batch_integration/api/comp_method.yaml b/src/batch_integration/api/comp_method.yaml deleted file mode 100644 index e7b682b541..0000000000 --- a/src/batch_integration/api/comp_method.yaml +++ /dev/null @@ -1,29 +0,0 @@ -functionality: - arguments: - - name: --input - type: file - description: Unintegrated AnnData HDF5 file. - required: true - example: input.h5ad - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Integrated AnnData HDF5 file. - required: true - example: "output.h5ad" - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false - - name: --scaling - type: boolean - description: Whether to scale the data or not - default: false - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: false - required: false \ No newline at end of file diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml new file mode 100644 index 0000000000..12e5118f90 --- /dev/null +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -0,0 +1,69 @@ +functionality: + info: + output_type: embedding + arguments: + - name: --input + __merge__: anndata_unintegrated.yaml + - name: --output + alternatives: [ -o ] + direction: output + __merge__: anndata_integrated_embedding.yaml + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + test_resources: + - path: ../../../../../resources_test/batch_integration/pancreas/ + - type: python_script + path: generic_test.py + text: | + from os import path + import subprocess + import numpy as np + import anndata as ad + + + print(">> Running script", flush=True) + + input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" + output_path = "embeddding.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] + + print(">> Checking whether input file exists", flush=True) + assert path.exists(input_path) + + print(">> Running script as test", flush=True) + subprocess.run(cmd, check=True) + + print(">> Checking whether output file exists", flush=True) + assert path.exists(output_path) + + print(">> Reading h5ad files", flush=True) + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + + print(f"input: {input}", flush=True) + print(f"output: {output}", flush=True) + + print(">> Checking whether predictions were added", flush=True) + assert 'dataset_id' in output.uns + assert 'X_pca' in output.obsm + assert 'X_emb' in output.obsm + assert 'normalization_id' in output.uns + assert 'method_id' in output.uns + assert meta['fuctionality_name'] == output.uns['method_id'] + + assert 'hvg' in output.uns + + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) + + print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml new file mode 100644 index 0000000000..24a471a694 --- /dev/null +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -0,0 +1,57 @@ +functionality: + namespace: batch_integration/graph/methods + info: + output_type: graph + arguments: + - __merge__: anndata_unintegrated.yaml + name: --input + - __merge__: anndata_integrated_graph.yaml + name: --output + direction: output + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + test_resources: + - path: ../../../../../resources_test/batch_integration/pancreas/ + - type: python_script + path: generic_test.py + text: | + import os + import subprocess + import anndata as ad + + input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" + output_path = "inegrated.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] + + print(">> Checking whether input file exists", flush=True) + assert os.path.exists(input_path) + + print(">> Running script as test", flush=True) + subprocess.run(cmd, check=True) + + print(">> Checking whether file exists", flush=True) + assert os.path.exists(output_path) + + print(">> Reading h5ad files", flush=True) + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + print(f"input: {input}", flush=True) + print(f"output: {output}", flush=True) + + print(">> Checking whether predictions were added", flush=True) + # TODO: use helper function to check whether the required fields are defined + assert 'connectivities' in output.obsp + assert 'distances' in output.obsp + + print(">> Check values", flush=True) + assert meta['functionality_name'] == output.uns['method_id'] + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print(">> All tests passed successfully") diff --git a/src/batch_integration/api/comp_metric.yaml b/src/batch_integration/api/comp_metric.yaml index 40f9011ceb..545264aa83 100644 --- a/src/batch_integration/api/comp_metric.yaml +++ b/src/batch_integration/api/comp_metric.yaml @@ -12,8 +12,80 @@ functionality: description: Output tsv file of the metric required: true example: output.tsv - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false \ No newline at end of file + test_resources: + - path: ../../../../../resources_test/batch_integration + - type: python_script + dest: test.py + text: | + import sys + from os import path + import subprocess + import numpy as np + import anndata as ad + import yaml + + ## VIASH START + meta = { + "resources_dir": "resources_test/batch_integration/graph/methods", + "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" + } + ## VIASH END + + np.random.seed(42) + + print(">> Read metric config", flush=True) + with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + + output_type = config["functionality"].get("info", {}).get("output_type") + + print(">> Construct input arguments", flush=True) + if output_type == "graph": + input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" + elif output_type == "embedding": + input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" + else: + sys.exit("Unrecognized .functionality.info.output_type") + output_file = "output.h5ad" + + cmd_args = [ + meta["executable"], + "--input", input_file, + "--output", output_file + ] + + print(">> Running script", flush=True) + subprocess.run(cmd_args, check=True) + + print(">> Checking whether file exists", flush=True) + assert path.exists(output_file) + input = ad.read_h5ad(input_file) + output = ad.read_h5ad(output_file) + + print(">> Print AnnData contents", flush=True) + print("input:", input, flush=True) + print("output:", output, flush=True) + + print(">> Checking whether metrics were added", flush=True) + assert "metric_ids" in output.uns + assert "metric_values" in output.uns + assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.uns["dataset_id"] == output.uns["dataset_id"] + assert input.uns["method_id"] == output.uns["method_id"] + + print(">> Check that score makes sense", flush=True) + metrics_info = { + metric["metric_id"]: metric + for metric in config["functionality"]["info"]["metrics"] + } + + for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + + print(">> All tests passed successfully") diff --git a/src/batch_integration/api/comp_split_dataset.yaml b/src/batch_integration/api/comp_split_dataset.yaml new file mode 100644 index 0000000000..997cf62918 --- /dev/null +++ b/src/batch_integration/api/comp_split_dataset.yaml @@ -0,0 +1,64 @@ +functionality: + arguments: + - name: "--input" + __merge__: anndata_dataset.yaml + - name: "--output_unintegrated" + __merge__: anndata_unintegrated.yaml + direction: output + - name: "--output_solution" + __merge__: anndata_solution.yaml + direction: output + # test_resources: + # - path: ../../../resources_test/common/pancreas/ + # - type: python_script + # path: generic_test.py + # text: | + # import anndata as ad + # import subprocess + # from os import path + + # input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + # output_train_path = "train.h5ad" + # output_test_path = "test.h5ad" + # cmd = [ + # meta['executable'], + # "--input", input_path, + # "--output_train", output_train_path, + # "--output_test", output_test_path + # ] + + # print(">> Checking whether input file exists", flush=True) + # assert path.exists(input_path) + + # print(">> Running script as test", flush=True) + # out = subprocess.run(cmd, check=True, capture_output=True, text=True) + + # print(">> Checking whether output files exist", flush=True) + # assert path.exists(output_train_path) + # assert path.exists(output_test_path) + + # print(">> Reading h5ad files", flush=True) + # input = ad.read_h5ad(input_path) + # output_train = ad.read_h5ad(output_train_path) + # output_test = ad.read_h5ad(output_test_path) + + # print("input:", input, flush=True) + # print("output_train:", output_train, flush=True) + # print("output_test:", output_test, flush=True) + + # print(">> Checking whether data from input was copied properly to output", flush=True) + # assert input.n_obs == output_train.n_obs + # assert input.n_obs == output_test.n_obs + # assert input.uns["dataset_id"] == output_train.uns["dataset_id"] + # assert input.uns["dataset_id"] == output_test.uns["dataset_id"] + + + # print(">> Check whether certain slots exist", flush=True) + # assert "counts" in output_train.layers + # assert "normalized" in output_train.layers + # assert 'hvg_score' in output_train.var + # assert "counts" in output_test.layers + # assert "normalized" in output_test.layers + # assert 'hvg_score' in output_test.var + + # print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/batch_integration/changes.md b/src/batch_integration/changes.md new file mode 100644 index 0000000000..a33ca3dc84 --- /dev/null +++ b/src/batch_integration/changes.md @@ -0,0 +1,24 @@ +# Batch integration changes + +Already done +* move imports to the top of the file +* remove pprint on debug +* wrote generic unit test for metrics +* merged NMI and ARI metric +* changed metric outputs to h5ad +* added .functionality.info.output_type to methods and metrics +* use anndata when scanpy is not needed +* Add 'flush=True' to all print statements +* write generic unit test for methods + +TODO: +* split up api for different output types +* add file specs +* Copy descriptions from openproblems v1 for methods and metrics +* add .functionality.info to methods and metrics +* Change `split_dataset` so it uses the normalization, hvg, pca from the given object rather than recompute. +* Change `split_dataset` to output two AnnData objects: unintegrated and solution? +* Create a normalization variant: + log_cpm -> log_cpm_batchscaled +* Rename knn_connectivities to connectivities in solution +* Simplify renaming fields in split_dataset, e.g. celltype -> label, knn_connectivities -> connectivities. \ No newline at end of file diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/datasets/README.md index 7d5836489d..6dd89140c7 100644 --- a/src/batch_integration/datasets/README.md +++ b/src/batch_integration/datasets/README.md @@ -25,7 +25,7 @@ This module creates Anndata objects that contain: And transformations of the data: -* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.obsm['X_pca']`: PCA embedding of the log-normalized counts * `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['pca_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['pca_distances']`: distance matrix generated by `scanpy.pp.neighbors()` diff --git a/src/batch_integration/datasets/preprocessing/config.vsh.yaml b/src/batch_integration/datasets/preprocessing/config.vsh.yaml deleted file mode 100644 index 83bd58abf7..0000000000 --- a/src/batch_integration/datasets/preprocessing/config.vsh.yaml +++ /dev/null @@ -1,50 +0,0 @@ -functionality: - name: preprocessing - namespace: batch_integration/datasets - version: dev - description: Preprocess adata object for data integration - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output h5ad file of the cleaned dataset - required: true - - name: --input - type: file - description: Anndata HDF5 file - required: true - - name: --label - type: string - description: Cell annotation label in adata.obs - required: true - - name: --batch - type: string - description: Batch assignment in adata.obs - required: true - - name: --hvgs - type: integer - description: Number of highly variable genes - default: 2000 - required: false - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false - resources: - - type: python_script - path: script.py - - path: ../utils/_hvg_batch.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/ -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - - type: nextflow diff --git a/src/batch_integration/datasets/preprocessing/run_example.sh b/src/batch_integration/datasets/preprocessing/run_example.sh deleted file mode 100644 index bd12c9796c..0000000000 --- a/src/batch_integration/datasets/preprocessing/run_example.sh +++ /dev/null @@ -1,12 +0,0 @@ -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/resources/data_loader_pancreas.h5ad \ - --label celltype \ - --batch tech \ - --hvgs 100 \ - --output src/batch_integration/resources/datasets_pancreas.h5ad \ - --debug true diff --git a/src/batch_integration/datasets/preprocessing/script.py b/src/batch_integration/datasets/preprocessing/script.py deleted file mode 100644 index e54904b058..0000000000 --- a/src/batch_integration/datasets/preprocessing/script.py +++ /dev/null @@ -1,69 +0,0 @@ -## VIASH START -import os - -print(os.getcwd()) -par = { - 'input': './src/batch_integration/datasets/resources/data_loader_pancreas.h5ad', - 'label': 'celltype', - 'batch': 'tech', - 'hvgs': 2000, - 'output': './src/batch_integration/datasets/resources/datasets_pancreas.h5ad', - 'debug': True -} -meta = { - 'resources_dir': './resources_test/common/pancreas/', -} -## VIASH END - -print('Importing libraries') -import scanpy as sc -import scib -from pprint import pprint -import sys - -sys.path.append(meta['resources_dir']) -from _hvg_batch import hvg_batch - -if par['debug']: - pprint(par) - -adata_file = par['input'] -label = par['label'] -batch = par['batch'] -hvgs = par['hvgs'] -output = par['output'] - -print('Read adata') -adata = sc.read_h5ad(adata_file) - -# Rename columns -print('Rename columns') -adata.obs['label'] = adata.obs[label] -adata.obs['batch'] = adata.obs[batch] -adata.X = adata.layers['counts'].copy() - -print('Normalise and log-transform data') -sc.pp.normalize_total(adata) -sc.pp.log1p(adata) -adata.layers['logcounts'] = adata.X.copy() - -print(f'Select {hvgs} highly variable genes') -hvg_list = hvg_batch(adata, 'batch', n_hvg=hvgs) -adata.var['highly_variable'] = adata.var_names.isin(hvg_list) - -print('Scaling') -adata.layers['logcounts_scaled'] = scib.pp.scale_batch(adata, 'batch').X - -print('Transformation: PCA') -sc.tl.pca( - adata, - svd_solver='arpack', - return_info=True, -) -adata.obsm['X_uni'] = adata.obsm['X_pca'] - -print('Transformation: kNN') -sc.pp.neighbors(adata, use_rep='X_uni', key_added='uni') - -print('Writing adata to file') -adata.write(output, compression='gzip') diff --git a/src/batch_integration/datasets/preprocessing/test.py b/src/batch_integration/datasets/preprocessing/test.py deleted file mode 100644 index de8dacc7c6..0000000000 --- a/src/batch_integration/datasets/preprocessing/test.py +++ /dev/null @@ -1,45 +0,0 @@ -import os -from os import path -import subprocess -import scanpy as sc -import numpy as np - -name = 'preprocessing' -anndata_in = meta["resources_dir"] + '/pancreas/dataset.h5ad' -anndata_out = 'datasets_pancreas.h5ad' - -print('>> Running script') -n_hvgs = 100 -out = subprocess.check_output([ - './preprocessing', - '--input', anndata_in, - '--label', 'celltype', - '--batch', 'tech', - '--hvgs', str(n_hvgs), - '--output', anndata_out -]).decode('utf-8') - -print('>> Checking whether file exists') -assert path.exists(anndata_out) - -print('>> Check that output fits expected API') -adata = sc.read_h5ad(anndata_out) -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert adata.var['highly_variable'].dtype == 'bool' -assert adata.var['highly_variable'].sum() == n_hvgs -assert -0.0000001 <= np.mean(adata.layers['logcounts_scaled']) <= 0.0000001 -assert 0.75 <= np.var(adata.layers['logcounts_scaled']) <= 1 - -print('>> All tests passed successfully') diff --git a/src/batch_integration/datasets/subsample/config.vsh.yaml b/src/batch_integration/datasets/subsample/config.vsh.yaml deleted file mode 100644 index a74ed048b1..0000000000 --- a/src/batch_integration/datasets/subsample/config.vsh.yaml +++ /dev/null @@ -1,46 +0,0 @@ -functionality: - name: subsample - namespace: batch_integration/datasets - version: dev - description: Subset adata object for testing - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } - arguments: - - name: --output - alternatives: [ -o ] - type: file - direction: output - description: Output h5ad file of the cleaned dataset - required: true - - name: --input - type: file - description: Anndata HDF5 file - required: true - - name: --label - type: string - description: Cell annotation label in adata.obs - required: true - - name: --batch - type: string - description: Batch assignment in adata.obs - required: true - - name: --debug - type: boolean - description: Verbose output for debugging - default: False - required: false - resources: - - type: python_script - path: script.py - - path: utils/g2m_genes_tirosh_hm.txt - - path: utils/s_genes_tirosh_hm.txt - test_resources: - - type: python_script - path: test.py - - path: ../../../../resources_test/common/pancreas/dataset.h5ad -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - - type: nextflow diff --git a/src/batch_integration/datasets/subsample/run_example.sh b/src/batch_integration/datasets/subsample/run_example.sh deleted file mode 100644 index a2e9963121..0000000000 --- a/src/batch_integration/datasets/subsample/run_example.sh +++ /dev/null @@ -1,11 +0,0 @@ -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --adata src/common/dataset_loader/download/resources/pancreas.h5ad \ - --label celltype \ - --batch tech \ - --output src/batch_integration/resources/data_loader_pancreas.h5ad \ - --debug true diff --git a/src/batch_integration/datasets/subsample/script.py b/src/batch_integration/datasets/subsample/script.py deleted file mode 100644 index ca06541e55..0000000000 --- a/src/batch_integration/datasets/subsample/script.py +++ /dev/null @@ -1,55 +0,0 @@ -""" -This script subsets a downloaded dataset for testing all the batch integration modules -""" -## VIASH START -par = { - 'adata': 'src/common/dataset_loader/download/resources/pancreas.h5ad', - 'label': 'celltype', - 'batch': 'tech', - 'output': 'src/batch_integration/resources/data_loader_pancreas.h5ad', - 'debug': True -} -meta = { - 'resources_dir': './src/batch_integration/datasets', -} -## VIASH END - -print('Importing libraries') -import scanpy as sc -from pprint import pprint - -if par['debug']: - pprint(par) - -resources_dir = meta['resources_dir'] -adata_file = par['input'] -label = par['label'] -batch = par['batch'] -output = par['output'] -g2m_file = f'{resources_dir}/g2m_genes_tirosh_hm.txt' -s_file = f'{resources_dir}/s_genes_tirosh_hm.txt' - -print('Read adata') -adata = sc.read_h5ad(adata_file) - -print('Get batch and label subsets') -head_batches = adata.obs[batch].unique().tolist()[0:3] -head_labels = adata.obs[label].unique().tolist()[0:2] - -print('Get features subsets') -g2m_genes = [x.strip() for x in open(g2m_file).readlines()] -s_genes = [x.strip() for x in open(s_file).readlines()] - -all_genes = adata.var.index.tolist() -cc_genes = [x for x in g2m_genes + s_genes if x in all_genes] -head_genes = list(set(cc_genes + all_genes[:100])) - -print('Subset adata') -adata = adata[adata.obs[batch].isin(head_batches)] -adata = adata[adata.obs[label].isin(head_labels)] -adata = adata[:, head_genes] -sc.pp.subsample(adata, 0.3, random_state=42) - -print(adata) - -adata.write(output, compression='gzip') diff --git a/src/batch_integration/datasets/subsample/test.py b/src/batch_integration/datasets/subsample/test.py deleted file mode 100644 index 1ded02f287..0000000000 --- a/src/batch_integration/datasets/subsample/test.py +++ /dev/null @@ -1,27 +0,0 @@ -from os import path -import subprocess -import scanpy as sc -import numpy as np - -name = 'subsample' -anndata_in = 'dataset.h5ad' -anndata_out = 'dataset_sub.h5ad' - -print('>> Running script') -n_hvgs = 100 -out = subprocess.check_output([ - './subsample', - '--input', anndata_in, - '--label', 'celltype', - '--batch', 'tech', - '--output', anndata_out -]).decode('utf-8') - -print('>> Checking whether file exists') -assert path.exists(anndata_out) - -print('>> Check that output fits expected API') -adata = sc.read_h5ad(anndata_out) -assert 'dataset_id' in adata.uns - -print('>> All tests passed successfully') diff --git a/src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt b/src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt deleted file mode 100644 index 4053db0cf8..0000000000 --- a/src/batch_integration/datasets/subsample/utils/g2m_genes_tirosh_hm.txt +++ /dev/null @@ -1,54 +0,0 @@ -HMGB2 -CDK1 -NUSAP1 -UBE2C -BIRC5 -TPX2 -TOP2A -NDC80 -CKS2 -NUF2 -CKS1B -MKI67 -TMPO -CENPF -TACC3 -FAM64A -SMC4 -CCNB2 -CKAP2L -CKAP2 -AURKB -BUB1 -KIF11 -ANP32E -TUBB4B -GTSE1 -KIF20B -HJURP -CDCA3 -HN1 -CDC20 -TTK -CDC25C -KIF2C -RANGAP1 -NCAPD2 -DLGAP5 -CDCA2 -CDCA8 -ECT2 -KIF23 -HMMR -AURKA -PSRC1 -ANLN -LBR -CKAP5 -CENPE -CTCF -NEK2 -G2E3 -GAS2L3 -CBX5 -CENPA \ No newline at end of file diff --git a/src/batch_integration/datasets/subsample/utils/s_genes_tirosh_hm.txt b/src/batch_integration/datasets/subsample/utils/s_genes_tirosh_hm.txt deleted file mode 100644 index 35b4aa7eb8..0000000000 --- a/src/batch_integration/datasets/subsample/utils/s_genes_tirosh_hm.txt +++ /dev/null @@ -1,43 +0,0 @@ -MCM5 -PCNA -TYMS -FEN1 -MCM2 -MCM4 -RRM1 -UNG -GINS2 -MCM6 -CDCA7 -DTL -PRIM1 -UHRF1 -MLF1IP -HELLS -RFC2 -RPA2 -NASP -RAD51AP1 -GMNN -WDR76 -SLBP -CCNE2 -UBR7 -POLD3 -MSH2 -ATAD2 -RAD51 -RRM2 -CDC45 -CDC6 -EXO1 -TIPIN -DSCC1 -BLM -CASP8AP2 -USP1 -CLSPN -POLA1 -CHAF1B -BRIP1 -E2F8 \ No newline at end of file diff --git a/src/batch_integration/datasets/utils/_hvg_batch.py b/src/batch_integration/datasets/utils/_hvg_batch.py deleted file mode 100644 index ec59bfab49..0000000000 --- a/src/batch_integration/datasets/utils/_hvg_batch.py +++ /dev/null @@ -1,15 +0,0 @@ -import scib - - -def hvg_batch(adata, batch_key, n_hvg): - """ - Compute highly variable genes by batch - """ - if n_hvg > adata.n_vars or n_hvg == 0: - return adata.var_names.tolist() - return scib.pp.hvg_batch( - adata, - batch_key=batch_key, - target_genes=n_hvg, - adataOut=False - ) diff --git a/src/batch_integration/datasets/utils/_log_scran_pooling.py b/src/batch_integration/datasets/utils/_log_scran_pooling.py deleted file mode 100644 index 93e0cc3f73..0000000000 --- a/src/batch_integration/datasets/utils/_log_scran_pooling.py +++ /dev/null @@ -1,22 +0,0 @@ -import scanpy as sc -import scprep - - -def log_scran_pooling(adata): - """Normalize data with scran via rpy2.""" - _scran = scprep.run.RFunction( - setup="library('scran')", - args="sce, min.mean=0.1", - body=""" - sce <- computeSumFactors( - sce, min.mean=min.mean, - assay.type="X" - ) - sizeFactors(sce) - """, - ) - adata.obs["size_factors"] = _scran(adata) - adata.X = scprep.utils.matrix_vector_elementwise_multiply( - adata.X, adata.obs["size_factors"], axis=0 - ) - sc.pp.log1p(adata) diff --git a/src/batch_integration/embedding/methods/combat/config.vsh.yaml b/src/batch_integration/embedding/methods/combat/config.vsh.yaml index 0262434a74..f4a847857c 100644 --- a/src/batch_integration/embedding/methods/combat/config.vsh.yaml +++ b/src/batch_integration/embedding/methods/combat/config.vsh.yaml @@ -3,20 +3,20 @@ __merge__: ../../../api/comp_method.yaml functionality: name: combat namespace: batch_integration/embedding/methods - version: dev description: Run Combat - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + info: + output_type: embedding resources: - type: python_script path: script.py test_resources: - type: python_script path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad + - path: ../../../../../resources_test/batch_integration/pancreas/unintegrated.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: [ pyyaml ] - type: nextflow diff --git a/src/batch_integration/embedding/methods/combat/script.py b/src/batch_integration/embedding/methods/combat/script.py index 117a26bbe5..3361fdcb12 100644 --- a/src/batch_integration/embedding/methods/combat/script.py +++ b/src/batch_integration/embedding/methods/combat/script.py @@ -1,45 +1,43 @@ +import scanpy as sc +from scipy.sparse import csr_matrix + ## VIASH START par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', + 'output': 'output.h5ad', 'hvg': True, - 'scaling': True, - 'debug': True + 'scaling': True } -## VIASH END - -print('Importing libraries') -from pprint import pprint -import scanpy as sc -from scipy.sparse import csr_matrix -if par['debug']: - pprint(par) +meta = { + 'functionality_name' : 'foo' +} +## VIASH END adata_file = par['input'] output = par['output'] hvg = par['hvg'] scaling = par['scaling'] -print('Read adata') +print('Read input', flush=True) adata = sc.read_h5ad(adata_file) if hvg: - print('Select HVGs') + print('Select HVGs', flush=True) adata = adata[:, adata.var['highly_variable']].copy() if scaling: - print('Scale') + print('Scale', flush=True) adata.X = adata.layers['logcounts_scaled'] else: adata.X = adata.layers['logcounts'] -print('Integrate') +print('Integrate', flush=True) adata.X = sc.pp.combat(adata, key='batch', inplace=False) adata.X = csr_matrix(adata.X) -print('Postprocess data') -adata.obsm['X_emb'] = sc.pp.pca( +print('Postprocess data', flush=True) +X_emb = sc.pp.pca( adata.X, n_comps=50, use_highly_variable=False, @@ -47,9 +45,21 @@ return_info=False ) -print('Save HDF5') -adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling +print('Create output AnnData object', flush=True) +output = sc.AnnData( + obs= adata.obs[[]], + obsm={ + 'X_emb': X_emb + }, + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + 'scaled': par['scaling'], + 'hvg': par('hvg') + }, + layers = adata.layers +) -adata.write(output, compression='gzip') +print('Write to output', flush=True) +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/embedding/methods/combat/test.py b/src/batch_integration/embedding/methods/combat/test.py index 7f4179db31..1bf4ad0d62 100644 --- a/src/batch_integration/embedding/methods/combat/test.py +++ b/src/batch_integration/embedding/methods/combat/test.py @@ -1,47 +1,49 @@ from os import path import subprocess import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'combat' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_emb' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns - -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False - -unintegrated = sc.read('processed.h5ad') -assert len(unintegrated.X.data) != len(adata.X.data) -assert not np.any(np.not_equal(unintegrated.obsm['X_pca'], adata.obsm['X_pca'])) +import anndata as ad + + +print(">> Running script", flush=True) + +input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" +output_path = "inegrated.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path +] + +print(">> Checking whether input file exists", flush=True) +assert path.exists(input_path) + +print(">> Running script as test", flush=True) +subprocess.run(cmd, check=True) + +print(">> Checking whether output file exists", flush=True) +assert path.exists(output_path) + +print(">> Reading h5ad files", flush=True) +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) + +print(">> Checking whether predictions were added", flush=True) +assert 'dataset_id' in output.uns +assert 'X_pca' in output.obsm +assert 'X_emb' in output.obsm +assert 'normalization_id' in output.uns +assert 'method_id' in output.uns +assert meta['fuctionality_name'] == output.uns['method_id'] + +assert 'hvg' in output.uns +assert output.uns['hvg'] == False +assert 'scaled' in output.uns +assert output.uns['scaled'] == False + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.n_obs == output.n_obs +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index 9f803d4adc..42cc70541a 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -3,20 +3,17 @@ __merge__: ../../../api/comp_metric.yaml functionality: name: asw_batch namespace: batch_integration/embedding/metrics - version: dev description: Average silhouette of batches per label - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + info: + output_type: embedding + integrated_embedding: X_emb resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml - type: nextflow diff --git a/src/batch_integration/embedding/metrics/asw_batch/script.py b/src/batch_integration/embedding/metrics/asw_batch/script.py index ba871f7a12..45bd99d5b8 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/script.py +++ b/src/batch_integration/embedding/metrics/asw_batch/script.py @@ -1,40 +1,50 @@ +import pprint +import anndata as ad +from scib.metrics import silhouette_batch +import yaml + ## VIASH START par = { - 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/asw_batch_pancreas_mnn.tsv', - 'debug': True + 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', + 'output': 'output.h5ad', + 'hvg': False, + 'scaling': False +} +meta = { + 'functionality_name': 'foo', + 'config': 'src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml' } ## VIASH END -print('Importing libraries') -import pprint -import scanpy as sc -from scib.metrics import silhouette_batch - -if par['debug']: - pprint.pprint(par) - -OUTPUT_TYPE = 'embedding' -METRIC = 'asw_batch' -EMBEDDING = 'X_emb' +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) -adata_file = par['input'] -output = par['output'] +output_type = config["functionality"]["info"]["output_type"] +integrated_embedding = config["functionality"]["info"]["integrated_embedding"] -print('Read adata') -adata = sc.read(adata_file) -name = adata.uns['dataset_id'] +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) print('compute score') score = silhouette_batch( adata, batch_key='batch', group_key='label', - embed=EMBEDDING, + embed=integrated_embedding, +) + +print("Create output AnnData object") +output = ad.AnnData( + uns={ + "dataset_id": adata.uns['dataset_id'], + "method_id": adata.uns['method_id'], + "metric_ids": [ meta['functionality_name'] ], + "metric_values": [ score ], + "hvg": adata.uns['hvg'], + "scaled": adata.uns['scaled'], + "output_type": output_type, + } ) -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) +print("Write data to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py deleted file mode 100644 index 02fa724c3c..0000000000 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'asw_batch' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) - -print(">> Check that score makes sense") -result = pd.read_table(metric_file) -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml index 43dd8f84bc..9112bf2689 100644 --- a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml @@ -3,20 +3,14 @@ __merge__: ../../../api/comp_metric.yaml functionality: name: asw_label namespace: batch_integration/embedding/metrics - version: dev description: Average silhouette of labels - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml - type: nextflow diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/embedding/metrics/asw_label/script.py index 397bb174ba..f32dddb805 100644 --- a/src/batch_integration/embedding/metrics/asw_label/script.py +++ b/src/batch_integration/embedding/metrics/asw_label/script.py @@ -1,34 +1,54 @@ +import pprint +import anndata as ad +from scib.metrics import silhouette +import yaml + ## VIASH START par = { - 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/asw_label_pancreas_mnn.tsv', - 'debug': True + 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', + 'output': 'output.h5ad', + 'hvg': False, + 'scaling': False } -## VIASH END -print('Importing libraries') -import pprint -import scanpy as sc -from scib.metrics import silhouette +meta = { + 'functionality_name': 'foo', + 'config': 'src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml' +} +## VIASH END -if par['debug']: - pprint.pprint(par) +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) -OUTPUT_TYPE = 'embedding' -METRIC = 'asw_label' +output_type = config["functionality"]["info"]["output_type"] +integrated_embedding = config["functionality"]["info"]["integrated_embedding"] adata_file = par['input'] output = par['output'] -print('Read adata') -adata = sc.read(adata_file) +print('Read input', flush=True) +adata = ad.read_h5ad(adata_file) name = adata.uns['dataset_id'] print('compute score') -score = silhouette(adata, group_key='label', embed='X_emb') +score = silhouette( + adata, + group_key='label', + embed=integrated_embedding +) + +print("Create output AnnData object") +output = ad.AnnData( + uns={ + "dataset_id": adata.uns['dataset_id'], + "method_id": adata.uns['method_id'], + "hvg": adata.uns['hvg'], + "scaled": adata.uns['scaled'], + "output_type": output_type, + "metric_ids": meta['functionality_name'], + "metric_value": score + } +) -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) +print("Write data to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/batch_integration/embedding/metrics/asw_label/test.py b/src/batch_integration/embedding/metrics/asw_label/test.py deleted file mode 100644 index faba5a1139..0000000000 --- a/src/batch_integration/embedding/metrics/asw_label/test.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'asw_label' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) - -print(">> Check that score makes sense") -result = pd.read_table(metric_file) -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml index edda16b343..d7042df51f 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml @@ -3,12 +3,7 @@ __merge__: ../../../api/comp_metric.yaml functionality: name: cell_cycle_conservation namespace: batch_integration/embedding/metrics - version: dev description: Cell cycle conservation score based on cell cycle gene scoring - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } arguments: - name: --organism type: string @@ -17,11 +12,10 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml - type: nextflow diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py index 2431c04171..67766d21e3 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py @@ -2,20 +2,15 @@ par = { 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', - 'organism': 'human', - 'debug': True + 'organism': 'human' } ## VIASH END -print('Importing libraries') import pprint import scanpy as sc from scib.metrics import cell_cycle from scipy.sparse import csr_matrix -if par['debug']: - pprint.pprint(par) - OUTPUT_TYPE = 'embedding' METRIC = 'cell_cycle_conservation' @@ -23,7 +18,7 @@ organism = par['organism'] output = par['output'] -print('Read adata') +print('Read input', flush=True) adata = sc.read(adata_file) adata_int = adata.copy() name = adata.uns['dataset_id'] diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py b/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py deleted file mode 100644 index af491ce150..0000000000 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/test.py +++ /dev/null @@ -1,34 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np -import scanpy as sc - -np.random.seed(42) - -metric = 'cell_cycle_conservation' -metric_file = metric + '.tsv' - -print(sc.read('combat.h5ad')) - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--organism", "human", - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) - -print(">> Check that score makes sense") -result = pd.read_table(metric_file) -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - - -print(">> All tests passed successfully") diff --git a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml index a4efdfe1eb..4087743d7d 100644 --- a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml @@ -3,20 +3,14 @@ __merge__: ../../../api/comp_metric.yaml functionality: name: pcr namespace: batch_integration/embedding/metrics - version: dev description: PCA regression - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/embedding/methods/combat.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml - type: nextflow diff --git a/src/batch_integration/embedding/metrics/pcr/script.py b/src/batch_integration/embedding/metrics/pcr/script.py index b975302cf3..5749fa1d23 100644 --- a/src/batch_integration/embedding/metrics/pcr/script.py +++ b/src/batch_integration/embedding/metrics/pcr/script.py @@ -1,26 +1,21 @@ ## VIASH START par = { 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', - 'debug': True + 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv' } ## VIASH END -print('Importing libraries') import pprint import scanpy as sc from scib.metrics import pcr_comparison -if par['debug']: - pprint.pprint(par) - OUTPUT_TYPE = 'embedding' METRIC = 'pcr' adata_file = par['input'] output = par['output'] -print('Read adata') +print('Read input', flush=True) adata = sc.read(adata_file) adata_int = adata.copy() name = adata.uns['dataset_id'] diff --git a/src/batch_integration/embedding/metrics/pcr/test.py b/src/batch_integration/embedding/metrics/pcr/test.py deleted file mode 100644 index 0fc00d70b7..0000000000 --- a/src/batch_integration/embedding/metrics/pcr/test.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'pcr' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) - -print(">> Check that score makes sense") -result = pd.read_table(metric_file) -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/graph/README.md index 0a98da398b..eb61e893aa 100644 --- a/src/batch_integration/graph/README.md +++ b/src/batch_integration/graph/README.md @@ -23,10 +23,10 @@ Datasets should contain the following attributes: * `adata.layers['counts']` with raw, integer UMI count data * `adata.layers['logcounts']`: log-normalized count data * `adata.layers['logcounts_scaled']`: scaled log-normalized count data -* `adata.obsm['X_uni']`: PCA embedding of the log-normalized counts +* `adata.obsm['X_pca']`: PCA embedding of the log-normalized counts * `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['uni_distances']`: distance matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['pca_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` +* `adata.obsp['pca_distances']`: distance matrix generated by `scanpy.pp.neighbors()` The default count matrix in `adata.X` is assumed to contain the log normalised counts from `adata.layers['logcounts']`. diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml index 01749c049d..272a8aa9df 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/graph/methods/bbknn/config.vsh.yaml @@ -1,27 +1,27 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../../api/comp_method_graph.yaml functionality: name: bbknn - namespace: batch_integration/graph/methods description: Run BBKNN on adata object - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + info: + type: method + method_name: BBKNN + # paper_reference: "xxxxxxxxxxx" + # code_url: xxxxxxxxxxx + # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py + # v1_commit: xxxxxxxxxxxxxx + # preferred_normalization: log_cpm + # variants: + # bbknn: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - type: python_script - path: test_scaled_hvg.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - type: python - packages: + pypi: - bbknn + - pyyaml - type: nextflow diff --git a/src/batch_integration/graph/methods/bbknn/run_example.sh b/src/batch_integration/graph/methods/bbknn/run_example.sh deleted file mode 100644 index f5c341e495..0000000000 --- a/src/batch_integration/graph/methods/bbknn/run_example.sh +++ /dev/null @@ -1,12 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_bbknn.h5ad \ - --debug true diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/graph/methods/bbknn/script.py index 7ff650afce..0053019412 100644 --- a/src/batch_integration/graph/methods/bbknn/script.py +++ b/src/batch_integration/graph/methods/bbknn/script.py @@ -1,45 +1,29 @@ +import anndata as ad +from scib.integration import bbknn + ## VIASH START par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', 'hvg': True, - 'scaling': True, - 'debug': True +} +meta = { + 'functionality_name': 'foo' } ## VIASH END -print('Importing libraries') -from pprint import pprint -import scanpy as sc -from scib.integration import bbknn - -if par['debug']: - pprint(par) - -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] - -print('Read adata') -adata = sc.read_h5ad(adata_file) - -if hvg: - print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] - -if scaling: - print('Scale') - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) -print('Integrate') -adata = bbknn(adata, batch='batch') +if par['hvg']: + print('Select HVGs', flush=True) + input = input[:, input.var['hvg']].copy() -print('Save HDF5') -adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling +print('Run BBKNN', flush=True) +input.X = input.layers['normalized'] +input = bbknn(input, batch='batch') +del input.X -adata.write(output, compression='gzip') +print("Store outputs", flush=True) +input.uns['method_id'] = meta['functionality_name'] +input.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/graph/methods/bbknn/test.py b/src/batch_integration/graph/methods/bbknn/test.py deleted file mode 100644 index a1472a74ce..0000000000 --- a/src/batch_integration/graph/methods/bbknn/test.py +++ /dev/null @@ -1,46 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'bbknn' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert not adata.uns['hvg'] -assert 'scaled' in adata.uns -assert not adata.uns['scaled'] - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py b/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py deleted file mode 100644 index 51106111a7..0000000000 --- a/src/batch_integration/graph/methods/bbknn/test_scaled_hvg.py +++ /dev/null @@ -1,51 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'bbknn' -output_file = method + '_scaled_hvg.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'True', - "--scaling", 'True', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -adata.X = adata.X.todense() - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == True -assert adata.n_vars == 100 -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == True -assert -0.0000001 <= np.mean(adata.X) <= 0.0000001 -assert 0.8 <= np.var(adata.X) <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/graph/methods/combat/config.vsh.yaml index 416520a6a6..c87450ff5e 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/graph/methods/combat/config.vsh.yaml @@ -1,22 +1,25 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../../api/comp_method_graph.yaml functionality: name: combat - namespace: batch_integration/graph/methods - version: dev - description: Run Combat - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + info: + type: method + output_type: graph + method_name: Combat + # paper_reference: "xxxxxxxxxxx" + # code_url: xxxxxxxxxxx + # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py + # v1_commit: xxxxxxxxxxxxxx + # preferred_normalization: log_cpm + # variants: + # combat: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml - type: nextflow diff --git a/src/batch_integration/graph/methods/combat/run_example.sh b/src/batch_integration/graph/methods/combat/run_example.sh deleted file mode 100644 index ce00a91fac..0000000000 --- a/src/batch_integration/graph/methods/combat/run_example.sh +++ /dev/null @@ -1,14 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch batch \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_combat.h5ad \ - --debug true diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/graph/methods/combat/script.py index 18abf18f82..3af76ea9f1 100644 --- a/src/batch_integration/graph/methods/combat/script.py +++ b/src/batch_integration/graph/methods/combat/script.py @@ -1,44 +1,34 @@ -## VIASH START -par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', - 'hvg': True, - 'scaling': True, - 'debug': True -} -## VIASH END +# TODO: this should be a output_type: features method. -print('Importing libraries') -from pprint import pprint import scanpy as sc from scipy.sparse import csr_matrix -if par['debug']: - pprint(par) +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'hvg': True +} -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] +meta = { + 'funcionality_name': 'foo' +} -print('Read adata') -adata = sc.read_h5ad(adata_file) +## VIASH END -if hvg: - print('Select HVGs') - adata = adata[:, adata.var['highly_variable']].copy() +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) -if scaling: - print('Scale') - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']].copy() -print('Integrate') +print('Run Combat', flush=True) +adata.X = adata.layers['normalized'] adata.X = sc.pp.combat(adata, key='batch', inplace=False) adata.X = csr_matrix(adata.X) -print('Postprocess data') +print("Run PCA", flush=True) adata.obsm['X_emb'] = sc.pp.pca( adata.X, n_comps=50, @@ -46,11 +36,11 @@ svd_solver='arpack', return_info=False ) +del adata.X + +print("Run KNN", flush=True) sc.pp.neighbors(adata, use_rep='X_emb') -print('Save HDF5') +print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling - -adata.write(output, compression='gzip') +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/graph/methods/combat/test.py b/src/batch_integration/graph/methods/combat/test.py deleted file mode 100644 index bb5d279b4c..0000000000 --- a/src/batch_integration/graph/methods/combat/test.py +++ /dev/null @@ -1,50 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'combat' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file, as_sparse='X') - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False - -unintegrated = sc.read('processed.h5ad', as_sparse='X') -assert len(unintegrated.X.data) != len(adata.X.data) -assert not np.any(np.not_equal(unintegrated.obsm['X_pca'], adata.obsm['X_pca'])) - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/params.tsv b/src/batch_integration/graph/methods/params.tsv deleted file mode 100644 index ca79eb3d39..0000000000 --- a/src/batch_integration/graph/methods/params.tsv +++ /dev/null @@ -1,10 +0,0 @@ -# HVG, scaling preprocessing setupts for integration methods -hvg scaling method -True True bbknn -True False bbknn -False True bbknn -False False bbknn -True True combat -True False combat -False True combat -False False combat diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml index 38c0c62404..0f58c85656 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml @@ -1,26 +1,28 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../../api/comp_method_graph.yaml functionality: name: scanorama_embed - namespace: batch_integration/graph/methods - version: dev description: Run Scanorama on adata object, use embedding output - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + info: + type: method + output_type: graph + method_name: Scanorama + # paper_reference: "xxxxxxxxxxx" + # code_url: xxxxxxxxxxx + # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py + # v1_commit: xxxxxxxxxxxxxx + # preferred_normalization: log_cpm + # variants: + # combat: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - type: python - packages: + pypi: - scanorama + - pyyaml - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh b/src/batch_integration/graph/methods/scanorama_embed/run_example.sh deleted file mode 100644 index 6b9ec6c6eb..0000000000 --- a/src/batch_integration/graph/methods/scanorama_embed/run_example.sh +++ /dev/null @@ -1,12 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_scanorama_embed.h5ad \ - --debug true diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/graph/methods/scanorama_embed/script.py index e996893608..304e48c6be 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/script.py +++ b/src/batch_integration/graph/methods/scanorama_embed/script.py @@ -1,49 +1,33 @@ +# TODO: this should be a output_type: embedding method. +import scanpy as sc +from scib.integration import scanorama + ## VIASH START par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', 'hvg': True, - 'scaling': True, - 'debug': True +} +meta = { + 'functionality_name': 'foo' } ## VIASH END -print('Importing libraries') -from pprint import pprint -import scanpy as sc -from scib.integration import scanorama +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) -if par['debug']: - pprint(par) +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']].copy() -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] - -print('Read adata') -print(adata_file) -adata = sc.read_h5ad(adata_file) - -if hvg: - print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] - -if scaling: - print('Scale') - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] - -print('Integrate') +print('Run scanorama', flush=True) +adata.X = adata.layers['normalized'] adata.obsm['X_emb'] = scanorama(adata, batch='batch').obsm['X_emb'] +del adata.X -print('Postprocess data') +print('Run kNN', flush=True) sc.pp.neighbors(adata, use_rep='X_emb') -print('Save HDF5') +print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling - -adata.write(output, compression='gzip') +adata.write(par['output'], compression='gzip') diff --git a/src/batch_integration/graph/methods/scanorama_embed/test.py b/src/batch_integration/graph/methods/scanorama_embed/test.py deleted file mode 100644 index 502e0e52bc..0000000000 --- a/src/batch_integration/graph/methods/scanorama_embed/test.py +++ /dev/null @@ -1,46 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'scanorama_embed' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml index 25a071db8f..2845573e7d 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml @@ -1,26 +1,28 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../../api/comp_method_graph.yaml functionality: name: scanorama_feature - namespace: batch_integration/graph/methods - version: dev - description: Run Scanorama on adata object, use full feature output - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + description: Run Scanorama on adata object, use feature output + info: + type: method + output_type: graph + method_name: Scanorama + # paper_reference: "xxxxxxxxxxx" + # code_url: xxxxxxxxxxx + # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py + # v1_commit: xxxxxxxxxxxxxx + # preferred_normalization: log_cpm + # variants: + # combat: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - type: python - packages: + pypi: - scanorama + - pyyaml - type: nextflow diff --git a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh b/src/batch_integration/graph/methods/scanorama_feature/run_example.sh deleted file mode 100644 index 0494839c05..0000000000 --- a/src/batch_integration/graph/methods/scanorama_feature/run_example.sh +++ /dev/null @@ -1,12 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_scanorama_feature.h5ad \ - --debug true diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/graph/methods/scanorama_feature/script.py index fbf5b1962b..882c1baa66 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/script.py +++ b/src/batch_integration/graph/methods/scanorama_feature/script.py @@ -1,55 +1,42 @@ +# TODO: this should be a output_type: feature method. +import scanpy as sc +from scib.integration import scanorama + ## VIASH START par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', 'hvg': True, - 'scaling': True, - 'debug': True +} +meta = { + 'functionality_name': 'foo' } ## VIASH END -print('Importing libraries') -from pprint import pprint -import scanpy as sc -from scib.integration import scanorama - -if par['debug']: - pprint(par) - -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] - -print('Read adata') -adata = sc.read_h5ad(adata_file) +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) -if hvg: - print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']] -if scaling: - print('Scale') - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] - -print('Integrate') +print('Run scanorama', flush=True) +adata.X = adata.layers['normalized'] adata.X = scanorama(adata, batch='batch').X -print('Postprocess data') +print("Run PCA", flush=True) sc.pp.pca( adata, n_comps=50, - use_highly_variable=True, + use_highly_variable=False, svd_solver='arpack', return_info=True ) +del adata.X + +print("Run KNN", flush=True) sc.pp.neighbors(adata, use_rep='X_pca') -print('Save HDF5') +print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling - -adata.write(output, compression='gzip') +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/graph/methods/scanorama_feature/test.py b/src/batch_integration/graph/methods/scanorama_feature/test.py deleted file mode 100644 index dc58cce103..0000000000 --- a/src/batch_integration/graph/methods/scanorama_feature/test.py +++ /dev/null @@ -1,46 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'scanorama_feature' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/graph/methods/scvi/config.vsh.yaml index 9b067e801d..67913d2f95 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/graph/methods/scvi/config.vsh.yaml @@ -1,26 +1,28 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../../api/comp_method_graph.yaml functionality: name: scvi - namespace: batch_integration/graph/methods - version: dev - description: Run scVI on adata object - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } + description: Run scVI on adata object, use feature output + info: + type: method + output_type: graph + method_name: scVI + # paper_reference: "xxxxxxxxxxx" + # code_url: xxxxxxxxxxx + # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py + # v1_commit: xxxxxxxxxxxxxx + # preferred_normalization: log_cpm + # variants: + # combat: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/processed.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - type: python - packages: + pypi: - scvi + - pyyaml - type: nextflow diff --git a/src/batch_integration/graph/methods/scvi/run_example.sh b/src/batch_integration/graph/methods/scvi/run_example.sh deleted file mode 100644 index cf93de8974..0000000000 --- a/src/batch_integration/graph/methods/scvi/run_example.sh +++ /dev/null @@ -1,12 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_scvi.h5ad \ - --debug true diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/graph/methods/scvi/script.py index 3e7915a9af..960a6b3714 100644 --- a/src/batch_integration/graph/methods/scvi/script.py +++ b/src/batch_integration/graph/methods/scvi/script.py @@ -1,48 +1,32 @@ +# TODO: this should be a output_type: embedding method. +import scanpy as sc +from scib.integration import scvi + ## VIASH START par = { - 'input': './src/batch_integration/resources/datasets_pancreas.h5ad', - 'output': './src/batch_integration/resources/pancreas_bbknn.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', 'hvg': True, - 'scaling': True, - 'debug': True +} +meta = { + 'functionality_name' : 'foo' } ## VIASH END -print('Importing libraries') -from pprint import pprint -import scanpy as sc -from scib.integration import scvi +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) -if par['debug']: - pprint(par) +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']].copy() -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] - -print('Read adata') -adata = sc.read_h5ad(adata_file) - -if hvg: - print('Select HVGs') - adata = adata[:, adata.var['highly_variable']] - -if scaling: - print('Scale') - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] - -print('Integrate') +print('Run scvi', flush=True) +adata.X = adata.layers['normalized'] adata = scvi(adata, batch='batch') -print('Postprocess data') +print('Run kNN', flush=True) sc.pp.neighbors(adata, use_rep='X_emb') -print('Save HDF5') +print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] -adata.uns['hvg'] = hvg -adata.uns['scaled'] = scaling - -adata.write(output, compression='gzip') +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/graph/methods/scvi/test.py b/src/batch_integration/graph/methods/scvi/test.py deleted file mode 100644 index d1a7b35d2d..0000000000 --- a/src/batch_integration/graph/methods/scvi/test.py +++ /dev/null @@ -1,46 +0,0 @@ -from os import path -import subprocess -import numpy as np -import scanpy as sc - -np.random.seed(42) - -method = 'scvi' -output_file = method + '.h5ad' - -print(">> Running script") -out = subprocess.check_output([ - "./" + method, - "--input", 'processed.h5ad', - "--hvg", 'False', - "--scaling", 'False', - "--output", output_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_file) - -print('>> Checking API') -adata = sc.read(output_file) - -assert 'dataset_id' in adata.uns -assert 'label' in adata.obs.columns -assert 'batch' in adata.obs.columns -assert 'highly_variable' in adata.var -assert 'counts' in adata.layers -assert 'logcounts' in adata.layers -assert 'logcounts_scaled' in adata.layers -assert 'X_pca' in adata.obsm -assert 'X_uni' in adata.obsm -assert 'uni' in adata.uns -assert 'uni_distances' in adata.obsp -assert 'uni_connectivities' in adata.obsp - -assert 'connectivities' in adata.obsp -assert 'distances' in adata.obsp -assert 'hvg' in adata.uns -assert adata.uns['hvg'] == False -assert 'scaled' in adata.uns -assert adata.uns['scaled'] == False - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml deleted file mode 100644 index f7e0f48e02..0000000000 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ /dev/null @@ -1,25 +0,0 @@ -# use metric api spec -__merge__: ../../../api/comp_metric.yaml -functionality: - name: ari - namespace: batch_integration/graph/metrics - version: dev - description: Adjusted rand index (ARI) - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/graph/methods/bbknn.h5ad - - type: python_script - path: test_combat.py - - path: ../../../../../resources_test/batch_integration/graph/methods/combat.h5ad -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - - type: nextflow diff --git a/src/batch_integration/graph/metrics/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py deleted file mode 100644 index 8679e960a7..0000000000 --- a/src/batch_integration/graph/metrics/ari/script.py +++ /dev/null @@ -1,45 +0,0 @@ -## VIASH START -par = { - 'input': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/graph/resources/ari_pancreas_mnn.tsv', - 'debug': True -} -## VIASH END - -print('Importing libraries') -import pprint -import scanpy as sc -from scib.metrics.clustering import opt_louvain -from scib.metrics import ari - -if par['debug']: - pprint.pprint(par) - -OUTPUT_TYPE = 'graph' -METRIC = 'ari' - -adata_file = par['input'] -output = par['output'] - -print('Read adata') -adata = sc.read(adata_file) -name = adata.uns['dataset_id'] - -print('clustering') -opt_louvain( - adata, - label_key='label', - cluster_key='cluster', - plot=False, - inplace=True, - force=True -) - -print('compute score') -score = ari(adata, group1='cluster', group2='label') - -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py deleted file mode 100644 index 4398ac8254..0000000000 --- a/src/batch_integration/graph/metrics/ari/test.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'ari' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'bbknn.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) -result = pd.read_table(metric_file) - -print(">> Check that score makes sense") -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/test_combat.py b/src/batch_integration/graph/metrics/ari/test_combat.py deleted file mode 100644 index 6fc4bebbed..0000000000 --- a/src/batch_integration/graph/metrics/ari/test_combat.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'ari' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) -result = pd.read_table(metric_file) - -print(">> Check that score makes sense") -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml new file mode 100644 index 0000000000..ed21ca464c --- /dev/null +++ b/src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml @@ -0,0 +1,51 @@ +# use metric api spec +__merge__: ../../../api/comp_metric.yaml +functionality: + name: clustering_overlap + namespace: batch_integration/graph/metrics + description: Metrics that are based on computing the clustering overlap. + info: + output_type: graph + metrics: + - metric_id: ari + metric_name: ARI + metric_description: | + The Adjusted Rand Index (ARI) compares the overlap of two clusterings; + it considers both correct clustering overlaps while also counting correct + disagreements between two clusterings. + We compared the cell-type labels with the NMI-optimized + Louvain clustering computed on the integrated dataset. + The adjustment of the Rand index corrects for randomly correct labels. + An ARI of 0 or 1 corresponds to random labeling or a perfect match, + respectively. + We used the scikit-learn implementation of the ARI. + paper_reference: hubert1985comparing + min: 0 + max: 1 + maximize: true + - metric_id: nmi + metric_name: NMI + metric_description: | + Normalized Mutual Information (NMI) compares the overlap of two clusterings. + We used NMI to compare the cell-type labels with Louvain clusters computed on + the integrated dataset. The overlap was scaled using the mean of the entropy terms + for cell-type and cluster labels. Thus, NMI scores of 0 or 1 correspond to uncorrelated + clustering or a perfect match, respectively. We performed optimized Louvain clustering + for this metric to obtain the best match between clusters and labels. + Louvain clustering was performed at a resolution range of 0.1 to 2 in steps of 0.1, + and the clustering output with the highest NMI with the label set was used. We + the scikit-learn implementation of NMI. + paper_reference: amelio2015normalized + min: 0 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml + - type: nextflow diff --git a/src/batch_integration/graph/metrics/clustering_overlap/script.py b/src/batch_integration/graph/metrics/clustering_overlap/script.py new file mode 100644 index 0000000000..a4ddab9c4e --- /dev/null +++ b/src/batch_integration/graph/metrics/clustering_overlap/script.py @@ -0,0 +1,49 @@ +import yaml +import anndata as ad +from scib.metrics.clustering import opt_louvain +from scib.metrics import ari, nmi + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} +## VIASH END + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) + +print('Run Louvain clustering', flush=True) +opt_louvain( + input, + label_key='label', + cluster_key='cluster', + plot=False, + inplace=True, + force=True +) + +print('Compute ARI score', flush=True) +ari_score = ari(input, group1='cluster', group2='label') + +print('Compute NMI score', flush=True) +nmi_score = nmi(input, group1='cluster', group2='label') + +print("Create output AnnData object", flush=True) +output = ad.AnnData( + uns={ + "dataset_id": input.uns['dataset_id'], + "method_id": input.uns['method_id'], + "metric_ids": [ "ari", "nmi" ], + "metric_values": [ ari_score, nmi_score ], + "hvg": input.uns['hvg'], + "scaled": input.uns['scaled'], + "output_type": config["functionality"]["info"]["output_type"], + } +) + +print("Write data to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml deleted file mode 100644 index 340a69dbaa..0000000000 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ /dev/null @@ -1,25 +0,0 @@ -# use metric api spec -__merge__: ../../../api/comp_metric.yaml -functionality: - name: nmi - namespace: batch_integration/graph/metrics - version: dev - description: Normalized mutual information (NMI) - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/graph/methods/bbknn.h5ad - - type: python_script - path: test_combat.py - - path: ../../../../../resources_test/batch_integration/graph/methods/combat.h5ad -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - - type: nextflow diff --git a/src/batch_integration/graph/metrics/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py deleted file mode 100644 index 19653f58ea..0000000000 --- a/src/batch_integration/graph/metrics/nmi/script.py +++ /dev/null @@ -1,45 +0,0 @@ -## VIASH START -par = { - 'input': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/graph/resources/nmi_pancreas_mnn.tsv', - 'debug': True -} -## VIASH END - -print('Importing libraries') -import pprint -import scanpy as sc -from scib.metrics.clustering import opt_louvain -from scib.metrics import nmi - -if par['debug']: - pprint.pprint(par) - -OUTPUT_TYPE = 'graph' -METRIC = 'nmi' - -adata_file = par['input'] -output = par['output'] - -print('Read adata') -adata = sc.read(adata_file) -name = adata.uns['dataset_id'] - -print('clustering') -opt_louvain( - adata, - label_key='label', - cluster_key='cluster', - plot=False, - inplace=True, - force=True -) - -print('compute score') -score = nmi(adata, group1='cluster', group2='label') - -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py deleted file mode 100644 index bc13c152d5..0000000000 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'nmi' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'bbknn.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) - -print(">> Check that score makes sense") -result = pd.read_table(metric_file) -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/test_combat.py b/src/batch_integration/graph/metrics/nmi/test_combat.py deleted file mode 100644 index f925918e2d..0000000000 --- a/src/batch_integration/graph/metrics/nmi/test_combat.py +++ /dev/null @@ -1,29 +0,0 @@ -from os import path -import subprocess -import pandas as pd -import numpy as np - -np.random.seed(42) - -metric = 'nmi' -metric_file = metric + '.tsv' - -print(">> Running script") -out = subprocess.check_output([ - "./" + metric, - "--input", 'combat.h5ad', - "--output", metric_file -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(metric_file) -result = pd.read_table(metric_file) - -print(">> Check that score makes sense") -assert result.shape == (1, 4) -score = result.loc[0, 'value'] -print(score) - -assert 0 <= score <= 1 - -print(">> All tests passed successfully") diff --git a/src/batch_integration/library.bib b/src/batch_integration/library.bib new file mode 100644 index 0000000000..bc4144d931 --- /dev/null +++ b/src/batch_integration/library.bib @@ -0,0 +1,23 @@ +@article{hubert1985comparing, + doi = {10.1007/bf01908075}, + url = {https://doi.org/10.1007/bf01908075}, + year = {1985}, + month = dec, + publisher = {Springer Science and Business Media {LLC}}, + volume = {2}, + number = {1}, + pages = {193--218}, + author = {Lawrence Hubert and Phipps Arabie}, + title = {Comparing partitions}, + journal = {Journal of Classification} +} +@inproceedings{amelio2015normalized, + doi = {10.1145/2808797.2809344}, + url = {https://doi.org/10.1145/2808797.2809344}, + year = {2015}, + month = aug, + publisher = {{ACM}}, + author = {Alessia Amelio and Clara Pizzuti}, + title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?}, + booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015} +} \ No newline at end of file diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index 14fb196f35..c7257310c2 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -18,11 +18,10 @@ mkdir -p $DATASET_DIR # process dataset echo process data... -viash run src/batch_integration/datasets/preprocessing/config.vsh.yaml -- \ +viash run src/batch_integration/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ - --output $DATASET_DIR/pancreas/processed.h5ad \ - --label celltype \ - --batch tech \ + --output_unintegrated $DATASET_DIR/pancreas/unintegrated.h5ad \ + --output_solution $DATASET_DIR/pancreas/solution.h5ad \ --hvgs 100 # run methods @@ -30,16 +29,16 @@ echo run methods... # Graph methods viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/processed.h5ad \ + --input $DATASET_DIR/pancreas/unintegrated.h5ad \ --output $DATASET_DIR/graph/methods/bbknn.h5ad viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/processed.h5ad \ + --input $DATASET_DIR/pancreas/unintegrated.h5ad \ --output $DATASET_DIR/graph/methods/combat.h5ad # Embedding method viash run src/batch_integration/embedding/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/processed.h5ad \ + --input $DATASET_DIR/pancreas/unintegrated.h5ad \ --output $DATASET_DIR/embedding/methods/combat.h5ad # run one metric diff --git a/src/batch_integration/split_dataset/config.vsh.yaml b/src/batch_integration/split_dataset/config.vsh.yaml new file mode 100644 index 0000000000..0bf443ddf8 --- /dev/null +++ b/src/batch_integration/split_dataset/config.vsh.yaml @@ -0,0 +1,33 @@ +__merge__: ../api/comp_split_dataset.yaml +functionality: + name: split_dataset + namespace: batch_integration + description: Preprocess adata object for data integration + arguments: + - name: "--obs_label" + type: "string" + description: "Which .obs slot to use as label." + default: "celltype" + - name: "--obs_batch" + type: "string" + description: "Which .obs slot to use as batch covariate." + default: "batch" + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + required: false + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../resources_test/common/pancreas/ +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: pyyaml + - type: nextflow diff --git a/src/batch_integration/split_dataset/script.py b/src/batch_integration/split_dataset/script.py new file mode 100644 index 0000000000..10f716f4c8 --- /dev/null +++ b/src/batch_integration/split_dataset/script.py @@ -0,0 +1,104 @@ +import anndata as ad +import scib +import yaml +import re +import pandas as pd + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'hvgs': 2000, + 'output': 'output.h5ad' +} +meta = {} +## VIASH END + +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) + +def compute_batched_hvg(adata, n_hvgs): + adata = adata.copy() + adata.X = adata.layers['normalized'].copy() + if n_hvgs > adata.n_vars or n_hvgs <= 0: + hvg_list = adata.var_names.tolist() + else: + hvg_list = scib.pp.hvg_batch( + adata, + batch_key='batch', + target_genes=n_hvgs, + adataOut=False + ) + adata.var['hvg'] = adata.var_names.isin(hvg_list) + del adata.X + return adata + + +# read the .config.vsh.yaml to find out which output slots need to be copied to which output file +def read_slots(par, meta): + # read output spec from yaml + with open(meta["config"], "r") as file: + config = yaml.safe_load(file) + + output_struct_slots = {} + + # fetch info on which slots should be copied to which file + for arg in config["functionality"]["arguments"]: + if re.match("--output_", arg["name"]): + file = re.sub("--output_", "", arg["name"]) + + struct_slots = arg['info']['slots'] + out = {} + for (struct, slots) in struct_slots.items(): + out[struct] = { slot['name'] : slot['name'] for slot in slots } + + # rename source keys + if 'obs' in out: + if 'label' in out['obs']: + out['obs']['label'] = par['obs_label'] + if 'batch' in out['obs']: + out['obs']['batch'] = par['obs_batch'] + + output_struct_slots[file] = out + + return output_struct_slots + +# create new anndata objects according to api spec +def subset_anndata(adata_sub, slot_info): + structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] + kwargs = {} + + for struct in structs: + slot_mapping = slot_info.get(struct, {}) + data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} + if len(data) > 0: + if struct in ["obs", "var"]: + data = pd.concat(data, axis=1) + kwargs[struct] = data + elif struct in ["obs", "var"]: + # if no columns need to be copied, we still need an "obs" and a "var" + # to help determine the shape of the adata + kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] + + return ad.AnnData(**kwargs) + +print(f'Select {par["hvgs"]} highly variable genes', flush=True) +adata_with_hvg = compute_batched_hvg(input, n_hvgs=par['hvgs']) + +print(">> Figuring out which data needs to be copied to which output file", flush=True) +slot_info_per_output = read_slots(par, meta) + +print(">> Create unintegrated object", flush=True) +output_unintegrated = subset_anndata( + adata_sub=adata_with_hvg, + slot_info=slot_info_per_output["unintegrated"] +) + +print(">> Create solution object", flush=True) +output_solution = subset_anndata( + adata_sub=adata_with_hvg, + slot_info=slot_info_per_output["solution"] +) + +print('Writing adatas to file', flush=True) +output_unintegrated.write(par['output_unintegrated'], compression='gzip') +output_solution.write(par['output_solution'], compression='gzip') diff --git a/src/batch_integration/split_dataset/test.py b/src/batch_integration/split_dataset/test.py new file mode 100644 index 0000000000..e678e7a1c9 --- /dev/null +++ b/src/batch_integration/split_dataset/test.py @@ -0,0 +1,51 @@ +import os +import subprocess +import anndata as ad +import numpy as np + +input_file = meta["resources_dir"] + '/pancreas/dataset.h5ad' +unintegrated_file = 'unintegrated.h5ad' +solution_file = 'solution.h5ad' +n_hvgs = 100 + +cmd_args = [ + meta["executable"], + '--input', input_file, + '--hvgs', str(n_hvgs), + '--output_unintegrated', unintegrated_file, + '--output_solution', solution_file +] +print('>> Running script') +subprocess.run(cmd_args, check=True) + +print('>> Checking whether outputs exist') +assert os.path.exists(unintegrated_file) +assert os.path.exists(solution_file) + +print('>> Read anndata files') +input = ad.read_h5ad(input_file) +unintegrated = ad.read_h5ad(unintegrated_file) +solution = ad.read_h5ad(solution_file) + +print("input:", input) +print("unintegrated:", unintegrated) +print("solution:", solution) + +print(">> Checking dimensions, make sure no cells were dropped") +assert input.n_obs == unintegrated.n_obs +assert input.n_obs == solution.n_obs +assert input.n_vars == unintegrated.n_vars +assert input.n_vars == solution.n_vars + +print(">> Checking whether data from input was copied properly to output") +assert unintegrated.uns["dataset_id"] == input.uns["dataset_id"] +assert solution.uns["dataset_id"] == input.uns["dataset_id"] + +print(">> Check output") +assert unintegrated.var['hvg'].dtype == 'bool' +assert unintegrated.var['hvg'].sum() == n_hvgs + +print(">> Check whether certain slots exist") +# todo: use helper function for this + +print('>> All tests passed successfully') diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index e03c396010..38515bd7d3 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -4,18 +4,17 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" // import methods -include { bbknn } from "$targetDir/batch_integration/graph/methods/bbknn/main.nf" params(params) -include { combat } from "$targetDir/batch_integration/graph/methods/combat/main.nf" params(params) -include { scanorama_embed } from "$targetDir/batch_integration/graph/methods/scanorama_embed/main.nf" params(params) -include { scanorama_feature } from "$targetDir/batch_integration/graph/methods/scanorama_feature/main.nf" params(params) -include { scvi } from "$targetDir/batch_integration/graph/methods/scvi/main.nf" params(params) +include { bbknn } from "$targetDir/batch_integration/graph/methods/bbknn/main.nf" +include { combat } from "$targetDir/batch_integration/graph/methods/combat/main.nf" +include { scanorama_embed } from "$targetDir/batch_integration/graph/methods/scanorama_embed/main.nf" +include { scanorama_feature } from "$targetDir/batch_integration/graph/methods/scanorama_feature/main.nf" +include { scvi } from "$targetDir/batch_integration/graph/methods/scvi/main.nf" // import metrics -include { ari } from "$targetDir/batch_integration/graph/metrics/ari/main.nf" params(params) -include { nmi } from "$targetDir/batch_integration/graph/metrics/nmi/main.nf" params(params) +include { clustering_overlap } from "$targetDir/batch_integration/graph/metrics/clustering_overlap/main.nf" // tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" From 744da04cff6c325cb913e75fd4b19142255b1f08 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 9 Feb 2023 14:07:45 +0100 Subject: [PATCH 0734/1233] restructure Former-commit-id: c79c673ba824e62cbbe9b508ac26cbec3a8c117b --- .../api/anndata_integrated_graph.yaml | 6 +-- src/batch_integration/changes.md | 41 ++++++++++++++++++- .../combat/config.vsh.yaml | 2 +- .../combat/run_example.sh | 0 .../combat/script.py | 0 .../combat/test.py | 0 .../bbknn/config.vsh.yaml | 8 ++-- .../methods => methods_graph}/bbknn/script.py | 0 .../combat/config.vsh.yaml | 2 +- .../combat/script.py | 0 .../scanorama_embed/config.vsh.yaml | 2 +- .../scanorama_embed/script.py | 0 .../scanorama_feature/config.vsh.yaml | 2 +- .../scanorama_feature/script.py | 0 .../scvi/config.vsh.yaml | 2 +- .../methods => methods_graph}/scvi/script.py | 0 .../asw_batch/config.vsh.yaml | 2 +- .../asw_batch/script.py | 0 .../asw_label/config.vsh.yaml | 2 +- .../asw_label/script.py | 0 .../cell_cycle_conservation/config.vsh.yaml | 2 +- .../cell_cycle_conservation/script.py | 0 .../pcr/config.vsh.yaml | 2 +- .../pcr/script.py | 0 .../clustering_overlap/config.vsh.yaml | 2 +- .../clustering_overlap/script.py | 0 .../README.md => old_readmes/datasets.md} | 0 .../README.md => old_readmes/embedding.md} | 0 .../embedding_metrics.md} | 0 .../{graph/README.md => old_readmes/graph.md} | 0 .../graph_methods.md} | 0 .../graph_metrics.md} | 0 32 files changed, 55 insertions(+), 20 deletions(-) rename src/batch_integration/{embedding/methods => methods_embedding}/combat/config.vsh.yaml (92%) rename src/batch_integration/{embedding/methods => methods_embedding}/combat/run_example.sh (100%) rename src/batch_integration/{embedding/methods => methods_embedding}/combat/script.py (100%) rename src/batch_integration/{embedding/methods => methods_embedding}/combat/test.py (100%) rename src/batch_integration/{graph/methods => methods_graph}/bbknn/config.vsh.yaml (70%) rename src/batch_integration/{graph/methods => methods_graph}/bbknn/script.py (100%) rename src/batch_integration/{graph/methods => methods_graph}/combat/config.vsh.yaml (92%) rename src/batch_integration/{graph/methods => methods_graph}/combat/script.py (100%) rename src/batch_integration/{graph/methods => methods_graph}/scanorama_embed/config.vsh.yaml (93%) rename src/batch_integration/{graph/methods => methods_graph}/scanorama_embed/script.py (100%) rename src/batch_integration/{graph/methods => methods_graph}/scanorama_feature/config.vsh.yaml (93%) rename src/batch_integration/{graph/methods => methods_graph}/scanorama_feature/script.py (100%) rename src/batch_integration/{graph/methods => methods_graph}/scvi/config.vsh.yaml (93%) rename src/batch_integration/{graph/methods => methods_graph}/scvi/script.py (100%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/asw_batch/config.vsh.yaml (91%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/asw_batch/script.py (100%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/asw_label/config.vsh.yaml (89%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/asw_label/script.py (100%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/cell_cycle_conservation/config.vsh.yaml (92%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/cell_cycle_conservation/script.py (100%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/pcr/config.vsh.yaml (88%) rename src/batch_integration/{embedding/metrics => metrics_embedding}/pcr/script.py (100%) rename src/batch_integration/{graph/metrics => metrics_graph}/clustering_overlap/config.vsh.yaml (98%) rename src/batch_integration/{graph/metrics => metrics_graph}/clustering_overlap/script.py (100%) rename src/batch_integration/{datasets/README.md => old_readmes/datasets.md} (100%) rename src/batch_integration/{embedding/README.md => old_readmes/embedding.md} (100%) rename src/batch_integration/{embedding/metrics/README.md => old_readmes/embedding_metrics.md} (100%) rename src/batch_integration/{graph/README.md => old_readmes/graph.md} (100%) rename src/batch_integration/{graph/methods/README.md => old_readmes/graph_methods.md} (100%) rename src/batch_integration/{graph/metrics/README.md => old_readmes/graph_metrics.md} (100%) diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml index 5263417de8..dce7831365 100644 --- a/src/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -7,10 +7,6 @@ info: slots: obsp: - type: double - name: integration_distances - description: Neighbors distance matrix. - required: true - - type: double - name: integration_connectivities + name: connectivities description: Neighbors connectivities matrix. required: true diff --git a/src/batch_integration/changes.md b/src/batch_integration/changes.md index a33ca3dc84..124df564a4 100644 --- a/src/batch_integration/changes.md +++ b/src/batch_integration/changes.md @@ -21,4 +21,43 @@ TODO: * Create a normalization variant: log_cpm -> log_cpm_batchscaled * Rename knn_connectivities to connectivities in solution -* Simplify renaming fields in split_dataset, e.g. celltype -> label, knn_connectivities -> connectivities. \ No newline at end of file +* Simplify renaming fields in split_dataset, e.g. celltype -> label, knn_connectivities -> connectivities. + +## proposed batch integration structure + +* split_dataset + - input: common dataset + - output_unintegrated: for methods. important slots: + .layers["normalized"] + .obs["batch"] + .obs["label"]? (probably not) + .var["hvg"] + .obsm["X_pca"]? (probably not) + - output_solution: for metrics + .obs["batch"] + .obs["label"] + .obsp["knn_connectivities"] -- could be renamed to connectivities +* methods_graph + example: bbknn + output_slots: + .obsp["connectivities"] +* methods_embed + example: scanorama_embed + output_slots: + .obsm["X_emb"] +* methods_feature + example: scanorama_feature + output_slots: + .X +* converters + - feature_to_embed: runs PCA on .X + - embed_to_graph: runs sc.pp.neighbors on .obsm["X_emb"] +* metrics_graph +* metrics_embed +* metrics_feature + +New todos: + +- move methods and metrics to the correct folders (e.g. scanorama_embed to `methods_embed/scanorama_embed`) +- create API files for all of the above componenent types +- compare current components with v1, list the ones that are missing \ No newline at end of file diff --git a/src/batch_integration/embedding/methods/combat/config.vsh.yaml b/src/batch_integration/methods_embedding/combat/config.vsh.yaml similarity index 92% rename from src/batch_integration/embedding/methods/combat/config.vsh.yaml rename to src/batch_integration/methods_embedding/combat/config.vsh.yaml index f4a847857c..45f1b4e4d8 100644 --- a/src/batch_integration/embedding/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods_embedding/combat/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../../api/comp_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: combat namespace: batch_integration/embedding/methods diff --git a/src/batch_integration/embedding/methods/combat/run_example.sh b/src/batch_integration/methods_embedding/combat/run_example.sh similarity index 100% rename from src/batch_integration/embedding/methods/combat/run_example.sh rename to src/batch_integration/methods_embedding/combat/run_example.sh diff --git a/src/batch_integration/embedding/methods/combat/script.py b/src/batch_integration/methods_embedding/combat/script.py similarity index 100% rename from src/batch_integration/embedding/methods/combat/script.py rename to src/batch_integration/methods_embedding/combat/script.py diff --git a/src/batch_integration/embedding/methods/combat/test.py b/src/batch_integration/methods_embedding/combat/test.py similarity index 100% rename from src/batch_integration/embedding/methods/combat/test.py rename to src/batch_integration/methods_embedding/combat/test.py diff --git a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml b/src/batch_integration/methods_graph/bbknn/config.vsh.yaml similarity index 70% rename from src/batch_integration/graph/methods/bbknn/config.vsh.yaml rename to src/batch_integration/methods_graph/bbknn/config.vsh.yaml index 272a8aa9df..2ec1669053 100644 --- a/src/batch_integration/graph/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods_graph/bbknn/config.vsh.yaml @@ -1,13 +1,13 @@ # use method api spec -__merge__: ../../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_graph.yaml functionality: name: bbknn - description: Run BBKNN on adata object + description: "BBKNN: fast batch alignment of single cell transcriptomes" info: type: method method_name: BBKNN - # paper_reference: "xxxxxxxxxxx" - # code_url: xxxxxxxxxxx + paper_reference: "polanski2020bbknn" + code_url: https://github.com/Teichlab/bbknn # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py # v1_commit: xxxxxxxxxxxxxx # preferred_normalization: log_cpm diff --git a/src/batch_integration/graph/methods/bbknn/script.py b/src/batch_integration/methods_graph/bbknn/script.py similarity index 100% rename from src/batch_integration/graph/methods/bbknn/script.py rename to src/batch_integration/methods_graph/bbknn/script.py diff --git a/src/batch_integration/graph/methods/combat/config.vsh.yaml b/src/batch_integration/methods_graph/combat/config.vsh.yaml similarity index 92% rename from src/batch_integration/graph/methods/combat/config.vsh.yaml rename to src/batch_integration/methods_graph/combat/config.vsh.yaml index c87450ff5e..9b1c1feeec 100644 --- a/src/batch_integration/graph/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods_graph/combat/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_graph.yaml functionality: name: combat info: diff --git a/src/batch_integration/graph/methods/combat/script.py b/src/batch_integration/methods_graph/combat/script.py similarity index 100% rename from src/batch_integration/graph/methods/combat/script.py rename to src/batch_integration/methods_graph/combat/script.py diff --git a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods_graph/scanorama_embed/config.vsh.yaml similarity index 93% rename from src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml rename to src/batch_integration/methods_graph/scanorama_embed/config.vsh.yaml index 0f58c85656..b2d7a83e42 100644 --- a/src/batch_integration/graph/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods_graph/scanorama_embed/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_graph.yaml functionality: name: scanorama_embed description: Run Scanorama on adata object, use embedding output diff --git a/src/batch_integration/graph/methods/scanorama_embed/script.py b/src/batch_integration/methods_graph/scanorama_embed/script.py similarity index 100% rename from src/batch_integration/graph/methods/scanorama_embed/script.py rename to src/batch_integration/methods_graph/scanorama_embed/script.py diff --git a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml similarity index 93% rename from src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml rename to src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml index 2845573e7d..01f4646898 100644 --- a/src/batch_integration/graph/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_graph.yaml functionality: name: scanorama_feature description: Run Scanorama on adata object, use feature output diff --git a/src/batch_integration/graph/methods/scanorama_feature/script.py b/src/batch_integration/methods_graph/scanorama_feature/script.py similarity index 100% rename from src/batch_integration/graph/methods/scanorama_feature/script.py rename to src/batch_integration/methods_graph/scanorama_feature/script.py diff --git a/src/batch_integration/graph/methods/scvi/config.vsh.yaml b/src/batch_integration/methods_graph/scvi/config.vsh.yaml similarity index 93% rename from src/batch_integration/graph/methods/scvi/config.vsh.yaml rename to src/batch_integration/methods_graph/scvi/config.vsh.yaml index 67913d2f95..6cd55d2713 100644 --- a/src/batch_integration/graph/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods_graph/scvi/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_graph.yaml functionality: name: scvi description: Run scVI on adata object, use feature output diff --git a/src/batch_integration/graph/methods/scvi/script.py b/src/batch_integration/methods_graph/scvi/script.py similarity index 100% rename from src/batch_integration/graph/methods/scvi/script.py rename to src/batch_integration/methods_graph/scvi/script.py diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml similarity index 91% rename from src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml rename to src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml index 42cc70541a..0f62ac0590 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml @@ -1,5 +1,5 @@ # use metric api spec -__merge__: ../../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: asw_batch namespace: batch_integration/embedding/metrics diff --git a/src/batch_integration/embedding/metrics/asw_batch/script.py b/src/batch_integration/metrics_embedding/asw_batch/script.py similarity index 100% rename from src/batch_integration/embedding/metrics/asw_batch/script.py rename to src/batch_integration/metrics_embedding/asw_batch/script.py diff --git a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml similarity index 89% rename from src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml rename to src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml index 9112bf2689..ed61287b75 100644 --- a/src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml @@ -1,5 +1,5 @@ # use metric api spec -__merge__: ../../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: asw_label namespace: batch_integration/embedding/metrics diff --git a/src/batch_integration/embedding/metrics/asw_label/script.py b/src/batch_integration/metrics_embedding/asw_label/script.py similarity index 100% rename from src/batch_integration/embedding/metrics/asw_label/script.py rename to src/batch_integration/metrics_embedding/asw_label/script.py diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml similarity index 92% rename from src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml rename to src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml index d7042df51f..c334a690d1 100644 --- a/src/batch_integration/embedding/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml @@ -1,5 +1,5 @@ # use metric api spec -__merge__: ../../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: cell_cycle_conservation namespace: batch_integration/embedding/metrics diff --git a/src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py similarity index 100% rename from src/batch_integration/embedding/metrics/cell_cycle_conservation/script.py rename to src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py diff --git a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml similarity index 88% rename from src/batch_integration/embedding/metrics/pcr/config.vsh.yaml rename to src/batch_integration/metrics_embedding/pcr/config.vsh.yaml index 4087743d7d..f4e9467b52 100644 --- a/src/batch_integration/embedding/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml @@ -1,5 +1,5 @@ # use metric api spec -__merge__: ../../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: pcr namespace: batch_integration/embedding/metrics diff --git a/src/batch_integration/embedding/metrics/pcr/script.py b/src/batch_integration/metrics_embedding/pcr/script.py similarity index 100% rename from src/batch_integration/embedding/metrics/pcr/script.py rename to src/batch_integration/metrics_embedding/pcr/script.py diff --git a/src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml similarity index 98% rename from src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml rename to src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml index ed21ca464c..9e1c6c16e2 100644 --- a/src/batch_integration/graph/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml @@ -1,5 +1,5 @@ # use metric api spec -__merge__: ../../../api/comp_metric.yaml +__merge__: ../../api/comp_metric.yaml functionality: name: clustering_overlap namespace: batch_integration/graph/metrics diff --git a/src/batch_integration/graph/metrics/clustering_overlap/script.py b/src/batch_integration/metrics_graph/clustering_overlap/script.py similarity index 100% rename from src/batch_integration/graph/metrics/clustering_overlap/script.py rename to src/batch_integration/metrics_graph/clustering_overlap/script.py diff --git a/src/batch_integration/datasets/README.md b/src/batch_integration/old_readmes/datasets.md similarity index 100% rename from src/batch_integration/datasets/README.md rename to src/batch_integration/old_readmes/datasets.md diff --git a/src/batch_integration/embedding/README.md b/src/batch_integration/old_readmes/embedding.md similarity index 100% rename from src/batch_integration/embedding/README.md rename to src/batch_integration/old_readmes/embedding.md diff --git a/src/batch_integration/embedding/metrics/README.md b/src/batch_integration/old_readmes/embedding_metrics.md similarity index 100% rename from src/batch_integration/embedding/metrics/README.md rename to src/batch_integration/old_readmes/embedding_metrics.md diff --git a/src/batch_integration/graph/README.md b/src/batch_integration/old_readmes/graph.md similarity index 100% rename from src/batch_integration/graph/README.md rename to src/batch_integration/old_readmes/graph.md diff --git a/src/batch_integration/graph/methods/README.md b/src/batch_integration/old_readmes/graph_methods.md similarity index 100% rename from src/batch_integration/graph/methods/README.md rename to src/batch_integration/old_readmes/graph_methods.md diff --git a/src/batch_integration/graph/metrics/README.md b/src/batch_integration/old_readmes/graph_metrics.md similarity index 100% rename from src/batch_integration/graph/metrics/README.md rename to src/batch_integration/old_readmes/graph_metrics.md From c7f314364a17440dbe4c9bba12213ca1efaa2297 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 9 Feb 2023 16:45:43 +0100 Subject: [PATCH 0735/1233] rafactor to v2 Former-commit-id: c2e84c44c5e61fa9cde44e8ef7712d1c5fee2c21 --- .../api/anndata_integrated_feature.yaml | 11 +++ .../api/comp_method_embedding.yaml | 85 ++++++++++--------- .../api/comp_method_feature.yaml | 56 ++++++++++++ .../api/comp_method_graph.yaml | 2 +- .../methods_embedding/combat/config.vsh.yaml | 16 ++-- .../methods_embedding/combat/run_example.sh | 14 --- .../methods_embedding/combat/script.py | 28 ++---- .../methods_embedding/combat/test.py | 49 ----------- .../feature_to_embed/config.vsh.yaml | 23 +++++ .../feature_to_embed/script.py | 32 +++++++ .../scanorama_embed/config.vsh.yaml | 0 .../scanorama_embed/script.py | 0 .../methods_feature/combat/config.vsh.yaml | 34 ++++++++ .../combat/script.py | 13 --- .../methods_graph/bbknn/config.vsh.yaml | 18 ++-- .../methods_graph/combat/config.vsh.yaml | 25 ------ 16 files changed, 230 insertions(+), 176 deletions(-) create mode 100644 src/batch_integration/api/anndata_integrated_feature.yaml create mode 100644 src/batch_integration/api/comp_method_feature.yaml delete mode 100644 src/batch_integration/methods_embedding/combat/run_example.sh delete mode 100644 src/batch_integration/methods_embedding/combat/test.py create mode 100644 src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml create mode 100644 src/batch_integration/methods_embedding/feature_to_embed/script.py rename src/batch_integration/{methods_graph => methods_embedding}/scanorama_embed/config.vsh.yaml (100%) rename src/batch_integration/{methods_graph => methods_embedding}/scanorama_embed/script.py (100%) create mode 100644 src/batch_integration/methods_feature/combat/config.vsh.yaml rename src/batch_integration/{methods_graph => methods_feature}/combat/script.py (75%) delete mode 100644 src/batch_integration/methods_graph/combat/config.vsh.yaml diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml new file mode 100644 index 0000000000..40499faace --- /dev/null +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -0,0 +1,11 @@ +__merge__: "anndata_unintegrated.yaml" +type: file +description: Integrated AnnData HDF5 file. +example: input.h5ad +info: + short_description: "Integrated Graph" + slots: + X: + - type: double + description: integrated feature + required: true diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 12e5118f90..e4e8389dec 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -5,7 +5,6 @@ functionality: - name: --input __merge__: anndata_unintegrated.yaml - name: --output - alternatives: [ -o ] direction: output __merge__: anndata_integrated_embedding.yaml - name: --hvg @@ -13,57 +12,59 @@ functionality: description: Whether to subset to highly variable genes default: false required: false - test_resources: - - path: ../../../../../resources_test/batch_integration/pancreas/ - - type: python_script - path: generic_test.py - text: | - from os import path - import subprocess - import numpy as np - import anndata as ad + # ! Will not work with feature_to_embed + # test_resources: + # - path: ../../../../resources_test/batch_integration/pancreas/ + # - type: python_script + # path: generic_test.py + # text: | + # from os import path + # import subprocess + # import numpy as np + # import anndata as ad - print(">> Running script", flush=True) + # print(">> Running script", flush=True) - input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" - output_path = "embeddding.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path - ] + # input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" + # output_path = "embeddding.h5ad" + # cmd = [ + # meta['executable'], + # "--input", input_path, + # "--output", output_path + # ] - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) + # print(">> Checking whether input file exists", flush=True) + # assert path.exists(input_path) - print(">> Running script as test", flush=True) - subprocess.run(cmd, check=True) + # print(">> Running script as test", flush=True) + # out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout + # print(out) - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) + # print(">> Checking whether output file exists", flush=True) + # assert path.exists(output_path) - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) + # print(">> Reading h5ad files", flush=True) + # input = ad.read_h5ad(input_path) + # output = ad.read_h5ad(output_path) - print(f"input: {input}", flush=True) - print(f"output: {output}", flush=True) + # print(f"input: {input}", flush=True) + # print(f"output: {output}", flush=True) - print(">> Checking whether predictions were added", flush=True) - assert 'dataset_id' in output.uns - assert 'X_pca' in output.obsm - assert 'X_emb' in output.obsm - assert 'normalization_id' in output.uns - assert 'method_id' in output.uns - assert meta['fuctionality_name'] == output.uns['method_id'] + # print(">> Checking whether predictions were added", flush=True) + # assert 'dataset_id' in output.uns + # assert 'X_pca' in output.obsm + # assert 'X_emb' in output.obsm + # assert 'normalization_id' in output.uns + # assert 'method_id' in output.uns + # assert meta['fuctionality_name'] == output.uns['method_id'] - assert 'hvg' in output.uns + # assert 'hvg' in output.uns - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] + # print(">> Checking whether data from input was copied properly to output", flush=True) + # assert input.n_obs == output.n_obs + # assert input.uns["dataset_id"] == output.uns["dataset_id"] - assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) + # assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - print(">> All tests passed successfully") \ No newline at end of file + # print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml new file mode 100644 index 0000000000..d9295ca1fc --- /dev/null +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -0,0 +1,56 @@ +functionality: + namespace: batch_integration/methods_feature + info: + output_type: feature + arguments: + - __merge__: anndata_unintegrated.yaml + name: --input + - __merge__: anndata_integrated_feature.yaml + name: --output + direction: output + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + test_resources: + - path: ../../../../resources_test/batch_integration/feature/ + - type: python_script + path: generic_test.py + text: | + import os + import subprocess + import anndata as ad + + input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" + output_path = "inegrated.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] + + print(">> Checking whether input file exists", flush=True) + assert os.path.exists(input_path) + + print(">> Running script as test", flush=True) + subprocess.run(cmd, check=True) + + print(">> Checking whether file exists", flush=True) + assert os.path.exists(output_path) + + print(">> Reading h5ad files", flush=True) + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) + print(f"input: {input}", flush=True) + print(f"output: {output}", flush=True) + + print(">> Checking whether predictions were added", flush=True) + # TODO: use helper function to check whether the required fields are defined + assert output.X + + print(">> Check values", flush=True) + assert meta['functionality_name'] == output.uns['method_id'] + assert input.uns["dataset_id"] == output.uns["dataset_id"] + + print(">> All tests passed successfully") diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 24a471a694..58993c46c9 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -14,7 +14,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../../resources_test/batch_integration/pancreas/ + - path: ../../../../resources_test/batch_integration/pancreas/ - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/methods_embedding/combat/config.vsh.yaml b/src/batch_integration/methods_embedding/combat/config.vsh.yaml index 45f1b4e4d8..72a7ed61cd 100644 --- a/src/batch_integration/methods_embedding/combat/config.vsh.yaml +++ b/src/batch_integration/methods_embedding/combat/config.vsh.yaml @@ -1,18 +1,20 @@ # use method api spec -__merge__: ../../api/comp_method.yaml +__merge__: ../../api/comp_method_embedding.yaml functionality: name: combat - namespace: batch_integration/embedding/methods + namespace: batch_integration/methods_embedding description: Run Combat info: - output_type: embedding + type: method + method_name: Combat + paper_refernce: hansen2012removing + v1_url: + v1 commit: + variants: + combat: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../../../../resources_test/batch_integration/pancreas/unintegrated.h5ad platforms: - type: docker image: mumichae/scib-base:1.0.2 diff --git a/src/batch_integration/methods_embedding/combat/run_example.sh b/src/batch_integration/methods_embedding/combat/run_example.sh deleted file mode 100644 index ce00a91fac..0000000000 --- a/src/batch_integration/methods_embedding/combat/run_example.sh +++ /dev/null @@ -1,14 +0,0 @@ -set -e -SCRIPTPATH="$( - cd "$(dirname "$0")" >/dev/null 2>&1 || exit - pwd -P -)" - -bin/viash run ${SCRIPTPATH}/config.vsh.yaml -- \ - --input src/batch_integration/datasets/resources/datasets_pancreas.h5ad \ - --label celltype \ - --batch batch \ - --hvg true \ - --scaling true \ - --output src/batch_integration/resources/graph_pancreas_combat.h5ad \ - --debug true diff --git a/src/batch_integration/methods_embedding/combat/script.py b/src/batch_integration/methods_embedding/combat/script.py index 3361fdcb12..e9b7642c7a 100644 --- a/src/batch_integration/methods_embedding/combat/script.py +++ b/src/batch_integration/methods_embedding/combat/script.py @@ -6,7 +6,6 @@ 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', 'output': 'output.h5ad', 'hvg': True, - 'scaling': True } meta = { @@ -14,25 +13,15 @@ } ## VIASH END -adata_file = par['input'] -output = par['output'] -hvg = par['hvg'] -scaling = par['scaling'] - print('Read input', flush=True) -adata = sc.read_h5ad(adata_file) +adata = sc.read_h5ad(par['input']) -if hvg: +if par['hvg']: print('Select HVGs', flush=True) adata = adata[:, adata.var['highly_variable']].copy() -if scaling: - print('Scale', flush=True) - adata.X = adata.layers['logcounts_scaled'] -else: - adata.X = adata.layers['logcounts'] - -print('Integrate', flush=True) +print('Run Combat', flush=True) +adata.X = adata.layers['normalized'] adata.X = sc.pp.combat(adata, key='batch', inplace=False) adata.X = csr_matrix(adata.X) @@ -47,7 +36,7 @@ print('Create output AnnData object', flush=True) output = sc.AnnData( - obs= adata.obs[[]], + obs= adata.obs, obsm={ 'X_emb': X_emb }, @@ -55,11 +44,10 @@ 'dataset_id': adata.uns['dataset_id'], 'normalization_id': adata.uns['normalization_id'], 'method_id': meta['functionality_name'], - 'scaled': par['scaling'], - 'hvg': par('hvg') + 'hvg': par['hvg'] }, - layers = adata.layers + layers = {key: value for key, value in adata.layers.items()} ) print('Write to output', flush=True) -adata.write_h5ad(par['output'], compression='gzip') +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_embedding/combat/test.py b/src/batch_integration/methods_embedding/combat/test.py deleted file mode 100644 index 1bf4ad0d62..0000000000 --- a/src/batch_integration/methods_embedding/combat/test.py +++ /dev/null @@ -1,49 +0,0 @@ -from os import path -import subprocess -import numpy as np -import anndata as ad - - -print(">> Running script", flush=True) - -input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" -output_path = "inegrated.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] - -print(">> Checking whether input file exists", flush=True) -assert path.exists(input_path) - -print(">> Running script as test", flush=True) -subprocess.run(cmd, check=True) - -print(">> Checking whether output file exists", flush=True) -assert path.exists(output_path) - -print(">> Reading h5ad files", flush=True) -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) - -print(">> Checking whether predictions were added", flush=True) -assert 'dataset_id' in output.uns -assert 'X_pca' in output.obsm -assert 'X_emb' in output.obsm -assert 'normalization_id' in output.uns -assert 'method_id' in output.uns -assert meta['fuctionality_name'] == output.uns['method_id'] - -assert 'hvg' in output.uns -assert output.uns['hvg'] == False -assert 'scaled' in output.uns -assert output.uns['scaled'] == False - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - -print(">> All tests passed successfully") diff --git a/src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml b/src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml new file mode 100644 index 0000000000..7b4b1d5bd2 --- /dev/null +++ b/src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../api/comp_method_feature.yaml +functionality: + name: feature_to_embed + description: "Transform a feature integration to an embedded integration" + info: + type: method + method_name: Feature to Embed + preferred_normalization: log_cpm + variants: + feature_to_embed: + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.10 + setup: + - type: python + pypi: + - pyyaml + - scanpy + - type: nextflow diff --git a/src/batch_integration/methods_embedding/feature_to_embed/script.py b/src/batch_integration/methods_embedding/feature_to_embed/script.py new file mode 100644 index 0000000000..b911d9cdaf --- /dev/null +++ b/src/batch_integration/methods_embedding/feature_to_embed/script.py @@ -0,0 +1,32 @@ +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/feature/integrated.h5ad', + 'ouput': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo' +} + +## VIASH END + +print('Read input', flush=True) +adata= sc.read_h5ad(par['input']) + +print('Run PCA', flush=True) +adata.obsm['X_emb'] = sc.pp.pca( + adata.X, + n_comps=50, + use_highly_variable=False, + svd_solver='arpack', + return_info=False +) +del adata.X + +print('Store outputs', flush=True) +adata.uns['parent_method_id'] = adata.uns['method_id'] +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/methods_graph/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_graph/scanorama_embed/config.vsh.yaml rename to src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml diff --git a/src/batch_integration/methods_graph/scanorama_embed/script.py b/src/batch_integration/methods_embedding/scanorama_embed/script.py similarity index 100% rename from src/batch_integration/methods_graph/scanorama_embed/script.py rename to src/batch_integration/methods_embedding/scanorama_embed/script.py diff --git a/src/batch_integration/methods_feature/combat/config.vsh.yaml b/src/batch_integration/methods_feature/combat/config.vsh.yaml new file mode 100644 index 0000000000..ec2719a5b0 --- /dev/null +++ b/src/batch_integration/methods_feature/combat/config.vsh.yaml @@ -0,0 +1,34 @@ +# use method api spec +__merge__: ../../api/comp_method_graph.yaml +functionality: + name: combat + description: "Adjusting batch effects in microarray expression data using + empirical Bayes methods" + info: + type: method + method_name: Combat + paper_reference: "hansen2012removing" + code_url: https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + combat_full_unscaled: + combat_hvg_unscaled: + hvg: true + combat_full_scaled: + preferred_normalization: log_cpm_scaled + combat_hvg_scaled: + hvg: true + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: + - pyyaml + - type: nextflow diff --git a/src/batch_integration/methods_graph/combat/script.py b/src/batch_integration/methods_feature/combat/script.py similarity index 75% rename from src/batch_integration/methods_graph/combat/script.py rename to src/batch_integration/methods_feature/combat/script.py index 3af76ea9f1..7c8f178149 100644 --- a/src/batch_integration/methods_graph/combat/script.py +++ b/src/batch_integration/methods_feature/combat/script.py @@ -28,19 +28,6 @@ adata.X = sc.pp.combat(adata, key='batch', inplace=False) adata.X = csr_matrix(adata.X) -print("Run PCA", flush=True) -adata.obsm['X_emb'] = sc.pp.pca( - adata.X, - n_comps=50, - use_highly_variable=False, - svd_solver='arpack', - return_info=False -) -del adata.X - -print("Run KNN", flush=True) -sc.pp.neighbors(adata, use_rep='X_emb') - print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_graph/bbknn/config.vsh.yaml b/src/batch_integration/methods_graph/bbknn/config.vsh.yaml index 2ec1669053..68b600e6e1 100644 --- a/src/batch_integration/methods_graph/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods_graph/bbknn/config.vsh.yaml @@ -2,17 +2,25 @@ __merge__: ../../api/comp_method_graph.yaml functionality: name: bbknn + namespace: batch_integration/methods_graph description: "BBKNN: fast batch alignment of single cell transcriptomes" info: type: method method_name: BBKNN paper_reference: "polanski2020bbknn" code_url: https://github.com/Teichlab/bbknn - # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py - # v1_commit: xxxxxxxxxxxxxx - # preferred_normalization: log_cpm - # variants: - # bbknn: + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + bbknn_full_unscaled: + bbknn_hvg_unscaled: + hvg: true + bbknn_hvg_scaled: + preferred_normalization: log_cpm_scaled + bbknn_full_scaled: + hvg: true + preferred_normalization: log_cpm_scaled resources: - type: python_script path: script.py diff --git a/src/batch_integration/methods_graph/combat/config.vsh.yaml b/src/batch_integration/methods_graph/combat/config.vsh.yaml deleted file mode 100644 index 9b1c1feeec..0000000000 --- a/src/batch_integration/methods_graph/combat/config.vsh.yaml +++ /dev/null @@ -1,25 +0,0 @@ -# use method api spec -__merge__: ../../api/comp_method_graph.yaml -functionality: - name: combat - info: - type: method - output_type: graph - method_name: Combat - # paper_reference: "xxxxxxxxxxx" - # code_url: xxxxxxxxxxx - # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py - # v1_commit: xxxxxxxxxxxxxx - # preferred_normalization: log_cpm - # variants: - # combat: - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - setup: - - type: python - pypi: pyyaml - - type: nextflow From 14b7eab45117349ea5d74732a829e14f4607f3e8 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 9 Feb 2023 16:46:10 +0100 Subject: [PATCH 0736/1233] update scvi config Former-commit-id: db4bda1d79c6513006876ce604a7286213855abd --- .../methods_graph/scvi/config.vsh.yaml | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/batch_integration/methods_graph/scvi/config.vsh.yaml b/src/batch_integration/methods_graph/scvi/config.vsh.yaml index 6cd55d2713..39b723e79b 100644 --- a/src/batch_integration/methods_graph/scvi/config.vsh.yaml +++ b/src/batch_integration/methods_graph/scvi/config.vsh.yaml @@ -5,15 +5,16 @@ functionality: description: Run scVI on adata object, use feature output info: type: method - output_type: graph method_name: scVI - # paper_reference: "xxxxxxxxxxx" - # code_url: xxxxxxxxxxx - # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py - # v1_commit: xxxxxxxxxxxxxx - # preferred_normalization: log_cpm - # variants: - # combat: + paper_reference: "lopez2018deep" + code_url: https://github.com/YosefLab/scvi-tools" + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + scvi_full_unscaled: + scvi_hvg_unscaled: + hvg: true resources: - type: python_script path: script.py From 8d5eb606699b86a8293b9aa24cbcb0e771f81711 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 14 Feb 2023 10:35:23 +0100 Subject: [PATCH 0737/1233] refactor methods and metrics to v2 Former-commit-id: 11f6a6b6a4c97449155c0012b5929c79a0605657 --- .../api/anndata_integrated_embedding.yaml | 18 +++- .../api/anndata_integrated_feature.yaml | 17 ++++ .../api/anndata_integrated_graph.yaml | 17 ++++ src/batch_integration/api/anndata_score.yaml | 41 ++++++++ .../api/comp_method_embedding.yaml | 93 ++++++++++--------- .../api/comp_method_graph.yaml | 12 ++- ...metric.yaml => comp_metric_embedding.yaml} | 15 +-- .../api/comp_metric_feature.yaml | 86 +++++++++++++++++ .../api/comp_metric_graph.yaml | 86 +++++++++++++++++ .../methods_embedding/combat/config.vsh.yaml | 24 ----- .../methods_embedding/combat/script.py | 53 ----------- .../feature_to_embed/script.py | 10 +- .../scanorama_embed/config.vsh.yaml | 26 ++++-- .../scanorama_embed/script.py | 19 ++-- .../scvi/config.vsh.yaml | 4 +- .../scvi/script.py | 20 ++-- .../methods_feature/combat/script.py | 13 ++- .../scanorama_feature/config.vsh.yaml | 36 +++++++ .../scanorama_feature/script.py | 37 ++++---- .../methods_graph/bbknn/script.py | 11 ++- .../embed_to_graph/config.vsh.yaml | 23 +++++ .../methods_graph/embed_to_graph/script.py | 33 +++++++ .../scanorama_feature/config.vsh.yaml | 28 ------ .../asw_batch/config.vsh.yaml | 19 +++- .../metrics_embedding/asw_batch/script.py | 47 +++++----- .../asw_label/config.vsh.yaml | 18 +++- .../metrics_embedding/asw_label/script.py | 33 +++---- .../cell_cycle_conservation/config.vsh.yaml | 18 +++- .../cell_cycle_conservation/script.py | 60 +++++++----- .../metrics_embedding/pcr/script.py | 50 ++++++---- .../clustering_overlap/config.vsh.yaml | 13 ++- .../clustering_overlap/script.py | 26 ++++-- .../resources_test_scripts/pancreas.sh | 15 +-- 33 files changed, 697 insertions(+), 324 deletions(-) create mode 100644 src/batch_integration/api/anndata_score.yaml rename src/batch_integration/api/{comp_metric.yaml => comp_metric_embedding.yaml} (91%) create mode 100644 src/batch_integration/api/comp_metric_feature.yaml create mode 100644 src/batch_integration/api/comp_metric_graph.yaml delete mode 100644 src/batch_integration/methods_embedding/combat/config.vsh.yaml delete mode 100644 src/batch_integration/methods_embedding/combat/script.py rename src/batch_integration/{methods_graph => methods_embedding}/scvi/config.vsh.yaml (91%) rename src/batch_integration/{methods_graph => methods_embedding}/scvi/script.py (62%) create mode 100644 src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml rename src/batch_integration/{methods_graph => methods_feature}/scanorama_feature/script.py (52%) create mode 100644 src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml create mode 100644 src/batch_integration/methods_graph/embed_to_graph/script.py delete mode 100644 src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml diff --git a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/batch_integration/api/anndata_integrated_embedding.yaml index 0abb11e8b4..e1426f9bf1 100644 --- a/src/batch_integration/api/anndata_integrated_embedding.yaml +++ b/src/batch_integration/api/anndata_integrated_embedding.yaml @@ -10,4 +10,20 @@ info: name: X_emb description: integration embedding prediction required: true - + uns: + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: parent_method_id + description: if anndata passed from a previous method + required: false + - type: boolean + name: hvg + description: If the method was done on hvg or full + required: true + - type: string + name: output_id + description: what kind of output has been generated + required: true diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index 40499faace..1c3e690d7b 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -9,3 +9,20 @@ info: - type: double description: integrated feature required: true + uns: + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: parent_method_id + description: if anndata passed from a previous method + required: false + - type: boolean + name: hvg + description: If the method was done on hvg or full + required: true + - type: string + name: output_id + description: what kind of output has been generated + required: true \ No newline at end of file diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml index dce7831365..1d1a8c381b 100644 --- a/src/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -10,3 +10,20 @@ info: name: connectivities description: Neighbors connectivities matrix. required: true + uns: + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: parent_method_id + description: if anndata passed from a previous method + required: false + - type: boolean + name: hvg + description: If the method was done on hvg or full + required: true + - type: string + name: output_id + description: what kind of output has been generated + required: true diff --git a/src/batch_integration/api/anndata_score.yaml b/src/batch_integration/api/anndata_score.yaml new file mode 100644 index 0000000000..9c8518345f --- /dev/null +++ b/src/batch_integration/api/anndata_score.yaml @@ -0,0 +1,41 @@ +type: file +description: "Metric score file" +example: "score.h5ad" +info: + short_description: "Score" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + required: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true + required: true + - type: string + name: parent_method_id + description: previous method id if anndata is from a previous method + required: false + - type: boolean + name: hvg + description: If the method was done on hvg or full + required: true + - type: string + name: output_id + description: what kind of output has been generated + required: true \ No newline at end of file diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index e4e8389dec..ac56cb63b5 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -12,59 +12,64 @@ functionality: description: Whether to subset to highly variable genes default: false required: false - # ! Will not work with feature_to_embed - # test_resources: - # - path: ../../../../resources_test/batch_integration/pancreas/ - # - type: python_script - # path: generic_test.py - # text: | - # from os import path - # import subprocess - # import numpy as np - # import anndata as ad + test_resources: + - path: ../../../../resources_test/batch_integration/ + - type: python_script + path: generic_test.py + text: | + from os import path + import subprocess + import numpy as np + import anndata as ad - # print(">> Running script", flush=True) + print(">> Running script", flush=True) + if meta["functionality_name"] == 'feature_to_embed': + input_path = meta["resources_dir"] + "/batch_integration/feature/scvi.h5ad" + else: + input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" + output_path = "embeddding.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path + ] - # input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" - # output_path = "embeddding.h5ad" - # cmd = [ - # meta['executable'], - # "--input", input_path, - # "--output", output_path - # ] + print(">> Checking whether input file exists", flush=True) + assert path.exists(input_path) - # print(">> Checking whether input file exists", flush=True) - # assert path.exists(input_path) + print(">> Running script as test", flush=True) + out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout + print(out) - # print(">> Running script as test", flush=True) - # out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout - # print(out) + print(">> Checking whether output file exists", flush=True) + assert path.exists(output_path) - # print(">> Checking whether output file exists", flush=True) - # assert path.exists(output_path) + print(">> Reading h5ad files", flush=True) + input = ad.read_h5ad(input_path) + output = ad.read_h5ad(output_path) - # print(">> Reading h5ad files", flush=True) - # input = ad.read_h5ad(input_path) - # output = ad.read_h5ad(output_path) + print(f"input: {input}", flush=True) + print(f"output: {output}", flush=True) - # print(f"input: {input}", flush=True) - # print(f"output: {output}", flush=True) + print(">> Checking whether predictions were added", flush=True) + assert 'dataset_id' in output.uns + assert 'X_pca' in output.obsm + assert 'X_emb' in output.obsm + assert 'normalization_id' in output.uns + assert 'method_id' in output.uns + assert meta['fuctionality_name'] == output.uns['method_id'] + if meta["functionality_name"] == 'feature_to_embed': + assert 'parent_method_id' in output.uns - # print(">> Checking whether predictions were added", flush=True) - # assert 'dataset_id' in output.uns - # assert 'X_pca' in output.obsm - # assert 'X_emb' in output.obsm - # assert 'normalization_id' in output.uns - # assert 'method_id' in output.uns - # assert meta['fuctionality_name'] == output.uns['method_id'] + assert 'hvg' in output.uns - # assert 'hvg' in output.uns + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.n_obs == output.n_obs + assert input.uns["dataset_id"] == output.uns["dataset_id"] + - # print(">> Checking whether data from input was copied properly to output", flush=True) - # assert input.n_obs == output.n_obs - # assert input.uns["dataset_id"] == output.uns["dataset_id"] + assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - # assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - - # print(">> All tests passed successfully") \ No newline at end of file + print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 58993c46c9..2c2af15bc1 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -14,7 +14,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas/ + - path: ../../../../resources_test/batch_integration/ - type: python_script path: generic_test.py text: | @@ -22,7 +22,10 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" + if meta["functionality_name"] == 'embed_to_graph': + input_path = meta["resources_dir"] + "/batch_integration/embedding/scvi.h5ad" + else: + input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" output_path = "inegrated.h5ad" cmd = [ meta['executable'], @@ -34,7 +37,8 @@ functionality: assert os.path.exists(input_path) print(">> Running script as test", flush=True) - subprocess.run(cmd, check=True) + out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout + print(out, flush=True) print(">> Checking whether file exists", flush=True) assert os.path.exists(output_path) @@ -53,5 +57,7 @@ functionality: print(">> Check values", flush=True) assert meta['functionality_name'] == output.uns['method_id'] assert input.uns["dataset_id"] == output.uns["dataset_id"] + if meta["functionality_name"] == 'embed_to_graph': + assert 'parent_method_id' in output.uns print(">> All tests passed successfully") diff --git a/src/batch_integration/api/comp_metric.yaml b/src/batch_integration/api/comp_metric_embedding.yaml similarity index 91% rename from src/batch_integration/api/comp_metric.yaml rename to src/batch_integration/api/comp_metric_embedding.yaml index 545264aa83..dc79ad897c 100644 --- a/src/batch_integration/api/comp_metric.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -1,17 +1,12 @@ functionality: arguments: - - name: --input - type: file - description: Integrated AnnData HDF5 file. - required: true - example: input.h5ad + - name: --input_integrated + __merge__: anndata_integrated_embedding.yaml + - name: --input_solution + __merge__: anndata_solution.yaml - name: --output - alternatives: [ -o ] - type: file direction: output - description: Output tsv file of the metric - required: true - example: output.tsv + __merge__: anndata_score.yaml test_resources: - path: ../../../../../resources_test/batch_integration - type: python_script diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml new file mode 100644 index 0000000000..3a599a8d39 --- /dev/null +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -0,0 +1,86 @@ +functionality: + arguments: + - name: --input_integrated + __merge__: anndata_integrated_feature.yaml + - name: --input_solution + __merge__: anndata_solution.yaml + - name: --output + direction: output + __merge__: anndata_score.yaml + test_resources: + - path: ../../../../../resources_test/batch_integration + - type: python_script + dest: test.py + text: | + import sys + from os import path + import subprocess + import numpy as np + import anndata as ad + import yaml + + ## VIASH START + meta = { + "resources_dir": "resources_test/batch_integration/graph/methods", + "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" + } + ## VIASH END + + np.random.seed(42) + + print(">> Read metric config", flush=True) + with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + + output_type = config["functionality"].get("info", {}).get("output_type") + + print(">> Construct input arguments", flush=True) + if output_type == "graph": + input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" + elif output_type == "embedding": + input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" + else: + sys.exit("Unrecognized .functionality.info.output_type") + output_file = "output.h5ad" + + cmd_args = [ + meta["executable"], + "--input", input_file, + "--output", output_file + ] + + print(">> Running script", flush=True) + subprocess.run(cmd_args, check=True) + + print(">> Checking whether file exists", flush=True) + assert path.exists(output_file) + input = ad.read_h5ad(input_file) + output = ad.read_h5ad(output_file) + + print(">> Print AnnData contents", flush=True) + print("input:", input, flush=True) + print("output:", output, flush=True) + + print(">> Checking whether metrics were added", flush=True) + assert "metric_ids" in output.uns + assert "metric_values" in output.uns + assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.uns["dataset_id"] == output.uns["dataset_id"] + assert input.uns["method_id"] == output.uns["method_id"] + + print(">> Check that score makes sense", flush=True) + metrics_info = { + metric["metric_id"]: metric + for metric in config["functionality"]["info"]["metrics"] + } + + for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + + print(">> All tests passed successfully") diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml new file mode 100644 index 0000000000..49790016c3 --- /dev/null +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -0,0 +1,86 @@ +functionality: + arguments: + - name: --input_integrated + __merge__: anndata_integrated_graph.yaml + - name: --input_solution + __merge__: anndata_solution.yaml + - name: --output + direction: output + __merge__: anndata_score.yaml + test_resources: + - path: ../../../../../resources_test/batch_integration + - type: python_script + dest: test.py + text: | + import sys + from os import path + import subprocess + import numpy as np + import anndata as ad + import yaml + + ## VIASH START + meta = { + "resources_dir": "resources_test/batch_integration/graph/methods", + "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" + } + ## VIASH END + + np.random.seed(42) + + print(">> Read metric config", flush=True) + with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + + output_type = config["functionality"].get("info", {}).get("output_type") + + print(">> Construct input arguments", flush=True) + if output_type == "graph": + input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" + elif output_type == "embedding": + input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" + else: + sys.exit("Unrecognized .functionality.info.output_type") + output_file = "output.h5ad" + + cmd_args = [ + meta["executable"], + "--input", input_file, + "--output", output_file + ] + + print(">> Running script", flush=True) + subprocess.run(cmd_args, check=True) + + print(">> Checking whether file exists", flush=True) + assert path.exists(output_file) + input = ad.read_h5ad(input_file) + output = ad.read_h5ad(output_file) + + print(">> Print AnnData contents", flush=True) + print("input:", input, flush=True) + print("output:", output, flush=True) + + print(">> Checking whether metrics were added", flush=True) + assert "metric_ids" in output.uns + assert "metric_values" in output.uns + assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.uns["dataset_id"] == output.uns["dataset_id"] + assert input.uns["method_id"] == output.uns["method_id"] + + print(">> Check that score makes sense", flush=True) + metrics_info = { + metric["metric_id"]: metric + for metric in config["functionality"]["info"]["metrics"] + } + + for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + + print(">> All tests passed successfully") diff --git a/src/batch_integration/methods_embedding/combat/config.vsh.yaml b/src/batch_integration/methods_embedding/combat/config.vsh.yaml deleted file mode 100644 index 72a7ed61cd..0000000000 --- a/src/batch_integration/methods_embedding/combat/config.vsh.yaml +++ /dev/null @@ -1,24 +0,0 @@ -# use method api spec -__merge__: ../../api/comp_method_embedding.yaml -functionality: - name: combat - namespace: batch_integration/methods_embedding - description: Run Combat - info: - type: method - method_name: Combat - paper_refernce: hansen2012removing - v1_url: - v1 commit: - variants: - combat: - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - setup: - - type: python - pypi: [ pyyaml ] - - type: nextflow diff --git a/src/batch_integration/methods_embedding/combat/script.py b/src/batch_integration/methods_embedding/combat/script.py deleted file mode 100644 index e9b7642c7a..0000000000 --- a/src/batch_integration/methods_embedding/combat/script.py +++ /dev/null @@ -1,53 +0,0 @@ -import scanpy as sc -from scipy.sparse import csr_matrix - -## VIASH START -par = { - 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', - 'output': 'output.h5ad', - 'hvg': True, -} - -meta = { - 'functionality_name' : 'foo' -} -## VIASH END - -print('Read input', flush=True) -adata = sc.read_h5ad(par['input']) - -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['highly_variable']].copy() - -print('Run Combat', flush=True) -adata.X = adata.layers['normalized'] -adata.X = sc.pp.combat(adata, key='batch', inplace=False) -adata.X = csr_matrix(adata.X) - -print('Postprocess data', flush=True) -X_emb = sc.pp.pca( - adata.X, - n_comps=50, - use_highly_variable=False, - svd_solver='arpack', - return_info=False -) - -print('Create output AnnData object', flush=True) -output = sc.AnnData( - obs= adata.obs, - obsm={ - 'X_emb': X_emb - }, - uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': meta['functionality_name'], - 'hvg': par['hvg'] - }, - layers = {key: value for key, value in adata.layers.items()} -) - -print('Write to output', flush=True) -output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_embedding/feature_to_embed/script.py b/src/batch_integration/methods_embedding/feature_to_embed/script.py index b911d9cdaf..a28c7f4f60 100644 --- a/src/batch_integration/methods_embedding/feature_to_embed/script.py +++ b/src/batch_integration/methods_embedding/feature_to_embed/script.py @@ -1,4 +1,5 @@ import scanpy as sc +import yaml ## VIASH START @@ -8,11 +9,17 @@ } meta = { - 'functionality_name': 'foo' + 'functionality_name': 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) adata= sc.read_h5ad(par['input']) @@ -27,6 +34,7 @@ del adata.X print('Store outputs', flush=True) +adata.uns['output_type'] = output_type adata.uns['parent_method_id'] = adata.uns['method_id'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml index b2d7a83e42..92170df584 100644 --- a/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml @@ -2,18 +2,26 @@ __merge__: ../../api/comp_method_graph.yaml functionality: name: scanorama_embed - description: Run Scanorama on adata object, use embedding output + namespace: batch_integration/methods_embedding + description: "Efficient integration of heterogeneous single-cell + transcriptomes using Scanorama" info: type: method - output_type: graph method_name: Scanorama - # paper_reference: "xxxxxxxxxxx" - # code_url: xxxxxxxxxxx - # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py - # v1_commit: xxxxxxxxxxxxxx - # preferred_normalization: log_cpm - # variants: - # combat: + paper_reference: "hie2019efficient" + code_url: https://github.com/brianhie/scanorama + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + scanorama_embed_full_unscaled: + scanorama_embed_hvg_unscaled: + hvg: true + scanorama_embed_hvg_scaled: + hvg: true + preferred_normalization: log_cpm_scaled + scanorama_embed_full_scaled: + preferred_normalization: log_cpm_scaled resources: - type: python_script path: script.py diff --git a/src/batch_integration/methods_embedding/scanorama_embed/script.py b/src/batch_integration/methods_embedding/scanorama_embed/script.py index 304e48c6be..0bb0529fa2 100644 --- a/src/batch_integration/methods_embedding/scanorama_embed/script.py +++ b/src/batch_integration/methods_embedding/scanorama_embed/script.py @@ -1,5 +1,5 @@ -# TODO: this should be a output_type: embedding method. -import scanpy as sc +import yaml +import anndata as ad from scib.integration import scanorama ## VIASH START @@ -9,12 +9,18 @@ 'hvg': True, } meta = { - 'functionality_name': 'foo' + 'functionality_name': 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) -adata = sc.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input']) if par['hvg']: print('Select HVGs', flush=True) @@ -25,9 +31,8 @@ adata.obsm['X_emb'] = scanorama(adata, batch='batch').obsm['X_emb'] del adata.X -print('Run kNN', flush=True) -sc.pp.neighbors(adata, use_rep='X_emb') - print("Store outputs", flush=True) +adata.uns['output_type'] = output_type +adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_graph/scvi/config.vsh.yaml b/src/batch_integration/methods_embedding/scvi/config.vsh.yaml similarity index 91% rename from src/batch_integration/methods_graph/scvi/config.vsh.yaml rename to src/batch_integration/methods_embedding/scvi/config.vsh.yaml index 39b723e79b..5d9ed591ed 100644 --- a/src/batch_integration/methods_graph/scvi/config.vsh.yaml +++ b/src/batch_integration/methods_embedding/scvi/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_embedding.yaml functionality: name: scvi description: Run scVI on adata object, use feature output @@ -24,6 +24,6 @@ platforms: setup: - type: python pypi: - - scvi + - scvi-tools - pyyaml - type: nextflow diff --git a/src/batch_integration/methods_graph/scvi/script.py b/src/batch_integration/methods_embedding/scvi/script.py similarity index 62% rename from src/batch_integration/methods_graph/scvi/script.py rename to src/batch_integration/methods_embedding/scvi/script.py index 960a6b3714..f768c036e0 100644 --- a/src/batch_integration/methods_graph/scvi/script.py +++ b/src/batch_integration/methods_embedding/scvi/script.py @@ -1,5 +1,5 @@ -# TODO: this should be a output_type: embedding method. -import scanpy as sc +import yaml +import anndata as ad from scib.integration import scvi ## VIASH START @@ -9,12 +9,18 @@ 'hvg': True, } meta = { - 'functionality_name' : 'foo' + 'functionality_name' : 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) -adata = sc.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input']) if par['hvg']: print('Select HVGs', flush=True) @@ -23,10 +29,10 @@ print('Run scvi', flush=True) adata.X = adata.layers['normalized'] adata = scvi(adata, batch='batch') - -print('Run kNN', flush=True) -sc.pp.neighbors(adata, use_rep='X_emb') +del adata.X print("Store outputs", flush=True) +adata.uns['output_type'] = output_type +adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_feature/combat/script.py b/src/batch_integration/methods_feature/combat/script.py index 7c8f178149..fee9b9eef7 100644 --- a/src/batch_integration/methods_feature/combat/script.py +++ b/src/batch_integration/methods_feature/combat/script.py @@ -1,5 +1,4 @@ -# TODO: this should be a output_type: features method. - +import yaml import scanpy as sc from scipy.sparse import csr_matrix @@ -11,11 +10,17 @@ } meta = { - 'funcionality_name': 'foo' + 'funcionality_name': 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) adata = sc.read_h5ad(par['input']) @@ -29,5 +34,7 @@ adata.X = csr_matrix(adata.X) print("Store outputs", flush=True) +adata.uns['output_type'] = output_type +adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml new file mode 100644 index 0000000000..a48f0dc97d --- /dev/null +++ b/src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml @@ -0,0 +1,36 @@ +# use method api spec +__merge__: ../../api/comp_method_feature.yaml +functionality: + name: scanorama_feature + namespace: batch_integration/methods_feauture + description: "Efficient integration of heterogeneous single-cell + transcriptomes using Scanorama" + info: + type: method + method_name: Scanorama + paper_reference: "hie2019efficient" + code_url: https://github.com/brianhie/scanorama + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + scanorama_feature_full_unscaled: + scanorama_feature_hvg_unscaled: + hvg: true + scanorama_feature_hvg_scaled: + hvg: true + preferred_normalization: log_cpm_scaled + scanorama_feature_full_scaled: + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: mumichae/scib-base:1.0.2 + setup: + - type: python + pypi: + - scanorama + - pyyaml + - type: nextflow diff --git a/src/batch_integration/methods_graph/scanorama_feature/script.py b/src/batch_integration/methods_feature/scanorama_feature/script.py similarity index 52% rename from src/batch_integration/methods_graph/scanorama_feature/script.py rename to src/batch_integration/methods_feature/scanorama_feature/script.py index 882c1baa66..ce16a564f0 100644 --- a/src/batch_integration/methods_graph/scanorama_feature/script.py +++ b/src/batch_integration/methods_feature/scanorama_feature/script.py @@ -1,5 +1,5 @@ -# TODO: this should be a output_type: feature method. -import scanpy as sc +import yaml +import anndata as ad from scib.integration import scanorama ## VIASH START @@ -9,12 +9,18 @@ 'hvg': True, } meta = { - 'functionality_name': 'foo' + 'functionality_name': 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) -adata = sc.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input']) if par['hvg']: print('Select HVGs', flush=True) @@ -24,19 +30,18 @@ adata.X = adata.layers['normalized'] adata.X = scanorama(adata, batch='batch').X -print("Run PCA", flush=True) -sc.pp.pca( - adata, - n_comps=50, - use_highly_variable=False, - svd_solver='arpack', - return_info=True -) -del adata.X - -print("Run KNN", flush=True) -sc.pp.neighbors(adata, use_rep='X_pca') +# ? Create new comp feature_to_graph? +# print("Run PCA", flush=True) +# sc.pp.pca( +# adata, +# n_comps=50, +# use_highly_variable=False, +# svd_solver='arpack', +# return_info=True +# ) print("Store outputs", flush=True) +adata.uns['output_type'] = output_type +adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_graph/bbknn/script.py b/src/batch_integration/methods_graph/bbknn/script.py index 0053019412..137b9228f1 100644 --- a/src/batch_integration/methods_graph/bbknn/script.py +++ b/src/batch_integration/methods_graph/bbknn/script.py @@ -1,3 +1,4 @@ +import yaml import anndata as ad from scib.integration import bbknn @@ -8,10 +9,16 @@ 'hvg': True, } meta = { - 'functionality_name': 'foo' + 'functionality_name': 'foo', + 'config': 'bar' } ## VIASH END +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + print('Read input', flush=True) input = ad.read_h5ad(par['input']) @@ -25,5 +32,7 @@ del input.X print("Store outputs", flush=True) +input.uns['output_type'] = output_type +input.uns['hvg'] = par['hvg'] input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml b/src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml new file mode 100644 index 0000000000..111960c534 --- /dev/null +++ b/src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../api/comp_method_graph.yaml +functionality: + name: embed_to_graph + namespace: batch_integration/methods_graph + description: "Transform an embedded integration to a graph integration" + info: + type: method + method_name: Embedding to Graph + variants: + embed_to_graph: + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.10 + setup: + - type: python + pypi: + - scanpy + - pyyaml + - type: nextflow diff --git a/src/batch_integration/methods_graph/embed_to_graph/script.py b/src/batch_integration/methods_graph/embed_to_graph/script.py new file mode 100644 index 0000000000..30dfac16e9 --- /dev/null +++ b/src/batch_integration/methods_graph/embed_to_graph/script.py @@ -0,0 +1,33 @@ +import yaml +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'ouput': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar' +} + +## VIASH END + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["output_type"] + +print('read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print('Run kNN', flush=True) +sc.pp.neighbors(adata, use_rep='X_emb') + +print("Store outputs", flush=True) +adata.uns['output_type'] = output_type +adata.uns['parent_method_id'] = adata.uns['method_id'] +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml deleted file mode 100644 index 01f4646898..0000000000 --- a/src/batch_integration/methods_graph/scanorama_feature/config.vsh.yaml +++ /dev/null @@ -1,28 +0,0 @@ -# use method api spec -__merge__: ../../api/comp_method_graph.yaml -functionality: - name: scanorama_feature - description: Run Scanorama on adata object, use feature output - info: - type: method - output_type: graph - method_name: Scanorama - # paper_reference: "xxxxxxxxxxx" - # code_url: xxxxxxxxxxx - # v1_url: openproblems/tasks/xxxxxx/methods/xxxxxx.py - # v1_commit: xxxxxxxxxxxxxx - # preferred_normalization: log_cpm - # variants: - # combat: - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: mumichae/scib-base:1.0.2 - setup: - - type: python - pypi: - - scanorama - - pyyaml - - type: nextflow diff --git a/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml b/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml index 0f62ac0590..336242e3ed 100644 --- a/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml @@ -1,12 +1,20 @@ # use metric api spec -__merge__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_batch - namespace: batch_integration/embedding/metrics + namespace: batch_integration/metrics_embedding description: Average silhouette of batches per label info: - output_type: embedding - integrated_embedding: X_emb + type: metric + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + paper_reference: luecken2022benchmarking + metrics: + - metric_id: asw_batch + metric_name: ASW batch + min: 0 + max: 1 + maximize: true resources: - type: python_script path: script.py @@ -15,5 +23,6 @@ platforms: image: mumichae/scib-base:1.0.2 setup: - type: python - pypi: pyyaml + pypi: + - pyyaml - type: nextflow diff --git a/src/batch_integration/metrics_embedding/asw_batch/script.py b/src/batch_integration/metrics_embedding/asw_batch/script.py index 45bd99d5b8..5c8c3f0da0 100644 --- a/src/batch_integration/metrics_embedding/asw_batch/script.py +++ b/src/batch_integration/metrics_embedding/asw_batch/script.py @@ -1,50 +1,49 @@ -import pprint import anndata as ad from scib.metrics import silhouette_batch import yaml ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', + 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', - 'hvg': False, - 'scaling': False } meta = { 'functionality_name': 'foo', - 'config': 'src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml' } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["output_type"] -integrated_embedding = config["functionality"]["info"]["integrated_embedding"] - print('Read input', flush=True) -adata = ad.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input_integrated']) +adata_solution= ad.read_h5ad(par['input_solution']) -print('compute score') +print('Transfer obs annotations', flush=True) +adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] +adata.obs['label'] = adata_solution.obs['label'][adata.obs_names] + +print('compute score', flush=True) score = silhouette_batch( adata, batch_key='batch', group_key='label', - embed=integrated_embedding, + embed='X_emb', ) -print("Create output AnnData object") +print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - "dataset_id": adata.uns['dataset_id'], - "method_id": adata.uns['method_id'], - "metric_ids": [ meta['functionality_name'] ], - "metric_values": [ score ], - "hvg": adata.uns['hvg'], - "scaled": adata.uns['scaled'], - "output_type": output_type, + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ], + 'hvg': adata.uns['hvg'], + 'output_type': adata.uns['output_type'], } ) -print("Write data to file", flush=True) -output.write_h5ad(par["output"], compression="gzip") +if 'parent_method_id' in adata.uns: + output.uns['parent_method_id'] = adata.uns['parent_method_id'] + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml b/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml index ed61287b75..84586e17ce 100644 --- a/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml @@ -1,9 +1,20 @@ # use metric api spec -__merge__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_label - namespace: batch_integration/embedding/metrics + namespace: batch_integration/metrics_embedding description: Average silhouette of labels + info: + type: metric + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + paper_reference: luecken2022benchmarking + metrics: + - metric_id: asw_label + metric_name: ASW Label + min: 0 + max: 1 + maximize: true resources: - type: python_script path: script.py @@ -12,5 +23,6 @@ platforms: image: mumichae/scib-base:1.0.2 setup: - type: python - pypi: pyyaml + pypi: + - pyyaml - type: nextflow diff --git a/src/batch_integration/metrics_embedding/asw_label/script.py b/src/batch_integration/metrics_embedding/asw_label/script.py index f32dddb805..3b2b7bc7fb 100644 --- a/src/batch_integration/metrics_embedding/asw_label/script.py +++ b/src/batch_integration/metrics_embedding/asw_label/script.py @@ -1,54 +1,47 @@ -import pprint import anndata as ad from scib.metrics import silhouette -import yaml ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/processed.h5ad', + 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', - 'hvg': False, - 'scaling': False } meta = { 'functionality_name': 'foo', - 'config': 'src/batch_integration/embedding/metrics/asw_label/config.vsh.yaml' } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["output_type"] -integrated_embedding = config["functionality"]["info"]["integrated_embedding"] - -adata_file = par['input'] -output = par['output'] - print('Read input', flush=True) -adata = ad.read_h5ad(adata_file) -name = adata.uns['dataset_id'] +adata = ad.read_h5ad(par['input_integrated']) +adata_solution = ad.read_h5ad(par['input_solution']) + +print('Transfer obs annotations') +adata.obs['label'] = adata_solution.obs['label'][adata.obs_names] print('compute score') score = silhouette( adata, group_key='label', - embed=integrated_embedding + embed='X_emb' ) print("Create output AnnData object") output = ad.AnnData( uns={ "dataset_id": adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], "method_id": adata.uns['method_id'], "hvg": adata.uns['hvg'], - "scaled": adata.uns['scaled'], - "output_type": output_type, + "output_type": adata.uns['output_type'], "metric_ids": meta['functionality_name'], "metric_value": score } ) +if 'parent_method_id' in adata.uns: + output.uns['parent_method_id'] = adata.uns['parent_method_id'] + print("Write data to file", flush=True) output.write_h5ad(par["output"], compression="gzip") diff --git a/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml index c334a690d1..7531ea7db4 100644 --- a/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml @@ -1,9 +1,20 @@ # use metric api spec -__merge__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric_embedding.yaml functionality: name: cell_cycle_conservation - namespace: batch_integration/embedding/metrics + namespace: batch_integration/metrics_embedding description: Cell cycle conservation score based on cell cycle gene scoring + info: + type: metric + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + paper_reference: luecken2022benchmarking + metrics: + - metric_id: cell_cycle_conservation + metric_name: Cell Cycle Conservation + min: 0 + max: 1 + maximize: true arguments: - name: --organism type: string @@ -17,5 +28,6 @@ platforms: image: mumichae/scib-base:1.0.2 setup: - type: python - pypi: pyyaml + pypi: + - pyyaml - type: nextflow diff --git a/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py b/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py index 67766d21e3..eccfc8c9f2 100644 --- a/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py @@ -1,41 +1,55 @@ +import anndata as ad +from scib.metrics import cell_cycle + ## VIASH START par = { - 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv', + 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', + 'output': 'output.h5ad', 'organism': 'human' } + +meta = { + 'functionality_name': 'foo' +} ## VIASH END -import pprint -import scanpy as sc -from scib.metrics import cell_cycle -from scipy.sparse import csr_matrix +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) +adata_solution : ad.read_h5ad(par['input_solution']) -OUTPUT_TYPE = 'embedding' -METRIC = 'cell_cycle_conservation' -adata_file = par['input'] -organism = par['organism'] -output = par['output'] +adata.X = adata.layers['normalized'] -print('Read input', flush=True) -adata = sc.read(adata_file) -adata_int = adata.copy() -name = adata.uns['dataset_id'] +print('Transfer obs annotations', flush=True) +adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] -adata.X = adata.layers['logcounts'] +adata_int = adata.copy() -print('compute score') +print('compute score', flush=True) score = cell_cycle( adata, adata_int, batch_key='batch', embed='X_emb', - organism=organism + organism=par['organism'] ) -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ], + 'hvg': adata.uns['hvg'], + 'output_type': adata.uns['output_type'], + } +) + +if 'parent_method_id' in adata.uns: + output.uns['parent_method_id'] = adata.uns['parent_method_id'] + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/metrics_embedding/pcr/script.py b/src/batch_integration/metrics_embedding/pcr/script.py index 5749fa1d23..fc371aabaa 100644 --- a/src/batch_integration/metrics_embedding/pcr/script.py +++ b/src/batch_integration/metrics_embedding/pcr/script.py @@ -1,24 +1,27 @@ +import anndata as ad +from scib.metrics import pcr_comparison + ## VIASH START par = { - 'input': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', - 'output': './src/batch_integration/embedding/resources/cc_score_pancreas_mnn.tsv' + 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality_name': 'foo', } ## VIASH END -import pprint -import scanpy as sc -from scib.metrics import pcr_comparison +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) +adata_solution= ad.read_h5ad(par['input_solution']) -OUTPUT_TYPE = 'embedding' -METRIC = 'pcr' -adata_file = par['input'] -output = par['output'] +print('Transfer obs annotations', flush=True) +adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] -print('Read input', flush=True) -adata = sc.read(adata_file) adata_int = adata.copy() -name = adata.uns['dataset_id'] print('compute score') score = pcr_comparison( @@ -29,8 +32,21 @@ verbose=False ) -with open(output, 'w') as file: - header = ['dataset', 'output_type', 'metric', 'value'] - entry = [name, OUTPUT_TYPE, METRIC, score] - file.write('\t'.join(header) + '\n') - file.write('\t'.join([str(x) for x in entry])) +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ], + 'hvg': adata.uns['hvg'], + 'output_type': adata.uns['output_type'], + } +) + +if 'parent_method_id' in adata.uns: + output.uns['parent_method_id'] = adata.uns['parent_method_id'] + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml index 9e1c6c16e2..05d6d395a9 100644 --- a/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml @@ -1,11 +1,11 @@ # use metric api spec -__merge__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric_graph.yaml functionality: name: clustering_overlap - namespace: batch_integration/graph/metrics + namespace: batch_integration/metrics_graph description: Metrics that are based on computing the clustering overlap. info: - output_type: graph + type: metric metrics: - metric_id: ari metric_name: ARI @@ -23,6 +23,8 @@ functionality: min: 0 max: 1 maximize: true + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - metric_id: nmi metric_name: NMI metric_description: | @@ -39,6 +41,8 @@ functionality: min: 0 max: 1 maximize: true + v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py @@ -47,5 +51,6 @@ platforms: image: mumichae/scib-base:1.0.2 setup: - type: python - pypi: pyyaml + pypi: + - pyyaml - type: nextflow diff --git a/src/batch_integration/metrics_graph/clustering_overlap/script.py b/src/batch_integration/metrics_graph/clustering_overlap/script.py index a4ddab9c4e..57baccc1d9 100644 --- a/src/batch_integration/metrics_graph/clustering_overlap/script.py +++ b/src/batch_integration/metrics_graph/clustering_overlap/script.py @@ -1,20 +1,25 @@ -import yaml import anndata as ad from scib.metrics.clustering import opt_louvain from scib.metrics import ari, nmi ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - 'output': 'output.h5ad' + 'input_integrated': 'resources_test/batch_integration/graph/bbknn.h5ad', + 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', + 'output': 'output.h5ad', } -## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) +meta = { + 'functionality_name': 'foo' +} +## VIASH END print('Read input', flush=True) -input = ad.read_h5ad(par['input']) +input = ad.read_h5ad(par['input_integrated']) +solution = ad.read_h5ad(par['input_solution']) + +print('Transfer obs annotations', flush=True) +input.obs['label'] = solution.obs['label'][input.obs_names] print('Run Louvain clustering', flush=True) opt_louvain( @@ -36,14 +41,17 @@ output = ad.AnnData( uns={ "dataset_id": input.uns['dataset_id'], + 'normalization_id': input.uns['normalization_id'], "method_id": input.uns['method_id'], "metric_ids": [ "ari", "nmi" ], "metric_values": [ ari_score, nmi_score ], "hvg": input.uns['hvg'], - "scaled": input.uns['scaled'], - "output_type": config["functionality"]["info"]["output_type"], + 'output_type': input.uns['output_type'], } ) +if 'parent_method_id' in input.uns: + output.uns['parent_method_id'] = input.uns['parent_method_id'] + print("Write data to file", flush=True) output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index c7257310c2..a19189d3e2 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -28,18 +28,19 @@ viash run src/batch_integration/split_dataset/config.vsh.yaml -- \ echo run methods... # Graph methods -viash run src/batch_integration/graph/methods/bbknn/config.vsh.yaml -- \ +viash run src/batch_integration/methods_graph/bbknn/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/graph/methods/bbknn.h5ad + --output $DATASET_DIR/graph/bbknn.h5ad -viash run src/batch_integration/graph/methods/combat/config.vsh.yaml -- \ +# Embedding method +viash run src/batch_integration/methods_embedding/scvi/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/graph/methods/combat.h5ad + --output $DATASET_DIR/embedding/scvi.h5ad -# Embedding method -viash run src/batch_integration/embedding/methods/combat/config.vsh.yaml -- \ +# feature method +viash run src/batch_integration/methods_feature/combat/config.vsh.yaml -- \ --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/embedding/methods/combat.h5ad + --output $DATASET_DIR/feature/combat.h5ad # run one metric echo run metrics... From d3c2ce331145e443ca20e8dce75fbee2d4ea979a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 14 Feb 2023 11:42:53 +0100 Subject: [PATCH 0738/1233] fix metrics unit tests Former-commit-id: bbf49fcf03586b943eee54b9094403963b416ffd --- .../api/comp_metric_embedding.yaml | 20 +++++++------------ .../api/comp_metric_feature.yaml | 18 ++++++----------- .../api/comp_metric_graph.yaml | 14 +++++-------- 3 files changed, 18 insertions(+), 34 deletions(-) diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index dc79ad897c..2c45791a66 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -8,7 +8,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration - type: python_script dest: test.py text: | @@ -21,8 +21,8 @@ functionality: ## VIASH START meta = { - "resources_dir": "resources_test/batch_integration/graph/methods", - "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" + "resources_dir": "resources_test/batch_integration", + "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" } ## VIASH END @@ -32,20 +32,14 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - output_type = config["functionality"].get("info", {}).get("output_type") - - print(">> Construct input arguments", flush=True) - if output_type == "graph": - input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" - elif output_type == "embedding": - input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" - else: - sys.exit("Unrecognized .functionality.info.output_type") + input_file = f"{meta['resources_dir']}/batch_integration/embedding/scvi.h5ad" + sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], - "--input", input_file, + "--input_integrated", input_file, + "--input_solution", sol_file, "--output", output_file ] diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 3a599a8d39..14182458ba 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -8,7 +8,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration - type: python_script dest: test.py text: | @@ -21,7 +21,7 @@ functionality: ## VIASH START meta = { - "resources_dir": "resources_test/batch_integration/graph/methods", + "resources_dir": "resources_test/batch_integration", "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" } ## VIASH END @@ -32,20 +32,14 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - output_type = config["functionality"].get("info", {}).get("output_type") - - print(">> Construct input arguments", flush=True) - if output_type == "graph": - input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" - elif output_type == "embedding": - input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" - else: - sys.exit("Unrecognized .functionality.info.output_type") + input_file = f"{meta['resources_dir']}/batch_integration/feature/combat.h5ad" + sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], - "--input", input_file, + "--input_integrated", input_file, + "--input_solution", sol_file, "--output", output_file ] diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 49790016c3..0617bf4179 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -8,7 +8,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration - type: python_script dest: test.py text: | @@ -34,18 +34,14 @@ functionality: output_type = config["functionality"].get("info", {}).get("output_type") - print(">> Construct input arguments", flush=True) - if output_type == "graph": - input_file = f"{meta['resources_dir']}/batch_integration/graph/methods/bbknn.h5ad" - elif output_type == "embedding": - input_file = f"{meta['resources_dir']}/batch_integration/embedding/methods/combat.h5ad" - else: - sys.exit("Unrecognized .functionality.info.output_type") + input_file = f"{meta['resources_dir']}/batch_integration/graph/bbknn.h5ad" + sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], - "--input", input_file, + "--input_integrated", input_file, + "--input_solution", sol_file, "--output", output_file ] From 13d4f72236f77a02d08e119d927a0d69d23f8636 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 14 Feb 2023 17:03:32 +0100 Subject: [PATCH 0739/1233] update missing methods and metrics Former-commit-id: e6e610ea3af8c68ae673c16c7b369c7343dc6e80 --- src/batch_integration/changes.md | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/src/batch_integration/changes.md b/src/batch_integration/changes.md index 124df564a4..920b269318 100644 --- a/src/batch_integration/changes.md +++ b/src/batch_integration/changes.md @@ -60,4 +60,28 @@ New todos: - move methods and metrics to the correct folders (e.g. scanorama_embed to `methods_embed/scanorama_embed`) - create API files for all of the above componenent types -- compare current components with v1, list the ones that are missing \ No newline at end of file +- compare current components with v1, list the ones that are missing + +missing methods: + +- `control_methods`: add the baseline methods as control methods to all subtasks +- `fastmnn`: feature and embed method (convert to Rscript?) +- `harmony`: embed method (convert to Rscript?) +- `liger`: embed method (convert to Rscript?) +- `mnn`: feature method +- `scalex`: feature and embed method +- `scanvi`: embed method + +missing metrics: + +- `ari`: embedding, feature +- `graph_connectivity`: embedding, graph, feature +- `hvg_cons`: feature +- `isolabel_f1`: embedding, graph, feature +- `isolabel_sil`: embedding, feature +- `kBET`: embedding, feature +- `nmi`: embedding, feature +- `pcr`: feature +- `asw_batch`: feature +- `asw_label`: feature +- \ No newline at end of file From db08f8152ac38b160859cd325d957591f32b6146 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 15 Feb 2023 12:13:04 +0100 Subject: [PATCH 0740/1233] Move tranformer components Co-authored-by: Robrecht Cannoodt Former-commit-id: 0f8fd6bab02dd102fb321ac015eaf5b2e87fa1db --- .../embed_to_graph/config.vsh.yaml | 12 +++++++----- .../embed_to_graph/script.py | 0 .../feature_to_embed/config.vsh.yaml | 12 +++++++----- .../feature_to_embed/script.py | 0 4 files changed, 14 insertions(+), 10 deletions(-) rename src/batch_integration/{methods_graph => transformers}/embed_to_graph/config.vsh.yaml (61%) rename src/batch_integration/{methods_graph => transformers}/embed_to_graph/script.py (100%) rename src/batch_integration/{methods_embedding => transformers}/feature_to_embed/config.vsh.yaml (61%) rename src/batch_integration/{methods_embedding => transformers}/feature_to_embed/script.py (100%) diff --git a/src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml similarity index 61% rename from src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml rename to src/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 111960c534..3bced2c965 100644 --- a/src/batch_integration/methods_graph/embed_to_graph/config.vsh.yaml +++ b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -1,14 +1,16 @@ -# use method api spec -__merge__: ../../api/comp_method_graph.yaml functionality: name: embed_to_graph - namespace: batch_integration/methods_graph + namespace: batch_integration/transformers description: "Transform an embedded integration to a graph integration" info: type: method method_name: Embedding to Graph - variants: - embed_to_graph: + arguments: + - __merge__: ../../api/anndata_integrated_embedding.yaml + name: --input + - __merge__: ../../api/anndata_integrated_graph.yaml + name: --output + direction: output resources: - type: python_script path: script.py diff --git a/src/batch_integration/methods_graph/embed_to_graph/script.py b/src/batch_integration/transformers/embed_to_graph/script.py similarity index 100% rename from src/batch_integration/methods_graph/embed_to_graph/script.py rename to src/batch_integration/transformers/embed_to_graph/script.py diff --git a/src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml similarity index 61% rename from src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml rename to src/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 7b4b1d5bd2..a96ce1a610 100644 --- a/src/batch_integration/methods_embedding/feature_to_embed/config.vsh.yaml +++ b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -1,14 +1,16 @@ -# use method api spec -__merge__: ../../api/comp_method_feature.yaml functionality: name: feature_to_embed + namespace: batch_integration/transformers description: "Transform a feature integration to an embedded integration" info: type: method method_name: Feature to Embed - preferred_normalization: log_cpm - variants: - feature_to_embed: + arguments: + - __merge__: ../../api/anndata_integrated_feature.yaml + name: --input + - __merge__: ../../api/anndata_integrated_embedding.yaml + name: --output + direction: output resources: - type: python_script path: script.py diff --git a/src/batch_integration/methods_embedding/feature_to_embed/script.py b/src/batch_integration/transformers/feature_to_embed/script.py similarity index 100% rename from src/batch_integration/methods_embedding/feature_to_embed/script.py rename to src/batch_integration/transformers/feature_to_embed/script.py From 21ff429196cdab93e2af9121b0f765cb348800b6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 15 Feb 2023 12:13:44 +0100 Subject: [PATCH 0741/1233] fix typos and unit testing Co-authored-by: Robrecht Cannoodt Former-commit-id: 55c988771031a924af9169a3e351b0ae9a51313c --- .../api/anndata_dataset.yaml | 4 ++++ .../api/anndata_integrated_embedding.yaml | 1 + .../api/anndata_integrated_feature.yaml | 1 + .../api/anndata_integrated_graph.yaml | 1 + .../api/anndata_solution.yaml | 4 ++++ .../api/anndata_unintegrated.yaml | 4 ++++ .../api/comp_method_embedding.yaml | 11 ++--------- .../api/comp_method_feature.yaml | 8 ++++---- .../api/comp_method_graph.yaml | 7 +------ .../scanorama_embed/config.vsh.yaml | 2 +- .../methods_feature/combat/config.vsh.yaml | 3 ++- .../methods_feature/combat/script.py | 2 +- .../metrics_embedding/asw_label/script.py | 4 ++-- .../metrics_embedding/pcr/config.vsh.yaml | 19 ++++++++++++++++--- .../metrics_embedding/pcr/script.py | 2 +- 15 files changed, 45 insertions(+), 28 deletions(-) diff --git a/src/batch_integration/api/anndata_dataset.yaml b/src/batch_integration/api/anndata_dataset.yaml index 8b6d47c825..5d94736f7f 100644 --- a/src/batch_integration/api/anndata_dataset.yaml +++ b/src/batch_integration/api/anndata_dataset.yaml @@ -73,3 +73,7 @@ info: - type: object name: knn description: Neighbors data. + - type: string + name: organism + description: "Which normalization was used" + required: true diff --git a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/batch_integration/api/anndata_integrated_embedding.yaml index e1426f9bf1..024cef7fad 100644 --- a/src/batch_integration/api/anndata_integrated_embedding.yaml +++ b/src/batch_integration/api/anndata_integrated_embedding.yaml @@ -3,6 +3,7 @@ type: file description: Integrated AnnData HDF5 file. example: input.h5ad info: + prediction_type: embedding short_description: "Integrated embedding" slots: obsm: diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index 1c3e690d7b..c7aacc9675 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -3,6 +3,7 @@ type: file description: Integrated AnnData HDF5 file. example: input.h5ad info: + prediction_type: feature short_description: "Integrated Graph" slots: X: diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml index 1d1a8c381b..52a2632fe9 100644 --- a/src/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -3,6 +3,7 @@ type: file description: Integrated AnnData HDF5 file. example: input.h5ad info: + prediction_type: graph short_description: "Integrated Graph" slots: obsp: diff --git a/src/batch_integration/api/anndata_solution.yaml b/src/batch_integration/api/anndata_solution.yaml index 4914212565..db7acd54b4 100644 --- a/src/batch_integration/api/anndata_solution.yaml +++ b/src/batch_integration/api/anndata_solution.yaml @@ -50,3 +50,7 @@ info: name: normalization_id description: "Which normalization was used" required: true + - type: string + name: organism + description: "Which normalization was used" + required: true diff --git a/src/batch_integration/api/anndata_unintegrated.yaml b/src/batch_integration/api/anndata_unintegrated.yaml index 2ed8eadb87..974f2e59fe 100644 --- a/src/batch_integration/api/anndata_unintegrated.yaml +++ b/src/batch_integration/api/anndata_unintegrated.yaml @@ -41,3 +41,7 @@ info: name: normalization_id description: "Which normalization was used" required: true + - type: string + name: organism + description: "Which normalization was used" + required: true diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index ac56cb63b5..4e385122a0 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -23,12 +23,7 @@ functionality: import anndata as ad - print(">> Running script", flush=True) - if meta["functionality_name"] == 'feature_to_embed': - input_path = meta["resources_dir"] + "/batch_integration/feature/scvi.h5ad" - else: - input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" - input_path = meta["resources_dir"] + "/pancreas/processed.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" output_path = "embeddding.h5ad" cmd = [ meta['executable'], @@ -59,9 +54,7 @@ functionality: assert 'X_emb' in output.obsm assert 'normalization_id' in output.uns assert 'method_id' in output.uns - assert meta['fuctionality_name'] == output.uns['method_id'] - if meta["functionality_name"] == 'feature_to_embed': - assert 'parent_method_id' in output.uns + assert meta['functionality_name'] == output.uns['method_id'] assert 'hvg' in output.uns diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index d9295ca1fc..1f8d9c40ca 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -14,7 +14,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/feature/ + - path: ../../../../resources_test/batch_integration/ - type: python_script path: generic_test.py text: | @@ -22,8 +22,8 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" - output_path = "inegrated.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + output_path = "integrated.h5ad" cmd = [ meta['executable'], "--input", input_path, @@ -47,7 +47,7 @@ functionality: print(">> Checking whether predictions were added", flush=True) # TODO: use helper function to check whether the required fields are defined - assert output.X + assert output.X is not None print(">> Check values", flush=True) assert meta['functionality_name'] == output.uns['method_id'] diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 2c2af15bc1..ea3f85b766 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -22,10 +22,7 @@ functionality: import subprocess import anndata as ad - if meta["functionality_name"] == 'embed_to_graph': - input_path = meta["resources_dir"] + "/batch_integration/embedding/scvi.h5ad" - else: - input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" output_path = "inegrated.h5ad" cmd = [ meta['executable'], @@ -57,7 +54,5 @@ functionality: print(">> Check values", flush=True) assert meta['functionality_name'] == output.uns['method_id'] assert input.uns["dataset_id"] == output.uns["dataset_id"] - if meta["functionality_name"] == 'embed_to_graph': - assert 'parent_method_id' in output.uns print(">> All tests passed successfully") diff --git a/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml index 92170df584..c4b7d53fd5 100644 --- a/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml @@ -1,5 +1,5 @@ # use method api spec -__merge__: ../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_embedding.yaml functionality: name: scanorama_embed namespace: batch_integration/methods_embedding diff --git a/src/batch_integration/methods_feature/combat/config.vsh.yaml b/src/batch_integration/methods_feature/combat/config.vsh.yaml index ec2719a5b0..d284cb1054 100644 --- a/src/batch_integration/methods_feature/combat/config.vsh.yaml +++ b/src/batch_integration/methods_feature/combat/config.vsh.yaml @@ -1,7 +1,8 @@ # use method api spec -__merge__: ../../api/comp_method_graph.yaml +__merge__: ../../api/comp_method_feature.yaml functionality: name: combat + namespace: batch_integration/methods_feature description: "Adjusting batch effects in microarray expression data using empirical Bayes methods" info: diff --git a/src/batch_integration/methods_feature/combat/script.py b/src/batch_integration/methods_feature/combat/script.py index fee9b9eef7..6c7cf09ca9 100644 --- a/src/batch_integration/methods_feature/combat/script.py +++ b/src/batch_integration/methods_feature/combat/script.py @@ -10,7 +10,7 @@ } meta = { - 'funcionality_name': 'foo', + 'functionality_name': 'foo', 'config': 'bar' } diff --git a/src/batch_integration/metrics_embedding/asw_label/script.py b/src/batch_integration/metrics_embedding/asw_label/script.py index 3b2b7bc7fb..a34ffa9d4d 100644 --- a/src/batch_integration/metrics_embedding/asw_label/script.py +++ b/src/batch_integration/metrics_embedding/asw_label/script.py @@ -35,8 +35,8 @@ "method_id": adata.uns['method_id'], "hvg": adata.uns['hvg'], "output_type": adata.uns['output_type'], - "metric_ids": meta['functionality_name'], - "metric_value": score + "metric_ids": [meta['functionality_name']], + "metric_values": [score] } ) diff --git a/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml b/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml index f4e9467b52..6a1f927d83 100644 --- a/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml @@ -1,9 +1,21 @@ # use metric api spec -__merge__: ../../api/comp_metric.yaml +__merge__: ../../api/comp_metric_embedding.yaml functionality: name: pcr - namespace: batch_integration/embedding/metrics + namespace: batch_integration/metrics_embedding description: PCA regression + info: + type: metric + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + paper_reference: luecken2022benchmarking + metrics: + - metric_id: pcr + metric_name: PCR + min: 0 + max: 1 + maximize: true + resources: - type: python_script path: script.py @@ -12,5 +24,6 @@ platforms: image: mumichae/scib-base:1.0.2 setup: - type: python - pypi: pyyaml + pypi: + - pyyaml - type: nextflow diff --git a/src/batch_integration/metrics_embedding/pcr/script.py b/src/batch_integration/metrics_embedding/pcr/script.py index fc371aabaa..912b8c4293 100644 --- a/src/batch_integration/metrics_embedding/pcr/script.py +++ b/src/batch_integration/metrics_embedding/pcr/script.py @@ -20,7 +20,7 @@ print('Transfer obs annotations', flush=True) adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] - +adata.X = adata.layers['normalized'] adata_int = adata.copy() print('compute score') From 90e0a45a12503ed0d21fe139c71449bff463c0cb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 28 Feb 2023 12:17:53 +0100 Subject: [PATCH 0742/1233] switch to viash 0.7.0 Former-commit-id: 77d6cb65e1b0c956a8cc2926d320f55d6fa7ff1e --- _viash.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 200ea0ed73..0d9c3b3713 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.6.7 +viash_version: 0.7.0 source: src target: target From b49e6de3faabaca372227b3d46786b8c8bf41033 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 28 Feb 2023 12:48:55 +0100 Subject: [PATCH 0743/1233] update helpers Former-commit-id: 647be522b5c707308be9343a8d352cd203c23245 --- src/wf_utils/DataflowHelper.nf | 4 +- src/wf_utils/WorkflowHelper.nf | 492 +++++++++++++++++++++++++++++++-- 2 files changed, 473 insertions(+), 23 deletions(-) diff --git a/src/wf_utils/DataflowHelper.nf b/src/wf_utils/DataflowHelper.nf index 1057038288..213af64c7c 100644 --- a/src/wf_utils/DataflowHelper.nf +++ b/src/wf_utils/DataflowHelper.nf @@ -8,7 +8,7 @@ */ def setWorkflowArguments(Map args) { - wfKey = args.key ?: "setWorkflowArguments" + wfKey = args.key != null ? args.key : "setWorkflowArguments" args.keySet().removeAll(["key"]) @@ -68,7 +68,7 @@ def setWorkflowArguments(Map args) { def getWorkflowArguments(Map args) { - def inputKey = args.inputKey ?: "input" + def inputKey = args.inputKey != null ? args.inputKey : "input" def wfKey = "getWorkflowArguments_" + args.key workflow getWorkflowArgumentsInstance { diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index 0fb00586e4..69b9941abd 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -26,7 +26,8 @@ def getChild(parent, child) { if (child.contains("://") || Paths.get(child).isAbsolute()) { child } else { - parent.replaceAll('/[^/]*$', "/") + child + def parentAbsolute = Paths.get(parent).toAbsolutePath().toString() + parentAbsolute.replaceAll('/[^/]*$', "/") + child } } @@ -107,15 +108,15 @@ def readYaml(file) { // based on how Functionality.scala is implemented def processArgument(arg) { - arg.multiple = arg.multiple ?: false - arg.required = arg.required ?: false - arg.direction = arg.direction ?: "input" - arg.multiple_sep = arg.multiple_sep ?: ":" + arg.multiple = arg.multiple != null ? arg.multiple : false + arg.required = arg.required != null ? arg.required : false + arg.direction = arg.direction != null ? arg.direction : "input" + arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ":" arg.plainName = arg.name.replaceAll("^-*", "") if (arg.type == "file") { - arg.must_exist = arg.must_exist ?: true - arg.create_parent = arg.create_parent ?: true + arg.must_exist = arg.must_exist != null ? arg.must_exist : true + arg.create_parent = arg.create_parent != null ? arg.create_parent : true } if (arg.type == "file" && arg.direction == "output") { @@ -129,7 +130,8 @@ def processArgument(arg) { if (extSearch instanceof List) { extSearch = extSearch[0] } - def ext = extSearch.find("\\.[^\\.]+\$") ?: "" + def extSearchResult = extSearch.find("\\.[^\\.]+\$") + def ext = extSearchResult != null ? extSearchResult : "" arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" } @@ -191,27 +193,27 @@ def processConfig(config) { // set defaults for inputs config.functionality.inputs = - (config.functionality.inputs ?: []).collect{arg -> - arg.type = arg.type ?: "file" + (config.functionality.inputs != null ? config.functionality.inputs : []).collect{arg -> + arg.type = arg.type != null ? arg.type : "file" arg.direction = "input" processArgument(arg) } // set defaults for outputs config.functionality.outputs = - (config.functionality.outputs ?: []).collect{arg -> - arg.type = arg.type ?: "file" + (config.functionality.outputs != null ? config.functionality.outputs : []).collect{arg -> + arg.type = arg.type != null ? arg.type : "file" arg.direction = "output" processArgument(arg) } // set defaults for arguments config.functionality.arguments = - (config.functionality.arguments ?: []).collect{arg -> + (config.functionality.arguments != null ? config.functionality.arguments : []).collect{arg -> processArgument(arg) } // set defaults for argument_group arguments config.functionality.argument_groups = - (config.functionality.argument_groups ?: []).collect{grp -> - grp.arguments = (grp.arguments ?: []).collect{arg -> + (config.functionality.argument_groups != null ? config.functionality.argument_groups : []).collect{grp -> + grp.arguments = (grp.arguments != null ? grp.arguments : []).collect{arg -> arg instanceof String ? arg.replaceAll("^-*", "") : processArgument(arg) } grp @@ -238,7 +240,7 @@ def processConfig(config) { } def readConfig(file) { - def config = readYaml(file ?: "$projectDir/config.vsh.yaml") + def config = readYaml(file != null ? file : "$projectDir/config.vsh.yaml") processConfig(config) } @@ -359,7 +361,7 @@ def generateArgumentHelp(param) { def dflt = null if (param.default != null) { if (param.default instanceof List) { - dflt = param.default.join(param.multiple_sep ?: ", ") + dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") } else { dflt = param.default.toString() } @@ -367,7 +369,7 @@ def generateArgumentHelp(param) { def example = null if (param.example != null) { if (param.example instanceof List) { - example = param.example.join(param.multiple_sep ?: ", ") + example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") } else { example = param.example.toString() } @@ -457,7 +459,7 @@ def helpMessage(config) { } } -def guessMultiParamFormat(params) { +def _guessParamListFormat(params) { if (!params.containsKey("param_list") || params.param_list == null) { "none" } else { @@ -477,7 +479,14 @@ def guessMultiParamFormat(params) { } } +viashChannelDeprecationWarningPrinted = false + def paramsToList(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: paramsToList has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } // fetch default params from functionality def defaultArgs = config.functionality.allArguments .findAll { it.containsKey("default") } @@ -490,7 +499,7 @@ def paramsToList(params, config) { // check multi input params // objects should be closures and not functions, thanks to FunctionDef - def multiParamFormat = guessMultiParamFormat(params) + def multiParamFormat = _guessParamListFormat(params) def multiOptionFunctions = [ "csv": {[it, readCsv(it)]}, @@ -559,7 +568,7 @@ def paramsToList(params, config) { parData = parData.flatten() // cast types - if (par.type == "file" && ((par.direction ?: "input") == "input")) { + if (par.type == "file" && ((par.direction != null ? par.direction : "input") == "input")) { parData = parData.collect{path -> if (path !instanceof String) { path @@ -603,10 +612,451 @@ def paramsToList(params, config) { } def paramsToChannel(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: paramsToChannel has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } Channel.fromList(paramsToList(params, config)) } def viashChannel(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: viashChannel has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } paramsToChannel(params, config) | map{tup -> [tup.id, tup]} } + +/** + * Split parameters for arguments that accept multiple values using their separator + * + * @param paramList A Map containing parameters to split. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A Map of parameters where the parameter values have been split into a list using + * their seperator. + */ +Map _splitParams(Map parValues, Map config){ + def parsedParamValues = parValues.collectEntries { parName, parValue -> + def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) + + if (!parameterSettings) { + // if argument is not found, do not alter + return [parName, parValue] + } + if (parameterSettings.multiple) { // Check if parameter can accept multiple values + if (parValue instanceof Collection) { + parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } + } else if (parValue instanceof String) { + parValue = parValue.split(parameterSettings.multiple_sep) + } else if (parValue == null) { + parValue = [] + } else { + parValue = [ parValue ] + } + parValue = parValue.flatten() + } + // For all parameters check if multiple values are only passed for + // arguments that allow it. Quietly simplify lists of length 1. + if (!parameterSettings.multiple && parValue instanceof Collection) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + [parName, parValue] + } + return parsedParamValues +} + +/** + * Check if the ids are unique across parameter sets + * + * @param parameterSets a list of parameter sets. + */ +private void _checkUniqueIds(List>> parameterSets) { + def ppIds = parameterSets.collect{it[0]} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" +} + +/** + * Resolve the file paths in the parameters relative to given path + * + * @param paramList A Map containing parameters to process. + * This function assumes that files are still of type String. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * @param relativeTo path of a file to resolve the parameters values to. + * + * @return A map of parameters where the location of the input file parameters have been resolved + * resolved relatively to the provided path. + */ +private Map _resolvePathsRelativeTo(Map paramList, Map config, String relativeTo) { + paramList.collectEntries { parName, parValue -> + argSettings = config.functionality.allArguments.find{it.plainName == parName} + if (argSettings && argSettings.type == "file" && argSettings.direction == "input") { + if (parValue instanceof Collection) { + parValue = parValue.collect({path -> + path !instanceof String ? path : file(getChild(relativeTo, path)) + }) + } else { + parValue = parValue !instanceof String ? path : file(getChild(relativeTo, parValue)) + } + } + [parName, parValue] + } +} + +/** + * Parse nextflow parameters based on settings defined in a viash config + * and return a nextflow channel. + * + * @param params Input parameters from nextflow. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A list of parameter sets that were parsed from the 'param_list' argument value. + */ +private List> _parseParamListArguments(Map params, Map config){ + // first try to guess the format (if not set in params) + def paramListFormat = _guessParamListFormat(params) + + // get the correct parser function for the detected params_list format + def paramListParsers = [ + "csv": {[it, readCsv(it)]}, + "json": {[it, readJson(it)]}, + "yaml": {[it, readYaml(it)]}, + "yaml_blob": {[null, readYamlBlob(it)]}, + "asis": {[null, it]}, + "none": {[null, [[:]]]} + ] + assert paramListParsers.containsKey(paramListFormat): + "Format of provided --param_list not recognised.\n" + + "You can use '--param_list_format' to manually specify the format.\n" + + "Found: '$paramListFormat'. Expected: one of 'csv', 'json', "+ + "'yaml', 'yaml_blob', 'asis' or 'none'" + def paramListParser = paramListParsers.get(paramListFormat) + + // fetch multi param inputs + def paramListOut = paramListParser(params.containsKey("param_list") ? params.param_list : "") + // multiFile is null if the value passed to param_list was not a file (e.g a blob) + // If the value was indeed a file, multiFile contains the location that file (used later). + def paramListFile = paramListOut[0] + def paramSets = paramListOut[1] // these are the actual parameters from reading the blob/file + + // data checks + assert paramSets instanceof List: "--param_list should contain a list of maps" + for (value in paramSets) { + assert value instanceof Map: "--param_list should contain a list of maps" + } + + // Reformat from List to List> by adding the ID as first element of a Tuple2 + paramSets = paramSets.collect({ paramValues -> + [paramValues.get("id", null), paramValues.findAll{it.key != 'id'}] + }) + // Split parameters with 'multiple: true' + paramSets = paramSets.collect({ id, paramValues -> + def splitParamValues = _splitParams(paramValues, config) + [id, splitParamValues] + }) + + // The paths of input files inside a param_list file may have been specified relatively to the + // location of the param_list file. These paths must be made absolute. + if (paramListFile){ + paramSets = paramSets.collect({ id, paramValues -> + def relativeParamValues = _resolvePathsRelativeTo(paramValues, config, paramListFile) + [id, relativeParamValues] + }) + } + + return paramSets +} + +/** + * Cast parameters to the correct type as defined in the Viash config + * + * @param parValues A Map of input arguments. + * + * @return The input arguments that have been cast to the type from the viash config. + */ + +private Map _castParamTypes(Map parValues, Map config) { + // Cast the input to the correct type according to viash config + def castParValues = parValues.collectEntries({ parName, parValue -> + paramSettings = config.functionality.allArguments.find({it.plainName == parName}) + // dont parse parameters like publish_dir ( in which case paramSettings = null) + parType = paramSettings ? paramSettings.get("type", null) : null + if (parValue !instanceof Collection) { + parValue = [parValue] + } + if (parType == "file" && ((paramSettings.direction != null ? paramSettings.direction : "input") == "input")) { + parValue = parValue.collect{ path -> + if (path !instanceof String) { + path + } else { + file(path) + } + } + } else if (parType == "integer") { + parValue = parValue.collect{it as Integer} + } else if (parType == "double") { + parValue = parValue.collect{it as Double} + } else if (parType == "boolean" || + parType == "boolean_true" || + parType == "boolean_false") { + parValue = parValue.collect{it as Boolean} + } + + // simplify list to value if need be + if (paramSettings && !paramSettings.multiple) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + [parName, parValue] + }) + return castParValues +} + +/** + * Apply the argument settings specified in a Viash config to a single parameter set. + * - Split the parameter values according to their seperator if + * the parameter accepts multiple values + * - Cast the parameters to their corect types. + * - Assertions: + * ~ Check if any unknown parameters are found + * + * @param paramValues A Map of parameter to be processed. All parameters must + * also be specified in the Viash config. + * @param config: A Map of the Viash configuration. This Map can be generated from + * the config file using the readConfig() function. + * @return The input parameters that have been processed. + */ +Map applyConfigToOneParameterSet(Map paramValues, Map config){ + def splitParamValues = _splitParams(paramValues, config) + def castParamValues = _castParamTypes(splitParamValues, config) + + // Check if any unexpected arguments were passed + def knownParams = config.functionality.allArguments.collect({it.plainName}) + ["publishDir", "publish_dir"] + castParamValues.each({parName, parValue -> + assert parName in knownParams: "Unknown parameter. Parameter $parName should be in $knownParams" + }) + return castParamValues +} + +/** + * Apply the argument settings specified in a Viash config to a list of parameter sets. + * - Split the parameter values according to their seperator if + * the parameter accepts multiple values + * - Cast the parameters to their corect types. + * - Assertions: + * ~ Check if any unknown parameters are found + * ~ Check if the ID of the parameter set is unique across all sets. + * + * @return The input parameters that have been processed. + */ + +List applyConfig(List parameterSets, Map config){ + def processedparameterSets = parameterSets.collect({ parameterSet -> + def id = parameterSet[0] + def paramValues = parameterSet[1] + def passthrough = parameterSet.drop(2) + def processedSet = applyConfigToOneParameterSet(paramValues, config) + [id, processedSet] + passthrough + }) + + _checkUniqueIds(processedparameterSets) + return processedparameterSets +} + +/** + * Parse nextflow parameters based on settings defined in a viash config. + * Return a list of parameter sets, each parameter set corresponding to + * an event in a nextflow channel. The output from this function can be used + * with Channel.fromList to create a nextflow channel with Vdsl3 formatted + * events. + * + * This function performs: + * - A filtering of the params which can be found in the config file. + * - Process the params_list argument which allows a user to to initialise + * a Vsdl3 channel with multiple parameter sets. Possible formats are + * csv, json, yaml, or simply a yaml_blob. A csv should have column names + * which correspond to the different arguments of this pipeline. A json or a yaml + * file should be a list of maps, each of which has keys corresponding to the + * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. + * When passing a csv, json or yaml, relative path names are relativized to the + * location of the parameter file. + * - Combine the parameter sets into a vdsl3 Channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A list of parameters with the first element of the event being + * the event ID and the second element containing a map of the parsed parameters. + */ + +private List>> _paramsToParamSets(Map params, Map config){ + /* parse regular parameters (not in param_list) */ + /*************************************************/ + def globalParams = config.functionality.allArguments + .findAll { params.containsKey(it.plainName) } + .collectEntries { [ it.plainName, params[it.plainName] ] } + def globalID = params.get("id", null) + def globalParamsValues = applyConfigToOneParameterSet(globalParams.findAll{it.key != 'id'}, config) + + /* process params_list arguments */ + /*********************************/ + def paramSets = _parseParamListArguments(params, config) + def parameterSetsWithConfigApplied = applyConfig(paramSets, config) + + /* combine arguments into channel */ + /**********************************/ + def processedParams = parameterSetsWithConfigApplied.indexed().collect{ index, paramSet -> + def id = paramSet[0] + def parValues = paramSet[1] + id = [id, globalID].find({it != null}) // first non-null element + + if (workflow.stubRun) { + // if stub run, explicitly add an id if missing + id = id ? id : "stub" + index + } + assert id != null: "Each parameter set should have at least an ID." + // Add regular parameters together with parameters passed with 'param_list' + def combinedArgsValues = globalParamsValues + parValues + + // Remove parameters which are null, if the default is also null + combinedArgsValues = combinedArgsValues.collectEntries{paramName, paramValue -> + parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) + if ( paramValue != null || parameterSettings.get("default", null) != null ) { + [paramName, paramValue] + } + } + [id, combinedArgsValues] + } + + // Check if ids (first element of each list) is unique + _checkUniqueIds(processedParams) + return processedParams +} + +/** + * Parse nextflow parameters based on settings defined in a viash config + * and return a nextflow channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A nextflow Channel with events. Events are formatted as a tuple that contains + * first contains the ID of the event and as second element holds a parameter map. + * + * + */ +def channelFromParams(Map params, Map config) { + processedParams = _paramsToParamSets(params, config) + return Channel.fromList(processedParams) +} + +/** + * Process a list of Vdsl3 formatted parameters and apply a Viash config to them: + * - Gather default parameters from the Viash config and make + * sure that they are correctly formatted (see applyConfig method). + * - Format the input parameters (also using the applyConfig method). + * - Apply the default parameter to the input parameters. + * - Do some assertions: + * ~ Check if the event IDs in the channel are unique. + * + * @param params A list of parameter sets as Tuples. The first element of the tuples + * must be a unique id of the parameter set, and the second element + * must contain the parameters themselves. Optional extra elements + * of the tuples will be passed to the output as is. + * @param config A Map of the Viash configuration. This Map can be generated from + * the config file using the readConfig() function. + * + * @return A list of processed parameters sets as tuples. + */ + +private List _preprocessInputsList(List params, Map config) { + // Get different parameter types (used throughout this function) + def defaultArgs = config.functionality.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // Apply config to default parameters + def parsedDefaultValues = applyConfigToOneParameterSet(defaultArgs, config) + + // Apply config to input parameters + def parsedInputParamSets = applyConfig(params, config) + + // Merge two parameter sets together + def parsedArgs = parsedInputParamSets.collect({ parsedInputParamSet -> + def id = parsedInputParamSet[0] + def parValues = parsedInputParamSet[1] + def passthrough = parsedInputParamSet.drop(2) + def parValuesWithDefault = parsedDefaultValues + parValues + [id, parValuesWithDefault] + passthrough + }) + _checkUniqueIds(parsedArgs) + + return parsedArgs +} + +/** + * Generate a nextflow Workflow that allows processing a channel of + * Vdsl3 formatted events and apply a Viash config to them: + * - Gather default parameters from the Viash config and make + * sure that they are correctly formatted (see applyConfig method). + * - Format the input parameters (also using the applyConfig method). + * - Apply the default parameter to the input parameters. + * - Do some assertions: + * ~ Check if the event IDs in the channel are unique. + * + * The events in the channel are formatted as tuples, with the + * first element of the tuples being a unique id of the parameter set, + * and the second element containg the the parameters themselves. + * Optional extra elements of the tuples will be passed to the output as is. + * + * @param args A map that must contain a 'config' key that points + * to a parsed config (see readConfig()). Optionally, a + * 'key' key can be provided which can be used to create a unique + * name for the workflow process. + * + * @return A workflow that allows processing a channel of Vdsl3 formatted events + * and apply a Viash config to them. + */ +def preprocessInputs(Map args) { + wfKey = args.key != null ? args.key : "preprocessInputs" + config = args.config + workflow preprocessInputsInstance { + take: + input_ch + + main: + assert config instanceof Map : + "Error in preprocessInputs: config must be a map. " + + "Expected class: Map. Found: config.getClass() is ${config.getClass()}" + + output_ch = input_ch + | toSortedList + | map { paramList -> _preprocessInputsList(paramList, config) } + | flatMap + emit: + output_ch + } + + return preprocessInputsInstance.cloneWithName(wfKey) +} From fce64824c03ef62adfb227115c2ab0e8ce8d68f1 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 1 Mar 2023 15:16:02 +0100 Subject: [PATCH 0744/1233] update main nf workflow Former-commit-id: ebe71cc1dd9bc2f7e2d749e2152eb9175f929fe1 --- src/batch_integration/workflows/run/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index 38515bd7d3..fa0cd786e2 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -43,7 +43,7 @@ workflow run_wf { // split params for downstream components | setWorkflowArguments( method: ["input"], - metric: [], + metric: ["input_solution"], output: ["output"] ) From 32dcfe648d5380b17141d627ccae993c27a50e59 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 9 Mar 2023 10:45:54 +0100 Subject: [PATCH 0745/1233] add output parameter Former-commit-id: 172b46f33aee579c014f53f5f3f87e865191f256 --- src/common/create_skeleton/config.vsh.yaml | 11 +++++++++-- src/common/create_skeleton/script.py | 11 ++++++++--- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index d4182a744b..e80b536ecf 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -5,24 +5,31 @@ functionality: arguments: - type: string name: --task + description: Which task the component will be added example: denoising - description: - type: string name: --comp_type example: metric - description: + description: type of component to create choices: ['metric', 'method', 'negative_control', 'positive_control'] - type: string name: --language example: python description: script language + default: python - type: string name: --name example: new_comp description: name of the new method in snake case + - type: file + name: --output + direction: output + default: "my_method" resources: - type: python_script path: script.py + - path: ../../../src + dest: openproblems-v2/src platforms: - type: docker image: python:3.10 diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 127567cb1f..abb2e9528d 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -36,7 +36,7 @@ def add_method_config(tmpl): 'method_name': 'Method name', 'preferred_normalization': '', 'variants': { - 'method_name': '', + par['name']: '', 'method_variant1': { 'preferred_normalization': '' } @@ -199,7 +199,10 @@ def create_r_script(tmpl_par): ## Create script template -task_api = f'src/{par["task"]}/api' + +resource_dir = meta["resources_dir"] + "/openproblems-v2" + +task_api = f'{resource_dir}/src/{par["task"]}/api' api_conf = f'{task_api}/comp_{merge}.yaml' with open(api_conf, 'r') as f: @@ -223,7 +226,7 @@ def create_r_script(tmpl_par): ## Write output -out_dir= Path(par['name']) +out_dir= Path(par["output"]) out_dir.mkdir(exist_ok=True) @@ -232,5 +235,7 @@ def create_r_script(tmpl_par): script_f = config_out['functionality']['resources'][0]['path'] +print(script_f) + with open(f'{out_dir}/{script_f}', 'w') as fpy: fpy.write(script_out) \ No newline at end of file From 0f02410185d2b2899b8fc364d2e421952300fa05 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 9 Mar 2023 10:46:40 +0100 Subject: [PATCH 0746/1233] Update src/common/create_skeleton/script.py Co-authored-by: Robrecht Cannoodt Former-commit-id: ccb201bf2736ba9b1933f24fd723a1778df78cfe --- src/common/create_skeleton/script.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index abb2e9528d..272ac54e51 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -16,8 +16,6 @@ ## VIASH END -def add_metric_config(tmpl): - tmpl['functionality']['info']['metrics'] = [{ 'metric_id': 'metric_id', 'metric_name': 'Metric Name', @@ -25,8 +23,7 @@ def add_metric_config(tmpl): 'min': 0, 'max': 1, 'maximize': 'true', - } - ] + }] return tmpl From 8ef6a79379a71a4d46d0eb11c1c88ccddd8f1395 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 9 Mar 2023 10:47:00 +0100 Subject: [PATCH 0747/1233] Update src/common/create_skeleton/script.py Co-authored-by: Robrecht Cannoodt Former-commit-id: e5b5a065771905bf664c2a22b1f90ac5d8ca2d18 --- src/common/create_skeleton/script.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 272ac54e51..ee3e028fb5 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -58,11 +58,12 @@ def add_python_setup(conf): def add_r_setup(conf): + conf['functionality']['resources'][0]['type'] = 'r_script' - conf['functionality']['resources'][0]['path'] = 'script.r' + conf['functionality']['resources'][0]['path'] = 'script.R' conf['functionality']['test_resources'][0]['type'] = 'r_script' - conf['functionality']['test_resources'][0]['path'] = 'script.r' + conf['functionality']['test_resources'][0]['path'] = 'script.R' for i, platform in enumerate(conf['platforms']): if platform['type'] == 'docker': From 315d64e8b17e1b00271234a0d3154b7b044b7c61 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 9 Mar 2023 11:17:04 +0100 Subject: [PATCH 0748/1233] Move resource OPv2 to input Co-authored-by: Robrecht Cannoodt Former-commit-id: a4af22692bc141d85b989c66bf4ad4dc66d6ff11 --- src/common/create_skeleton/config.vsh.yaml | 8 +++++--- src/common/create_skeleton/script.py | 14 +++++++------- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index e80b536ecf..fe84a7ef97 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -3,6 +3,10 @@ functionality: namespace: common description: Create a skeleton directory containing a viash config file and python or r script file based on the task api. arguments: + - name: "--src" + type: "file" + default: "./src" + description: "The src directory of the openproblems-v2 repository." - type: string name: --task description: Which task the component will be added @@ -24,12 +28,10 @@ functionality: - type: file name: --output direction: output - default: "my_method" + required: true resources: - type: python_script path: script.py - - path: ../../../src - dest: openproblems-v2/src platforms: - type: docker image: python:3.10 diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index ee3e028fb5..fc8c6fdcba 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -5,10 +5,11 @@ ## VIASH START # The following code has been auto-generated by Viash. par = { + 'src': './src', 'task': 'denoising', 'comp_type': 'metric', 'language': 'python', - 'name': 'new_comp' + 'name': 'new_comp', } meta = { } @@ -16,6 +17,8 @@ ## VIASH END +def add_metric_config(tmpl): + tmpl['functionality']['info']['metrics'] = [{ 'metric_id': 'metric_id', 'metric_name': 'Metric Name', @@ -58,7 +61,6 @@ def add_python_setup(conf): def add_r_setup(conf): - conf['functionality']['resources'][0]['type'] = 'r_script' conf['functionality']['resources'][0]['path'] = 'script.R' @@ -181,7 +183,7 @@ def create_r_script(tmpl_par): else: config_out = add_method_config(conf_tmpl_dict) - + if par['comp_type'] == 'method': config_out['functionality']['info']['paper_reference']= '' @@ -198,9 +200,9 @@ def create_r_script(tmpl_par): ## Create script template -resource_dir = meta["resources_dir"] + "/openproblems-v2" +resource_dir = par['src'] -task_api = f'{resource_dir}/src/{par["task"]}/api' +task_api = f'{resource_dir}/{par["task"]}/api' api_conf = f'{task_api}/comp_{merge}.yaml' with open(api_conf, 'r') as f: @@ -233,7 +235,5 @@ def create_r_script(tmpl_par): script_f = config_out['functionality']['resources'][0]['path'] -print(script_f) - with open(f'{out_dir}/{script_f}', 'w') as fpy: fpy.write(script_out) \ No newline at end of file From 730a65882cdb506b998bbe16b8d7baeef3f0d79e Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Thu, 9 Mar 2023 21:54:55 +0100 Subject: [PATCH 0749/1233] add R_script template Former-commit-id: 6aea3101bcb8a67db491fca850661a54c74e5e43 --- src/common/create_skeleton/script.py | 116 +++++++++++++++++++++------ 1 file changed, 90 insertions(+), 26 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index fc8c6fdcba..f77ff1f1c6 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -76,12 +76,11 @@ def add_r_setup(conf): 'type': 'r', 'cran': [ 'anndata'], 'bioc': '' - }, - { + }) + pltf['setup'].append({ 'type': 'apt', 'packages': ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] - } - ) + }) return conf @@ -90,7 +89,12 @@ def create_python_script(tmpl_par): script_templ = f'''import anndata as ad ## VIASH START -par = {templ_par} +par = {{ + # Required arguments for the task + {templ_par} + # Optional method-specific arguments + 'n_neighbors': 5, + }} meta = {{ 'functionality_name': 'foo' @@ -98,33 +102,72 @@ def create_python_script(tmpl_par): ## VIASH END -print('Load input data', flush=True) -adata=ad.read_h5ad(par['{list(templ_par.keys())[0]}']) +## Data reader +print('Reading input files', flush=True) -print('Process data', flush=True) -# insert code block here where pred is the prediction +input_train =ad.read_h5ad(par['{list(templ_par.keys())[0]}']) -pred = adata +print('processing Data', flush=True) +# ... preprocessing ... +# ... train model ... +# ... generate predictions ... -# Create output anndata -output = ad.AnnData( - uns = {{ - 'dataset_id': adata.uns['dataset_id'], - 'method_id': meta['functionality_name'] - }}, - layers = adata.layers +# write output to file +adata = ad.AnnData( + X=y_pred, + uns={ + 'dataset_id': input_train.uns['dataset_id'], + 'method_id': meta['functionality_name'], + }, ) -output.layers['denoised'] = pred - -print('Write Data', flush=True) -output.write_h5ad(par['output'],compression='gzip') +print('writing to output files', flush=True) +adata.write_h5ad(par['output'], compress='gzip') ''' return script_templ def create_r_script(tmpl_par): - '' + newline = "\n" + script_templ = f'''library(anndata, warn.conflicts = FALSE) + +## VIASH START + +par <- list( + # Required arguments for the task + {newline.join(f"{key} = {value}," for key, value in tmpl_par.items())} + # Optional method-specific arguments + n_neighbors = 5, +) + +meta <- list( + functionality_name = "foo" +) + +## VIASH END + +## Data reader +cat("Reading input files\\n") +input_train <- read_h5ad(par["{list(templ_par.keys())[0]}"]) + +cat("processing Data\\n") +# ... preprocessing ... +# ... train model ... +# ... generate predictions ... + +# write output to file +adata <- anndata::AnnData( + X = y_pred, + uns = list( + dataset_id = input_train$uns$dataset_id, + method_id = meta$functionality_name, + ) +) + +cat("writing to output files\\n") +zzz <- adata$write_h5ad(par$output, compression = "gzip") +''' + return script_templ ## Create config file @@ -137,19 +180,32 @@ def create_r_script(tmpl_par): # points to global config e.g. parameters __merge__: ../../api/comp_{merge}.yaml functionality: + # a unique name for your method, same as what is being output by the script. + # must match the regex [a-z][a-z0-9_]* name: {par['name']} - namespace: {par["task"]}/{merge}s - description: # add description + namespace: {par["task"]}/{merge}s + # metadata for your method + description: A description for your method. info: type: {par["comp_type"]} - # additional parameters specific for method. always set default if required - parameters: + # component parameters + arguments: + # Method-specific parameters. + # Change these to expose parameters of your method to Nextflow (optional) + - name: "--n_neighbors" + type: "integer" + default: 5 + description: Number of neighbors to use. # files your script needs resources: + # the script itself - type: path: + # additional resources your script needs (optional) + - type: file + path: weights.pt # resources for unit testing your component test_resources: @@ -159,13 +215,21 @@ def create_r_script(tmpl_par): # target platforms platforms: + # By specifying 'docker' platform, viash will build a standalone + # executable which uses docker in the back end to run your method. - type: docker + # you need to specify a base image that contains at least bash and python image: + # You can specify additional dependencies with 'setup'. setup: - type: python pip: - pyyaml - anndata>=0.8 + + # By specifying a 'nextflow', viash will also build a viash module + # which uses the docker container built above to also be able to + # run your method as part of a nextflow pipeline. - type: nextflow directives: label: ['midmem', 'midcpu'] From 9fdc78ac49c517d43d4e7b383cfb8ecaa00d479e Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 10 Mar 2023 11:30:05 +0100 Subject: [PATCH 0750/1233] add script comp specific output Former-commit-id: b93ec80bee32d25a3b3f3c2dbe20573ca03f205d --- src/common/create_skeleton/script.py | 79 +++++++++++++++++++++------- 1 file changed, 61 insertions(+), 18 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index f77ff1f1c6..66b33dd489 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -85,13 +85,14 @@ def add_r_setup(conf): return conf -def create_python_script(tmpl_par): +def create_python_script(tmpl_par, comp_type): + newline = "\n" script_templ = f'''import anndata as ad ## VIASH START par = {{ # Required arguments for the task - {templ_par} + {newline.join(f"'{key}': '{value}'," for key, value in tmpl_par.items())} # Optional method-specific arguments 'n_neighbors': 5, }} @@ -105,29 +106,47 @@ def create_python_script(tmpl_par): ## Data reader print('Reading input files', flush=True) -input_train =ad.read_h5ad(par['{list(templ_par.keys())[0]}']) +adata = ad.read_h5ad(par['{list(templ_par.keys())[0]}']) print('processing Data', flush=True) # ... preprocessing ... # ... train model ... # ... generate predictions ... -# write output to file -adata = ad.AnnData( +''' + + if comp_type == 'metric': + script_templ = script_templ + '''# write output to file +out = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'method_id': adata.uns['method_id'], + 'metric_values': [''], + 'metric_ids': [meta['functionality_name']], # if multiple values, add ids explicitly e.g. ['asw', 'asw_batch'] + }, +) + +print('writing to output files', flush=True) +out.write_h5ad(par['output'], compress='gzip') + ''' + else : + script_templ = script_templ + '''# write output to file +out = ad.AnnData( X=y_pred, uns={ - 'dataset_id': input_train.uns['dataset_id'], + 'dataset_id': adata.uns['dataset_id'], 'method_id': meta['functionality_name'], }, ) print('writing to output files', flush=True) -adata.write_h5ad(par['output'], compress='gzip') -''' +out.write_h5ad(par['output'], compress='gzip') + ''' + return script_templ -def create_r_script(tmpl_par): +def create_r_script(tmpl_par, comp_type): newline = "\n" script_templ = f'''library(anndata, warn.conflicts = FALSE) @@ -135,7 +154,7 @@ def create_r_script(tmpl_par): par <- list( # Required arguments for the task - {newline.join(f"{key} = {value}," for key, value in tmpl_par.items())} + {newline.join(f'{key} = "{value}",' for key, value in tmpl_par.items())} # Optional method-specific arguments n_neighbors = 5, ) @@ -148,25 +167,49 @@ def create_r_script(tmpl_par): ## Data reader cat("Reading input files\\n") -input_train <- read_h5ad(par["{list(templ_par.keys())[0]}"]) +adata <- read_h5ad(par["{list(templ_par.keys())[0]}"]) cat("processing Data\\n") # ... preprocessing ... # ... train model ... # ... generate predictions ... -# write output to file -adata <- anndata::AnnData( +''' + + if comp_type == 'metric': + script_templ = script_templ + '''# write output to file +out <- anndata::AnnData( + shape = c(0, 0), + uns = list( + dataset_id = adata$uns$dataset_id, + method_id = adata$uns$method_id, + metric_values = list(""), + metric_ids = list(meta$functionality_name), # if multiple values, add ids explicitly e.g. list('asw', 'asw_batch') + ) +) + +out("writing to output files\\n") +zzz <- adata$write_h5ad(par$output, compression = "gzip") + ''' + + else: + script_templ = script_templ + '''# write output to file +out <- anndata::AnnData( X = y_pred, uns = list( - dataset_id = input_train$uns$dataset_id, + dataset_id = adata$uns$dataset_id, method_id = meta$functionality_name, ) ) -cat("writing to output files\\n") +out("writing to output files\\n") zzz <- adata$write_h5ad(par$output, compression = "gzip") -''' + ''' + + + + + return script_templ @@ -281,11 +324,11 @@ def create_r_script(tmpl_par): if par['language'] == 'python': - script_out = create_python_script(templ_par) + script_out = create_python_script(templ_par, par['comp_type']) if par['language'] == 'r': - script_out = create_r_script(templ_par) + script_out = create_r_script(templ_par, par['comp_type']) From fe7a6c76d4749a3bb72c1b798d3f1291e68b4c2b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 10 Mar 2023 13:46:29 +0100 Subject: [PATCH 0751/1233] move X to layers Co-authored-by: Kai Waldrant Co-authored-by: Michaela Mueller Former-commit-id: e8c13d5793873978f60639fe36fa3dad62ab8717 --- src/batch_integration/api/anndata_integrated_feature.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index c7aacc9675..d02a5c780d 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -6,9 +6,10 @@ info: prediction_type: feature short_description: "Integrated Graph" slots: - X: + layers: - type: double - description: integrated feature + name: corrected_counts + description: Corrected counts after integration required: true uns: - type: string From b5841afa1eacfaee8ab2085ef875ab134944e271 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 10 Mar 2023 13:46:35 +0100 Subject: [PATCH 0752/1233] Fix label Former-commit-id: b19b907e0a9efea3be8ea8d1ebd3eb8791b36d2e --- src/batch_integration/api/anndata_solution.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/batch_integration/api/anndata_solution.yaml b/src/batch_integration/api/anndata_solution.yaml index db7acd54b4..6a6600fbfa 100644 --- a/src/batch_integration/api/anndata_solution.yaml +++ b/src/batch_integration/api/anndata_solution.yaml @@ -1,8 +1,8 @@ type: file -description: Unintegrated AnnData HDF5 file. +description: Solution AnnData HDF5 file. example: input.h5ad info: - short_description: "Unintegrated" + short_description: "Solution" slots: layers: - type: integer From 3a5f4eb75abb3edcb58a04a958989bba4737c5e6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 10 Mar 2023 14:11:02 +0100 Subject: [PATCH 0753/1233] combine methods and metrics into one folder Former-commit-id: 62e8318f4d3d998edd68f953e93d95be701897ee --- .../{methods_graph => methods}/bbknn/config.vsh.yaml | 0 src/batch_integration/{methods_graph => methods}/bbknn/script.py | 0 .../{methods_feature => methods}/combat/config.vsh.yaml | 0 .../{methods_feature => methods}/combat/script.py | 0 .../scanorama_embed/config.vsh.yaml | 0 .../{methods_embedding => methods}/scanorama_embed/script.py | 0 .../scanorama_feature/config.vsh.yaml | 0 .../{methods_feature => methods}/scanorama_feature/script.py | 0 .../{methods_embedding => methods}/scvi/config.vsh.yaml | 0 .../{methods_embedding => methods}/scvi/script.py | 0 .../{metrics_embedding => metrics}/asw_batch/config.vsh.yaml | 0 .../{metrics_embedding => metrics}/asw_batch/script.py | 0 .../{metrics_embedding => metrics}/asw_label/config.vsh.yaml | 0 .../{metrics_embedding => metrics}/asw_label/script.py | 0 .../cell_cycle_conservation/config.vsh.yaml | 0 .../cell_cycle_conservation/script.py | 0 .../{metrics_graph => metrics}/clustering_overlap/config.vsh.yaml | 0 .../{metrics_graph => metrics}/clustering_overlap/script.py | 0 .../{metrics_embedding => metrics}/pcr/config.vsh.yaml | 0 .../{metrics_embedding => metrics}/pcr/script.py | 0 20 files changed, 0 insertions(+), 0 deletions(-) rename src/batch_integration/{methods_graph => methods}/bbknn/config.vsh.yaml (100%) rename src/batch_integration/{methods_graph => methods}/bbknn/script.py (100%) rename src/batch_integration/{methods_feature => methods}/combat/config.vsh.yaml (100%) rename src/batch_integration/{methods_feature => methods}/combat/script.py (100%) rename src/batch_integration/{methods_embedding => methods}/scanorama_embed/config.vsh.yaml (100%) rename src/batch_integration/{methods_embedding => methods}/scanorama_embed/script.py (100%) rename src/batch_integration/{methods_feature => methods}/scanorama_feature/config.vsh.yaml (100%) rename src/batch_integration/{methods_feature => methods}/scanorama_feature/script.py (100%) rename src/batch_integration/{methods_embedding => methods}/scvi/config.vsh.yaml (100%) rename src/batch_integration/{methods_embedding => methods}/scvi/script.py (100%) rename src/batch_integration/{metrics_embedding => metrics}/asw_batch/config.vsh.yaml (100%) rename src/batch_integration/{metrics_embedding => metrics}/asw_batch/script.py (100%) rename src/batch_integration/{metrics_embedding => metrics}/asw_label/config.vsh.yaml (100%) rename src/batch_integration/{metrics_embedding => metrics}/asw_label/script.py (100%) rename src/batch_integration/{metrics_embedding => metrics}/cell_cycle_conservation/config.vsh.yaml (100%) rename src/batch_integration/{metrics_embedding => metrics}/cell_cycle_conservation/script.py (100%) rename src/batch_integration/{metrics_graph => metrics}/clustering_overlap/config.vsh.yaml (100%) rename src/batch_integration/{metrics_graph => metrics}/clustering_overlap/script.py (100%) rename src/batch_integration/{metrics_embedding => metrics}/pcr/config.vsh.yaml (100%) rename src/batch_integration/{metrics_embedding => metrics}/pcr/script.py (100%) diff --git a/src/batch_integration/methods_graph/bbknn/config.vsh.yaml b/src/batch_integration/methods/bbknn/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_graph/bbknn/config.vsh.yaml rename to src/batch_integration/methods/bbknn/config.vsh.yaml diff --git a/src/batch_integration/methods_graph/bbknn/script.py b/src/batch_integration/methods/bbknn/script.py similarity index 100% rename from src/batch_integration/methods_graph/bbknn/script.py rename to src/batch_integration/methods/bbknn/script.py diff --git a/src/batch_integration/methods_feature/combat/config.vsh.yaml b/src/batch_integration/methods/combat/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_feature/combat/config.vsh.yaml rename to src/batch_integration/methods/combat/config.vsh.yaml diff --git a/src/batch_integration/methods_feature/combat/script.py b/src/batch_integration/methods/combat/script.py similarity index 100% rename from src/batch_integration/methods_feature/combat/script.py rename to src/batch_integration/methods/combat/script.py diff --git a/src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_embedding/scanorama_embed/config.vsh.yaml rename to src/batch_integration/methods/scanorama_embed/config.vsh.yaml diff --git a/src/batch_integration/methods_embedding/scanorama_embed/script.py b/src/batch_integration/methods/scanorama_embed/script.py similarity index 100% rename from src/batch_integration/methods_embedding/scanorama_embed/script.py rename to src/batch_integration/methods/scanorama_embed/script.py diff --git a/src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_feature/scanorama_feature/config.vsh.yaml rename to src/batch_integration/methods/scanorama_feature/config.vsh.yaml diff --git a/src/batch_integration/methods_feature/scanorama_feature/script.py b/src/batch_integration/methods/scanorama_feature/script.py similarity index 100% rename from src/batch_integration/methods_feature/scanorama_feature/script.py rename to src/batch_integration/methods/scanorama_feature/script.py diff --git a/src/batch_integration/methods_embedding/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods_embedding/scvi/config.vsh.yaml rename to src/batch_integration/methods/scvi/config.vsh.yaml diff --git a/src/batch_integration/methods_embedding/scvi/script.py b/src/batch_integration/methods/scvi/script.py similarity index 100% rename from src/batch_integration/methods_embedding/scvi/script.py rename to src/batch_integration/methods/scvi/script.py diff --git a/src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/asw_batch/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics_embedding/asw_batch/config.vsh.yaml rename to src/batch_integration/metrics/asw_batch/config.vsh.yaml diff --git a/src/batch_integration/metrics_embedding/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py similarity index 100% rename from src/batch_integration/metrics_embedding/asw_batch/script.py rename to src/batch_integration/metrics/asw_batch/script.py diff --git a/src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics_embedding/asw_label/config.vsh.yaml rename to src/batch_integration/metrics/asw_label/config.vsh.yaml diff --git a/src/batch_integration/metrics_embedding/asw_label/script.py b/src/batch_integration/metrics/asw_label/script.py similarity index 100% rename from src/batch_integration/metrics_embedding/asw_label/script.py rename to src/batch_integration/metrics/asw_label/script.py diff --git a/src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics_embedding/cell_cycle_conservation/config.vsh.yaml rename to src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml diff --git a/src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py similarity index 100% rename from src/batch_integration/metrics_embedding/cell_cycle_conservation/script.py rename to src/batch_integration/metrics/cell_cycle_conservation/script.py diff --git a/src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics_graph/clustering_overlap/config.vsh.yaml rename to src/batch_integration/metrics/clustering_overlap/config.vsh.yaml diff --git a/src/batch_integration/metrics_graph/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py similarity index 100% rename from src/batch_integration/metrics_graph/clustering_overlap/script.py rename to src/batch_integration/metrics/clustering_overlap/script.py diff --git a/src/batch_integration/metrics_embedding/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics_embedding/pcr/config.vsh.yaml rename to src/batch_integration/metrics/pcr/config.vsh.yaml diff --git a/src/batch_integration/metrics_embedding/pcr/script.py b/src/batch_integration/metrics/pcr/script.py similarity index 100% rename from src/batch_integration/metrics_embedding/pcr/script.py rename to src/batch_integration/metrics/pcr/script.py From 251aab1a7b4df3de3ee00aad16d4f83c9d69c147 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 10 Mar 2023 14:13:40 +0100 Subject: [PATCH 0754/1233] remove solution object Former-commit-id: 627de047abf9f35fa6374c426aa91b5ef0a86f9a --- .../api/anndata_solution.yaml | 56 ------------------- .../api/anndata_unintegrated.yaml | 5 ++ .../api/comp_metric_embedding.yaml | 2 +- .../api/comp_metric_feature.yaml | 2 +- .../api/comp_metric_graph.yaml | 2 +- .../api/comp_split_dataset.yaml | 5 +- src/batch_integration/split_dataset/script.py | 15 ++--- 7 files changed, 13 insertions(+), 74 deletions(-) delete mode 100644 src/batch_integration/api/anndata_solution.yaml diff --git a/src/batch_integration/api/anndata_solution.yaml b/src/batch_integration/api/anndata_solution.yaml deleted file mode 100644 index 6a6600fbfa..0000000000 --- a/src/batch_integration/api/anndata_solution.yaml +++ /dev/null @@ -1,56 +0,0 @@ -type: file -description: Solution AnnData HDF5 file. -example: input.h5ad -info: - short_description: "Solution" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalized expression values - required: true - obs: - - type: string - name: batch - description: Batch information - required: true - - type: string - name: label - description: label information - required: true - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - obsp: - - type: double - name: knn_distances - description: K nearest neighbors distance matrix. - required: true - - type: double - name: knn_connectivities - description: K nearest neighbors connectivities matrix. - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: string - name: organism - description: "Which normalization was used" - required: true diff --git a/src/batch_integration/api/anndata_unintegrated.yaml b/src/batch_integration/api/anndata_unintegrated.yaml index 974f2e59fe..aead1cdcad 100644 --- a/src/batch_integration/api/anndata_unintegrated.yaml +++ b/src/batch_integration/api/anndata_unintegrated.yaml @@ -32,6 +32,11 @@ info: name: X_pca description: The resulting PCA embedding. required: true + obsp: + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true uns: - type: string name: dataset_id diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 2c45791a66..0547d05475 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -3,7 +3,7 @@ functionality: - name: --input_integrated __merge__: anndata_integrated_embedding.yaml - name: --input_solution - __merge__: anndata_solution.yaml + __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 14182458ba..a33b8565b1 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -3,7 +3,7 @@ functionality: - name: --input_integrated __merge__: anndata_integrated_feature.yaml - name: --input_solution - __merge__: anndata_solution.yaml + __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 0617bf4179..8788d26a04 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -3,7 +3,7 @@ functionality: - name: --input_integrated __merge__: anndata_integrated_graph.yaml - name: --input_solution - __merge__: anndata_solution.yaml + __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml diff --git a/src/batch_integration/api/comp_split_dataset.yaml b/src/batch_integration/api/comp_split_dataset.yaml index 997cf62918..d96e954278 100644 --- a/src/batch_integration/api/comp_split_dataset.yaml +++ b/src/batch_integration/api/comp_split_dataset.yaml @@ -2,12 +2,9 @@ functionality: arguments: - name: "--input" __merge__: anndata_dataset.yaml - - name: "--output_unintegrated" + - name: "--output" __merge__: anndata_unintegrated.yaml direction: output - - name: "--output_solution" - __merge__: anndata_solution.yaml - direction: output # test_resources: # - path: ../../../resources_test/common/pancreas/ # - type: python_script diff --git a/src/batch_integration/split_dataset/script.py b/src/batch_integration/split_dataset/script.py index 10f716f4c8..35379af8b8 100644 --- a/src/batch_integration/split_dataset/script.py +++ b/src/batch_integration/split_dataset/script.py @@ -87,18 +87,11 @@ def subset_anndata(adata_sub, slot_info): print(">> Figuring out which data needs to be copied to which output file", flush=True) slot_info_per_output = read_slots(par, meta) -print(">> Create unintegrated object", flush=True) -output_unintegrated = subset_anndata( +print(">> Create output object", flush=True) +output = subset_anndata( adata_sub=adata_with_hvg, - slot_info=slot_info_per_output["unintegrated"] -) - -print(">> Create solution object", flush=True) -output_solution = subset_anndata( - adata_sub=adata_with_hvg, - slot_info=slot_info_per_output["solution"] + slot_info=slot_info_per_output["output"] ) print('Writing adatas to file', flush=True) -output_unintegrated.write(par['output_unintegrated'], compression='gzip') -output_solution.write(par['output_solution'], compression='gzip') +output.write(par['output'], compression='gzip') From 7ea111860064d1311c7e25dafb1cd105cd0662b0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 10 Mar 2023 14:14:08 +0100 Subject: [PATCH 0755/1233] pseudo code for nxf pipeline Former-commit-id: a763e2c3c66143978ab46d08d4a86c346697a262 --- src/batch_integration/workflows/run/main.nf | 65 ++++++++++++--------- 1 file changed, 38 insertions(+), 27 deletions(-) diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index fa0cd786e2..8e4c871cbb 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -38,34 +38,45 @@ workflow run_wf { input_ch main: - output_ch = input_ch - - // split params for downstream components - | setWorkflowArguments( - method: ["input"], - metric: ["input_solution"], - output: ["output"] - ) - - // multiply events by the number of method - | add_methods - - // run methods - | getWorkflowArguments(key: "method") - | run_methods - // construct tuples for metrics - | pmap{ id, file, passthrough -> - // derive unique ids from output filenames - def newId = file.getName().replaceAll(".output.*", "") - // combine prediction with solution - def newData = [ input: file ] - [ newId, newData, passthrough ] - } - - // run metrics - | getWorkflowArguments(key: "metric") - | run_metrics + // run feature methods + meth_feature = input_ch + | (combat & scanorama_feature) + | mix + // run embed methods + meth_embed = input_ch + | (scanorama_embed & scvi) + | mix + // run graph methods + meth_graph = input_ch + | (bbknn) + + // apply feature metrics on feature outputs + // metr_feat = meth_feature + // | (asw_batch & asw_label & cell_cycle_conservation & pcr) + + // convert feature outputs to embedding outputs + meth_feat_to_embed = meth_feature + | feature_to_embed + + // apply embedding metrics to embedding outputs + metr_embed = meth_embed + | mix(meth_feat_to_embed) + | (asw_batch & asw_label & cell_cycle_conservation & pcr) + | mix + + // convert embedding outputs to graph outputs + meth_embed_to_graph = meth_embed + | mix(meth_feat_to_embed) + | embed_to_graph + + // apply graph metrics to graph outputs + metr_graph = meth_graph + | mix(meth_embed_to_graph) + | (clustering_overlap) + + + output_ch = metr_embed.mix(metr_graph) // convert to tsv | aggregate_results From 83d079a552e96ebf0e231c94e601ac2a743ba8eb Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 10 Mar 2023 16:16:31 +0100 Subject: [PATCH 0756/1233] add basic unit test Former-commit-id: e6dec5e5625d6c6e7398e9fdaa143648c02a47ae --- src/common/create_skeleton/config.vsh.yaml | 5 +++ src/common/create_skeleton/test.py | 38 ++++++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 src/common/create_skeleton/test.py diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index fe84a7ef97..13019740f6 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -32,6 +32,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - type: python_script + path: test.py + - path: ../../../src + dest: openproblems-v2/src platforms: - type: docker image: python:3.10 diff --git a/src/common/create_skeleton/test.py b/src/common/create_skeleton/test.py new file mode 100644 index 0000000000..da99957e8f --- /dev/null +++ b/src/common/create_skeleton/test.py @@ -0,0 +1,38 @@ +import subprocess +from os import path + + +## VIASH START + +meta = { + 'executable': 'foo' +} + +## VIASH END + +src_path = meta["resources_dir"] + "/openproblems-v2/src" +output_path= 'test_method' + + +cmd = [ + meta['executable'], + '--src', src_path, + '--task', 'label_projection', + '--comp_type', 'method', + '--name', 'test_method', + '--language', 'python', + '--output', output_path, +] + +print('>> Running the script as test', flush=True) +out= subprocess.run(cmd, check=True) + +print('>> Checking whether output files exist', flush=True) +assert path.exists(output_path) +conf_f = path.join(output_path, 'config.vsh.yaml') +assert path.exists(conf_f) +script_f = path.join(output_path, "script.py") +assert path.exists(script_f) + +print('all checks succeeded!', flush=True) + From 0f6001628e82a72420ae7aa51c33aa0746cc67e7 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 10 Mar 2023 16:46:34 +0100 Subject: [PATCH 0757/1233] update test with file content check Former-commit-id: e44745acb66004b00ca8e81e3aec060b2fbf9f50 --- src/common/create_skeleton/test.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/common/create_skeleton/test.py b/src/common/create_skeleton/test.py index da99957e8f..7825388392 100644 --- a/src/common/create_skeleton/test.py +++ b/src/common/create_skeleton/test.py @@ -1,5 +1,6 @@ import subprocess from os import path +from ruamel.yaml import YAML ## VIASH START @@ -34,5 +35,18 @@ script_f = path.join(output_path, "script.py") assert path.exists(script_f) +print('>> Checking file contents', flush=True) +yaml = YAML() +with open(conf_f) as f: + conf_data = yaml.load(f) + +assert conf_data['functionality']['name'] == 'test_method' +assert conf_data['functionality']['namespace'] == 'label_projection/methods' +assert conf_data['functionality']['info']['type'] == 'method' + +assert conf_data['platforms'][0]['image'] == 'python:3.10' + + + print('all checks succeeded!', flush=True) From 28c956f112b3eabb078b3927120f046aa965b1b6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 10 Mar 2023 17:50:01 +0100 Subject: [PATCH 0758/1233] remove solution anndata Former-commit-id: ea23854bc72767c113ca075bf7d7ffdc729333a1 --- src/batch_integration/api/comp_metric_embedding.yaml | 4 ---- src/batch_integration/api/comp_metric_feature.yaml | 4 ---- src/batch_integration/api/comp_metric_graph.yaml | 4 ---- 3 files changed, 12 deletions(-) diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 0547d05475..daa40e8f62 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -2,8 +2,6 @@ functionality: arguments: - name: --input_integrated __merge__: anndata_integrated_embedding.yaml - - name: --input_solution - __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml @@ -33,13 +31,11 @@ functionality: config = yaml.safe_load(file) input_file = f"{meta['resources_dir']}/batch_integration/embedding/scvi.h5ad" - sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], "--input_integrated", input_file, - "--input_solution", sol_file, "--output", output_file ] diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index a33b8565b1..df482c9ffc 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -2,8 +2,6 @@ functionality: arguments: - name: --input_integrated __merge__: anndata_integrated_feature.yaml - - name: --input_solution - __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml @@ -33,13 +31,11 @@ functionality: config = yaml.safe_load(file) input_file = f"{meta['resources_dir']}/batch_integration/feature/combat.h5ad" - sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], "--input_integrated", input_file, - "--input_solution", sol_file, "--output", output_file ] diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 8788d26a04..5cf44a2d23 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -2,8 +2,6 @@ functionality: arguments: - name: --input_integrated __merge__: anndata_integrated_graph.yaml - - name: --input_solution - __merge__: anndata_unintegrated.yaml - name: --output direction: output __merge__: anndata_score.yaml @@ -35,13 +33,11 @@ functionality: output_type = config["functionality"].get("info", {}).get("output_type") input_file = f"{meta['resources_dir']}/batch_integration/graph/bbknn.h5ad" - sol_file = f"{meta['resources_dir']}/batch_integration/pancreas/solution.h5ad" output_file = "output.h5ad" cmd_args = [ meta["executable"], "--input_integrated", input_file, - "--input_solution", sol_file, "--output", output_file ] From 0dfdd76526c4721a7e12d3b5cb04e93f5bda53ac Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Sun, 12 Mar 2023 22:58:07 +0100 Subject: [PATCH 0759/1233] fix unit testing Former-commit-id: a42ccbd5e04d6f16bb2758c049bd065fb63f2fa6 --- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/methods/combat/script.py | 4 +++- .../methods/scanorama_feature/script.py | 4 +++- src/batch_integration/metrics/asw_batch/script.py | 9 --------- src/batch_integration/metrics/asw_label/script.py | 8 -------- .../metrics/cell_cycle_conservation/script.py | 8 -------- .../metrics/clustering_overlap/script.py | 5 ----- src/batch_integration/metrics/pcr/script.py | 7 +------ src/batch_integration/split_dataset/script.py | 4 ++-- src/batch_integration/split_dataset/test.py | 14 +++----------- .../transformers/embed_to_graph/script.py | 2 -- .../transformers/feature_to_embed/script.py | 6 ++---- 12 files changed, 15 insertions(+), 58 deletions(-) diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 1f8d9c40ca..4188529036 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -47,7 +47,7 @@ functionality: print(">> Checking whether predictions were added", flush=True) # TODO: use helper function to check whether the required fields are defined - assert output.X is not None + assert output.layers['corrected_counts'] is not None print(">> Check values", flush=True) assert meta['functionality_name'] == output.uns['method_id'] diff --git a/src/batch_integration/methods/combat/script.py b/src/batch_integration/methods/combat/script.py index 6c7cf09ca9..0277493dcf 100644 --- a/src/batch_integration/methods/combat/script.py +++ b/src/batch_integration/methods/combat/script.py @@ -31,7 +31,9 @@ print('Run Combat', flush=True) adata.X = adata.layers['normalized'] adata.X = sc.pp.combat(adata, key='batch', inplace=False) -adata.X = csr_matrix(adata.X) +adata.layers['corrected_counts'] = csr_matrix(adata.X) + +del(adata.X) print("Store outputs", flush=True) adata.uns['output_type'] = output_type diff --git a/src/batch_integration/methods/scanorama_feature/script.py b/src/batch_integration/methods/scanorama_feature/script.py index ce16a564f0..ba3433b8c3 100644 --- a/src/batch_integration/methods/scanorama_feature/script.py +++ b/src/batch_integration/methods/scanorama_feature/script.py @@ -28,7 +28,9 @@ print('Run scanorama', flush=True) adata.X = adata.layers['normalized'] -adata.X = scanorama(adata, batch='batch').X +adata.layers['corrected_counts'] = scanorama(adata, batch='batch').X + +del(adata.X) # ? Create new comp feature_to_graph? # print("Run PCA", flush=True) diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py index 5c8c3f0da0..ccf68e6fe8 100644 --- a/src/batch_integration/metrics/asw_batch/script.py +++ b/src/batch_integration/metrics/asw_batch/script.py @@ -5,7 +5,6 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', - 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', } meta = { @@ -15,11 +14,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input_integrated']) -adata_solution= ad.read_h5ad(par['input_solution']) - -print('Transfer obs annotations', flush=True) -adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] -adata.obs['label'] = adata_solution.obs['label'][adata.obs_names] print('compute score', flush=True) score = silhouette_batch( @@ -42,8 +36,5 @@ } ) -if 'parent_method_id' in adata.uns: - output.uns['parent_method_id'] = adata.uns['parent_method_id'] - print('Write data to file', flush=True) output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/metrics/asw_label/script.py b/src/batch_integration/metrics/asw_label/script.py index a34ffa9d4d..88b450bca3 100644 --- a/src/batch_integration/metrics/asw_label/script.py +++ b/src/batch_integration/metrics/asw_label/script.py @@ -4,7 +4,6 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', - 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', } @@ -15,10 +14,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input_integrated']) -adata_solution = ad.read_h5ad(par['input_solution']) - -print('Transfer obs annotations') -adata.obs['label'] = adata_solution.obs['label'][adata.obs_names] print('compute score') score = silhouette( @@ -40,8 +35,5 @@ } ) -if 'parent_method_id' in adata.uns: - output.uns['parent_method_id'] = adata.uns['parent_method_id'] - print("Write data to file", flush=True) output.write_h5ad(par["output"], compression="gzip") diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py index eccfc8c9f2..bfb978fbe7 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics/cell_cycle_conservation/script.py @@ -4,7 +4,6 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', - 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', 'organism': 'human' } @@ -16,14 +15,9 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input_integrated']) -adata_solution : ad.read_h5ad(par['input_solution']) - adata.X = adata.layers['normalized'] -print('Transfer obs annotations', flush=True) -adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] - adata_int = adata.copy() print('compute score', flush=True) @@ -48,8 +42,6 @@ } ) -if 'parent_method_id' in adata.uns: - output.uns['parent_method_id'] = adata.uns['parent_method_id'] print('Write data to file', flush=True) output.write_h5ad(par['output'], compression='gzip') diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py index 57baccc1d9..ff0218865b 100644 --- a/src/batch_integration/metrics/clustering_overlap/script.py +++ b/src/batch_integration/metrics/clustering_overlap/script.py @@ -5,7 +5,6 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/graph/bbknn.h5ad', - 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', } @@ -16,10 +15,6 @@ print('Read input', flush=True) input = ad.read_h5ad(par['input_integrated']) -solution = ad.read_h5ad(par['input_solution']) - -print('Transfer obs annotations', flush=True) -input.obs['label'] = solution.obs['label'][input.obs_names] print('Run Louvain clustering', flush=True) opt_louvain( diff --git a/src/batch_integration/metrics/pcr/script.py b/src/batch_integration/metrics/pcr/script.py index 912b8c4293..e8ca5ce074 100644 --- a/src/batch_integration/metrics/pcr/script.py +++ b/src/batch_integration/metrics/pcr/script.py @@ -4,7 +4,6 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', - 'input_solution': 'resources_test/batch_integration/pancreas/solution.h5ad', 'output': 'output.h5ad', } @@ -15,11 +14,9 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input_integrated']) -adata_solution= ad.read_h5ad(par['input_solution']) -print('Transfer obs annotations', flush=True) -adata.obs['batch'] = adata_solution.obs['batch'][adata.obs_names] +print('preprocess data', flush=True) adata.X = adata.layers['normalized'] adata_int = adata.copy() @@ -45,8 +42,6 @@ } ) -if 'parent_method_id' in adata.uns: - output.uns['parent_method_id'] = adata.uns['parent_method_id'] print('Write data to file', flush=True) output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/split_dataset/script.py b/src/batch_integration/split_dataset/script.py index 35379af8b8..1d06456bdf 100644 --- a/src/batch_integration/split_dataset/script.py +++ b/src/batch_integration/split_dataset/script.py @@ -43,8 +43,8 @@ def read_slots(par, meta): # fetch info on which slots should be copied to which file for arg in config["functionality"]["arguments"]: - if re.match("--output_", arg["name"]): - file = re.sub("--output_", "", arg["name"]) + if re.match("--output", arg["name"]): + file = "output" struct_slots = arg['info']['slots'] out = {} diff --git a/src/batch_integration/split_dataset/test.py b/src/batch_integration/split_dataset/test.py index e678e7a1c9..6468070831 100644 --- a/src/batch_integration/split_dataset/test.py +++ b/src/batch_integration/split_dataset/test.py @@ -4,42 +4,34 @@ import numpy as np input_file = meta["resources_dir"] + '/pancreas/dataset.h5ad' -unintegrated_file = 'unintegrated.h5ad' -solution_file = 'solution.h5ad' +unintegrated_file = 'output.h5ad' n_hvgs = 100 cmd_args = [ meta["executable"], '--input', input_file, '--hvgs', str(n_hvgs), - '--output_unintegrated', unintegrated_file, - '--output_solution', solution_file + '--output', unintegrated_file, ] print('>> Running script') subprocess.run(cmd_args, check=True) print('>> Checking whether outputs exist') assert os.path.exists(unintegrated_file) -assert os.path.exists(solution_file) print('>> Read anndata files') input = ad.read_h5ad(input_file) unintegrated = ad.read_h5ad(unintegrated_file) -solution = ad.read_h5ad(solution_file) print("input:", input) -print("unintegrated:", unintegrated) -print("solution:", solution) +print("output:", unintegrated) print(">> Checking dimensions, make sure no cells were dropped") assert input.n_obs == unintegrated.n_obs -assert input.n_obs == solution.n_obs assert input.n_vars == unintegrated.n_vars -assert input.n_vars == solution.n_vars print(">> Checking whether data from input was copied properly to output") assert unintegrated.uns["dataset_id"] == input.uns["dataset_id"] -assert solution.uns["dataset_id"] == input.uns["dataset_id"] print(">> Check output") assert unintegrated.var['hvg'].dtype == 'bool' diff --git a/src/batch_integration/transformers/embed_to_graph/script.py b/src/batch_integration/transformers/embed_to_graph/script.py index 30dfac16e9..c4878aa1a8 100644 --- a/src/batch_integration/transformers/embed_to_graph/script.py +++ b/src/batch_integration/transformers/embed_to_graph/script.py @@ -28,6 +28,4 @@ print("Store outputs", flush=True) adata.uns['output_type'] = output_type -adata.uns['parent_method_id'] = adata.uns['method_id'] -adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/batch_integration/transformers/feature_to_embed/script.py b/src/batch_integration/transformers/feature_to_embed/script.py index a28c7f4f60..031a015b46 100644 --- a/src/batch_integration/transformers/feature_to_embed/script.py +++ b/src/batch_integration/transformers/feature_to_embed/script.py @@ -23,18 +23,16 @@ print('Read input', flush=True) adata= sc.read_h5ad(par['input']) + print('Run PCA', flush=True) adata.obsm['X_emb'] = sc.pp.pca( - adata.X, + adata.layers["corrected_counts"], n_comps=50, use_highly_variable=False, svd_solver='arpack', return_info=False ) -del adata.X print('Store outputs', flush=True) adata.uns['output_type'] = output_type -adata.uns['parent_method_id'] = adata.uns['method_id'] -adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file From bde2726e9da7e939b6ef94fbdd61b9bdf5b749a2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 13 Mar 2023 10:37:07 +0100 Subject: [PATCH 0760/1233] wip update nextflow WF Former-commit-id: 6a6ac7a390dd006189697e1e9eca4e30fb69f99a --- .../methods/scanorama_feature/config.vsh.yaml | 2 +- .../methods/scvi/config.vsh.yaml | 1 + src/batch_integration/workflows/run/main.nf | 20 +++++++++++++------ 3 files changed, 16 insertions(+), 7 deletions(-) diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index a48f0dc97d..fb884a8b4c 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: scanorama_feature - namespace: batch_integration/methods_feauture + namespace: batch_integration/methods_feature description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index 5d9ed591ed..18e51569e6 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -2,6 +2,7 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scvi + namespace: batch_integration/methods_graph description: Run scVI on adata object, use feature output info: type: method diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index 8e4c871cbb..455fea88e3 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -4,14 +4,22 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" // import methods -include { bbknn } from "$targetDir/batch_integration/graph/methods/bbknn/main.nf" -include { combat } from "$targetDir/batch_integration/graph/methods/combat/main.nf" -include { scanorama_embed } from "$targetDir/batch_integration/graph/methods/scanorama_embed/main.nf" -include { scanorama_feature } from "$targetDir/batch_integration/graph/methods/scanorama_feature/main.nf" -include { scvi } from "$targetDir/batch_integration/graph/methods/scvi/main.nf" +include { bbknn } from "$targetDir/batch_integration/methods_graph/bbknn/main.nf" +include { combat } from "$targetDir/batch_integration/methods_feature/combat/main.nf" +include { scanorama_embed } from "$targetDir/batch_integration/methods_embedding/scanorama_embed/main.nf" +include { scanorama_feature } from "$targetDir/batch_integration/methods_feature/scanorama_feature/main.nf" +include { scvi } from "$targetDir/batch_integration/methods_graph/scvi/main.nf" + +// import transformers +include ( feature_to_embed ) from "$targetDir/batch_integration/methods_feature/feature_to_embed/main.nf" +include ( embed_to_graph ) from "$targetDir/batch_integration/methods_graph/embed_to_graph/main.nf" // import metrics -include { clustering_overlap } from "$targetDir/batch_integration/graph/metrics/clustering_overlap/main.nf" +include { clustering_overlap } from "$targetDir/batch_integration/metrics_graph/clustering_overlap/main.nf" +include { asw_batch } from "$targetDir/batch_integration/metrics_embedding/asw_batch/main.nf" +include { asw_label } from "$targetDir/batch_integration/metrics_embedding/asw_label/main.nf" +include { ccc } from "$targetDir/batch_integration/metrics_embedding/cel_cycle_conservation/main.nf" +include { pcr } from "$targetDir/batch_integration/metrics_embedding/pcr/main.nf" // tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" From a3d12d21a9554a3f75094178a9602851ff5ae8c8 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 13 Mar 2023 22:10:34 +0100 Subject: [PATCH 0761/1233] add task info Former-commit-id: dba3cd5a9feeff2565869e59243c85b5e2822126 --- src/batch_integration/api/task_info.yaml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 src/batch_integration/api/task_info.yaml diff --git a/src/batch_integration/api/task_info.yaml b/src/batch_integration/api/task_info.yaml new file mode 100644 index 0000000000..83cf0351be --- /dev/null +++ b/src/batch_integration/api/task_info.yaml @@ -0,0 +1,17 @@ +task_id: batch_integration +task_name: Batch Integration +v1_url: openproblems/tasks/batch_integration/README.md +v1_commit: 637163fba7d74ab5393c2adbee5354dcf4d46f85 +summary: Batch integration methods integrate datasets across batches that arise from various biological and technical sources. +description: | + Batch (or data) integration methods integrate datasets across batches that arise from various biological (e.g., tissue, location, individual, species) and technical (e.g., ambient RNA, lab, protocol) sources. The goal of a batch integration method is to remove unwanted batch effects in the data, while retaining biologically-meaningful variation that can help us to detect cell identities, fit cellular trajectories, or understand patterns of gene or pathway activity. + + Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have divided the batch integration task into three subtasks. These subtasks are: + + * [Batch integration graphs](graph/), + * [Batch integration embeddings](embedding/), and + * [Batch integrated feature matrices](feature/) + + These subtasks collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. Information on the task API for datasets, methods, and metrics can be found in the individual subtask pages. + + Metrics for this task either assess the removal of batch effects or assess the conservation of biological variation. This can be a helpful distinction when devising new metrics. This task, including the subtask structure, was taken from a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2), which is a useful reference for more background reading on this task and the above concepts. \ No newline at end of file From b58bf0cb767929a40608b6526ab9c958265a1061 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 14 Mar 2023 10:06:41 +0100 Subject: [PATCH 0762/1233] WIP NF workflow Former-commit-id: 9c7a76aea4c81d8f66904a4969445b301875371c --- src/batch_integration/workflows/run/main.nf | 50 +++++++++++++++++-- .../workflows/run/run_nextflow.sh | 2 + 2 files changed, 47 insertions(+), 5 deletions(-) diff --git a/src/batch_integration/workflows/run/main.nf b/src/batch_integration/workflows/run/main.nf index 455fea88e3..f88d77c7f3 100644 --- a/src/batch_integration/workflows/run/main.nf +++ b/src/batch_integration/workflows/run/main.nf @@ -30,6 +30,13 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } f config = readConfig("$projectDir/config.vsh.yaml") + +// construct a map of methods (id -> method_module) +methods = [ bbknn, combat, scanorama_embed, scanorama_feature, scvi] + .collectEntries{method -> + [method.config.functionality.name, method] + } + workflow { helpMessage(config) @@ -47,6 +54,26 @@ workflow run_wf { main: + output_ch = input_ch + + // split params for downstream components + | setWorkflowArguments( + preprocess: ["normalization_id", "dataset_id"], + method: ["input"], + output: ["output"] + ) + + // multiply events by the number of method + | getWorkflowArguments(key: "preprocess") + | add_methods + + // filter the normalization methods that a method actually prefers + | check_filtered_normalization_id + + // run methods + | getWorkflowArguments(key: "method") + | run_methods + // run feature methods meth_feature = input_ch | (combat & scanorama_feature) @@ -109,11 +136,7 @@ workflow run_wf { * Sub workflows * *******************************************************/ -// construct a map of methods (id -> method_module) -methods = [ bbknn, combat, scanorama_embed, scanorama_feature, scvi] - .collectEntries{method -> - [method.config.functionality.name, method] - } + workflow add_methods { take: input_ch @@ -131,6 +154,23 @@ workflow add_methods { emit: output_ch } +workflow check_filtered_normalization_id { + take: input_ch + main: + output_ch = input_ch + | pfilter{id, data -> + data = data.clone() + def method = methods[data.method_id] + def preferred = method.config.functionality.info.preferred_normalization + // if a method is just using the counts, we can use any normalization method + if (preferred == "counts") { + preferred = "log_cpm" + } + data.normalization_id == preferred + } + emit: output_ch +} + workflow run_methods { take: input_ch main: diff --git a/src/batch_integration/workflows/run/run_nextflow.sh b/src/batch_integration/workflows/run/run_nextflow.sh index edc9fbefd4..1df0c7a125 100755 --- a/src/batch_integration/workflows/run/run_nextflow.sh +++ b/src/batch_integration/workflows/run/run_nextflow.sh @@ -23,6 +23,8 @@ nextflow run . \ -c src/wf_utils/labels_ci.config \ -resume \ --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ --input $DATASET_DIR/processed.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ From e01e7a515040e9c4559278d4a02dfab279be0cd6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 14 Mar 2023 11:59:50 +0100 Subject: [PATCH 0763/1233] openproblemsv1 multimodal data loader (#71) * add initial component for fetching multimodal datasets from openproblemsv1 * fix components, add uns metadata * try manual setup * fix typo in v1 * wip changes to v1 script * add organism * refactor apis * fill in metadata * don't forget to pass arguments * improve changelog, remove old dataset * fix test resource script, fix unit tests * fix scripts * temporarily add matplotlib<3.7 to the dependencies * Revert "temporarily add matplotlib<3.7 to the dependencies" This reverts commit c3ff97ef4a592856b421cfb67eff903d0cbc3bad. * update changelog Former-commit-id: ee16578ccf1a1e7b001cebeccb74bed84bc5bd0b --- CHANGELOG.md | 45 +++--- src/datasets/api/anndata_dataset.yaml | 57 +------- src/datasets/api/anndata_hvg.yaml | 49 +------ src/datasets/api/anndata_normalized.yaml | 30 +--- src/datasets/api/anndata_pca.yaml | 34 +---- src/datasets/api/anndata_raw.yaml | 29 +++- .../loaders/openproblems_v1/config.vsh.yaml | 41 +++++- src/datasets/loaders/openproblems_v1/run.sh | 17 --- .../loaders/openproblems_v1/script.py | 22 ++- src/datasets/loaders/openproblems_v1/test.py | 10 +- .../config.vsh.yaml | 80 +++++++++++ .../openproblems_v1_multimodal/script.py | 133 ++++++++++++++++++ .../openproblems_v1_multimodal/test.py | 66 +++++++++ .../resource_scripts/openproblems_v1.sh | 86 ++++++++++- .../openproblems_v1_multimodal.sh | 46 ++++++ .../resource_test_scripts/pancreas.sh | 8 +- .../resource_test_scripts/pancreas_tasks.sh | 5 + .../process_openproblems_v1/config.vsh.yaml | 30 ++++ .../workflows/process_openproblems_v1/main.nf | 5 +- 19 files changed, 565 insertions(+), 228 deletions(-) delete mode 100755 src/datasets/loaders/openproblems_v1/run.sh create mode 100644 src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml create mode 100644 src/datasets/loaders/openproblems_v1_multimodal/script.py create mode 100644 src/datasets/loaders/openproblems_v1_multimodal/test.py create mode 100755 src/datasets/resource_scripts/openproblems_v1_multimodal.sh create mode 100644 src/datasets/resource_test_scripts/pancreas_tasks.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index aa367f2377..ed39079378 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,30 @@ * `get_task_info`: extract task info +## datasets + +### NEW FUNCTIONALITY + +* `workflows/process_openproblems_v1`: Fetch and process legacy OpenProblems v1 datasets, whilst adding extra information to the `.uns`. + +* `normalization/log_cpm`: A log CPM normalization method. + +* `normalization/log_scran_pooling`: A log scran pooling normalization method. + +* `normalization/sqrt_cpm`: A sqrt CPM normalization method. + +* `normalization/l1_sqrt`: A scaled L1 sqrt normalization. extracted from Alra method in the denoising task from v1 + +* `subsample`: Subsample an h5ad file. Allows keeping observations from specific batches and celltypes, + also allows keeping certain features. + +### V1 MIGRATION + +* `loaders/openproblems_v1`: Fetch a dataset from OpenProblems v1, whilst adding extra information to the `.uns`. + +* `loaders/openproblems_v1_multimodal`: Fetch a multimodal dataset from OpenProblems v1, whilst adding extra information to the `.uns`. + + ## label_projection @@ -62,27 +86,6 @@ * `metric/f1`: Migrated from v1. -## datasets - -### NEW FUNCTIONALITY - -* `workflows/process_openproblems_v1`: Fetch and process legacy OpenProblems v1 datasets - -* `normalization/log_cpm`: A log CPM normalization method. - -* `normalization/log_scran_pooling`: A log scran pooling normalization method. - -* `normalization/sqrt_cpm`: A sqrt CPM normalization method. - -* `normalization/l1_sqrt`: A scaled L1 sqrt normalization. extracted from Alra method in the denoising task from v1 - -* `subsample`: Subsample an h5ad file. Allows keeping observations from specific batches and celltypes, - also allows keeping certain features. - -### V1 MIGRATION - -* `loaders/openproblems_v1`: Fetch a dataset from OpenProblems v1 - ## denoising ### NEW FUNCTIONALITY diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index 8b6d47c825..d6bb88eab8 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -1,48 +1,10 @@ +__merge__: anndata_hvg.yaml type: file description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" example: "dataset.h5ad" info: label: "Dataset+PCA+HVG+kNN" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalised expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalisation method, if any. - required: false - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true obsp: - type: double name: knn_distances @@ -52,24 +14,7 @@ info: name: knn_connectivities description: K nearest neighbors connectivities matrix. required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: double - name: pca_variance - description: The PCA variance objects. - required: true - type: object name: knn description: Neighbors data. diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_hvg.yaml index e770e877fd..a49c38a680 100644 --- a/src/datasets/api/anndata_hvg.yaml +++ b/src/datasets/api/anndata_hvg.yaml @@ -1,34 +1,10 @@ +__merge__: anndata_pca.yaml type: file description: "A normalised dataset with a PCA embedding and HVG selection" example: "dataset.h5ad" info: label: "Dataset+PCA+HVG" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalised expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalisation method, if any. - required: false var: - type: boolean name: hvg @@ -38,26 +14,3 @@ info: name: hvg_score description: A ranking of the features by hvg. required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: double - name: pca_variance - description: The PCA variance objects. - required: true diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/anndata_normalized.yaml index 58aaa077ad..5698abb1f4 100644 --- a/src/datasets/api/anndata_normalized.yaml +++ b/src/datasets/api/anndata_normalized.yaml @@ -1,40 +1,16 @@ +__merge__: anndata_raw.yaml type: file description: "A normalized dataset" example: "dataset.h5ad" info: label: "Normalized dataset" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true + layers: - type: double name: normalized description: Normalised expression values obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - type: double name: size_factors description: The size factors created by the normalisation method, if any. - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true + required: false \ No newline at end of file diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/anndata_pca.yaml index 41fdc680e4..97c9730e62 100644 --- a/src/datasets/api/anndata_pca.yaml +++ b/src/datasets/api/anndata_pca.yaml @@ -1,34 +1,10 @@ +__merge__: anndata_normalized.yaml type: file description: "A normalised dataset with a PCA embedding" example: "dataset.h5ad" info: label: "Dataset+PCA" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalised expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalisation method, if any. - required: false obsm: - type: double name: X_pca @@ -40,14 +16,6 @@ info: description: The PCA loadings matrix. required: true uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - type: double name: pca_variance description: The PCA variance objects. diff --git a/src/datasets/api/anndata_raw.yaml b/src/datasets/api/anndata_raw.yaml index 2e46e64cff..6320921cce 100644 --- a/src/datasets/api/anndata_raw.yaml +++ b/src/datasets/api/anndata_raw.yaml @@ -27,8 +27,27 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true - # todo: ? - # - dataset_label - # - dataset_description - # - dataset_doi - # - dataset_url (if doi not available) + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: data_url + description: Link to the original source of the dataset. + required: false + - name: data_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the dataset. + required: false diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index eb16a1ec88..54cb6bc3c6 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" + - name: "--dataset_id" type: "string" description: "The ID of the dataset" required: true @@ -26,6 +26,32 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--data_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--data_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false - name: Outputs arguments: - name: "--output" @@ -39,10 +65,13 @@ functionality: path: test.py platforms: - type: docker - image: singlecellopenproblems/openproblems + image: python:3.8 setup: - - type: python - packages: - - scanpy - - "anndata>=0.8" + - type: apt + packages: git + - type: docker + run: | + git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ + pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ + pip install --no-cache-dir --editable /opt/openproblems - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/run.sh b/src/datasets/loaders/openproblems_v1/run.sh deleted file mode 100755 index 1edd5e5efb..0000000000 --- a/src/datasets/loaders/openproblems_v1/run.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -export NXF_VER=22.04.5 - -nextflow \ - run . \ - -main-script target/nextflow/datasets/loaders/openproblems_v1/main.nf \ - -resume \ - -profile docker \ - --param_list src/datasets/loaders/openproblems_v1/datasets.csv \ - --publish_dir output/datasets \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 1dccba8ecb..927816780f 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { - "id": "pancreas", + "dataset_id": "pancreas", "obs_celltype": "celltype", "obs_batch": "tech", "obs_tissue": "tissue", @@ -23,7 +23,7 @@ "allen_brain_atlas": (op.data.allen_brain_atlas.load_mouse_brain_atlas, {}), "cengen": (op.data.cengen.load_cengen, {}), "immune_cells": (op.data.immune_cells.load_immune, {}), - "mouse_blood_olssen_labelled": (op.data.mouse_blood_olssen_labelled.load_olsson_2016_mouse_blood, {}), + "mouse_blood_olsson_labelled": (op.data.mouse_blood_olsson_labelled.load_olsson_2016_mouse_blood, {}), "mouse_hspc_nestorowa2016": (op.data.mouse_hspc_nestorowa2016.load_mouse_hspc_nestorowa2016, {}), "pancreas": (op.data.pancreas.load_pancreas, {}), # "tabula_muris_senis": op.data.tabula_muris_senis.load_tabula_muris_senis, @@ -34,19 +34,15 @@ "tenx_1k_pbmc": (op.data.tenx.load_tenx_1k_pbmc, {}), "tenx_5k_pbmc": (op.data.tenx.load_tenx_5k_pbmc, {}), "tnbc_wu2021": (op.data.tnbc_wu2021.load_tnbc_data, {}), - # "Wagner_2018_zebrafish_embryo_CRISPR": op.data.Wagner_2018_zebrafish_embryo_CRISPR.load_zebrafish_chd_tyr, "zebrafish": (op.data.zebrafish.load_zebrafish, {}) } # fetch dataset -dataset_fun, kwargs = dataset_funs[par["id"]] +dataset_fun, kwargs = dataset_funs[par["dataset_id"]] print("Fetch dataset", flush=True) adata = dataset_fun(**kwargs) -print("Setting .uns['dataset_id']", flush=True) -adata.uns["dataset_id"] = par["id"] - # override values one by one because adata.uns and # metadata are two different classes. for key, value in dataset_fun.metadata.items(): @@ -93,5 +89,17 @@ adata.layers["counts"] = adata.X del adata.X +print("Add metadata to uns", flush=True) +metadata_fields = [ + "dataset_id", "dataset_name", "data_url", "data_reference", + "dataset_summary", "dataset_description", "dataset_organism" +] +uns_metadata = { + id: par[id] + for id in metadata_fields + if id in par +} +adata.uns.update(uns_metadata) + print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index 6606bc47d8..ffa018455c 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -11,11 +11,17 @@ out = subprocess.run( [ meta["executable"], - "--id", name, + "--dataset_id", name, "--obs_celltype", obs_celltype, "--obs_batch", obs_batch, "--layer_counts", "counts", - "--output", output + "--output", output, + "--dataset_name", "Pancreas", + "--data_url", "http://foo.org", + "--data_reference", "foo2000bar", + "--dataset_summary", "A short summary.", + "--dataset_description", "A couple of paragraphs worth of text.", + "--dataset_organism", "homo_sapiens", ], check=True ) diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml new file mode 100644 index 0000000000..5bb626d3e1 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -0,0 +1,80 @@ +functionality: + name: "openproblems_v1_multimodal" + namespace: "datasets/loaders" + description: "Fetch a dataset from OpenProblems v1" + argument_groups: + - name: Inputs + arguments: + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "In which layer to find the counts matrix. Leave undefined to use `.X`." + example: counts + - name: "--sparse" + type: boolean + default: true + description: Convert layers to a sparse CSR format. + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--data_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--data_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Outputs + arguments: + - name: "--output_mod1" + __merge__: ../../api/anndata_raw.yaml + direction: "output" + - name: "--output_mod2" + __merge__: ../../api/anndata_raw.yaml + direction: "output" + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + image: python:3.8 + setup: + - type: apt + packages: git + - type: docker + run: | + git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ + pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ + pip install --no-cache-dir --editable /opt/openproblems + - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py new file mode 100644 index 0000000000..8c0dbefa37 --- /dev/null +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -0,0 +1,133 @@ +from typing import Any, Callable, Dict, Tuple +import openproblems as op +import scanpy as sc +import scipy +import pandas as pd + +## VIASH START +par = { + "dataset_id": "scicar_mouse_kidney", + "obs_celltype": "celltype", + "obs_batch": "replicate", + "obs_tissue": None, + "layer_counts": "counts", + "output": "test_data.h5ad", +} +meta = { + "resources_dir": "src/datasets/loaders/openproblems_v1/" +} +## VIASH END + + +# make dataset lookup table +# If need be, this could be stored in a separate yaml file +dataset_funs: Dict[str, Tuple[Callable, Dict[str, Any]]] = { + "citeseq_cbmc": (op.data.multimodal.citeseq.load_citeseq_cbmc, {}), + "scicar_cell_lines": (op.data.multimodal.scicar.load_scicar_cell_lines, {}), + "scicar_mouse_kidney": (op.data.multimodal.scicar.load_scicar_mouse_kidney, {}), +} + +# fetch dataset +dataset_fun, kwargs = dataset_funs[par["dataset_id"]] + +print("Fetch dataset", flush=True) +adata = dataset_fun(**kwargs) + +print(f"source adata: {adata}", flush=True) + +# construct modality2 dataset +mod2_var_data = { + key.replace("mode2_var_", ""): adata.uns[key] + for key in adata.uns.keys() + if key.startswith("mode2_var_") +} +mod2_var = pd.DataFrame( + mod2_var_data, + index=adata.uns["mode2_var"] +) +mod2_obs = adata.obs.loc[adata.uns["mode2_obs"]] +mod2 = sc.AnnData( + obs=mod2_obs, + var=mod2_var, + layers={ "counts": adata.obsm["mode2"] } +) + +# construct modality1 dataset +mod1 = adata.copy() +mod1.uns = { key: value for key, value in mod1.uns.items() if not key.startswith("mode2_")} +mod1.obsm = { key: value for key, value in mod1.obsm.items() if not key.startswith("mode2_")} +mod1.obsp = { key: value for key, value in mod1.obsp.items() if not key.startswith("mode2_")} +mod1.varm = { key: value for key, value in mod1.varm.items() if not key.startswith("mode2_")} +mod1.varp = { key: value for key, value in mod1.varp.items() if not key.startswith("mode2_")} + +# override values one by one because adata.uns and +# metadata are two different classes. +for key, value in dataset_fun.metadata.items(): + print(f"Setting .uns['{key}']", flush=True) + mod1.uns[key] = value + mod2.uns[key] = value + +print("Setting .obs['celltype']", flush=True) +if par["obs_celltype"]: + if par["obs_celltype"] in mod1.obs: + mod1.obs["celltype"] = mod1.obs[par["obs_celltype"]] + mod2.obs["celltype"] = mod2.obs[par["obs_celltype"]] + else: + print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.", flush=True) + +print("Setting .obs['batch']", flush=True) +if par["obs_batch"]: + if par["obs_batch"] in mod1.obs: + mod1.obs["batch"] = mod1.obs[par["obs_batch"]] + mod2.obs["batch"] = mod2.obs[par["obs_batch"]] + else: + print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.", flush=True) + +print("Setting .obs['tissue']", flush=True) +if par["obs_tissue"]: + if par["obs_tissue"] in mod1.obs: + mod1.obs["tissue"] = mod1.obs[par["obs_tissue"]] + mod2.obs["tissue"] = mod2.obs[par["obs_tissue"]] + else: + print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.", flush=True) + +if par["layer_counts"] and par["layer_counts"] in mod1.layers: + print(f"Temporarily moving mod1.layers['{par['layer_counts']}']", flush=True) + mod1_X = mod1.layers[par["layer_counts"]] + del mod1.layers[par["layer_counts"]] +else: + print("Temporarily moving mod1.X", flush=True) + mod1_X = mod1.X + del mod1.X + +if par["sparse"] and not scipy.sparse.issparse(mod1_X): + print("Make mod1 counts sparse", flush=True) + mod1_X = scipy.sparse.csr_matrix(mod1_X) + +if par["sparse"] and not scipy.sparse.issparse(mod2.layers["counts"]): + print("Make mod2 counts sparse", flush=True) + mod2.layers["counts"] = scipy.sparse.csr_matrix(mod2.layers["counts"]) + +print("Moving .X to .layers['counts']", flush=True) +mod1.layers["counts"] = mod1_X + +# just in case +del mod1.X +del mod2.X + +print("Add metadata to uns", flush=True) +metadata_fields = [ + "dataset_id", "dataset_name", "data_url", "data_reference", + "dataset_summary", "dataset_description" "dataset_organism" +] +uns_metadata = { + id: par[id] + for id in metadata_fields + if id in par +} +mod1.uns.update(uns_metadata) +mod2.uns.update(uns_metadata) + +print("Writing adata to file", flush=True) +mod1.write_h5ad(par["output_mod1"], compression="gzip") +mod2.write_h5ad(par["output_mod2"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1_multimodal/test.py b/src/datasets/loaders/openproblems_v1_multimodal/test.py new file mode 100644 index 0000000000..1f22f6732a --- /dev/null +++ b/src/datasets/loaders/openproblems_v1_multimodal/test.py @@ -0,0 +1,66 @@ +from os import path +import subprocess +import anndata as ad + +name = "scicar_mouse_kidney" +obs_celltype = "cell_name" +obs_batch = "replicate" +obs_tissue = None + +output_mod1_file = "output_mod1.h5ad" +output_mod2_file = "output_mod2.h5ad" + +print(">> Running script", flush=True) +out = subprocess.run( + [ + meta["executable"], + "--dataset_id", name, + "--obs_celltype", obs_celltype, + "--obs_batch", obs_batch, + "--layer_counts", "counts", + "--output_mod1", output_mod1_file, + "--output_mod2", output_mod2_file, + "--dataset_name", "Pancreas", + "--data_url", "http://foo.org", + "--data_reference", "foo2000bar", + "--dataset_summary", "A short summary.", + "--dataset_description", "A couple of paragraphs worth of text.", + "--dataset_organism", "homo_sapiens", + ], + check=True +) + +print(">> Checking whether files exist", flush=True) +assert path.exists(output_mod1_file) +assert path.exists(output_mod2_file) + +print(">> Read output anndata", flush=True) +output_mod1 = ad.read_h5ad(output_mod1_file) +output_mod2 = ad.read_h5ad(output_mod2_file) + +print(f"output_mod1: {output_mod1}", flush=True) +print(f"output_mod2: {output_mod2}", flush=True) + +print(">> Check that output mod1 fits expected API", flush=True) +assert output_mod1.X is None +assert "counts" in output_mod1.layers +assert output_mod1.uns["dataset_id"] == name +if obs_celltype: + assert "celltype" in output_mod1.obs.columns +if obs_batch: + assert "batch" in output_mod1.obs.columns +if obs_tissue: + assert "tissue" in output_mod1.obs.columns + +print(">> Check that output mod2 fits expected API", flush=True) +assert output_mod2.X is None +assert "counts" in output_mod2.layers +assert output_mod2.uns["dataset_id"] == name +if obs_celltype: + assert "celltype" in output_mod2.obs.columns +if obs_batch: + assert "batch" in output_mod2.obs.columns +if obs_tissue: + assert "tissue" in output_mod2.obs.columns + +print(">> All tests passed successfully", flush=True) diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 420da43210..89f4888555 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -22,51 +22,128 @@ param_list: - id: allen_brain_atlas obs_celltype: label layer_counts: counts + dataset_id: allen_brain_atlas + dataset_name: Mouse Brain Atlas + data_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 + data_reference: tasic2016adult + dataset_summary: Adult mouse primary visual cortex + dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). + dataset_organism: mus_musculus - id: cengen obs_celltype: cell_type obs_batch: experiment_code obs_tissue: tissue layer_counts: counts + dataset_id: cengen + dataset_name: CeNGEN + data_url: https://www.cengen.org + data_reference: hammarlund2018cengen + dataset_summary: Complete Gene Expression Map of an Entire Nervous System + dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. + dataset_organism: caenorhabditis_elegans - id: immune_cells obs_celltype: final_annotation obs_batch: batch obs_tissue: tissue layer_counts: counts - - - id: mouse_blood_olssen_labelled + dataset_id: immune_cells + dataset_name: Human immune + data_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html + data_reference: luecken2022benchmarking + dataset_summary: Human immune cells dataset from the scIB benchmarks + dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). + dataset_organism: homo_sapiens + + - id: mouse_blood_olsson_labelled obs_celltype: celltype layer_counts: counts + dataset_id: mouse_blood_olsson_labelled + dataset_name: Mouse myeloid + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 + data_reference: olsson2016single + dataset_summary: Myeloid lineage differentiation from mouse blood + dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. + dataset_organism: mus_musculus - id: mouse_hspc_nestorowa2016 obs_celltype: cell_type_label layer_counts: counts + dataset_id: mouse_hspc_nestorowa2016 + dataset_name: Mouse HSPC + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 + data_reference: nestorowa2016single + dataset_summary: Haematopoeitic stem and progenitor cells from mouse bone marrow + dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. + dataset_organism: mus_musculus - id: pancreas obs_celltype: celltype obs_batch: tech layer_counts: counts + dataset_id: pancreas + dataset_name: Human pancreas + data_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html + data_reference: luecken2022benchmarking + dataset_summary: Human pancreas cells dataset from the scIB benchmarks + dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). + dataset_organism: homo_sapiens - id: tabula_muris_senis_droplet_lung obs_celltype: cell_type obs_batch: donor_id layer_counts: counts + dataset_id: tabula_muris_senis_droplet_lung + dataset_name: Tabula Muris Senis Lung + data_url: https://tabula-muris-senis.ds.czbiohub.org + data_reference: tabula2020single + dataset_summary: Aging mouse lung cells from Tabula Muris Senis + dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. + dataset_organism: mus_musculus - id: tenx_1k_pbmc layer_counts: counts + dataset_id: tenx_1k_pbmc + dataset_name: 1k PBMCs + data_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 + data_reference: 10x2018pbmc + dataset_summary: 1k peripheral blood mononuclear cells from a healthy donor + dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. + dataset_organism: homo_sapiens - id: tenx_5k_pbmc layer_counts: counts + dataset_id: tenx_5k_pbmc + dataset_name: 5k PBMCs + data_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 + data_reference: 10x2019pbmc + dataset_summary: 5k peripheral blood mononuclear cells from a healthy donor + dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. + dataset_organism: homo_sapiens - id: tnbc_wu2021 obs_celltype: celltype_minor layer_counts: counts + dataset_id: tnbc_wu2021 + dataset_name: Triple-Negative Breast Cancer + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 + data_reference: wu2021single + dataset_summary: 1535 cells from six fresh triple-negative breast cancer tumors. + dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). + dataset_organism: homo_sapiens - id: zebrafish obs_celltype: cell_type obs_batch: lab layer_counts: counts + dataset_id: zebrafish + dataset_name: Zebrafish embryonic cells + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 + data_reference: wagner2018single + dataset_summary: Single-cell mRNA sequencing of zebrafish embryonic cells. + dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. + dataset_organism: danio_rerio output: '$id.h5ad' HERE @@ -79,5 +156,6 @@ nextflow \ -profile docker \ -resume \ -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ - -with-tower + --publish_dir "$OUTPUT_DIR" + + # -with-tower diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh new file mode 100755 index 0000000000..1598c3091d --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -0,0 +1,46 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="resources/datasets/openproblems_v1_multimodal" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + cat > "$params_file" << 'HERE' +param_list: + - id: citeseq_cbmc + layer_counts: counts + + - id: scicar_cell_lines + obs_celltype: cell_name + layer_counts: counts + + - id: scicar_mouse_kidney + obs_celltype: cell_name + obs_batch: replicate + layer_counts: counts + +output: '$id.h5ad' +HERE +fi + +export NXF_VER=22.04.5 +nextflow \ + run . \ + -main-script src/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" \ + -with-tower diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 81677a13bd..7f5eb3c720 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -17,10 +17,16 @@ mkdir -p $DATASET_DIR # download dataset viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ - --id "pancreas" \ --obs_celltype "celltype" \ --obs_batch "tech" \ --layer_counts "counts" \ + --dataset_id pancreas \ + --dataset_name "Human pancreas" \ + --data_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ + --data_reference "luecken2022benchmarking" \ + --dataset_summary "Human pancreas cells dataset from the scIB benchmarks" \ + --dataset_description "Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq)." \ + --dataset_organism "homo_sapiens" \ --output $DATASET_DIR/temp_dataset_full.h5ad wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/g2m_genes_tirosh_hm.txt -O $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt diff --git a/src/datasets/resource_test_scripts/pancreas_tasks.sh b/src/datasets/resource_test_scripts/pancreas_tasks.sh new file mode 100644 index 0000000000..1b73a2e8d7 --- /dev/null +++ b/src/datasets/resource_test_scripts/pancreas_tasks.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +src/denoising/resources_test_scripts/pancreas.sh +src/dimensionality_reduction/resources_test_scripts/pancreas.sh +src/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 7d83919119..3373083b25 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -10,6 +10,10 @@ functionality: type: "string" description: "The ID of the dataset" required: true + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true - name: "--obs_celltype" type: "string" description: "Location of where to find the observation cell types." @@ -27,6 +31,32 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--data_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--data_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false - name: Outputs arguments: - name: "--output" diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 5a2bd14b24..edbcfa8bd7 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -32,7 +32,10 @@ workflow run_wf { // split params for downstream components | setWorkflowArguments( - loader: ["id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse"], + loader: [ + "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse", + "dataset_name", "data_url", "data_reference", "dataset_summary", "dataset_description", "dataset_organism" + ], output: [ "output" ] ) From cedd6924f54cbe8874de983bb790799dc9eab41f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 09:35:32 +0100 Subject: [PATCH 0764/1233] make script executable Former-commit-id: fe46cec94377b99a3c0f311cbbe0f47fa828471a --- src/datasets/resource_test_scripts/pancreas_tasks.sh | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 src/datasets/resource_test_scripts/pancreas_tasks.sh diff --git a/src/datasets/resource_test_scripts/pancreas_tasks.sh b/src/datasets/resource_test_scripts/pancreas_tasks.sh old mode 100644 new mode 100755 From 3fb1269a00d660dd1972988a2f17e2ffa604c05c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 09:43:41 +0100 Subject: [PATCH 0765/1233] add documentation to component Former-commit-id: e3f1b7069047335601135c43a1d3a34987035b57 --- src/common/create_skeleton/config.vsh.yaml | 26 +++++++++++++--------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index 13019740f6..bbfd93c677 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -1,34 +1,41 @@ functionality: name: create_skeleton namespace: common - description: Create a skeleton directory containing a viash config file and python or r script file based on the task api. + description: | + Create a skeleton Viash component. + + Usage: + ``` + bin/create_skeleton --task denoising --comp_type method --language r --name foo --output src/denoising/method/foo + ``` arguments: - name: "--src" type: "file" default: "./src" - description: "The src directory of the openproblems-v2 repository." + description: "The source directory of the openproblems-v2 repository." - type: string name: --task - description: Which task the component will be added + description: Which task the component will be added to. example: denoising - type: string name: --comp_type example: metric - description: type of component to create + description: The type of component to create. choices: ['metric', 'method', 'negative_control', 'positive_control'] - type: string name: --language - example: python - description: script language + description: Which scripting language to use. Options are 'python', 'r'. default: python + choices: [python, r] - type: string name: --name example: new_comp - description: name of the new method in snake case + description: Name of the new method, formatted in snake case. - type: file name: --output direction: output required: true + description: Path to the component directory. resources: - type: python_script path: script.py @@ -39,11 +46,10 @@ functionality: dest: openproblems-v2/src platforms: - type: docker - image: python:3.10 + image: python:3.10-slim setup: - type: python - pip: - - ruamel.yaml + pip: ruamel.yaml - type: nextflow From d60d8fe8618e00ad0a7d40186a751f71670c4952 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 13:35:16 +0100 Subject: [PATCH 0766/1233] update skeleton code Former-commit-id: 02d7875f96be2dbc076669165ee3d4ed6ae8f1d4 --- src/common/create_skeleton/config.vsh.yaml | 24 +- src/common/create_skeleton/script.py | 644 +++++++++++---------- 2 files changed, 346 insertions(+), 322 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index bbfd93c677..726f1090dd 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -6,22 +6,19 @@ functionality: Usage: ``` - bin/create_skeleton --task denoising --comp_type method --language r --name foo --output src/denoising/method/foo + bin/create_skeleton --task denoising --type method --language r --name foo + bin/create_skeleton --task denoising --type metric --language python --name bar ``` arguments: - - name: "--src" - type: "file" - default: "./src" - description: "The source directory of the openproblems-v2 repository." - type: string name: --task description: Which task the component will be added to. example: denoising - type: string - name: --comp_type + name: --type example: metric description: The type of component to create. - choices: ['metric', 'method', 'negative_control', 'positive_control'] + choices: ['metric', 'method', 'control_method'] - type: string name: --language description: Which scripting language to use. Options are 'python', 'r'. @@ -34,8 +31,17 @@ functionality: - type: file name: --output direction: output - required: true - description: Path to the component directory. + # required: true + description: Path to the component directory. Suggested location is `src//s/`. + default: src/${VIASH_PAR_TASK}/${VIASH_PAR_TYPE}s/${VIASH_PAR_NAME} + - type: file + name: --api_file + description: | + Which API file to use. Defaults to `src//api/comp_.yaml`. + In tasks with different subtypes of method, this location might not exist and you might need + to manually specify a different API file to inherit from. + # required: true + default: src/${VIASH_PAR_TASK}/api/comp_${VIASH_PAR_TYPE}.yaml resources: - type: python_script path: script.py diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 66b33dd489..161d6a2363 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -1,346 +1,364 @@ +from typing import Any from ruamel.yaml import YAML from pathlib import Path - +import os +import re ## VIASH START -# The following code has been auto-generated by Viash. par = { - 'src': './src', 'task': 'denoising', - 'comp_type': 'metric', + 'type': 'metric', 'language': 'python', 'name': 'new_comp', + 'output': 'src/denoising/methods/new_comp', + 'api_file': 'src/denoising/api/comp_method.yaml' } -meta = { -} - ## VIASH END - -def add_metric_config(tmpl): - - tmpl['functionality']['info']['metrics'] = [{ - 'metric_id': 'metric_id', - 'metric_name': 'Metric Name', - 'metric_description': 'metric description', +# TODO: fix adata -> detect input file + +def strip_margin(text: str) -> str: + return re.sub('(\n?)[ \t]*\|', '\\1', text) + +def create_config_template(par): + yaml = YAML() + config_template = yaml.load(strip_margin(f'''\ + |# The API specifies which type of component this is. + |# It contains specifications for: + |# - The input/output files + |# - Common parameters + |# - A unit test + |__merge__: {os.path.relpath(par["api_file"], par["output"])} + | + |functionality: + | name: {par["name"]} + | namespace: {par["task"]}/{par['type']}s + | + | # Metadata for your component (required) + | info: + | xx: xx + | + | # Component-specific parameters (optional) + | # arguments: + | # - name: "--n_neighbors" + | # type: "integer" + | # default: 5 + | # description: Number of neighbors to use. + | + | # Resources required to run the component + | resources: + | # The script of your component + | - type: xx + | path: xx + | # Additional resources your script needs (optional) + | # - type: file + | # path: weights.pt + | + |# Target platforms. For more information, see . + |platforms: + | - type: docker + | image: + | # Add custom dependencies here + | setup: + | - type: nextflow + | directives: + | label: [midmem, midcpu] + |''' + )) + return config_template + +def add_method_info(conf, par, pretty_name) -> None: + """Set up the functionality info for a method.""" + conf['functionality']['info'] = { + 'pretty_name': pretty_name, + 'summary': 'FILL IN: A one sentence summary of this method.', + 'description': 'FILL IN: A (multiline) description of how this method works.', + 'reference': 'bibtex_reference_key', + 'documentation_url': 'https://url.to/the/documentation', + 'repository_url': 'https://github.com/organisation/repository', + 'preferred_normalization': 'log_cpm' + } + if par["type"] == "control_method": + del conf['functionality']['info']['reference'] + del conf['functionality']['info']['documentation_url'] + del conf['functionality']['info']['repository_url'] + +def add_metric_info(conf, par, pretty_name) -> None: + """Set up the functionality info for a metric.""" + conf['functionality']['info'] = { + 'metrics': [{ + 'name': f'{par["name"]}', + 'pretty_name': pretty_name, + 'summary': 'FILL IN: A one sentence summary of this metric.', + 'description': 'FILL IN: A (multiline) description of how this metric works.', + 'reference': 'bibtex_reference_key', + 'documentation_url': 'https://url.to/the/documentation', + 'repository_url': 'https://github.com/organisation/repository', 'min': 0, 'max': 1, 'maximize': 'true', }] - - return tmpl - -def add_method_config(tmpl): - - tmpl['functionality']['info'].update({ - 'method_name': 'Method name', - 'preferred_normalization': '', - 'variants': { - par['name']: '', - 'method_variant1': { - 'preferred_normalization': '' - } - } - }) - - return tmpl - -def add_python_setup(conf): - - conf['functionality']['resources'][0]['type'] = 'python_script' - conf['functionality']['resources'][0]['path'] = 'script.py' - - conf['functionality']['test_resources'][0]['type'] = 'python_script' - conf['functionality']['test_resources'][0]['path'] = 'script.py' - - for i, platform in enumerate(conf['platforms']): - if platform['type'] == 'docker': - conf['platforms'][i]['image'] = 'python:3.10' - - return conf - -def add_r_setup(conf): - - conf['functionality']['resources'][0]['type'] = 'r_script' - conf['functionality']['resources'][0]['path'] = 'script.R' - - conf['functionality']['test_resources'][0]['type'] = 'r_script' - conf['functionality']['test_resources'][0]['path'] = 'script.R' - - for i, platform in enumerate(conf['platforms']): - if platform['type'] == 'docker': - pltf = conf['platforms'][i] - pltf['image'] = 'eddelbuettel/r2u:22.04' - pltf['setup'].append( - { - 'type': 'r', - 'cran': [ 'anndata'], - 'bioc': '' - }) - pltf['setup'].append({ - 'type': 'apt', - 'packages': ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] - }) - - return conf - - -def create_python_script(tmpl_par, comp_type): - newline = "\n" - script_templ = f'''import anndata as ad -## VIASH START - -par = {{ - # Required arguments for the task - {newline.join(f"'{key}': '{value}'," for key, value in tmpl_par.items())} - # Optional method-specific arguments - 'n_neighbors': 5, - }} - -meta = {{ - 'functionality_name': 'foo' -}} - -## VIASH END - -## Data reader -print('Reading input files', flush=True) - -adata = ad.read_h5ad(par['{list(templ_par.keys())[0]}']) - -print('processing Data', flush=True) -# ... preprocessing ... -# ... train model ... -# ... generate predictions ... - -''' + } + +def add_script_resource(conf, par) -> None: + """Add the script to the functionality resources.""" + if par['language'] == 'python': + conf['functionality']['resources'] = [{ + "type": "python_script", + "path": "script.py", + }] + if par['language'] == 'r': + conf['functionality']['resources'] = [{ + "type": "r_script", + "path": "script.R", + }] - if comp_type == 'metric': - script_templ = script_templ + '''# write output to file -out = ad.AnnData( - uns={ - 'dataset_id': adata.uns['dataset_id'], - 'method_id': adata.uns['method_id'], - 'metric_values': [''], - 'metric_ids': [meta['functionality_name']], # if multiple values, add ids explicitly e.g. ['asw', 'asw_batch'] - }, -) - -print('writing to output files', flush=True) -out.write_h5ad(par['output'], compress='gzip') - ''' - else : - script_templ = script_templ + '''# write output to file -out = ad.AnnData( - X=y_pred, - uns={ - 'dataset_id': adata.uns['dataset_id'], - 'method_id': meta['functionality_name'], +def add_python_setup(conf) -> None: + """Set up the docker platform for Python.""" + conf['platforms'][0]["image"] = 'python:3.10' + conf['platforms'][0]["setup"] = [ + { + "type": "python", + "pypi": "anndata>=0.8" + } + ] + +def add_r_setup(conf) -> None: + """Set up the docker platform for R.""" + conf['platforms'][0]["image"] = 'eddelbuettel/r2u:22.04' + conf['platforms'][0]["setup"] = [ + { + "type": "apt", + "packages": ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] }, -) - -print('writing to output files', flush=True) -out.write_h5ad(par['output'], compress='gzip') - ''' - - - return script_templ - -def create_r_script(tmpl_par, comp_type): - newline = "\n" - script_templ = f'''library(anndata, warn.conflicts = FALSE) - -## VIASH START - -par <- list( - # Required arguments for the task - {newline.join(f'{key} = "{value}",' for key, value in tmpl_par.items())} - # Optional method-specific arguments - n_neighbors = 5, -) - -meta <- list( - functionality_name = "foo" -) - -## VIASH END - -## Data reader -cat("Reading input files\\n") -adata <- read_h5ad(par["{list(templ_par.keys())[0]}"]) - -cat("processing Data\\n") -# ... preprocessing ... -# ... train model ... -# ... generate predictions ... - -''' - - if comp_type == 'metric': - script_templ = script_templ + '''# write output to file -out <- anndata::AnnData( - shape = c(0, 0), - uns = list( - dataset_id = adata$uns$dataset_id, - method_id = adata$uns$method_id, - metric_values = list(""), - metric_ids = list(meta$functionality_name), # if multiple values, add ids explicitly e.g. list('asw', 'asw_batch') + { + "type": "r", + "cran": "anndata", + "script": "anndata::install_anndata()" # TODO: does this work? + } + ] + +def read_api_spec(par): + with open(par['api_file'], 'r') as f: + api_spec = YAML().load(f) + return api_spec + +def set_par_values(api_spec) -> dict[str, Any]: + """Reads in the API file and returns default values for the par object.""" + args = api_spec['functionality']['arguments'] + for argi, arg in enumerate(args): + arg_type = arg.get("type", "file") + direction = arg.get("direction", "input") + key = re.sub("^-*", "", arg['name']) + + # find value + if arg_type != "file": + value = arg.get("default", arg.get("example", "...")) + elif direction == "input": + key_strip = key.replace("input_", "") + value = f'resources_test/{par["task"]}/pancreas/{key_strip}.h5ad' + else: + key_strip = key.replace("output_", "") + value = f'{key_strip}.h5ad' + + # store key and value + api_spec['functionality']['arguments'][argi]["type"] = arg_type + api_spec['functionality']['arguments'][argi]["direction"] = direction + api_spec['functionality']['arguments'][argi]["key"] = key + api_spec['functionality']['arguments'][argi]["value"] = value + +def create_python_script(par, api_spec, type): + args = api_spec['functionality']['arguments'] + par_string = ",\n ".join(f"'{arg['key']}': '{arg['value']}'" for arg in args) + read_h5ad_string = "\n".join( + f"{arg['key']} = ad.read_h5ad(par['{arg['key']}'])" + for arg in args + if arg['type'] == "file" + and arg['direction'] == "input" ) -) -out("writing to output files\\n") -zzz <- adata$write_h5ad(par$output, compression = "gzip") - ''' - + if type == 'metric': + output_string = strip_margin(f'''\ + |print('Compute metrics', flush=True) + |# metric_ids and metric_values can have length > 1 + |# but should be of equal length + |metric_ids = [ '{par['name']}' ] + |metric_values = [ 0.5 ] + | + |print('Create output anndata', flush=True) + |out = ad.AnnData( + | uns={{ + | 'dataset_id': adata.uns['dataset_id'], + | 'method_id': adata.uns['method_id'], + | 'metric_ids': metric_ids, + | 'metric_values': metric_values, + | }}, + |)''') else: - script_templ = script_templ + '''# write output to file -out <- anndata::AnnData( - X = y_pred, - uns = list( - dataset_id = adata$uns$dataset_id, - method_id = meta$functionality_name, + # TODO: fix output slots + output_string = strip_margin('''\ + |print('Preprocess data', flush=True) + |# ... preprocessing ... + | + |print('Train model', flush=True) + |# ... train model ... + | + |print('Generate predictions', flush=True) + |# ... generate predictions ... + | + |print('Create output anndata', flush=True) + |out = ad.AnnData( + | X=y_pred, + | uns={ + | 'dataset_id': adata.uns['dataset_id'], + | 'method_id': meta['functionality_name'], + | }, + |)''') + + script = strip_margin(f'''\ + |import anndata as ad + | + |## VIASH START + |par = {{ + | {par_string} + |}} + |meta = {{ + | 'functionality_name': '{par["name"]}' + |}} + |## VIASH END + | + |print('Reading input files', flush=True) + |{read_h5ad_string} + | + |{output_string} + | + |print('Write output to file', flush=True) + |out.write_h5ad(par['output'], compress='gzip') + |''') + + return script + + +def create_r_script(par, api_spec, type): + args = api_spec['functionality']['arguments'] + par_string = ",\n ".join(f'{arg["key"]} = "{arg["value"]}"' for arg in args) + read_h5ad_string = "\n".join( + f'{arg["key"]} <- anndata::read_h5ad(par[["{arg["key"]}"]])' + for arg in args + if arg['type'] == "file" + and arg['direction'] == "input" ) -) - -out("writing to output files\\n") -zzz <- adata$write_h5ad(par$output, compression = "gzip") - ''' - - - - - - return script_templ - - -## Create config file -if 'control' in par['comp_type']: - merge = 'control_method' -else: - merge = par['comp_type'] - -config_tmpl = f''' -# points to global config e.g. parameters -__merge__: ../../api/comp_{merge}.yaml -functionality: - # a unique name for your method, same as what is being output by the script. - # must match the regex [a-z][a-z0-9_]* - name: {par['name']} - namespace: {par["task"]}/{merge}s - # metadata for your method - description: A description for your method. - info: - type: {par["comp_type"]} - - # component parameters - arguments: - # Method-specific parameters. - # Change these to expose parameters of your method to Nextflow (optional) - - name: "--n_neighbors" - type: "integer" - default: 5 - description: Number of neighbors to use. - - # files your script needs - resources: - # the script itself - - type: - path: - # additional resources your script needs (optional) - - type: file - path: weights.pt - - # resources for unit testing your component - test_resources: - - type: python_script - path: test.py - - path: sample_data - -# target platforms -platforms: - # By specifying 'docker' platform, viash will build a standalone - # executable which uses docker in the back end to run your method. - - type: docker - # you need to specify a base image that contains at least bash and python - image: - # You can specify additional dependencies with 'setup'. - setup: - - type: python - pip: - - pyyaml - - anndata>=0.8 - - # By specifying a 'nextflow', viash will also build a viash module - # which uses the docker container built above to also be able to - # run your method as part of a nextflow pipeline. - - type: nextflow - directives: - label: ['midmem', 'midcpu'] -''' - -yaml = YAML() -conf_tmpl_dict = yaml.load(config_tmpl) -# Add component specific config data - -if par['comp_type'] == 'metric': - - config_out = add_metric_config(conf_tmpl_dict) - -else: - - config_out = add_method_config(conf_tmpl_dict) - - if par['comp_type'] == 'method': - config_out['functionality']['info']['paper_reference']= '' - - -# add elements depending on language -if par['language'] == 'python': - - config_out = add_python_setup(config_out) - -if par['language'] == 'r': - - config_out = add_r_setup(config_out) - - -## Create script template - -resource_dir = par['src'] - -task_api = f'{resource_dir}/{par["task"]}/api' -api_conf = f'{task_api}/comp_{merge}.yaml' - -with open(api_conf, 'r') as f: - api_data = yaml.load(f) - -args = api_data['functionality']['arguments'] - -templ_par = {} - -for arg in args: - templ_par[arg['name'].replace('--','')] = '' + if type == 'metric': + output_string = strip_margin(f'''\ + |cat("Compute metrics\\n") + |# metric_ids and metric_values can have length > 1 + |# but should be of equal length + |metric_ids <- c( "{par['name']}" ) + |metric_values <- c( 0.5 ) + | + |cat("Create output anndata\\n") + |out <- anndata::AnnData( + | uns = list( + | dataset_id = adata$uns[["dataset_id"]], + | method_id = adata$uns[["method_id"]], + | metric_ids = metric_ids, + | metric_values = metric_values, + | ) + |)''') + else: + # TODO: fix output slots + output_string = strip_margin('''\ + |cat("Preprocess data\\n") + |# ... preprocessing ... + | + |cat("Train model\\n") + |# ... train model ... + | + |cat("Generate predictions\\n") + |# ... generate predictions ... + | + |cat("Create output anndata\\n") + |out <- anndata::AnnData( + | X = y_pred, + | uns = list( + | dataset_id = adata$uns[["dataset_id"]], + | method_id = meta[["functionality_name"]], + | ) + |)''') + + script = strip_margin(f'''\ + |library(anndata) + | + |## VIASH START + |par <- list( + | {par_string} + |) + |meta <- list( + | functionality_name = "{par["name"]}" + |) + |## VIASH END + | + |cat("Reading input files\\n") + |{read_h5ad_string} + | + |{output_string} + | + |cat("Write output to file\\n") + |out$write_h5ad(par[["output"]], compress = "gzip") + |''') + + return script + + +def main(par): + ####### CHECK INPUTS ####### + assert re.match("[a-z][a-z0-9_]*", par["name"]), "Name should match the regular expression '[a-z][a-z0-9_]*'. Example: 'my_component'." + assert len(par['name']) <= 50, "Method name should be at most 50 characters." + + pretty_name = re.sub("_", " ", par['name']).title() + + api_spec = read_api_spec(par) + + ####### CREATE CONFIG ####### + config_template = create_config_template(par) + + # Add component specific info + if par['type'] == 'metric': + add_metric_info(config_template, par, pretty_name) + else: + add_method_info(config_template, par, pretty_name) -if par['language'] == 'python': + # add script to resources + add_script_resource(config_template, par) - script_out = create_python_script(templ_par, par['comp_type']) + # add elements depending on language + if par['language'] == 'python': + add_python_setup(config_template) -if par['language'] == 'r': + if par['language'] == 'r': + add_r_setup(config_template) - script_out = create_r_script(templ_par, par['comp_type']) + ####### CREATE SCRIPT ####### + set_par_values(api_spec) + if par['language'] == 'python': + script_out = create_python_script(par, api_spec, par['type']) + if par['language'] == 'r': + script_out = create_r_script(par, api_spec, par['type']) -## Write output -out_dir= Path(par["output"]) + ####### WRITE OUTPUTS ####### + out_dir = Path(par["output"]) + out_dir.mkdir(exist_ok=True) -out_dir.mkdir(exist_ok=True) + with open(f'{out_dir}/config.vsh.yaml', 'w') as f: + YAML().dump(config_template, f) -with open(f'{out_dir}/config.vsh.yaml', 'w') as f: - yaml.dump(config_out, f) + script_name = config_template['functionality']['resources'][0]['path'] -script_f = config_out['functionality']['resources'][0]['path'] + with open(f'{out_dir}/{script_name}', 'w') as f: + f.write(script_out) -with open(f'{out_dir}/{script_f}', 'w') as fpy: - fpy.write(script_out) \ No newline at end of file +if __name__ == "__main__": + main(par) \ No newline at end of file From ba34b82c0f49548e857e6f17c0f167c1e999d961 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 18:38:05 +0100 Subject: [PATCH 0767/1233] include types in api (#92) Former-commit-id: fb1f7bd323469931003d6e4a807733f717486322 --- src/denoising/api/comp_control_method.yaml | 2 ++ src/denoising/api/comp_method.yaml | 2 ++ src/denoising/api/comp_metric.yaml | 2 ++ src/denoising/api/comp_split_dataset.yaml | 2 ++ src/denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- src/denoising/control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/denoising/methods/alra/config.vsh.yaml | 1 - src/denoising/methods/dca/config.vsh.yaml | 1 - src/denoising/methods/knn_smoothing/config.vsh.yaml | 1 - src/denoising/methods/magic/config.vsh.yaml | 1 - src/dimensionality_reduction/api/comp_control_method.yaml | 2 ++ src/dimensionality_reduction/api/comp_method.yaml | 2 ++ src/dimensionality_reduction/api/comp_metric.yaml | 2 ++ src/dimensionality_reduction/api/comp_split_dataset.yaml | 2 ++ .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/densmap/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/ivis/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/neuralee/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/pca/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/phate/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 1 - src/dimensionality_reduction/methods/umap/config.vsh.yaml | 1 - src/label_projection/api/comp_control_method.yaml | 2 ++ src/label_projection/api/comp_method.yaml | 2 ++ src/label_projection/api/comp_metric.yaml | 2 ++ src/label_projection/api/comp_split_dataset.yaml | 2 ++ .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/label_projection/methods/knn/config.vsh.yaml | 1 - .../methods/logistic_regression/config.vsh.yaml | 1 - src/label_projection/methods/mlp/config.vsh.yaml | 1 - src/label_projection/methods/scanvi/config.vsh.yaml | 1 - .../methods/seurat_transferdata/config.vsh.yaml | 1 - src/label_projection/methods/xgboost/config.vsh.yaml | 1 - 36 files changed, 31 insertions(+), 24 deletions(-) diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 157f076452..c21488d131 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: control_method arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 0b8dabfb2c..52222c2582 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: method arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 4717fc9ab1..63a72c7dfc 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: "--input_test" __merge__: anndata_test.yaml diff --git a/src/denoising/api/comp_split_dataset.yaml b/src/denoising/api/comp_split_dataset.yaml index 3752f06386..78c4120bfc 100644 --- a/src/denoising/api/comp_split_dataset.yaml +++ b/src/denoising/api/comp_split_dataset.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: split_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 64e601f7ab..dec30dccac 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "denoising/control_methods" description: "negative control by copying train counts" info: - type: negative_control + subtype: negative_control method_name: No Denoising v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index e24fb9cf9c..3cf248ed8b 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "denoising/control_methods" description: "Negative control by copying the train counts" info: - type: positive_control + subtype: positive_control method_name: Perfect Denoising v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 394193e458..d2112f92fd 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -12,7 +12,6 @@ functionality: Next, each row (gene) is thresholded by the magnitude of the most negative value of that gene. Finally, the matrix is rescaled. info: - type: method method_name: ALRA paper_reference: "linderman2018zero" code_url: "https://github.com/KlugerLab/ALRA" diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 0ce04986bd..cbdfe27d76 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -8,7 +8,6 @@ functionality: Removes the dropout effect by taking the count structure, overdispersed nature and sparsity of the data into account using a deep autoencoder with zero-inflated negative binomial (ZINB) loss function. info: - type: method method_name: DCA paper_reference: "https://www.nature.com/articles/s41467-018-07931-2" code_url: "https://github.com/theislab/dca" diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 2fd5c0ed6e..b269b112b5 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "denoising/methods" description: "iterative K-nearest neighbor smoothing" info: - type: method method_name: KNN Smoothing paper_reference: "wagner2018knearest" code_url: "https://github.com/yanailab/knn-smoothing" diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index d9b820ed07..c03c916fdf 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "denoising/methods" description: "MAGIC: Markov affinity-based graph imputation of cells" info: - type: method method_name: MAGIC paper_reference: "https://doi.org/10.1016/j.cell.2018.05.061" code_url: "https://github.com/KrishnaswamyLab/MAGIC" diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 6918aba03e..439a841913 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: control_method arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index e9c6776d3a..f5cfc5fa7f 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: method arguments: - name: "--input" __merge__: anndata_train.yaml diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 48d07e06bc..8041ad6e4b 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: "--input_reduced" __merge__: anndata_reduced.yaml diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_split_dataset.yaml index 6a2bc619fb..8705ca3e35 100644 --- a/src/dimensionality_reduction/api/comp_split_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_split_dataset.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: split_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index d4224281b5..72a0919d93 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "dimensionality_reduction/control_methods" description: "Uses a normal distribution to generate random embeddings." info: - type: negative_control + subtype: negative_control method_name: Random Features v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 92fb2cae71..0075729262 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "dimensionality_reduction/control_methods" description: "Positive control method which generates high-dimensional (full data) embedding" info: - type: positive_control + subtype: positive_control label: True Features v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_comp_id: "True Features" diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index eb6695275c..f25a90587d 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "Density-preserving UMAP" info: - type: method method_name: densMAP paper_reference: "narayan2021assessing" code_url: https://github.com/lmcinnes/umap diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index b397c0a0f4..1160229870 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -9,7 +9,6 @@ functionality: ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using a parametric mapping function, and scales linearly to millions of observations. info: - type: method method_name: "ivis" paper_reference: szubert2019structurepreserving code_url: https://github.com/beringresearch/ivis diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 6b083bd880..afbd4ff1f1 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/)." info: - type: method method_name: NeuralEE paper_reference: "xiong2020neuralee" code_url: https://github.com/HiBearME/NeuralEE diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index c066a90b9f..964e3e6eaf 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "Principal component analysis (PCA)" info: - type: method method_name: "PCA" paper_reference: pearson1901pca code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index cdc43b3be9..99ebbc5f77 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "Potential of heat-diffusion for affinity-based transition embedding" info: - type: method method_name: PHATE paper_reference: "moon2019visualizing" code_url: https://github.com/KrishnaswamyLab/PHATE/ diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 9f67413462..0191321519 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "t-Distributed Stochastic Neighbor Embedding (t-SNE)" info: - type: method method_name: t-SNE paper_reference: vandermaaten2008visualizing code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 0d21b52625..a4fa7269e1 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "dimensionality_reduction/methods" description: "Uniform Manifold Approximation and Projection for Dimension Reduction" info: - type: method label: UMAP paper_doi: "10.1038/s41587-020-00801-7" code_url: https://github.com/lmcinnes/umap diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index bdf3fa2b4a..a1a1d3454e 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: control_method arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index a685d6230e..8db6b57f1f 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: method arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 148903f9db..6609052435 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: "--input_solution" __merge__: anndata_solution.yaml diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_split_dataset.yaml index 7092ccf19a..79ab59f2ee 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_split_dataset.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: split_dataset arguments: - name: "--input" __merge__: ../../datasets/api/anndata_dataset.yaml diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index a3c5c9fbd8..efba61636e 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "label_projection/control_methods" description: "Baseline method using majority voting" info: - type: negative_control + subtype: negative_control label: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index b602fc6137..b2f2417b18 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "label_projection/control_methods" description: "Negative control method which generates random labels" info: - type: negative_control + subtype: negative_control label: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 4576b54483..96cb322eb5 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "label_projection/control_methods" description: "Positive control method by returning the true labels" info: - type: positive_control + subtype: positive_control label: True labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index f73583c5de..3999a7d052 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "label_projection/methods" description: "K-Nearest Neighbors classifier" info: - type: method label: KNN # paper_name: "Nearest neighbor pattern classification" # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 6ec8d66bdd..791c6395f8 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "label_projection/methods" description: "Logistic regression method" info: - type: method label: Logistic Regression paper_name: "Applied Logistic Regression" paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index df5eab7516..e414e51d71 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "label_projection/methods" description: "Multilayer perceptron" info: - type: method label: Multilayer perceptron # paper_name: "Connectionist learning procedures" # paper_url: "https://doi.org/10.1016/0004-3702(89)90049-0" diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index f09dc9fe04..a75f36ddbe 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -6,7 +6,6 @@ functionality: Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. info: - type: method label: SCANVI paper_doi: "10.1101/2020.07.16.205997" code_url: "https://github.com/YosefLab/scvi-tools" diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index c6cb19baf3..96927476de 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -6,7 +6,6 @@ functionality: The Seurat v3 anchoring procedure is designed to integrate diverse single-cell datasets across technologies and modalities. info: - type: method label: Seurat TransferData paper_doi: "10.1101/460147" code_url: "https://github.com/satijalab/seurat" diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index caeb1395c1..beae608e19 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -4,7 +4,6 @@ functionality: namespace: "label_projection/methods" description: "XGBoost: A Scalable Tree Boosting System" info: - type: method label: XGBoost paper_doi: 10.1145/2939672.2939785 code_url: "https://github.com/dmlc/xgboost" From 7156e37ad787d763134a184be941da783b845a00 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 22:59:49 +0100 Subject: [PATCH 0768/1233] resolve remaining todos in skeleton component Former-commit-id: 1af02c9b326f126b6cbc638e12c2386ee3281a40 --- src/common/create_skeleton/config.vsh.yaml | 1 + src/common/create_skeleton/script.py | 268 +++++++++++++-------- src/common/create_skeleton/test.py | 18 +- 3 files changed, 176 insertions(+), 111 deletions(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index 726f1090dd..e395b00542 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -51,6 +51,7 @@ functionality: - path: ../../../src dest: openproblems-v2/src platforms: + - type: native - type: docker image: python:3.10-slim setup: diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 161d6a2363..16d74ce7d2 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -3,11 +3,15 @@ from pathlib import Path import os import re +import subprocess + +yaml = YAML() +yaml.indent(mapping=2, sequence=4, offset=2) ## VIASH START par = { 'task': 'denoising', - 'type': 'metric', + 'type': 'method', 'language': 'python', 'name': 'new_comp', 'output': 'src/denoising/methods/new_comp', @@ -15,13 +19,10 @@ } ## VIASH END -# TODO: fix adata -> detect input file - def strip_margin(text: str) -> str: return re.sub('(\n?)[ \t]*\|', '\\1', text) def create_config_template(par): - yaml = YAML() config_template = yaml.load(strip_margin(f'''\ |# The API specifies which type of component this is. |# It contains specifications for: @@ -35,8 +36,7 @@ def create_config_template(par): | namespace: {par["task"]}/{par['type']}s | | # Metadata for your component (required) - | info: - | xx: xx + | info: | | # Component-specific parameters (optional) | # arguments: @@ -119,7 +119,7 @@ def add_python_setup(conf) -> None: conf['platforms'][0]["setup"] = [ { "type": "python", - "pypi": "anndata>=0.8" + "pypi": "anndata~=0.8" } ] @@ -131,30 +131,26 @@ def add_r_setup(conf) -> None: "type": "apt", "packages": ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] }, + { + "type": "python", + "pypi": "anndata~=0.8" + }, { "type": "r", - "cran": "anndata", - "script": "anndata::install_anndata()" # TODO: does this work? + "cran": "anndata" } ] -def read_api_spec(par): - with open(par['api_file'], 'r') as f: - api_spec = YAML().load(f) - return api_spec - -def set_par_values(api_spec) -> dict[str, Any]: - """Reads in the API file and returns default values for the par object.""" - args = api_spec['functionality']['arguments'] +def set_par_values(config) -> dict[str, Any]: + """Adds values to each of the arguments in a config file.""" + args = config['functionality']['arguments'] for argi, arg in enumerate(args): - arg_type = arg.get("type", "file") - direction = arg.get("direction", "input") key = re.sub("^-*", "", arg['name']) # find value - if arg_type != "file": + if arg["type"] != "file": value = arg.get("default", arg.get("example", "...")) - elif direction == "input": + elif arg["direction"] == "input": key_strip = key.replace("input_", "") value = f'resources_test/{par["task"]}/pancreas/{key_strip}.h5ad' else: @@ -162,14 +158,83 @@ def set_par_values(api_spec) -> dict[str, Any]: value = f'{key_strip}.h5ad' # store key and value - api_spec['functionality']['arguments'][argi]["type"] = arg_type - api_spec['functionality']['arguments'][argi]["direction"] = direction - api_spec['functionality']['arguments'][argi]["key"] = key - api_spec['functionality']['arguments'][argi]["value"] = value + config['functionality']['arguments'][argi]["key"] = key + config['functionality']['arguments'][argi]["value"] = value + +def look_for_adata_arg(args, uns_field): + """Look for an argument that has a .uns[uns_field] in its info.slots.""" + for arg in args: + uns = arg.get("info", {}).get("slots", {}).get("uns", []) + for unval in uns: + if unval.get("name") == uns_field: + return arg["key"] + return "adata" + +def write_output_python(arg, copy_from_adata, is_metric): + """Create code for writing the output h5ad files.""" + slots = arg.get("info", {}).get("slots", {}) + outer = [] + for group_name, slots in slots.items(): + inner = [] + for slot in slots: + if group_name == "uns" and slot["name"] == "dataset_id": + value = f"{copy_from_adata}.uns['{slot['name']}']" + elif group_name == "uns" and slot["name"] == "method_id": + if is_metric: + value = f"{copy_from_adata}.uns['{slot['name']}']" + else: + value = "meta['functionality_name']" + else: + value = group_name + "_" + slot["name"] + inner.append(f"'{slot['name']}': {value}") + inner_values = ',\n '.join(inner) + outer.append(f"{group_name}={{\n {inner_values}\n }}") + outer_values = ',\n '.join(outer) + return strip_margin( + f'''\ + |print("Write {arg["key"]} AnnData to file", flush=True) + |{arg["key"]} = ad.AnnData( + | {outer_values} + |) + |{arg["key"]}.write_h5ad(par['{arg["key"]}'], compression='gzip')''' + ) -def create_python_script(par, api_spec, type): - args = api_spec['functionality']['arguments'] +def write_output_r(arg, copy_from_adata, is_metric): + """Create code for writing the output h5ad files.""" + slots = arg.get("info", {}).get("slots", {}) + outer = [] + for group_name, slots in slots.items(): + inner = [] + for slot in slots: + if group_name == "uns" and slot["name"] == "dataset_id": + value = f"{copy_from_adata}$uns[[\"{slot['name']}\"]]" + elif group_name == "uns" and slot["name"] == "method_id": + if is_metric: + value = f"{copy_from_adata}$uns[[\"{slot['name']}\"]]" + else: + value = "meta[[\"functionality_name\"]]" + else: + value = group_name + "_" + slot["name"] + inner.append(f"{slot['name']} = {value}") + inner_values = ',\n '.join(inner) + outer.append(f"{group_name} = list(\n {inner_values}\n )") + outer_values = ',\n '.join(outer) + return strip_margin( + f'''\ + |cat("Write {arg["key"]} AnnData to file\\n") + |{arg["key"]} <- anndata::AnnData( + | {outer_values} + |) + |{arg["key"]}$write_h5ad(par[["{arg["key"]}"]], compression = "gzip")''' + ) + +def create_python_script(par, config, type): + args = config['functionality']['arguments'] + + # create the arguments of the par string par_string = ",\n ".join(f"'{arg['key']}': '{arg['value']}'" for arg in args) + + # create code for reading the input h5ad file read_h5ad_string = "\n".join( f"{arg['key']} = ad.read_h5ad(par['{arg['key']}'])" for arg in args @@ -177,26 +242,26 @@ def create_python_script(par, api_spec, type): and arg['direction'] == "input" ) + # determine which adata to copy from + copy_from_adata = look_for_adata_arg(args, "method_id" if type == "metric" else "dataset_id") + + # create code for writing the output h5ad files + write_h5ad_string = "\n".join( + write_output_python(arg, copy_from_adata, type == "metric") + for arg in args + if arg["type"] == "file" + and arg["direction"] == "output" + ) + if type == 'metric': - output_string = strip_margin(f'''\ + processing_string = strip_margin(f'''\ |print('Compute metrics', flush=True) |# metric_ids and metric_values can have length > 1 |# but should be of equal length - |metric_ids = [ '{par['name']}' ] - |metric_values = [ 0.5 ] - | - |print('Create output anndata', flush=True) - |out = ad.AnnData( - | uns={{ - | 'dataset_id': adata.uns['dataset_id'], - | 'method_id': adata.uns['method_id'], - | 'metric_ids': metric_ids, - | 'metric_values': metric_values, - | }}, - |)''') + |uns_metric_ids = [ '{par['name']}' ] + |uns_metric_values = [ 0.5 ]''') else: - # TODO: fix output slots - output_string = strip_margin('''\ + processing_string = strip_margin(f'''\ |print('Preprocess data', flush=True) |# ... preprocessing ... | @@ -204,16 +269,7 @@ def create_python_script(par, api_spec, type): |# ... train model ... | |print('Generate predictions', flush=True) - |# ... generate predictions ... - | - |print('Create output anndata', flush=True) - |out = ad.AnnData( - | X=y_pred, - | uns={ - | 'dataset_id': adata.uns['dataset_id'], - | 'method_id': meta['functionality_name'], - | }, - |)''') + |# ... generate predictions ...''') script = strip_margin(f'''\ |import anndata as ad @@ -230,18 +286,20 @@ def create_python_script(par, api_spec, type): |print('Reading input files', flush=True) |{read_h5ad_string} | - |{output_string} + |{processing_string} | - |print('Write output to file', flush=True) - |out.write_h5ad(par['output'], compress='gzip') + |{write_h5ad_string} |''') return script - def create_r_script(par, api_spec, type): args = api_spec['functionality']['arguments'] + + # create the arguments of the par string par_string = ",\n ".join(f'{arg["key"]} = "{arg["value"]}"' for arg in args) + + # create helpers for reading the h5ad file read_h5ad_string = "\n".join( f'{arg["key"]} <- anndata::read_h5ad(par[["{arg["key"]}"]])' for arg in args @@ -249,26 +307,26 @@ def create_r_script(par, api_spec, type): and arg['direction'] == "input" ) + # determine which adata to copy from + copy_from_adata = look_for_adata_arg(args, "method_id" if type == "metric" else "dataset_id") + + # create code for writing the output h5ad files + write_h5ad_string = "\n".join( + write_output_r(arg, copy_from_adata, type == "metric") + for arg in args + if arg["type"] == "file" + and arg["direction"] == "output" + ) + if type == 'metric': - output_string = strip_margin(f'''\ + processing_string = strip_margin(f'''\ |cat("Compute metrics\\n") |# metric_ids and metric_values can have length > 1 |# but should be of equal length - |metric_ids <- c( "{par['name']}" ) - |metric_values <- c( 0.5 ) - | - |cat("Create output anndata\\n") - |out <- anndata::AnnData( - | uns = list( - | dataset_id = adata$uns[["dataset_id"]], - | method_id = adata$uns[["method_id"]], - | metric_ids = metric_ids, - | metric_values = metric_values, - | ) - |)''') + |uns_metric_ids <- c("{par['name']}") + |uns_metric_values <- c(0.5)''') else: - # TODO: fix output slots - output_string = strip_margin('''\ + processing_string = strip_margin(f'''\ |cat("Preprocess data\\n") |# ... preprocessing ... | @@ -276,16 +334,7 @@ def create_r_script(par, api_spec, type): |# ... train model ... | |cat("Generate predictions\\n") - |# ... generate predictions ... - | - |cat("Create output anndata\\n") - |out <- anndata::AnnData( - | X = y_pred, - | uns = list( - | dataset_id = adata$uns[["dataset_id"]], - | method_id = meta[["functionality_name"]], - | ) - |)''') + |# ... generate predictions ...''') script = strip_margin(f'''\ |library(anndata) @@ -302,14 +351,25 @@ def create_r_script(par, api_spec, type): |cat("Reading input files\\n") |{read_h5ad_string} | - |{output_string} + |{processing_string} | - |cat("Write output to file\\n") - |out$write_h5ad(par[["output"]], compress = "gzip") + |{write_h5ad_string} |''') return script +def read_viash_config(file): + # read in config + command = ["viash", "config", "view", str(file)] + + # Execute the command and capture the output + output = subprocess.check_output(command, universal_newlines=True) + + # Parse the output as YAML + config = yaml.load(output) + + return config + def main(par): ####### CHECK INPUTS ####### @@ -318,11 +378,16 @@ def main(par): pretty_name = re.sub("_", " ", par['name']).title() - api_spec = read_api_spec(par) + ####### CREATE OUTPUT DIR ####### + out_dir = Path(par["output"]) + out_dir.mkdir(exist_ok=True) ####### CREATE CONFIG ####### - config_template = create_config_template(par) + config_file = out_dir / 'config.vsh.yaml' + # get config template + config_template = create_config_template(par) + # Add component specific info if par['type'] == 'metric': add_metric_info(config_template, par, pretty_name) @@ -339,26 +404,31 @@ def main(par): if par['language'] == 'r': add_r_setup(config_template) + with open(config_file, 'w') as f: + yaml.dump(config_template, f) + ####### CREATE SCRIPT ####### - set_par_values(api_spec) + script_file = out_dir / config_template['functionality']['resources'][0]['path'] - if par['language'] == 'python': - script_out = create_python_script(par, api_spec, par['type']) + # touch file + script_file.touch() - if par['language'] == 'r': - script_out = create_r_script(par, api_spec, par['type']) + # read config with viash + final_config = read_viash_config(config_file) - ####### WRITE OUTPUTS ####### - out_dir = Path(par["output"]) - out_dir.mkdir(exist_ok=True) - - with open(f'{out_dir}/config.vsh.yaml', 'w') as f: - YAML().dump(config_template, f) + # set reasonable values + set_par_values(final_config) - script_name = config_template['functionality']['resources'][0]['path'] + if par['language'] == 'python': + script_out = create_python_script(par, final_config, par['type']) - with open(f'{out_dir}/{script_name}', 'w') as f: + if par['language'] == 'r': + script_out = create_r_script(par, final_config, par['type']) + + # write script + with open(script_file, 'w') as f: f.write(script_out) + if __name__ == "__main__": main(par) \ No newline at end of file diff --git a/src/common/create_skeleton/test.py b/src/common/create_skeleton/test.py index 7825388392..39c6a34e59 100644 --- a/src/common/create_skeleton/test.py +++ b/src/common/create_skeleton/test.py @@ -2,31 +2,27 @@ from os import path from ruamel.yaml import YAML - ## VIASH START - meta = { 'executable': 'foo' } - ## VIASH END -src_path = meta["resources_dir"] + "/openproblems-v2/src" -output_path= 'test_method' - +api_file = meta["resources_dir"] + "/openproblems-v2/src/label_projection/api/comp_method.yaml" +output_path = 'method_py' cmd = [ meta['executable'], - '--src', src_path, '--task', 'label_projection', - '--comp_type', 'method', + '--type', 'method', '--name', 'test_method', '--language', 'python', '--output', output_path, + '--api_file', api_file ] print('>> Running the script as test', flush=True) -out= subprocess.run(cmd, check=True) +out = subprocess.run(cmd, check=True) print('>> Checking whether output files exist', flush=True) assert path.exists(output_path) @@ -42,11 +38,9 @@ assert conf_data['functionality']['name'] == 'test_method' assert conf_data['functionality']['namespace'] == 'label_projection/methods' -assert conf_data['functionality']['info']['type'] == 'method' - assert conf_data['platforms'][0]['image'] == 'python:3.10' -print('all checks succeeded!', flush=True) +print('All checks succeeded!', flush=True) From 70d256cba59f97e9cba91553e6c275708fb48acc Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 16 Mar 2023 23:13:27 +0100 Subject: [PATCH 0769/1233] update skeleton component Former-commit-id: 1196404f98bcee95bb328a1a823a304eed0d9fea --- src/common/create_skeleton/config.vsh.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_skeleton/config.vsh.yaml index e395b00542..9f6d672f8d 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_skeleton/config.vsh.yaml @@ -1,3 +1,4 @@ +# TODO: project config is no longer mounted functionality: name: create_skeleton namespace: common @@ -51,10 +52,13 @@ functionality: - path: ../../../src dest: openproblems-v2/src platforms: - - type: native - type: docker image: python:3.10-slim setup: + - type: apt + packages: [ curl, default-jre, unzip ] + - type: docker + run: [ cd /usr/bin && curl -fsSL dl.viash.io | bash ] - type: python pip: ruamel.yaml - type: nextflow From c33e9c1e40cce9fc5d87168aad0078bccbdc86b6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 17 Mar 2023 11:36:33 +0100 Subject: [PATCH 0770/1233] move info type Former-commit-id: 320af128c0dae70927ec334bf87935f9d761a64a --- src/batch_integration/api/comp_method_embedding.yaml | 1 + src/batch_integration/api/comp_method_feature.yaml | 1 + src/batch_integration/api/comp_method_graph.yaml | 1 + src/batch_integration/api/comp_metric_embedding.yaml | 2 ++ src/batch_integration/api/comp_metric_feature.yaml | 2 ++ src/batch_integration/api/comp_metric_graph.yaml | 2 ++ src/batch_integration/api/comp_split_dataset.yaml | 2 ++ src/batch_integration/methods/bbknn/config.vsh.yaml | 1 - src/batch_integration/methods/combat/config.vsh.yaml | 1 - src/batch_integration/methods/scanorama_embed/config.vsh.yaml | 1 - src/batch_integration/methods/scanorama_feature/config.vsh.yaml | 1 - src/batch_integration/methods/scvi/config.vsh.yaml | 1 - src/batch_integration/metrics/asw_batch/config.vsh.yaml | 1 - src/batch_integration/metrics/asw_label/config.vsh.yaml | 1 - .../metrics/cell_cycle_conservation/config.vsh.yaml | 1 - .../metrics/clustering_overlap/config.vsh.yaml | 1 - src/batch_integration/metrics/pcr/config.vsh.yaml | 1 - 17 files changed, 11 insertions(+), 10 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 4e385122a0..407076933c 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -1,5 +1,6 @@ functionality: info: + type: method output_type: embedding arguments: - name: --input diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 4188529036..068e31dd81 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -1,6 +1,7 @@ functionality: namespace: batch_integration/methods_feature info: + type: method output_type: feature arguments: - __merge__: anndata_unintegrated.yaml diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index ea3f85b766..d085a3c8f5 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -1,6 +1,7 @@ functionality: namespace: batch_integration/graph/methods info: + type: method output_type: graph arguments: - __merge__: anndata_unintegrated.yaml diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index daa40e8f62..17bfcb06b4 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: --input_integrated __merge__: anndata_integrated_embedding.yaml diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index df482c9ffc..4bc6ce612b 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: --input_integrated __merge__: anndata_integrated_feature.yaml diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 5cf44a2d23..5d20facb35 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: metric arguments: - name: --input_integrated __merge__: anndata_integrated_graph.yaml diff --git a/src/batch_integration/api/comp_split_dataset.yaml b/src/batch_integration/api/comp_split_dataset.yaml index d96e954278..2471f70dc3 100644 --- a/src/batch_integration/api/comp_split_dataset.yaml +++ b/src/batch_integration/api/comp_split_dataset.yaml @@ -1,4 +1,6 @@ functionality: + info: + type: split_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/batch_integration/methods/bbknn/config.vsh.yaml b/src/batch_integration/methods/bbknn/config.vsh.yaml index 68b600e6e1..81ace76079 100644 --- a/src/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods/bbknn/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/methods_graph description: "BBKNN: fast batch alignment of single cell transcriptomes" info: - type: method method_name: BBKNN paper_reference: "polanski2020bbknn" code_url: https://github.com/Teichlab/bbknn diff --git a/src/batch_integration/methods/combat/config.vsh.yaml b/src/batch_integration/methods/combat/config.vsh.yaml index d284cb1054..7929fb3a54 100644 --- a/src/batch_integration/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods/combat/config.vsh.yaml @@ -6,7 +6,6 @@ functionality: description: "Adjusting batch effects in microarray expression data using empirical Bayes methods" info: - type: method method_name: Combat paper_reference: "hansen2012removing" code_url: https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml index c4b7d53fd5..f7095762e3 100644 --- a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -6,7 +6,6 @@ functionality: description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: - type: method method_name: Scanorama paper_reference: "hie2019efficient" code_url: https://github.com/brianhie/scanorama diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index fb884a8b4c..44576e854a 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -6,7 +6,6 @@ functionality: description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: - type: method method_name: Scanorama paper_reference: "hie2019efficient" code_url: https://github.com/brianhie/scanorama diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index 18e51569e6..a5065846e9 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/methods_graph description: Run scVI on adata object, use feature output info: - type: method method_name: scVI paper_reference: "lopez2018deep" code_url: https://github.com/YosefLab/scvi-tools" diff --git a/src/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/asw_batch/config.vsh.yaml index 336242e3ed..bf791ae2d7 100644 --- a/src/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/metrics_embedding description: Average silhouette of batches per label info: - type: metric v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf paper_reference: luecken2022benchmarking diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml index 84586e17ce..8b1cb954fa 100644 --- a/src/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_label/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/metrics_embedding description: Average silhouette of labels info: - type: metric v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf paper_reference: luecken2022benchmarking diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 7531ea7db4..886bf1c2bd 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/metrics_embedding description: Cell cycle conservation score based on cell cycle gene scoring info: - type: metric v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf paper_reference: luecken2022benchmarking diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 05d6d395a9..d1c5f5bc95 100644 --- a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/metrics_graph description: Metrics that are based on computing the clustering overlap. info: - type: metric metrics: - metric_id: ari metric_name: ARI diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml index 6a1f927d83..394fc40497 100644 --- a/src/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics/pcr/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: namespace: batch_integration/metrics_embedding description: PCA regression info: - type: metric v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf paper_reference: luecken2022benchmarking From 590a27386188cc122680a0f436bf029f91f307f0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:07:44 +0100 Subject: [PATCH 0771/1233] Fix organism in the API Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: 3f582c56affaf9acb2b236769c34718ceed30c8e --- src/batch_integration/api/anndata_dataset.yaml | 4 ++-- src/batch_integration/api/anndata_unintegrated.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/batch_integration/api/anndata_dataset.yaml b/src/batch_integration/api/anndata_dataset.yaml index 5d94736f7f..c17b2b15e3 100644 --- a/src/batch_integration/api/anndata_dataset.yaml +++ b/src/batch_integration/api/anndata_dataset.yaml @@ -74,6 +74,6 @@ info: name: knn description: Neighbors data. - type: string - name: organism - description: "Which normalization was used" + name: dataset_organism + description: The organism of the sample in the dataset. required: true diff --git a/src/batch_integration/api/anndata_unintegrated.yaml b/src/batch_integration/api/anndata_unintegrated.yaml index aead1cdcad..68f7bfba1e 100644 --- a/src/batch_integration/api/anndata_unintegrated.yaml +++ b/src/batch_integration/api/anndata_unintegrated.yaml @@ -47,6 +47,6 @@ info: description: "Which normalization was used" required: true - type: string - name: organism + name: dataset_organism description: "Which normalization was used" required: true From 6ea9bdd9a42835897124e8b2488ff45fa6ca54bd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:07:52 +0100 Subject: [PATCH 0772/1233] Update description Former-commit-id: f04528a830ccb87e76400d7a4fd55601dddd5881 --- src/datasets/api/anndata_raw.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/api/anndata_raw.yaml b/src/datasets/api/anndata_raw.yaml index 6320921cce..d22d350564 100644 --- a/src/datasets/api/anndata_raw.yaml +++ b/src/datasets/api/anndata_raw.yaml @@ -49,5 +49,5 @@ info: required: true - name: dataset_organism type: string - description: The organism of the dataset. + description: The organism of the sample in the dataset. required: false From 81dad64a072c2e81db322a2484a71d0b4f1527ab Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:08:08 +0100 Subject: [PATCH 0773/1233] Organism is now in the anndata instead of a parameter Former-commit-id: c7878e985719e36659c1d203cdd633ab139cce03 --- .../metrics/cell_cycle_conservation/config.vsh.yaml | 10 +++++----- .../metrics/cell_cycle_conservation/script.py | 5 ++--- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 886bf1c2bd..0e824df4eb 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -14,11 +14,11 @@ functionality: min: 0 max: 1 maximize: true - arguments: - - name: --organism - type: string - description: Name of organism to compute cell cycle scores on - required: true + # arguments: + # - name: --organism + # type: string + # description: Name of organism to compute cell cycle scores on + # required: true resources: - type: python_script path: script.py diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py index bfb978fbe7..93c93d2368 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics/cell_cycle_conservation/script.py @@ -4,8 +4,7 @@ ## VIASH START par = { 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', - 'output': 'output.h5ad', - 'organism': 'human' + 'output': 'output.h5ad' } meta = { @@ -26,7 +25,7 @@ adata_int, batch_key='batch', embed='X_emb', - organism=par['organism'] + organism=adata.uns['dataset_organism'] ) print('Create output AnnData object', flush=True) From 66ebb9bcc4120be77b2d619354c2b65188a94cac Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:08:15 +0100 Subject: [PATCH 0774/1233] Update resource test script Former-commit-id: 277b86d1a9f06a6a3088c673adb9f690d6e45002 --- .../resources_test_scripts/pancreas.sh | 30 ++++++++----------- 1 file changed, 13 insertions(+), 17 deletions(-) diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index a19189d3e2..3961f5660a 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -20,27 +20,23 @@ mkdir -p $DATASET_DIR echo process data... viash run src/batch_integration/split_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ - --output_unintegrated $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output_solution $DATASET_DIR/pancreas/solution.h5ad \ + --output $DATASET_DIR/unintegrated.h5ad \ --hvgs 100 -# run methods -echo run methods... +echo Running BBKNN +viash run src/batch_integration/methods/bbknn/config.vsh.yaml -- \ + --input $DATASET_DIR/unintegrated.h5ad \ + --output $DATASET_DIR/bbknn.h5ad -# Graph methods -viash run src/batch_integration/methods_graph/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/graph/bbknn.h5ad +echo Running SCVI +viash run src/batch_integration/methods/scvi/config.vsh.yaml -- \ + --input $DATASET_DIR/unintegrated.h5ad \ + --output $DATASET_DIR/scvi.h5ad -# Embedding method -viash run src/batch_integration/methods_embedding/scvi/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/embedding/scvi.h5ad - -# feature method -viash run src/batch_integration/methods_feature/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/unintegrated.h5ad \ - --output $DATASET_DIR/feature/combat.h5ad +echo Running combat +viash run src/batch_integration/methods/combat/config.vsh.yaml -- \ + --input $DATASET_DIR/unintegrated.h5ad \ + --output $DATASET_DIR/combat.h5ad # run one metric echo run metrics... From 4c5922cbd4e0e62dccd3ea47a2fa40269ba189e4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:13:28 +0100 Subject: [PATCH 0775/1233] Refactor test resource paths Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: abb37088da41eee8c6ab942f23ea6ef0e127a8b9 --- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 2 +- src/batch_integration/api/comp_metric_feature.yaml | 2 +- src/batch_integration/api/comp_metric_graph.yaml | 2 +- src/batch_integration/methods/bbknn/script.py | 2 +- src/batch_integration/methods/combat/script.py | 2 +- src/batch_integration/methods/scanorama_embed/script.py | 2 +- src/batch_integration/methods/scanorama_feature/script.py | 2 +- src/batch_integration/methods/scvi/script.py | 2 +- src/batch_integration/metrics/asw_batch/script.py | 2 +- src/batch_integration/metrics/asw_label/script.py | 2 +- src/batch_integration/metrics/cell_cycle_conservation/script.py | 2 +- src/batch_integration/metrics/clustering_overlap/script.py | 2 +- src/batch_integration/metrics/pcr/script.py | 2 +- src/batch_integration/transformers/embed_to_graph/script.py | 2 +- src/batch_integration/transformers/feature_to_embed/script.py | 2 +- 18 files changed, 18 insertions(+), 18 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 407076933c..bdbeb4b9d6 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -24,7 +24,7 @@ functionality: import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" output_path = "embeddding.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 068e31dd81..ceca84748c 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -23,7 +23,7 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" output_path = "integrated.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index d085a3c8f5..35d6b050e2 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -23,7 +23,7 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/pancreas/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" output_path = "inegrated.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 17bfcb06b4..06bc0ecb12 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -32,7 +32,7 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - input_file = f"{meta['resources_dir']}/batch_integration/embedding/scvi.h5ad" + input_file = f"{meta['resources_dir']}/batch_integration/scvi.h5ad" output_file = "output.h5ad" cmd_args = [ diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 4bc6ce612b..3c28615fe0 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -32,7 +32,7 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - input_file = f"{meta['resources_dir']}/batch_integration/feature/combat.h5ad" + input_file = f"{meta['resources_dir']}/batch_integration/combat.h5ad" output_file = "output.h5ad" cmd_args = [ diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 5d20facb35..8628609698 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -34,7 +34,7 @@ functionality: output_type = config["functionality"].get("info", {}).get("output_type") - input_file = f"{meta['resources_dir']}/batch_integration/graph/bbknn.h5ad" + input_file = f"{meta['resources_dir']}/batch_integration/bbknn.h5ad" output_file = "output.h5ad" cmd_args = [ diff --git a/src/batch_integration/methods/bbknn/script.py b/src/batch_integration/methods/bbknn/script.py index 137b9228f1..25941fb14a 100644 --- a/src/batch_integration/methods/bbknn/script.py +++ b/src/batch_integration/methods/bbknn/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/combat/script.py b/src/batch_integration/methods/combat/script.py index 0277493dcf..1d0179b322 100644 --- a/src/batch_integration/methods/combat/script.py +++ b/src/batch_integration/methods/combat/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True } diff --git a/src/batch_integration/methods/scanorama_embed/script.py b/src/batch_integration/methods/scanorama_embed/script.py index 0bb0529fa2..75e83e5da2 100644 --- a/src/batch_integration/methods/scanorama_embed/script.py +++ b/src/batch_integration/methods/scanorama_embed/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/scanorama_feature/script.py b/src/batch_integration/methods/scanorama_feature/script.py index ba3433b8c3..904972e6d1 100644 --- a/src/batch_integration/methods/scanorama_feature/script.py +++ b/src/batch_integration/methods/scanorama_feature/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/scvi/script.py b/src/batch_integration/methods/scvi/script.py index f768c036e0..9f0a5c2b71 100644 --- a/src/batch_integration/methods/scvi/script.py +++ b/src/batch_integration/methods/scvi/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py index ccf68e6fe8..537cd2a486 100644 --- a/src/batch_integration/metrics/asw_batch/script.py +++ b/src/batch_integration/metrics/asw_batch/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/batch_integration/metrics/asw_label/script.py b/src/batch_integration/metrics/asw_label/script.py index 88b450bca3..49261bbdbe 100644 --- a/src/batch_integration/metrics/asw_label/script.py +++ b/src/batch_integration/metrics/asw_label/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py index 93c93d2368..b773f9abf8 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics/cell_cycle_conservation/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', 'output': 'output.h5ad' } diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py index ff0218865b..e050b56aff 100644 --- a/src/batch_integration/metrics/clustering_overlap/script.py +++ b/src/batch_integration/metrics/clustering_overlap/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/graph/bbknn.h5ad', + 'input_integrated': 'resources_test/batch_integration/bbknn.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/metrics/pcr/script.py b/src/batch_integration/metrics/pcr/script.py index e8ca5ce074..17efe452c1 100644 --- a/src/batch_integration/metrics/pcr/script.py +++ b/src/batch_integration/metrics/pcr/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/transformers/embed_to_graph/script.py b/src/batch_integration/transformers/embed_to_graph/script.py index c4878aa1a8..b859bf58f6 100644 --- a/src/batch_integration/transformers/embed_to_graph/script.py +++ b/src/batch_integration/transformers/embed_to_graph/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/embedding/scvi.h5ad', + 'input': 'resources_test/batch_integration/scvi.h5ad', 'ouput': 'output.h5ad' } diff --git a/src/batch_integration/transformers/feature_to_embed/script.py b/src/batch_integration/transformers/feature_to_embed/script.py index 031a015b46..71f80a30a6 100644 --- a/src/batch_integration/transformers/feature_to_embed/script.py +++ b/src/batch_integration/transformers/feature_to_embed/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/feature/integrated.h5ad', + 'input': 'resources_test/batch_integration/combat.h5ad', 'ouput': 'output.h5ad' } From 87856aa06f82f603afd2a99aa5160499a0362e49 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:23:01 +0100 Subject: [PATCH 0776/1233] fix namespaces Former-commit-id: a3d14f3f3bdcfa0d37d9f2d7ca4d94ebcfbf455f --- .../api/comp_method_embedding.yaml | 1 + src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/methods/bbknn/config.vsh.yaml | 1 - .../methods/combat/config.vsh.yaml | 1 - .../methods/scanorama_embed/config.vsh.yaml | 1 - .../methods/scanorama_feature/config.vsh.yaml | 1 - src/batch_integration/methods/scvi/config.vsh.yaml | 13 +++++++------ 8 files changed, 10 insertions(+), 12 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index bdbeb4b9d6..259abd327e 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -1,4 +1,5 @@ functionality: + namespace: batch_integration/methods info: type: method output_type: embedding diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index ceca84748c..16c57e89ce 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -1,5 +1,5 @@ functionality: - namespace: batch_integration/methods_feature + namespace: batch_integration/methods info: type: method output_type: feature diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 35d6b050e2..3ca44735ad 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -1,5 +1,5 @@ functionality: - namespace: batch_integration/graph/methods + namespace: batch_integration/methods info: type: method output_type: graph diff --git a/src/batch_integration/methods/bbknn/config.vsh.yaml b/src/batch_integration/methods/bbknn/config.vsh.yaml index 81ace76079..929a476f5b 100644 --- a/src/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods/bbknn/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_method_graph.yaml functionality: name: bbknn - namespace: batch_integration/methods_graph description: "BBKNN: fast batch alignment of single cell transcriptomes" info: method_name: BBKNN diff --git a/src/batch_integration/methods/combat/config.vsh.yaml b/src/batch_integration/methods/combat/config.vsh.yaml index 7929fb3a54..85587eb0a0 100644 --- a/src/batch_integration/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods/combat/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: combat - namespace: batch_integration/methods_feature description: "Adjusting batch effects in microarray expression data using empirical Bayes methods" info: diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml index f7095762e3..436d374606 100644 --- a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scanorama_embed - namespace: batch_integration/methods_embedding description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index 44576e854a..05342d3013 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: scanorama_feature - namespace: batch_integration/methods_feature description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index a5065846e9..57b41f14a8 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -2,8 +2,7 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scvi - namespace: batch_integration/methods_graph - description: Run scVI on adata object, use feature output + description: Run scVI on adata object info: method_name: scVI paper_reference: "lopez2018deep" @@ -22,8 +21,10 @@ platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - - type: python - pypi: - - scvi-tools - - pyyaml + # - type: python + # pypi: + # - scvi-tools<0.20 + # - pyyaml + - type: docker + run: micromamba install -c conda-forge "scvi-tools<0.20" "pyyaml" - type: nextflow From 0240b8b45202ecc72874a77dacd3349150745e4f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:24:33 +0100 Subject: [PATCH 0777/1233] update metrics namespaces Former-commit-id: 6a99b7f6f72bda95a5b50dc12046d678dda07684 --- src/batch_integration/api/comp_metric_embedding.yaml | 1 + src/batch_integration/api/comp_metric_feature.yaml | 1 + src/batch_integration/api/comp_metric_graph.yaml | 1 + src/batch_integration/metrics/asw_batch/config.vsh.yaml | 1 - src/batch_integration/metrics/asw_label/config.vsh.yaml | 1 - .../metrics/cell_cycle_conservation/config.vsh.yaml | 1 - src/batch_integration/metrics/clustering_overlap/config.vsh.yaml | 1 - src/batch_integration/metrics/pcr/config.vsh.yaml | 1 - 8 files changed, 3 insertions(+), 5 deletions(-) diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 06bc0ecb12..9cc80499fc 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -1,4 +1,5 @@ functionality: + namespace: batch_integration/metrics info: type: metric arguments: diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 3c28615fe0..430c838c19 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -1,4 +1,5 @@ functionality: + namespace: batch_integration/metrics info: type: metric arguments: diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 8628609698..3102a0cba7 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -1,4 +1,5 @@ functionality: + namespace: batch_integration/metrics info: type: metric arguments: diff --git a/src/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/asw_batch/config.vsh.yaml index bf791ae2d7..6146e5c5ff 100644 --- a/src/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_batch - namespace: batch_integration/metrics_embedding description: Average silhouette of batches per label info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml index 8b1cb954fa..e3cb81e31a 100644 --- a/src/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_label/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_label - namespace: batch_integration/metrics_embedding description: Average silhouette of labels info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 0e824df4eb..a06057bd08 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: cell_cycle_conservation - namespace: batch_integration/metrics_embedding description: Cell cycle conservation score based on cell cycle gene scoring info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml index d1c5f5bc95..e04c20af26 100644 --- a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric_graph.yaml functionality: name: clustering_overlap - namespace: batch_integration/metrics_graph description: Metrics that are based on computing the clustering overlap. info: metrics: diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml index 394fc40497..e591589d69 100644 --- a/src/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics/pcr/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: pcr - namespace: batch_integration/metrics_embedding description: PCA regression info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py From a3e845b256a41c3ceac154e15e728ee01a7ee0fd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 13:44:22 +0100 Subject: [PATCH 0778/1233] change BI test resource location Former-commit-id: 1d48a47211e730eb0570b1451ba3c160998baa90 --- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 4 ++-- src/batch_integration/api/comp_metric_feature.yaml | 4 ++-- src/batch_integration/api/comp_metric_graph.yaml | 4 ++-- src/batch_integration/methods/bbknn/script.py | 2 +- src/batch_integration/methods/combat/script.py | 2 +- .../methods/scanorama_embed/script.py | 2 +- .../methods/scanorama_feature/script.py | 2 +- src/batch_integration/methods/scvi/config.vsh.yaml | 11 +++++------ src/batch_integration/methods/scvi/script.py | 2 +- src/batch_integration/metrics/asw_batch/script.py | 2 +- src/batch_integration/metrics/asw_label/script.py | 2 +- .../metrics/cell_cycle_conservation/script.py | 2 +- .../metrics/clustering_overlap/script.py | 2 +- src/batch_integration/metrics/pcr/script.py | 2 +- .../resources_test_scripts/pancreas.sh | 2 +- .../transformers/embed_to_graph/script.py | 2 +- .../transformers/feature_to_embed/script.py | 2 +- 20 files changed, 27 insertions(+), 28 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 259abd327e..e868bb724f 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -15,7 +15,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/ + - path: ../../../../resources_test/batch_integration/pancreas/ - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 16c57e89ce..d6c1ee0597 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -15,7 +15,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/ + - path: ../../../../resources_test/batch_integration/pancreas/ - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 3ca44735ad..9a66bdb296 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -15,7 +15,7 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/ + - path: ../../../../resources_test/batch_integration/pancreas/ - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 9cc80499fc..53b86a2a60 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -9,7 +9,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration/pancreas - type: python_script dest: test.py text: | @@ -22,7 +22,7 @@ functionality: ## VIASH START meta = { - "resources_dir": "resources_test/batch_integration", + "resources_dir": "resources_test/batch_integration/pancreas", "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" } ## VIASH END diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 430c838c19..4ca591a05c 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -9,7 +9,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration/pancreas - type: python_script dest: test.py text: | @@ -22,7 +22,7 @@ functionality: ## VIASH START meta = { - "resources_dir": "resources_test/batch_integration", + "resources_dir": "resources_test/batch_integration/pancreas", "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" } ## VIASH END diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 3102a0cba7..9c97df45c1 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -9,7 +9,7 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration + - path: ../../../../resources_test/batch_integration/pancreas - type: python_script dest: test.py text: | @@ -22,7 +22,7 @@ functionality: ## VIASH START meta = { - "resources_dir": "resources_test/batch_integration/graph/methods", + "resources_dir": "resources_test/batch_integration/pancreas/graph/methods", "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" } ## VIASH END diff --git a/src/batch_integration/methods/bbknn/script.py b/src/batch_integration/methods/bbknn/script.py index 25941fb14a..137b9228f1 100644 --- a/src/batch_integration/methods/bbknn/script.py +++ b/src/batch_integration/methods/bbknn/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/combat/script.py b/src/batch_integration/methods/combat/script.py index 1d0179b322..0277493dcf 100644 --- a/src/batch_integration/methods/combat/script.py +++ b/src/batch_integration/methods/combat/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True } diff --git a/src/batch_integration/methods/scanorama_embed/script.py b/src/batch_integration/methods/scanorama_embed/script.py index 75e83e5da2..0bb0529fa2 100644 --- a/src/batch_integration/methods/scanorama_embed/script.py +++ b/src/batch_integration/methods/scanorama_embed/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/scanorama_feature/script.py b/src/batch_integration/methods/scanorama_feature/script.py index 904972e6d1..ba3433b8c3 100644 --- a/src/batch_integration/methods/scanorama_feature/script.py +++ b/src/batch_integration/methods/scanorama_feature/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index 57b41f14a8..2e64f09012 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -21,10 +21,9 @@ platforms: - type: docker image: mumichae/scib-base:1.0.2 setup: - # - type: python - # pypi: - # - scvi-tools<0.20 - # - pyyaml - - type: docker - run: micromamba install -c conda-forge "scvi-tools<0.20" "pyyaml" + - type: python + pypi: + - scvi-tools + - pyyaml + - scib - type: nextflow diff --git a/src/batch_integration/methods/scvi/script.py b/src/batch_integration/methods/scvi/script.py index 9f0a5c2b71..f768c036e0 100644 --- a/src/batch_integration/methods/scvi/script.py +++ b/src/batch_integration/methods/scvi/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', 'hvg': True, } diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py index 537cd2a486..d723e1ccb7 100644 --- a/src/batch_integration/metrics/asw_batch/script.py +++ b/src/batch_integration/metrics/asw_batch/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/batch_integration/metrics/asw_label/script.py b/src/batch_integration/metrics/asw_label/script.py index 49261bbdbe..f534c0c79e 100644 --- a/src/batch_integration/metrics/asw_label/script.py +++ b/src/batch_integration/metrics/asw_label/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py index b773f9abf8..3f582936b2 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics/cell_cycle_conservation/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'output': 'output.h5ad' } diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py index e050b56aff..87f4d48b6b 100644 --- a/src/batch_integration/metrics/clustering_overlap/script.py +++ b/src/batch_integration/metrics/clustering_overlap/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/bbknn.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/bbknn.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/metrics/pcr/script.py b/src/batch_integration/metrics/pcr/script.py index 17efe452c1..6750c22349 100644 --- a/src/batch_integration/metrics/pcr/script.py +++ b/src/batch_integration/metrics/pcr/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'output': 'output.h5ad', } diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index 3961f5660a..fdebf31c31 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -7,7 +7,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/batch_integration +DATASET_DIR=resources_test/batch_integration/pancreas if [ ! -f $RAW_DATA ]; then echo "Error! Could not find raw data" diff --git a/src/batch_integration/transformers/embed_to_graph/script.py b/src/batch_integration/transformers/embed_to_graph/script.py index b859bf58f6..44fd1a93ce 100644 --- a/src/batch_integration/transformers/embed_to_graph/script.py +++ b/src/batch_integration/transformers/embed_to_graph/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/scvi.h5ad', + 'input': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'ouput': 'output.h5ad' } diff --git a/src/batch_integration/transformers/feature_to_embed/script.py b/src/batch_integration/transformers/feature_to_embed/script.py index 71f80a30a6..c883909e18 100644 --- a/src/batch_integration/transformers/feature_to_embed/script.py +++ b/src/batch_integration/transformers/feature_to_embed/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/combat.h5ad', + 'input': 'resources_test/batch_integration/pancreas/combat.h5ad', 'ouput': 'output.h5ad' } From 66bc6900d151f43cd638c5e9c6770c7541124f0f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 14:47:15 +0100 Subject: [PATCH 0779/1233] fix unit tests Former-commit-id: 691a5b0b863a7fac6ead53bb7af4c28225e54f8f --- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 2 +- src/batch_integration/api/comp_metric_feature.yaml | 2 +- src/batch_integration/api/comp_metric_graph.yaml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index e868bb724f..c61e76a370 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -25,7 +25,7 @@ functionality: import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" output_path = "embeddding.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index d6c1ee0597..e7a09eb631 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -23,7 +23,7 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" output_path = "integrated.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 9a66bdb296..0b28dcdb94 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -23,7 +23,7 @@ functionality: import subprocess import anndata as ad - input_path = meta["resources_dir"] + "/batch_integration/unintegrated.h5ad" + input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" output_path = "inegrated.h5ad" cmd = [ meta['executable'], diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 53b86a2a60..84a319515d 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -33,7 +33,7 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - input_file = f"{meta['resources_dir']}/batch_integration/scvi.h5ad" + input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" output_file = "output.h5ad" cmd_args = [ diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 4ca591a05c..910315f981 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -33,7 +33,7 @@ functionality: with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) - input_file = f"{meta['resources_dir']}/batch_integration/combat.h5ad" + input_file = f"{meta['resources_dir']}/pancreas/combat.h5ad" output_file = "output.h5ad" cmd_args = [ diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 9c97df45c1..47b5907fbf 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -35,7 +35,7 @@ functionality: output_type = config["functionality"].get("info", {}).get("output_type") - input_file = f"{meta['resources_dir']}/batch_integration/bbknn.h5ad" + input_file = f"{meta['resources_dir']}/pancreas/bbknn.h5ad" output_file = "output.h5ad" cmd_args = [ From 5fb5d594f5e5ce3958415316a71f3ef508c25e0a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 14:47:24 +0100 Subject: [PATCH 0780/1233] add translator for the organism Former-commit-id: b15584ba902e0ff1cb1feba96138642630b905f0 --- .../metrics/cell_cycle_conservation/script.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/batch_integration/metrics/cell_cycle_conservation/script.py index 3f582936b2..54df10fd9e 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/batch_integration/metrics/cell_cycle_conservation/script.py @@ -19,13 +19,18 @@ adata_int = adata.copy() +translator = { + "homo_sapiens": "human", + "mus_musculus": "mouse" +} + print('compute score', flush=True) score = cell_cycle( adata, adata_int, batch_key='batch', embed='X_emb', - organism=adata.uns['dataset_organism'] + organism=translator[adata.uns['dataset_organism']] ) print('Create output AnnData object', flush=True) From 313d38dc27cb1f8f51375a76afbe76ced0346f30 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 15:15:55 +0100 Subject: [PATCH 0781/1233] Update metadata Former-commit-id: 5a6fca276686ce6cc6641039eaa1a2dffba27a01 --- src/batch_integration/README.md | 8 +-- src/batch_integration/changes.md | 87 -------------------------------- 2 files changed, 2 insertions(+), 93 deletions(-) delete mode 100644 src/batch_integration/changes.md diff --git a/src/batch_integration/README.md b/src/batch_integration/README.md index 1693cf2231..56a4500c51 100644 --- a/src/batch_integration/README.md +++ b/src/batch_integration/README.md @@ -2,12 +2,8 @@ Batch (or data) integration methods integrate datasets across batches that arise from various biological (e.g., tissue, location, individual, species) and technical (e.g., ambient RNA, lab, protocol) sources. The goal of a batch integration method is to remove unwanted batch effects in the data, while retaining biologically-meaningful variation that can help us to detect cell identities, fit cellular trajectories, or understand patterns of gene or pathway activity. -Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have divided the batch integration task into three subtasks. These subtasks are: +Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have created separate component subtypes for each of the three method types: "graph", "embedding" and "feature". -* [Batch integration graphs](graph/), -* [Batch integration embeddings](embedding/), and -* [Batch integrated feature matrices](feature/) - -These subtasks collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. Information on the task API for datasets, methods, and metrics can be found in the individual subtask pages. +These subtypes collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. Metrics for this task either assess the removal of batch effects or assess the conservation of biological variation. This can be a helpful distinction when devising new metrics. This task, including the subtask structure, was taken from a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2), which is a useful reference for more background reading on this task and the above concepts. diff --git a/src/batch_integration/changes.md b/src/batch_integration/changes.md deleted file mode 100644 index 920b269318..0000000000 --- a/src/batch_integration/changes.md +++ /dev/null @@ -1,87 +0,0 @@ -# Batch integration changes - -Already done -* move imports to the top of the file -* remove pprint on debug -* wrote generic unit test for metrics -* merged NMI and ARI metric -* changed metric outputs to h5ad -* added .functionality.info.output_type to methods and metrics -* use anndata when scanpy is not needed -* Add 'flush=True' to all print statements -* write generic unit test for methods - -TODO: -* split up api for different output types -* add file specs -* Copy descriptions from openproblems v1 for methods and metrics -* add .functionality.info to methods and metrics -* Change `split_dataset` so it uses the normalization, hvg, pca from the given object rather than recompute. -* Change `split_dataset` to output two AnnData objects: unintegrated and solution? -* Create a normalization variant: - log_cpm -> log_cpm_batchscaled -* Rename knn_connectivities to connectivities in solution -* Simplify renaming fields in split_dataset, e.g. celltype -> label, knn_connectivities -> connectivities. - -## proposed batch integration structure - -* split_dataset - - input: common dataset - - output_unintegrated: for methods. important slots: - .layers["normalized"] - .obs["batch"] - .obs["label"]? (probably not) - .var["hvg"] - .obsm["X_pca"]? (probably not) - - output_solution: for metrics - .obs["batch"] - .obs["label"] - .obsp["knn_connectivities"] -- could be renamed to connectivities -* methods_graph - example: bbknn - output_slots: - .obsp["connectivities"] -* methods_embed - example: scanorama_embed - output_slots: - .obsm["X_emb"] -* methods_feature - example: scanorama_feature - output_slots: - .X -* converters - - feature_to_embed: runs PCA on .X - - embed_to_graph: runs sc.pp.neighbors on .obsm["X_emb"] -* metrics_graph -* metrics_embed -* metrics_feature - -New todos: - -- move methods and metrics to the correct folders (e.g. scanorama_embed to `methods_embed/scanorama_embed`) -- create API files for all of the above componenent types -- compare current components with v1, list the ones that are missing - -missing methods: - -- `control_methods`: add the baseline methods as control methods to all subtasks -- `fastmnn`: feature and embed method (convert to Rscript?) -- `harmony`: embed method (convert to Rscript?) -- `liger`: embed method (convert to Rscript?) -- `mnn`: feature method -- `scalex`: feature and embed method -- `scanvi`: embed method - -missing metrics: - -- `ari`: embedding, feature -- `graph_connectivity`: embedding, graph, feature -- `hvg_cons`: feature -- `isolabel_f1`: embedding, graph, feature -- `isolabel_sil`: embedding, feature -- `kBET`: embedding, feature -- `nmi`: embedding, feature -- `pcr`: feature -- `asw_batch`: feature -- `asw_label`: feature -- \ No newline at end of file From c55df0688490243863387cc311291a826512a323 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 15:24:09 +0100 Subject: [PATCH 0782/1233] remove deprecated component Former-commit-id: 4ea622803c4a387227bcb9b1e78137a4d0ad2ad7 --- src/common/dataset_loader/download/README.md | 9 -- .../dataset_loader/download/config.vsh.yaml | 88 ------------------- .../dataset_loader/download/datasets.tsv | 5 -- .../dataset_loader/download/run_example.sh | 6 -- src/common/dataset_loader/download/script.py | 76 ---------------- src/common/dataset_loader/download/test.py | 46 ---------- 6 files changed, 230 deletions(-) delete mode 100644 src/common/dataset_loader/download/README.md delete mode 100644 src/common/dataset_loader/download/config.vsh.yaml delete mode 100644 src/common/dataset_loader/download/datasets.tsv delete mode 100644 src/common/dataset_loader/download/run_example.sh delete mode 100644 src/common/dataset_loader/download/script.py delete mode 100644 src/common/dataset_loader/download/test.py diff --git a/src/common/dataset_loader/download/README.md b/src/common/dataset_loader/download/README.md deleted file mode 100644 index 7670fafd6e..0000000000 --- a/src/common/dataset_loader/download/README.md +++ /dev/null @@ -1,9 +0,0 @@ -# Universal Data Loader - -Download data from URL and ensure that matrices are stored as expected. - -## API -Downloaded datasets contain: - -* `adata.X`: raw counts -* `adata.layers['lognorm']`: log-normalized counts, only if available diff --git a/src/common/dataset_loader/download/config.vsh.yaml b/src/common/dataset_loader/download/config.vsh.yaml deleted file mode 100644 index 81921b031a..0000000000 --- a/src/common/dataset_loader/download/config.vsh.yaml +++ /dev/null @@ -1,88 +0,0 @@ -functionality: - name: "download" - status: deprecated - namespace: "common/dataset_loader" - version: "dev" - description: "Download a dataset." - authors: - - name: "Michaela Mueller" - roles: [ maintainer, author ] - props: { github: mumichae } - argument_groups: - - name: Inputs - arguments: - - name: "--url" - type: "string" - description: "URL of dataset" - required: true - - name: "--name" - type: "string" - example: "pbmc" - description: "Name of dataset" - required: true - - name: "--obs_celltype" - type: "string" - description: "Location of where to find the observation cell types." - - name: "--obs_batch" - type: "string" - description: "Location of where to find the observation batch IDs." - - name: "--obs_tissue" - type: "string" - description: "Location of where to find the observation tissue information." - - name: "--layer_counts" - type: "string" - description: "In which layer to find the counts matrix. Leave undefined to use `.X`." - example: counts - - name: Outputs - arguments: - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file of the cleaned dataset" - required: true - info: - slots: - layers: - - type: integer - name: $par_layer_counts_output - description: Raw counts - required: false - obs: - - type: string - name: celltype - description: Cell type labels - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: false - - name: "--layer_counts_output" - type: "string" - description: "Location of where to store the counts data. Leave undefined to store in `.X`, else it will be stored in `.layers[par['layer_counts_output']]`." - example: counts - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test.py -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scanpy - - "anndata>=0.8" - - type: nextflow diff --git a/src/common/dataset_loader/download/datasets.tsv b/src/common/dataset_loader/download/datasets.tsv deleted file mode 100644 index a9a4934684..0000000000 --- a/src/common/dataset_loader/download/datasets.tsv +++ /dev/null @@ -1,5 +0,0 @@ -processor name url obs_celltype obs_batch obs_tissue -anndata_loader pancreas https://ndownloader.figshare.com/files/24539828 celltype tech NA -anndata_loader immune_cells https://ndownloader.figshare.com/files/25717328 final_annotation batch tissue -anndata_loader pbmc https://ndownloader.figshare.com/files/24974582 NA NA NA -anndata_loader tenx_5k_pbmc https://ndownloader.figshare.com/files/25555739 NA NA NA diff --git a/src/common/dataset_loader/download/run_example.sh b/src/common/dataset_loader/download/run_example.sh deleted file mode 100644 index 6130cb3925..0000000000 --- a/src/common/dataset_loader/download/run_example.sh +++ /dev/null @@ -1,6 +0,0 @@ -bin/viash run src/common/dataset_loader/download/config.vsh.yaml -- \ - --output src/common/dataset_loader/download/resources/pancreas.h5ad \ - --url https://ndownloader.figshare.com/files/24539828 \ - --name pancreas \ - --obs_cell_type celltype \ - --obs_batch tech diff --git a/src/common/dataset_loader/download/script.py b/src/common/dataset_loader/download/script.py deleted file mode 100644 index 48e340f95f..0000000000 --- a/src/common/dataset_loader/download/script.py +++ /dev/null @@ -1,76 +0,0 @@ -print("Importing libraries") -import scanpy as sc -import tempfile -import os -import urllib - -_FAKE_HEADERS = [("User-Agent", "Mozilla/5.0")] - -## VIASH START -par = { - "url": "https://ndownloader.figshare.com/files/24539828", - "name": "pancreas", - "obs_celltype": "celltype", - "obs_batch": "tech", - "layer_counts": "counts", - "output": "test_data.h5ad", - "layer_counts_output": "counts" -} -## VIASH END - -with tempfile.TemporaryDirectory() as tempdir: - print("Downloading", par['url'], flush=True) - filepath = os.path.join(tempdir, "dataset.h5ad") - - with open(filepath, "wb") as filehandle: - opener = urllib.request.build_opener() - opener.addheaders = _FAKE_HEADERS - urllib.request.install_opener(opener) - with urllib.request.urlopen(par["url"]) as urlhandle: - filehandle.write(urlhandle.read()) - - print("Reading file") - adata = sc.read_h5ad(filepath) - -print("Setting .uns['dataset_id']") -adata.uns["dataset_id"] = par["name"] - -print("Setting .obs['celltype']") -if par["obs_celltype"]: - if par["obs_celltype"] in adata.obs: - adata.obs["celltype"] = adata.obs[par["obs_celltype"]] - else: - print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.") - -print("Setting .obs['batch']") -if par["obs_batch"]: - if par["obs_batch"] in adata.obs: - adata.obs["batch"] = adata.obs[par["obs_batch"]] - else: - print(f"Warning: key '{par['obs_batch']}' could not be found in adata.obs.") - -print("Setting .obs['tissue']") -if par["obs_tissue"]: - if par["obs_tissue"] in adata.obs: - adata.obs["tissue"] = adata.obs[par["obs_tissue"]] - else: - print(f"Warning: key '{par['obs_tissue']}' could not be found in adata.obs.") - -print("Remove cells or genes with 0 counts") -if par["layer_counts"] and par["layer_counts"] in adata.layers: - print(f" Temporarily copying .layers['{par['layer_counts']}'] to .X") - adata.X = adata.layers[par["layer_counts"]] - del adata.layers[par["layer_counts"]] - -print(" Removing empty genes") -sc.pp.filter_genes(adata, min_cells=1) -print(" Removing empty cells") -sc.pp.filter_cells(adata, min_counts=2) - -if par["layer_counts_output"]: - print(f" Copying .X back to .layers['{par['layer_counts_output']}']") - adata.layers[par["layer_counts_output"]] = adata.X - del adata.X - -print("Writing adata to file") -adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/common/dataset_loader/download/test.py b/src/common/dataset_loader/download/test.py deleted file mode 100644 index a52ca203cb..0000000000 --- a/src/common/dataset_loader/download/test.py +++ /dev/null @@ -1,46 +0,0 @@ -from os import path -import subprocess -import scanpy as sc - -name = "pancreas" -output = "dataset.h5ad" -url = "https://ndownloader.figshare.com/files/24539828" -obs_celltype = "celltype" -obs_batch = "tech" - -layer_counts_output = "foobar" - -print(">> Running script") -out = subprocess.check_output([ - meta["executable"], - "--url", url, - "--name", name, - "--obs_celltype", obs_celltype, - "--obs_batch", obs_batch, - "--layer_counts", "counts", - "--layer_counts_output", layer_counts_output, - "--output", output -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output) - -print(">> Read output anndata") -adata = sc.read_h5ad(output) - -print(adata) - -print(">> Check that output fits expected API") -if layer_counts_output is not None: - assert adata.X is None - assert layer_counts_output in adata.layers -else: - assert adata.X is not None - assert layer_counts_output not in adata.layers -assert adata.uns["dataset_id"] == name -if obs_celltype: - assert "celltype" in adata.obs.columns -if obs_batch: - assert "batch" in adata.obs.columns - -print(">> All tests passed successfully") From 11de142125ce1957c4cea8450112ce44c7a7fde1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 17 Mar 2023 15:49:31 +0100 Subject: [PATCH 0783/1233] Fix issue where normalization_id was not being copied from the upstream anndata. Former-commit-id: 02b97bcc59cd5ce70b79c8f7a72f1a79ed7d4ebc --- src/common/create_skeleton/script.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/create_skeleton/script.py b/src/common/create_skeleton/script.py index 16d74ce7d2..d5983d3a84 100644 --- a/src/common/create_skeleton/script.py +++ b/src/common/create_skeleton/script.py @@ -177,7 +177,7 @@ def write_output_python(arg, copy_from_adata, is_metric): for group_name, slots in slots.items(): inner = [] for slot in slots: - if group_name == "uns" and slot["name"] == "dataset_id": + if group_name == "uns" and slot["name"] in ["dataset_id", "normalization_id"]: value = f"{copy_from_adata}.uns['{slot['name']}']" elif group_name == "uns" and slot["name"] == "method_id": if is_metric: @@ -206,7 +206,7 @@ def write_output_r(arg, copy_from_adata, is_metric): for group_name, slots in slots.items(): inner = [] for slot in slots: - if group_name == "uns" and slot["name"] == "dataset_id": + if group_name == "uns" and slot["name"] in ["dataset_id", "normalization_id"]: value = f"{copy_from_adata}$uns[[\"{slot['name']}\"]]" elif group_name == "uns" and slot["name"] == "method_id": if is_metric: From c221554df575a36a95f592a62e6e26213378c021 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 17 Mar 2023 22:02:35 +0000 Subject: [PATCH 0784/1233] Bump tj-actions/changed-files from 35.5.0 to 35.7.2 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.5.0 to 35.7.2. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.5.0...v35.7.2) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: 12a7c98b79cc88604862826bdd74c7cad7437cfe --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index e8dd80c20d..1161f06690 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.5.0 + uses: tj-actions/changed-files@v35.7.2 with: separator: ";" diff_relative: true From 38b9de424597e9bbe4be7c684d5841f9808fef9a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 18 Mar 2023 19:56:50 +0100 Subject: [PATCH 0785/1233] Update src/batch_integration/api/anndata_integrated_feature.yaml Co-authored-by: Kai Waldrant Former-commit-id: 7432fba39ec14f0cbaa3da4127116add548932c4 --- src/batch_integration/api/anndata_integrated_feature.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index d02a5c780d..aea42f846f 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -4,7 +4,7 @@ description: Integrated AnnData HDF5 file. example: input.h5ad info: prediction_type: feature - short_description: "Integrated Graph" + short_description: "Integrated Feature" slots: layers: - type: double From 7961a33a7cb32e480e010278d3500e55708db659 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 21 Mar 2023 10:45:40 +0100 Subject: [PATCH 0786/1233] Apply suggestions from code review Co-authored-by: Kai Waldrant Former-commit-id: f565c88d7dc7638640c854529d3c021a4db3429e --- src/batch_integration/api/anndata_integrated_embedding.yaml | 6 +----- src/batch_integration/api/anndata_integrated_feature.yaml | 6 +----- src/batch_integration/api/anndata_integrated_graph.yaml | 6 +----- src/batch_integration/api/anndata_score.yaml | 6 +----- src/batch_integration/methods/scanorama_feature/script.py | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 5 ----- src/batch_integration/metrics/clustering_overlap/script.py | 3 --- 7 files changed, 5 insertions(+), 29 deletions(-) diff --git a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/batch_integration/api/anndata_integrated_embedding.yaml index 024cef7fad..9b9208c0fa 100644 --- a/src/batch_integration/api/anndata_integrated_embedding.yaml +++ b/src/batch_integration/api/anndata_integrated_embedding.yaml @@ -16,15 +16,11 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: string - name: parent_method_id - description: if anndata passed from a previous method - required: false - type: boolean name: hvg description: If the method was done on hvg or full required: true - type: string - name: output_id + name: output_type description: what kind of output has been generated required: true diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index aea42f846f..bfebdcd038 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -16,15 +16,11 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: string - name: parent_method_id - description: if anndata passed from a previous method - required: false - type: boolean name: hvg description: If the method was done on hvg or full required: true - type: string - name: output_id + name: output_type description: what kind of output has been generated required: true \ No newline at end of file diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml index 52a2632fe9..0f09941cee 100644 --- a/src/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -16,15 +16,11 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: string - name: parent_method_id - description: if anndata passed from a previous method - required: false - type: boolean name: hvg description: If the method was done on hvg or full required: true - type: string - name: output_id + name: output_type description: what kind of output has been generated required: true diff --git a/src/batch_integration/api/anndata_score.yaml b/src/batch_integration/api/anndata_score.yaml index 9c8518345f..116694ff51 100644 --- a/src/batch_integration/api/anndata_score.yaml +++ b/src/batch_integration/api/anndata_score.yaml @@ -27,15 +27,11 @@ info: description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." multiple: true required: true - - type: string - name: parent_method_id - description: previous method id if anndata is from a previous method - required: false - type: boolean name: hvg description: If the method was done on hvg or full required: true - type: string - name: output_id + name: output_type description: what kind of output has been generated required: true \ No newline at end of file diff --git a/src/batch_integration/methods/scanorama_feature/script.py b/src/batch_integration/methods/scanorama_feature/script.py index ba3433b8c3..85a743af8d 100644 --- a/src/batch_integration/methods/scanorama_feature/script.py +++ b/src/batch_integration/methods/scanorama_feature/script.py @@ -30,7 +30,7 @@ adata.X = adata.layers['normalized'] adata.layers['corrected_counts'] = scanorama(adata, batch='batch').X -del(adata.X) +del adata.X # ? Create new comp feature_to_graph? # print("Run PCA", flush=True) diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index a06057bd08..a3dea7593a 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -13,11 +13,6 @@ functionality: min: 0 max: 1 maximize: true - # arguments: - # - name: --organism - # type: string - # description: Name of organism to compute cell cycle scores on - # required: true resources: - type: python_script path: script.py diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py index 87f4d48b6b..bef625f893 100644 --- a/src/batch_integration/metrics/clustering_overlap/script.py +++ b/src/batch_integration/metrics/clustering_overlap/script.py @@ -45,8 +45,5 @@ } ) -if 'parent_method_id' in input.uns: - output.uns['parent_method_id'] = input.uns['parent_method_id'] - print("Write data to file", flush=True) output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file From 0fa6c9d55324cbb79d16659ebdecd638d363459c Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 14:46:14 +0100 Subject: [PATCH 0787/1233] update with requested changes Former-commit-id: dc2c1ee26ea0ab4b227b2d8a4e08d288936d8a1f --- .../check_dataset_schema/config.vsh.yaml | 9 ++++--- src/common/check_dataset_schema/script.py | 24 +++++++------------ 2 files changed, 13 insertions(+), 20 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index d71569d5cc..17b57dd475 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -19,23 +19,22 @@ functionality: type: boolean default: false description: Whether or not to stop with exit code 1 if the input file does not adhere to the schema. - - name: --copy_output - type: boolean_true - description: Wether a output needs to be created for further analysis. - name: Output arguments: - - name: --json + - name: --checks type: file required: false description: If specified, this file will contain a structured log of which checks succeeded (or not). + example: checks.json - name: --output type: file required: false description: If specified, the output file will be a copy of the input file. + example: output.h5ad resources: - type: python_script path: script.py -platform: +platforms: - type: docker image: python:3.10 setup: diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 44d72c5573..105d88c380 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -9,9 +9,8 @@ par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', 'schema': 'src/denoising/api/anndata_dataset.yaml', - 'stop_on_error': 'false', - 'copy_output': 'false', - 'json': 'output/error.json', + 'stop_on_error': False, + 'checks': 'output/error.json', 'output': 'output/output.h5ad' } meta = { @@ -29,11 +28,6 @@ def check_structure (slot_info, adata_slot): return missing -def write_json(output): - if par['json'] is not None: - with open(par["json"], "w") as outf: - json.dump(output, outf, indent=2) - print('Load data', flush=True) adata = ad.read_h5ad(par['input']) @@ -59,12 +53,12 @@ def write_json(output): out['data_schema'] = 'not ok' out['error'][slot] = check -if par['stop_on_error'] == 'true': - write_json(out) - exit(out['exit_code']) +if par['json'] is not None: + with open(par["checks"], "w") as f: + json.dump(out, f, indent=2) -if par['copy_output'] == 'true': - assert par['output'] is not None, 'No output defined' - write_json(out) +if par['output'] is not None: shutil.copyfile(par["input"], par["output"]) - + +if par['stop_on_error']: + exit(out['exit_code']) From 52875d19a2d9f9be5367e597883cd994a24dbb70 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 15:21:30 +0100 Subject: [PATCH 0788/1233] update expected types Former-commit-id: 7b6d9bb35445f82e819d346fa3e8f7aaab2de740 --- src/common/unit_test/check_method_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/unit_test/check_method_config.py b/src/common/unit_test/check_method_config.py index ad4968642b..47dce63ec9 100644 --- a/src/common/unit_test/check_method_config.py +++ b/src/common/unit_test/check_method_config.py @@ -20,7 +20,7 @@ print("Check info fields", flush=True) info = config['functionality']['info'] assert "type" in info, "type not an info field" -info_types = ["method", "negative_control", "positive_control"] +info_types = ["method", "control_method"] assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" assert "method_name" in info, "method_name not an info field" assert "variants" in info, "variants not an info field" From 088f2257ef3377728fa857419c7ee9f6a36c43c3 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 15:23:55 +0100 Subject: [PATCH 0789/1233] fix dim_red configs Former-commit-id: 667a5ed1d289cfa389abd4c3f042a591149ab607 --- .../control_methods/true_features/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index b3d3e71553..4000c6b6a8 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: "Positive control method which generates high-dimensional (full data) embedding" info: subtype: positive_control - label: True Features + method_name: True Features v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_comp_id: "True Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index a57a77dc7b..79801fd661 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: namespace: "dimensionality_reduction/methods" description: "Uniform Manifold Approximation and Projection for Dimension Reduction" info: - label: UMAP + method_name: UMAP paper_doi: "10.1038/s41587-020-00801-7" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index a17e54cf0e..7433e4ec00 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a v1_note: This metric is already included in the 'coranking' component and can be removed. metrics: - - method_id: trustworthiness + - metric_id: trustworthiness metric_name: Trustworthiness at k=15 paper_reference: venna2006local min: 0 From ff6638cab6988a12823a9ba072590edfaa73a9c2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 15:30:59 +0100 Subject: [PATCH 0790/1233] add paper ref to dim_red umap Former-commit-id: d6acc4bba9b3df10acb23a5df506a7b185d04ec3 --- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 79801fd661..8a126590d9 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: "Uniform Manifold Approximation and Projection for Dimension Reduction" info: method_name: UMAP - paper_doi: "10.1038/s41587-020-00801-7" + paper_reference : "mcinnes2018umap" code_url: https://github.com/lmcinnes/umap v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf From 7de42ddd2a5f68d1b1cccc125775186f6892a2d0 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 16:00:20 +0100 Subject: [PATCH 0791/1233] updat info field lab_proj control_methods Former-commit-id: 76c7b3a9d05e64058b3f069b4c8796b55481756b --- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 7ff037a908..642f430fca 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: "Baseline method using majority voting" info: subtype: negative_control - label: Majority Vote + method_name: Majority Vote v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c variants: diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 78e294fbf4..25c280f574 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: "Negative control method which generates random labels" info: subtype: negative_control - label: Random Labels + method_name: Random Labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 2c29ef6dfe..68abd74498 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: description: "Positive control method by returning the true labels" info: subtype: positive_control - label: True labels + method_name: True labels v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts From b2ed30d91a979cd5fe9825a0e63b85ea03d4d4a5 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 16:05:52 +0100 Subject: [PATCH 0792/1233] update method info fields lab_proj Former-commit-id: 8247293d86c37b2a0ef4c8de73daf2cc9389b488 --- src/label_projection/methods/knn/config.vsh.yaml | 4 ++-- .../methods/logistic_regression/config.vsh.yaml | 9 +++++---- src/label_projection/methods/mlp/config.vsh.yaml | 4 ++-- src/label_projection/methods/scanvi/config.vsh.yaml | 4 ++-- .../methods/seurat_transferdata/config.vsh.yaml | 4 ++-- src/label_projection/methods/xgboost/config.vsh.yaml | 4 ++-- 6 files changed, 15 insertions(+), 14 deletions(-) diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 5a8dcd0998..1555da9c31 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -4,11 +4,11 @@ functionality: namespace: "label_projection/methods" description: "K-Nearest Neighbors classifier" info: - label: KNN + method_name: KNN # paper_name: "Nearest neighbor pattern classification" # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" # paper_year: 1967 - paper_doi: "10.1109/TIT.1967.1053964" + paper_reference : "cover1967nearest" code_url: https://github.com/scikit-learn/scikit-learn doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 90d54f77b1..8cab5126db 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -4,10 +4,11 @@ functionality: namespace: "label_projection/methods" description: "Logistic regression method" info: - label: Logistic Regression - paper_name: "Applied Logistic Regression" - paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" - paper_year: 2013 + method_name: Logistic Regression + # paper_name: "Applied Logistic Regression" + # paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" + # paper_year: 2013 + paper_reference: "hosmer2013applied" code_url: https://github.com/scikit-learn/scikit-learn doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 642e3b6777..ff2751ffcd 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -4,11 +4,11 @@ functionality: namespace: "label_projection/methods" description: "Multilayer perceptron" info: - label: Multilayer perceptron + method_name: Multilayer perceptron # paper_name: "Connectionist learning procedures" # paper_url: "https://doi.org/10.1016/0004-3702(89)90049-0" # paper_year: 1990 - paper_doi: "10.1016/0004-3702(89)90049-0" + paper_reference: "hinton1989connectionist" code_url: https://github.com/scikit-learn/scikit-learn doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1_url: openproblems/tasks/label_projection/methods/mlp.py diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index a70f5d71de..54a03b2474 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -6,8 +6,8 @@ functionality: Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. info: - label: SCANVI - paper_doi: "10.1101/2020.07.16.205997" + method_name: SCANVI + paper_reference: "lotfollahi2020query" code_url: "https://github.com/YosefLab/scvi-tools" doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index d75516b2c0..d7fed1239e 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -6,8 +6,8 @@ functionality: The Seurat v3 anchoring procedure is designed to integrate diverse single-cell datasets across technologies and modalities. info: - label: Seurat TransferData - paper_doi: "10.1101/460147" + method_name: Seurat TransferData + paper_reference: "hao2021integrated" code_url: "https://github.com/satijalab/seurat" doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" v1_url: openproblems/tasks/label_projection/methods/seurat.py diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index 11740dc609..3a3d9e2970 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -4,8 +4,8 @@ functionality: namespace: "label_projection/methods" description: "XGBoost: A Scalable Tree Boosting System" info: - label: XGBoost - paper_doi: 10.1145/2939672.2939785 + method_name: XGBoost + paper_reference: "chen2016xgboost" code_url: "https://github.com/dmlc/xgboost" doc_url: "https://xgboost.readthedocs.io/en/stable/index.html" v1_url: openproblems/tasks/label_projection/methods/xgboost.py From ed763fd38111488458d94de973f320449bb7bc10 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 16:07:55 +0100 Subject: [PATCH 0793/1233] remove typo Former-commit-id: d2c504b8a66eb6df27d883fce131ba0a74505770 --- src/common/unit_test/check_metric_config.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/common/unit_test/check_metric_config.py b/src/common/unit_test/check_metric_config.py index 55e5ad2dbe..3407ddb62a 100644 --- a/src/common/unit_test/check_metric_config.py +++ b/src/common/unit_test/check_metric_config.py @@ -12,10 +12,10 @@ def check_metric(metric: Dict[str, str]) -> str: assert "metric_id" in metric, "metric_id not a field" - assert "metric_name" in metric, f"metric_name not a field in metric['metric_id']" - assert "min" in metric, f"min not a field in metric['metric_id']" - assert "max" in metric, f"max not a field in metric['metric_id']" - assert "maximize" in metric, f"maximize not a field in metric['metric_id']" + assert "metric_name" in metric, f"metric_name not a field in metric" + assert "min" in metric, f"min not a field in metric" + assert "max" in metric, f"max not a field in metric" + assert "maximize" in metric, f"maximize not a field in metric" assert isinstance(metric['metric_id'], str), "not a string" assert isinstance(metric['metric_name'], str), "not a string" assert isinstance(metric['min'], int), "not an int" From 18e4e1e36cbe2ca11da2f6bcd419bef292e14fec Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 16:09:43 +0100 Subject: [PATCH 0794/1233] update metric info fields lab_proj Former-commit-id: 5d1c3c9965da5116c99ee6128da103412235eb27 --- .../metrics/accuracy/config.vsh.yaml | 4 ++-- src/label_projection/metrics/f1/config.vsh.yaml | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index c6f756b6ac..f4994ec4f1 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -7,8 +7,8 @@ functionality: v1_url: openproblems/tasks/label_projection/metrics/accuracy.py v1_commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 metrics: - - id: accuracy - label: Accuracy + - metric_id: accuracy + metric_name: Accuracy description: The percentage of correctly predicted labels. min: 0 max: 1 diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index e830c9cbc7..742123317d 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -7,20 +7,20 @@ functionality: v1_url: openproblems/tasks/label_projection/metrics/f1.py v1_commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 metrics: - - id: f1_weighted - label: F1 weighted + - metric_id: f1_weighted + metric_name: F1 weighted description: Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall. min: 0 max: 1 maximize: true - - id: f1_macro - label: F1 macro + - metric_id: f1_macro + metric_name: F1 macro description: Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. min: 0 max: 1 maximize: true - - id: f1_micro - label: F1 micro + - metric_id: f1_micro + metric_name: F1 micro description: Calculates the F1 score globally by counting the total true positives, false negatives and false positives. min: 0 max: 1 From 556cd92ac957acca3dca13206370390293d659af Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 22:06:27 +0100 Subject: [PATCH 0795/1233] add unit testing Former-commit-id: c87a72d0510f2d17dee963f9d7924d2a98c42b22 --- .../check_dataset_schema/config.vsh.yaml | 10 +++- src/common/check_dataset_schema/script.py | 2 +- src/common/check_dataset_schema/test.py | 58 +++++++++++++++++++ .../check_schema_resources.sh | 57 ++++++++++++++++++ 4 files changed, 125 insertions(+), 2 deletions(-) create mode 100644 src/common/check_dataset_schema/test.py create mode 100644 src/common/resources_test_scripts/check_schema_resources.sh diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 17b57dd475..9f054db087 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -26,14 +26,22 @@ functionality: required: false description: If specified, this file will contain a structured log of which checks succeeded (or not). example: checks.json + direction: output - name: --output type: file required: false description: If specified, the output file will be a copy of the input file. - example: output.h5ad + example: output.h5ad + direction: output resources: - type: python_script path: script.py + test_resources: + - path: ../../../resources_test + - path: ../../../src + dest: src + - type: python_script + path: test.py platforms: - type: docker image: python:3.10 diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 105d88c380..a0159c99b7 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -53,7 +53,7 @@ def check_structure (slot_info, adata_slot): out['data_schema'] = 'not ok' out['error'][slot] = check -if par['json'] is not None: +if par['checks'] is not None: with open(par["checks"], "w") as f: json.dump(out, f, indent=2) diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py new file mode 100644 index 0000000000..a154f341df --- /dev/null +++ b/src/common/check_dataset_schema/test.py @@ -0,0 +1,58 @@ +import subprocess +from os import path +import json + +input_path = meta["resources_dir"] + "resources_test/common/pancreas/dataset.h5ad" +input_correct_schema = meta["resources_dir"] + "resources_test/common/check_schema/anndata_correct.yaml" +input_error_schema = meta["resources_dir"] + "resources_test/common/check_schema/anndata_error.yaml" +output_checks = "checks.json" +output_path = "output.h5ad" + + +cmd = [ + meta['executable'], + "--input", input_path, + "--schema", input_correct_schema, + "--checks", output_checks, + "--output", output_path, +] + +print(">> Running script as test", flush=True) +subprocess.run(cmd, check=True) + +print(">> Checking whether output file exists", flush=True) +assert path.exists(output_checks) +assert path.exists(output_path) + +print(">> Reading json file", flush=True) +with open(output_checks, 'r') as f: + out = json.load(f) + print(out) + + +# Check if an incomplete h5ad is captured +cmd_error = [ + meta['executable'], + "--input", input_path, + "--schema", input_error_schema, + "--stop_on_error", 'true', + "--checks", output_checks, + "--output", output_path, +] + +print(">> Running script as test", flush=True) +out_error = subprocess.run(cmd_error) + +print(">> Checking whether output file exists", flush=True) +assert path.exists(output_checks) +assert path.exists(output_path) + +assert out_error.returncode == 1 + +print(">> Reading json file", flush=True) +with open(output_checks, 'r') as f: + out = json.load(f) + print(out) + + +print("All checks succeeded!") diff --git a/src/common/resources_test_scripts/check_schema_resources.sh b/src/common/resources_test_scripts/check_schema_resources.sh new file mode 100644 index 0000000000..c11dcdd389 --- /dev/null +++ b/src/common/resources_test_scripts/check_schema_resources.sh @@ -0,0 +1,57 @@ +#!/bin/bash + +# make sure folloewing command has been executed +# viash ns build -q 'common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +OUTPUT_DIR="resources_test/common/check_schema" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +# Create small git sha input file +correct_file="$OUTPUT_DIR/anndata_correct.yaml" +error_file="$OUTPUT_DIR/anndata_error.yaml" + +cat < $correct_file +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" +EOT + +cat < $error_file +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: error_test + description: "A made up uns variable to test if error is picked up" +EOT \ No newline at end of file From 9b381e1ec1263f52442d12fbf343689fd2e15208 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 21 Mar 2023 22:12:21 +0100 Subject: [PATCH 0796/1233] update changelog Former-commit-id: 986387574303e9458f8a2c11432feaef8048d7d4 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed39079378..57e7ac1c54 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,8 @@ * `get_task_info`: extract task info +* `check_dataset_schema`: check if the dataset used has the required fields defined in the api `anndata_*.yaml` files + ## datasets ### NEW FUNCTIONALITY From 32d32a4b292ffd0402d9aecb506ca434156410ec Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 22 Mar 2023 14:01:31 +0100 Subject: [PATCH 0797/1233] add test resource to unit test Former-commit-id: 655305ec7f64c7b7bc9daa8f145631fe03511088 --- src/common/check_dataset_schema/test.py | 46 ++++++++++++++- .../check_schema_resources.sh | 57 ------------------- 2 files changed, 44 insertions(+), 59 deletions(-) delete mode 100644 src/common/resources_test_scripts/check_schema_resources.sh diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index a154f341df..30b201ac16 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -3,12 +3,54 @@ import json input_path = meta["resources_dir"] + "resources_test/common/pancreas/dataset.h5ad" -input_correct_schema = meta["resources_dir"] + "resources_test/common/check_schema/anndata_correct.yaml" -input_error_schema = meta["resources_dir"] + "resources_test/common/check_schema/anndata_error.yaml" +input_correct_schema = meta["resources_dir"] + "resources_test/common/anndata_correct.yaml" +input_error_schema = meta["resources_dir"] + "resources_test/common/anndata_error.yaml" output_checks = "checks.json" output_path = "output.h5ad" + +with open(input_correct_schema, "w") as f: + f.write(''' +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + ''') + + +with open(input_error_schema, "w") as f: + f.write(''' +type: file +description: "A preprocessed dataset" +example: "preprocessed.h5ad" +info: + short_description: "Preprocessed dataset" + slots: + layers: + - type: integer + name: counts + description: Raw counts + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + - type: string + name: error_test + description: "A made up uns variable to test if error is picked up" + ''') + + cmd = [ meta['executable'], "--input", input_path, diff --git a/src/common/resources_test_scripts/check_schema_resources.sh b/src/common/resources_test_scripts/check_schema_resources.sh deleted file mode 100644 index c11dcdd389..0000000000 --- a/src/common/resources_test_scripts/check_schema_resources.sh +++ /dev/null @@ -1,57 +0,0 @@ -#!/bin/bash - -# make sure folloewing command has been executed -# viash ns build -q 'common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -OUTPUT_DIR="resources_test/common/check_schema" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -# Create small git sha input file -correct_file="$OUTPUT_DIR/anndata_correct.yaml" -error_file="$OUTPUT_DIR/anndata_error.yaml" - -cat < $correct_file -type: file -description: "A preprocessed dataset" -example: "preprocessed.h5ad" -info: - short_description: "Preprocessed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" -EOT - -cat < $error_file -type: file -description: "A preprocessed dataset" -example: "preprocessed.h5ad" -info: - short_description: "Preprocessed dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - - type: string - name: error_test - description: "A made up uns variable to test if error is picked up" -EOT \ No newline at end of file From afbe79c389d5fa6a78994a0cd74c5c08f48df83f Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 22 Mar 2023 14:50:09 +0100 Subject: [PATCH 0798/1233] add suggestions Former-commit-id: 653f2b7250a8c8b7feb6a35070174043412ff55b --- src/common/check_dataset_schema/config.vsh.yaml | 4 +--- src/common/check_dataset_schema/test.py | 6 +++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 9f054db087..6b18e5faed 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -37,9 +37,7 @@ functionality: - type: python_script path: script.py test_resources: - - path: ../../../resources_test - - path: ../../../src - dest: src + - path: ../../../resources_test/common/pancreas - type: python_script path: test.py platforms: diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 30b201ac16..aad0e7f81e 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -2,9 +2,9 @@ from os import path import json -input_path = meta["resources_dir"] + "resources_test/common/pancreas/dataset.h5ad" -input_correct_schema = meta["resources_dir"] + "resources_test/common/anndata_correct.yaml" -input_error_schema = meta["resources_dir"] + "resources_test/common/anndata_error.yaml" +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +input_correct_schema = "anndata_correct.yaml" +input_error_schema = "anndata_error.yaml" output_checks = "checks.json" output_path = "output.h5ad" From 844498f7485a3204a2b8adedce276c8b0b6fda39 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 22 Mar 2023 15:19:54 +0100 Subject: [PATCH 0799/1233] bump version container Former-commit-id: 15d7ac16cd2a1d6216b16fa3aad9f42065f16951 --- src/label_projection/methods/scanvi/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 54a03b2474..2ec00a3dfb 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: nvcr.io/nvidia/pytorch:22.09-py3 + image: nvcr.io/nvidia/pytorch:22.12-py3 setup: - type: python packages: From c43ec3bb9edd681879bd34f334589cadeb559d6c Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 22 Mar 2023 17:26:58 +0100 Subject: [PATCH 0800/1233] add general unit test for split_dataset Former-commit-id: a91a8af56b15c669c0860fa9562d5d77fc4c825d --- .../api/comp_split_dataset.yaml | 99 +++++++++---------- 1 file changed, 45 insertions(+), 54 deletions(-) diff --git a/src/batch_integration/api/comp_split_dataset.yaml b/src/batch_integration/api/comp_split_dataset.yaml index 2471f70dc3..5d869be713 100644 --- a/src/batch_integration/api/comp_split_dataset.yaml +++ b/src/batch_integration/api/comp_split_dataset.yaml @@ -7,57 +7,48 @@ functionality: - name: "--output" __merge__: anndata_unintegrated.yaml direction: output - # test_resources: - # - path: ../../../resources_test/common/pancreas/ - # - type: python_script - # path: generic_test.py - # text: | - # import anndata as ad - # import subprocess - # from os import path - - # input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - # output_train_path = "train.h5ad" - # output_test_path = "test.h5ad" - # cmd = [ - # meta['executable'], - # "--input", input_path, - # "--output_train", output_train_path, - # "--output_test", output_test_path - # ] - - # print(">> Checking whether input file exists", flush=True) - # assert path.exists(input_path) - - # print(">> Running script as test", flush=True) - # out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - # print(">> Checking whether output files exist", flush=True) - # assert path.exists(output_train_path) - # assert path.exists(output_test_path) - - # print(">> Reading h5ad files", flush=True) - # input = ad.read_h5ad(input_path) - # output_train = ad.read_h5ad(output_train_path) - # output_test = ad.read_h5ad(output_test_path) - - # print("input:", input, flush=True) - # print("output_train:", output_train, flush=True) - # print("output_test:", output_test, flush=True) - - # print(">> Checking whether data from input was copied properly to output", flush=True) - # assert input.n_obs == output_train.n_obs - # assert input.n_obs == output_test.n_obs - # assert input.uns["dataset_id"] == output_train.uns["dataset_id"] - # assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - - - # print(">> Check whether certain slots exist", flush=True) - # assert "counts" in output_train.layers - # assert "normalized" in output_train.layers - # assert 'hvg_score' in output_train.var - # assert "counts" in output_test.layers - # assert "normalized" in output_test.layers - # assert 'hvg_score' in output_test.var - - # print("All checks succeeded!", flush=True) \ No newline at end of file + test_resources: + - path: ../../../resources_test/common/pancreas/ + - type: python_script + path: generic_test.py + text: | + import anndata as ad + import subprocess + from os import path + + input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" + output_unintegrated_path = "unintegrated.h5ad" + cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_unintegrated_path + ] + + print(">> Checking whether input file exists", flush=True) + assert path.exists(input_path) + + print(">> Running script as test", flush=True) + out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout + print(out) + + print(">> Checking whether output files exist", flush=True) + assert path.exists(output_unintegrated_path) + + print(">> Reading h5ad files", flush=True) + input = ad.read_h5ad(input_path) + output_unintegrated = ad.read_h5ad(output_unintegrated_path) + + print("input:", input, flush=True) + print("output_unintegrated:", output_unintegrated, flush=True) + + print(">> Checking whether data from input was copied properly to output", flush=True) + assert input.n_obs == output_unintegrated.n_obs + assert input.uns["dataset_id"] == output_unintegrated.uns["dataset_id"] + + + print(">> Check whether certain slots exist", flush=True) + assert "counts" in output_unintegrated.layers + assert "normalized" in output_unintegrated.layers + assert 'hvg' in output_unintegrated.var + + print("All checks succeeded!", flush=True) \ No newline at end of file From 2e9b6bedb6aa1e673087dbb8adf504cc9969209e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 23 Mar 2023 22:03:42 +0000 Subject: [PATCH 0801/1233] Bump tj-actions/changed-files from 35.7.2 to 35.7.6 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.7.2 to 35.7.6. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.7.2...v35.7.6) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: f883caec9535ce740eb0778636e73374a1f8e68a --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 1161f06690..25b17b6472 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.7.2 + uses: tj-actions/changed-files@v35.7.6 with: separator: ";" diff_relative: true From 31749acfbfebb7b4b4fdc9e3aa84d5610e8ea9ae Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:06:56 +0100 Subject: [PATCH 0802/1233] Update task description Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: 2d9bf0d3accd9b88c116d1b53d970a8d8a176869 --- src/batch_integration/api/task_info.yaml | 29 ++++++++----- src/batch_integration/library.bib | 52 ++++++++++++++++++++++++ 2 files changed, 70 insertions(+), 11 deletions(-) diff --git a/src/batch_integration/api/task_info.yaml b/src/batch_integration/api/task_info.yaml index 83cf0351be..2a68e5ed9c 100644 --- a/src/batch_integration/api/task_info.yaml +++ b/src/batch_integration/api/task_info.yaml @@ -2,16 +2,23 @@ task_id: batch_integration task_name: Batch Integration v1_url: openproblems/tasks/batch_integration/README.md v1_commit: 637163fba7d74ab5393c2adbee5354dcf4d46f85 -summary: Batch integration methods integrate datasets across batches that arise from various biological and technical sources. +summary: Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. description: | - Batch (or data) integration methods integrate datasets across batches that arise from various biological (e.g., tissue, location, individual, species) and technical (e.g., ambient RNA, lab, protocol) sources. The goal of a batch integration method is to remove unwanted batch effects in the data, while retaining biologically-meaningful variation that can help us to detect cell identities, fit cellular trajectories, or understand patterns of gene or pathway activity. + ## Motivation + + As single-cell technologies advance, single-cell datasets are growing both in size and complexity. + Especially in consortia such as the Human Cell Atlas, individual studies combine data from multiple labs, each sequencing multiple individuals possibly with different technologies. + This gives rise to complex batch effects in the data that must be computationally removed to perform a joint analysis. + These batch integration methods must remove the batch effect while not removing relevant biological information. + Currently, over 200 tools exist that aim to remove batch effects scRNA-seq datasets [@zappia2018exploring]. + These methods balance the removal of batch effects with the conservation of nuanced biological information in different ways. + This abundance of tools has complicated batch integration method choice, leading to several benchmarks on this topic [@luecken2020benchmarking; @tran2020benchmark; @chazarragil2021flexible; @mereu2020benchmarking]. + Yet, benchmarks use different metrics, method implementations and datasets. Here we build a living benchmarking task for batch integration methods with the vision of improving the consistency of method evaluation. - Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have divided the batch integration task into three subtasks. These subtasks are: - - * [Batch integration graphs](graph/), - * [Batch integration embeddings](embedding/), and - * [Batch integrated feature matrices](feature/) - - These subtasks collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. Information on the task API for datasets, methods, and metrics can be found in the individual subtask pages. - - Metrics for this task either assess the removal of batch effects or assess the conservation of biological variation. This can be a helpful distinction when devising new metrics. This task, including the subtask structure, was taken from a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2), which is a useful reference for more background reading on this task and the above concepts. \ No newline at end of file + ## Task Description + + In this task we evaluate batch integration methods on their ability to remove batch effects in the data while conserving variation attributed to biological effects. + As input, methods require either normalised or unnormalised data with multiple batches and consistent cell type labels. + The batch integrated output can be a feature matrix, a low dimensional embedding and/or a neighbourhood graph. + The respective batch-integrated representation is then evaluated using sets of metrics that capture how well batch effects are removed and whether biological variance is conserved. + We have based this particular task on the latest, and most extensive benchmark of single-cell data integration methods [@luecken2022benchmarking]. diff --git a/src/batch_integration/library.bib b/src/batch_integration/library.bib index bc4144d931..0081cf3aa2 100644 --- a/src/batch_integration/library.bib +++ b/src/batch_integration/library.bib @@ -20,4 +20,56 @@ @inproceedings{amelio2015normalized author = {Alessia Amelio and Clara Pizzuti}, title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?}, booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015} +} +@article{zappia2018exploring, + doi = {10.1371/journal.pcbi.1006245}, + url = {https://doi.org/10.1371/journal.pcbi.1006245}, + year = {2018}, + month = jun, + publisher = {Public Library of Science ({PLoS})}, + volume = {14}, + number = {6}, + pages = {e1006245}, + author = {Luke Zappia and Belinda Phipson and Alicia Oshlack}, + editor = {Dina Schneidman}, + title = {Exploring the single-cell {RNA}-seq analysis landscape with the {scRNA}-tools database}, + journal = {{PLOS} Computational Biology} +} +@article{tran2020benchmark, + doi = {10.1186/s13059-019-1850-9}, + url = {https://doi.org/10.1186/s13059-019-1850-9}, + year = {2020}, + month = jan, + publisher = {Springer Science and Business Media {LLC}}, + volume = {21}, + number = {1}, + author = {Hoa Thi Nhu Tran and Kok Siong Ang and Marion Chevrier and Xiaomeng Zhang and Nicole Yee Shin Lee and Michelle Goh and Jinmiao Chen}, + title = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data}, + journal = {Genome Biology} +} +@article{chazarragil2021flexible, + doi = {10.1093/nar/gkab004}, + url = {https://doi.org/10.1093/nar/gkab004}, + year = {2021}, + month = feb, + publisher = {Oxford University Press ({OUP})}, + volume = {49}, + number = {7}, + pages = {e42--e42}, + author = {Ruben Chazarra-Gil and Stijn van~Dongen and Vladimir~Yu Kiselev and Martin Hemberg}, + title = {Flexible comparison of batch correction methods for single-cell {RNA}-seq using {BatchBench}}, + journal = {Nucleic Acids Research} +} +@article{mereu2020benchmarking, + doi = {10.1038/s41587-020-0469-4}, + url = {https://doi.org/10.1038/s41587-020-0469-4}, + year = {2020}, + month = apr, + publisher = {Springer Science and Business Media {LLC}}, + volume = {38}, + number = {6}, + pages = {747--755}, + author = {Elisabetta Mereu and Atefeh Lafzi and Catia Moutinho and Christoph Ziegenhain and Davis J. McCarthy and Adri{\'{a}}n {\'{A}}lvarez-Varela and Eduard Batlle and Sagar and Dominic Gr\"{u}n and Julia K. Lau and St{\'{e}}phane C. Boutet and Chad Sanada and Aik Ooi and Robert C. Jones and Kelly Kaihara and Chris Brampton and Yasha Talaga and Yohei Sasagawa and Kaori Tanaka and Tetsutaro Hayashi and Caroline Braeuning and Cornelius Fischer and Sascha Sauer and Timo Trefzer and Christian Conrad and Xian Adiconis and Lan T. Nguyen and Aviv Regev and Joshua Z. Levin and Swati Parekh and Aleksandar Janjic and Lucas E. Wange and Johannes W. Bagnoli and Wolfgang Enard and Marta Gut and Rickard Sandberg and Itoshi Nikaido and Ivo Gut and Oliver Stegle and Holger Heyn}, + title = {Benchmarking single-cell {RNA}-sequencing protocols for cell atlas projects}, + journal = {Nature Biotechnology} } \ No newline at end of file From a32108e1b496f74c63530c70a88118ca3e1e5bb8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:19:12 +0100 Subject: [PATCH 0803/1233] update to scib 1.1.3 Former-commit-id: 3cc116b170b299c4c81852dfbd0ba1f1264aa1b7 --- src/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/batch_integration/methods/combat/config.vsh.yaml | 2 +- src/batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../methods/scanorama_feature/config.vsh.yaml | 2 +- src/batch_integration/methods/scvi/config.vsh.yaml | 3 +-- src/batch_integration/metrics/asw_batch/config.vsh.yaml | 2 +- src/batch_integration/metrics/asw_label/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 2 +- .../metrics/clustering_overlap/config.vsh.yaml | 2 +- src/batch_integration/metrics/pcr/config.vsh.yaml | 2 +- src/batch_integration/split_dataset/config.vsh.yaml | 2 +- 11 files changed, 11 insertions(+), 12 deletions(-) diff --git a/src/batch_integration/methods/bbknn/config.vsh.yaml b/src/batch_integration/methods/bbknn/config.vsh.yaml index 929a476f5b..50854683b3 100644 --- a/src/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods/bbknn/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/methods/combat/config.vsh.yaml b/src/batch_integration/methods/combat/config.vsh.yaml index 85587eb0a0..2dc5897394 100644 --- a/src/batch_integration/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods/combat/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml index 436d374606..3e07d09dc9 100644 --- a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index 05342d3013..d1ba995088 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index 2e64f09012..cc9744eb78 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -19,11 +19,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: - scvi-tools - pyyaml - - scib - type: nextflow diff --git a/src/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/asw_batch/config.vsh.yaml index 6146e5c5ff..816429e85d 100644 --- a/src/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml index e3cb81e31a..0c5a8bfb0d 100644 --- a/src/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_label/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index a3dea7593a..61d278e477 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml index e04c20af26..fef72343dd 100644 --- a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml index e591589d69..4e31a7ff8e 100644 --- a/src/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics/pcr/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: diff --git a/src/batch_integration/split_dataset/config.vsh.yaml b/src/batch_integration/split_dataset/config.vsh.yaml index 0bf443ddf8..184dea0904 100644 --- a/src/batch_integration/split_dataset/config.vsh.yaml +++ b/src/batch_integration/split_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: ../../../resources_test/common/pancreas/ platforms: - type: docker - image: mumichae/scib-base:1.0.2 + image: mumichae/scib-base:1.1.3 setup: - type: python pypi: pyyaml From c8bc8f1ac9e6983c0e788f467760c5c4a432629b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:20:02 +0100 Subject: [PATCH 0804/1233] remove unneeded files Former-commit-id: 3efc7aa8e7f92a993de1fd918476abd2afc6edf0 --- src/batch_integration/old_readmes/datasets.md | 31 ----------- .../old_readmes/embedding.md | 38 ------------- .../old_readmes/embedding_metrics.md | 24 -------- src/batch_integration/old_readmes/graph.md | 55 ------------------- .../old_readmes/graph_methods.md | 23 -------- .../old_readmes/graph_metrics.md | 23 -------- src/batch_integration/workflows/download.tsv | 2 - src/common/create_skeleton/script.sh | 5 ++ 8 files changed, 5 insertions(+), 196 deletions(-) delete mode 100644 src/batch_integration/old_readmes/datasets.md delete mode 100644 src/batch_integration/old_readmes/embedding.md delete mode 100644 src/batch_integration/old_readmes/embedding_metrics.md delete mode 100644 src/batch_integration/old_readmes/graph.md delete mode 100644 src/batch_integration/old_readmes/graph_methods.md delete mode 100644 src/batch_integration/old_readmes/graph_metrics.md delete mode 100644 src/batch_integration/workflows/download.tsv create mode 100755 src/common/create_skeleton/script.sh diff --git a/src/batch_integration/old_readmes/datasets.md b/src/batch_integration/old_readmes/datasets.md deleted file mode 100644 index 6dd89140c7..0000000000 --- a/src/batch_integration/old_readmes/datasets.md +++ /dev/null @@ -1,31 +0,0 @@ -# Datasets - -Viash component for preparing data **before** running data integration methods. - -## API - -### Requires - -* `adata.X`: raw counts -* batch label in `adata.obs` that is specified as a parameter to the script -* cell identity label in `adata.obs` that is specified as a parameter to the script - -### Returns - -This module creates Anndata objects that contain: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']`: batch covariate -* `adata.obs['label']`: cell identity label -* `adata.var['highly_variable']`: label whether a gene is identified as highly variable -* `adata.layers['counts']`: raw, integer UMI count data -* `adata.layers['logcounts']`: log-normalized count data -* `adata.layers['logcounts_scaled']`: log-normalized count data scaled to unit variance and zero mean -* `adata.X`: same as in `adata.layers['logcounts']` - -And transformations of the data: - -* `adata.obsm['X_pca']`: PCA embedding of the log-normalized counts -* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['pca_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['pca_distances']`: distance matrix generated by `scanpy.pp.neighbors()` diff --git a/src/batch_integration/old_readmes/embedding.md b/src/batch_integration/old_readmes/embedding.md deleted file mode 100644 index 90a25de046..0000000000 --- a/src/batch_integration/old_readmes/embedding.md +++ /dev/null @@ -1,38 +0,0 @@ -# Batch Integration with Embedding Output - -This sub-task focuses on all methods that can output integrated embeddings. -Additionally, metrics can also be applied to PCA embeddings of the feature matrix output. -Other sub-tasks for batch integration can be found for: - -* [graph](../graph/), and -* [corrected features](../feature/) - -This sub-task was taken from -a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2). - -## API - -Datasets should contain the following attributes: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']` with the batch covariate, -* `adata.obs['label']` with the cell identity label, -* `adata.layers['counts']` with raw, integer UMI count data, and -* `adata.X` with log-normalized data - -Methods should assign output to: - -* `adata.obsm['X_emb']` - -Methods are run in four different scenarios that include scaling and highly variable gene selection: - -* `full_unscaled` -* `hvg_unscaled` -* `full_scaled` -* `hvg_scaled` - -Metrics can compare: - -* `adata.obsm['X_emb']` to `adata.obsm['X_pca']` -* `adata.obsm['X_emb']` to `adata.obs['label']` -* `adata.obsm['X_emb']` to `adata.obs['batch']` diff --git a/src/batch_integration/old_readmes/embedding_metrics.md b/src/batch_integration/old_readmes/embedding_metrics.md deleted file mode 100644 index 5fc16ca7b2..0000000000 --- a/src/batch_integration/old_readmes/embedding_metrics.md +++ /dev/null @@ -1,24 +0,0 @@ -# Evaluation of Batch Integration with Embedding Output - -Metrics on embedding output include: - -* Average silhouette width on batches ASW_batch -* Average silhouette width on labels ASW_label -* Cell cycle conservation -* Principle component regression PCR - -## API - -All datasets should contain the following attributes: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']`: the batch covariate -* `adata.obs['label']`: the cell identity label -* `adata.obsm['X_pca']`: the PCA embedding before integration -* `adata.obsm['X_emb']`: the embedding after integration - -Metrics compare: - -* `adata.obsm['X_emb']` to `adata.obsm['X_pca']` -* `adata.obsm['X_emb']` to `adata.obs['label']` -* `adata.obsm['X_emb']` to `adata.obs['batch']` diff --git a/src/batch_integration/old_readmes/graph.md b/src/batch_integration/old_readmes/graph.md deleted file mode 100644 index eb61e893aa..0000000000 --- a/src/batch_integration/old_readmes/graph.md +++ /dev/null @@ -1,55 +0,0 @@ -# Batch Integration with Graph Output - -The output of all batch integration tasks can be represented as a graph. This sub-task focuses on all methods that can -output integrated graphs, and includes methods that canonically output the other two data formats with subsequent -postprocessing to generate a graph. Other sub-tasks for batch integration can be found for: - -* [embeddings](../embedding/), and -* [corrected features](../feature/) - -This sub-task was taken from -a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2). - -## API - -### Input - -Datasets should contain the following attributes: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']` with the batch covariate -* `adata.obs['label']` with the cell identity label - * `adata.var['highly_variable']`: label whether a gene is identified as highly variable -* `adata.layers['counts']` with raw, integer UMI count data -* `adata.layers['logcounts']`: log-normalized count data -* `adata.layers['logcounts_scaled']`: scaled log-normalized count data -* `adata.obsm['X_pca']`: PCA embedding of the log-normalized counts -* `adata.uns['uni']`: neighbors data generated by `scanpy.pp.neighbors()` -* `adata.obsp['pca_connectivities']`: connectivity matrix generated by `scanpy.pp.neighbors()` -* `adata.obsp['pca_distances']`: distance matrix generated by `scanpy.pp.neighbors()` - -The default count matrix in `adata.X` is assumed to contain the log normalised counts from `adata.layers['logcounts']`. - -### Output - -For each integration method, the count matrix can be used as-is, feature selected for highly variable genes (HVGs) -and/or scaled to unit variance and zero mean. -As a result, there are four different preprocessing scenarios per dataset -and method that include scaling and HVG selection: - -* `full_unscaled`: no HVG selection or scaling -* `hvg_unscaled`: HVG selected -* `full_scaled`: scaled -* `hvg_scaled`: HVG selected and scaled - -The user should be able to specify which of the four scenarios to run the method with. - -Methods should assign integration output to: - -* `adata.obsp['connectivities']` and `adata.obsp['distances']` - -Metrics can compare: - -* `adata.obsp['connectivities']` to `adata.obs['uni_connectivies']`, -* `adata.obsp['connectivities']` to `adata.obs['label']`, and/or -* `adata.obsp['connectivities']` to `adata.obs['batch']`. diff --git a/src/batch_integration/old_readmes/graph_methods.md b/src/batch_integration/old_readmes/graph_methods.md deleted file mode 100644 index cea477ff1e..0000000000 --- a/src/batch_integration/old_readmes/graph_methods.md +++ /dev/null @@ -1,23 +0,0 @@ -# Run Graph Integration Methods - -Viash component for running integration methods. - -## API - -### Input data formats - -The components before integration must contain: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']`: batch covariate -* `adata.X`: log-normalized expression - -Whether a dataset is scaled or selected for highly-variable genes before integration is passed by parameters to the -script. - -### Output data formats - -* `adata.obsp['connectivities']`: Integrated graph connectivities -* `adata.obsp['distances']`: Integrated graph distances -* `adata.uns['hvg']`: Number of highly variable genes selected before integration (0 meaning that no HVG selection was performed) -* `adata.uns['scaled']`: Boolean entry whether scaling was performed before integration diff --git a/src/batch_integration/old_readmes/graph_metrics.md b/src/batch_integration/old_readmes/graph_metrics.md deleted file mode 100644 index 1701dd23da..0000000000 --- a/src/batch_integration/old_readmes/graph_metrics.md +++ /dev/null @@ -1,23 +0,0 @@ -# Evaluation of Batch Integration with Graph Output - -Metrics on graph output include: - -* adjusted rand index ARI -* normalized mutual information NMI - -## API - -All datasets should contain the following attributes: - -* `adata.uns['name']`: name of the dataset -* `adata.obs['batch']`: the batch covariate -* `adata.obs['label']`: the cell identity label -* `adata.obs['uni_connectivies']`: graph connectivities before integration -* `adata.obsp['connectivities']`: graph connectivities after integration -* `adata.obsp['distances']`: graph distances after integration - -Metrics compare: - -* `adata.obsp['connectivities']` to `adata.obs['uni_connectivies']`, -* `adata.obsp['connectivities']` to `adata.obs['label']`, and/or -* `adata.obsp['connectivities']` to `adata.obs['batch']`. diff --git a/src/batch_integration/workflows/download.tsv b/src/batch_integration/workflows/download.tsv deleted file mode 100644 index 1d07a3165a..0000000000 --- a/src/batch_integration/workflows/download.tsv +++ /dev/null @@ -1,2 +0,0 @@ -name obs_cell_type obs_batch url -pancreas celltype tech https://ndownloader.figshare.com/files/24539828 diff --git a/src/common/create_skeleton/script.sh b/src/common/create_skeleton/script.sh new file mode 100755 index 0000000000..a8e58fae07 --- /dev/null +++ b/src/common/create_skeleton/script.sh @@ -0,0 +1,5 @@ +TASK=dimensionality_reduction +viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type metric --name foor --language r +viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type method --name foor --language r +viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type method --name foopy +viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type metric --name foopy \ No newline at end of file From 255c01b3dd0b11fd6d617e1e497d93279d03d03f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:25:51 +0100 Subject: [PATCH 0805/1233] remove unneeded type Former-commit-id: 249f7015f4ba078a6a8ed54f78cd19f2a2254abf --- src/batch_integration/workflows/run/preprocessing.tsv | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 src/batch_integration/workflows/run/preprocessing.tsv diff --git a/src/batch_integration/workflows/run/preprocessing.tsv b/src/batch_integration/workflows/run/preprocessing.tsv deleted file mode 100644 index 422356511b..0000000000 --- a/src/batch_integration/workflows/run/preprocessing.tsv +++ /dev/null @@ -1,6 +0,0 @@ -name label batch hvgs scaling -pancreas celltype tech 0 false -pancreas celltype tech 0 true -pancreas celltype tech 2000 false -pancreas celltype tech 2000 true -pancreas celltype tech 2000 true \ No newline at end of file From d72e31f9ca292bf7fcb29ebb82c2ce144bda16b4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:30:46 +0100 Subject: [PATCH 0806/1233] Fix clustering overlap metrics Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: 3e90a77467384f4e2b5630bd90e73b6aa986067a --- .../metrics/clustering_overlap/script.py | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/batch_integration/metrics/clustering_overlap/script.py index bef625f893..9e57be8496 100644 --- a/src/batch_integration/metrics/clustering_overlap/script.py +++ b/src/batch_integration/metrics/clustering_overlap/script.py @@ -1,5 +1,6 @@ import anndata as ad -from scib.metrics.clustering import opt_louvain +import scanpy as sc +from scib.metrics.clustering import cluster_optimal_resolution from scib.metrics import ari, nmi ## VIASH START @@ -16,14 +17,12 @@ print('Read input', flush=True) input = ad.read_h5ad(par['input_integrated']) -print('Run Louvain clustering', flush=True) -opt_louvain( - input, +print('Run optimal Leiden clustering', flush=True) +cluster_optimal_resolution( + adata=input, label_key='label', cluster_key='cluster', - plot=False, - inplace=True, - force=True + cluster_function=sc.tl.leiden, ) print('Compute ARI score', flush=True) From e906a82577bb50de69cec8665506a8502d195e9f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:32:59 +0100 Subject: [PATCH 0807/1233] Fix renamed parameters Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: 7544b3083397cffd06c884ea08f13af69393dddd --- src/batch_integration/metrics/asw_batch/script.py | 2 +- src/batch_integration/metrics/asw_label/script.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py index d723e1ccb7..40169e9808 100644 --- a/src/batch_integration/metrics/asw_batch/script.py +++ b/src/batch_integration/metrics/asw_batch/script.py @@ -19,7 +19,7 @@ score = silhouette_batch( adata, batch_key='batch', - group_key='label', + lable_key='label', embed='X_emb', ) diff --git a/src/batch_integration/metrics/asw_label/script.py b/src/batch_integration/metrics/asw_label/script.py index f534c0c79e..be878f105b 100644 --- a/src/batch_integration/metrics/asw_label/script.py +++ b/src/batch_integration/metrics/asw_label/script.py @@ -18,7 +18,7 @@ print('compute score') score = silhouette( adata, - group_key='label', + label_key='label', embed='X_emb' ) From 8747cac89955436ce431f56107ba31faa452df90 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Mar 2023 13:36:46 +0100 Subject: [PATCH 0808/1233] Fix typo Co-authored-by: Michaela Mueller Co-authored-by: Kai Waldrant Former-commit-id: ca52475dff24592ba0e978edea8a9269f43eaa2c --- src/batch_integration/metrics/asw_batch/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/batch_integration/metrics/asw_batch/script.py index 40169e9808..82860ccc24 100644 --- a/src/batch_integration/metrics/asw_batch/script.py +++ b/src/batch_integration/metrics/asw_batch/script.py @@ -19,7 +19,7 @@ score = silhouette_batch( adata, batch_key='batch', - lable_key='label', + label_key='label', embed='X_emb', ) From 7ea76ccc258db87f94c8cbca2859ffddf84a0e30 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 29 Mar 2023 16:55:26 +0200 Subject: [PATCH 0809/1233] fix missing data in method info Former-commit-id: 3119a6ac9a110d23d810f2c65c623e0296bf74e5 --- src/common/get_method_info/script.R | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 97150f7d1b..a155182c0c 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -18,7 +18,14 @@ configs <- yaml::yaml.load(ns_list$stdout) df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) - info <- as_tibble(config$functionality$info) + info <- config$functionality$info + # remove empty fields + for (n in names(info)) { + if (length(info[[n]]) == 0) { + info[[n]] <- NA + } + } + info <- as_tibble(info) info$config_path <- gsub(".*\\./", "", config$info$config) info$task_id <- par$task_id info$method_id <- config$functionality$name From 641c7e94904b44ad95117e99423081905a93d3d6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 29 Mar 2023 21:27:35 +0200 Subject: [PATCH 0810/1233] update config unit test Former-commit-id: 64ae9791d54062da72140615b80771f5500d6931 --- src/common/unit_test/check_method_config.py | 12 +++++++--- src/common/unit_test/check_metric_config.py | 26 +++++++++++++-------- 2 files changed, 25 insertions(+), 13 deletions(-) diff --git a/src/common/unit_test/check_method_config.py b/src/common/unit_test/check_method_config.py index 47dce63ec9..0c49f3b779 100644 --- a/src/common/unit_test/check_method_config.py +++ b/src/common/unit_test/check_method_config.py @@ -15,6 +15,7 @@ print("check general fields", flush=True) +assert "name" in config["functionality"] is not None, "Name not a field or is empty" assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" print("Check info fields", flush=True) @@ -22,11 +23,16 @@ assert "type" in info, "type not an info field" info_types = ["method", "control_method"] assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" -assert "method_name" in info, "method_name not an info field" +assert "pretty_name" in info is not None, "pretty_name not an info field or is empty" +assert "summary" in info is not None, "summary not an info field or is empty" +assert "description" in info is not None, "description not an info field or is empty" +if ("control" not in info["type"]): + assert "reference" in info, "reference not an info field" + assert "documentation_url" in info is not None, "documentation_url not an info field or is empty" + assert "repository_url" in info is not None, "repository_url not an info field or is empty" assert "variants" in info, "variants not an info field" assert "preferred_normalization" in info, "preferred_normalization not an info field" -if ("control" not in info["type"]): - assert "paper_reference" in info, "paper_reference not an info field" + diff --git a/src/common/unit_test/check_metric_config.py b/src/common/unit_test/check_metric_config.py index 3407ddb62a..0b46c911ec 100644 --- a/src/common/unit_test/check_metric_config.py +++ b/src/common/unit_test/check_metric_config.py @@ -11,29 +11,35 @@ ## VIASH END def check_metric(metric: Dict[str, str]) -> str: - assert "metric_id" in metric, "metric_id not a field" - assert "metric_name" in metric, f"metric_name not a field in metric" - assert "min" in metric, f"min not a field in metric" - assert "max" in metric, f"max not a field in metric" - assert "maximize" in metric, f"maximize not a field in metric" - assert isinstance(metric['metric_id'], str), "not a string" - assert isinstance(metric['metric_name'], str), "not a string" + assert "name" in metric is not None, "metric_id not a field or is empty" + assert "pretty_name" in metric is not None, "pretty_name not a field in metric or is empty" + assert "summary" in metric is not None, "summary not a field in metric or is empty" + assert "description" in metric is not None, "description not a field in metric or is empty" + assert "reference" in metric, "reference not a field in metric" + assert "documentation_url" in metric , "documentation_url not a field in metric" + assert "repository_url" in metric , "repository_url not an info field" + assert "min" in metric is not None, f"min not a field in metric or is emtpy" + assert "max" in metric is not None, f"max not a field in metric or is empty" + assert "maximize" in metric is not None, f"maximize not a field in metric or is emtpy" assert isinstance(metric['min'], int), "not an int" assert isinstance(metric['max'], (int, str)), "not an int or string (+inf)" - assert isinstance(metric['maximize'], bool), "not a bool" + assert isinstance(metric['maximize'], bool) or metric["maximize"] not in ["-inf", "+inf"], "not a bool" print("Load config data", flush=True) with open(meta["config"], "r") as file: config = yaml.safe_load(file) -info = config['functionality']['info'] - print("check general fields", flush=True) +assert "name" in config["functionality"] is not None, "Name not a field or is empty" assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" print("Check info fields", flush=True) +info = config['functionality']['info'] +print(info) +assert "type" in info, "type not an info field" +assert info["type"] == "metric" , f"got {info['type']} expected 'metric'" assert "metrics" in info, "metrics not an info field" for metric in info["metrics"]: check_metric(metric) From c8a3322c65df2a44521eea407bf23daa1359e60f Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Wed, 29 Mar 2023 21:28:16 +0200 Subject: [PATCH 0811/1233] update denoising configs Former-commit-id: 126a5fb3b2b61207c94a5bdd27cb9a97312c2800 --- CONTRIBUTING.qmd | 2 +- .../no_denoising/config.vsh.yaml | 6 ++-- .../perfect_denoising/config.vsh.yaml | 7 +++-- src/denoising/methods/alra/config.vsh.yaml | 31 +++++++++---------- src/denoising/methods/dca/config.vsh.yaml | 18 ++++++----- .../methods/knn_smoothing/config.vsh.yaml | 20 +++++++++--- src/denoising/methods/magic/config.vsh.yaml | 20 +++++++++--- src/denoising/metrics/mse/config.vsh.yaml | 16 +++++----- src/denoising/metrics/poisson/config.vsh.yaml | 18 ++++++----- 9 files changed, 85 insertions(+), 53 deletions(-) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 7f52701b1b..60fd63d583 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -174,7 +174,7 @@ functionality: # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" # paper_year: 1967 - code_url: "https://github.com/my_organisation/foo" + repository_url: "https://github.com/my_organisation/foo" resources: - type: python_script path: script.py diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 0c63fde42f..6ddc6bbdb5 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -2,10 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "no_denoising" namespace: "denoising/control_methods" - description: "negative control by copying train counts" + info: subtype: negative_control - method_name: No Denoising + pretty_name: No Denoising + summary: "negative control by copying train counts" + description: "This baseline method serves as a negative control, where the denoised data is a copy of the unaltered training data. This represents the scoring threshold if denoising was not performed on the data." v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index af457bb973..a3bbda6645 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -1,11 +1,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "perfect_denoising" - namespace: "denoising/control_methods" - description: "Negative control by copying the train counts" + namespace: "denoising/control_methods" info: subtype: positive_control - method_name: Perfect Denoising + pretty_name: Perfect Denoising + summary: "Positive control by copying the test counts" + description: "This baseline serves as a positive control, where the test data is copied 1-to-1 to the denoised data. This makes it seem as if the data is perfectly denoised as it will be compared to the test data in the metrics." v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index 11f2b75ca3..f686d809b1 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -2,30 +2,27 @@ __merge__: ../../api/comp_method.yaml functionality: name: "alra" namespace: "denoising/methods" - description: | - Adaptively-thresholded Low Rank Approximation (ALRA). - - ALRA is a method for imputation of missing values in single cell RNA-sequencing data, - described in the preprint, "Zero-preserving imputation of scRNA-seq data using low-rank approximation" - available [here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a - scRNA-seq expression matrix, ALRA first computes its rank-k approximation using randomized SVD. - Next, each row (gene) is thresholded by the magnitude of the most negative value of that gene. - Finally, the matrix is rescaled. info: - method_name: ALRA - paper_reference: "linderman2018zero" - code_url: "https://github.com/KlugerLab/ALRA" - doc_url: https://github.com/KlugerLab/ALRA/blob/master/README.md + pretty_name: ALRA + summary: "ALRA imputes missing values in scRNA-seq data by computing rank-k approximation, thresholding by gene, and rescaling the matrix." + description: | + "Adaptively-thresholded Low Rank Approximation (ALRA). + + ALRA is a method for imputation of missing values in single cell RNA-sequencing data, + described in the preprint, "Zero-preserving imputation of scRNA-seq data using low-rank approximation" + available [here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a + scRNA-seq expression matrix, ALRA first computes its rank-k approximation using randomized SVD. + Next, each row (gene) is thresholded by the magnitude of the most negative value of that gene. + Finally, the matrix is rescaled." + reference: "linderman2018zero" + repository_url: "https://github.com/KlugerLab/ALRA" + documentation_url: https://github.com/KlugerLab/ALRA/blob/master/README.md v1_url: openproblems/tasks/denoising/methods/alra.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: alra: preferred_normalization: counts arguments: - - name: "--layer_input" - type: string - default: "counts" - description: Which layer to use as input. - name: "--epochs" type: "integer" default: 300 diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 6e2fff5b4c..da088fa8f2 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -2,15 +2,17 @@ __merge__: ../../api/comp_method.yaml functionality: name: "dca" namespace: "denoising/methods" - description: | - Deep Count Autoencoder - - Removes the dropout effect by taking the count structure, overdispersed nature and sparsity of the data into account - using a deep autoencoder with zero-inflated negative binomial (ZINB) loss function. info: - method_name: DCA - paper_reference: "https://www.nature.com/articles/s41467-018-07931-2" - code_url: "https://github.com/theislab/dca" + pretty_name: DCA + summary: "A deep autoencoder with ZINB loss function to address the dropout effect in count data" + description: | + "Deep Count Autoencoder + + Removes the dropout effect by taking the count structure, overdispersed nature and sparsity of the data into account + using a deep autoencoder with zero-inflated negative binomial (ZINB) loss function." + reference: "eraslan2019single" + documentation_url: "https://github.com/theislab/dca#readme" + repository_url: "https://github.com/theislab/dca" v1_url: openproblems/tasks/denoising/methods/dca.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 61ee627cc8..9bab76224b 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -2,11 +2,23 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn_smoothing" namespace: "denoising/methods" - description: "iterative K-nearest neighbor smoothing" info: - method_name: KNN Smoothing - paper_reference: "wagner2018knearest" - code_url: "https://github.com/yanailab/knn-smoothing" + pretty_name: KNN Smoothing + summary: "Iterative kNN-smoothing denoises scRNA-seq data by iteratively increasing the size of neighbourhoods for smoothing until a maximum k value is reached." + description: "Iterative kNN-smoothing is a method to repair or denoise noisy scRNA-seq + expression matrices. Given a scRNA-seq expression matrix, KNN-smoothing first + applies initial normalisation and smoothing. Then, a chosen number of + principal components is used to calculate Euclidean distances between cells. + Minimally sized neighbourhoods are initially determined from these Euclidean + distances, and expression profiles are shared between neighbouring cells. + Then, the resultant smoothed matrix is used as input to the next step of + smoothing, where the size (k) of the considered neighbourhoods is increased, + leading to greater smoothing. This process continues until a chosen maximum k + value has been reached, at which point the iteratively smoothed object is + then optionally scaled to yield a final result." + reference: "wagner2018knearest" + documentation_url: "https://github.com/yanailab/knn-smoothing#readme" + repository_url: "https://github.com/yanailab/knn-smoothing" v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index b479e8a1e2..365bb6fb2a 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -2,11 +2,23 @@ __merge__: ../../api/comp_method.yaml functionality: name: "magic" namespace: "denoising/methods" - description: "MAGIC: Markov affinity-based graph imputation of cells" info: - method_name: MAGIC - paper_reference: "https://doi.org/10.1016/j.cell.2018.05.061" - code_url: "https://github.com/KrishnaswamyLab/MAGIC" + pretty_name: MAGIC + summary: "MAGIC imputes and denoises scRNA-seq data using Euclidean distances and a Gaussian kernel to calculate the affinity matrix, followed by a Markov process and multiplication with the normalised data to obtain imputed values." + description: "MAGIC (Markov Affinity-based Graph Imputation of Cells) is a method for + imputation and denoising of noisy or dropout-prone single cell RNA-sequencing + data. Given a normalised scRNA-seq expression matrix, it first calculates + Euclidean distances between each pair of cells in the dataset, which is then + augmented using a Gaussian kernel (function) and row-normalised to give a + normalised affinity matrix. A t-step markov process is then calculated, by + powering this affinity matrix t times. Finally, the powered affinity matrix + is right-multiplied by the normalised data, causing the final imputed values + to take the value of a per-gene average weighted by the affinities of cells. + The resultant imputed matrix is then rescaled, to more closely match the + magnitude of measurements in the normalised (input) matrix." + reference: "van2018recovering" + documentation_url: "https://github.com/KrishnaswamyLab/MAGIC#readme" + repository_url: "https://github.com/KrishnaswamyLab/MAGIC" v1_url: openproblems/tasks/denoising/methods/magic.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 0db45933d2..4d4e4004b1 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -2,15 +2,17 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "mse" namespace: "denoising/metrics" - description: "Mean Squared Error." info: - paper_reference: "batson2019molecular" - v1_url: openproblems/tasks/denoising/metrics/mse.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - - metric_id: mse - metric_name: Mean-squared error - metric_description: The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio + - name: mse + pretty_name: Mean-squared error + summary: "The mean squared error between the denoised counts and the true counts." + description: "The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio" + reference: batson2019molecular + documentation_url: "" + repository_url: "" + v1_url: openproblems/tasks/denoising/metrics/mse.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf maximize: false min: 0 max: +inf diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index e56dccebbe..8494f24621 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -2,15 +2,19 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "poisson" namespace: "denoising/metrics" - description: "Poisson loss" info: - paper_reference: "batson2019molecular" - v1_url: openproblems/tasks/denoising/metrics/poisson.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + reference: "batson2019molecular" metrics: - - metric_id: poisson - metric_name: Poisson Loss - metric_description: "Poisson loss: measure the mean of the inconsistencies between predicted and target" + - name: poisson + pretty_name: Poisson Loss + summary: "The Poisson log lieklihood of the true counts observed in the distribution of denoised counts" + description: "The Poisson log likelihood of observing the true counts of the test dataset + given the distribution given in the denoised dataset." + reference: batson2019molecular + documentation_url: "" + repository_url: "" + v1_url: openproblems/tasks/denoising/metrics/poisson.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf maximize: false min: 0 max: +inf From ac18ab0e0f05f97f08bae69b9765cbfa07ca09d9 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 31 Mar 2023 09:03:59 +0200 Subject: [PATCH 0812/1233] update dim_red Former-commit-id: 95184a73bfb65e508db4809a4308401e11df1031 --- .../random_features/config.vsh.yaml | 7 +- .../true_features/config.vsh.yaml | 4 +- .../methods/densmap/config.vsh.yaml | 10 +-- .../methods/ivis/config.vsh.yaml | 12 +++- .../methods/neuralee/config.vsh.yaml | 18 +++-- .../methods/pca/config.vsh.yaml | 16 +++-- .../methods/phate/config.vsh.yaml | 18 +++-- .../methods/tsne/config.vsh.yaml | 16 +++-- .../methods/umap/config.vsh.yaml | 15 ++-- .../metrics/coranking/config.vsh.yaml | 72 +++++++++++++------ .../density_preservation/config.vsh.yaml | 18 ++--- .../metrics/rmse/config.vsh.yaml | 22 +++--- .../metrics/trustworthiness/config.vsh.yaml | 8 ++- .../workflows/run/main.nf | 4 +- 14 files changed, 165 insertions(+), 75 deletions(-) diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 51b6865a6f..fdac452995 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -2,10 +2,11 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_features" namespace: "dimensionality_reduction/control_methods" - description: "Uses a normal distribution to generate random embeddings." info: subtype: negative_control - method_name: Random Features + pretty_name: Random Features + summary: "Negative control by randomly embedding into a 2D space." + description: "This method serves as a negative control, where the data is randomly embedded into a two-dimensional space, with no attempt to preserve the original structure." v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: counts @@ -24,4 +25,4 @@ platforms: - "anndata>=0.8" - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 4000c6b6a8..4bdd1e22ed 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -5,7 +5,9 @@ functionality: description: "Positive control method which generates high-dimensional (full data) embedding" info: subtype: positive_control - method_name: True Features + pretty_name: True Features + summary: "Positive control by retaining the dimensionality without loss of information." + description: "This serves as a positive control since the original high-dimensional data is retained as is, without any loss of information" v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py v1_comp_id: "True Features" v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 63c5d3424a..4be7bb71ad 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -2,11 +2,13 @@ __merge__: ../../api/comp_method.yaml functionality: name: "densmap" namespace: "dimensionality_reduction/methods" - description: "Density-preserving UMAP" info: - method_name: densMAP - paper_reference: "narayan2021assessing" - code_url: https://github.com/lmcinnes/umap + pretty_name: densMAP + summary: "Modified UMAP with preservation of local density information" + description: "A modification of UMAP that adds an extra cost term in order to preserve information about the relative local density of the data. It is performed on the same inputs as UMAP." + reference: "narayan2021assessing" + repository_url: https://github.com/lmcinnes/umap + documentation_url: https://github.com/lmcinnes/umap#readme v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index 61b0f1465a..2b934f3527 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -1,6 +1,7 @@ # see https://github.com/openproblems-bio/openproblems/blob/9ebb777b3b76337e731a3b99f4bf39462a15c4cc/openproblems/tasks/dimensionality_reduction/methods/ivis.py __merge__: ../../api/comp_method.yaml +status: disabled #Temporarily removed from OPv1 see commit 93d2161a08da3edf249abedff5111fb5ce527552 functionality: name: "ivis" namespace: "dimensionality_reduction/methods" @@ -9,9 +10,14 @@ functionality: ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using a parametric mapping function, and scales linearly to millions of observations. info: - method_name: "ivis" - paper_reference: szubert2019structurepreserving - code_url: https://github.com/beringresearch/ivis + pretty_name: "ivis" + summary: + description: | + "ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. + ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using + a parametric mapping function, and scales linearly to millions of observations." + reference: szubert2019structurepreserving + repository_url: https://github.com/beringresearch/ivis v1_url: openproblems/tasks/dimensionality_reduction/methods/ivis.py v1_commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 378ef026f9..f195f449cf 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -2,11 +2,21 @@ __merge__: ../../api/comp_method.yaml functionality: name: "neuralee" namespace: "dimensionality_reduction/methods" - description: "A neural network implementation of elastic embedding implemented in the [NeuralEE package](https://neuralee.readthedocs.io/en/latest/)." info: - method_name: NeuralEE - paper_reference: "xiong2020neuralee" - code_url: https://github.com/HiBearME/NeuralEE + pretty_name: NeuralEE + summary: "Non-linear method that uses a neural network to preserve pairwise distances between data points in a high-dimensional space." + description: | + "A neural network implementation of elastic embedding. It is a + non-linear method that preserves pairwise distances between data points. + NeuralEE uses a neural network to optimize an objective function that + measures the difference between pairwise distances in the original + high-dimensional space and the two-dimensional space. It is computed on both + the recommended input from the package authors of 500 HVGs selected from a + logged expression matrix (without sequencing depth scaling) and the default + logCPM matrix with 1000 HVGs." + reference: "xiong2020neuralee" + repository_url: "https://github.com/HiBearME/NeuralEE" + documentation_url: "https://github.com/HiBearME/NeuralEE#readme" v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 1b5cced743..658f575412 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -2,11 +2,19 @@ __merge__: ../../api/comp_method.yaml functionality: name: "pca" namespace: "dimensionality_reduction/methods" - description: "Principal component analysis (PCA)" info: - method_name: "PCA" - paper_reference: pearson1901pca - code_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html + pretty_name: "PCA" + summary: "A linear method that finds orthogonal directions to compute the two-dimensional embedding, capturing maximum variance from logCPM expression matrix with/without selecting 1000 HVGs." + description: | + 'Principal Component Analysis is a linear method that finds orthogonal + directions in the data that capture the most variance. The first two + principal components are chosen as the two-dimensional embedding. We select + only the first two principal components as the two-dimensional embedding. PCA + is calculated on the logCPM expression matrix with and without selecting 1000 + HVGs.' + reference: pearson1901pca + repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" + documentatoin_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index c0dd529295..9ae1b1d6ea 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -2,11 +2,21 @@ __merge__: ../../api/comp_method.yaml functionality: name: "phate" namespace: "dimensionality_reduction/methods" - description: "Potential of heat-diffusion for affinity-based transition embedding" info: - method_name: PHATE - paper_reference: "moon2019visualizing" - code_url: https://github.com/KrishnaswamyLab/PHATE/ + pretty_name: PHATE + summary: "Preservating trajectories in a dataset by using heat diffusion potential via an affinity-based method that creates an embedding from dominant eigenvalues of a Markov transition matrix." + description: | + "PHATE or “Potential of Heat - diffusion for Affinity - based Transition + Embedding” uses the potential of heat diffusion to preserve trajectories in a + dataset via a diffusion process. It is an affinity - based method that + creates an embedding by finding the dominant eigenvalues of a Markov + transition matrix. We evaluate several variants including using the + recommended square - root transformed CPM matrix as input, this input with + the gamma parameter set to zero and the normal logCPM transformed matrix with + and without HVG selection." + reference: "moon2019visualizing" + repository_url: "https://github.com/KrishnaswamyLab/PHATE" + documentation_url: "https://github.com/KrishnaswamyLab/PHATE#readme" v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: sqrt_cpm diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index b876ff685c..786c56dc8e 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -2,11 +2,19 @@ __merge__: ../../api/comp_method.yaml functionality: name: "tsne" namespace: "dimensionality_reduction/methods" - description: "t-Distributed Stochastic Neighbor Embedding (t-SNE)" info: - method_name: t-SNE - paper_reference: vandermaaten2008visualizing - code_url: https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE + pretty_name: t-SNE + summary: "Minimizing Kullback-Leibler divergence by converting similarities into joint probabilities between data points and the low/high dimensional embedding." + description: | + "t-distributed Stochastic Neighbor Embedding converts similarities + between data points to joint probabilities and tries to minimize the + Kullback-Leibler divergence between the joint probabilities of the + low-dimensional embedding and the high-dimensional data. We use the + implementation in the scanpy package with the result of PCA on the logCPM + expression matrix (with and without HVG selection)." + reference: vandermaaten2008visualizing + repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE" + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE" v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 8a126590d9..4684209d2b 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -2,11 +2,18 @@ __merge__: ../../api/comp_method.yaml functionality: name: "umap" namespace: "dimensionality_reduction/methods" - description: "Uniform Manifold Approximation and Projection for Dimension Reduction" info: - method_name: UMAP - paper_reference : "mcinnes2018umap" - code_url: https://github.com/lmcinnes/umap + pretty_name: UMAP + summary: "A manifold learning algorithm that utilizes topological data analysis for dimension reduction." + description: | + "Uniform Manifold Approximation and Projection is an algorithm for + dimension reduction based on manifold learning techniques and ideas from + topological data analysis. We perform UMAP on the logCPM expression matrix + before and after HVG selection and with and without PCA as a pre-processing + step." + reference : "mcinnes2018umap" + repository_url: "https://github.com/lmcinnes/umap" + documentation_url: "https://github.com/lmcinnes/umap#readme" v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 6bfc3b0ec0..d190d6183d 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -15,47 +15,75 @@ functionality: In addition, the references for each of the metrics were looked up to properly attribute the original authors of each of the metrics. - paper_reference: kraemer2018dimred + reference: kraemer2018dimred metrics: - - metric_id: continuity_at_k30 - metric_name: Continuity at k=30 - paper_reference: venna2006local + - name: continuity_at_k30 + pretty_name: Continuity at k=30 + reference: venna2006local + summary: "" + description: "" + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true - - metric_id: trustworthiness_at_k30 - metric_name: Trustworthiness at k=30 - paper_reference: venna2006local + - name: trustworthiness_at_k30 + pretty_name: Trustworthiness at k=30 + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: venna2006local min: 0 max: 1 maximize: true - - metric_id: qnx_at_k30 - metric_name: The value for QNX at k=30 - paper_reference: lee2009quality + - name: qnx_at_k30 + pretty_name: The value for QNX at k=30 + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: lee2009quality min: 0 max: 1 maximize: true - - metric_id: lcmc_at_k30 - metric_name: The value for LCMC at k=30 - paper_reference: chen2009local + - name: lcmc_at_k30 + pretty_name: The value for LCMC at k=30 + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: chen2009local min: 0 max: 1 maximize: true - - metric_id: qnx_auc - metric_name: Area under the QNX curve - paper_reference: lueks2011evaluate + - name: qnx_auc + pretty_name: Area under the QNX curve + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: lueks2011evaluate min: 0 max: 1 maximize: true - - metric_id: qlocal - metric_name: Local quality measure - paper_reference: lueks2011evaluate + - name: qlocal + pretty_name: Local quality measure + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: lueks2011evaluate min: 0 max: 1 maximize: true - - metric_id: qglobal - metric_name: Global quality measure - paper_reference: lueks2011evaluate + - name: qglobal + pretty_name: Global quality measure + summary: "" + description: "" + repository_url: "" + documentation_url: "" + reference: lueks2011evaluate min: 0 max: 1 maximize: true diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 3c1c9c78b5..53cede8a1f 100644 --- a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -2,19 +2,19 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "density_preservation" namespace: "dimensionality_reduction/metrics" - description: | - Similarity between local densities in the high-dimensional data and the reduced data. info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - - metric_id: density_preservation - metric_name: Density preservation - metric_description: | - Similarity between local densities in the high-dimensional data and the reduced data. - - This is computed as the pearson correlation of local radii with the local radii in the original data space. - paper_reference: narayan2021assessing + - name: density_preservation + pretty_name: Density preservation + summary: "Similarity between local densities in the high-dimensional data and the reduced data." + description: | + "Similarity between local densities in the high-dimensional data and the reduced data. + This is computed as the pearson correlation of local radii with the local radii in the original data space." + repository_url: "" + documentation_url: "" + reference: narayan2021assessing min: -1 max: 1 maximize: true diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index aecfaadb1c..30cb3bc133 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -8,17 +8,23 @@ functionality: v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b v1_note: This metric was ported but will probably be removed soon. metrics: - - metric_id: rmse - metric_name: RMSE - metric_description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." - paper_reference: kruskal1964mds + - name: rmse + pretty_name: RMSE + summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." + description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." + reference: kruskal1964mds + repository_url: "" + documentation_url: "" min: 0 max: +inf maximize: false - - metric_id: rmse_spectral - metric_name: RMSE Spectral - metric_description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." - paper_reference: coifman2006diffusion + - name: rmse_spectral + pretty_name: RMSE Spectral + summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." + description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." + reference: coifman2006diffusion + repository_url: "" + documentation_url: "" min: 0 max: +inf maximize: false diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 7433e4ec00..dc16765138 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -8,9 +8,11 @@ functionality: v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a v1_note: This metric is already included in the 'coranking' component and can be removed. metrics: - - metric_id: trustworthiness - metric_name: Trustworthiness at k=15 - paper_reference: venna2006local + - name: trustworthiness + pretty_name: Trustworthiness at k=15 + summary: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." + description: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." + reference: venna2006local min: 0 max: 1 maximize: true diff --git a/src/dimensionality_reduction/workflows/run/main.nf b/src/dimensionality_reduction/workflows/run/main.nf index 742695a9c7..f89ff9a7b5 100644 --- a/src/dimensionality_reduction/workflows/run/main.nf +++ b/src/dimensionality_reduction/workflows/run/main.nf @@ -14,7 +14,7 @@ include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.n include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" -include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" +// include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" // import metrics include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" @@ -32,7 +32,7 @@ include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; pa config = readConfig("$projectDir/config.vsh.yaml") // construct a map of methods (id -> method_module) -methods = [ random_features, true_features, umap, densmap, phate, tsne, pca, neuralee, ivis ] +methods = [ random_features, true_features, umap, densmap, phate, tsne, pca, neuralee ] .collectEntries{method -> [method.config.functionality.name, method] } From b3b1d861b5b244239b78eb6bc343a942d5736e28 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 31 Mar 2023 09:51:36 +0200 Subject: [PATCH 0813/1233] fix config dim_red Former-commit-id: 7252ed7d67f070a7ec40b663a63eb8b4fd18dc7b --- .../methods/ivis/config.vsh.yaml | 13 ++++++------- .../methods/pca/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 ++ 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index 2b934f3527..c688f4cfaa 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -1,23 +1,22 @@ # see https://github.com/openproblems-bio/openproblems/blob/9ebb777b3b76337e731a3b99f4bf39462a15c4cc/openproblems/tasks/dimensionality_reduction/methods/ivis.py __merge__: ../../api/comp_method.yaml -status: disabled #Temporarily removed from OPv1 see commit 93d2161a08da3edf249abedff5111fb5ce527552 functionality: + #Temporarily removed from OPv1 see commit 93d2161a08da3edf249abedff5111fb5ce527552 + status: disabled name: "ivis" namespace: "dimensionality_reduction/methods" - description: | - ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. - ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using - a parametric mapping function, and scales linearly to millions of observations. info: pretty_name: "ivis" - summary: + summary: "" description: | "ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using a parametric mapping function, and scales linearly to millions of observations." reference: szubert2019structurepreserving - repository_url: https://github.com/beringresearch/ivis + repository_url: "https://github.com/beringresearch/ivis" + documentation_url: "https://github.com/beringresearch/ivis#readme" + reference: "" v1_url: openproblems/tasks/dimensionality_reduction/methods/ivis.py v1_commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 658f575412..5527d14a84 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: HVGs.' reference: pearson1901pca repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" - documentatoin_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index dc16765138..d37ce37638 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -13,6 +13,8 @@ functionality: summary: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." description: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." reference: venna2006local + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true From 36c2525dea00b4a80e4245ff548ca2105ef2232d Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 31 Mar 2023 11:11:05 +0200 Subject: [PATCH 0814/1233] update label_projection Former-commit-id: 2c3610bb0e58675661cdbedfb4dce432e5153131 --- .../majority_vote/config.vsh.yaml | 5 +-- .../random_labels/config.vsh.yaml | 5 +-- .../true_labels/config.vsh.yaml | 4 ++- .../methods/knn/config.vsh.yaml | 21 ++++++++----- .../logistic_regression/config.vsh.yaml | 18 ++++++----- .../methods/mlp/config.vsh.yaml | 21 ++++++++----- .../methods/scanvi/config.vsh.yaml | 20 +++++++----- .../seurat_transferdata/config.vsh.yaml | 17 +++++++--- .../methods/xgboost/config.vsh.yaml | 14 ++++++--- .../metrics/accuracy/config.vsh.yaml | 11 ++++--- .../metrics/f1/config.vsh.yaml | 31 +++++++++++++------ 11 files changed, 109 insertions(+), 58 deletions(-) diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index 642f430fca..ad4edc6604 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -2,10 +2,11 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "majority_vote" namespace: "label_projection/control_methods" - description: "Baseline method using majority voting" info: subtype: negative_control - method_name: Majority Vote + pretty_name: Majority Vote + summary: "A baseline-type method that predicts all cells to belong to the most abundant cell type in the dataset" + description: "A baseline-type method that predicts all cells to belong to the most abundant cell type in the dataset" v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c variants: diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 25c280f574..837e1f82cf 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -2,10 +2,11 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_labels" namespace: "label_projection/control_methods" - description: "Negative control method which generates random labels" info: subtype: negative_control - method_name: Random Labels + pretty_name: Random Labels + summary: "a negative control, where the labels are randomly predicted." + description: "A negative control, where the labels are randomly predicted without training the data." v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 68abd74498..62e4e97f9c 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -5,7 +5,9 @@ functionality: description: "Positive control method by returning the true labels" info: subtype: positive_control - method_name: True labels + pretty_name: True labels + summary: "a positive control, solution labels are copied 1 to 1 to the predicted data." + description: "A positive control, where the solution labels are copied 1 to 1 to the predicted data." v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 1555da9c31..507e18d730 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -2,15 +2,20 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn" namespace: "label_projection/methods" - description: "K-Nearest Neighbors classifier" info: - method_name: KNN - # paper_name: "Nearest neighbor pattern classification" - # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" - # paper_year: 1967 - paper_reference : "cover1967nearest" - code_url: https://github.com/scikit-learn/scikit-learn - doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" + pretty_name: KNN + summary: "Assumes cells with similar gene expression belong to the same cell type, and assigns an unlabelled cell the most common cell type among its k nearest neighbors in PCA space." + description: | + 'Using the "k-nearest neighbours" approach, which is a + popular machine learning algorithm for classification and regression tasks. + The assumption underlying KNN in this context is that cells with similar gene + expression profiles tend to belong to the same cell type. For each unlabelled + cell, this method computes the $k$ labelled cells (in this case, 5) with the + smallest distance in PCA space, and assigns that cell the most common cell + type among its $k$ nearest neighbors.' + reference : "cover1967nearest" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 8cab5126db..d3d1f45441 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -2,15 +2,17 @@ __merge__: ../../api/comp_method.yaml functionality: name: "logistic_regression" namespace: "label_projection/methods" - description: "Logistic regression method" info: - method_name: Logistic Regression - # paper_name: "Applied Logistic Regression" - # paper_url: "https://books.google.com/books?id=64JYAwAAQBAJ" - # paper_year: 2013 - paper_reference: "hosmer2013applied" - code_url: https://github.com/scikit-learn/scikit-learn - doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" + pretty_name: Logistic Regression + summary: "Logistic Regression with 100-dimensional PCA coordinates estimates parameters for multivariate classification by minimizing cross entropy loss over cell type classes." + description: | + "Logistic Regression estimates parameters of a logistic function for + multivariate classification tasks. Here, we use 100-dimensional whitened PCA + coordinates as independent variables, and the model minimises the cross + entropy loss over all cell type classes." + reference: "hosmer2013applied" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index ff2751ffcd..b7a30091bd 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -2,15 +2,20 @@ __merge__: ../../api/comp_method.yaml functionality: name: "mlp" namespace: "label_projection/methods" - description: "Multilayer perceptron" info: - method_name: Multilayer perceptron - # paper_name: "Connectionist learning procedures" - # paper_url: "https://doi.org/10.1016/0004-3702(89)90049-0" - # paper_year: 1990 - paper_reference: "hinton1989connectionist" - code_url: https://github.com/scikit-learn/scikit-learn - doc_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" + pretty_name: Multilayer perceptron + summary: "A neural network with 100-dimensional PCA input, two hidden layers, and gradient descent weight updates to minimize cross entropy loss." + description: | + "Multi-Layer Perceptron is a type of artificial neural network that + consists of multiple layers of interconnected neurons. Each neuron computes a + weighted sum of all neurons in the previous layer and transforms it with + nonlinear activation function. The output layer provides the final + prediction, and network weights are updated by gradient descent to minimize + the cross entropy loss. Here, the input data is 100-dimensional whitened PCA + coordinates for each cell, and we use two hidden layers of 100 neurons each." + reference: "hinton1989connectionist" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1_url: openproblems/tasks/label_projection/methods/mlp.py v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 2ec00a3dfb..cd3afbbdbf 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -2,14 +2,20 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" namespace: "label_projection/methods" - description: | - Probabilistic harmonization and annotation of single-cell - transcriptomics data with deep generative models. info: - method_name: SCANVI - paper_reference: "lotfollahi2020query" - code_url: "https://github.com/YosefLab/scvi-tools" - doc_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html + pretty_name: SCANVI + summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." + description: | + "single-cell ANnotation using Variational Inference is a + semi-supervised variant of the scVI(Lopez et al. 2018) algorithm. Like scVI, + scANVI uses deep neural networks and stochastic optimization to model + uncertainty caused by technical noise and bias in single - cell + transcriptomics measurements. However, scANVI also leverages cell type labels + in the generative modelling. In this approach, scANVI is used to predict the + cell type labels of the unlabelled test data." + reference: "lotfollahi2020query" + repository_url: "https://github.com/YosefLab/scvi-tools" + documentation_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 v1_comp_id: scarches_scanvi_hvg diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index d7fed1239e..28c6c17346 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -6,10 +6,19 @@ functionality: The Seurat v3 anchoring procedure is designed to integrate diverse single-cell datasets across technologies and modalities. info: - method_name: Seurat TransferData - paper_reference: "hao2021integrated" - code_url: "https://github.com/satijalab/seurat" - doc_url: "https://satijalab.org/seurat/articles/integration_mapping.html" + pretty_name: Seurat TransferData + summary: "Seurat reference mapping predicts cell types for unlabelled cells using PCA distances, labelled anchors, and transfer anchors from Seurat, with SCTransform normalization." + description: | + "Seurat reference mapping is a cell type label transfer method provided by the + Seurat package. Gene expression counts are first normalised by SCTransform + before computing PCA. Then it finds mutual nearest neighbours, known as + transfer anchors, between the labelled and unlabelled part of the data in PCA + space, and computes each cell’s distance to each of the anchor pairs. + Finally, it uses the labelled anchors to predict cell types for unlabelled + cells based on these distances." + reference: "hao2021integrated" + repository_url: "https://github.com/satijalab/seurat" + documentation_url: "https://satijalab.org/seurat/articles/integration_mapping.html" v1_url: openproblems/tasks/label_projection/methods/seurat.py v1_commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 preferred_normalization: log_cpm diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index 3a3d9e2970..b28f410b23 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -4,10 +4,16 @@ functionality: namespace: "label_projection/methods" description: "XGBoost: A Scalable Tree Boosting System" info: - method_name: XGBoost - paper_reference: "chen2016xgboost" - code_url: "https://github.com/dmlc/xgboost" - doc_url: "https://xgboost.readthedocs.io/en/stable/index.html" + pretty_name: XGBoost + summary: "XGBoost is a decision tree model that averages multiple trees with gradient boosting." + description: | + "XGBoost is a gradient boosting decision tree model that learns multiple tree + structures in the form of a series of input features and their values, + leading to a prediction decision, and averages predictions from all its + trees. Here, input features are normalised gene expression values." + reference: "chen2016xgboost" + repository_url: "https://github.com/dmlc/xgboost" + documentation_url: "https://xgboost.readthedocs.io/en/stable/index.html" v1_url: openproblems/tasks/label_projection/methods/xgboost.py v1_commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c preferred_normalization: log_cpm diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index f4994ec4f1..edcd9bcd03 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -2,14 +2,17 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "accuracy" namespace: "label_projection/metrics" - description: "The percentage of correctly predicted labels." info: v1_url: openproblems/tasks/label_projection/metrics/accuracy.py v1_commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 metrics: - - metric_id: accuracy - metric_name: Accuracy - description: The percentage of correctly predicted labels. + - name: accuracy + pretty_name: Accuracy + summary: "The percentage of correctly predicted labels." + description: "The percentage of correctly predicted labels." + reference: "" + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 742123317d..d74681b359 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -2,26 +2,37 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "f1" namespace: "label_projection/metrics" - description: "balanced F-score or F-measure" info: v1_url: openproblems/tasks/label_projection/metrics/f1.py v1_commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 metrics: - - metric_id: f1_weighted - metric_name: F1 weighted - description: Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall. + - name: f1_weighted + pretty_name: F1 weighted + summary: "Average weigthed support between each labels F1 score" + description: "Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall." + reference: "" + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true - - metric_id: f1_macro - metric_name: F1 macro - description: Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account. + - name: f1_macro + pretty_name: F1 macro + summary: "Unweighted mean of each label F1-score" + description: "Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account." + reference: "" + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true - - metric_id: f1_micro - metric_name: F1 micro - description: Calculates the F1 score globally by counting the total true positives, false negatives and false positives. + - name: f1_micro + pretty_name: F1 micro + summary: "Calculation of TP, FN and FP." + description: "Calculates the F1 score globally by counting the total true positives, false negatives and false positives." + reference: "" + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true From 3c34ea3b01f24d6eb94dca64a4a06597987b8d97 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Fri, 31 Mar 2023 11:44:24 +0200 Subject: [PATCH 0815/1233] update batch_integration Former-commit-id: 87c15b623eaf3d371240c9f0e6ab1ab695a616bd --- .../methods/bbknn/config.vsh.yaml | 14 ++++++++++---- .../methods/combat/config.vsh.yaml | 18 +++++++++++++----- .../methods/scanorama_embed/config.vsh.yaml | 12 +++++++----- .../methods/scanorama_feature/config.vsh.yaml | 10 +++++++--- .../methods/scvi/config.vsh.yaml | 6 +++--- .../metrics/asw_batch/config.vsh.yaml | 12 ++++++++---- .../metrics/asw_label/config.vsh.yaml | 11 ++++++++--- .../cell_cycle_conservation/config.vsh.yaml | 12 ++++++++---- .../embed_to_graph/config.vsh.yaml | 2 +- .../feature_to_embed/config.vsh.yaml | 2 +- 10 files changed, 66 insertions(+), 33 deletions(-) diff --git a/src/batch_integration/methods/bbknn/config.vsh.yaml b/src/batch_integration/methods/bbknn/config.vsh.yaml index 50854683b3..63a2c1d44c 100644 --- a/src/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/batch_integration/methods/bbknn/config.vsh.yaml @@ -2,11 +2,17 @@ __merge__: ../../api/comp_method_graph.yaml functionality: name: bbknn - description: "BBKNN: fast batch alignment of single cell transcriptomes" info: - method_name: BBKNN - paper_reference: "polanski2020bbknn" - code_url: https://github.com/Teichlab/bbknn + pretty_name: BBKNN + summary: "BBKNN creates k nearest neighbours graph by identifying neighbours within batches, then combining and processing them with UMAP for visualization." + description: | + "BBKNN or batch balanced k nearest neighbours graph is built for each cell by + identifying its k nearest neighbours within each defined batch separately, + creating independent neighbour sets for each cell in each batch. These sets + are then combined and processed with the UMAP algorithm for visualisation." + reference: "polanski2020bbknn" + repository_url: "https://github.com/Teichlab/bbknn" + documentation_url: "https://github.com/Teichlab/bbknn#readme" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/methods/combat/config.vsh.yaml b/src/batch_integration/methods/combat/config.vsh.yaml index 2dc5897394..5479814861 100644 --- a/src/batch_integration/methods/combat/config.vsh.yaml +++ b/src/batch_integration/methods/combat/config.vsh.yaml @@ -2,12 +2,20 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: combat - description: "Adjusting batch effects in microarray expression data using - empirical Bayes methods" info: - method_name: Combat - paper_reference: "hansen2012removing" - code_url: https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html + pretty_name: Combat + summary: "Adjusting batch effects in microarray expression data using + empirical Bayes methods" + description: | + "An Empirical Bayes (EB) approach to correct for batch effects. It + estimates batch-specific parameters by pooling information across genes in + each batch and shrinks the estimates towards the overall mean of the batch + effect estimates across all genes. These parameters are then used to adjust + the data for batch effects, leading to more accurate and reproducible + results." + reference: "hansen2012removing" + repository_url: "https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html" + documentation_url: "https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml index 3e07d09dc9..5d8132905f 100644 --- a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -2,12 +2,14 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scanorama_embed - description: "Efficient integration of heterogeneous single-cell - transcriptomes using Scanorama" info: - method_name: Scanorama - paper_reference: "hie2019efficient" - code_url: https://github.com/brianhie/scanorama + pretty_name: Scanorama + summary: "Efficient integration of heterogeneous single-cell + transcriptomes using Scanorama" + description: + reference: "hie2019efficient" + repository_url: "https://github.com/brianhie/scanorama" + documentation_url: "https://github.com/brianhie/scanorama#readme" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index d1ba995088..73f5812c79 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -5,9 +5,13 @@ functionality: description: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" info: - method_name: Scanorama - paper_reference: "hie2019efficient" - code_url: https://github.com/brianhie/scanorama + pretty_name: Scanorama + summary: "Efficient integration of heterogeneous single-cell + transcriptomes using Scanorama" + description: + reference: "hie2019efficient" + repository_url: "https://github.com/brianhie/scanorama" + documentation_url: "https://github.com/brianhie/scanorama#readme" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index cc9744eb78..f9ad96ffe2 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -4,9 +4,9 @@ functionality: name: scvi description: Run scVI on adata object info: - method_name: scVI - paper_reference: "lopez2018deep" - code_url: https://github.com/YosefLab/scvi-tools" + pretty_name: scVI + reference: "lopez2018deep" + repository_url: https://github.com/YosefLab/scvi-tools" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/metrics/asw_batch/config.vsh.yaml index 816429e85d..da3e7ec6c1 100644 --- a/src/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -2,14 +2,18 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_batch - description: Average silhouette of batches per label info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - paper_reference: luecken2022benchmarking metrics: - - metric_id: asw_batch - metric_name: ASW batch + - name: asw_batch + pretty_name: ASW batch + summary: Average silhouette of batches per label + description: | + "A batch correction metric that computes the silhouette score over all batch labels per cell type. Here, 0 indicates that batches are well mixed and any deviation from 0 indicates there remains a separation between batch labels. This is rescaled to a score between 0 and 1 by taking." + reference: luecken2022benchmarking + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml index 0c5a8bfb0d..1c6d6381e7 100644 --- a/src/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_label/config.vsh.yaml @@ -6,10 +6,15 @@ functionality: info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - paper_reference: luecken2022benchmarking + metrics: - - metric_id: asw_label - metric_name: ASW Label + - name: asw_label + pretty_name: ASW Label + summary: "Average silhouette of labels" + description: "The absolute silhouette width is computed on cell identity labels, measuring their compactness." + reference: luecken2022benchmarking + repository_url: + description_url: min: 0 max: 1 maximize: true diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 61d278e477..e04a48e3b8 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -2,14 +2,18 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: cell_cycle_conservation - description: Cell cycle conservation score based on cell cycle gene scoring info: v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - paper_reference: luecken2022benchmarking + reference: luecken2022benchmarking metrics: - - metric_id: cell_cycle_conservation - metric_name: Cell Cycle Conservation + - name: cell_cycle_conservation + pretty_name: Cell Cycle Conservation + summary: "Cell cycle conservation score based on cell cycle gene scoring" + description: "The cell-cycle conservation score evaluates how well the cell-cycle effect can be captured before and after integration." + reference: + repository_url: + documentation_url: min: 0 max: 1 maximize: true diff --git a/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 3bced2c965..2056dd4ea2 100644 --- a/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: description: "Transform an embedded integration to a graph integration" info: type: method - method_name: Embedding to Graph + pretty_name: Embedding to Graph arguments: - __merge__: ../../api/anndata_integrated_embedding.yaml name: --input diff --git a/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml index a96ce1a610..adc1c14cd5 100644 --- a/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -4,7 +4,7 @@ functionality: description: "Transform a feature integration to an embedded integration" info: type: method - method_name: Feature to Embed + pretty_name: Feature to Embed arguments: - __merge__: ../../api/anndata_integrated_feature.yaml name: --input From 069f66669e99a8fedb08b110fd06e04f766a30c6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 10:16:39 +0200 Subject: [PATCH 0816/1233] update batc_integration Former-commit-id: 05458913878f0ed6f2269829d5258f2b1884a29a --- .../clustering_overlap/config.vsh.yaml | 22 ++++++++++++------- .../metrics/pcr/config.vsh.yaml | 18 ++++++++++----- 2 files changed, 27 insertions(+), 13 deletions(-) diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml index fef72343dd..104b1ff96a 100644 --- a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -5,9 +5,10 @@ functionality: description: Metrics that are based on computing the clustering overlap. info: metrics: - - metric_id: ari - metric_name: ARI - metric_description: | + - name: ari + pretty_name: ARI + summary: "Adjusted Rand Index compares clustering overlap, correcting for random labels and considering correct overlaps and disagreements." + description: | The Adjusted Rand Index (ARI) compares the overlap of two clusterings; it considers both correct clustering overlaps while also counting correct disagreements between two clusterings. @@ -17,15 +18,18 @@ functionality: An ARI of 0 or 1 corresponds to random labeling or a perfect match, respectively. We used the scikit-learn implementation of the ARI. - paper_reference: hubert1985comparing + reference: hubert1985comparing + repostiory_url: "" + documentation_url: "" min: 0 max: 1 maximize: true v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - - metric_id: nmi - metric_name: NMI - metric_description: | + - name: nmi + pretty_name: NMI + summary: "NMI compares overlap by scaling using mean entropy terms and optimizing Louvain clustering to obtain the best match between clusters and labels." + description: | Normalized Mutual Information (NMI) compares the overlap of two clusterings. We used NMI to compare the cell-type labels with Louvain clusters computed on the integrated dataset. The overlap was scaled using the mean of the entropy terms @@ -35,7 +39,9 @@ functionality: Louvain clustering was performed at a resolution range of 0.1 to 2 in steps of 0.1, and the clustering output with the highest NMI with the label set was used. We the scikit-learn implementation of NMI. - paper_reference: amelio2015normalized + reference: amelio2015normalized + documentation_url: "" + repository_url: "" min: 0 max: 1 maximize: true diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml index 4e31a7ff8e..21a933110b 100644 --- a/src/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics/pcr/config.vsh.yaml @@ -4,12 +4,20 @@ functionality: name: pcr description: PCA regression info: - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - paper_reference: luecken2022benchmarking metrics: - - metric_id: pcr - metric_name: PCR + - name: pcr + pretty_name: PCR + summary: + description: + reference: luecken2022benchmarking + repository_url: "The comparison of explained variance by batch before and after integration." + documentation_url: | + "This compares the explained variance by batch before and after integration. It + returns a score between 0 and 1 (scaled=True) with 0 if the variance + contribution hasn’t changed. The larger the score, the more different the + variance contributions are before and after integration." + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf min: 0 max: 1 maximize: true From af9c4d9920c2416518c8f7f8f039a41b5d183fb2 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 10:24:27 +0200 Subject: [PATCH 0817/1233] fix typo Former-commit-id: 072556bb37ff3785ce24492cce8e23cb27990196 --- src/common/unit_test/check_metric_config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/unit_test/check_metric_config.py b/src/common/unit_test/check_metric_config.py index 0b46c911ec..54508425ab 100644 --- a/src/common/unit_test/check_metric_config.py +++ b/src/common/unit_test/check_metric_config.py @@ -11,7 +11,7 @@ ## VIASH END def check_metric(metric: Dict[str, str]) -> str: - assert "name" in metric is not None, "metric_id not a field or is empty" + assert "name" in metric is not None, "name not a field or is empty" assert "pretty_name" in metric is not None, "pretty_name not a field in metric or is empty" assert "summary" in metric is not None, "summary not a field in metric or is empty" assert "description" in metric is not None, "description not a field in metric or is empty" From cff8d379018c51599500f40f252e4f6af954efd8 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 13:41:16 +0200 Subject: [PATCH 0818/1233] update get_info scripts Former-commit-id: 70a417e2bfe8e32bc706aed9853813ba2c618a69 --- src/common/get_method_info/script.R | 8 ++++++-- src/common/get_metric_info/script.R | 12 +++++++++--- src/label_projection/methods/scanvi/config.vsh.yaml | 1 - 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index a155182c0c..04a7b8f670 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -30,11 +30,15 @@ df <- map_df(configs, function(config) { info$task_id <- par$task_id info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace - info$description <- config$functionality$description info$is_baseline <- grepl("control", info$type) info }) %>% - select(method_id, type, one_of("method_name"), everything()) + rename( + method_name = pretty_name, + method_summary = description, + paper_reference = reference, + code_url = repository_url, + ) jsonlite::write_json( purrr::transpose(df), diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 1872f90872..4693268ab9 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -4,8 +4,8 @@ library(rlang) ## VIASH START par <- list( input = ".", - task_id = "label_projection", - output = "output/metrics.json" + task_id = "batch_integration", + output = "output/metric_info.json" ) ## VIASH END @@ -27,8 +27,14 @@ df <- map_df(configs, function(config) { info$v1_url <- config$functionality$info$v1_url info$v1_commit <- config$functionality$info$v1_commit info + info }) %>% - select(metric_id, everything()) +rename( + metric_id = name, + metric_name = pretty_name, + metric_summary = description, + paper_reference = reference, +) jsonlite::write_json( purrr::transpose(df), diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index cd3afbbdbf..50cda68e73 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -18,7 +18,6 @@ functionality: documentation_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 - v1_comp_id: scarches_scanvi_hvg preferred_normalization: log_cpm variants: scanvi_all_genes: From 9d40bfe3d0813681a11bac377e3fb81a6418851b Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 13:45:00 +0200 Subject: [PATCH 0819/1233] rename create_skeleton to create_component Former-commit-id: 9b50b41e216dc425794a5f9985fa53074f0bf73e --- .../{create_skeleton => create_component}/config.vsh.yaml | 8 ++++---- .../{create_skeleton => create_component}/script.py | 0 src/common/create_component/script.sh | 5 +++++ src/common/{create_skeleton => create_component}/test.py | 0 src/common/create_skeleton/script.sh | 5 ----- 5 files changed, 9 insertions(+), 9 deletions(-) rename src/common/{create_skeleton => create_component}/config.vsh.yaml (88%) rename src/common/{create_skeleton => create_component}/script.py (100%) create mode 100755 src/common/create_component/script.sh rename src/common/{create_skeleton => create_component}/test.py (100%) delete mode 100755 src/common/create_skeleton/script.sh diff --git a/src/common/create_skeleton/config.vsh.yaml b/src/common/create_component/config.vsh.yaml similarity index 88% rename from src/common/create_skeleton/config.vsh.yaml rename to src/common/create_component/config.vsh.yaml index 9f6d672f8d..fd67acf685 100644 --- a/src/common/create_skeleton/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -1,14 +1,14 @@ # TODO: project config is no longer mounted functionality: - name: create_skeleton + name: create_component namespace: common description: | - Create a skeleton Viash component. + Create a component Viash component. Usage: ``` - bin/create_skeleton --task denoising --type method --language r --name foo - bin/create_skeleton --task denoising --type metric --language python --name bar + bin/create_component --task denoising --type method --language r --name foo + bin/create_component --task denoising --type metric --language python --name bar ``` arguments: - type: string diff --git a/src/common/create_skeleton/script.py b/src/common/create_component/script.py similarity index 100% rename from src/common/create_skeleton/script.py rename to src/common/create_component/script.py diff --git a/src/common/create_component/script.sh b/src/common/create_component/script.sh new file mode 100755 index 0000000000..9fef9ef3a7 --- /dev/null +++ b/src/common/create_component/script.sh @@ -0,0 +1,5 @@ +TASK=dimensionality_reduction +viash run src/common/create_component/config.vsh.yaml -- --task $TASK --type metric --name foor --language r +viash run src/common/create_component/config.vsh.yaml -- --task $TASK --type method --name foor --language r +viash run src/common/create_component/config.vsh.yaml -- --task $TASK --type method --name foopy +viash run src/common/create_component/config.vsh.yaml -- --task $TASK --type metric --name foopy \ No newline at end of file diff --git a/src/common/create_skeleton/test.py b/src/common/create_component/test.py similarity index 100% rename from src/common/create_skeleton/test.py rename to src/common/create_component/test.py diff --git a/src/common/create_skeleton/script.sh b/src/common/create_skeleton/script.sh deleted file mode 100755 index a8e58fae07..0000000000 --- a/src/common/create_skeleton/script.sh +++ /dev/null @@ -1,5 +0,0 @@ -TASK=dimensionality_reduction -viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type metric --name foor --language r -viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type method --name foor --language r -viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type method --name foopy -viash run src/common/create_skeleton/config.vsh.yaml -- --task $TASK --type metric --name foopy \ No newline at end of file From bcd4c4613e99b2ccf15b6ef213871ccab8b3db4f Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 14:09:23 +0200 Subject: [PATCH 0820/1233] move git_sha and check_migration to migration namsepace Former-commit-id: 82704cda681f49365dc316e73b2a24866740474f --- .../check_migration_status/config.vsh.yaml | 2 +- src/{common => migration}/check_migration_status/script.py | 0 src/{common => migration}/check_migration_status/test.py | 0 src/{common => migration}/list_git_shas/config.vsh.yaml | 2 +- src/{common => migration}/list_git_shas/script.py | 0 src/{common => migration}/list_git_shas/test.py | 0 6 files changed, 2 insertions(+), 2 deletions(-) rename src/{common => migration}/check_migration_status/config.vsh.yaml (97%) rename src/{common => migration}/check_migration_status/script.py (100%) rename src/{common => migration}/check_migration_status/test.py (100%) rename src/{common => migration}/list_git_shas/config.vsh.yaml (98%) rename src/{common => migration}/list_git_shas/script.py (100%) rename src/{common => migration}/list_git_shas/test.py (100%) diff --git a/src/common/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml similarity index 97% rename from src/common/check_migration_status/config.vsh.yaml rename to src/migration/check_migration_status/config.vsh.yaml index 93cbb77097..e072f78b74 100644 --- a/src/common/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "check_migration_status" - namespace: "common" + namespace: "migration" description: "Check migration status" arguments: - name: "--git_sha" diff --git a/src/common/check_migration_status/script.py b/src/migration/check_migration_status/script.py similarity index 100% rename from src/common/check_migration_status/script.py rename to src/migration/check_migration_status/script.py diff --git a/src/common/check_migration_status/test.py b/src/migration/check_migration_status/test.py similarity index 100% rename from src/common/check_migration_status/test.py rename to src/migration/check_migration_status/test.py diff --git a/src/common/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml similarity index 98% rename from src/common/list_git_shas/config.vsh.yaml rename to src/migration/list_git_shas/config.vsh.yaml index 233c8099f4..20050c1007 100644 --- a/src/common/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: list_git_shas - namespace: common + namespace: migration description: "Extract git file info from a git repo" arguments: - name: --input diff --git a/src/common/list_git_shas/script.py b/src/migration/list_git_shas/script.py similarity index 100% rename from src/common/list_git_shas/script.py rename to src/migration/list_git_shas/script.py diff --git a/src/common/list_git_shas/test.py b/src/migration/list_git_shas/test.py similarity index 100% rename from src/common/list_git_shas/test.py rename to src/migration/list_git_shas/test.py From 4d8d98d721912a5cf94d76b7f775334a589b1bae Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 14:09:57 +0200 Subject: [PATCH 0821/1233] remove dataset_concatenate Former-commit-id: e93dde50f4fef50890a3127e19d8db9782b17fbc --- .../dataset_concatenate/config.vsh.yaml | 34 ------------------- src/common/dataset_concatenate/script.py | 21 ------------ src/common/dataset_concatenate/test_script.py | 26 -------------- 3 files changed, 81 deletions(-) delete mode 100644 src/common/dataset_concatenate/config.vsh.yaml delete mode 100644 src/common/dataset_concatenate/script.py delete mode 100644 src/common/dataset_concatenate/test_script.py diff --git a/src/common/dataset_concatenate/config.vsh.yaml b/src/common/dataset_concatenate/config.vsh.yaml deleted file mode 100644 index 6800806f11..0000000000 --- a/src/common/dataset_concatenate/config.vsh.yaml +++ /dev/null @@ -1,34 +0,0 @@ -functionality: - name: "dataset_concatenate" - status: deprecated - namespace: "common/data_processing" - description: "Concatenate datasets" - arguments: - - name: "--inputs" - alternatives: ["-i"] - type: "file" - multiple: true - required: true - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file" - required: true - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test_script.py - - type: file - path: "../../../resources_test/common/pancreas" -platforms: - - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - "anndata>=0.8" - - type: nextflow diff --git a/src/common/dataset_concatenate/script.py b/src/common/dataset_concatenate/script.py deleted file mode 100644 index 78faf143ca..0000000000 --- a/src/common/dataset_concatenate/script.py +++ /dev/null @@ -1,21 +0,0 @@ -import anndata as ad - -## VIASH START -par = { - "inputs": ["resources_test/common/pancreas/dataset.h5ad", "resources_test/common/pancreas/dataset.h5ad"], - "output": "output.h5ad" -} -## VIASH END - -adata_list = [] -for input in par["inputs"]: - print("Loading {}".format(input)) - adata_list.append(ad.read_h5ad(input)) - -print("Concatenate anndatas") -adata = ad.concat(adata_list) - -print("Concatenated anndata: ", adata) - -print("Writing result file") -adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/common/dataset_concatenate/test_script.py b/src/common/dataset_concatenate/test_script.py deleted file mode 100644 index 12c26a8501..0000000000 --- a/src/common/dataset_concatenate/test_script.py +++ /dev/null @@ -1,26 +0,0 @@ -import subprocess -import anndata as ad -from os import path - -## VIASH START -## VIASH END - -input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" -output_path = "toy_data_concatenated.h5ad" - -print(">> Runing script as test") -out = subprocess.check_output([ - meta["executable"], - "--inputs", f"{input_path}:{input_path}", - "--output", output_path -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_path) - -print(">> Check that test output fits expected API") -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) - -assert output.n_obs == input.n_obs * 2 -assert output.n_vars == input.n_vars From be245a5fececb0289afca79929e0e220ac7cecc9 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 14:32:25 +0200 Subject: [PATCH 0822/1233] rename split_dataset to process_dataset Former-commit-id: 3aaca7c2d9e9cfa753a73ec2153e8fb1f43e788d --- CONTRIBUTING.qmd | 4 ++-- .../{comp_split_dataset.yaml => comp_process_dataset.yaml} | 2 +- .../{split_dataset => process_dataset}/config.vsh.yaml | 4 ++-- .../{split_dataset => process_dataset}/script.py | 0 .../{split_dataset => process_dataset}/test.py | 0 src/batch_integration/resources_test_scripts/pancreas.sh | 2 +- src/denoising/README.md | 2 +- .../{comp_split_dataset.yaml => comp_process_dataset.yaml} | 2 +- .../{split_dataset => process_dataset}/config.vsh.yaml | 4 ++-- src/denoising/{split_dataset => process_dataset}/helper.py | 0 src/denoising/{split_dataset => process_dataset}/script.py | 2 +- .../{split_datasets.sh => process_datasets.sh} | 2 +- src/denoising/resources_test_scripts/pancreas.sh | 2 +- src/dimensionality_reduction/README.md | 2 +- .../{comp_split_dataset.yaml => comp_process_dataset.yaml} | 2 +- .../{split_dataset => process_dataset}/config.vsh.yaml | 4 ++-- .../{split_dataset => process_dataset}/script.py | 2 +- .../{split_dataset => process_dataset}/test.py | 0 .../{split_datasets.sh => process_datasets.sh} | 2 +- .../resources_test_scripts/pancreas.sh | 2 +- src/label_projection/README.md | 2 +- .../{comp_split_dataset.yaml => comp_process_dataset.yaml} | 2 +- .../{split_dataset => process_dataset}/config.vsh.yaml | 4 ++-- .../{split_dataset => process_dataset}/script.py | 4 ++-- .../{split_datasets.sh => process_datasets.sh} | 2 +- src/label_projection/resources_test_scripts/pancreas.sh | 2 +- src/multimodal_data_integration/README.md | 2 +- 27 files changed, 29 insertions(+), 29 deletions(-) rename src/batch_integration/api/{comp_split_dataset.yaml => comp_process_dataset.yaml} (98%) rename src/batch_integration/{split_dataset => process_dataset}/config.vsh.yaml (92%) rename src/batch_integration/{split_dataset => process_dataset}/script.py (100%) rename src/batch_integration/{split_dataset => process_dataset}/test.py (100%) rename src/denoising/api/{comp_split_dataset.yaml => comp_process_dataset.yaml} (98%) rename src/denoising/{split_dataset => process_dataset}/config.vsh.yaml (93%) rename src/denoising/{split_dataset => process_dataset}/helper.py (100%) rename src/denoising/{split_dataset => process_dataset}/script.py (97%) rename src/denoising/resources_scripts/{split_datasets.sh => process_datasets.sh} (95%) rename src/dimensionality_reduction/api/{comp_split_dataset.yaml => comp_process_dataset.yaml} (98%) rename src/dimensionality_reduction/{split_dataset => process_dataset}/config.vsh.yaml (82%) rename src/dimensionality_reduction/{split_dataset => process_dataset}/script.py (96%) rename src/dimensionality_reduction/{split_dataset => process_dataset}/test.py (100%) rename src/dimensionality_reduction/resources_scripts/{split_datasets.sh => process_datasets.sh} (94%) rename src/label_projection/api/{comp_split_dataset.yaml => comp_process_dataset.yaml} (99%) rename src/label_projection/{split_dataset => process_dataset}/config.vsh.yaml (92%) rename src/label_projection/{split_dataset => process_dataset}/script.py (96%) rename src/label_projection/resources_scripts/{split_datasets.sh => process_datasets.sh} (95%) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 60fd63d583..17688607b4 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -64,7 +64,7 @@ viash ns build --query 'label_projection|common' --parallel --setup cachedbuild ``` In development mode with 'dev'. - Exporting split_dataset (label_projection) =docker=> target/docker/label_projection/split_dataset + Exporting process_dataset (label_projection) =docker=> target/docker/label_projection/process_dataset Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile @@ -126,7 +126,7 @@ Detailed overview of a task folder (e.g. `src/label_projection`): ├── metrics Label projection metric components. ├── resources_scripts The scripts needed to run the benchmark. ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - ├── split_dataset A component that masks a common dataset for use in the benchmark + ├── process_dataset A component that masks a common dataset for use in the benchmark └── workflows The benchmarking workflow. diff --git a/src/batch_integration/api/comp_split_dataset.yaml b/src/batch_integration/api/comp_process_dataset.yaml similarity index 98% rename from src/batch_integration/api/comp_split_dataset.yaml rename to src/batch_integration/api/comp_process_dataset.yaml index 5d869be713..6ae3736b1a 100644 --- a/src/batch_integration/api/comp_split_dataset.yaml +++ b/src/batch_integration/api/comp_process_dataset.yaml @@ -1,6 +1,6 @@ functionality: info: - type: split_dataset + type: process_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/batch_integration/split_dataset/config.vsh.yaml b/src/batch_integration/process_dataset/config.vsh.yaml similarity index 92% rename from src/batch_integration/split_dataset/config.vsh.yaml rename to src/batch_integration/process_dataset/config.vsh.yaml index 184dea0904..1dac6dc8a3 100644 --- a/src/batch_integration/split_dataset/config.vsh.yaml +++ b/src/batch_integration/process_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ -__merge__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_process_dataset.yaml functionality: - name: split_dataset + name: process_dataset namespace: batch_integration description: Preprocess adata object for data integration arguments: diff --git a/src/batch_integration/split_dataset/script.py b/src/batch_integration/process_dataset/script.py similarity index 100% rename from src/batch_integration/split_dataset/script.py rename to src/batch_integration/process_dataset/script.py diff --git a/src/batch_integration/split_dataset/test.py b/src/batch_integration/process_dataset/test.py similarity index 100% rename from src/batch_integration/split_dataset/test.py rename to src/batch_integration/process_dataset/test.py diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/batch_integration/resources_test_scripts/pancreas.sh index fdebf31c31..1ad7a75ede 100755 --- a/src/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/batch_integration/resources_test_scripts/pancreas.sh @@ -18,7 +18,7 @@ mkdir -p $DATASET_DIR # process dataset echo process data... -viash run src/batch_integration/split_dataset/config.vsh.yaml -- \ +viash run src/batch_integration/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output $DATASET_DIR/unintegrated.h5ad \ --hvgs 100 diff --git a/src/denoising/README.md b/src/denoising/README.md index 84038fdbb6..562e5cc45f 100644 --- a/src/denoising/README.md +++ b/src/denoising/README.md @@ -10,7 +10,7 @@ Structure of this task: ├── README.md This file ├── resources_scripts Scripts to process the datasets ├── resources_test_scripts Scripts to process the test resources - ├── split_dataset Component to prepare common datasets + ├── process_dataset Component to prepare common datasets └── workflows Pipelines to run the full benchmark Relevant links: diff --git a/src/denoising/api/comp_split_dataset.yaml b/src/denoising/api/comp_process_dataset.yaml similarity index 98% rename from src/denoising/api/comp_split_dataset.yaml rename to src/denoising/api/comp_process_dataset.yaml index 78c4120bfc..7578e161eb 100644 --- a/src/denoising/api/comp_split_dataset.yaml +++ b/src/denoising/api/comp_process_dataset.yaml @@ -1,6 +1,6 @@ functionality: info: - type: split_dataset + type: process_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/denoising/split_dataset/config.vsh.yaml b/src/denoising/process_dataset/config.vsh.yaml similarity index 93% rename from src/denoising/split_dataset/config.vsh.yaml rename to src/denoising/process_dataset/config.vsh.yaml index bd80df46d2..1c19af5f4c 100644 --- a/src/denoising/split_dataset/config.vsh.yaml +++ b/src/denoising/process_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ -__merge__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_process_dataset.yaml functionality: - name: "split_dataset" + name: "process_dataset" namespace: "denoising" description: | Split data using molecular cross-validation. diff --git a/src/denoising/split_dataset/helper.py b/src/denoising/process_dataset/helper.py similarity index 100% rename from src/denoising/split_dataset/helper.py rename to src/denoising/process_dataset/helper.py diff --git a/src/denoising/split_dataset/script.py b/src/denoising/process_dataset/script.py similarity index 97% rename from src/denoising/split_dataset/script.py rename to src/denoising/process_dataset/script.py index 95fcd0544d..54c3958bdb 100644 --- a/src/denoising/split_dataset/script.py +++ b/src/denoising/process_dataset/script.py @@ -13,7 +13,7 @@ } meta = { "functionality_name": "split_data", - "resources_dir": "src/denoising/split_dataset" + "resources_dir": "src/denoising/process_dataset" } ## VIASH END diff --git a/src/denoising/resources_scripts/split_datasets.sh b/src/denoising/resources_scripts/process_datasets.sh similarity index 95% rename from src/denoising/resources_scripts/split_datasets.sh rename to src/denoising/resources_scripts/process_datasets.sh index 0e0333a825..0cb7073463 100755 --- a/src/denoising/resources_scripts/split_datasets.sh +++ b/src/denoising/resources_scripts/process_datasets.sh @@ -54,7 +54,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script target/nextflow/denoising/split_dataset/main.nf \ + -main-script target/nextflow/denoising/process_dataset/main.nf \ -profile docker \ -resume \ -params-file $params_file \ diff --git a/src/denoising/resources_test_scripts/pancreas.sh b/src/denoising/resources_test_scripts/pancreas.sh index 9fa4796e15..50bb68e735 100755 --- a/src/denoising/resources_test_scripts/pancreas.sh +++ b/src/denoising/resources_test_scripts/pancreas.sh @@ -20,7 +20,7 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/denoising/split_dataset/config.vsh.yaml -- \ +viash run src/denoising/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ diff --git a/src/dimensionality_reduction/README.md b/src/dimensionality_reduction/README.md index 957b9e3b69..a9783ea4b2 100644 --- a/src/dimensionality_reduction/README.md +++ b/src/dimensionality_reduction/README.md @@ -10,7 +10,7 @@ Structure of this task: ├── README.md This file ├── resources_scripts Scripts to process the datasets ├── resources_test_scripts Scripts to process the test resources - ├── split_dataset Component to prepare common datasets + ├── process_dataset Component to prepare common datasets └── workflows Pipelines to run the full benchmark Relevant links: diff --git a/src/dimensionality_reduction/api/comp_split_dataset.yaml b/src/dimensionality_reduction/api/comp_process_dataset.yaml similarity index 98% rename from src/dimensionality_reduction/api/comp_split_dataset.yaml rename to src/dimensionality_reduction/api/comp_process_dataset.yaml index 8705ca3e35..abea8c028b 100644 --- a/src/dimensionality_reduction/api/comp_split_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_process_dataset.yaml @@ -1,6 +1,6 @@ functionality: info: - type: split_dataset + type: process_dataset arguments: - name: "--input" __merge__: anndata_dataset.yaml diff --git a/src/dimensionality_reduction/split_dataset/config.vsh.yaml b/src/dimensionality_reduction/process_dataset/config.vsh.yaml similarity index 82% rename from src/dimensionality_reduction/split_dataset/config.vsh.yaml rename to src/dimensionality_reduction/process_dataset/config.vsh.yaml index 7fb8cd56d2..09ef02c139 100644 --- a/src/dimensionality_reduction/split_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ -__merge__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_process_dataset.yaml functionality: - name: "split_dataset" + name: "process_dataset" namespace: "dimensionality_reduction" resources: - type: python_script diff --git a/src/dimensionality_reduction/split_dataset/script.py b/src/dimensionality_reduction/process_dataset/script.py similarity index 96% rename from src/dimensionality_reduction/split_dataset/script.py rename to src/dimensionality_reduction/process_dataset/script.py index d51e7471a0..7981010b6a 100644 --- a/src/dimensionality_reduction/split_dataset/script.py +++ b/src/dimensionality_reduction/process_dataset/script.py @@ -13,7 +13,7 @@ } meta = { "functionality_name": "split_data", - "config": "src/dimensionality_reduction/split_dataset/.config.vsh.yaml" + "config": "src/dimensionality_reduction/process_dataset/.config.vsh.yaml" } ## VIASH END diff --git a/src/dimensionality_reduction/split_dataset/test.py b/src/dimensionality_reduction/process_dataset/test.py similarity index 100% rename from src/dimensionality_reduction/split_dataset/test.py rename to src/dimensionality_reduction/process_dataset/test.py diff --git a/src/dimensionality_reduction/resources_scripts/split_datasets.sh b/src/dimensionality_reduction/resources_scripts/process_datasets.sh similarity index 94% rename from src/dimensionality_reduction/resources_scripts/split_datasets.sh rename to src/dimensionality_reduction/resources_scripts/process_datasets.sh index c447076c02..dd0de0ddbc 100755 --- a/src/dimensionality_reduction/resources_scripts/split_datasets.sh +++ b/src/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -59,7 +59,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script target/nextflow/dimensionality_reduction/split_dataset/main.nf \ + -main-script target/nextflow/dimensionality_reduction/process_dataset/main.nf \ -profile docker \ -resume \ -params-file $params_file \ diff --git a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh index e1a455b88b..909946635e 100755 --- a/src/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -19,7 +19,7 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/dimensionality_reduction/split_dataset/config.vsh.yaml -- \ +viash run src/dimensionality_reduction/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad diff --git a/src/label_projection/README.md b/src/label_projection/README.md index e2c73b365e..e7be28c7b1 100644 --- a/src/label_projection/README.md +++ b/src/label_projection/README.md @@ -10,7 +10,7 @@ Structure of this task: ├── README.md This file ├── resources_scripts Scripts to process the datasets ├── resources_test_scripts Scripts to process the test resources - ├── split_dataset Component to prepare common datasets + ├── process_dataset Component to prepare common datasets └── workflows Pipelines to run the full benchmark Relevant links: diff --git a/src/label_projection/api/comp_split_dataset.yaml b/src/label_projection/api/comp_process_dataset.yaml similarity index 99% rename from src/label_projection/api/comp_split_dataset.yaml rename to src/label_projection/api/comp_process_dataset.yaml index 79ab59f2ee..45c921566e 100644 --- a/src/label_projection/api/comp_split_dataset.yaml +++ b/src/label_projection/api/comp_process_dataset.yaml @@ -1,6 +1,6 @@ functionality: info: - type: split_dataset + type: process_dataset arguments: - name: "--input" __merge__: ../../datasets/api/anndata_dataset.yaml diff --git a/src/label_projection/split_dataset/config.vsh.yaml b/src/label_projection/process_dataset/config.vsh.yaml similarity index 92% rename from src/label_projection/split_dataset/config.vsh.yaml rename to src/label_projection/process_dataset/config.vsh.yaml index d11a48eb30..ac3485ff4a 100644 --- a/src/label_projection/split_dataset/config.vsh.yaml +++ b/src/label_projection/process_dataset/config.vsh.yaml @@ -1,6 +1,6 @@ -__merge__: ../api/comp_split_dataset.yaml +__merge__: ../api/comp_process_dataset.yaml functionality: - name: "split_dataset" + name: "process_dataset" namespace: "label_projection" arguments: - name: "--method" diff --git a/src/label_projection/split_dataset/script.py b/src/label_projection/process_dataset/script.py similarity index 96% rename from src/label_projection/split_dataset/script.py rename to src/label_projection/process_dataset/script.py index 7451c0e97a..6aab6afac5 100644 --- a/src/label_projection/split_dataset/script.py +++ b/src/label_projection/process_dataset/script.py @@ -18,8 +18,8 @@ 'output_solution': 'solution.h5ad' } meta = { - 'resources_dir': 'src/label_projection/split_dataset', - 'config': 'src/label_projection/split_dataset/.config.vsh.yaml' + 'resources_dir': 'src/label_projection/process_dataset', + 'config': 'src/label_projection/process_dataset/.config.vsh.yaml' } ## VIASH END diff --git a/src/label_projection/resources_scripts/split_datasets.sh b/src/label_projection/resources_scripts/process_datasets.sh similarity index 95% rename from src/label_projection/resources_scripts/split_datasets.sh rename to src/label_projection/resources_scripts/process_datasets.sh index d561760373..9e16f606d0 100755 --- a/src/label_projection/resources_scripts/split_datasets.sh +++ b/src/label_projection/resources_scripts/process_datasets.sh @@ -58,7 +58,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script target/nextflow/label_projection/split_dataset/main.nf \ + -main-script target/nextflow/label_projection/process_dataset/main.nf \ -profile docker \ -resume \ -params-file $params_file \ diff --git a/src/label_projection/resources_test_scripts/pancreas.sh b/src/label_projection/resources_test_scripts/pancreas.sh index d0040dca43..4faf188eb5 100755 --- a/src/label_projection/resources_test_scripts/pancreas.sh +++ b/src/label_projection/resources_test_scripts/pancreas.sh @@ -20,7 +20,7 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/label_projection/split_dataset/config.vsh.yaml -- \ +viash run src/label_projection/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ diff --git a/src/multimodal_data_integration/README.md b/src/multimodal_data_integration/README.md index d8d0d58cc5..19b60f3614 100644 --- a/src/multimodal_data_integration/README.md +++ b/src/multimodal_data_integration/README.md @@ -10,7 +10,7 @@ Structure of this task: ├── README.md This file ├── resources_scripts Scripts to process the datasets ├── resources_test_scripts Scripts to process the test resources - ├── split_dataset Component to prepare common datasets + ├── process_dataset Component to prepare common datasets └── workflows Pipelines to run the full benchmark Relevant links: From c256f933383f5a75d574b254bb2eeba00a30b04a Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 15:05:12 +0200 Subject: [PATCH 0823/1233] update batch_int unit tests Former-commit-id: d10cff13e573bb92e7717b57241f1cdbe9179bf1 --- src/batch_integration/api/comp_method_embedding.yaml | 4 +++- src/batch_integration/api/comp_method_feature.yaml | 4 +++- src/batch_integration/api/comp_method_graph.yaml | 4 +++- src/batch_integration/api/comp_metric_embedding.yaml | 4 +++- src/batch_integration/api/comp_metric_feature.yaml | 4 +++- src/batch_integration/api/comp_metric_graph.yaml | 4 +++- 6 files changed, 18 insertions(+), 6 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index c61e76a370..1b88852491 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -15,7 +15,9 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas/ + - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index e7a09eb631..a2fafe1c46 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -15,7 +15,9 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas/ + - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 0b28dcdb94..5bbb1883b9 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -15,7 +15,9 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas/ + - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 84a319515d..f679d14d25 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -10,6 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script dest: test.py text: | @@ -65,7 +67,7 @@ functionality: print(">> Check that score makes sense", flush=True) metrics_info = { - metric["metric_id"]: metric + metric["name"]: metric for metric in config["functionality"]["info"]["metrics"] } diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 910315f981..4dd7700a1e 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -10,6 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script dest: test.py text: | @@ -65,7 +67,7 @@ functionality: print(">> Check that score makes sense", flush=True) metrics_info = { - metric["metric_id"]: metric + metric["name"]: metric for metric in config["functionality"]["info"]["metrics"] } diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 47b5907fbf..b7702bc7eb 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -10,6 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: ../../../../resources_test/batch_integration/pancreas + - type: python_script + path: ../../../common/unit_test/check_metric_config.py - type: python_script dest: test.py text: | @@ -67,7 +69,7 @@ functionality: print(">> Check that score makes sense", flush=True) metrics_info = { - metric["metric_id"]: metric + metric["name"]: metric for metric in config["functionality"]["info"]["metrics"] } From 23aa1b3275a3b18764a3ba720dacc116127e23d3 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Mon, 3 Apr 2023 15:48:09 +0200 Subject: [PATCH 0824/1233] fix failed unit_tests batch_int Former-commit-id: caf228dc12f3e6155e632ee97c583ef172cdea60 --- .../methods/scanorama_embed/config.vsh.yaml | 3 ++- .../methods/scanorama_feature/config.vsh.yaml | 3 ++- src/batch_integration/methods/scvi/config.vsh.yaml | 6 +++++- .../metrics/asw_label/config.vsh.yaml | 4 ++-- .../metrics/cell_cycle_conservation/config.vsh.yaml | 11 +++++------ .../metrics/clustering_overlap/config.vsh.yaml | 2 +- src/batch_integration/metrics/pcr/config.vsh.yaml | 11 +++++------ 7 files changed, 22 insertions(+), 18 deletions(-) diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml index 5d8132905f..d9a06473a8 100644 --- a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -6,7 +6,8 @@ functionality: pretty_name: Scanorama summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" - description: + description: | + "Scanorama is an extension of the MNN method. Other then MNN, it finds mutual nearest neighbours over all batches and embeds observations into a joint hyperplane." reference: "hie2019efficient" repository_url: "https://github.com/brianhie/scanorama" documentation_url: "https://github.com/brianhie/scanorama#readme" diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml index 73f5812c79..4796d527fd 100644 --- a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -8,7 +8,8 @@ functionality: pretty_name: Scanorama summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" - description: + description: | + "Scanorama is an extension of the MNN method. Other then MNN, it finds mutual nearest neighbours over all batches and embeds observations into a joint hyperplane." reference: "hie2019efficient" repository_url: "https://github.com/brianhie/scanorama" documentation_url: "https://github.com/brianhie/scanorama#readme" diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/batch_integration/methods/scvi/config.vsh.yaml index f9ad96ffe2..ca02439af7 100644 --- a/src/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/batch_integration/methods/scvi/config.vsh.yaml @@ -5,8 +5,12 @@ functionality: description: Run scVI on adata object info: pretty_name: scVI + summary: "scVI combines a variational autoencoder with a hierarchical Bayesian model." + description: | + scVI combines a variational autoencoder with a hierarchical Bayesian model. It uses the negative binomial distribution to describe gene expression of each cell, conditioned on unobserved factors and the batch variable. ScVI is run as implemented in Luecken et al. reference: "lopez2018deep" - repository_url: https://github.com/YosefLab/scvi-tools" + repository_url: "https://github.com/YosefLab/scvi-tools" + documentation_url: "https://github.com/YosefLab/scvi-tools#readme" v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/batch_integration/metrics/asw_label/config.vsh.yaml index 1c6d6381e7..767e426304 100644 --- a/src/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/batch_integration/metrics/asw_label/config.vsh.yaml @@ -13,8 +13,8 @@ functionality: summary: "Average silhouette of labels" description: "The absolute silhouette width is computed on cell identity labels, measuring their compactness." reference: luecken2022benchmarking - repository_url: - description_url: + repository_url: "" + documentation_url: "" min: 0 max: 1 maximize: true diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index e04a48e3b8..5f7c03173b 100644 --- a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -3,17 +3,16 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: cell_cycle_conservation info: - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - reference: luecken2022benchmarking metrics: - name: cell_cycle_conservation pretty_name: Cell Cycle Conservation summary: "Cell cycle conservation score based on cell cycle gene scoring" description: "The cell-cycle conservation score evaluates how well the cell-cycle effect can be captured before and after integration." - reference: - repository_url: - documentation_url: + reference: luecken2022benchmarking + repository_url: "" + documentation_url: "" + v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py + v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf min: 0 max: 1 maximize: true diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 104b1ff96a..4fda99a7d3 100644 --- a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: respectively. We used the scikit-learn implementation of the ARI. reference: hubert1985comparing - repostiory_url: "" + repository_url: "" documentation_url: "" min: 0 max: 1 diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/batch_integration/metrics/pcr/config.vsh.yaml index 21a933110b..6cd0dc37aa 100644 --- a/src/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/batch_integration/metrics/pcr/config.vsh.yaml @@ -7,21 +7,20 @@ functionality: metrics: - name: pcr pretty_name: PCR - summary: - description: - reference: luecken2022benchmarking - repository_url: "The comparison of explained variance by batch before and after integration." - documentation_url: | + summary: "The comparison of explained variance by batch before and after integration." + description: | "This compares the explained variance by batch before and after integration. It returns a score between 0 and 1 (scaled=True) with 0 if the variance contribution hasn’t changed. The larger the score, the more different the variance contributions are before and after integration." + reference: luecken2022benchmarking + repository_url: "" + documentation_url: "" v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf min: 0 max: 1 maximize: true - resources: - type: python_script path: script.py From 11310e2e1bfe0156d8b9f5c688813492dfa3f72b Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Tue, 4 Apr 2023 14:26:43 +0200 Subject: [PATCH 0825/1233] remove map_df from get_method_info Former-commit-id: cc540aa6af2730a59f793948259e334b253f827a --- src/common/get_method_info/script.R | 35 ++++++++++++++++------------- 1 file changed, 19 insertions(+), 16 deletions(-) diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 04a7b8f670..5287c7d51a 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -16,32 +16,35 @@ ns_list <- processx::run( ) configs <- yaml::yaml.load(ns_list$stdout) -df <- map_df(configs, function(config) { +out <- map(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) info <- config$functionality$info - # remove empty fields - for (n in names(info)) { - if (length(info[[n]]) == 0) { - info[[n]] <- NA - } - } - info <- as_tibble(info) + + # add extra info info$config_path <- gsub(".*\\./", "", config$info$config) info$task_id <- par$task_id info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace info$is_baseline <- grepl("control", info$type) + + # rename fields to v1 format + info$method_name <- info$pretty_name + info$pretty_name <- NULL + info$method_summary <- info$description + info$description <- NULL + info$paper_reference <- info$reference + info$reference <- NULL + info$code_url <- info$repository_url + info$repository_url <- NULL + + # todo: show warning when certain data is missing and return null? + + # return output info -}) %>% - rename( - method_name = pretty_name, - method_summary = description, - paper_reference = reference, - code_url = repository_url, - ) +}) jsonlite::write_json( - purrr::transpose(df), + out, par$output, auto_unbox = TRUE, pretty = TRUE From 5387ab9eb36ba428deff17e1d26ccc4efdb16e98 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 5 Apr 2023 22:02:29 +0000 Subject: [PATCH 0826/1233] Bump tj-actions/changed-files from 35.7.6 to 35.7.11 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.7.6 to 35.7.11. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.7.6...v35.7.11) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: 58d61685243ebcffa9488fa73e8531e8e34f376a --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 25b17b6472..a260180054 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.7.6 + uses: tj-actions/changed-files@v35.7.11 with: separator: ";" diff_relative: true From 9ab7584962695f0ad9d8168ae80657798d76635a Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 7 Apr 2023 15:38:04 +0200 Subject: [PATCH 0827/1233] Update CONTRIBUTING.qmd Co-authored-by: Robrecht Cannoodt Former-commit-id: ab3451b4a7b03a4607a17f32a36c714c8ff80659 --- CONTRIBUTING.qmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 17688607b4..605726d008 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -126,7 +126,7 @@ Detailed overview of a task folder (e.g. `src/label_projection`): ├── metrics Label projection metric components. ├── resources_scripts The scripts needed to run the benchmark. ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - ├── process_dataset A component that masks a common dataset for use in the benchmark + ├── process_dataset A component that masks a common dataset for use in the benchmark └── workflows The benchmarking workflow. From f16f20b781fba35a196e2e74c508f000e3a60962 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 7 Apr 2023 22:11:41 +0000 Subject: [PATCH 0828/1233] Bump tj-actions/changed-files from 35.7.11 to 35.7.12 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.7.11 to 35.7.12. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.7.11...v35.7.12) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: 971c39b641df24d40d1b1ebd31613e1eecd058fb --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index a260180054..32e2c50321 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.7.11 + uses: tj-actions/changed-files@v35.7.12 with: separator: ";" diff_relative: true From d73cc3b72c032bfd5e163534b64ad92459be5ed6 Mon Sep 17 00:00:00 2001 From: KaiWaldrant Date: Sat, 8 Apr 2023 11:03:48 +0200 Subject: [PATCH 0829/1233] update changelog Former-commit-id: 34664d34441a0fb47159b5cdb4502cf00054a6c6 --- CHANGELOG.md | 32 ++++++++++++++++++-------------- 1 file changed, 18 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 50ad391008..5feed78fb3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,26 +1,22 @@ # openproblems-v2 0.1.0 +* updated method and metric info fields according to [#93](https://github.com/openproblems-bio/openproblems-v2/issues/93) + ## common ### NEW FUNCTIONALITY * `extract_scores`: Summarise a metrics output tsv. -* `dataset_concatenate`: Concatenate N AnnData datasets. - * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. -* `list_git_shas`: create list of latest commit hashes of all files in repo. - * `get_api_info`: extract api info from tasks * `get_method_info`: extract method info from config yaml * `get_metric_info`: extract metric info from config yaml -* `check_migration_status`: compare git shas from methods with v1 - * `get_results`: extract benchmark scores * `get_task_info`: extract task info @@ -28,6 +24,16 @@ * `unit_test`: Common unit test that can be used by all tasks * `check_dataset_schema`: check if the dataset used has the required fields defined in the api `anndata_*.yaml` files + +* `Create_component`: creates a template folder with a viash config and script file depending on the task api. + +## migration + +### NEW FUNCTIONALITY + +* `list_git_shas`: create list of latest commit hashes of all files in repo. + +* `check_migration_status`: compare git shas from methods with v1 ## datasets @@ -52,17 +58,15 @@ * `loaders/openproblems_v1_multimodal`: Fetch a multimodal dataset from OpenProblems v1, whilst adding extra information to the `.uns`. - - ## label_projection ### NEW FUNCTIONALITY * `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. -* `api/comp_*`: Created an api definition for the split, method and metric components. +* `api/comp_*`: Created an api definition for the process, method and metric components. -* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. * `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. @@ -98,7 +102,7 @@ * `api/comp_*`: Created an api definition for the split, method and metric components. -* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. * `resources_test/denoising/pancreas` with `src/denoising/resources_test_scripts/pancreas.sh`. @@ -126,7 +130,7 @@ * extended the use of sparse data in methods unless it was not possible -* split_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. +* process_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. ## Dimensionality reduction @@ -135,7 +139,7 @@ * `api/comp_*`: Created an api definition for the split, control method, method and metric components. -* `split_dataset`: Added a component for splitting raw datasets into task-ready dataset objects. +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. * `control_methods`: Added a component for baseline methods specifically. @@ -175,7 +179,7 @@ * Raw counts and normalized expression data is stored in `.layers["counts"]` and `.layers["normalized"]`, respectively, instead of in `.X`. -* A `split_dataset` has been implemented to make a distinction between the data a method is allowed to see +* A `process_dataset` has been implemented to make a distinction between the data a method is allowed to see (here called the train data) and what a metric is allowed to see (here called the test data). * `methods/ivis` had originally been removed from the v1 (temporarily) but has been added back to the v2. From 9f942ef424917f138eb999f48718799b33a7aa74 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 11 Apr 2023 13:05:04 +0200 Subject: [PATCH 0830/1233] Update CHANGELOG.md Former-commit-id: a7cc6cc87a460141d8e02cdfea6344d79f86786b --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5feed78fb3..97c2f70a3b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,7 @@ # openproblems-v2 0.1.0 -* updated method and metric info fields according to [#93](https://github.com/openproblems-bio/openproblems-v2/issues/93) + ## common @@ -27,6 +27,10 @@ * `Create_component`: creates a template folder with a viash config and script file depending on the task api. +### MINOR CHANGES + +* Refactor and standardize metric and method info fields (#99). + ## migration ### NEW FUNCTIONALITY From 28a80dc15a0fea9d980d71a21efa763a46601564 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 12 Apr 2023 22:02:26 +0000 Subject: [PATCH 0831/1233] Bump tj-actions/changed-files from 35.7.12 to 35.8.0 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.7.12 to 35.8.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.7.12...v35.8.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Former-commit-id: f75b1723580385e944fdc3012d72af1d8c1a1d84 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 32e2c50321..c67f329ed4 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.7.12 + uses: tj-actions/changed-files@v35.8.0 with: separator: ";" diff_relative: true From 46f420918cfe9c9294bc1e384e973855c75135d8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 19 Apr 2023 11:03:09 +0200 Subject: [PATCH 0832/1233] use viashpy in subsample test Former-commit-id: 8a8025d94373b51a5e540f3090be4ee8654642a0 --- src/datasets/subsample/config.vsh.yaml | 4 + src/datasets/subsample/test_script.py | 121 ++++++++++++++----------- 2 files changed, 70 insertions(+), 55 deletions(-) diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index 9971e34d3c..75c2773045 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -59,4 +59,8 @@ platforms: packages: - scanpy - "anndata>=0.8" + test_setup: + - type: python + packages: + - viashpy - type: nextflow diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index be631b2bbf..3ef6a7eac2 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -1,58 +1,69 @@ -import subprocess -import scanpy as sc -from os import path +import sys +import os +import pytest +import anndata as ad -### VIASH START -meta = { - "resources_dir": "resources_test/common" -} -### VIASH END input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" -input = sc.read_h5ad(input_path) - -print(">> Running script as test for even") -output_path = "output.h5ad" -out = subprocess.check_output([ - meta["executable"], - "--input", input_path, - "--output", output_path, - "--even", - "--seed", "123", - "--n_obs", "100", - "--n_vars", "120" -]).decode("utf-8") - -print(">> Checking whether file exists") -assert path.exists(output_path) - -print(">> Check that test output fits expected API") -output = sc.read_h5ad(output_path) - -assert output.n_obs <= 100 -assert output.n_vars <= 120 - - - -print(">> Runing script as test for specific batch and celltype categories") -output2_path = "output.h5ad" - -keep_features = list(input.var_names[:10]) -out = subprocess.check_output([ - meta["executable"], - "--input", input_path, - "--keep_celltype_categories", "acinar:beta", - "--keep_batch_categories", "celseq:inDrop4:smarter", - "--keep_features", ":".join(keep_features), - "--output", output_path, - "--seed", "123" -]).decode("utf-8") -print(">> Checking whether file exists") -assert path.exists(output2_path) - -print(">> Check that test output fits expected API") -output2 = sc.read_h5ad(output2_path) - -assert output2.n_obs <= 500 -assert output2.n_vars <= 500 -assert set(keep_features).issubset(output2.var_names) +input = ad.read_h5ad(input_path) + +def test_even_sampling(run_component): + output_path = "output.h5ad" + run_component([ + "--input", input_path, + "--output", output_path, + "--even", + "--seed", "123", + "--n_obs", "100", + "--n_vars", "120" + ]) + + print(">> Checking whether file exists") + assert os.path.exists(output_path) + + print(">> Check that test output fits expected API") + output = ad.read_h5ad(output_path) + + assert output.n_obs <= 100 + assert output.n_vars <= 120 + + print(f"output: {output}", flush=True) + + +def test_keep_functionality(run_component): + output_path = "output.h5ad" + + keep_features = list(input.var_names[:10]) + run_component([ + "--input", input_path, + "--keep_celltype_categories", "acinar:beta", + "--keep_batch_categories", "celseq:inDrop4:smarter", + "--keep_features", ":".join(keep_features), + "--output", output_path, + "--seed", "123" + ]) + + print(">> Checking whether file exists") + assert os.path.exists(output_path) + + print(">> Check that test output fits expected API") + output = ad.read_h5ad(output_path) + + assert output.n_obs <= 500 + assert output.n_vars <= 500 + assert set(keep_features).issubset(output.var_names) + + print(f"output: {output}", flush=True) + +if __name__ == '__main__': + sys.exit(pytest.main([__file__, "--capture=no"], plugins=["viashpy"])) + + + + + + + + + + From f492354742dba25c2ecb4ff88c632e1726fb1259 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 19 Apr 2023 11:03:39 +0200 Subject: [PATCH 0833/1233] update to viash 0.7.2 Former-commit-id: f79962e7724344fdaec4174c5dcca968ddf79cee --- _viash.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 0d9c3b3713..8d64d59236 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.0 +viash_version: 0.7.2 source: src target: target From 9840a405c9403235bafc70ab5525de9730010895 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 19 Apr 2023 11:10:39 +0200 Subject: [PATCH 0834/1233] use project relative paths in label proj task Former-commit-id: a9047b18f9b8a0ab61a56559328dc02cb6aaf6d2 --- .../api/comp_control_method.yaml | 49 +------------ src/label_projection/api/comp_method.yaml | 49 +------------ src/label_projection/api/comp_metric.yaml | 41 +---------- .../api/comp_process_dataset.yaml | 68 +------------------ .../unit_tests/test_method.py | 42 ++++++++++++ .../unit_tests/test_metric.py | 34 ++++++++++ .../unit_tests/test_process_dataset.py | 62 +++++++++++++++++ 7 files changed, 150 insertions(+), 195 deletions(-) create mode 100644 src/label_projection/unit_tests/test_method.py create mode 100644 src/label_projection/unit_tests/test_metric.py create mode 100644 src/label_projection/unit_tests/test_process_dataset.py diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index 83e4e029fd..6ce4fbc46d 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -12,51 +12,8 @@ functionality: __merge__: anndata_prediction.yaml direction: output test_resources: - - path: ../../../../resources_test/label_projection/pancreas + - path: /resources_test/label_projection/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: /src/common/unit_test/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--input_test", input_test_path, - "--output", output_path - ] - - # todo: if we could access the viash config, we could check whether - # .functionality.info.type == "positive_control" - if meta['functionality_name'] == 'true_labels': - cmd = cmd + ["--input_solution", input_solution_path] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input_test = ad.read_h5ad(input_test_path) - output = ad.read_h5ad(output_path) - print("input_test:", input_test) - print("output:", output) - - print(">> Checking whether predictions were added") - assert "label_pred" in output.obs - assert meta['functionality_name'] == output.uns["method_id"] - - print("Checking whether data from input was copied properly to output") - assert input_test.n_obs == output.n_obs - assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") + path: /src/label_projection/unit_tests/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index b30a559398..a5543098b6 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -10,51 +10,8 @@ functionality: __merge__: anndata_prediction.yaml direction: output test_resources: - - path: ../../../../resources_test/label_projection/pancreas + - path: /resources_test/label_projection/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: /src/common/unit_test/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--input_test", input_test_path, - "--output", output_path - ] - - # todo: if we could access the viash config, we could check whether - # .functionality.info.type == "positive_control" - if meta['functionality_name'] == 'true_labels': - cmd = cmd + ["--input_solution", input_solution_path] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input_test = ad.read_h5ad(input_test_path) - output = ad.read_h5ad(output_path) - print("input_test:", input_test) - print("output:", output) - - print(">> Checking whether predictions were added") - assert "label_pred" in output.obs - assert meta['functionality_name'] == output.uns["method_id"] - - print("Checking whether data from input was copied properly to output") - assert input_test.n_obs == output.n_obs - assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") + path: /src/label_projection/unit_tests/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 7d72cab3fa..34cf3ca18f 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -10,43 +10,8 @@ functionality: __merge__: anndata_score.yaml direction: output test_resources: - - path: ../../../../resources_test/label_projection/pancreas + - path: /resources_test/label_projection/pancreas - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: /src/common/unit_test/check_metric_config.py - type: python_script - path: format_check.py - text: | - import anndata as ad - import subprocess - from os import path - - input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" - input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_prediction", input_prediction_path, - "--input_solution", input_solution_path, - "--output", output_path - ] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - input_solution = ad.read_h5ad(input_solution_path) - input_prediction = ad.read_h5ad(input_prediction_path) - output = ad.read_h5ad(output_path) - - print("Checking whether data from input was copied properly to output") - assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] - assert output.uns["method_id"] == input_prediction.uns["method_id"] - assert output.uns["metric_ids"] is not None - assert output.uns["metric_values"] is not None - - # TODO: check whether the metric ids are all in .functionality.info - - print("All checks succeeded!") + path: /src/label_projection/unit_tests/test_metric.py diff --git a/src/label_projection/api/comp_process_dataset.yaml b/src/label_projection/api/comp_process_dataset.yaml index 45c921566e..829919a034 100644 --- a/src/label_projection/api/comp_process_dataset.yaml +++ b/src/label_projection/api/comp_process_dataset.yaml @@ -3,7 +3,7 @@ functionality: type: process_dataset arguments: - name: "--input" - __merge__: ../../datasets/api/anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output @@ -14,69 +14,7 @@ functionality: __merge__: anndata_solution.yaml direction: output test_resources: + - path: /resources_test/common/pancreas - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_train_path = "output_train.h5ad" - output_test_path = "output_test.h5ad" - output_solution_path = "output_solution.h5ad" - - cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path, - "--output_solution", output_solution_path - ] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_train_path) - assert path.exists(output_test_path) - assert path.exists(output_solution_path) - - print(">> Reading h5ad files") - input = ad.read_h5ad(input_path) - output_train = ad.read_h5ad(output_train_path) - output_test = ad.read_h5ad(output_test_path) - output_solution = ad.read_h5ad(output_solution_path) - - print("input:", input) - print("output_train:", output_train) - print("output_test:", output_test) - print("output_solution:", output_solution) - - print(">> Checking dimensions, make sure no cells were dropped") - assert input.n_obs == output_train.n_obs + output_test.n_obs - assert output_test.n_obs == output_solution.n_obs - assert input.n_vars == output_train.n_vars - assert input.n_vars == output_test.n_vars + path: /src/label_projection/unit_tests/test_process_dataset.py - print(">> Checking whether data from input was copied properly to output") - assert output_train.uns["dataset_id"] == input.uns["dataset_id"] - assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] - - print(">> Check whether certain slots exist") - assert "counts" in output_train.layers - assert "normalized" in output_train.layers - assert "label" in output_train.obs - assert "batch" in output_train.obs - assert "counts" in output_test.layers - assert "normalized" in output_test.layers - assert "label" not in output_test.obs # make sure label is /not/ here - assert "batch" in output_test.obs - assert "counts" in output_solution.layers - assert "normalized" in output_solution.layers - assert "label" in output_solution.obs - assert "batch" in output_solution.obs - - print(">> All checks succeeded!") - - path: ../../../resources_test/common/pancreas diff --git a/src/label_projection/unit_tests/test_method.py b/src/label_projection/unit_tests/test_method.py new file mode 100644 index 0000000000..251875f767 --- /dev/null +++ b/src/label_projection/unit_tests/test_method.py @@ -0,0 +1,42 @@ +import anndata as ad +import subprocess +from os import path + +input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" +input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" +input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" +output_path = "output.h5ad" + +cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--input_test", input_test_path, + "--output", output_path +] + +# todo: if we could access the viash config, we could check whether +# .functionality.info.type == "positive_control" +if meta['functionality_name'] == 'true_labels': + cmd = cmd + ["--input_solution", input_solution_path] + +print(">> Running script as test") +out = subprocess.check_output(cmd).decode("utf-8") + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input_test = ad.read_h5ad(input_test_path) +output = ad.read_h5ad(output_path) +print("input_test:", input_test) +print("output:", output) + +print(">> Checking whether predictions were added") +assert "label_pred" in output.obs +assert meta['functionality_name'] == output.uns["method_id"] + +print("Checking whether data from input was copied properly to output") +assert input_test.n_obs == output.n_obs +assert input_test.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") \ No newline at end of file diff --git a/src/label_projection/unit_tests/test_metric.py b/src/label_projection/unit_tests/test_metric.py new file mode 100644 index 0000000000..7a19f3d950 --- /dev/null +++ b/src/label_projection/unit_tests/test_metric.py @@ -0,0 +1,34 @@ +import anndata as ad +import subprocess +from os import path + +input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" +input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" +output_path = "output.h5ad" + +cmd = [ + meta['executable'], + "--input_prediction", input_prediction_path, + "--input_solution", input_solution_path, + "--output", output_path +] + +print(">> Running script as test") +out = subprocess.check_output(cmd).decode("utf-8") + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +input_solution = ad.read_h5ad(input_solution_path) +input_prediction = ad.read_h5ad(input_prediction_path) +output = ad.read_h5ad(output_path) + +print("Checking whether data from input was copied properly to output") +assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] +assert output.uns["method_id"] == input_prediction.uns["method_id"] +assert output.uns["metric_ids"] is not None +assert output.uns["metric_values"] is not None + +# TODO: check whether the metric ids are all in .functionality.info + +print("All checks succeeded!") diff --git a/src/label_projection/unit_tests/test_process_dataset.py b/src/label_projection/unit_tests/test_process_dataset.py new file mode 100644 index 0000000000..86d3591a9e --- /dev/null +++ b/src/label_projection/unit_tests/test_process_dataset.py @@ -0,0 +1,62 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +output_train_path = "output_train.h5ad" +output_test_path = "output_test.h5ad" +output_solution_path = "output_solution.h5ad" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path, + "--output_solution", output_solution_path +] + +print(">> Running script as test") +out = subprocess.check_output(cmd).decode("utf-8") + +print(">> Checking whether output file exists") +assert path.exists(output_train_path) +assert path.exists(output_test_path) +assert path.exists(output_solution_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output_train = ad.read_h5ad(output_train_path) +output_test = ad.read_h5ad(output_test_path) +output_solution = ad.read_h5ad(output_solution_path) + +print("input:", input) +print("output_train:", output_train) +print("output_test:", output_test) +print("output_solution:", output_solution) + +print(">> Checking dimensions, make sure no cells were dropped") +assert input.n_obs == output_train.n_obs + output_test.n_obs +assert output_test.n_obs == output_solution.n_obs +assert input.n_vars == output_train.n_vars +assert input.n_vars == output_test.n_vars + +print(">> Checking whether data from input was copied properly to output") +assert output_train.uns["dataset_id"] == input.uns["dataset_id"] +assert output_test.uns["dataset_id"] == input.uns["dataset_id"] +assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] + +print(">> Check whether certain slots exist") +assert "counts" in output_train.layers +assert "normalized" in output_train.layers +assert "label" in output_train.obs +assert "batch" in output_train.obs +assert "counts" in output_test.layers +assert "normalized" in output_test.layers +assert "label" not in output_test.obs # make sure label is /not/ here +assert "batch" in output_test.obs +assert "counts" in output_solution.layers +assert "normalized" in output_solution.layers +assert "label" in output_solution.obs +assert "batch" in output_solution.obs + +print(">> All checks succeeded!") \ No newline at end of file From 8670907b032edaff92ec03f646e2b77e0d47c857 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 09:24:58 +0200 Subject: [PATCH 0835/1233] test with branch Former-commit-id: 23ab929628de18b274b750fdae1915c4241223f6 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 32e2c50321..f96a327362 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -64,7 +64,7 @@ jobs: format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@v3 + uses: viash-io/viash-actions/project/detect-changed-components@fix/detect-resources with: input_file: "${{ steps.ns_list.outputs.output_file }}" From 0309bd3a6abddf2781cf59e30e5ba3c86eeeff19 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 09:37:56 +0200 Subject: [PATCH 0836/1233] switch to viash 0.7.3 instead Former-commit-id: 48d83228800ec7a670dda30736aff81e9fc11fe4 --- _viash.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 8d64d59236..f116ef6c2e 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.2 +viash_version: 0.7.3 source: src target: target From 64032fb7437073c53bb763eb77081a9583f9198c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 10:29:57 +0200 Subject: [PATCH 0837/1233] switch to main Former-commit-id: 4932df420adde3c7b17d590a6c55d66b65be4801 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f96a327362..1db518323d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -64,7 +64,7 @@ jobs: format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@fix/detect-resources + uses: viash-io/viash-actions/project/detect-changed-components@main with: input_file: "${{ steps.ns_list.outputs.output_file }}" From 84c5e5063c1d518b6c5cdabeb78c4e630e71895d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 10:48:05 +0200 Subject: [PATCH 0838/1233] refactor test Former-commit-id: f606c272104b64cec04e17eaf90addaa9d71c289 --- src/datasets/subsample/config.vsh.yaml | 2 +- src/datasets/subsample/script.py | 2 +- src/datasets/subsample/test_script.py | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index 75c2773045..e6d5a64df7 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -53,7 +53,7 @@ functionality: - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/datasets/subsample/script.py b/src/datasets/subsample/script.py index 60d238581d..84940205d7 100644 --- a/src/datasets/subsample/script.py +++ b/src/datasets/subsample/script.py @@ -5,7 +5,7 @@ ### VIASH START par = { - "input": "resources_test/common/pancreas/temp_dataset_full.h5ad", + "input": "resources_test/common/pancreas/dataset.h5ad", "keep_celltype_categories": None, "keep_batch_categories": None, "keep_features": ["HMGB2", "CDK1", "NUSAP1", "UBE2C"], diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index 3ef6a7eac2..ec8cd1e4ea 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -2,7 +2,7 @@ import os import pytest import anndata as ad - +import numpy as np input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" input = ad.read_h5ad(input_path) @@ -51,7 +51,7 @@ def test_keep_functionality(run_component): assert output.n_obs <= 500 assert output.n_vars <= 500 - assert set(keep_features).issubset(output.var_names) + assert np.all([ f in output.var_names for f in keep_features]) print(f"output: {output}", flush=True) From b1badc2241e55d00fb8876bef50a8889d3b5d178 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 10:55:16 +0200 Subject: [PATCH 0839/1233] remove unneeded newlines Former-commit-id: 73df5ffb3ebd7fb9f974b92a6c33edfa045719e5 --- src/datasets/subsample/test_script.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index ec8cd1e4ea..a12d07dc17 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -57,13 +57,3 @@ def test_keep_functionality(run_component): if __name__ == '__main__': sys.exit(pytest.main([__file__, "--capture=no"], plugins=["viashpy"])) - - - - - - - - - - From 1d0db1287603d9447d3ac77d41bb3f7873d8bac1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 13:22:29 +0200 Subject: [PATCH 0840/1233] rename unit_tests to comp_test Former-commit-id: 21734b914fedbedfacea5d82d410560c9b7c1e2f --- src/label_projection/api/comp_control_method.yaml | 2 +- src/label_projection/api/comp_method.yaml | 2 +- src/label_projection/api/comp_metric.yaml | 2 +- src/label_projection/api/comp_process_dataset.yaml | 2 +- src/label_projection/{unit_tests => comp_tests}/test_method.py | 0 src/label_projection/{unit_tests => comp_tests}/test_metric.py | 0 .../{unit_tests => comp_tests}/test_process_dataset.py | 0 7 files changed, 4 insertions(+), 4 deletions(-) rename src/label_projection/{unit_tests => comp_tests}/test_method.py (100%) rename src/label_projection/{unit_tests => comp_tests}/test_metric.py (100%) rename src/label_projection/{unit_tests => comp_tests}/test_process_dataset.py (100%) diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index 6ce4fbc46d..1c50f03c2d 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -16,4 +16,4 @@ functionality: - type: python_script path: /src/common/unit_test/check_method_config.py - type: python_script - path: /src/label_projection/unit_tests/test_method.py \ No newline at end of file + path: /src/label_projection/comp_test/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index a5543098b6..32aec2e95f 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -14,4 +14,4 @@ functionality: - type: python_script path: /src/common/unit_test/check_method_config.py - type: python_script - path: /src/label_projection/unit_tests/test_method.py \ No newline at end of file + path: /src/label_projection/comp_test/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 34cf3ca18f..963e537ac3 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -14,4 +14,4 @@ functionality: - type: python_script path: /src/common/unit_test/check_metric_config.py - type: python_script - path: /src/label_projection/unit_tests/test_metric.py + path: /src/label_projection/comp_test/test_metric.py diff --git a/src/label_projection/api/comp_process_dataset.yaml b/src/label_projection/api/comp_process_dataset.yaml index 829919a034..ff97c4eb2b 100644 --- a/src/label_projection/api/comp_process_dataset.yaml +++ b/src/label_projection/api/comp_process_dataset.yaml @@ -16,5 +16,5 @@ functionality: test_resources: - path: /resources_test/common/pancreas - type: python_script - path: /src/label_projection/unit_tests/test_process_dataset.py + path: /src/label_projection/comp_test/test_process_dataset.py diff --git a/src/label_projection/unit_tests/test_method.py b/src/label_projection/comp_tests/test_method.py similarity index 100% rename from src/label_projection/unit_tests/test_method.py rename to src/label_projection/comp_tests/test_method.py diff --git a/src/label_projection/unit_tests/test_metric.py b/src/label_projection/comp_tests/test_metric.py similarity index 100% rename from src/label_projection/unit_tests/test_metric.py rename to src/label_projection/comp_tests/test_metric.py diff --git a/src/label_projection/unit_tests/test_process_dataset.py b/src/label_projection/comp_tests/test_process_dataset.py similarity index 100% rename from src/label_projection/unit_tests/test_process_dataset.py rename to src/label_projection/comp_tests/test_process_dataset.py From e6fef37e92fdd2cf470b387db81ddccd990dd463 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 13:23:10 +0200 Subject: [PATCH 0841/1233] also rename `src/common/unit_test` to `src/common/comp_test` Former-commit-id: 5fea5910a1c9f94e233c4ffe7698a16374d615bd --- CHANGELOG.md | 2 +- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 2 +- src/batch_integration/api/comp_metric_feature.yaml | 2 +- src/batch_integration/api/comp_metric_graph.yaml | 2 +- src/common/{unit_test => comp_test}/check_method_config.py | 0 src/common/{unit_test => comp_test}/check_metric_config.py | 0 src/denoising/api/comp_control_method.yaml | 2 +- src/denoising/api/comp_method.yaml | 2 +- src/denoising/api/comp_metric.yaml | 2 +- src/dimensionality_reduction/api/comp_control_method.yaml | 2 +- src/dimensionality_reduction/api/comp_method.yaml | 2 +- src/dimensionality_reduction/api/comp_metric.yaml | 2 +- src/label_projection/api/comp_control_method.yaml | 2 +- src/label_projection/api/comp_method.yaml | 2 +- src/label_projection/api/comp_metric.yaml | 2 +- 18 files changed, 16 insertions(+), 16 deletions(-) rename src/common/{unit_test => comp_test}/check_method_config.py (100%) rename src/common/{unit_test => comp_test}/check_metric_config.py (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 97c2f70a3b..95d441b171 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ * `get_task_info`: extract task info -* `unit_test`: Common unit test that can be used by all tasks +* `comp_test`: Common unit test that can be used by all tasks * `check_dataset_schema`: check if the dataset used has the required fields defined in the api `anndata_*.yaml` files diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 1b88852491..02b82412ed 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index a2fafe1c46..22f4d99318 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 5bbb1883b9..2043bfca9d 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index f679d14d25..fb9c8238b1 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: ../../../common/comp_test/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 4dd7700a1e..c9675e7ccd 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: ../../../common/comp_test/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index b7702bc7eb..df3a5c0ba6 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: ../../../common/comp_test/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/common/unit_test/check_method_config.py b/src/common/comp_test/check_method_config.py similarity index 100% rename from src/common/unit_test/check_method_config.py rename to src/common/comp_test/check_method_config.py diff --git a/src/common/unit_test/check_metric_config.py b/src/common/comp_test/check_metric_config.py similarity index 100% rename from src/common/unit_test/check_metric_config.py rename to src/common/comp_test/check_metric_config.py diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 908a3507a6..a636006dd9 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index f91a2365f5..2050126660 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 589e57d503..c428b07e8e 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: ../../../common/comp_test/check_metric_config.py - type: python_script path: format_check.py text: | diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 01518c4e62..e93b074b58 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 708dc19948..69c142f871 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/unit_test/check_method_config.py + path: ../../../common/comp_test/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 8be36bedee..29a6158283 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/unit_test/check_metric_config.py + path: ../../../common/comp_test/check_metric_config.py - type: python_script path: generic_test.py text: | diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index 1c50f03c2d..4c4fe3167f 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -14,6 +14,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/unit_test/check_method_config.py + path: /src/common/comp_test/check_method_config.py - type: python_script path: /src/label_projection/comp_test/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 32aec2e95f..0dd56f7156 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -12,6 +12,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/unit_test/check_method_config.py + path: /src/common/comp_test/check_method_config.py - type: python_script path: /src/label_projection/comp_test/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 963e537ac3..08509c2d14 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -12,6 +12,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/unit_test/check_metric_config.py + path: /src/common/comp_test/check_metric_config.py - type: python_script path: /src/label_projection/comp_test/test_metric.py From df866defcc50031a45cd8212c0e53cf85df3235c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 13:33:29 +0200 Subject: [PATCH 0842/1233] fix folder naming Former-commit-id: 2d24bfe9c20e86d113b79cf8a61493d59576e6cf --- CHANGELOG.md | 2 +- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 2 +- src/batch_integration/api/comp_metric_feature.yaml | 2 +- src/batch_integration/api/comp_metric_graph.yaml | 2 +- src/common/{comp_test => comp_tests}/check_method_config.py | 0 src/common/{comp_test => comp_tests}/check_metric_config.py | 0 src/denoising/api/comp_control_method.yaml | 2 +- src/denoising/api/comp_method.yaml | 2 +- src/denoising/api/comp_metric.yaml | 2 +- src/dimensionality_reduction/api/comp_control_method.yaml | 2 +- src/dimensionality_reduction/api/comp_method.yaml | 2 +- src/dimensionality_reduction/api/comp_metric.yaml | 2 +- src/label_projection/api/comp_control_method.yaml | 4 ++-- src/label_projection/api/comp_method.yaml | 4 ++-- src/label_projection/api/comp_metric.yaml | 4 ++-- src/label_projection/api/comp_process_dataset.yaml | 2 +- 19 files changed, 20 insertions(+), 20 deletions(-) rename src/common/{comp_test => comp_tests}/check_method_config.py (100%) rename src/common/{comp_test => comp_tests}/check_metric_config.py (100%) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95d441b171..5585fa7ce6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ * `get_task_info`: extract task info -* `comp_test`: Common unit test that can be used by all tasks +* `comp_tests`: Common unit test that can be used by all tasks * `check_dataset_schema`: check if the dataset used has the required fields defined in the api `anndata_*.yaml` files diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 02b82412ed..6e7b72bf44 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 22f4d99318..1534136d4b 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 2043bfca9d..59972b6f38 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -17,7 +17,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index fb9c8238b1..1703182632 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_metric_config.py + path: ../../../common/comp_tests/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index c9675e7ccd..7f08a83f00 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_metric_config.py + path: ../../../common/comp_tests/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index df3a5c0ba6..d383efcb25 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -11,7 +11,7 @@ functionality: test_resources: - path: ../../../../resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_test/check_metric_config.py + path: ../../../common/comp_tests/check_metric_config.py - type: python_script dest: test.py text: | diff --git a/src/common/comp_test/check_method_config.py b/src/common/comp_tests/check_method_config.py similarity index 100% rename from src/common/comp_test/check_method_config.py rename to src/common/comp_tests/check_method_config.py diff --git a/src/common/comp_test/check_metric_config.py b/src/common/comp_tests/check_metric_config.py similarity index 100% rename from src/common/comp_test/check_metric_config.py rename to src/common/comp_tests/check_metric_config.py diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index a636006dd9..7d553a9330 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 2050126660..0f5b1e51d3 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index c428b07e8e..ef4c8833ae 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_test/check_metric_config.py + path: ../../../common/comp_tests/check_metric_config.py - type: python_script path: format_check.py text: | diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index e93b074b58..a2e873f105 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index 69c142f871..f52a21f284 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_test/check_method_config.py + path: ../../../common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 29a6158283..8b8c838eda 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: ../../../../resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_test/check_metric_config.py + path: ../../../common/comp_tests/check_metric_config.py - type: python_script path: generic_test.py text: | diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index 4c4fe3167f..fa647e5003 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -14,6 +14,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/comp_test/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/label_projection/comp_test/test_method.py \ No newline at end of file + path: /src/label_projection/comp_tests/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 0dd56f7156..0aec11fa2f 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -12,6 +12,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/comp_test/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/label_projection/comp_test/test_method.py \ No newline at end of file + path: /src/label_projection/comp_tests/test_method.py \ No newline at end of file diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 08509c2d14..6b6008d539 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -12,6 +12,6 @@ functionality: test_resources: - path: /resources_test/label_projection/pancreas - type: python_script - path: /src/common/comp_test/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/label_projection/comp_test/test_metric.py + path: /src/label_projection/comp_tests/test_metric.py diff --git a/src/label_projection/api/comp_process_dataset.yaml b/src/label_projection/api/comp_process_dataset.yaml index ff97c4eb2b..707a5c46d5 100644 --- a/src/label_projection/api/comp_process_dataset.yaml +++ b/src/label_projection/api/comp_process_dataset.yaml @@ -16,5 +16,5 @@ functionality: test_resources: - path: /resources_test/common/pancreas - type: python_script - path: /src/label_projection/comp_test/test_process_dataset.py + path: /src/label_projection/comp_tests/test_process_dataset.py From 1212858d7ce3dcf8e1c6a5992170521b7e63d89f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 14:09:51 +0200 Subject: [PATCH 0843/1233] switch to v3 afain Former-commit-id: 7163fbde68bdcaf21a7ef31526026e0f47f4921f --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 1db518323d..32e2c50321 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -64,7 +64,7 @@ jobs: format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@main + uses: viash-io/viash-actions/project/detect-changed-components@v3 with: input_file: "${{ steps.ns_list.outputs.output_file }}" From 00b345b737099f83e3925ec98ca19b6fe481fa95 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 14:15:42 +0200 Subject: [PATCH 0844/1233] set the required anndata version to 'anndata~=0.8.0' (#130) * set the required anndata version to 'anndata~=0.8.0' * remove extra space Former-commit-id: 0b2e837b258b96631a790b0128143ab1b772b7b9 --- CONTRIBUTING.md | 6 +++--- CONTRIBUTING.qmd | 2 +- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 4 ++-- src/common/extract_scores/config.vsh.yaml | 2 +- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 2 +- src/datasets/normalization/log_cpm/config.vsh.yaml | 2 +- .../normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- src/datasets/subsample/config.vsh.yaml | 2 +- src/denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- .../control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/denoising/methods/alra/config.vsh.yaml | 2 +- src/denoising/methods/dca/config.vsh.yaml | 2 +- src/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/denoising/methods/magic/config.vsh.yaml | 2 +- src/denoising/metrics/mse/config.vsh.yaml | 2 +- src/denoising/metrics/poisson/config.vsh.yaml | 2 +- src/denoising/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../methods/densmap/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/ivis/config.vsh.yaml | 2 +- .../methods/neuralee/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- src/dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 2 +- src/dimensionality_reduction/metrics/rmse/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/label_projection/methods/mlp/config.vsh.yaml | 2 +- src/label_projection/methods/scanvi/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/label_projection/methods/xgboost/config.vsh.yaml | 2 +- src/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/label_projection/process_dataset/config.vsh.yaml | 2 +- 48 files changed, 51 insertions(+), 51 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a325e89f4f..b9aae91646 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -215,7 +215,7 @@ platforms: setup: - type: python packages: - - anndata>=0.8 + - anndata~=0.8.0 - scikit-learn - type: nextflow ``` @@ -383,7 +383,7 @@ viash test src/label_projection/methods/foo/config.vsh.yaml Step 1/7 : FROM python:3.10 ---> 465483cdaa4e - Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" + Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata~=0.8.0" "scikit-learn" ---> Using cache ---> 91f658ec0590 Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" @@ -480,7 +480,7 @@ viash test src/label_projection/methods/foo/config.vsh.yaml Step 1/7 : FROM python:3.10 ---> 465483cdaa4e - Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata>=0.8" "scikit-learn" + Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata~=0.8.0" "scikit-learn" ---> Using cache ---> 91f658ec0590 Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 605726d008..a4d8b4c32e 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -184,7 +184,7 @@ platforms: setup: - type: python packages: - - anndata>=0.8 + - anndata~=0.8.0 - scikit-learn - type: nextflow HERE diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 6b18e5faed..0f833cdb0f 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -45,6 +45,6 @@ platforms: image: python:3.10 setup: - type: python - pip: [anndata>=0.8, pyyaml] + pip: [anndata~=0.8.0, pyyaml] - type: nextflow diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index d5983d3a84..f6273d58cb 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -119,7 +119,7 @@ def add_python_setup(conf) -> None: conf['platforms'][0]["setup"] = [ { "type": "python", - "pypi": "anndata~=0.8" + "pypi": "anndata~=0.8.0" } ] @@ -133,7 +133,7 @@ def add_r_setup(conf) -> None: }, { "type": "python", - "pypi": "anndata~=0.8" + "pypi": "anndata~=0.8.0" }, { "type": "r", diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 3e1a336106..124becb00a 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -33,5 +33,5 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8 ] + pip: [ anndata~=0.8.0 ] - type: nextflow diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index be227766af..af993a4888 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -22,7 +22,7 @@ platforms: - type: python packages: - scprep - - "anndata>=0.8" + - "anndata~=0.8.0" - numpy - type: nextflow directives: diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 824809bcb4..0f29529355 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -13,7 +13,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 6ded643aa4..91d4d414a2 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -17,7 +17,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8, scanpy ] + pip: [ anndata~=0.8.0, scanpy ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 8ceaf85bc8..88acda2039 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -13,7 +13,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 500d33f5fa..434a2bc402 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -13,6 +13,6 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 7b7743df17..2f9f4a0d01 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -13,6 +13,6 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index b6cff9bfb6..ebd719b1a7 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -17,5 +17,5 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index e6d5a64df7..2023b2edf2 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -58,7 +58,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" test_setup: - type: python packages: diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 6ddc6bbdb5..2afb33c41e 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -22,7 +22,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - type: nextflow directives: diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index a3bbda6645..ccf7425b65 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -21,7 +21,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - type: nextflow directives: diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index f686d809b1..d596164e87 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -37,7 +37,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] - type: python - pip: [ anndata>=0.8, pyyaml ] + pip: [ anndata~=0.8.0, pyyaml ] - type: r cran: [ Matrix, anndata, bit64, rsvd ] - type: docker diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index da088fa8f2..997b1aeb1f 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -32,7 +32,7 @@ platforms: setup: - type: python packages: - - anndata>=0.8 + - anndata~=0.8.0 - pyyaml - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 9bab76224b..32a05fd97f 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -33,7 +33,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - scipy github: diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 365bb6fb2a..8b3f3252fb 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -57,7 +57,7 @@ platforms: image: "python:3.10" setup: - type: python - pip: [ "anndata>=0.8", pyyaml, scprep, magic-impute, scipy, scikit-learn<1.2] + pip: [ "anndata~=0.8.0", pyyaml, scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index 4d4e4004b1..b2a2a5ed4a 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -26,7 +26,7 @@ platforms: - type: python packages: - scikit-learn - - "anndata>=0.8" + - "anndata~=0.8.0" - scanpy - scprep - pyyaml diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 8494f24621..94d29ce1b7 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -27,7 +27,7 @@ platforms: setup: - type: python pip: - - "anndata>=0.8" + - "anndata~=0.8.0" - scprep - pyyaml - type: nextflow diff --git a/src/denoising/process_dataset/config.vsh.yaml b/src/denoising/process_dataset/config.vsh.yaml index 1c19af5f4c..61a74d0b74 100644 --- a/src/denoising/process_dataset/config.vsh.yaml +++ b/src/denoising/process_dataset/config.vsh.yaml @@ -31,7 +31,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - numpy - scipy - type: nextflow diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index fdac452995..a923da0432 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -22,7 +22,7 @@ platforms: - type: python packages: - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 4bdd1e22ed..d81953e413 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -41,7 +41,7 @@ platforms: packages: - scanpy - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index 4be7bb71ad..ed1c08da4b 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -38,7 +38,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - umap-learn - type: nextflow diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index c688f4cfaa..b723076b95 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -41,7 +41,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - ivis[cpu] - pyyaml - type: nextflow diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index f195f449cf..adbf7aebc3 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -49,7 +49,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - torch - "git+https://github.com/michalk8/neuralee@8946abf" diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 5527d14a84..9b8351c65b 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -37,7 +37,7 @@ platforms: packages: - scanpy - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 9ae1b1d6ea..08f10799be 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -50,7 +50,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - phate==1.0.* - scprep - pyyaml diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 786c56dc8e..3d350af7f5 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -44,7 +44,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - MulticoreTSNE - type: nextflow diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index 4684209d2b..c6f2c2fb8f 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -44,7 +44,7 @@ platforms: - type: python packages: - scanpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - umap-learn - type: nextflow diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index d190d6183d..177b4cf41c 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -99,7 +99,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8, pyyaml ] + pip: [ anndata~=0.8.0, pyyaml ] - type: nextflow directives: label: [ highmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 53cede8a1f..0aba9dec57 100644 --- a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -29,7 +29,7 @@ platforms: packages: - scipy - numpy - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - umap-learn - type: nextflow diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 30cb3bc133..43b2b50910 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -46,7 +46,7 @@ platforms: - numpy - scipy - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index d37ce37638..32c7b0078b 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -30,7 +30,7 @@ platforms: - scikit-learn - numpy - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/dimensionality_reduction/process_dataset/config.vsh.yaml index 09ef02c139..9d2df6f66a 100644 --- a/src/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -12,7 +12,7 @@ platforms: - type: python packages: - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index ad4edc6604..d8fc6464ab 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -21,7 +21,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - type: nextflow directives: diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 837e1f82cf..0d5f3999bb 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -23,7 +23,7 @@ platforms: packages: - scanpy - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index 62e4e97f9c..c031c8faa2 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -23,7 +23,7 @@ platforms: - type: python packages: - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index 507e18d730..d327024545 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -34,7 +34,7 @@ platforms: packages: - scikit-learn - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index d3d1f45441..6238e49690 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -31,7 +31,7 @@ platforms: packages: - scikit-learn - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index b7a30091bd..62a77df0af 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -44,7 +44,7 @@ platforms: packages: - scikit-learn - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 50cda68e73..0d324b805b 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -37,7 +37,7 @@ platforms: - type: python packages: - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - scarches - type: nextflow directives: diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index 28c6c17346..8198ae25bc 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -36,7 +36,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata>=0.8, pyyaml ] + pip: [ anndata~=0.8.0, pyyaml ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index b28f410b23..ca044ace50 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -30,7 +30,7 @@ platforms: setup: - type: python packages: - - "anndata>=0.8" + - "anndata~=0.8.0" - pyyaml - xgboost - type: nextflow diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index edcd9bcd03..7d762a2c74 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -27,5 +27,5 @@ platforms: packages: - pyyaml - scikit-learn - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index d74681b359..9e271b2a84 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -47,5 +47,5 @@ platforms: packages: - scikit-learn - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow diff --git a/src/label_projection/process_dataset/config.vsh.yaml b/src/label_projection/process_dataset/config.vsh.yaml index ac3485ff4a..cedd6d3c6f 100644 --- a/src/label_projection/process_dataset/config.vsh.yaml +++ b/src/label_projection/process_dataset/config.vsh.yaml @@ -30,5 +30,5 @@ platforms: - type: python packages: - pyyaml - - "anndata>=0.8" + - "anndata~=0.8.0" - type: nextflow From 3e2508a6cebd04be6dc5e95fcb2460cd70f5a094 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 14:39:49 +0200 Subject: [PATCH 0845/1233] add PR template (#135) Former-commit-id: 447e502f1a2e8285b02fa891ddac2803baffa632 --- .github/PULL_REQUEST_TEMPLATE.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 .github/PULL_REQUEST_TEMPLATE.md diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000000..43caae6b44 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,18 @@ +## Describe your changes + +## Issue ticket number and link +Closes #xxxx (Replace xxxx with the GitHub issue number) + +## Checklist before requesting a review +- [ ] I have performed a self-review of my code + +- Check the correct box. Does this PR contain: + - [ ] Breaking changes + - [ ] New functionality + - [ ] Major changes + - [ ] Minor changes + - [ ] Bug fixes + +- [ ] Proposed changes are described in the CHANGELOG.md + +- [ ] CI Tests succeed and look good! \ No newline at end of file From 58172263343ba22320911b767223ca76109eb97a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 15:03:43 +0200 Subject: [PATCH 0846/1233] move tests Former-commit-id: 082860dd599f61da20189e38be2413095dda2d84 --- .../api/comp_method_embedding.yaml | 56 +------------- .../api/comp_method_feature.yaml | 43 +---------- .../api/comp_method_graph.yaml | 45 +----------- .../api/comp_metric_embedding.yaml | 71 +----------------- .../api/comp_metric_feature.yaml | 71 +----------------- .../api/comp_metric_graph.yaml | 73 +------------------ .../api/comp_process_dataset.yaml | 45 +----------- .../comp_tests/test_method_embedding.py | 64 ++++++++++++++++ .../comp_tests/test_method_feature.py | 36 +++++++++ .../comp_tests/test_method_graph.py | 38 ++++++++++ .../comp_tests/test_metric_embedding.py | 64 ++++++++++++++++ .../comp_tests/test_metric_feature.py | 64 ++++++++++++++++ .../comp_tests/test_metric_graph.py | 66 +++++++++++++++++ .../comp_tests/test_process_dataset.py | 40 ++++++++++ .../process_dataset/config.vsh.yaml | 1 - .../check_dataset_schema/config.vsh.yaml | 2 +- src/datasets/api/comp_normalization.yaml | 2 +- src/datasets/api/comp_processor_hvg.yaml | 2 +- src/denoising/api/comp_control_method.yaml | 46 +----------- src/denoising/api/comp_method.yaml | 41 +---------- src/denoising/api/comp_metric.yaml | 42 +---------- src/denoising/api/comp_process_dataset.yaml | 44 +---------- src/denoising/comp_tests/test_method.py | 34 +++++++++ src/denoising/comp_tests/test_metric.py | 34 +++++++++ .../comp_tests/test_process_dataset.py | 40 ++++++++++ .../api/comp_control_method.yaml | 4 +- .../api/comp_method.yaml | 4 +- .../api/comp_metric.yaml | 4 +- .../api/comp_process_dataset.yaml | 2 +- 29 files changed, 522 insertions(+), 556 deletions(-) create mode 100644 src/batch_integration/comp_tests/test_method_embedding.py create mode 100644 src/batch_integration/comp_tests/test_method_feature.py create mode 100644 src/batch_integration/comp_tests/test_method_graph.py create mode 100644 src/batch_integration/comp_tests/test_metric_embedding.py create mode 100644 src/batch_integration/comp_tests/test_metric_feature.py create mode 100644 src/batch_integration/comp_tests/test_metric_graph.py create mode 100644 src/batch_integration/comp_tests/test_process_dataset.py create mode 100644 src/denoising/comp_tests/test_method.py create mode 100644 src/denoising/comp_tests/test_metric.py create mode 100644 src/denoising/comp_tests/test_process_dataset.py diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 6e7b72bf44..6a39f2dfab 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -15,58 +15,8 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - from os import path - import subprocess - import numpy as np - import anndata as ad - - - input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" - output_path = "embeddding.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path - ] - - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout - print(out) - - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - - print(f"input: {input}", flush=True) - print(f"output: {output}", flush=True) - - print(">> Checking whether predictions were added", flush=True) - assert 'dataset_id' in output.uns - assert 'X_pca' in output.obsm - assert 'X_emb' in output.obsm - assert 'normalization_id' in output.uns - assert 'method_id' in output.uns - assert meta['functionality_name'] == output.uns['method_id'] - - assert 'hvg' in output.uns - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - - assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - - print(">> All tests passed successfully") \ No newline at end of file + path: /src/batch_integration/comp_tests/test_method_embedding.py diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 1534136d4b..07152f9b8d 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -15,45 +15,8 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import os - import subprocess - import anndata as ad - - input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" - output_path = "integrated.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path - ] - - print(">> Checking whether input file exists", flush=True) - assert os.path.exists(input_path) - - print(">> Running script as test", flush=True) - subprocess.run(cmd, check=True) - - print(">> Checking whether file exists", flush=True) - assert os.path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - print(f"input: {input}", flush=True) - print(f"output: {output}", flush=True) - - print(">> Checking whether predictions were added", flush=True) - # TODO: use helper function to check whether the required fields are defined - assert output.layers['corrected_counts'] is not None - - print(">> Check values", flush=True) - assert meta['functionality_name'] == output.uns['method_id'] - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print(">> All tests passed successfully") + path: /src/batch_integration/comp_tests/test_method_feature.py diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 59972b6f38..f6b00c2d72 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -15,47 +15,8 @@ functionality: default: false required: false test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import os - import subprocess - import anndata as ad - - input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" - output_path = "inegrated.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path - ] - - print(">> Checking whether input file exists", flush=True) - assert os.path.exists(input_path) - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout - print(out, flush=True) - - print(">> Checking whether file exists", flush=True) - assert os.path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - print(f"input: {input}", flush=True) - print(f"output: {output}", flush=True) - - print(">> Checking whether predictions were added", flush=True) - # TODO: use helper function to check whether the required fields are defined - assert 'connectivities' in output.obsp - assert 'distances' in output.obsp - - print(">> Check values", flush=True) - assert meta['functionality_name'] == output.uns['method_id'] - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print(">> All tests passed successfully") + path: /src/batch_integration/comp_tests/test_method_graph.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 1703182632..4ae56d3e08 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -9,73 +9,8 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_metric_config.py + path: /common/comp_tests/check_metric_config.py - type: python_script - dest: test.py - text: | - import sys - from os import path - import subprocess - import numpy as np - import anndata as ad - import yaml - - ## VIASH START - meta = { - "resources_dir": "resources_test/batch_integration/pancreas", - "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" - } - ## VIASH END - - np.random.seed(42) - - print(">> Read metric config", flush=True) - with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - - input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" - output_file = "output.h5ad" - - cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file - ] - - print(">> Running script", flush=True) - subprocess.run(cmd_args, check=True) - - print(">> Checking whether file exists", flush=True) - assert path.exists(output_file) - input = ad.read_h5ad(input_file) - output = ad.read_h5ad(output_file) - - print(">> Print AnnData contents", flush=True) - print("input:", input, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether metrics were added", flush=True) - assert "metric_ids" in output.uns - assert "metric_values" in output.uns - assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.uns["dataset_id"] == output.uns["dataset_id"] - assert input.uns["method_id"] == output.uns["method_id"] - - print(">> Check that score makes sense", flush=True) - metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] - } - - for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - - print(">> All tests passed successfully") + path: /src/batch_integration/comp_tests/test_metric_embedding.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 7f08a83f00..8a3c4bcdc7 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -9,73 +9,8 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_metric_config.py + path: /common/comp_tests/check_metric_config.py - type: python_script - dest: test.py - text: | - import sys - from os import path - import subprocess - import numpy as np - import anndata as ad - import yaml - - ## VIASH START - meta = { - "resources_dir": "resources_test/batch_integration/pancreas", - "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" - } - ## VIASH END - - np.random.seed(42) - - print(">> Read metric config", flush=True) - with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - - input_file = f"{meta['resources_dir']}/pancreas/combat.h5ad" - output_file = "output.h5ad" - - cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file - ] - - print(">> Running script", flush=True) - subprocess.run(cmd_args, check=True) - - print(">> Checking whether file exists", flush=True) - assert path.exists(output_file) - input = ad.read_h5ad(input_file) - output = ad.read_h5ad(output_file) - - print(">> Print AnnData contents", flush=True) - print("input:", input, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether metrics were added", flush=True) - assert "metric_ids" in output.uns - assert "metric_values" in output.uns - assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.uns["dataset_id"] == output.uns["dataset_id"] - assert input.uns["method_id"] == output.uns["method_id"] - - print(">> Check that score makes sense", flush=True) - metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] - } - - for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - - print(">> All tests passed successfully") + path: /src/batch_integration/comp_tests/test_metric_feature.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index d383efcb25..9f3a18e3b1 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -9,75 +9,8 @@ functionality: direction: output __merge__: anndata_score.yaml test_resources: - - path: ../../../../resources_test/batch_integration/pancreas + - path: /resources_test/batch_integration/pancreas - type: python_script - path: ../../../common/comp_tests/check_metric_config.py + path: /common/comp_tests/check_metric_config.py - type: python_script - dest: test.py - text: | - import sys - from os import path - import subprocess - import numpy as np - import anndata as ad - import yaml - - ## VIASH START - meta = { - "resources_dir": "resources_test/batch_integration/pancreas/graph/methods", - "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" - } - ## VIASH END - - np.random.seed(42) - - print(">> Read metric config", flush=True) - with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - - output_type = config["functionality"].get("info", {}).get("output_type") - - input_file = f"{meta['resources_dir']}/pancreas/bbknn.h5ad" - output_file = "output.h5ad" - - cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file - ] - - print(">> Running script", flush=True) - subprocess.run(cmd_args, check=True) - - print(">> Checking whether file exists", flush=True) - assert path.exists(output_file) - input = ad.read_h5ad(input_file) - output = ad.read_h5ad(output_file) - - print(">> Print AnnData contents", flush=True) - print("input:", input, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether metrics were added", flush=True) - assert "metric_ids" in output.uns - assert "metric_values" in output.uns - assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.uns["dataset_id"] == output.uns["dataset_id"] - assert input.uns["method_id"] == output.uns["method_id"] - - print(">> Check that score makes sense", flush=True) - metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] - } - - for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - - print(">> All tests passed successfully") + path: /src/batch_integration/comp_tests/test_metric_graph.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_process_dataset.yaml b/src/batch_integration/api/comp_process_dataset.yaml index 6ae3736b1a..3ec6345ff3 100644 --- a/src/batch_integration/api/comp_process_dataset.yaml +++ b/src/batch_integration/api/comp_process_dataset.yaml @@ -8,47 +8,6 @@ functionality: __merge__: anndata_unintegrated.yaml direction: output test_resources: - - path: ../../../resources_test/common/pancreas/ + - path: /resources_test/common/pancreas/ - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_unintegrated_path = "unintegrated.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_unintegrated_path - ] - - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout - print(out) - - print(">> Checking whether output files exist", flush=True) - assert path.exists(output_unintegrated_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output_unintegrated = ad.read_h5ad(output_unintegrated_path) - - print("input:", input, flush=True) - print("output_unintegrated:", output_unintegrated, flush=True) - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output_unintegrated.n_obs - assert input.uns["dataset_id"] == output_unintegrated.uns["dataset_id"] - - - print(">> Check whether certain slots exist", flush=True) - assert "counts" in output_unintegrated.layers - assert "normalized" in output_unintegrated.layers - assert 'hvg' in output_unintegrated.var - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/batch_integration/comp_tests/test_process_dataset.py \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_method_embedding.py b/src/batch_integration/comp_tests/test_method_embedding.py new file mode 100644 index 0000000000..d8825af182 --- /dev/null +++ b/src/batch_integration/comp_tests/test_method_embedding.py @@ -0,0 +1,64 @@ +import sys +from os import path +import subprocess +import numpy as np +import anndata as ad +import yaml + +## VIASH START +meta = { + "resources_dir": "resources_test/batch_integration/pancreas", + "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" +} +## VIASH END + +np.random.seed(42) + +print(">> Read metric config", flush=True) +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" +output_file = "output.h5ad" + +cmd_args = [ + meta["executable"], + "--input_integrated", input_file, + "--output", output_file +] + +print(">> Running script", flush=True) +subprocess.run(cmd_args, check=True) + +print(">> Checking whether file exists", flush=True) +assert path.exists(output_file) +input = ad.read_h5ad(input_file) +output = ad.read_h5ad(output_file) + +print(">> Print AnnData contents", flush=True) +print("input:", input, flush=True) +print("output:", output, flush=True) + +print(">> Checking whether metrics were added", flush=True) +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input.uns["method_id"] == output.uns["method_id"] + +print(">> Check that score makes sense", flush=True) +metrics_info = { + metric["name"]: metric + for metric in config["functionality"]["info"]["metrics"] +} + +for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + +print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_method_feature.py b/src/batch_integration/comp_tests/test_method_feature.py new file mode 100644 index 0000000000..ddd49102d9 --- /dev/null +++ b/src/batch_integration/comp_tests/test_method_feature.py @@ -0,0 +1,36 @@ +import os +import subprocess +import anndata as ad + +input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" +output_path = "integrated.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path +] + +print(">> Checking whether input file exists", flush=True) +assert os.path.exists(input_path) + +print(">> Running script as test", flush=True) +subprocess.run(cmd, check=True) + +print(">> Checking whether file exists", flush=True) +assert os.path.exists(output_path) + +print(">> Reading h5ad files", flush=True) +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) +print(f"input: {input}", flush=True) +print(f"output: {output}", flush=True) + +print(">> Checking whether predictions were added", flush=True) +# TODO: use helper function to check whether the required fields are defined +assert output.layers['corrected_counts'] is not None + +print(">> Check values", flush=True) +assert meta['functionality_name'] == output.uns['method_id'] +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_method_graph.py b/src/batch_integration/comp_tests/test_method_graph.py new file mode 100644 index 0000000000..9b3d5f7de8 --- /dev/null +++ b/src/batch_integration/comp_tests/test_method_graph.py @@ -0,0 +1,38 @@ +import os +import subprocess +import anndata as ad + +input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" +output_path = "inegrated.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path +] + +print(">> Checking whether input file exists", flush=True) +assert os.path.exists(input_path) + +print(">> Running script as test", flush=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout +print(out, flush=True) + +print(">> Checking whether file exists", flush=True) +assert os.path.exists(output_path) + +print(">> Reading h5ad files", flush=True) +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) +print(f"input: {input}", flush=True) +print(f"output: {output}", flush=True) + +print(">> Checking whether predictions were added", flush=True) +# TODO: use helper function to check whether the required fields are defined +assert 'connectivities' in output.obsp +assert 'distances' in output.obsp + +print(">> Check values", flush=True) +assert meta['functionality_name'] == output.uns['method_id'] +assert input.uns["dataset_id"] == output.uns["dataset_id"] + +print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_embedding.py b/src/batch_integration/comp_tests/test_metric_embedding.py new file mode 100644 index 0000000000..347c85c0d6 --- /dev/null +++ b/src/batch_integration/comp_tests/test_metric_embedding.py @@ -0,0 +1,64 @@ +import sys +from os import path +import subprocess +import numpy as np +import anndata as ad +import yaml + +## VIASH START +meta = { + "resources_dir": "resources_test/batch_integration/pancreas", + "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" +} +## VIASH END + +np.random.seed(42) + +print(">> Read metric config", flush=True) +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" +output_file = "output.h5ad" + +cmd_args = [ + meta["executable"], + "--input_integrated", input_file, + "--output", output_file +] + +print(">> Running script", flush=True) +subprocess.run(cmd_args, check=True) + +print(">> Checking whether file exists", flush=True) +assert path.exists(output_file) +input = ad.read_h5ad(input_file) +output = ad.read_h5ad(output_file) + +print(">> Print AnnData contents", flush=True) +print("input:", input, flush=True) +print("output:", output, flush=True) + +print(">> Checking whether metrics were added", flush=True) +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input.uns["method_id"] == output.uns["method_id"] + +print(">> Check that score makes sense", flush=True) +metrics_info = { + metric["name"]: metric + for metric in config["functionality"]["info"]["metrics"] +} + +for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + +print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_feature.py b/src/batch_integration/comp_tests/test_metric_feature.py new file mode 100644 index 0000000000..13498ab22a --- /dev/null +++ b/src/batch_integration/comp_tests/test_metric_feature.py @@ -0,0 +1,64 @@ +import sys +from os import path +import subprocess +import numpy as np +import anndata as ad +import yaml + +## VIASH START +meta = { + "resources_dir": "resources_test/batch_integration/pancreas", + "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" +} +## VIASH END + +np.random.seed(42) + +print(">> Read metric config", flush=True) +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +input_file = f"{meta['resources_dir']}/pancreas/combat.h5ad" +output_file = "output.h5ad" + +cmd_args = [ + meta["executable"], + "--input_integrated", input_file, + "--output", output_file +] + +print(">> Running script", flush=True) +subprocess.run(cmd_args, check=True) + +print(">> Checking whether file exists", flush=True) +assert path.exists(output_file) +input = ad.read_h5ad(input_file) +output = ad.read_h5ad(output_file) + +print(">> Print AnnData contents", flush=True) +print("input:", input, flush=True) +print("output:", output, flush=True) + +print(">> Checking whether metrics were added", flush=True) +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input.uns["method_id"] == output.uns["method_id"] + +print(">> Check that score makes sense", flush=True) +metrics_info = { + metric["name"]: metric + for metric in config["functionality"]["info"]["metrics"] +} + +for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + +print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_graph.py b/src/batch_integration/comp_tests/test_metric_graph.py new file mode 100644 index 0000000000..399f7c1ce8 --- /dev/null +++ b/src/batch_integration/comp_tests/test_metric_graph.py @@ -0,0 +1,66 @@ +import sys +from os import path +import subprocess +import numpy as np +import anndata as ad +import yaml + +## VIASH START +meta = { + "resources_dir": "resources_test/batch_integration/pancreas/graph/methods", + "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" +} +## VIASH END + +np.random.seed(42) + +print(">> Read metric config", flush=True) +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"].get("info", {}).get("output_type") + +input_file = f"{meta['resources_dir']}/pancreas/bbknn.h5ad" +output_file = "output.h5ad" + +cmd_args = [ + meta["executable"], + "--input_integrated", input_file, + "--output", output_file +] + +print(">> Running script", flush=True) +subprocess.run(cmd_args, check=True) + +print(">> Checking whether file exists", flush=True) +assert path.exists(output_file) +input = ad.read_h5ad(input_file) +output = ad.read_h5ad(output_file) + +print(">> Print AnnData contents", flush=True) +print("input:", input, flush=True) +print("output:", output, flush=True) + +print(">> Checking whether metrics were added", flush=True) +assert "metric_ids" in output.uns +assert "metric_values" in output.uns +assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.uns["dataset_id"] == output.uns["dataset_id"] +assert input.uns["method_id"] == output.uns["method_id"] + +print(">> Check that score makes sense", flush=True) +metrics_info = { + metric["name"]: metric + for metric in config["functionality"]["info"]["metrics"] +} + +for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): + assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" + info = metrics_info[metric_id] + + assert info["min"] <= metric_value + assert metric_value <= info["max"] + +print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_process_dataset.py b/src/batch_integration/comp_tests/test_process_dataset.py new file mode 100644 index 0000000000..2897326337 --- /dev/null +++ b/src/batch_integration/comp_tests/test_process_dataset.py @@ -0,0 +1,40 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +output_unintegrated_path = "unintegrated.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_unintegrated_path +] + +print(">> Checking whether input file exists", flush=True) +assert path.exists(input_path) + +print(">> Running script as test", flush=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout +print(out) + +print(">> Checking whether output files exist", flush=True) +assert path.exists(output_unintegrated_path) + +print(">> Reading h5ad files", flush=True) +input = ad.read_h5ad(input_path) +output_unintegrated = ad.read_h5ad(output_unintegrated_path) + +print("input:", input, flush=True) +print("output_unintegrated:", output_unintegrated, flush=True) + +print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.n_obs == output_unintegrated.n_obs +assert input.uns["dataset_id"] == output_unintegrated.uns["dataset_id"] + + +print(">> Check whether certain slots exist", flush=True) +assert "counts" in output_unintegrated.layers +assert "normalized" in output_unintegrated.layers +assert 'hvg' in output_unintegrated.var + +print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/batch_integration/process_dataset/config.vsh.yaml b/src/batch_integration/process_dataset/config.vsh.yaml index 1dac6dc8a3..848c6fe1b9 100644 --- a/src/batch_integration/process_dataset/config.vsh.yaml +++ b/src/batch_integration/process_dataset/config.vsh.yaml @@ -23,7 +23,6 @@ functionality: test_resources: - type: python_script path: test.py - - path: ../../../resources_test/common/pancreas/ platforms: - type: docker image: mumichae/scib-base:1.1.3 diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 6b18e5faed..6d221456fc 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -37,7 +37,7 @@ functionality: - type: python_script path: script.py test_resources: - - path: ../../../resources_test/common/pancreas + - path: /resources_test/common/pancreas - type: python_script path: test.py platforms: diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index 77414e5001..0047fd16ba 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -52,4 +52,4 @@ functionality: assert input.uns["dataset_id"] == output.uns["dataset_id"] print("All checks succeeded!") - - path: ../../../../resources_test/common/pancreas + - path: /resources_test/common/pancreas diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index db7ff6e3e6..c4fc313806 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -22,7 +22,7 @@ functionality: default: 1000 description: "The number of HVG to select" test_resources: - - path: ../../../../resources_test/common/pancreas + - path: /resources_test/common/pancreas - type: python_script path: generic_test.py text: | diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index 7d553a9330..ca0a960f58 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -10,48 +10,8 @@ functionality: __merge__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/train.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--output", output_path - ] - - if meta['functionality_name'] == 'perfect_denoising': - cmd = cmd + ["--input_test", input_test_path] - - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input_test = ad.read_h5ad(input_test_path) - output = ad.read_h5ad(output_path) - print("input_test:", input_test) - print("output:", output) - - print(">> Checking whether predictions were added") - assert "denoised" in output.layers - assert meta['functionality_name'] == output.uns["method_id"] - - print("Checking whether data from input was copied properly to output") - assert input_test.n_obs == output.n_obs - assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") + path: /src/denoising/comp_tests/test_method.py + - path: /resources_test/denoising/pancreas \ No newline at end of file diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index 0f5b1e51d3..b2eaf8c316 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -8,43 +8,8 @@ functionality: __merge__: anndata_denoised.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--output", output_path - ] - - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input_train = ad.read_h5ad(input_train_path) - output = ad.read_h5ad(output_path) - print("input_train:", input_train) - print("output:", output) - - print(">> Checking whether predictions were added") - assert "denoised" in output.layers - assert meta['functionality_name'] == output.uns["method_id"] - - print("Checking whether data from input was copied properly to output") - assert input_train.n_obs == output.n_obs - assert input_train.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") + path: /src/denoising/comp_tests/test_method.py + - path: /resources_test/denoising/pancreas \ No newline at end of file diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index ef4c8833ae..1a4ede1fc6 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -10,43 +10,9 @@ functionality: __merge__: anndata_score.yaml direction: output test_resources: - - path: ../../../../resources_test/denoising/pancreas - type: python_script - path: ../../../common/comp_tests/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: format_check.py - text: | - import anndata as ad - import subprocess - from os import path - - input_denoised_path = meta["resources_dir"] + "/pancreas/magic.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input_denoised", input_denoised_path, - "--input_test", input_test_path, - "--output", output_path - ] - - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - input_denoised = ad.read_h5ad(input_denoised_path) - input_test = ad.read_h5ad(input_test_path) - output = ad.read_h5ad(output_path) - - print("Checking whether data from input was copied properly to output") - assert output.uns["dataset_id"] == input_denoised.uns["dataset_id"] - assert output.uns["method_id"] == input_denoised.uns["method_id"] - assert output.uns["metric_ids"] is not None - assert output.uns["metric_values"] is not None - - # TODO: check whether the metric ids are all in .functionality.info - - print("All checks succeeded!") \ No newline at end of file + path: /src/label_projection/comp_tests/test_metric.py + - path: /resources_test/denoising/pancreas + \ No newline at end of file diff --git a/src/denoising/api/comp_process_dataset.yaml b/src/denoising/api/comp_process_dataset.yaml index 7578e161eb..a283f99d17 100644 --- a/src/denoising/api/comp_process_dataset.yaml +++ b/src/denoising/api/comp_process_dataset.yaml @@ -11,46 +11,6 @@ functionality: __merge__: anndata_test.yaml direction: output test_resources: - - path: ../../../resources_test/common/pancreas - type: python_script - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_train_path = "output_train.h5ad" - output_test_path = "output_test.h5ad" - - cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path, - ] - - print(">> Running script as test") - out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - print(">> Checking whether output file exists") - assert path.exists(output_train_path) - assert path.exists(output_test_path) - - print(">> Reading h5ad files") - input = ad.read_h5ad(input_path) - output_train = ad.read_h5ad(output_train_path) - output_test = ad.read_h5ad(output_test_path) - - print("input:", input) - print("output_train:", output_train) - print("output_test:", output_test) - - print(">> Checking whether data from input was copied properly to output") - assert output_train.uns["dataset_id"] == input.uns["dataset_id"] - assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - - print(">> Check whether certain slots exist") - assert "counts" in output_train.layers - assert "counts" in output_test.layers - - print(">> All checks succeeded!") + path: /src/label_projection/comp_tests/test_process_dataset.py + - path: /resources_test/common/pancreas diff --git a/src/denoising/comp_tests/test_method.py b/src/denoising/comp_tests/test_method.py new file mode 100644 index 0000000000..d44f7595ec --- /dev/null +++ b/src/denoising/comp_tests/test_method.py @@ -0,0 +1,34 @@ +import anndata as ad +import subprocess +from os import path + +input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" +output_path = "output.h5ad" + +cmd = [ + meta['executable'], + "--input_train", input_train_path, + "--output", output_path +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +print(">> Reading h5ad files") +input_train = ad.read_h5ad(input_train_path) +output = ad.read_h5ad(output_path) +print("input_train:", input_train) +print("output:", output) + +print(">> Checking whether predictions were added") +assert "denoised" in output.layers +assert meta['functionality_name'] == output.uns["method_id"] + +print("Checking whether data from input was copied properly to output") +assert input_train.n_obs == output.n_obs +assert input_train.uns["dataset_id"] == output.uns["dataset_id"] + +print("All checks succeeded!") diff --git a/src/denoising/comp_tests/test_metric.py b/src/denoising/comp_tests/test_metric.py new file mode 100644 index 0000000000..71e0b49941 --- /dev/null +++ b/src/denoising/comp_tests/test_metric.py @@ -0,0 +1,34 @@ +import anndata as ad +import subprocess +from os import path + +input_denoised_path = meta["resources_dir"] + "/pancreas/magic.h5ad" +input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" +output_path = "output.h5ad" + +cmd = [ + meta['executable'], + "--input_denoised", input_denoised_path, + "--input_test", input_test_path, + "--output", output_path +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_path) + +input_denoised = ad.read_h5ad(input_denoised_path) +input_test = ad.read_h5ad(input_test_path) +output = ad.read_h5ad(output_path) + +print("Checking whether data from input was copied properly to output") +assert output.uns["dataset_id"] == input_denoised.uns["dataset_id"] +assert output.uns["method_id"] == input_denoised.uns["method_id"] +assert output.uns["metric_ids"] is not None +assert output.uns["metric_values"] is not None + +# TODO: check whether the metric ids are all in .functionality.info + +print("All checks succeeded!") \ No newline at end of file diff --git a/src/denoising/comp_tests/test_process_dataset.py b/src/denoising/comp_tests/test_process_dataset.py new file mode 100644 index 0000000000..419500641a --- /dev/null +++ b/src/denoising/comp_tests/test_process_dataset.py @@ -0,0 +1,40 @@ +import anndata as ad +import subprocess +from os import path + +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +output_train_path = "output_train.h5ad" +output_test_path = "output_test.h5ad" + +cmd = [ + meta['executable'], + "--input", input_path, + "--output_train", output_train_path, + "--output_test", output_test_path, +] + +print(">> Running script as test") +out = subprocess.run(cmd, check=True, capture_output=True, text=True) + +print(">> Checking whether output file exists") +assert path.exists(output_train_path) +assert path.exists(output_test_path) + +print(">> Reading h5ad files") +input = ad.read_h5ad(input_path) +output_train = ad.read_h5ad(output_train_path) +output_test = ad.read_h5ad(output_test_path) + +print("input:", input) +print("output_train:", output_train) +print("output_test:", output_test) + +print(">> Checking whether data from input was copied properly to output") +assert output_train.uns["dataset_id"] == input.uns["dataset_id"] +assert output_test.uns["dataset_id"] == input.uns["dataset_id"] + +print(">> Check whether certain slots exist") +assert "counts" in output_train.layers +assert "counts" in output_test.layers + +print(">> All checks succeeded!") diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index a2e873f105..304ab25912 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -8,9 +8,9 @@ functionality: __merge__: anndata_reduced.yaml direction: output test_resources: - - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index f52a21f284..cf130f3633 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -8,9 +8,9 @@ functionality: __merge__: anndata_reduced.yaml direction: output test_resources: - - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_tests/check_method_config.py + path: /common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 8b8c838eda..720cb9b62c 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -10,9 +10,9 @@ functionality: __merge__: anndata_score.yaml direction: output test_resources: - - path: ../../../../resources_test/dimensionality_reduction/pancreas/ + - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: ../../../common/comp_tests/check_metric_config.py + path: /common/comp_tests/check_metric_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_process_dataset.yaml b/src/dimensionality_reduction/api/comp_process_dataset.yaml index abea8c028b..e4c69822b4 100644 --- a/src/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_process_dataset.yaml @@ -11,7 +11,7 @@ functionality: __merge__: anndata_test.yaml direction: output test_resources: - - path: ../../../resources_test/common/pancreas/ + - path: /resources_test/common/pancreas/ - type: python_script path: generic_test.py text: | From 9b8258c79b2fd5acf8de541c275aa06c91268565 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 15:10:44 +0200 Subject: [PATCH 0847/1233] fix refactoring issue Former-commit-id: ad80520a5d65fedc3cac455ee88b7ac28f2d46b2 --- src/batch_integration/api/comp_method_embedding.yaml | 2 +- src/batch_integration/api/comp_method_feature.yaml | 2 +- src/batch_integration/api/comp_method_graph.yaml | 2 +- src/batch_integration/api/comp_metric_embedding.yaml | 2 +- src/batch_integration/api/comp_metric_feature.yaml | 2 +- src/batch_integration/api/comp_metric_graph.yaml | 2 +- src/dimensionality_reduction/api/comp_control_method.yaml | 2 +- src/dimensionality_reduction/api/comp_method.yaml | 2 +- src/dimensionality_reduction/api/comp_metric.yaml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 6a39f2dfab..9d447cb838 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -17,6 +17,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/batch_integration/comp_tests/test_method_embedding.py diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 07152f9b8d..47b1f01ab1 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -17,6 +17,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/batch_integration/comp_tests/test_method_feature.py diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index f6b00c2d72..9ed6ac2807 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -17,6 +17,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/batch_integration/comp_tests/test_method_graph.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 4ae56d3e08..7fc50ec7b5 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -11,6 +11,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/batch_integration/comp_tests/test_metric_embedding.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 8a3c4bcdc7..71eb04bf80 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -11,6 +11,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/batch_integration/comp_tests/test_metric_feature.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index 9f3a18e3b1..c61bb9a5ec 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -11,6 +11,6 @@ functionality: test_resources: - path: /resources_test/batch_integration/pancreas - type: python_script - path: /common/comp_tests/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/batch_integration/comp_tests/test_metric_graph.py \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index 304ab25912..be24821d8a 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: /common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index cf130f3633..e9fc4136e5 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -10,7 +10,7 @@ functionality: test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: /common/comp_tests/check_method_config.py + path: /src/common/comp_tests/check_method_config.py - type: python_script path: generic_test.py text: | diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 720cb9b62c..151e840a67 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -12,7 +12,7 @@ functionality: test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ - type: python_script - path: /common/comp_tests/check_metric_config.py + path: /src/common/comp_tests/check_metric_config.py - type: python_script path: generic_test.py text: | From df68e40f2c7647cc6e8c7c93315e4f58b9fe6242 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 16:37:19 +0200 Subject: [PATCH 0848/1233] fix path Former-commit-id: ad2f26379f81c44a5681ec1521b0799d97c7db72 --- src/denoising/api/comp_metric.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 1a4ede1fc6..65ec8ab268 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -13,6 +13,6 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/label_projection/comp_tests/test_metric.py + path: /src/denoising/comp_tests/test_metric.py - path: /resources_test/denoising/pancreas \ No newline at end of file From b58293564472d355c5c8c9a7db41775937960ff0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 16:38:24 +0200 Subject: [PATCH 0849/1233] fix test Former-commit-id: b4439498b3eb53d1c0338a25c3d18412c1e7faa4 --- src/batch_integration/comp_tests/test_method_embedding.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/batch_integration/comp_tests/test_method_embedding.py b/src/batch_integration/comp_tests/test_method_embedding.py index d8825af182..16b3031ed8 100644 --- a/src/batch_integration/comp_tests/test_method_embedding.py +++ b/src/batch_integration/comp_tests/test_method_embedding.py @@ -23,7 +23,7 @@ cmd_args = [ meta["executable"], - "--input_integrated", input_file, + "--input", input_file, "--output", output_file ] From 47e53ec5566fc020bc8b37b7484568695115fe0d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 16:39:37 +0200 Subject: [PATCH 0850/1233] fix test Former-commit-id: eb87f273c5030342b76f4b9e4a89693c5652fcde --- src/common/create_component/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index fd67acf685..b688768199 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -49,7 +49,7 @@ functionality: test_resources: - type: python_script path: test.py - - path: ../../../src + - path: /src dest: openproblems-v2/src platforms: - type: docker From c6004c21bcde0ae723212ab7c64d82a2fac588ba Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Apr 2023 16:41:36 +0200 Subject: [PATCH 0851/1233] fix path to unit test Former-commit-id: e843f0d80d7c71ff05039c9a7419468229d3b410 --- src/denoising/api/comp_process_dataset.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/denoising/api/comp_process_dataset.yaml b/src/denoising/api/comp_process_dataset.yaml index a283f99d17..a395da32a2 100644 --- a/src/denoising/api/comp_process_dataset.yaml +++ b/src/denoising/api/comp_process_dataset.yaml @@ -12,5 +12,5 @@ functionality: direction: output test_resources: - type: python_script - path: /src/label_projection/comp_tests/test_process_dataset.py + path: /src/denoising/comp_tests/test_process_dataset.py - path: /resources_test/common/pancreas From f7cfcbea942640d83d7c9040d11200e79b384123 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 14:27:00 +0200 Subject: [PATCH 0852/1233] fix unit test Former-commit-id: ea0222f33ef291f292f1172c2c0b73365917049f --- .../comp_tests/test_method_embedding.py | 86 +++++++------------ .../comp_tests/test_method_feature.py | 3 +- 2 files changed, 34 insertions(+), 55 deletions(-) diff --git a/src/batch_integration/comp_tests/test_method_embedding.py b/src/batch_integration/comp_tests/test_method_embedding.py index 16b3031ed8..fff0ebc231 100644 --- a/src/batch_integration/comp_tests/test_method_embedding.py +++ b/src/batch_integration/comp_tests/test_method_embedding.py @@ -1,64 +1,42 @@ -import sys from os import path import subprocess import numpy as np import anndata as ad -import yaml - -## VIASH START -meta = { - "resources_dir": "resources_test/batch_integration/pancreas", - "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" -} -## VIASH END - -np.random.seed(42) - -print(">> Read metric config", flush=True) -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" -output_file = "output.h5ad" - -cmd_args = [ - meta["executable"], - "--input", input_file, - "--output", output_file +input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" +output_path = "embeddding.h5ad" +cmd = [ + meta['executable'], + "--input", input_path, + "--output", output_path ] - -print(">> Running script", flush=True) -subprocess.run(cmd_args, check=True) - -print(">> Checking whether file exists", flush=True) -assert path.exists(output_file) -input = ad.read_h5ad(input_file) -output = ad.read_h5ad(output_file) - -print(">> Print AnnData contents", flush=True) -print("input:", input, flush=True) -print("output:", output, flush=True) - -print(">> Checking whether metrics were added", flush=True) -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) +print(">> Checking whether input file exists", flush=True) +assert path.exists(input_path) + +print(">> Running script as test", flush=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout +print(out) + +print(">> Checking whether output file exists", flush=True) +assert path.exists(output_path) + +print(">> Reading h5ad files", flush=True) +input = ad.read_h5ad(input_path) +output = ad.read_h5ad(output_path) +print(f"input: {input}", flush=True) +print(f"output: {output}", flush=True) + +print(">> Checking whether predictions were added", flush=True) +assert 'dataset_id' in output.uns +assert 'X_pca' in output.obsm +assert 'X_emb' in output.obsm +assert 'normalization_id' in output.uns +assert 'method_id' in output.uns +assert meta['functionality_name'] == output.uns['method_id'] +assert 'hvg' in output.uns print(">> Checking whether data from input was copied properly to output", flush=True) +assert input.n_obs == output.n_obs assert input.uns["dataset_id"] == output.uns["dataset_id"] -assert input.uns["method_id"] == output.uns["method_id"] - -print(">> Check that score makes sense", flush=True) -metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] -} - -for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] +assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_method_feature.py b/src/batch_integration/comp_tests/test_method_feature.py index ddd49102d9..cc55f29822 100644 --- a/src/batch_integration/comp_tests/test_method_feature.py +++ b/src/batch_integration/comp_tests/test_method_feature.py @@ -14,7 +14,8 @@ assert os.path.exists(input_path) print(">> Running script as test", flush=True) -subprocess.run(cmd, check=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout +print(out) print(">> Checking whether file exists", flush=True) assert os.path.exists(output_path) From 65e4026fb0f00daa1b2a15c8af49f91aecc97a77 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 14:31:33 +0200 Subject: [PATCH 0853/1233] refactor relative paths into project-relative Former-commit-id: ef472b4bc58193503905425b809e4100c73eb5e4 --- src/common/api/get_info.yaml | 4 ++-- src/migration/check_migration_status/config.vsh.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml index e0545712bf..2b83c745d4 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/api/get_info.yaml @@ -15,9 +15,9 @@ functionality: default: "output.json" description: "Output json" test_resources: - - path: ../../../src + - path: /src dest: openproblems-v2/src - - path: ../../../_viash.yaml + - path: /_viash.yaml dest: openproblems-v2/_viash.yaml - type: python_script path: generic_test.py diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index e072f78b74..26457f3e78 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: - type: python_script path: script.py test_resources: - - path: ../../../resources_test + - path: /resources_test - type: python_script path: test.py platforms: From 28705374b14e4e2c448ffcdd7c596de45ec80e6f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 20:55:18 +0200 Subject: [PATCH 0854/1233] make generic generic unit test Former-commit-id: 9fc4f2164a418c88e58c292e67a1407cc7cf642c --- .../api/anndata_dataset.yaml | 79 ----------------- .../api/anndata_integrated_embedding.yaml | 2 +- .../api/anndata_integrated_feature.yaml | 2 +- .../api/anndata_integrated_graph.yaml | 2 +- .../api/anndata_unintegrated.yaml | 2 +- .../api/comp_method_embedding.yaml | 3 +- .../api/comp_method_feature.yaml | 3 +- .../api/comp_method_graph.yaml | 3 +- .../api/comp_metric_embedding.yaml | 3 +- .../api/comp_metric_feature.yaml | 3 +- .../api/comp_metric_graph.yaml | 3 +- .../api/comp_process_dataset.yaml | 6 +- .../comp_tests/test_method_embedding.py | 42 --------- .../comp_tests/test_method_feature.py | 37 -------- .../comp_tests/test_method_graph.py | 38 -------- .../comp_tests/test_metric_embedding.py | 64 -------------- .../comp_tests/test_metric_feature.py | 64 -------------- .../comp_tests/test_metric_graph.py | 66 -------------- .../comp_tests/test_process_dataset.py | 40 --------- .../process_dataset/config.vsh.yaml | 4 - src/batch_integration/process_dataset/test.py | 43 --------- .../embed_to_graph/config.vsh.yaml | 8 +- .../transformers/embed_to_graph/script.py | 9 +- .../feature_to_embed/config.vsh.yaml | 8 +- .../transformers/feature_to_embed/script.py | 7 -- src/common/comp_tests/check_method_config.py | 2 +- src/common/comp_tests/run_and_check_adata.py | 88 +++++++++++++++++++ src/datasets/api/anndata_dataset.yaml | 2 +- .../loaders/openproblems_v1/config.vsh.yaml | 2 +- .../config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- src/datasets/subsample/config.vsh.yaml | 2 +- src/denoising/api/anndata_dataset.yaml | 2 +- src/denoising/api/anndata_denoised.yaml | 2 +- src/denoising/api/anndata_score.yaml | 2 +- src/denoising/api/anndata_test.yaml | 2 +- src/denoising/api/anndata_train.yaml | 2 +- src/denoising/api/comp_control_method.yaml | 6 +- src/denoising/api/comp_method.yaml | 5 +- src/denoising/api/comp_metric.yaml | 3 +- src/denoising/api/comp_process_dataset.yaml | 6 +- src/denoising/comp_tests/test_method.py | 34 ------- src/denoising/comp_tests/test_metric.py | 34 ------- .../comp_tests/test_process_dataset.py | 40 --------- .../no_denoising/config.vsh.yaml | 2 - .../perfect_denoising/config.vsh.yaml | 1 - src/denoising/methods/alra/config.vsh.yaml | 1 - src/denoising/methods/dca/config.vsh.yaml | 1 - .../methods/knn_smoothing/config.vsh.yaml | 1 - src/denoising/methods/magic/config.vsh.yaml | 1 - src/denoising/metrics/mse/config.vsh.yaml | 1 - src/denoising/metrics/poisson/config.vsh.yaml | 1 - src/denoising/process_dataset/config.vsh.yaml | 2 +- .../api/anndata_dataset.yaml | 63 ------------- .../api/anndata_reduced.yaml | 2 +- .../api/anndata_score.yaml | 2 +- .../api/anndata_test.yaml | 2 +- .../api/anndata_train.yaml | 2 +- .../api/comp_control_method.yaml | 47 +--------- .../api/comp_method.yaml | 43 +-------- .../api/comp_metric.yaml | 50 +---------- .../api/comp_process_dataset.yaml | 56 +----------- .../random_features/config.vsh.yaml | 1 - .../true_features/config.vsh.yaml | 1 - .../methods/densmap/config.vsh.yaml | 1 - .../methods/ivis/config.vsh.yaml | 1 - .../methods/neuralee/config.vsh.yaml | 1 - .../methods/pca/config.vsh.yaml | 1 - .../methods/phate/config.vsh.yaml | 1 - .../methods/tsne/config.vsh.yaml | 1 - .../methods/umap/config.vsh.yaml | 1 - .../metrics/coranking/config.vsh.yaml | 1 - .../density_preservation/config.vsh.yaml | 1 - .../metrics/rmse/config.vsh.yaml | 1 - .../metrics/trustworthiness/config.vsh.yaml | 1 - .../process_dataset/config.vsh.yaml | 1 - src/label_projection/api/anndata_dataset.yaml | 63 ------------- .../api/anndata_prediction.yaml | 2 +- src/label_projection/api/anndata_score.yaml | 2 +- .../api/anndata_solution.yaml | 2 +- src/label_projection/api/anndata_test.yaml | 2 +- src/label_projection/api/anndata_train.yaml | 2 +- .../api/comp_control_method.yaml | 4 +- src/label_projection/api/comp_method.yaml | 4 +- src/label_projection/api/comp_metric.yaml | 4 +- .../api/comp_process_dataset.yaml | 4 +- .../comp_tests/test_method.py | 42 --------- .../comp_tests/test_metric.py | 34 ------- .../comp_tests/test_process_dataset.py | 62 ------------- .../majority_vote/config.vsh.yaml | 3 +- .../random_labels/config.vsh.yaml | 3 +- .../true_labels/config.vsh.yaml | 3 +- .../methods/knn/config.vsh.yaml | 1 - .../logistic_regression/config.vsh.yaml | 1 - .../methods/mlp/config.vsh.yaml | 1 - .../methods/scanvi/config.vsh.yaml | 1 - .../seurat_transferdata/config.vsh.yaml | 1 - .../methods/xgboost/config.vsh.yaml | 1 - .../metrics/accuracy/config.vsh.yaml | 1 - .../metrics/f1/config.vsh.yaml | 1 - .../process_dataset/config.vsh.yaml | 1 - 103 files changed, 188 insertions(+), 1132 deletions(-) delete mode 100644 src/batch_integration/api/anndata_dataset.yaml delete mode 100644 src/batch_integration/comp_tests/test_method_embedding.py delete mode 100644 src/batch_integration/comp_tests/test_method_feature.py delete mode 100644 src/batch_integration/comp_tests/test_method_graph.py delete mode 100644 src/batch_integration/comp_tests/test_metric_embedding.py delete mode 100644 src/batch_integration/comp_tests/test_metric_feature.py delete mode 100644 src/batch_integration/comp_tests/test_metric_graph.py delete mode 100644 src/batch_integration/comp_tests/test_process_dataset.py delete mode 100644 src/batch_integration/process_dataset/test.py create mode 100644 src/common/comp_tests/run_and_check_adata.py delete mode 100644 src/denoising/comp_tests/test_method.py delete mode 100644 src/denoising/comp_tests/test_metric.py delete mode 100644 src/denoising/comp_tests/test_process_dataset.py delete mode 100644 src/dimensionality_reduction/api/anndata_dataset.yaml delete mode 100644 src/label_projection/api/anndata_dataset.yaml delete mode 100644 src/label_projection/comp_tests/test_method.py delete mode 100644 src/label_projection/comp_tests/test_metric.py delete mode 100644 src/label_projection/comp_tests/test_process_dataset.py diff --git a/src/batch_integration/api/anndata_dataset.yaml b/src/batch_integration/api/anndata_dataset.yaml deleted file mode 100644 index c17b2b15e3..0000000000 --- a/src/batch_integration/api/anndata_dataset.yaml +++ /dev/null @@ -1,79 +0,0 @@ -type: file -description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" -example: "dataset.h5ad" -info: - label: "Dataset+PCA+HVG+kNN" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalised expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalisation method, if any. - required: false - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - obsp: - - type: double - name: knn_distances - description: K nearest neighbors distance matrix. - required: true - - type: double - name: knn_connectivities - description: K nearest neighbors connectivities matrix. - required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: double - name: pca_variance - description: The PCA variance objects. - required: true - - type: object - name: knn - description: Neighbors data. - - type: string - name: dataset_organism - description: The organism of the sample in the dataset. - required: true diff --git a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/batch_integration/api/anndata_integrated_embedding.yaml index 9b9208c0fa..8caacc6d16 100644 --- a/src/batch_integration/api/anndata_integrated_embedding.yaml +++ b/src/batch_integration/api/anndata_integrated_embedding.yaml @@ -1,7 +1,7 @@ __merge__: "anndata_unintegrated.yaml" type: file description: Integrated AnnData HDF5 file. -example: input.h5ad +example: "resources_test/batch_integration/pancreas/scvi.h5ad" info: prediction_type: embedding short_description: "Integrated embedding" diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/batch_integration/api/anndata_integrated_feature.yaml index bfebdcd038..7d71a54700 100644 --- a/src/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/batch_integration/api/anndata_integrated_feature.yaml @@ -1,7 +1,7 @@ __merge__: "anndata_unintegrated.yaml" type: file description: Integrated AnnData HDF5 file. -example: input.h5ad +example: "resources_test/batch_integration/pancreas/combat.h5ad" info: prediction_type: feature short_description: "Integrated Feature" diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/batch_integration/api/anndata_integrated_graph.yaml index 0f09941cee..26bb89b385 100644 --- a/src/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/batch_integration/api/anndata_integrated_graph.yaml @@ -1,7 +1,7 @@ __merge__: "anndata_unintegrated.yaml" type: file description: Integrated AnnData HDF5 file. -example: input.h5ad +example: "resources_test/batch_integration/pancreas/bbknn.h5ad" info: prediction_type: graph short_description: "Integrated Graph" diff --git a/src/batch_integration/api/anndata_unintegrated.yaml b/src/batch_integration/api/anndata_unintegrated.yaml index 68f7bfba1e..f2e0e8f9c3 100644 --- a/src/batch_integration/api/anndata_unintegrated.yaml +++ b/src/batch_integration/api/anndata_unintegrated.yaml @@ -1,6 +1,6 @@ type: file description: Unintegrated AnnData HDF5 file. -example: input.h5ad +example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" info: short_description: "Unintegrated" slots: diff --git a/src/batch_integration/api/comp_method_embedding.yaml b/src/batch_integration/api/comp_method_embedding.yaml index 9d447cb838..a3e2e87ff2 100644 --- a/src/batch_integration/api/comp_method_embedding.yaml +++ b/src/batch_integration/api/comp_method_embedding.yaml @@ -16,7 +16,8 @@ functionality: required: false test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_method_embedding.py + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/batch_integration/api/comp_method_feature.yaml b/src/batch_integration/api/comp_method_feature.yaml index 47b1f01ab1..94984233a8 100644 --- a/src/batch_integration/api/comp_method_feature.yaml +++ b/src/batch_integration/api/comp_method_feature.yaml @@ -16,7 +16,8 @@ functionality: required: false test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_method_feature.py + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/batch_integration/api/comp_method_graph.yaml index 9ed6ac2807..dfb00f40e0 100644 --- a/src/batch_integration/api/comp_method_graph.yaml +++ b/src/batch_integration/api/comp_method_graph.yaml @@ -16,7 +16,8 @@ functionality: required: false test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_method_graph.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/batch_integration/api/comp_metric_embedding.yaml index 7fc50ec7b5..384f3abb58 100644 --- a/src/batch_integration/api/comp_metric_embedding.yaml +++ b/src/batch_integration/api/comp_metric_embedding.yaml @@ -10,7 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_metric_embedding.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/batch_integration/api/comp_metric_feature.yaml index 71eb04bf80..32ac928477 100644 --- a/src/batch_integration/api/comp_metric_feature.yaml +++ b/src/batch_integration/api/comp_metric_feature.yaml @@ -10,7 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_metric_feature.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_metric_graph.yaml b/src/batch_integration/api/comp_metric_graph.yaml index c61bb9a5ec..fbc05334e8 100644 --- a/src/batch_integration/api/comp_metric_graph.yaml +++ b/src/batch_integration/api/comp_metric_graph.yaml @@ -10,7 +10,8 @@ functionality: __merge__: anndata_score.yaml test_resources: - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/batch_integration/comp_tests/test_metric_graph.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/batch_integration/api/comp_process_dataset.yaml b/src/batch_integration/api/comp_process_dataset.yaml index 3ec6345ff3..3dca90c7df 100644 --- a/src/batch_integration/api/comp_process_dataset.yaml +++ b/src/batch_integration/api/comp_process_dataset.yaml @@ -1,13 +1,15 @@ functionality: + namespace: batch_integration info: type: process_dataset arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_dataset.yaml - name: "--output" __merge__: anndata_unintegrated.yaml direction: output test_resources: - path: /resources_test/common/pancreas/ + dest: resources_test/common/pancreas/ - type: python_script - path: /src/batch_integration/comp_tests/test_process_dataset.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_method_embedding.py b/src/batch_integration/comp_tests/test_method_embedding.py deleted file mode 100644 index fff0ebc231..0000000000 --- a/src/batch_integration/comp_tests/test_method_embedding.py +++ /dev/null @@ -1,42 +0,0 @@ -from os import path -import subprocess -import numpy as np -import anndata as ad -input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" -output_path = "embeddding.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] -print(">> Checking whether input file exists", flush=True) -assert path.exists(input_path) - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout -print(out) - -print(">> Checking whether output file exists", flush=True) -assert path.exists(output_path) - -print(">> Reading h5ad files", flush=True) -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) -print(f"input: {input}", flush=True) -print(f"output: {output}", flush=True) - -print(">> Checking whether predictions were added", flush=True) -assert 'dataset_id' in output.uns -assert 'X_pca' in output.obsm -assert 'X_emb' in output.obsm -assert 'normalization_id' in output.uns -assert 'method_id' in output.uns -assert meta['functionality_name'] == output.uns['method_id'] -assert 'hvg' in output.uns - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.n_obs == output.n_obs -assert input.uns["dataset_id"] == output.uns["dataset_id"] -assert not np.any(np.not_equal(input.obsm['X_pca'], output.obsm['X_pca'])) - -print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_method_feature.py b/src/batch_integration/comp_tests/test_method_feature.py deleted file mode 100644 index cc55f29822..0000000000 --- a/src/batch_integration/comp_tests/test_method_feature.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -import subprocess -import anndata as ad - -input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" -output_path = "integrated.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] - -print(">> Checking whether input file exists", flush=True) -assert os.path.exists(input_path) - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout -print(out) - -print(">> Checking whether file exists", flush=True) -assert os.path.exists(output_path) - -print(">> Reading h5ad files", flush=True) -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) -print(f"input: {input}", flush=True) -print(f"output: {output}", flush=True) - -print(">> Checking whether predictions were added", flush=True) -# TODO: use helper function to check whether the required fields are defined -assert output.layers['corrected_counts'] is not None - -print(">> Check values", flush=True) -assert meta['functionality_name'] == output.uns['method_id'] -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_method_graph.py b/src/batch_integration/comp_tests/test_method_graph.py deleted file mode 100644 index 9b3d5f7de8..0000000000 --- a/src/batch_integration/comp_tests/test_method_graph.py +++ /dev/null @@ -1,38 +0,0 @@ -import os -import subprocess -import anndata as ad - -input_path = meta["resources_dir"] + "/pancreas/unintegrated.h5ad" -output_path = "inegrated.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path -] - -print(">> Checking whether input file exists", flush=True) -assert os.path.exists(input_path) - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout -print(out, flush=True) - -print(">> Checking whether file exists", flush=True) -assert os.path.exists(output_path) - -print(">> Reading h5ad files", flush=True) -input = ad.read_h5ad(input_path) -output = ad.read_h5ad(output_path) -print(f"input: {input}", flush=True) -print(f"output: {output}", flush=True) - -print(">> Checking whether predictions were added", flush=True) -# TODO: use helper function to check whether the required fields are defined -assert 'connectivities' in output.obsp -assert 'distances' in output.obsp - -print(">> Check values", flush=True) -assert meta['functionality_name'] == output.uns['method_id'] -assert input.uns["dataset_id"] == output.uns["dataset_id"] - -print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_embedding.py b/src/batch_integration/comp_tests/test_metric_embedding.py deleted file mode 100644 index 347c85c0d6..0000000000 --- a/src/batch_integration/comp_tests/test_metric_embedding.py +++ /dev/null @@ -1,64 +0,0 @@ -import sys -from os import path -import subprocess -import numpy as np -import anndata as ad -import yaml - -## VIASH START -meta = { - "resources_dir": "resources_test/batch_integration/pancreas", - "config": "src/batch_integration/metric_graph/ari/config.vsh.yaml" -} -## VIASH END - -np.random.seed(42) - -print(">> Read metric config", flush=True) -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -input_file = f"{meta['resources_dir']}/pancreas/scvi.h5ad" -output_file = "output.h5ad" - -cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file -] - -print(">> Running script", flush=True) -subprocess.run(cmd_args, check=True) - -print(">> Checking whether file exists", flush=True) -assert path.exists(output_file) -input = ad.read_h5ad(input_file) -output = ad.read_h5ad(output_file) - -print(">> Print AnnData contents", flush=True) -print("input:", input, flush=True) -print("output:", output, flush=True) - -print(">> Checking whether metrics were added", flush=True) -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.uns["dataset_id"] == output.uns["dataset_id"] -assert input.uns["method_id"] == output.uns["method_id"] - -print(">> Check that score makes sense", flush=True) -metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] -} - -for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - -print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_feature.py b/src/batch_integration/comp_tests/test_metric_feature.py deleted file mode 100644 index 13498ab22a..0000000000 --- a/src/batch_integration/comp_tests/test_metric_feature.py +++ /dev/null @@ -1,64 +0,0 @@ -import sys -from os import path -import subprocess -import numpy as np -import anndata as ad -import yaml - -## VIASH START -meta = { - "resources_dir": "resources_test/batch_integration/pancreas", - "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" -} -## VIASH END - -np.random.seed(42) - -print(">> Read metric config", flush=True) -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -input_file = f"{meta['resources_dir']}/pancreas/combat.h5ad" -output_file = "output.h5ad" - -cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file -] - -print(">> Running script", flush=True) -subprocess.run(cmd_args, check=True) - -print(">> Checking whether file exists", flush=True) -assert path.exists(output_file) -input = ad.read_h5ad(input_file) -output = ad.read_h5ad(output_file) - -print(">> Print AnnData contents", flush=True) -print("input:", input, flush=True) -print("output:", output, flush=True) - -print(">> Checking whether metrics were added", flush=True) -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.uns["dataset_id"] == output.uns["dataset_id"] -assert input.uns["method_id"] == output.uns["method_id"] - -print(">> Check that score makes sense", flush=True) -metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] -} - -for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - -print(">> All tests passed successfully") diff --git a/src/batch_integration/comp_tests/test_metric_graph.py b/src/batch_integration/comp_tests/test_metric_graph.py deleted file mode 100644 index 399f7c1ce8..0000000000 --- a/src/batch_integration/comp_tests/test_metric_graph.py +++ /dev/null @@ -1,66 +0,0 @@ -import sys -from os import path -import subprocess -import numpy as np -import anndata as ad -import yaml - -## VIASH START -meta = { - "resources_dir": "resources_test/batch_integration/pancreas/graph/methods", - "config": "src/batch_integration/graph/metrics/ari/config.vsh.yaml" -} -## VIASH END - -np.random.seed(42) - -print(">> Read metric config", flush=True) -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"].get("info", {}).get("output_type") - -input_file = f"{meta['resources_dir']}/pancreas/bbknn.h5ad" -output_file = "output.h5ad" - -cmd_args = [ - meta["executable"], - "--input_integrated", input_file, - "--output", output_file -] - -print(">> Running script", flush=True) -subprocess.run(cmd_args, check=True) - -print(">> Checking whether file exists", flush=True) -assert path.exists(output_file) -input = ad.read_h5ad(input_file) -output = ad.read_h5ad(output_file) - -print(">> Print AnnData contents", flush=True) -print("input:", input, flush=True) -print("output:", output, flush=True) - -print(">> Checking whether metrics were added", flush=True) -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert len(output.uns["metric_ids"]) == len(output.uns["metric_values"]) - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.uns["dataset_id"] == output.uns["dataset_id"] -assert input.uns["method_id"] == output.uns["method_id"] - -print(">> Check that score makes sense", flush=True) -metrics_info = { - metric["name"]: metric - for metric in config["functionality"]["info"]["metrics"] -} - -for metric_id, metric_value in zip(output.uns["metric_ids"], output.uns["metric_values"]): - assert metric_id in metrics_info, f"Metric id {metric_id} not found in .functionality.info.metrics" - info = metrics_info[metric_id] - - assert info["min"] <= metric_value - assert metric_value <= info["max"] - -print(">> All tests passed successfully") \ No newline at end of file diff --git a/src/batch_integration/comp_tests/test_process_dataset.py b/src/batch_integration/comp_tests/test_process_dataset.py deleted file mode 100644 index 2897326337..0000000000 --- a/src/batch_integration/comp_tests/test_process_dataset.py +++ /dev/null @@ -1,40 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -output_unintegrated_path = "unintegrated.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_unintegrated_path -] - -print(">> Checking whether input file exists", flush=True) -assert path.exists(input_path) - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT).stdout -print(out) - -print(">> Checking whether output files exist", flush=True) -assert path.exists(output_unintegrated_path) - -print(">> Reading h5ad files", flush=True) -input = ad.read_h5ad(input_path) -output_unintegrated = ad.read_h5ad(output_unintegrated_path) - -print("input:", input, flush=True) -print("output_unintegrated:", output_unintegrated, flush=True) - -print(">> Checking whether data from input was copied properly to output", flush=True) -assert input.n_obs == output_unintegrated.n_obs -assert input.uns["dataset_id"] == output_unintegrated.uns["dataset_id"] - - -print(">> Check whether certain slots exist", flush=True) -assert "counts" in output_unintegrated.layers -assert "normalized" in output_unintegrated.layers -assert 'hvg' in output_unintegrated.var - -print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/batch_integration/process_dataset/config.vsh.yaml b/src/batch_integration/process_dataset/config.vsh.yaml index 848c6fe1b9..bf2c5098b4 100644 --- a/src/batch_integration/process_dataset/config.vsh.yaml +++ b/src/batch_integration/process_dataset/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: process_dataset - namespace: batch_integration description: Preprocess adata object for data integration arguments: - name: "--obs_label" @@ -20,9 +19,6 @@ functionality: resources: - type: python_script path: script.py - test_resources: - - type: python_script - path: test.py platforms: - type: docker image: mumichae/scib-base:1.1.3 diff --git a/src/batch_integration/process_dataset/test.py b/src/batch_integration/process_dataset/test.py deleted file mode 100644 index 6468070831..0000000000 --- a/src/batch_integration/process_dataset/test.py +++ /dev/null @@ -1,43 +0,0 @@ -import os -import subprocess -import anndata as ad -import numpy as np - -input_file = meta["resources_dir"] + '/pancreas/dataset.h5ad' -unintegrated_file = 'output.h5ad' -n_hvgs = 100 - -cmd_args = [ - meta["executable"], - '--input', input_file, - '--hvgs', str(n_hvgs), - '--output', unintegrated_file, -] -print('>> Running script') -subprocess.run(cmd_args, check=True) - -print('>> Checking whether outputs exist') -assert os.path.exists(unintegrated_file) - -print('>> Read anndata files') -input = ad.read_h5ad(input_file) -unintegrated = ad.read_h5ad(unintegrated_file) - -print("input:", input) -print("output:", unintegrated) - -print(">> Checking dimensions, make sure no cells were dropped") -assert input.n_obs == unintegrated.n_obs -assert input.n_vars == unintegrated.n_vars - -print(">> Checking whether data from input was copied properly to output") -assert unintegrated.uns["dataset_id"] == input.uns["dataset_id"] - -print(">> Check output") -assert unintegrated.var['hvg'].dtype == 'bool' -assert unintegrated.var['hvg'].sum() == n_hvgs - -print(">> Check whether certain slots exist") -# todo: use helper function for this - -print('>> All tests passed successfully') diff --git a/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 2056dd4ea2..b21885f3cc 100644 --- a/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -3,8 +3,9 @@ functionality: namespace: batch_integration/transformers description: "Transform an embedded integration to a graph integration" info: - type: method + type: transformer pretty_name: Embedding to Graph + output_type: graph arguments: - __merge__: ../../api/anndata_integrated_embedding.yaml name: --input @@ -14,6 +15,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - path: /resources_test/batch_integration/pancreas/ + dest: resources_test/batch_integration/pancreas/ + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker image: python:3.10 diff --git a/src/batch_integration/transformers/embed_to_graph/script.py b/src/batch_integration/transformers/embed_to_graph/script.py index 44fd1a93ce..eae49d968e 100644 --- a/src/batch_integration/transformers/embed_to_graph/script.py +++ b/src/batch_integration/transformers/embed_to_graph/script.py @@ -2,17 +2,10 @@ import scanpy as sc ## VIASH START - par = { 'input': 'resources_test/batch_integration/pancreas/scvi.h5ad', 'ouput': 'output.h5ad' } - -meta = { - 'functionality_name': 'foo', - 'config': 'bar' -} - ## VIASH END with open(meta['config'], 'r', encoding="utf8") as file: @@ -20,7 +13,7 @@ output_type = config["functionality"]["info"]["output_type"] -print('read input', flush=True) +print('Read input', flush=True) adata = sc.read_h5ad(par['input']) print('Run kNN', flush=True) diff --git a/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml index adc1c14cd5..5bad68c5ac 100644 --- a/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -3,8 +3,9 @@ functionality: namespace: batch_integration/transformers description: "Transform a feature integration to an embedded integration" info: - type: method + type: transformer pretty_name: Feature to Embed + output_type: embedding arguments: - __merge__: ../../api/anndata_integrated_feature.yaml name: --input @@ -14,6 +15,11 @@ functionality: resources: - type: python_script path: script.py + test_resources: + - path: /resources_test/batch_integration/pancreas/ + dest: resources_test/batch_integration/pancreas/ + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker image: python:3.10 diff --git a/src/batch_integration/transformers/feature_to_embed/script.py b/src/batch_integration/transformers/feature_to_embed/script.py index c883909e18..7c61d3e67e 100644 --- a/src/batch_integration/transformers/feature_to_embed/script.py +++ b/src/batch_integration/transformers/feature_to_embed/script.py @@ -2,17 +2,10 @@ import yaml ## VIASH START - par = { 'input': 'resources_test/batch_integration/pancreas/combat.h5ad', 'ouput': 'output.h5ad' } - -meta = { - 'functionality_name': 'foo', - 'config': 'bar' -} - ## VIASH END with open(meta['config'], 'r', encoding="utf8") as file: diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 0c49f3b779..6fc217d1d4 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -14,7 +14,7 @@ config = yaml.safe_load(file) -print("check general fields", flush=True) +print("Check general fields", flush=True) assert "name" in config["functionality"] is not None, "Name not a field or is empty" assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py new file mode 100644 index 0000000000..446a2bcf20 --- /dev/null +++ b/src/common/comp_tests/run_and_check_adata.py @@ -0,0 +1,88 @@ +import anndata as ad +import subprocess +from os import path +import yaml +import re + +## VIASH START +meta = { + "executable": "target/docker/denoising/methods/dca/dca", + "config": "target/docker/denoising/methods/dca/.config.vsh.yaml", + "resources_dir": "resources_test/denoising" +} +## VIASH END + +# helper functions +def check_slots(adata, slot_metadata): + """Check whether an AnnData file contains all for the required + slots in the corresponding .info.slots field. + """ + for struc_name, slot_items in slot_metadata.items(): + struc_dict = getattr(adata, struc_name) + + for slot_item in slot_items: + if slot_item.get("required", False): + assert slot_item["name"] in struc_dict,\ + f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']" + + +# read viash config +with open(meta["config"], "r") as stream: + config = yaml.safe_load(stream) + +# get resources +arguments = [] + +for arg in config["functionality"]["arguments"]: + new_arg = arg.copy() + + # set clean name + clean_name = re.sub("^--", "", arg["name"]) + new_arg["clean_name"] = clean_name + + # use example to find test resource file + if arg["type"] == "file": + if arg["direction"] == "input": + value = f"{meta['resources_dir']}/{arg['example'][0]}" + else: + value = f"{clean_name}.h5ad" + new_arg["value"] = value + + arguments.append(new_arg) + +# construct command +cmd = [ meta["executable"] ] +for arg in arguments: + if arg["type"] == "file": + cmd.extend([arg["name"], arg["value"]]) + + +print(">> Checking whether input files exist", flush=True) +for arg in arguments: + if arg["type"] == "file" and arg["direction"] == "input": + assert path.exists(arg["value"]), f"Input file '{arg['value']}' does not exist" + +print(">> Running script as test", flush=True) +# out = subprocess.run(cmd, check=True, capture_output=True, text=True) +subprocess.run(cmd, check=True) + +print(">> Checking whether output file exists", flush=True) +for arg in arguments: + if arg["type"] == "file" and arg["direction"] == "output": + assert path.exists(arg["value"]), f"Output file '{arg['value']}' does not exist" + +print(">> Reading h5ad files and checking formats", flush=True) +adatas = {} +for arg in arguments: + if arg["type"] == "file": + print(f"Reading and checking {arg['clean_name']}", flush=True) + adata = ad.read_h5ad(arg["value"]) + slots = arg["info"]["slots"] + + print(f" {adata}") + + check_slots(adata, slots) + + adatas[arg["clean_name"]] = adata + +print("All checks succeeded!", flush=True) diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_dataset.yaml index d6bb88eab8..b686e89d1f 100644 --- a/src/datasets/api/anndata_dataset.yaml +++ b/src/datasets/api/anndata_dataset.yaml @@ -1,7 +1,7 @@ __merge__: anndata_hvg.yaml type: file description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" -example: "dataset.h5ad" +example: "/resources_test/common/pancreas/dataset.h5ad" info: label: "Dataset+PCA+HVG+kNN" slots: diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 54cb6bc3c6..fdb8e1d33b 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -65,7 +65,7 @@ functionality: path: test.py platforms: - type: docker - image: python:3.8 + image: python:3.10 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 5bb626d3e1..cd16a9de7c 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: path: test.py platforms: - type: docker - image: python:3.8 + image: python:3.10 setup: - type: apt packages: git diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 434a2bc402..815c3dfe44 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 2f9f4a0d01..36d13e6b36 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index ebd719b1a7..2b93951da5 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/subsample/config.vsh.yaml index 2023b2edf2..f7595ac54e 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/subsample/config.vsh.yaml @@ -50,7 +50,7 @@ functionality: test_resources: - type: python_script path: test_script.py - - path: "../../../resources_test/common/pancreas" + - path: /resources_test/common/pancreas platforms: - type: docker image: "python:3.10" diff --git a/src/denoising/api/anndata_dataset.yaml b/src/denoising/api/anndata_dataset.yaml index cf0a3a4eb0..ddaec78b4a 100644 --- a/src/denoising/api/anndata_dataset.yaml +++ b/src/denoising/api/anndata_dataset.yaml @@ -1,6 +1,6 @@ type: file description: "A preprocessed dataset" -example: "preprocessed.h5ad" +example: "resources_test/common/pancreas/dataset.h5ad" info: short_description: "Preprocessed dataset" slots: diff --git a/src/denoising/api/anndata_denoised.yaml b/src/denoising/api/anndata_denoised.yaml index a107af982a..fe0a4f3f29 100644 --- a/src/denoising/api/anndata_denoised.yaml +++ b/src/denoising/api/anndata_denoised.yaml @@ -1,6 +1,6 @@ type: file description: "The denoised data" -example: "denoised.h5ad" +example: "resources_test/denoising/pancreas/magic.h5ad" info: short_description: "Denoised data" slots: diff --git a/src/denoising/api/anndata_score.yaml b/src/denoising/api/anndata_score.yaml index a3f1af8399..d372473de4 100644 --- a/src/denoising/api/anndata_score.yaml +++ b/src/denoising/api/anndata_score.yaml @@ -1,6 +1,6 @@ type: file description: "Metric score file" -example: "output.h5ad" +example: "resources_test/denoising/pancreas/magic_poisson.h5ad" info: short_description: "Score" slots: diff --git a/src/denoising/api/anndata_test.yaml b/src/denoising/api/anndata_test.yaml index 1bee7651db..cf1096bf95 100644 --- a/src/denoising/api/anndata_test.yaml +++ b/src/denoising/api/anndata_test.yaml @@ -1,6 +1,6 @@ type: file description: "The test data" -example: "test.h5ad" +example: "resources_test/denoising/pancreas/test.h5ad" info: short_description: "Test data" slots: diff --git a/src/denoising/api/anndata_train.yaml b/src/denoising/api/anndata_train.yaml index 09383b02d7..78a185e334 100644 --- a/src/denoising/api/anndata_train.yaml +++ b/src/denoising/api/anndata_train.yaml @@ -1,6 +1,6 @@ type: file description: "The training data" -example: "training.h5ad" +example: "resources_test/denoising/pancreas/train.h5ad" info: short_description: "Training data" slots: diff --git a/src/denoising/api/comp_control_method.yaml b/src/denoising/api/comp_control_method.yaml index ca0a960f58..b97b38c358 100644 --- a/src/denoising/api/comp_control_method.yaml +++ b/src/denoising/api/comp_control_method.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "denoising/control_methods" info: type: control_method arguments: @@ -13,5 +14,6 @@ functionality: - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/denoising/comp_tests/test_method.py - - path: /resources_test/denoising/pancreas \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/denoising/pancreas + dest: resources_test/denoising/pancreas \ No newline at end of file diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index b2eaf8c316..ffea8e1fc3 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -11,5 +11,6 @@ functionality: - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/denoising/comp_tests/test_method.py - - path: /resources_test/denoising/pancreas \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/denoising/pancreas + dest: resources_test/denoising/pancreas \ No newline at end of file diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 65ec8ab268..061f322a06 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -13,6 +13,7 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/denoising/comp_tests/test_metric.py + path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/denoising/pancreas + dest: resources_test/denoising/pancreas \ No newline at end of file diff --git a/src/denoising/api/comp_process_dataset.yaml b/src/denoising/api/comp_process_dataset.yaml index a395da32a2..e2af1979e5 100644 --- a/src/denoising/api/comp_process_dataset.yaml +++ b/src/denoising/api/comp_process_dataset.yaml @@ -1,9 +1,10 @@ functionality: + namespace: "denoising" info: type: process_dataset arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output @@ -12,5 +13,6 @@ functionality: direction: output test_resources: - type: python_script - path: /src/denoising/comp_tests/test_process_dataset.py + path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas diff --git a/src/denoising/comp_tests/test_method.py b/src/denoising/comp_tests/test_method.py deleted file mode 100644 index d44f7595ec..0000000000 --- a/src/denoising/comp_tests/test_method.py +++ /dev/null @@ -1,34 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" -output_path = "output.h5ad" - -cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--output", output_path -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input_train = ad.read_h5ad(input_train_path) -output = ad.read_h5ad(output_path) -print("input_train:", input_train) -print("output:", output) - -print(">> Checking whether predictions were added") -assert "denoised" in output.layers -assert meta['functionality_name'] == output.uns["method_id"] - -print("Checking whether data from input was copied properly to output") -assert input_train.n_obs == output.n_obs -assert input_train.uns["dataset_id"] == output.uns["dataset_id"] - -print("All checks succeeded!") diff --git a/src/denoising/comp_tests/test_metric.py b/src/denoising/comp_tests/test_metric.py deleted file mode 100644 index 71e0b49941..0000000000 --- a/src/denoising/comp_tests/test_metric.py +++ /dev/null @@ -1,34 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_denoised_path = meta["resources_dir"] + "/pancreas/magic.h5ad" -input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" -output_path = "output.h5ad" - -cmd = [ - meta['executable'], - "--input_denoised", input_denoised_path, - "--input_test", input_test_path, - "--output", output_path -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -input_denoised = ad.read_h5ad(input_denoised_path) -input_test = ad.read_h5ad(input_test_path) -output = ad.read_h5ad(output_path) - -print("Checking whether data from input was copied properly to output") -assert output.uns["dataset_id"] == input_denoised.uns["dataset_id"] -assert output.uns["method_id"] == input_denoised.uns["method_id"] -assert output.uns["metric_ids"] is not None -assert output.uns["metric_values"] is not None - -# TODO: check whether the metric ids are all in .functionality.info - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/denoising/comp_tests/test_process_dataset.py b/src/denoising/comp_tests/test_process_dataset.py deleted file mode 100644 index 419500641a..0000000000 --- a/src/denoising/comp_tests/test_process_dataset.py +++ /dev/null @@ -1,40 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -output_train_path = "output_train.h5ad" -output_test_path = "output_test.h5ad" - -cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path, -] - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_train_path) -assert path.exists(output_test_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output_train = ad.read_h5ad(output_train_path) -output_test = ad.read_h5ad(output_test_path) - -print("input:", input) -print("output_train:", output_train) -print("output_test:", output_test) - -print(">> Checking whether data from input was copied properly to output") -assert output_train.uns["dataset_id"] == input.uns["dataset_id"] -assert output_test.uns["dataset_id"] == input.uns["dataset_id"] - -print(">> Check whether certain slots exist") -assert "counts" in output_train.layers -assert "counts" in output_test.layers - -print(">> All checks succeeded!") diff --git a/src/denoising/control_methods/no_denoising/config.vsh.yaml b/src/denoising/control_methods/no_denoising/config.vsh.yaml index 2afb33c41e..3dc526115c 100644 --- a/src/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/no_denoising/config.vsh.yaml @@ -1,8 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "no_denoising" - namespace: "denoising/control_methods" - info: subtype: negative_control pretty_name: No Denoising diff --git a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml index ccf7425b65..fc69898bd7 100644 --- a/src/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "perfect_denoising" - namespace: "denoising/control_methods" info: subtype: positive_control pretty_name: Perfect Denoising diff --git a/src/denoising/methods/alra/config.vsh.yaml b/src/denoising/methods/alra/config.vsh.yaml index d596164e87..d5ec0cd3c2 100644 --- a/src/denoising/methods/alra/config.vsh.yaml +++ b/src/denoising/methods/alra/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "alra" - namespace: "denoising/methods" info: pretty_name: ALRA summary: "ALRA imputes missing values in scRNA-seq data by computing rank-k approximation, thresholding by gene, and rescaling the matrix." diff --git a/src/denoising/methods/dca/config.vsh.yaml b/src/denoising/methods/dca/config.vsh.yaml index 997b1aeb1f..c9c09bdd00 100644 --- a/src/denoising/methods/dca/config.vsh.yaml +++ b/src/denoising/methods/dca/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "dca" - namespace: "denoising/methods" info: pretty_name: DCA summary: "A deep autoencoder with ZINB loss function to address the dropout effect in count data" diff --git a/src/denoising/methods/knn_smoothing/config.vsh.yaml b/src/denoising/methods/knn_smoothing/config.vsh.yaml index 32a05fd97f..d003db0b4b 100644 --- a/src/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/denoising/methods/knn_smoothing/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn_smoothing" - namespace: "denoising/methods" info: pretty_name: KNN Smoothing summary: "Iterative kNN-smoothing denoises scRNA-seq data by iteratively increasing the size of neighbourhoods for smoothing until a maximum k value is reached." diff --git a/src/denoising/methods/magic/config.vsh.yaml b/src/denoising/methods/magic/config.vsh.yaml index 8b3f3252fb..5824eb8dfe 100644 --- a/src/denoising/methods/magic/config.vsh.yaml +++ b/src/denoising/methods/magic/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "magic" - namespace: "denoising/methods" info: pretty_name: MAGIC summary: "MAGIC imputes and denoises scRNA-seq data using Euclidean distances and a Gaussian kernel to calculate the affinity matrix, followed by a Markov process and multiplication with the normalised data to obtain imputed values." diff --git a/src/denoising/metrics/mse/config.vsh.yaml b/src/denoising/metrics/mse/config.vsh.yaml index b2a2a5ed4a..f3b86c40ce 100644 --- a/src/denoising/metrics/mse/config.vsh.yaml +++ b/src/denoising/metrics/mse/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "mse" - namespace: "denoising/metrics" info: metrics: - name: mse diff --git a/src/denoising/metrics/poisson/config.vsh.yaml b/src/denoising/metrics/poisson/config.vsh.yaml index 94d29ce1b7..f116ade916 100644 --- a/src/denoising/metrics/poisson/config.vsh.yaml +++ b/src/denoising/metrics/poisson/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "poisson" - namespace: "denoising/metrics" info: reference: "batson2019molecular" metrics: diff --git a/src/denoising/process_dataset/config.vsh.yaml b/src/denoising/process_dataset/config.vsh.yaml index 61a74d0b74..9a470c7134 100644 --- a/src/denoising/process_dataset/config.vsh.yaml +++ b/src/denoising/process_dataset/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: "process_dataset" - namespace: "denoising" description: | Split data using molecular cross-validation. @@ -34,4 +33,5 @@ platforms: - "anndata~=0.8.0" - numpy - scipy + - pyyaml - type: nextflow diff --git a/src/dimensionality_reduction/api/anndata_dataset.yaml b/src/dimensionality_reduction/api/anndata_dataset.yaml deleted file mode 100644 index 774179aa5c..0000000000 --- a/src/dimensionality_reduction/api/anndata_dataset.yaml +++ /dev/null @@ -1,63 +0,0 @@ -type: file -description: "A normalized data with a PCA embedding and HVG selection" -example: "dataset.h5ad" -info: - short_description: "Dataset+PCA+HVG" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalized expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalization method, if any. - required: false - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: double - name: hvg_score - description: High variability gene score (normalized dispersion). The greater, the more variable. - required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: double - name: pca_variance - description: The PCA variance objects. - required: true diff --git a/src/dimensionality_reduction/api/anndata_reduced.yaml b/src/dimensionality_reduction/api/anndata_reduced.yaml index a806c442c9..efca248406 100644 --- a/src/dimensionality_reduction/api/anndata_reduced.yaml +++ b/src/dimensionality_reduction/api/anndata_reduced.yaml @@ -1,6 +1,6 @@ type: file description: "A dimensionally reduced dataset" -example: "reduced.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/reduced.h5ad" info: short_description: "Training data" slots: diff --git a/src/dimensionality_reduction/api/anndata_score.yaml b/src/dimensionality_reduction/api/anndata_score.yaml index 8c14dc9b1d..4e0c848e38 100644 --- a/src/dimensionality_reduction/api/anndata_score.yaml +++ b/src/dimensionality_reduction/api/anndata_score.yaml @@ -1,6 +1,6 @@ type: file description: "Metric score file" -example: "score.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/score.h5ad" info: short_description: "Score" slots: diff --git a/src/dimensionality_reduction/api/anndata_test.yaml b/src/dimensionality_reduction/api/anndata_test.yaml index 3454b7d87e..f51c130e8d 100644 --- a/src/dimensionality_reduction/api/anndata_test.yaml +++ b/src/dimensionality_reduction/api/anndata_test.yaml @@ -1,6 +1,6 @@ type: file description: "The test data" -example: "test.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/test.h5ad" info: short_description: "Test data" slots: diff --git a/src/dimensionality_reduction/api/anndata_train.yaml b/src/dimensionality_reduction/api/anndata_train.yaml index 7387d03ee0..5c0dd0fe05 100644 --- a/src/dimensionality_reduction/api/anndata_train.yaml +++ b/src/dimensionality_reduction/api/anndata_train.yaml @@ -1,6 +1,6 @@ type: file description: "The training data" -example: "train.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/train.h5ad" info: short_description: "Training data" slots: diff --git a/src/dimensionality_reduction/api/comp_control_method.yaml b/src/dimensionality_reduction/api/comp_control_method.yaml index be24821d8a..b2b2958d32 100644 --- a/src/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/dimensionality_reduction/api/comp_control_method.yaml @@ -1,56 +1,17 @@ functionality: + namespace: dimensionality_reduction/control_methods info: type: control_method arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: anndata_train.yaml - name: "--output" __merge__: anndata_reduced.yaml direction: output test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ + dest: resources_test/dimensionality_reduction/pancreas/ - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/train.h5ad" - output_path = "reduced.h5ad" - n_pca = 50 - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path, - "--n_pca", str(n_pca) - ] - - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd) - # out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - - print("input:", input, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether predictions were added", flush=True) - assert "X_emb" in output.obsm - assert meta['functionality_name'] == output.uns["method_id"] - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_method.yaml b/src/dimensionality_reduction/api/comp_method.yaml index e9fc4136e5..9a7764d81b 100644 --- a/src/dimensionality_reduction/api/comp_method.yaml +++ b/src/dimensionality_reduction/api/comp_method.yaml @@ -1,4 +1,5 @@ functionality: + namespace: dimensionality_reduction/methods info: type: method arguments: @@ -9,46 +10,8 @@ functionality: direction: output test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ + dest: resources_test/dimensionality_reduction/pancreas/ - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/train.h5ad" - output_path = "reduced.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path - ] - - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) - - print(">> Running script as test", flush=True) - subprocess.run(cmd, check=True) - - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - - print("input:", input, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether predictions were added", flush=True) - assert "X_emb" in output.obsm - assert meta['functionality_name'] == output.uns["method_id"] - assert 'normalization_id' in output.uns - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_metric.yaml b/src/dimensionality_reduction/api/comp_metric.yaml index 151e840a67..d056eb80dc 100644 --- a/src/dimensionality_reduction/api/comp_metric.yaml +++ b/src/dimensionality_reduction/api/comp_metric.yaml @@ -1,4 +1,5 @@ functionality: + namespace: dimensionality_reduction/metrics info: type: metric arguments: @@ -11,53 +12,8 @@ functionality: direction: output test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ + dest: resources_test/dimensionality_reduction/pancreas/ - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_reduced_path = meta["resources_dir"] + "/pancreas/reduced.h5ad" - input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" - output_path = "score.h5ad" - cmd = [ - meta['executable'], - "--input_reduced", input_reduced_path, - "--input_test", input_test_path, - "--output", output_path, - ] - - print(">> Checking whether input files exist", flush=True) - assert path.exists(input_reduced_path) - assert path.exists(input_test_path) - - print(">> Running script as test", flush=True) - subprocess.run(cmd, check=True) - - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) - - print(">> Reading h5ad files", flush=True) - input_reduced = ad.read_h5ad(input_reduced_path) - input_test = ad.read_h5ad(input_test_path) - output = ad.read_h5ad(output_path) - - print("input reduced:", input_reduced, flush=True) - print("input test:", input_test, flush=True) - print("output:", output, flush=True) - - print(">> Checking whether metrics were added", flush=True) - assert "metric_ids" in output.uns - assert "metric_values" in output.uns - # assert meta['functionality_name'] in output.uns["metric_ids"] - # todo: look at config to check whether all metric ids are available - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] - assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] - assert input_reduced.uns["method_id"] == output.uns["method_id"] - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/dimensionality_reduction/api/comp_process_dataset.yaml b/src/dimensionality_reduction/api/comp_process_dataset.yaml index e4c69822b4..13f68339a4 100644 --- a/src/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/dimensionality_reduction/api/comp_process_dataset.yaml @@ -1,9 +1,10 @@ functionality: + namespace: dimensionality_reduction info: type: process_dataset arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output @@ -12,55 +13,6 @@ functionality: direction: output test_resources: - path: /resources_test/common/pancreas/ + dest: resources_test/common/pancreas/ - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_train_path = "train.h5ad" - output_test_path = "test.h5ad" - cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path - ] - - print(">> Checking whether input file exists", flush=True) - assert path.exists(input_path) - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd, check=True, capture_output=True, text=True) - - print(">> Checking whether output files exist", flush=True) - assert path.exists(output_train_path) - assert path.exists(output_test_path) - - print(">> Reading h5ad files", flush=True) - input = ad.read_h5ad(input_path) - output_train = ad.read_h5ad(output_train_path) - output_test = ad.read_h5ad(output_test_path) - - print("input:", input, flush=True) - print("output_train:", output_train, flush=True) - print("output_test:", output_test, flush=True) - - print(">> Checking whether data from input was copied properly to output", flush=True) - assert input.n_obs == output_train.n_obs - assert input.n_obs == output_test.n_obs - assert input.uns["dataset_id"] == output_train.uns["dataset_id"] - assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - - - print(">> Check whether certain slots exist", flush=True) - assert "counts" in output_train.layers - assert "normalized" in output_train.layers - assert 'hvg_score' in output_train.var - assert "counts" in output_test.layers - assert "normalized" in output_test.layers - assert 'hvg_score' in output_test.var - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index a923da0432..61a5f9582d 100644 --- a/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_features" - namespace: "dimensionality_reduction/control_methods" info: subtype: negative_control pretty_name: Random Features diff --git a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index d81953e413..a33eeae015 100644 --- a/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "true_features" - namespace: "dimensionality_reduction/control_methods" description: "Positive control method which generates high-dimensional (full data) embedding" info: subtype: positive_control diff --git a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml index ed1c08da4b..248995b8ec 100644 --- a/src/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "densmap" - namespace: "dimensionality_reduction/methods" info: pretty_name: densMAP summary: "Modified UMAP with preservation of local density information" diff --git a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml index b723076b95..b440b17fa5 100644 --- a/src/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -5,7 +5,6 @@ functionality: #Temporarily removed from OPv1 see commit 93d2161a08da3edf249abedff5111fb5ce527552 status: disabled name: "ivis" - namespace: "dimensionality_reduction/methods" info: pretty_name: "ivis" summary: "" diff --git a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml index adbf7aebc3..dd74a3e76c 100644 --- a/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "neuralee" - namespace: "dimensionality_reduction/methods" info: pretty_name: NeuralEE summary: "Non-linear method that uses a neural network to preserve pairwise distances between data points in a high-dimensional space." diff --git a/src/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/dimensionality_reduction/methods/pca/config.vsh.yaml index 9b8351c65b..28483e00bf 100644 --- a/src/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "pca" - namespace: "dimensionality_reduction/methods" info: pretty_name: "PCA" summary: "A linear method that finds orthogonal directions to compute the two-dimensional embedding, capturing maximum variance from logCPM expression matrix with/without selecting 1000 HVGs." diff --git a/src/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/dimensionality_reduction/methods/phate/config.vsh.yaml index 08f10799be..244179f574 100644 --- a/src/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "phate" - namespace: "dimensionality_reduction/methods" info: pretty_name: PHATE summary: "Preservating trajectories in a dataset by using heat diffusion potential via an affinity-based method that creates an embedding from dominant eigenvalues of a Markov transition matrix." diff --git a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml index 3d350af7f5..448962cdfe 100644 --- a/src/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "tsne" - namespace: "dimensionality_reduction/methods" info: pretty_name: t-SNE summary: "Minimizing Kullback-Leibler divergence by converting similarities into joint probabilities between data points and the low/high dimensional embedding." diff --git a/src/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/dimensionality_reduction/methods/umap/config.vsh.yaml index c6f2c2fb8f..c6fa67e553 100644 --- a/src/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "umap" - namespace: "dimensionality_reduction/methods" info: pretty_name: UMAP summary: "A manifold learning algorithm that utilizes topological data analysis for dimension reduction." diff --git a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 177b4cf41c..417b4ae583 100644 --- a/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "coranking" - namespace: "dimensionality_reduction/metrics" description: | This is a set of metrics which all use a co-ranking matrix as the basis of the metric. info: diff --git a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 0aba9dec57..7fe3904975 100644 --- a/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "density_preservation" - namespace: "dimensionality_reduction/metrics" info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf diff --git a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 43b2b50910..a6c1b6044b 100644 --- a/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "rmse" - namespace: "dimensionality_reduction/metrics" description: The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py diff --git a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 32c7b0078b..29c8bbdcd9 100644 --- a/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "trustworthiness" - namespace: "dimensionality_reduction/metrics" description: "To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1." info: v1_url: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py diff --git a/src/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/dimensionality_reduction/process_dataset/config.vsh.yaml index 9d2df6f66a..fae70fcf52 100644 --- a/src/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: "process_dataset" - namespace: "dimensionality_reduction" resources: - type: python_script path: script.py diff --git a/src/label_projection/api/anndata_dataset.yaml b/src/label_projection/api/anndata_dataset.yaml deleted file mode 100644 index 9a65630b80..0000000000 --- a/src/label_projection/api/anndata_dataset.yaml +++ /dev/null @@ -1,63 +0,0 @@ -type: file -description: "A normalised data with a PCA embedding and HVG selection" -example: "dataset.h5ad" -info: - label: "Dataset+PCA+HVG" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalised expression values - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - - type: double - name: size_factors - description: The size factors created by the normalisation method, if any. - required: false - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true - obsm: - - type: double - name: X_pca - description: The resulting PCA embedding. - required: true - varm: - - type: double - name: pca_loadings - description: The PCA loadings matrix. - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: normalization_id - description: "Which normalization was used" - required: true - - type: double - name: pca_variance - description: The PCA variance objects. - required: true diff --git a/src/label_projection/api/anndata_prediction.yaml b/src/label_projection/api/anndata_prediction.yaml index de033195d0..bc305cd04d 100644 --- a/src/label_projection/api/anndata_prediction.yaml +++ b/src/label_projection/api/anndata_prediction.yaml @@ -1,6 +1,6 @@ type: file description: "The prediction file" -example: "prediction.h5ad" +example: "resources_test/label_projection/pancreas/knn.h5ad" info: short_description: "Prediction" slots: diff --git a/src/label_projection/api/anndata_score.yaml b/src/label_projection/api/anndata_score.yaml index 39181c68ba..34801c5396 100644 --- a/src/label_projection/api/anndata_score.yaml +++ b/src/label_projection/api/anndata_score.yaml @@ -1,6 +1,6 @@ type: file description: "Metric score file" -example: "output.h5ad" +example: "resources_test/label_projection/pancreas/knn_accuracy.h5ad" info: short_description: "Score" slots: diff --git a/src/label_projection/api/anndata_solution.yaml b/src/label_projection/api/anndata_solution.yaml index bed612a67b..69468001d1 100644 --- a/src/label_projection/api/anndata_solution.yaml +++ b/src/label_projection/api/anndata_solution.yaml @@ -1,6 +1,6 @@ type: file description: "The solution for the test data" -example: "solution.h5ad" +example: "resources_test/label_projection/pancreas/solution.h5ad" info: short_description: "Solution" slots: diff --git a/src/label_projection/api/anndata_test.yaml b/src/label_projection/api/anndata_test.yaml index 0c48edb999..d82811f356 100644 --- a/src/label_projection/api/anndata_test.yaml +++ b/src/label_projection/api/anndata_test.yaml @@ -1,6 +1,6 @@ type: file description: "The test data (without labels)" -example: "test.h5ad" +example: "resources_test/label_projection/pancreas/test.h5ad" info: short_description: "Test data" slots: diff --git a/src/label_projection/api/anndata_train.yaml b/src/label_projection/api/anndata_train.yaml index eece0bb34c..83fb4deb66 100644 --- a/src/label_projection/api/anndata_train.yaml +++ b/src/label_projection/api/anndata_train.yaml @@ -1,6 +1,6 @@ type: file description: "The training data" -example: "training.h5ad" +example: "resources_test/label_projection/pancreas/train.h5ad" info: short_description: "Training data" slots: diff --git a/src/label_projection/api/comp_control_method.yaml b/src/label_projection/api/comp_control_method.yaml index fa647e5003..4aa8e9b732 100644 --- a/src/label_projection/api/comp_control_method.yaml +++ b/src/label_projection/api/comp_control_method.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "label_projection/control_methods" info: type: control_method arguments: @@ -13,7 +14,8 @@ functionality: direction: output test_resources: - path: /resources_test/label_projection/pancreas + dest: resources_test/label_projection/pancreas - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/label_projection/comp_tests/test_method.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/label_projection/api/comp_method.yaml b/src/label_projection/api/comp_method.yaml index 0aec11fa2f..23e655b38a 100644 --- a/src/label_projection/api/comp_method.yaml +++ b/src/label_projection/api/comp_method.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "label_projection/methods" info: type: method arguments: @@ -11,7 +12,8 @@ functionality: direction: output test_resources: - path: /resources_test/label_projection/pancreas + dest: resources_test/label_projection/pancreas - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/label_projection/comp_tests/test_method.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file diff --git a/src/label_projection/api/comp_metric.yaml b/src/label_projection/api/comp_metric.yaml index 6b6008d539..21ebc5534a 100644 --- a/src/label_projection/api/comp_metric.yaml +++ b/src/label_projection/api/comp_metric.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "label_projection/metrics" info: type: metric arguments: @@ -11,7 +12,8 @@ functionality: direction: output test_resources: - path: /resources_test/label_projection/pancreas + dest: resources_test/label_projection/pancreas - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/label_projection/comp_tests/test_metric.py + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/label_projection/api/comp_process_dataset.yaml b/src/label_projection/api/comp_process_dataset.yaml index 707a5c46d5..70153f5d47 100644 --- a/src/label_projection/api/comp_process_dataset.yaml +++ b/src/label_projection/api/comp_process_dataset.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "label_projection" info: type: process_dataset arguments: @@ -15,6 +16,7 @@ functionality: direction: output test_resources: - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas - type: python_script - path: /src/label_projection/comp_tests/test_process_dataset.py + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/label_projection/comp_tests/test_method.py b/src/label_projection/comp_tests/test_method.py deleted file mode 100644 index 251875f767..0000000000 --- a/src/label_projection/comp_tests/test_method.py +++ /dev/null @@ -1,42 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_train_path = meta["resources_dir"] + "/pancreas/train.h5ad" -input_test_path = meta["resources_dir"] + "/pancreas/test.h5ad" -input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" -output_path = "output.h5ad" - -cmd = [ - meta['executable'], - "--input_train", input_train_path, - "--input_test", input_test_path, - "--output", output_path -] - -# todo: if we could access the viash config, we could check whether -# .functionality.info.type == "positive_control" -if meta['functionality_name'] == 'true_labels': - cmd = cmd + ["--input_solution", input_solution_path] - -print(">> Running script as test") -out = subprocess.check_output(cmd).decode("utf-8") - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input_test = ad.read_h5ad(input_test_path) -output = ad.read_h5ad(output_path) -print("input_test:", input_test) -print("output:", output) - -print(">> Checking whether predictions were added") -assert "label_pred" in output.obs -assert meta['functionality_name'] == output.uns["method_id"] - -print("Checking whether data from input was copied properly to output") -assert input_test.n_obs == output.n_obs -assert input_test.uns["dataset_id"] == output.uns["dataset_id"] - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/label_projection/comp_tests/test_metric.py b/src/label_projection/comp_tests/test_metric.py deleted file mode 100644 index 7a19f3d950..0000000000 --- a/src/label_projection/comp_tests/test_metric.py +++ /dev/null @@ -1,34 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_prediction_path = meta["resources_dir"] + "/pancreas/knn.h5ad" -input_solution_path = meta["resources_dir"] + "/pancreas/solution.h5ad" -output_path = "output.h5ad" - -cmd = [ - meta['executable'], - "--input_prediction", input_prediction_path, - "--input_solution", input_solution_path, - "--output", output_path -] - -print(">> Running script as test") -out = subprocess.check_output(cmd).decode("utf-8") - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -input_solution = ad.read_h5ad(input_solution_path) -input_prediction = ad.read_h5ad(input_prediction_path) -output = ad.read_h5ad(output_path) - -print("Checking whether data from input was copied properly to output") -assert output.uns["dataset_id"] == input_prediction.uns["dataset_id"] -assert output.uns["method_id"] == input_prediction.uns["method_id"] -assert output.uns["metric_ids"] is not None -assert output.uns["metric_values"] is not None - -# TODO: check whether the metric ids are all in .functionality.info - -print("All checks succeeded!") diff --git a/src/label_projection/comp_tests/test_process_dataset.py b/src/label_projection/comp_tests/test_process_dataset.py deleted file mode 100644 index 86d3591a9e..0000000000 --- a/src/label_projection/comp_tests/test_process_dataset.py +++ /dev/null @@ -1,62 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -output_train_path = "output_train.h5ad" -output_test_path = "output_test.h5ad" -output_solution_path = "output_solution.h5ad" - -cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path, - "--output_solution", output_solution_path -] - -print(">> Running script as test") -out = subprocess.check_output(cmd).decode("utf-8") - -print(">> Checking whether output file exists") -assert path.exists(output_train_path) -assert path.exists(output_test_path) -assert path.exists(output_solution_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output_train = ad.read_h5ad(output_train_path) -output_test = ad.read_h5ad(output_test_path) -output_solution = ad.read_h5ad(output_solution_path) - -print("input:", input) -print("output_train:", output_train) -print("output_test:", output_test) -print("output_solution:", output_solution) - -print(">> Checking dimensions, make sure no cells were dropped") -assert input.n_obs == output_train.n_obs + output_test.n_obs -assert output_test.n_obs == output_solution.n_obs -assert input.n_vars == output_train.n_vars -assert input.n_vars == output_test.n_vars - -print(">> Checking whether data from input was copied properly to output") -assert output_train.uns["dataset_id"] == input.uns["dataset_id"] -assert output_test.uns["dataset_id"] == input.uns["dataset_id"] -assert output_solution.uns["dataset_id"] == input.uns["dataset_id"] - -print(">> Check whether certain slots exist") -assert "counts" in output_train.layers -assert "normalized" in output_train.layers -assert "label" in output_train.obs -assert "batch" in output_train.obs -assert "counts" in output_test.layers -assert "normalized" in output_test.layers -assert "label" not in output_test.obs # make sure label is /not/ here -assert "batch" in output_test.obs -assert "counts" in output_solution.layers -assert "normalized" in output_solution.layers -assert "label" in output_solution.obs -assert "batch" in output_solution.obs - -print(">> All checks succeeded!") \ No newline at end of file diff --git a/src/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/label_projection/control_methods/majority_vote/config.vsh.yaml index d8fc6464ab..c7bf2e855b 100644 --- a/src/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "majority_vote" - namespace: "label_projection/control_methods" info: subtype: negative_control pretty_name: Majority Vote @@ -17,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/label_projection/control_methods/random_labels/config.vsh.yaml b/src/label_projection/control_methods/random_labels/config.vsh.yaml index 0d5f3999bb..f2d33c663f 100644 --- a/src/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/random_labels/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_labels" - namespace: "label_projection/control_methods" info: subtype: negative_control pretty_name: Random Labels @@ -17,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/label_projection/control_methods/true_labels/config.vsh.yaml b/src/label_projection/control_methods/true_labels/config.vsh.yaml index c031c8faa2..03f08e8d3a 100644 --- a/src/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/label_projection/control_methods/true_labels/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "true_labels" - namespace: "label_projection/control_methods" description: "Positive control method by returning the true labels" info: subtype: positive_control @@ -18,7 +17,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.8" + image: "python:3.10" setup: - type: python packages: diff --git a/src/label_projection/methods/knn/config.vsh.yaml b/src/label_projection/methods/knn/config.vsh.yaml index d327024545..e4d080822d 100644 --- a/src/label_projection/methods/knn/config.vsh.yaml +++ b/src/label_projection/methods/knn/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn" - namespace: "label_projection/methods" info: pretty_name: KNN summary: "Assumes cells with similar gene expression belong to the same cell type, and assigns an unlabelled cell the most common cell type among its k nearest neighbors in PCA space." diff --git a/src/label_projection/methods/logistic_regression/config.vsh.yaml b/src/label_projection/methods/logistic_regression/config.vsh.yaml index 6238e49690..5b3899b318 100644 --- a/src/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/label_projection/methods/logistic_regression/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "logistic_regression" - namespace: "label_projection/methods" info: pretty_name: Logistic Regression summary: "Logistic Regression with 100-dimensional PCA coordinates estimates parameters for multivariate classification by minimizing cross entropy loss over cell type classes." diff --git a/src/label_projection/methods/mlp/config.vsh.yaml b/src/label_projection/methods/mlp/config.vsh.yaml index 62a77df0af..cf1b855a5a 100644 --- a/src/label_projection/methods/mlp/config.vsh.yaml +++ b/src/label_projection/methods/mlp/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "mlp" - namespace: "label_projection/methods" info: pretty_name: Multilayer perceptron summary: "A neural network with 100-dimensional PCA input, two hidden layers, and gradient descent weight updates to minimize cross entropy loss." diff --git a/src/label_projection/methods/scanvi/config.vsh.yaml b/src/label_projection/methods/scanvi/config.vsh.yaml index 0d324b805b..ddcfedc2b9 100644 --- a/src/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/label_projection/methods/scanvi/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" - namespace: "label_projection/methods" info: pretty_name: SCANVI summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." diff --git a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml index 8198ae25bc..3160fe0638 100644 --- a/src/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "seurat_transferdata" - namespace: "label_projection/methods" description: | The Seurat v3 anchoring procedure is designed to integrate diverse single-cell datasets across technologies and modalities. diff --git a/src/label_projection/methods/xgboost/config.vsh.yaml b/src/label_projection/methods/xgboost/config.vsh.yaml index ca044ace50..b900dad81e 100644 --- a/src/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/label_projection/methods/xgboost/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "xgboost" - namespace: "label_projection/methods" description: "XGBoost: A Scalable Tree Boosting System" info: pretty_name: XGBoost diff --git a/src/label_projection/metrics/accuracy/config.vsh.yaml b/src/label_projection/metrics/accuracy/config.vsh.yaml index 7d762a2c74..16fe6a596f 100644 --- a/src/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/label_projection/metrics/accuracy/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "accuracy" - namespace: "label_projection/metrics" info: v1_url: openproblems/tasks/label_projection/metrics/accuracy.py v1_commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 diff --git a/src/label_projection/metrics/f1/config.vsh.yaml b/src/label_projection/metrics/f1/config.vsh.yaml index 9e271b2a84..3ba7618439 100644 --- a/src/label_projection/metrics/f1/config.vsh.yaml +++ b/src/label_projection/metrics/f1/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "f1" - namespace: "label_projection/metrics" info: v1_url: openproblems/tasks/label_projection/metrics/f1.py v1_commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 diff --git a/src/label_projection/process_dataset/config.vsh.yaml b/src/label_projection/process_dataset/config.vsh.yaml index cedd6d3c6f..66f8a02cc3 100644 --- a/src/label_projection/process_dataset/config.vsh.yaml +++ b/src/label_projection/process_dataset/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: "process_dataset" - namespace: "label_projection" arguments: - name: "--method" type: "string" From 2c5dd79d92c4267809899ace9097d495cd2a80e4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Apr 2023 21:03:49 +0200 Subject: [PATCH 0855/1233] Bump tj-actions/changed-files from 35.8.0 to 35.9.0 (#136) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.8.0 to 35.9.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.8.0...v35.9.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 1f893093aea97564faa584054dcc90fff7f9b0f9 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index c67f329ed4..f02df5086d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.8.0 + uses: tj-actions/changed-files@v35.9.0 with: separator: ";" diff_relative: true From 142cc87505a01ac0bcd62e9831a11faf4b610488 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 21:32:20 +0200 Subject: [PATCH 0856/1233] fix missing namespace Former-commit-id: 4ea7251931a89055d66552fa06359af15651c2fd --- src/denoising/api/comp_method.yaml | 1 + src/denoising/api/comp_metric.yaml | 1 + 2 files changed, 2 insertions(+) diff --git a/src/denoising/api/comp_method.yaml b/src/denoising/api/comp_method.yaml index ffea8e1fc3..7dc5c0e4b9 100644 --- a/src/denoising/api/comp_method.yaml +++ b/src/denoising/api/comp_method.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "denoising/methods" info: type: method arguments: diff --git a/src/denoising/api/comp_metric.yaml b/src/denoising/api/comp_metric.yaml index 061f322a06..8c608ae3d5 100644 --- a/src/denoising/api/comp_metric.yaml +++ b/src/denoising/api/comp_metric.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "denoising/metrics" info: type: metric arguments: From 345106dbd2af7cf7dd127fabcf7d06a50b49ddd4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 22:10:18 +0200 Subject: [PATCH 0857/1233] refactor subsample test Former-commit-id: d4326faa99e146f1c2d60006bfa14061777e4e73 --- src/datasets/subsample/test_script.py | 33 +++++++++++++++------------ 1 file changed, 18 insertions(+), 15 deletions(-) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index a12d07dc17..2206882f5a 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -4,6 +4,12 @@ import anndata as ad import numpy as np +## VIASH START +meta = { + "resources_dir": "resources_test/common" +} +## VIASH END + input_path = f"{meta['resources_dir']}/pancreas/dataset.h5ad" input = ad.read_h5ad(input_path) @@ -18,16 +24,14 @@ def test_even_sampling(run_component): "--n_vars", "120" ]) - print(">> Checking whether file exists") - assert os.path.exists(output_path) + # Checking whether file exists + assert os.path.exists(output_path), "Output file not found" - print(">> Check that test output fits expected API") + # Check that test output fits expected API output = ad.read_h5ad(output_path) - assert output.n_obs <= 100 - assert output.n_vars <= 120 - - print(f"output: {output}", flush=True) + assert output.n_obs <= 100, "n_obs should be <= 100" + assert output.n_vars <= 120, "n_vars should be <= 100" def test_keep_functionality(run_component): @@ -43,17 +47,16 @@ def test_keep_functionality(run_component): "--seed", "123" ]) - print(">> Checking whether file exists") - assert os.path.exists(output_path) + # Checking whether file exists + assert os.path.exists(output_path), "Output file not found" - print(">> Check that test output fits expected API") + # Check that test output fits expected API output = ad.read_h5ad(output_path) - assert output.n_obs <= 500 - assert output.n_vars <= 500 - assert np.all([ f in output.var_names for f in keep_features]) - - print(f"output: {output}", flush=True) + assert output.n_obs <= 500, "n_obs should be <= 500" + assert output.n_vars <= 500, "n_vars should be <= 500" + for feat in keep_features: + assert feat in output.var_names, f"{feat} should be in output.var_names" if __name__ == '__main__': sys.exit(pytest.main([__file__, "--capture=no"], plugins=["viashpy"])) From 73bb0e62ddbdffbbc96a48022dd820d4fb82894c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 22:10:35 +0200 Subject: [PATCH 0858/1233] remove unused import Former-commit-id: 4173b2ccff4680bf584a043f3d9be5c42c6a1ebe --- src/datasets/subsample/test_script.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/subsample/test_script.py index 2206882f5a..c2f3697dcc 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/subsample/test_script.py @@ -2,7 +2,6 @@ import os import pytest import anndata as ad -import numpy as np ## VIASH START meta = { From 09eb7dcc61386e7b47b8d75cbdfc99db3e2ed20b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 24 Apr 2023 22:20:38 +0200 Subject: [PATCH 0859/1233] try adding project config as resource Former-commit-id: b184170d8e795962f0b828a4e0884b1d9cfcebff --- src/common/create_component/config.vsh.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index b688768199..4127981618 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -51,6 +51,8 @@ functionality: path: test.py - path: /src dest: openproblems-v2/src + - path: /_viash.yaml + dest: openproblems-v2/_viash.yaml platforms: - type: docker image: python:3.10-slim From 63acb8537a3a1046d312938a34847662dc82de9f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Apr 2023 10:48:27 +0200 Subject: [PATCH 0860/1233] add viash_yaml path Former-commit-id: fd35d51b9f0b8a7d6999b65e410e87ebf05c886a --- src/common/create_component/config.vsh.yaml | 6 ++++++ src/common/create_component/test.py | 4 +++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index 4127981618..c24e1e932a 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -43,6 +43,12 @@ functionality: to manually specify a different API file to inherit from. # required: true default: src/${VIASH_PAR_TASK}/api/comp_${VIASH_PAR_TYPE}.yaml + - type: file + name: --viash_yaml + description: | + Path to the project config file. Needed for knowing the relative location of a file to the project root. + # required: true + default: "_viash.yaml" resources: - type: python_script path: script.py diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 39c6a34e59..e328e41fd5 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -9,6 +9,7 @@ ## VIASH END api_file = meta["resources_dir"] + "/openproblems-v2/src/label_projection/api/comp_method.yaml" +viash_yaml = meta["resources_dir"] + "/openproblems-v2/_viash.yaml" output_path = 'method_py' cmd = [ @@ -18,7 +19,8 @@ '--name', 'test_method', '--language', 'python', '--output', output_path, - '--api_file', api_file + '--api_file', api_file, + '--viash_yaml', viash_yaml ] print('>> Running the script as test', flush=True) From f7cff680ee9d4a32cc4c415e63b1c5ee357aafc2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Apr 2023 11:08:58 +0200 Subject: [PATCH 0861/1233] fix scripts Former-commit-id: 1576d61c5a8b6be6c1e7f57e99449e5ce997b99c --- src/common/create_component/script.py | 1 - src/common/create_component/test.py | 27 ++++++++++++--------------- 2 files changed, 12 insertions(+), 16 deletions(-) diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index f6273d58cb..4f7dba3546 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -33,7 +33,6 @@ def create_config_template(par): | |functionality: | name: {par["name"]} - | namespace: {par["task"]}/{par['type']}s | | # Metadata for your component (required) | info: diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index e328e41fd5..4598152f78 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -1,3 +1,4 @@ +import os import subprocess from os import path from ruamel.yaml import YAML @@ -8,40 +9,36 @@ } ## VIASH END -api_file = meta["resources_dir"] + "/openproblems-v2/src/label_projection/api/comp_method.yaml" -viash_yaml = meta["resources_dir"] + "/openproblems-v2/_viash.yaml" -output_path = 'method_py' +opv2 = f"{meta['resources_dir']}/openproblems-v2" +output_path = f"{opv2}/src/label_projection/methods/test_method" cmd = [ meta['executable'], '--task', 'label_projection', '--type', 'method', '--name', 'test_method', - '--language', 'python', - '--output', output_path, - '--api_file', api_file, - '--viash_yaml', viash_yaml + '--language', 'python' ] print('>> Running the script as test', flush=True) -out = subprocess.run(cmd, check=True) +out = subprocess.run(cmd, check=True, cwd=opv2) print('>> Checking whether output files exist', flush=True) -assert path.exists(output_path) +assert os.path.exists(output_path), "Output dir does not exist" + conf_f = path.join(output_path, 'config.vsh.yaml') -assert path.exists(conf_f) +assert os.path.exists(conf_f), "Config file does not exist" + script_f = path.join(output_path, "script.py") -assert path.exists(script_f) +assert os.path.exists(script_f), "Script file does not exist" print('>> Checking file contents', flush=True) yaml = YAML() with open(conf_f) as f: conf_data = yaml.load(f) -assert conf_data['functionality']['name'] == 'test_method' -assert conf_data['functionality']['namespace'] == 'label_projection/methods' -assert conf_data['platforms'][0]['image'] == 'python:3.10' - +assert conf_data['functionality']['name'] == 'test_method', "Name should be equal to 'test_method'" +assert conf_data['platforms'][0]['image'] == 'python:3.10', "Python image should be equal to python:3.10" print('All checks succeeded!', flush=True) From 2f05a22d1f21e41b0c164f6628d7f6b1bd35450c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Apr 2023 11:50:40 +0200 Subject: [PATCH 0862/1233] make subsample test more robust Former-commit-id: 84429bb4adde767b335fe954bf313777b320da03 --- src/datasets/{ => processors}/subsample/config.vsh.yaml | 2 +- src/datasets/{ => processors}/subsample/script.py | 4 +++- src/datasets/{ => processors}/subsample/test_script.py | 5 ++++- src/datasets/resource_test_scripts/pancreas.sh | 2 +- 4 files changed, 9 insertions(+), 4 deletions(-) rename src/datasets/{ => processors}/subsample/config.vsh.yaml (98%) rename src/datasets/{ => processors}/subsample/script.py (96%) rename src/datasets/{ => processors}/subsample/test_script.py (91%) diff --git a/src/datasets/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml similarity index 98% rename from src/datasets/subsample/config.vsh.yaml rename to src/datasets/processors/subsample/config.vsh.yaml index f7595ac54e..c367830400 100644 --- a/src/datasets/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: name: "subsample" - namespace: "datasets" + namespace: "datasets/processors" description: "Subsample an h5ad file" arguments: - name: "--input" diff --git a/src/datasets/subsample/script.py b/src/datasets/processors/subsample/script.py similarity index 96% rename from src/datasets/subsample/script.py rename to src/datasets/processors/subsample/script.py index 84940205d7..fd73d54b4d 100644 --- a/src/datasets/subsample/script.py +++ b/src/datasets/processors/subsample/script.py @@ -1,11 +1,12 @@ import scanpy as sc import random -import anndata as ad import numpy as np ### VIASH START par = { "input": "resources_test/common/pancreas/dataset.h5ad", + "n_obs": 500, + "n_vars": 500, "keep_celltype_categories": None, "keep_batch_categories": None, "keep_features": ["HMGB2", "CDK1", "NUSAP1", "UBE2C"], @@ -70,6 +71,7 @@ adata_output = adata_input[obs_index, var_ix].copy() +# todo: this should not remove features in keep_features! print(">> Remove empty observations and features", flush=True) sc.pp.filter_genes(adata_output, min_cells=1) sc.pp.filter_cells(adata_output, min_counts=2) diff --git a/src/datasets/subsample/test_script.py b/src/datasets/processors/subsample/test_script.py similarity index 91% rename from src/datasets/subsample/test_script.py rename to src/datasets/processors/subsample/test_script.py index c2f3697dcc..2e643205b5 100644 --- a/src/datasets/subsample/test_script.py +++ b/src/datasets/processors/subsample/test_script.py @@ -36,7 +36,10 @@ def test_even_sampling(run_component): def test_keep_functionality(run_component): output_path = "output.h5ad" - keep_features = list(input.var_names[:10]) + # keep_features = list(input.var_names[:10]) + # use genes with high enough expression + keep_features = ["ARHGEF12", "PPM1L", "HMGB2", "NEURL4"] + run_component([ "--input", input_path, "--keep_celltype_categories", "acinar:beta", diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 7f5eb3c720..41746677f5 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -34,7 +34,7 @@ wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722 KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s_genes_tirosh_hm.txt | paste -sd ":" -` # subsample -viash run src/datasets/subsample/config.vsh.yaml -- \ +viash run src/datasets/processors/subsample/config.vsh.yaml -- \ --input $DATASET_DIR/temp_dataset_full.h5ad \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ From 7479a0a2470c0c3d28095d6208b5aade0afb268a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Apr 2023 12:14:37 +0200 Subject: [PATCH 0863/1233] update changelog Former-commit-id: e57411f0e0cdfa755a458b1535a712c65970c173 --- CHANGELOG.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5585fa7ce6..b13d81ba7e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,21 +11,21 @@ * Created test data `resources_test/pancreas` with `src/common/resources_test_scripts/pancreas.sh`. -* `get_api_info`: extract api info from tasks +* `get_api_info`: Extract api info from tasks. -* `get_method_info`: extract method info from config yaml +* `get_method_info`: Extract method info from config yaml. -* `get_metric_info`: extract metric info from config yaml +* `get_metric_info`: Extract metric info from config yaml. -* `get_results`: extract benchmark scores +* `get_results`: Extract benchmark scores. -* `get_task_info`: extract task info +* `get_task_info`: Extract task info. -* `comp_tests`: Common unit test that can be used by all tasks +* `comp_tests`: Common unit tests that can be used by all tasks. -* `check_dataset_schema`: check if the dataset used has the required fields defined in the api `anndata_*.yaml` files +* `check_dataset_schema`: Check if the dataset used has the required fields defined in the api `anndata_*.yaml` files. -* `Create_component`: creates a template folder with a viash config and script file depending on the task api. +* `Create_component`: Creates a template folder with a viash config and script file depending on the task api. ### MINOR CHANGES From f3d8dcb484ae9b30fec317ff89b82a547d142c7f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 25 Apr 2023 12:20:39 +0200 Subject: [PATCH 0864/1233] check when required is not defined Former-commit-id: 746600f639c083b98aaac6418a0d57a4ee6ff07e --- src/common/comp_tests/run_and_check_adata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py index 446a2bcf20..61d3a8a9db 100644 --- a/src/common/comp_tests/run_and_check_adata.py +++ b/src/common/comp_tests/run_and_check_adata.py @@ -21,7 +21,7 @@ def check_slots(adata, slot_metadata): struc_dict = getattr(adata, struc_name) for slot_item in slot_items: - if slot_item.get("required", False): + if slot_item.get("required", True): assert slot_item["name"] in struc_dict,\ f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']" From aa90eca26a1ca28806ff548d8954ca954c6b19e4 Mon Sep 17 00:00:00 2001 From: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> Date: Tue, 25 Apr 2023 06:53:05 -0400 Subject: [PATCH 0865/1233] Add scanvi+scarches (#127) * add scvi+scarches * remove debug print * Update CHANGELOG.md * namespace no longer needed as it's already defined in the api --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: b11dfdb977d512516b24910a5115ce5e37c3f615 --- CHANGELOG.md | 2 + .../methods/scanvi_scarches/config.vsh.yaml | 63 +++++++++++++++++++ .../methods/scanvi_scarches/script.py | 61 ++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 src/label_projection/methods/scanvi_scarches/config.vsh.yaml create mode 100644 src/label_projection/methods/scanvi_scarches/script.py diff --git a/CHANGELOG.md b/CHANGELOG.md index b13d81ba7e..978031c939 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -84,6 +84,8 @@ * `methods/scanvi`: Migrated and adapted from v1. +* `methods/scanvi_scarches`: Migrated and adapted from v1. + * `methods/seurat_transferdata`: Migrated and adapted from v1. * `methods/xgboost`: Migrated from v1. diff --git a/src/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/label_projection/methods/scanvi_scarches/config.vsh.yaml new file mode 100644 index 0000000000..e6df0a1bb7 --- /dev/null +++ b/src/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -0,0 +1,63 @@ +# The API specifies which type of component this is. +# It contains specifications for: +# - The input/output files +# - Common parameters +# - A unit test +__merge__: ../../api/comp_method.yaml + +functionality: + name: scanvi_scarches + + # Metadata for your component (required) + info: + pretty_name: scANVI+scArches + summary: 'Query to reference single-cell integration with transfer learning with scANVI and scArches' + description: 'scArches+scANVI or "Single-cell architecture surgery" is a deep learning method for mapping new datasets onto a pre-existing reference model, using transfer learning and parameter optimization. It first uses scANVI to build a reference model from the training data, and then apply scArches to map the test data onto the reference model and make predictions.' + reference: lotfollahi2020query + documentation_url: https://docs.scvi-tools.org + repository_url: https://github.com/scverse/scvi-tools + preferred_normalization: none + variants: + scanvi_scarches: + + # Component-specific parameters (optional) + arguments: + - name: "--n_latent" + type: "integer" + default: 30 + description: "Number of units in the latent layer" + - name: "--n_layers" + type: "integer" + default: 2 + description: "Number of hidden layers" + - name: "--n_hidden" + type: "integer" + default: 128 + description: "Number of units in the hidden layers" + - name: "--dropout_rate" + type: "double" + default: 0.2 + description: "Rate of dropout applied in training" + - name: "--max_epochs" + type: "integer" + default: 2 + description: "Maximum number of training epochs" + + # Resources required to run the component + resources: + # The script of your component + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.10 + # Add custom dependencies here + setup: + - type: python + pypi: + - anndata~=0.8 + - pyyaml + - scvi-tools + - type: nextflow + directives: + label: [midmem, midcpu] diff --git a/src/label_projection/methods/scanvi_scarches/script.py b/src/label_projection/methods/scanvi_scarches/script.py new file mode 100644 index 0000000000..73c9c0f1fa --- /dev/null +++ b/src/label_projection/methods/scanvi_scarches/script.py @@ -0,0 +1,61 @@ +import anndata as ad +import numpy as np +import scvi + +## VIASH START +par = { + "input_train": "resources_test/label_projection/pancreas/train.h5ad", + "input_test": "resources_test/label_projection/pancreas/test.h5ad", + "output": "output.h5ad", + "n_latent": 30, + "n_layers": 2, + "n_hidden": 128, + "dropout_rate": 0.2, + "max_epochs": 200, +} +meta = {"functionality_name": "scanvi_xgboost"} +## VIASH END + +print("Reading input files", flush=True) +input_train = ad.read_h5ad(par["input_train"]) +input_test = ad.read_h5ad(par["input_test"]) +input_train.X = input_train.layers["counts"] +input_test.X = input_test.layers["counts"] + +print("Train model", flush=True) +unlabeled_category = "Unknown" + +scvi.model.SCVI.setup_anndata(input_train, batch_key="batch", labels_key="label") + +# specific scArches parameters +arches_params = dict( + use_layer_norm="both", + use_batch_norm="none", + encode_covariates=True, + dropout_rate=par["dropout_rate"], + n_hidden=par["n_hidden"], + n_layers=par["n_layers"], + n_latent=par["n_latent"], +) +scvi_model = scvi.model.SCVI(input_train, **arches_params) +train_kwargs = dict( + train_size=0.9, + early_stopping=True, +) +scvi_model.train(**train_kwargs) +model = scvi.model.SCANVI.from_scvi_model( + scvi_model, unlabeled_category=unlabeled_category +) +model.train(**train_kwargs) + +query_model = scvi.model.SCANVI.load_query_data(input_test, model) +train_kwargs = dict(max_epochs=par["max_epochs"], early_stopping=True) +query_model.train(plan_kwargs=dict(weight_decay=0.0), **train_kwargs) + +print("Generate predictions", flush=True) +input_test.obs["label"] = "Unknown" +input_test.obs["label_pred"] = query_model.predict(input_test) + +print("Write output AnnData to file", flush=True) +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par["output"], compression="gzip") From 038d106bbf1d69435df073cd8960d68899797628 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 Apr 2023 15:53:07 +0200 Subject: [PATCH 0866/1233] add_cwd_to_config_view Former-commit-id: cc93866acb75ef6cbb28e366018f889c0cb25e19 --- src/common/create_component/script.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 4f7dba3546..00f4ee06c4 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -362,7 +362,11 @@ def read_viash_config(file): command = ["viash", "config", "view", str(file)] # Execute the command and capture the output - output = subprocess.check_output(command, universal_newlines=True) + output = subprocess.check_output( + command, + universal_newlines=True, + cwd=str(file.parent) + ) # Parse the output as YAML config = yaml.load(output) From a50b681452e54cc92fad6a1e5318d78a155fd7d2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 27 Apr 2023 16:16:43 +0200 Subject: [PATCH 0867/1233] make file absolute Former-commit-id: 22a989ffd0017da04103f8ea574f378ecbe5b0cc --- src/common/create_component/script.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 00f4ee06c4..104d86c4b4 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -358,6 +358,8 @@ def create_r_script(par, api_spec, type): return script def read_viash_config(file): + file = file.absolute() + # read in config command = ["viash", "config", "view", str(file)] From 0c506714a8a1e7f24afe7d5cbbb411244245e5b4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 May 2023 22:12:12 +0000 Subject: [PATCH 0868/1233] Bump tj-actions/changed-files from 35.9.0 to 35.9.2 Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.9.0 to 35.9.2. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.9.0...v35.9.2) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Former-commit-id: be1c7ef544d3a7119794c16b340c3a8d4f97a60c --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f02df5086d..89bb75b3f1 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.9.0 + uses: tj-actions/changed-files@v35.9.2 with: separator: ";" diff_relative: true From 35135cfa994db1b15a2f610a8d9c3b7200678d24 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 11 May 2023 16:36:07 +0200 Subject: [PATCH 0869/1233] relocate denoising Former-commit-id: 9c9cf880f9c5889200efd34d99a03504efe5dc6d --- src/{ => tasks}/denoising/README.md | 0 src/{ => tasks}/denoising/api/anndata_dataset.yaml | 0 src/{ => tasks}/denoising/api/anndata_denoised.yaml | 0 src/{ => tasks}/denoising/api/anndata_score.yaml | 0 src/{ => tasks}/denoising/api/anndata_test.yaml | 0 src/{ => tasks}/denoising/api/anndata_train.yaml | 0 src/{ => tasks}/denoising/api/authors.yaml | 0 src/{ => tasks}/denoising/api/comp_control_method.yaml | 0 src/{ => tasks}/denoising/api/comp_method.yaml | 0 src/{ => tasks}/denoising/api/comp_metric.yaml | 0 src/{ => tasks}/denoising/api/comp_process_dataset.yaml | 0 src/{ => tasks}/denoising/api/task_info.yaml | 0 .../denoising/control_methods/no_denoising/config.vsh.yaml | 0 src/{ => tasks}/denoising/control_methods/no_denoising/script.py | 0 .../denoising/control_methods/perfect_denoising/config.vsh.yaml | 0 .../denoising/control_methods/perfect_denoising/script.py | 0 src/{ => tasks}/denoising/methods/alra/config.vsh.yaml | 0 src/{ => tasks}/denoising/methods/alra/script.R | 0 src/{ => tasks}/denoising/methods/dca/config.vsh.yaml | 0 src/{ => tasks}/denoising/methods/dca/script.py | 0 src/{ => tasks}/denoising/methods/knn_smoothing/config.vsh.yaml | 0 src/{ => tasks}/denoising/methods/knn_smoothing/script.py | 0 src/{ => tasks}/denoising/methods/magic/config.vsh.yaml | 0 src/{ => tasks}/denoising/methods/magic/script.py | 0 src/{ => tasks}/denoising/metrics/mse/config.vsh.yaml | 0 src/{ => tasks}/denoising/metrics/mse/script.py | 0 src/{ => tasks}/denoising/metrics/poisson/config.vsh.yaml | 0 src/{ => tasks}/denoising/metrics/poisson/script.py | 0 src/{ => tasks}/denoising/process_dataset/config.vsh.yaml | 0 src/{ => tasks}/denoising/process_dataset/helper.py | 0 src/{ => tasks}/denoising/process_dataset/script.py | 0 src/{ => tasks}/denoising/resources_scripts/process_datasets.sh | 0 src/{ => tasks}/denoising/resources_scripts/run_benchmark.sh | 0 src/{ => tasks}/denoising/resources_test_scripts/pancreas.sh | 0 src/{ => tasks}/denoising/workflows/run/config.vsh.yaml | 0 src/{ => tasks}/denoising/workflows/run/main.nf | 0 src/{ => tasks}/denoising/workflows/run/nextflow.config | 0 37 files changed, 0 insertions(+), 0 deletions(-) rename src/{ => tasks}/denoising/README.md (100%) rename src/{ => tasks}/denoising/api/anndata_dataset.yaml (100%) rename src/{ => tasks}/denoising/api/anndata_denoised.yaml (100%) rename src/{ => tasks}/denoising/api/anndata_score.yaml (100%) rename src/{ => tasks}/denoising/api/anndata_test.yaml (100%) rename src/{ => tasks}/denoising/api/anndata_train.yaml (100%) rename src/{ => tasks}/denoising/api/authors.yaml (100%) rename src/{ => tasks}/denoising/api/comp_control_method.yaml (100%) rename src/{ => tasks}/denoising/api/comp_method.yaml (100%) rename src/{ => tasks}/denoising/api/comp_metric.yaml (100%) rename src/{ => tasks}/denoising/api/comp_process_dataset.yaml (100%) rename src/{ => tasks}/denoising/api/task_info.yaml (100%) rename src/{ => tasks}/denoising/control_methods/no_denoising/config.vsh.yaml (100%) rename src/{ => 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src/denoising/api/anndata_dataset.yaml rename to src/tasks/denoising/api/anndata_dataset.yaml diff --git a/src/denoising/api/anndata_denoised.yaml b/src/tasks/denoising/api/anndata_denoised.yaml similarity index 100% rename from src/denoising/api/anndata_denoised.yaml rename to src/tasks/denoising/api/anndata_denoised.yaml diff --git a/src/denoising/api/anndata_score.yaml b/src/tasks/denoising/api/anndata_score.yaml similarity index 100% rename from src/denoising/api/anndata_score.yaml rename to src/tasks/denoising/api/anndata_score.yaml diff --git a/src/denoising/api/anndata_test.yaml b/src/tasks/denoising/api/anndata_test.yaml similarity index 100% rename from src/denoising/api/anndata_test.yaml rename to src/tasks/denoising/api/anndata_test.yaml diff --git a/src/denoising/api/anndata_train.yaml b/src/tasks/denoising/api/anndata_train.yaml similarity index 100% rename from src/denoising/api/anndata_train.yaml rename to src/tasks/denoising/api/anndata_train.yaml diff --git 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src/tasks/denoising/resources_test_scripts/pancreas.sh diff --git a/src/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run/config.vsh.yaml similarity index 100% rename from src/denoising/workflows/run/config.vsh.yaml rename to src/tasks/denoising/workflows/run/config.vsh.yaml diff --git a/src/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf similarity index 100% rename from src/denoising/workflows/run/main.nf rename to src/tasks/denoising/workflows/run/main.nf diff --git a/src/denoising/workflows/run/nextflow.config b/src/tasks/denoising/workflows/run/nextflow.config similarity index 100% rename from src/denoising/workflows/run/nextflow.config rename to src/tasks/denoising/workflows/run/nextflow.config From 4ca76937965e895fff5873c3dd8832adb65c1619 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 11 May 2023 16:49:29 +0200 Subject: [PATCH 0870/1233] relocate multimodal Former-commit-id: e927a2dcf1536a8e842ae9c150188e2650eba2d6 --- .../resources/sample_dataset.h5ad | Bin 137726 -> 0 bytes .../resources/sample_output.h5ad | Bin 159452 -> 0 bytes .../multimodal_data_integration/README.md | 0 .../datasets/datasets_scprep_csv.tsv | 0 .../datasets/sample_dataset/config.vsh.yaml | 0 .../datasets/sample_dataset/script.py | 0 .../datasets/sample_dataset/test.py | 0 .../datasets/scprep_csv/config.vsh.yaml | 0 .../datasets/scprep_csv/script.py | 0 .../datasets/scprep_csv/test.py | 0 .../methods/harmonic_alignment/config.vsh.yaml | 0 .../methods/harmonic_alignment/script.py | 0 .../methods/harmonic_alignment/test.py | 0 .../methods/mnn/config.vsh.yaml | 0 .../methods/mnn/script.R | 0 .../methods/mnn/test.py | 0 .../methods/sample_method/config.vsh.yaml | 0 .../methods/sample_method/script.py | 0 .../methods/sample_method/test.py | 0 .../methods/scot/config.vsh.yaml | 0 .../methods/scot/script.py | 0 .../methods/scot/test.py | 0 .../metrics/knn_auc/config.vsh.yaml | 0 .../metrics/knn_auc/script.py | 0 .../metrics/knn_auc/test.py | 0 .../metrics/mse/config.vsh.yaml | 0 .../metrics/mse/script.py | 0 .../metrics/mse/test.py | 0 .../utils/preprocessing.py | 0 .../multimodal_data_integration/utils/utils.py | 0 .../workflows/run/main.nf | 0 .../workflows/run/nextflow.config | 0 .../workflows/run/run_nextflow.sh | 0 33 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 src/multimodal_data_integration/resources/sample_dataset.h5ad delete mode 100644 src/multimodal_data_integration/resources/sample_output.h5ad rename src/{ => tasks}/multimodal_data_integration/README.md (100%) rename src/{ => tasks}/multimodal_data_integration/datasets/datasets_scprep_csv.tsv (100%) rename src/{ => tasks}/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml (100%) rename src/{ => tasks}/multimodal_data_integration/datasets/sample_dataset/script.py (100%) rename src/{ => tasks}/multimodal_data_integration/datasets/sample_dataset/test.py (100%) rename src/{ => 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tasks}/multimodal_data_integration/workflows/run/main.nf (100%) rename src/{ => tasks}/multimodal_data_integration/workflows/run/nextflow.config (100%) rename src/{ => tasks}/multimodal_data_integration/workflows/run/run_nextflow.sh (100%) diff --git a/src/multimodal_data_integration/resources/sample_dataset.h5ad b/src/multimodal_data_integration/resources/sample_dataset.h5ad deleted file mode 100644 index b23b1beeb8edc1797c734c4a8d4e8b3269ab78b9..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 137726 zcmeEv2S5}@`}ZOWDhl?BfF%+|;ChiJqMnF=5fDKIk>*939KEW<7DZI-2xx2(3kED8 zO+c{#f+AL=DI%bBq;ucQ?JnqX-1)x$hnS{wlWBU1VrYjdO zMgSJqkDsyIkkTROFI*2U7oYz(7+AVkcLmJpYAm}1?EC<;GwiZA+;szoC-Sm!=bgc| zGyLJ{g357w{gD?s@E-|eD6q;t`yGYZ?~l^xJ^9$JqU`tBWE3d2UyQK-u@k@jDq;EG zg|%xq9dZ8|W156KkLi7s1#bxWEnrjxLXS{xSanNf#-YD!k)f1KA^}+y<0rh{;~m*9ECnNwrJ&D*48 zqIp6~0?!|><3&Zh@Da!gOyB5l^?BL5bJ(sfShOPb@`@AFi#Czi1+D-)v-FIY^U{J9 z{5RBR5D8is2-JF0{qAGzv 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z9~VmbwdbOIy*B;vh_BnX`HjtagkPRCx_N46ff_Ns?+&Ed5zfL~nITuXL@ztgnimGWt`hlU-G8JrOKD1SZKe(~o= zhrNp3s_cJv^n)7#%X>UX9~RR(YehnlluduM?e7Jc2 z>aPXwjoWsl;ohiC4caU&{@LBzS%q^SwwXU~_OD%V|6v{b2i1E@^!f+XdvdCuoXO$5 z>~I%P{p26!(jIj@7VucWV*!r^JQnyLw}89+$^7|P^ZLK=_wKtGe_Nh3S;RDe^}VBx z=B@wMYfkx7l^j~RT|4^?(@svsv)}f7^H{)R0gnYd7VucWV}XBx1#;mxrIPor%@9@wv(FXeVfc++?zCQq&@#;*p+o=I5qplSaoD|YVS*E|<~TVyLks|!Ba>q~!C i)_i-sM618Y4K*Hot>@q4#u~Wh1O6WOS3Uk|-~S7 Date: Thu, 11 May 2023 16:50:08 +0200 Subject: [PATCH 0871/1233] relocate label_projection Former-commit-id: 06dd9c9b440d308bf5eef6c19682e7f2a33ae59f --- src/{ => tasks}/label_projection/README.md | 0 src/{ => tasks}/label_projection/api/anndata_prediction.yaml | 0 src/{ => tasks}/label_projection/api/anndata_score.yaml | 0 src/{ => tasks}/label_projection/api/anndata_solution.yaml | 0 src/{ => tasks}/label_projection/api/anndata_test.yaml | 0 src/{ => tasks}/label_projection/api/anndata_train.yaml | 0 src/{ => tasks}/label_projection/api/authors.yaml | 0 src/{ 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tasks}/label_projection/methods/mlp/script.py | 0 src/{ => tasks}/label_projection/methods/scanvi/config.vsh.yaml | 0 src/{ => tasks}/label_projection/methods/scanvi/script.py | 0 .../label_projection/methods/scanvi_scarches/config.vsh.yaml | 0 .../label_projection/methods/scanvi_scarches/script.py | 0 .../label_projection/methods/seurat_transferdata/config.vsh.yaml | 0 .../label_projection/methods/seurat_transferdata/script.R | 0 src/{ => tasks}/label_projection/methods/xgboost/config.vsh.yaml | 0 src/{ => tasks}/label_projection/methods/xgboost/script.py | 0 src/{ => tasks}/label_projection/metrics/accuracy/config.vsh.yaml | 0 src/{ => tasks}/label_projection/metrics/accuracy/script.py | 0 src/{ => tasks}/label_projection/metrics/f1/config.vsh.yaml | 0 src/{ => tasks}/label_projection/metrics/f1/script.py | 0 src/{ => tasks}/label_projection/process_dataset/config.vsh.yaml | 0 src/{ => tasks}/label_projection/process_dataset/script.py | 0 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tasks}/batch_integration/README.md (100%) rename src/{ => tasks}/batch_integration/api/anndata_integrated_embedding.yaml (100%) rename src/{ => tasks}/batch_integration/api/anndata_integrated_feature.yaml (100%) rename src/{ => tasks}/batch_integration/api/anndata_integrated_graph.yaml (100%) rename src/{ => tasks}/batch_integration/api/anndata_score.yaml (100%) rename src/{ => tasks}/batch_integration/api/anndata_unintegrated.yaml (100%) rename src/{ => tasks}/batch_integration/api/authors.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_method_embedding.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_method_feature.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_method_graph.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_metric_embedding.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_metric_feature.yaml (100%) rename src/{ => tasks}/batch_integration/api/comp_metric_graph.yaml (100%) rename src/{ => 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a/src/batch_integration/api/anndata_integrated_embedding.yaml b/src/tasks/batch_integration/api/anndata_integrated_embedding.yaml similarity index 100% rename from src/batch_integration/api/anndata_integrated_embedding.yaml rename to src/tasks/batch_integration/api/anndata_integrated_embedding.yaml diff --git a/src/batch_integration/api/anndata_integrated_feature.yaml b/src/tasks/batch_integration/api/anndata_integrated_feature.yaml similarity index 100% rename from src/batch_integration/api/anndata_integrated_feature.yaml rename to src/tasks/batch_integration/api/anndata_integrated_feature.yaml diff --git a/src/batch_integration/api/anndata_integrated_graph.yaml b/src/tasks/batch_integration/api/anndata_integrated_graph.yaml similarity index 100% rename from src/batch_integration/api/anndata_integrated_graph.yaml rename to src/tasks/batch_integration/api/anndata_integrated_graph.yaml diff --git a/src/batch_integration/api/anndata_score.yaml 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a/src/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml similarity index 100% rename from src/batch_integration/api/comp_method_feature.yaml rename to src/tasks/batch_integration/api/comp_method_feature.yaml diff --git a/src/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml similarity index 100% rename from src/batch_integration/api/comp_method_graph.yaml rename to src/tasks/batch_integration/api/comp_method_graph.yaml diff --git a/src/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml similarity index 100% rename from src/batch_integration/api/comp_metric_embedding.yaml rename to src/tasks/batch_integration/api/comp_metric_embedding.yaml diff --git a/src/batch_integration/api/comp_metric_feature.yaml b/src/tasks/batch_integration/api/comp_metric_feature.yaml similarity index 100% rename from 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b/src/tasks/batch_integration/methods/combat/script.py similarity index 100% rename from src/batch_integration/methods/combat/script.py rename to src/tasks/batch_integration/methods/combat/script.py diff --git a/src/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods/scanorama_embed/config.vsh.yaml rename to src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml diff --git a/src/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py similarity index 100% rename from src/batch_integration/methods/scanorama_embed/script.py rename to src/tasks/batch_integration/methods/scanorama_embed/script.py diff --git a/src/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods/scanorama_feature/config.vsh.yaml rename to src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml diff --git a/src/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py similarity index 100% rename from src/batch_integration/methods/scanorama_feature/script.py rename to src/tasks/batch_integration/methods/scanorama_feature/script.py diff --git a/src/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml similarity index 100% rename from src/batch_integration/methods/scvi/config.vsh.yaml rename to src/tasks/batch_integration/methods/scvi/config.vsh.yaml diff --git a/src/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py similarity index 100% rename from src/batch_integration/methods/scvi/script.py rename to src/tasks/batch_integration/methods/scvi/script.py diff --git a/src/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/asw_batch/config.vsh.yaml rename to src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml diff --git a/src/batch_integration/metrics/asw_batch/script.py b/src/tasks/batch_integration/metrics/asw_batch/script.py similarity index 100% rename from src/batch_integration/metrics/asw_batch/script.py rename to src/tasks/batch_integration/metrics/asw_batch/script.py diff --git a/src/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/asw_label/config.vsh.yaml rename to src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml diff --git a/src/batch_integration/metrics/asw_label/script.py b/src/tasks/batch_integration/metrics/asw_label/script.py similarity index 100% rename from src/batch_integration/metrics/asw_label/script.py rename to src/tasks/batch_integration/metrics/asw_label/script.py diff --git a/src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml rename to src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml diff --git a/src/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py similarity index 100% rename from src/batch_integration/metrics/cell_cycle_conservation/script.py rename to src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py diff --git a/src/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/clustering_overlap/config.vsh.yaml rename to src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml diff --git a/src/batch_integration/metrics/clustering_overlap/script.py b/src/tasks/batch_integration/metrics/clustering_overlap/script.py similarity index 100% rename from src/batch_integration/metrics/clustering_overlap/script.py rename to src/tasks/batch_integration/metrics/clustering_overlap/script.py diff --git a/src/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml similarity index 100% rename from src/batch_integration/metrics/pcr/config.vsh.yaml rename to src/tasks/batch_integration/metrics/pcr/config.vsh.yaml diff --git a/src/batch_integration/metrics/pcr/script.py b/src/tasks/batch_integration/metrics/pcr/script.py similarity index 100% rename from src/batch_integration/metrics/pcr/script.py rename to src/tasks/batch_integration/metrics/pcr/script.py diff --git a/src/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml similarity index 100% rename from src/batch_integration/process_dataset/config.vsh.yaml rename to src/tasks/batch_integration/process_dataset/config.vsh.yaml diff --git a/src/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py similarity index 100% rename from src/batch_integration/process_dataset/script.py rename to src/tasks/batch_integration/process_dataset/script.py diff --git a/src/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh similarity index 100% rename from src/batch_integration/resources_test_scripts/pancreas.sh rename to src/tasks/batch_integration/resources_test_scripts/pancreas.sh diff --git a/src/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml similarity index 100% rename from src/batch_integration/transformers/embed_to_graph/config.vsh.yaml rename to src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml diff --git a/src/batch_integration/transformers/embed_to_graph/script.py b/src/tasks/batch_integration/transformers/embed_to_graph/script.py similarity index 100% rename from src/batch_integration/transformers/embed_to_graph/script.py rename to src/tasks/batch_integration/transformers/embed_to_graph/script.py diff --git a/src/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml similarity index 100% rename from src/batch_integration/transformers/feature_to_embed/config.vsh.yaml rename to src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml diff --git a/src/batch_integration/transformers/feature_to_embed/script.py b/src/tasks/batch_integration/transformers/feature_to_embed/script.py similarity index 100% rename from src/batch_integration/transformers/feature_to_embed/script.py rename to src/tasks/batch_integration/transformers/feature_to_embed/script.py diff --git a/src/batch_integration/workflows/run/config.vsh.yaml b/src/tasks/batch_integration/workflows/run/config.vsh.yaml similarity index 100% rename from src/batch_integration/workflows/run/config.vsh.yaml rename to src/tasks/batch_integration/workflows/run/config.vsh.yaml diff --git a/src/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run/main.nf similarity index 100% rename from src/batch_integration/workflows/run/main.nf rename to src/tasks/batch_integration/workflows/run/main.nf diff --git a/src/batch_integration/workflows/run/nextflow.config b/src/tasks/batch_integration/workflows/run/nextflow.config similarity index 100% rename from src/batch_integration/workflows/run/nextflow.config rename to src/tasks/batch_integration/workflows/run/nextflow.config diff --git a/src/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run/run_nextflow.sh similarity index 100% rename from src/batch_integration/workflows/run/run_nextflow.sh rename to src/tasks/batch_integration/workflows/run/run_nextflow.sh From fefdc50b305be93337b4e7bf847e293b0f0a9f88 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 11 May 2023 17:22:58 +0200 Subject: [PATCH 0874/1233] update paths to inlcude "/tasks/" Former-commit-id: 67e6ad8987ea271ee19e274961ff113ac20546e6 --- src/common/check_dataset_schema/script.py | 2 +- src/common/create_component/config.vsh.yaml | 5 ++--- src/common/create_component/script.py | 4 ++-- src/common/create_component/test.py | 2 +- src/common/get_api_info/script.R | 4 ++-- src/common/get_method_info/script.R | 2 +- src/common/get_metric_info/script.R | 2 +- src/common/get_task_info/script.py | 2 +- 8 files changed, 11 insertions(+), 12 deletions(-) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index a0159c99b7..52d92e936c 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -8,7 +8,7 @@ # The following code has been auto-generated by Viash. par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'schema': 'src/denoising/api/anndata_dataset.yaml', + 'schema': 'src/tasks/denoising/api/anndata_dataset.yaml', 'stop_on_error': False, 'checks': 'output/error.json', 'output': 'output/output.h5ad' diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index c24e1e932a..b8ce762bd0 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -1,4 +1,3 @@ -# TODO: project config is no longer mounted functionality: name: create_component namespace: common @@ -34,7 +33,7 @@ functionality: direction: output # required: true description: Path to the component directory. Suggested location is `src//s/`. - default: src/${VIASH_PAR_TASK}/${VIASH_PAR_TYPE}s/${VIASH_PAR_NAME} + default: src/tasks/${VIASH_PAR_TASK}/${VIASH_PAR_TYPE}s/${VIASH_PAR_NAME} - type: file name: --api_file description: | @@ -42,7 +41,7 @@ functionality: In tasks with different subtypes of method, this location might not exist and you might need to manually specify a different API file to inherit from. # required: true - default: src/${VIASH_PAR_TASK}/api/comp_${VIASH_PAR_TYPE}.yaml + default: src/tasks/${VIASH_PAR_TASK}/api/comp_${VIASH_PAR_TYPE}.yaml - type: file name: --viash_yaml description: | diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 104d86c4b4..c55c03626b 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -14,8 +14,8 @@ 'type': 'method', 'language': 'python', 'name': 'new_comp', - 'output': 'src/denoising/methods/new_comp', - 'api_file': 'src/denoising/api/comp_method.yaml' + 'output': 'src/tasks/denoising/methods/new_comp', + 'api_file': 'src/tasks/denoising/api/comp_method.yaml' } ## VIASH END diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 4598152f78..483133305e 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -10,7 +10,7 @@ ## VIASH END opv2 = f"{meta['resources_dir']}/openproblems-v2" -output_path = f"{opv2}/src/label_projection/methods/test_method" +output_path = f"{opv2}/src/tasks/label_projection/methods/test_method" cmd = [ meta['executable'], diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index 623684225d..abaa718e84 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -9,8 +9,8 @@ par <- list( ) ## VIASH END -comp_yamls <- list.files(paste(par$input, "src", par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste(par$input, "src", par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) +comp_yamls <- list.files(paste(par$input, "src/tasks", par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) +file_yamls <- list.files(paste(par$input, "src/tasks", par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) # list component - file args links comp_file <- map_df(comp_yamls, function(yaml_file) { diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 5287c7d51a..01b7731956 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -11,7 +11,7 @@ par <- list( ns_list <- processx::run( "viash", - c("ns", "list", "-q", "methods", "--src", paste("src", par$task_id, sep = "/")), + c("ns", "list", "-q", "methods", "--src", paste("src/tasks", par$task_id, sep = "/")), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 4693268ab9..c6b85b8a63 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -11,7 +11,7 @@ par <- list( ns_list <- processx::run( "viash", - c("ns", "list", "-q", "metrics", "--src", paste("src", par$task_id, sep = "/")), + c("ns", "list", "-q", "metrics", "--src", paste("src/tasks", par$task_id, sep = "/")), wd = par$input ) configs <- yaml::yaml.load(ns_list$stdout) diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py index 4b906c6e5a..f05eaef7bc 100644 --- a/src/common/get_task_info/script.py +++ b/src/common/get_task_info/script.py @@ -13,7 +13,7 @@ ## VIASH END -task_info_path = path.join(par["input"], "src", par["task_id"], "api", "task_info.yaml") +task_info_path = path.join(par["input"], "src/tasks", par["task_id"], "api", "task_info.yaml") with open(task_info_path, "r") as f: task_info = load(f, Loader=CSafeLoader ) From 2e41e1142ce70ffe25cd45497684450c8998a4d5 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 11 May 2023 17:33:38 +0200 Subject: [PATCH 0875/1233] update changelog Former-commit-id: 3d7120dc7cfe118ebebeae235e57433c90458dd3 --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 978031c939..01fad0ba8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,11 @@ # openproblems-v2 0.1.0 +## general +### MAJOR CHANGES + +* Relocate task directories to new `src/tasks/` location. (PR #142) ## common From 869022ccc7e5ae3a510c4d1af53dfd54af789b05 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 11 May 2023 19:40:11 +0200 Subject: [PATCH 0876/1233] Update CHANGELOG.md Former-commit-id: 769aa54bf5e0cf26a6ce0a64497582062b237024 --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 01fad0ba8c..b1ef20bb08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ ### MAJOR CHANGES -* Relocate task directories to new `src/tasks/` location. (PR #142) +* Relocate task directories to new `src/tasks/` location (PR #142). ## common From 8e1ecb362b7f1c62ff431605add7144bc5688c08 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 May 2023 11:23:57 +0200 Subject: [PATCH 0877/1233] refactor process_dataset components to make use of helper functions (#147) Former-commit-id: d657e692f24e03ee90aab844589cbd6bee5b2814 --- src/common/helper_functions/subset_anndata.py | 83 +++++++++++++++++++ .../process_dataset/config.vsh.yaml | 1 + .../process_dataset/script.py | 73 ++++------------ src/tasks/denoising/process_dataset/script.py | 3 +- .../process_dataset/config.vsh.yaml | 1 + .../process_dataset/script.py | 61 ++------------ .../process_dataset/config.vsh.yaml | 1 + .../process_dataset/script.py | 82 +++++------------- 8 files changed, 130 insertions(+), 175 deletions(-) create mode 100644 src/common/helper_functions/subset_anndata.py diff --git a/src/common/helper_functions/subset_anndata.py b/src/common/helper_functions/subset_anndata.py new file mode 100644 index 0000000000..d183a02525 --- /dev/null +++ b/src/common/helper_functions/subset_anndata.py @@ -0,0 +1,83 @@ +"""Helper functions related to subsetting AnnData objects based on the file format +specifications in the .config.vsh.yaml and slot mapping overrides.""" + +def read_config_slots_info(config_file, slot_mapping = {}): + """Read the .config.vsh.yaml to find out which output slots need to be copied to which output file. + + Arguments: + config_file -- Path to the .config.vsh.yaml file (required). + slot_mapping -- Which slots to retain. Must be a dictionary whose keys are the names + of the AnnData structs, and values is another dictionary with destination value + names as keys and source value names as values. + Example of slot_mapping: + ``` + slot_mapping = { + "layers": { + "counts": par["layer_counts"], + }, + "obs": { + "celltype": par["obs_celltype"], + "batch": par["obs_batch"], + } + } + ``` + """ + import yaml + import re + + # read output spec from yaml + with open(config_file, "r") as object_name: + config = yaml.safe_load(object_name) + + output_struct_slots = {} + + # fetch info on which slots should be copied to which file + for arg in config["functionality"]["arguments"]: + # argument is an output file with a slot specification + if arg["direction"] == "output" and arg.get("info", {}).get("slots"): + object_name = re.sub("--", "", arg["name"]) + + struct_slots = arg['info']['slots'] + out = {} + for (struct, slots) in struct_slots.items(): + out_struct = {} + for slot in slots: + # if slot_mapping[struct][slot['name']] exists, use that as the source slot name + # otherwise use slot['name'] + source_slot = slot_mapping.get(struct, {}).get(slot["name"], slot["name"]) + out_struct[slot["name"]] = source_slot + out[struct] = out_struct + + output_struct_slots[object_name] = out + + return output_struct_slots + +# create new anndata objects according to api spec +def subset_anndata(adata, slot_info): + """Create new anndata object according to slot info specifications. + + Arguments: + adata -- An AnnData object to subset (required) + slot_info -- Which slots to retain, typically one of the items in the output of read_config_slots_info. + Must be a dictionary whose keys are the names of the AnnData structs, and values is another + dictionary with destination value names as keys and source value names as values. + """ + import pandas as pd + import anndata as ad + + structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] + kwargs = {} + + for struct in structs: + slot_mapping = slot_info.get(struct, {}) + data = {dest : getattr(adata, struct)[src] for (dest, src) in slot_mapping.items()} + if len(data) > 0: + if struct in ['obs', 'var']: + data = pd.concat(data, axis=1) + kwargs[struct] = data + elif struct in ['obs', 'var']: + # if no columns need to be copied, we still need an 'obs' and a 'var' + # to help determine the shape of the adata + kwargs[struct] = getattr(adata, struct).iloc[:,[]] + + return ad.AnnData(**kwargs) \ No newline at end of file diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index bf2c5098b4..2eb95f19f0 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -19,6 +19,7 @@ functionality: resources: - type: python_script path: script.py + - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker image: mumichae/scib-base:1.1.3 diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index 1d06456bdf..34bd3f07dd 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -1,8 +1,6 @@ -import anndata as ad +import sys import scib -import yaml -import re -import pandas as pd +import anndata as ad ## VIASH START par = { @@ -13,6 +11,10 @@ meta = {} ## VIASH END +# import helper functions +sys.path.append(meta['resources_dir']) +from subset_anndata import read_config_slots_info, subset_anndata + print('Read input', flush=True) input = ad.read_h5ad(par['input']) @@ -32,66 +34,21 @@ def compute_batched_hvg(adata, n_hvgs): del adata.X return adata - -# read the .config.vsh.yaml to find out which output slots need to be copied to which output file -def read_slots(par, meta): - # read output spec from yaml - with open(meta["config"], "r") as file: - config = yaml.safe_load(file) - - output_struct_slots = {} - - # fetch info on which slots should be copied to which file - for arg in config["functionality"]["arguments"]: - if re.match("--output", arg["name"]): - file = "output" - - struct_slots = arg['info']['slots'] - out = {} - for (struct, slots) in struct_slots.items(): - out[struct] = { slot['name'] : slot['name'] for slot in slots } - - # rename source keys - if 'obs' in out: - if 'label' in out['obs']: - out['obs']['label'] = par['obs_label'] - if 'batch' in out['obs']: - out['obs']['batch'] = par['obs_batch'] - - output_struct_slots[file] = out - - return output_struct_slots - -# create new anndata objects according to api spec -def subset_anndata(adata_sub, slot_info): - structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] - kwargs = {} - - for struct in structs: - slot_mapping = slot_info.get(struct, {}) - data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} - if len(data) > 0: - if struct in ["obs", "var"]: - data = pd.concat(data, axis=1) - kwargs[struct] = data - elif struct in ["obs", "var"]: - # if no columns need to be copied, we still need an "obs" and a "var" - # to help determine the shape of the adata - kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] - - return ad.AnnData(**kwargs) - print(f'Select {par["hvgs"]} highly variable genes', flush=True) adata_with_hvg = compute_batched_hvg(input, n_hvgs=par['hvgs']) print(">> Figuring out which data needs to be copied to which output file", flush=True) -slot_info_per_output = read_slots(par, meta) +# use par arguments to look for label and batch value in different slots +slot_mapping = { + "obs": { + "label": par["obs_label"], + "batch": par["obs_batch"], + } +} +slot_info = read_config_slots_info(meta["config"], slot_mapping) print(">> Create output object", flush=True) -output = subset_anndata( - adata_sub=adata_with_hvg, - slot_info=slot_info_per_output["output"] -) +output = subset_anndata(adata_with_hvg, slot_info["output"]) print('Writing adatas to file', flush=True) output.write(par['output'], compression='gzip') diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index 54c3958bdb..3c817acb63 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -1,7 +1,6 @@ +import sys import anndata as ad import numpy as np -import sys -import scipy.sparse ## VIASH START par = { diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index fae70fcf52..956fcf9cb2 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -4,6 +4,7 @@ functionality: resources: - type: python_script path: script.py + - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker image: "python:3.10" diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index 7981010b6a..b088643f9e 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -1,9 +1,5 @@ +import sys import anndata as ad -import re -import yaml -import random -import pandas as pd -import numpy as np ## VIASH START par = { @@ -17,64 +13,21 @@ } ## VIASH END -# read the .config.vsh.yaml to find out which output slots need to be copied to which output file -def read_slots(par, meta): - # read output spec from yaml - with open(meta["config"], "r") as file: - config = yaml.safe_load(file) - - output_struct_slots = {} - - # fetch info on which slots should be copied to which file - for arg in config["functionality"]["arguments"]: - if re.match("--output_", arg["name"]): - file = re.sub("--output_", "", arg["name"]) - - struct_slots = arg["info"]["slots"] - out = {} - for (struct, slots) in struct_slots.items(): - out[struct] = { slot["name"] : slot["name"] for slot in slots } - - output_struct_slots[file] = out - - return output_struct_slots - -# create new anndata objects according to api spec -def subset_anndata(adata_sub, slot_info): - structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] - kwargs = {} - - for struct in structs: - slot_mapping = slot_info.get(struct, {}) - data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} - if len(data) > 0: - if struct in ["obs", "var"]: - data = pd.concat(data, axis=1) - kwargs[struct] = data - elif struct in ["obs", "var"]: - # if no columns need to be copied, we still need an "obs" and a "var" - # to help determine the shape of the adata - kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] - - return ad.AnnData(**kwargs) +# import helper functions +sys.path.append(meta['resources_dir']) +from subset_anndata import read_config_slots_info, subset_anndata print(">> Load Data", flush=True) adata = ad.read_h5ad(par["input"]) print(">> Figuring out which data needs to be copied to which output file", flush=True) -slot_info_per_output = read_slots(par, meta) +slot_info = read_config_slots_info(meta["config"]) print(">> Creating train data", flush=True) -output_train = subset_anndata( - adata_sub=adata, - slot_info=slot_info_per_output["train"] -) +output_train = subset_anndata(adata, slot_info["output_train"]) print(">> Creating test data", flush=True) -output_test = subset_anndata( - adata_sub=adata, - slot_info=slot_info_per_output["test"] -) +output_test = subset_anndata(adata, slot_info["output_test"]) print(">> Writing", flush=True) output_train.write_h5ad(par["output_train"]) diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 66f8a02cc3..0f41c7b696 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -22,6 +22,7 @@ functionality: resources: - type: python_script path: script.py + - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker image: "python:3.10" diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 6aab6afac5..71584f5d4d 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -1,10 +1,7 @@ -import re -import yaml +import sys import random -import pandas as pd import numpy as np import anndata as ad -# Todo: throw error when not all slots are available? ## VIASH START par = { @@ -18,58 +15,14 @@ 'output_solution': 'solution.h5ad' } meta = { - 'resources_dir': 'src/label_projection/process_dataset', - 'config': 'src/label_projection/process_dataset/.config.vsh.yaml' + 'resources_dir': 'src/tasks/label_projection/process_dataset', + 'config': 'src/tasks/label_projection/process_dataset/.config.vsh.yaml' } ## VIASH END -# read the .config.vsh.yaml to find out which output slots need to be copied to which output file -def read_slots(par, meta): - # read output spec from yaml - with open(meta["config"], "r") as file: - config = yaml.safe_load(file) - - output_struct_slots = {} - - # fetch info on which slots should be copied to which file - for arg in config["functionality"]["arguments"]: - if re.match("--output_", arg["name"]): - file = re.sub("--output_", "", arg["name"]) - - struct_slots = arg['info']['slots'] - out = {} - for (struct, slots) in struct_slots.items(): - out[struct] = { slot['name'] : slot['name'] for slot in slots } - - # rename source keys - if 'obs' in out: - if 'label' in out['obs']: - out['obs']['label'] = par['obs_label'] - if 'batch' in out['obs']: - out['obs']['batch'] = par['obs_batch'] - - output_struct_slots[file] = out - - return output_struct_slots - -# create new anndata objects according to api spec -def subset_anndata(adata_sub, slot_info): - structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"] - kwargs = {} - - for struct in structs: - slot_mapping = slot_info.get(struct, {}) - data = {dest : getattr(adata_sub, struct)[src] for (dest, src) in slot_mapping.items()} - if len(data) > 0: - if struct in ['obs', 'var']: - data = pd.concat(data, axis=1) - kwargs[struct] = data - elif struct in ['obs', 'var']: - # if no columns need to be copied, we still need an 'obs' and a 'var' - # to help determine the shape of the adata - kwargs[struct] = getattr(adata_sub, struct).iloc[:,[]] - - return ad.AnnData(**kwargs) +# import helper functions +sys.path.append(meta['resources_dir']) +from subset_anndata import read_config_slots_info, subset_anndata # set seed if need be if par["seed"]: @@ -78,7 +31,7 @@ def subset_anndata(adata_sub, slot_info): print(">> Load data") adata = ad.read_h5ad(par["input"]) -print("adata:", adata) +print("input:", adata) print(f">> Process data using {par['method']} method") if par["method"] == "batch": @@ -92,24 +45,31 @@ def subset_anndata(adata_sub, slot_info): # subset the different adatas print(">> Figuring which data needs to be copied to which output file") -slot_info_per_output = read_slots(par, meta) +# use par arguments to look for label and batch value in different slots +slot_mapping = { + "obs": { + "label": par["obs_label"], + "batch": par["obs_batch"], + } +} +slot_info = read_config_slots_info(meta["config"], slot_mapping) print(">> Creating train data") output_train = subset_anndata( - adata_sub=adata[[not x for x in is_test]], - slot_info=slot_info_per_output['train'] + adata[[not x for x in is_test]], + slot_info["output_train"] ) print(">> Creating test data") output_test = subset_anndata( - adata_sub=adata[is_test], - slot_info=slot_info_per_output['test'] + adata[is_test], + slot_info["output_test"] ) print(">> Creating solution data") output_solution = subset_anndata( - adata_sub=adata[is_test], - slot_info=slot_info_per_output['solution'] + adata[is_test], + slot_info['output_solution'] ) print(">> Writing data") From 1ae58ccd0c4d99b6610710d6094659c4fc54eec9 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 25 May 2023 11:32:23 +0200 Subject: [PATCH 0878/1233] update baseline to control (#146) * update baseline to control * update changelog * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: cfea96537d354171cab5c7b1e810eee95bbd6945 --- CHANGELOG.md | 4 ++++ src/tasks/denoising/README.md | 2 +- .../denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- src/tasks/denoising/control_methods/no_denoising/script.py | 2 +- .../control_methods/perfect_denoising/config.vsh.yaml | 2 +- .../denoising/control_methods/perfect_denoising/script.py | 2 +- src/tasks/dimensionality_reduction/README.md | 2 +- src/tasks/label_projection/README.md | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 4 ++-- src/tasks/multimodal_data_integration/README.md | 2 +- 10 files changed, 14 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b1ef20bb08..ce4b35e7ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,10 @@ * Relocate task directories to new `src/tasks/` location (PR #142). +### MINOR CHANGES + +* Update "baseline" to "control" (PR #146) + ## common ### NEW FUNCTIONALITY diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 562e5cc45f..39858c3591 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -4,7 +4,7 @@ Structure of this task: src/denoising ├── api Interface specifications for components and datasets in this task - ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked ├── metrics Metrics used to quantify performance of methods ├── README.md This file diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index 3dc526115c..cb8e187352 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: subtype: negative_control pretty_name: No Denoising summary: "negative control by copying train counts" - description: "This baseline method serves as a negative control, where the denoised data is a copy of the unaltered training data. This represents the scoring threshold if denoising was not performed on the data." + description: "This method serves as a negative control, where the denoised data is a copy of the unaltered training data. This represents the scoring threshold if denoising was not performed on the data." v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/tasks/denoising/control_methods/no_denoising/script.py b/src/tasks/denoising/control_methods/no_denoising/script.py index 63a17750aa..f99452c094 100644 --- a/src/tasks/denoising/control_methods/no_denoising/script.py +++ b/src/tasks/denoising/control_methods/no_denoising/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { 'input_train': 'output_train.h5ad', - 'output': 'output_baseline_ND.h5ad', + 'output': 'output_ND.h5ad', } meta = { 'functionality_name': 'foo', diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index fc69898bd7..68f51a8c5c 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: subtype: positive_control pretty_name: Perfect Denoising summary: "Positive control by copying the test counts" - description: "This baseline serves as a positive control, where the test data is copied 1-to-1 to the denoised data. This makes it seem as if the data is perfectly denoised as it will be compared to the test data in the metrics." + description: "This method serves as a positive control, where the test data is copied 1-to-1 to the denoised data. This makes it seem as if the data is perfectly denoised as it will be compared to the test data in the metrics." v1_url: openproblems/tasks/denoising/methods/baseline.py v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: diff --git a/src/tasks/denoising/control_methods/perfect_denoising/script.py b/src/tasks/denoising/control_methods/perfect_denoising/script.py index 251bf87c07..97223c965a 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/script.py +++ b/src/tasks/denoising/control_methods/perfect_denoising/script.py @@ -4,7 +4,7 @@ par = { 'input_train': 'resources_test/denoising/pancreas/train.h5ad', 'input_test': 'resources_test/denoising/pancreas/test.h5ad', - 'output': 'output_baseline_PD.h5ad', + 'output': 'output_PD.h5ad', } meta = { 'functionality_name': 'foo', diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index a9783ea4b2..b34f1807a3 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -4,7 +4,7 @@ Structure of this task: src/dimensionality_reduction ├── api Interface specifications for components and datasets in this task - ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked ├── metrics Metrics used to quantify performance of methods ├── README.md This file diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index e7be28c7b1..342fca1675 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -4,7 +4,7 @@ Structure of this task: src/label_projection ├── api Interface specifications for components and datasets in this task - ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked ├── metrics Metrics used to quantify performance of methods ├── README.md This file diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index c7bf2e855b..c98afb822c 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -4,8 +4,8 @@ functionality: info: subtype: negative_control pretty_name: Majority Vote - summary: "A baseline-type method that predicts all cells to belong to the most abundant cell type in the dataset" - description: "A baseline-type method that predicts all cells to belong to the most abundant cell type in the dataset" + summary: "A control-type method that predicts all cells to belong to the most abundant cell type in the dataset" + description: "A control-type method that predicts all cells to belong to the most abundant cell type in the dataset" v1_url: openproblems/tasks/label_projection/methods/baseline.py v1_commit: b460ecb183328c857cbbf653488f522a4034a61c variants: diff --git a/src/tasks/multimodal_data_integration/README.md b/src/tasks/multimodal_data_integration/README.md index 19b60f3614..26bcd6b907 100644 --- a/src/tasks/multimodal_data_integration/README.md +++ b/src/tasks/multimodal_data_integration/README.md @@ -4,7 +4,7 @@ Structure of this task: src/multimodal_data_integration ├── api Interface specifications for components and datasets in this task - ├── control_methods Baseline (random/ground truth) methods to compare methods against + ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked ├── metrics Metrics used to quantify performance of methods ├── README.md This file From a2a3c24c3978e989d34ec217c1947b72eecce5db Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 May 2023 14:54:59 +0200 Subject: [PATCH 0879/1233] Fix ALRA (#148) Former-commit-id: 70f2e77aa973a3952119ae89572e7b4197f13fff --- src/tasks/denoising/methods/alra/config.vsh.yaml | 3 +-- src/tasks/denoising/methods/alra/script.R | 7 +------ 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index d5ec0cd3c2..c18a2f2945 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -39,8 +39,7 @@ platforms: pip: [ anndata~=0.8.0, pyyaml ] - type: r cran: [ Matrix, anndata, bit64, rsvd ] - - type: docker - run: git clone https://github.com/KlugerLab/ALRA.git /ALRA + github: KlugerLab/ALRA - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/denoising/methods/alra/script.R b/src/tasks/denoising/methods/alra/script.R index 10b311d296..6252cefffd 100644 --- a/src/tasks/denoising/methods/alra/script.R +++ b/src/tasks/denoising/methods/alra/script.R @@ -2,14 +2,9 @@ cat(">> Loading dependencies\n") library(anndata, warn.conflicts = FALSE) library(Matrix, warn.conflicts = FALSE) - -# load alra script from within the Docker container -source("/ALRA/alra.R") +library(ALRA, warn.conflicts = FALSE) ## VIASH START -# load directly from github when testing locally -source("https://raw.githubusercontent.com/KlugerLab/ALRA/master/alra.R") - par <- list( input_train = "resources_test/denoising/pancreas/train.h5ad", # input_train = "resources_test/common/pancreas/dataset.h5ad", From 91edf363916059b98ae88e2e0ef41c2db7a557f3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 May 2023 10:00:06 +0200 Subject: [PATCH 0880/1233] make explicit anndata spec for the common dataset, separate from the knn one (#150) Former-commit-id: 798d643cb7fd5c5bcbfcf1a84fc4cd458449a197 --- src/common/check_dataset_schema/script.py | 2 +- src/datasets/api/anndata_common_dataset.yaml | 9 +++++++++ .../api/{anndata_dataset.yaml => anndata_knn.yaml} | 0 src/datasets/api/comp_processor_knn.yaml | 2 +- .../batch_integration/api/comp_process_dataset.yaml | 2 +- src/tasks/denoising/api/comp_process_dataset.yaml | 2 +- .../api/comp_process_dataset.yaml | 2 +- src/tasks/label_projection/api/comp_process_dataset.yaml | 2 +- 8 files changed, 15 insertions(+), 6 deletions(-) create mode 100644 src/datasets/api/anndata_common_dataset.yaml rename src/datasets/api/{anndata_dataset.yaml => anndata_knn.yaml} (100%) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 52d92e936c..64a1aec674 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -8,7 +8,7 @@ # The following code has been auto-generated by Viash. par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'schema': 'src/tasks/denoising/api/anndata_dataset.yaml', + 'schema': 'src/tasks/denoising/api/anndata_common_dataset.yaml', 'stop_on_error': False, 'checks': 'output/error.json', 'output': 'output/output.h5ad' diff --git a/src/datasets/api/anndata_common_dataset.yaml b/src/datasets/api/anndata_common_dataset.yaml new file mode 100644 index 0000000000..8682bef378 --- /dev/null +++ b/src/datasets/api/anndata_common_dataset.yaml @@ -0,0 +1,9 @@ +__merge__: anndata_knn.yaml +type: file +description: | + A dataset processed by the common dataset processing pipeline. + This dataset contains both raw counts and normalized data matrices, + as well as a PCA embedding, HVG selection and a kNN graph. +example: "/resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common dataset" diff --git a/src/datasets/api/anndata_dataset.yaml b/src/datasets/api/anndata_knn.yaml similarity index 100% rename from src/datasets/api/anndata_dataset.yaml rename to src/datasets/api/anndata_knn.yaml diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index b8c7323711..f75e2afba2 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -8,7 +8,7 @@ functionality: description: Which layer to use as input. - name: "--output" direction: output - __merge__: anndata_dataset.yaml + __merge__: anndata_knn.yaml - name: "--key_added" type: string default: "knn" diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 3dca90c7df..5b1911f8e8 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -4,7 +4,7 @@ functionality: type: process_dataset arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_common_dataset.yaml - name: "--output" __merge__: anndata_unintegrated.yaml direction: output diff --git a/src/tasks/denoising/api/comp_process_dataset.yaml b/src/tasks/denoising/api/comp_process_dataset.yaml index e2af1979e5..566537dfd6 100644 --- a/src/tasks/denoising/api/comp_process_dataset.yaml +++ b/src/tasks/denoising/api/comp_process_dataset.yaml @@ -4,7 +4,7 @@ functionality: type: process_dataset arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_common_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output diff --git a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml index 13f68339a4..85fadac38d 100644 --- a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml @@ -4,7 +4,7 @@ functionality: type: process_dataset arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_common_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output diff --git a/src/tasks/label_projection/api/comp_process_dataset.yaml b/src/tasks/label_projection/api/comp_process_dataset.yaml index 70153f5d47..01331774a2 100644 --- a/src/tasks/label_projection/api/comp_process_dataset.yaml +++ b/src/tasks/label_projection/api/comp_process_dataset.yaml @@ -4,7 +4,7 @@ functionality: type: process_dataset arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_dataset.yaml + __merge__: /src/datasets/api/anndata_common_dataset.yaml - name: "--output_train" __merge__: anndata_train.yaml direction: output From a18db8ad56c0f692c29e6179f1b22cba6c628ee9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 May 2023 10:51:07 +0200 Subject: [PATCH 0881/1233] refactor components Former-commit-id: 4b22882de50bb852931b085b5f31791b1b240d4e --- src/datasets/api/anndata_common_dataset.yaml | 2 +- src/datasets/api/anndata_hvg.yaml | 4 ++-- src/datasets/api/anndata_knn.yaml | 2 +- src/datasets/api/anndata_normalized.yaml | 2 +- src/datasets/api/anndata_pca.yaml | 2 +- src/datasets/api/anndata_raw.yaml | 2 +- src/datasets/api/comp_dataset_loader.yaml | 11 +++++++---- src/datasets/api/comp_normalization.yaml | 1 + src/datasets/api/comp_processor_hvg.yaml | 1 + src/datasets/api/comp_processor_knn.yaml | 1 + src/datasets/api/comp_processor_pca.yaml | 1 + src/datasets/loaders/openproblems_v1/config.vsh.yaml | 1 - src/datasets/normalization/l1_sqrt/config.vsh.yaml | 1 - src/datasets/normalization/log_cpm/config.vsh.yaml | 1 - .../normalization/log_scran_pooling/config.vsh.yaml | 1 - src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 1 - src/datasets/processors/hvg/config.vsh.yaml | 1 - src/datasets/processors/knn/config.vsh.yaml | 1 - src/datasets/processors/pca/config.vsh.yaml | 1 - src/datasets/processors/subsample/config.vsh.yaml | 1 - 20 files changed, 18 insertions(+), 20 deletions(-) diff --git a/src/datasets/api/anndata_common_dataset.yaml b/src/datasets/api/anndata_common_dataset.yaml index 8682bef378..df7dba9736 100644 --- a/src/datasets/api/anndata_common_dataset.yaml +++ b/src/datasets/api/anndata_common_dataset.yaml @@ -4,6 +4,6 @@ description: | A dataset processed by the common dataset processing pipeline. This dataset contains both raw counts and normalized data matrices, as well as a PCA embedding, HVG selection and a kNN graph. -example: "/resources_test/common/pancreas/dataset.h5ad" +example: "resources_test/common/pancreas/dataset.h5ad" info: label: "Common dataset" diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/anndata_hvg.yaml index a49c38a680..ef4d10ce53 100644 --- a/src/datasets/api/anndata_hvg.yaml +++ b/src/datasets/api/anndata_hvg.yaml @@ -1,7 +1,7 @@ __merge__: anndata_pca.yaml type: file -description: "A normalised dataset with a PCA embedding and HVG selection" -example: "dataset.h5ad" +description: "A normalised dataset with a PCA embedding and HVG selection." +example: "resources_test/common/pancreas/hvg.h5ad" info: label: "Dataset+PCA+HVG" slots: diff --git a/src/datasets/api/anndata_knn.yaml b/src/datasets/api/anndata_knn.yaml index b686e89d1f..e158c837d0 100644 --- a/src/datasets/api/anndata_knn.yaml +++ b/src/datasets/api/anndata_knn.yaml @@ -1,7 +1,7 @@ __merge__: anndata_hvg.yaml type: file description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" -example: "/resources_test/common/pancreas/dataset.h5ad" +example: "resources_test/common/pancreas/dataset.h5ad" info: label: "Dataset+PCA+HVG+kNN" slots: diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/anndata_normalized.yaml index 5698abb1f4..4e0f9accf6 100644 --- a/src/datasets/api/anndata_normalized.yaml +++ b/src/datasets/api/anndata_normalized.yaml @@ -1,7 +1,7 @@ __merge__: anndata_raw.yaml type: file description: "A normalized dataset" -example: "dataset.h5ad" +example: "resources_test/common/pancreas/normalized.h5ad" info: label: "Normalized dataset" slots: diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/anndata_pca.yaml index 97c9730e62..9c486190e1 100644 --- a/src/datasets/api/anndata_pca.yaml +++ b/src/datasets/api/anndata_pca.yaml @@ -1,7 +1,7 @@ __merge__: anndata_normalized.yaml type: file description: "A normalised dataset with a PCA embedding" -example: "dataset.h5ad" +example: "resources_test/common/pancreas/pca.h5ad" info: label: "Dataset+PCA" slots: diff --git a/src/datasets/api/anndata_raw.yaml b/src/datasets/api/anndata_raw.yaml index d22d350564..0e41c8269a 100644 --- a/src/datasets/api/anndata_raw.yaml +++ b/src/datasets/api/anndata_raw.yaml @@ -1,6 +1,6 @@ type: file description: "An unprocessed dataset as output by a dataset loader." -example: "raw_dataset.h5ad" +example: "resources_test/common/pancreas/raw.h5ad" info: label: "Raw dataset" slots: diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 1fce66c7fb..18444606cd 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -1,5 +1,8 @@ functionality: - arguments: - - name: "--output" - direction: output - __merge__: anndata_raw.yaml + namespace: "datasets/loaders" + argument_groups: + - name: Outputs + arguments: + - name: "--output" + __merge__: ../../api/anndata_raw.yaml + direction: "output" diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index 0047fd16ba..a13ee25fbe 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "common/normalization" arguments: - name: "--input" __merge__: anndata_raw.yaml diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index c4fc313806..2664784588 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "datasets/processors" arguments: - name: "--input" __merge__: anndata_pca.yaml diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index f75e2afba2..76f496b877 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "datasets/processors" arguments: - name: "--input" __merge__: anndata_hvg.yaml diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index efc9202722..c3c762506a 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -1,4 +1,5 @@ functionality: + namespace: "datasets/processors" arguments: - name: "--input" __merge__: anndata_normalized.yaml diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index fdb8e1d33b..27314caff2 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -1,6 +1,5 @@ functionality: name: "openproblems_v1" - namespace: "datasets/loaders" description: "Fetch a dataset from OpenProblems v1" argument_groups: - name: Inputs diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index af993a4888..f27cf9e0cf 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_normalization.yaml functionality: name: "l1_sqrt" - namespace: "common/normalization" description: | Scaled L1 sqrt normalization. diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 0f29529355..19f3991fed 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_normalization.yaml functionality: name: "log_cpm" - namespace: "datasets/normalization" description: "Normalize data using Log CPM" resources: - type: python_script diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 91d4d414a2..cdd1dadd36 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_normalization.yaml functionality: name: "log_scran_pooling" - namespace: "datasets/normalization" description: "Normalize data using scran pooling" resources: - type: r_script diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 88acda2039..df28ec28e3 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_normalization.yaml functionality: name: "sqrt_cpm" - namespace: "datasets/normalization" description: "Normalize data using Log Sqrt" resources: - type: python_script diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 815c3dfe44..ea03c68d55 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_processor_hvg.yaml functionality: name: "hvg" - namespace: "datasets/processors" description: "Compute HVG" resources: - type: python_script diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 36d13e6b36..82742831b2 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_processor_knn.yaml functionality: name: "knn" - namespace: "datasets/processors" description: "Compute KNN" resources: - type: python_script diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 2b93951da5..d9afa0d838 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_processor_pca.yaml functionality: name: "pca" - namespace: "datasets/processors" description: "Compute PCA" resources: - type: python_script diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index c367830400..20a9e8df9e 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -1,6 +1,5 @@ functionality: name: "subsample" - namespace: "datasets/processors" description: "Subsample an h5ad file" arguments: - name: "--input" From 3bf706089b5f6c0b1ec6d372c4194d5bc33f001e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 May 2023 10:51:32 +0200 Subject: [PATCH 0882/1233] fix namespace Former-commit-id: 87b00d79bd639cda426d1ceba6870fc767600e49 --- src/datasets/api/comp_normalization.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index a13ee25fbe..0f73bba541 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,5 +1,5 @@ functionality: - namespace: "common/normalization" + namespace: "datasets/normalization" arguments: - name: "--input" __merge__: anndata_raw.yaml From f7944ab7b3d2f3cf5452633be0461a417a134d92 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 May 2023 11:05:11 +0200 Subject: [PATCH 0883/1233] fix argument Former-commit-id: 8e4e6bac2fa43a20e4b860c2b1e0b93231a73d58 --- src/datasets/api/comp_dataset_loader.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 18444606cd..f8aa91e027 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -4,5 +4,5 @@ functionality: - name: Outputs arguments: - name: "--output" - __merge__: ../../api/anndata_raw.yaml + __merge__: anndata_raw.yaml direction: "output" From 1e40f78da30e3cd7c840c8bd6880468ee38e4e3f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Sat, 27 May 2023 01:44:16 +0200 Subject: [PATCH 0884/1233] update test scripts (#143) * update test subprocess to print the output * improve assertion messages * use comp_tests in dataset components * remove variants check * check whether preferred_normalization is valid * add assertion messages * sanitize checks * make method/metric config check stricter * update changelog * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt * update assertion messages * update keep_feature in subsample test * update keep_features * update variants check * fix variants check --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: f81c8bcc2d6d434d24c14aedc86f151cd9562de4 --- CHANGELOG.md | 2 + src/common/api/get_info.yaml | 12 +++- src/common/check_dataset_schema/test.py | 27 ++++++--- src/common/comp_tests/check_method_config.py | 39 +++++++++++-- src/common/comp_tests/check_metric_config.py | 12 ++++ src/common/comp_tests/run_and_check_adata.py | 10 +++- src/common/create_component/test.py | 9 ++- src/datasets/api/comp_normalization.yaml | 41 +------------- src/datasets/api/comp_processor_hvg.yaml | 54 +----------------- src/datasets/api/comp_processor_knn.yaml | 7 ++- src/datasets/api/comp_processor_pca.yaml | 6 ++ .../loaders/openproblems_v1/config.vsh.yaml | 3 + src/datasets/loaders/openproblems_v1/test.py | 21 ++++--- .../config.vsh.yaml | 4 +- .../openproblems_v1_multimodal/test.py | 37 ++++++++----- .../normalization/l1_sqrt/config.vsh.yaml | 1 + .../normalization/log_cpm/config.vsh.yaml | 1 + .../log_scran_pooling/config.vsh.yaml | 2 +- .../normalization/sqrt_cpm/config.vsh.yaml | 1 + src/datasets/processors/pca/config.vsh.yaml | 1 + .../processors/subsample/config.vsh.yaml | 1 + .../processors/subsample/test_script.py | 2 +- .../resource_test_scripts/pancreas.sh | 16 +++--- src/migration/check_migration_status/test.py | 11 +++- src/migration/list_git_shas/test.py | 11 +++- .../metrics/rmse/test.py | 55 ------------------- .../metrics/trustworthiness/test.py | 55 ------------------- .../process_dataset/test.py | 54 ------------------ .../methods/scanvi_scarches/config.vsh.yaml | 2 +- .../metrics/accuracy/script.py | 2 +- .../label_projection/metrics/f1/script.py | 2 +- .../datasets/sample_dataset/test.py | 14 +++-- .../datasets/scprep_csv/test.py | 11 +++- .../methods/harmonic_alignment/test.py | 11 +++- .../methods/mnn/test.py | 11 +++- .../methods/sample_method/test.py | 11 +++- .../methods/scot/test.py | 11 +++- .../metrics/knn_auc/test.py | 11 +++- .../metrics/mse/test.py | 11 +++- 39 files changed, 259 insertions(+), 333 deletions(-) delete mode 100644 src/tasks/dimensionality_reduction/metrics/rmse/test.py delete mode 100644 src/tasks/dimensionality_reduction/metrics/trustworthiness/test.py delete mode 100644 src/tasks/dimensionality_reduction/process_dataset/test.py diff --git a/CHANGELOG.md b/CHANGELOG.md index ce4b35e7ea..0a276f1d14 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ ### MINOR CHANGES +* Update test scripts (PR #143) + * Update "baseline" to "control" (PR #146) ## common diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml index 2b83c745d4..eac870dad4 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/api/get_info.yaml @@ -38,11 +38,17 @@ functionality: ] print(">> Running script as test", flush=True) - out = subprocess.run(cmd, capture_output=True, text=True) - print(out.stderr) + out = subprocess.run(cmd, stderr=subprocess.STDOUT) + + if out.stdout: + print(out.stdout) + + if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path) + assert path.exists(output_path), "Output does not exist" print(">> Reading json file", flush=True) with open(output_path, 'r') as f: diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index aad0e7f81e..52a0ed9891 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -7,6 +7,8 @@ input_error_schema = "anndata_error.yaml" output_checks = "checks.json" output_path = "output.h5ad" +output_error_checks = "error_checks.json" +output_error_path = "error_output.h5ad" @@ -60,11 +62,18 @@ ] print(">> Running script as test", flush=True) -subprocess.run(cmd, check=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print(">> Checking whether output file exists", flush=True) -assert path.exists(output_checks) -assert path.exists(output_path) +assert path.exists(output_checks), "Output checks file does not exist" +assert path.exists(output_path), "Output path does not exist" print(">> Reading json file", flush=True) with open(output_checks, 'r') as f: @@ -78,21 +87,21 @@ "--input", input_path, "--schema", input_error_schema, "--stop_on_error", 'true', - "--checks", output_checks, - "--output", output_path, + "--checks", output_error_checks, + "--output", output_error_path, ] print(">> Running script as test", flush=True) out_error = subprocess.run(cmd_error) print(">> Checking whether output file exists", flush=True) -assert path.exists(output_checks) -assert path.exists(output_path) +assert path.exists(output_error_checks), "Output checks file does not exist" +assert path.exists(output_error_path), "Output path does not exist" -assert out_error.returncode == 1 +assert out_error.returncode == 1, "Exit code should be 1" print(">> Reading json file", flush=True) -with open(output_checks, 'r') as f: +with open(output_error_checks, 'r') as f: out = json.load(f) print(out) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 6fc217d1d4..c953ac8ca7 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -9,13 +9,35 @@ ## VIASH END +NAME_MAXLEN = 50 + +SUMMARY_MAXLEN = 400 + +DESCRIPTION_MAXLEN = 1000 + + +def assert_dict(dict, functionality): + + arg_names = [] + args = functionality["arguments"] + + for i in args: + arg_names.append(i["name"].replace("--","")) + + info = functionality["info"] + if dict: + for key in dict: + assert key in arg_names or info, f"{key} is not a defined argument or .functionality.info field" + + + print("Load config data", flush=True) with open(meta["config"], "r") as file: - config = yaml.safe_load(file) + config = yaml.safe_load(file) print("Check general fields", flush=True) -assert "name" in config["functionality"] is not None, "Name not a field or is empty" +assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters." assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" print("Check info fields", flush=True) @@ -25,14 +47,23 @@ assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" assert "pretty_name" in info is not None, "pretty_name not an info field or is empty" assert "summary" in info is not None, "summary not an info field or is empty" +assert "FILL IN:" not in info["summary"], "Summary not filled in" +assert len(info["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.summary) should not exceed {SUMMARY_MAXLEN} characters." assert "description" in info is not None, "description not an info field or is empty" +assert "FILL IN:" not in info["description"], "description not filled in" +assert len(info["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.description) should not exceed {DESCRIPTION_MAXLEN} characters." if ("control" not in info["type"]): assert "reference" in info, "reference not an info field" assert "documentation_url" in info is not None, "documentation_url not an info field or is empty" assert "repository_url" in info is not None, "repository_url not an info field or is empty" -assert "variants" in info, "variants not an info field" -assert "preferred_normalization" in info, "preferred_normalization not an info field" +if "variants" in info: + for key in info["variants"]: + assert_dict(info["variants"][key], config['functionality']) + +assert "preferred_normalization" in info, "preferred_normalization not an info field" +norm_methods = ["log_cpm", "counts", "log_scran_pooling", "sqrt_cpm", "l1_sqrt"] +assert info["preferred_normalization"] in norm_methods, "info['preferred_normalization'] not one of '" + "', '".join(norm_methods) + "'." diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 54508425ab..d03a553f66 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -10,11 +10,22 @@ ## VIASH END +NAME_MAXLEN = 50 + +SUMMARY_MAXLEN = 400 + +DESCRIPTION_MAXLEN = 1000 + def check_metric(metric: Dict[str, str]) -> str: assert "name" in metric is not None, "name not a field or is empty" + assert len(metric["name"]) <= NAME_MAXLEN, f"Component id (.functionality.info.metrics.metric.name) should not exceed {NAME_MAXLEN} characters." assert "pretty_name" in metric is not None, "pretty_name not a field in metric or is empty" assert "summary" in metric is not None, "summary not a field in metric or is empty" + assert "FILL IN:" not in metric["summary"], "Summary not filled in" + assert len(metric["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.metrics.metric.summary) should not exceed {SUMMARY_MAXLEN} characters." assert "description" in metric is not None, "description not a field in metric or is empty" + assert len(metric["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.metrics.metric.description) should not exceed {DESCRIPTION_MAXLEN} characters." + assert "FILL IN:" not in metric["description"], "description not filled in" assert "reference" in metric, "reference not a field in metric" assert "documentation_url" in metric , "documentation_url not a field in metric" assert "repository_url" in metric , "repository_url not an info field" @@ -32,6 +43,7 @@ def check_metric(metric: Dict[str, str]) -> str: print("check general fields", flush=True) assert "name" in config["functionality"] is not None, "Name not a field or is empty" +assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters." assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py index 61d3a8a9db..1bbc11fe1b 100644 --- a/src/common/comp_tests/run_and_check_adata.py +++ b/src/common/comp_tests/run_and_check_adata.py @@ -63,8 +63,14 @@ def check_slots(adata, slot_metadata): assert path.exists(arg["value"]), f"Input file '{arg['value']}' does not exist" print(">> Running script as test", flush=True) -# out = subprocess.run(cmd, check=True, capture_output=True, text=True) -subprocess.run(cmd, check=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print(">> Checking whether output file exists", flush=True) for arg in arguments: diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 483133305e..2aaadfbffe 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -21,7 +21,14 @@ ] print('>> Running the script as test', flush=True) -out = subprocess.run(cmd, check=True, cwd=opv2) +out = subprocess.run(cmd, stderr=subprocess.STDOUT, cwd=opv2) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print('>> Checking whether output files exist', flush=True) assert os.path.exists(output_path), "Output dir does not exist" diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index 0f73bba541..e2f27b86b3 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -15,42 +15,7 @@ functionality: default: "size_factors" description: In which .obs slot to store the size factors (if any). test_resources: - - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_path = "output.h5ad" - output_layer = "norm_layer" - - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path, - "--layer_output", output_layer - ] - - print(">> Running script as test") - out = subprocess.check_output(cmd).decode("utf-8") - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - print("input:", input) - print("output:", output) - - print(">> Checking whether output data structures were added") - assert output_layer in output.layers - - print("Checking whether data from input was copied properly to output") - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index 2664784588..05e757a900 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -24,56 +24,6 @@ functionality: description: "The number of HVG to select" test_resources: - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas - type: python_script - path: generic_test.py - text: | - import anndata as ad - import subprocess - from os import path - import yaml - - input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" - output_path = "output.h5ad" - - cmd = [ - meta['executable'], - "--input", input_path, - "--output", output_path, - ] - - with open(meta["config"], "r") as file: - config = yaml.safe_load(file) - - for arg in config["functionality"]["arguments"]: - if arg['name'] == '--layer_input': - layer_input = arg['default'][0] - cmd += ['--layer_input', layer_input] - elif arg['name'] == '--var_hvg': - var_hvg = arg['default'][0] - cmd += ['--var_hvg', var_hvg] - elif arg['name'] == '--var_hvg_score': - var_hvg_score = arg['default'][0] - cmd += ['--var_hvg_score', var_hvg_score] - - print(">> Running script as test") - out = subprocess.check_output(cmd) - - print(">> Checking whether output file exists") - assert path.exists(output_path) - - print(">> Reading h5ad files") - input = ad.read_h5ad(input_path) - output = ad.read_h5ad(output_path) - print("input:", input) - print("output:", output) - - print(">> Checking whether output data structures were added") - assert layer_input in output.layers - assert var_hvg in output.var - assert var_hvg_score in output.var - - print("Checking whether data from input was copied properly to output") - assert input.n_obs == output.n_obs - assert input.uns["dataset_id"] == output.uns["dataset_id"] - - print("All checks succeeded!") \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 76f496b877..000c167eb3 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -20,4 +20,9 @@ functionality: - name: "--num_neighbors" type: integer default: 15 - description: "The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation." \ No newline at end of file + description: "The size of local neighborhood (in terms of number of neighboring data points) used for manifold approximation." + test_resources: + - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index c3c762506a..73fbb42570 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -26,3 +26,9 @@ functionality: type: integer example: 25 description: Number of principal components to compute. Defaults to 50, or 1 - minimum dimension size of selected representation. + test_resources: + - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 27314caff2..bea378f233 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -73,4 +73,7 @@ platforms: git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems + - type: python + pypi: + - pyyaml - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index ffa018455c..1e50081b06 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -23,11 +23,18 @@ "--dataset_description", "A couple of paragraphs worth of text.", "--dataset_organism", "homo_sapiens", ], - check=True + stderr=subprocess.STDOUT ) +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) + print(">> Checking whether file exists", flush=True) -assert path.exists(output) +assert path.exists(output), "Output does not exist" print(">> Read output anndata", flush=True) adata = ad.read_h5ad(output) @@ -35,12 +42,12 @@ print(adata) print(">> Check that output fits expected API", flush=True) -assert adata.X is None -assert "counts" in adata.layers -assert adata.uns["dataset_id"] == name +assert adata.X is None, "adata.X should be None/empty" +assert "counts" in adata.layers, "Counts layer not found in output layers" +assert adata.uns["dataset_id"] == name, f"Expected {name} as value" if obs_celltype: - assert "celltype" in adata.obs.columns + assert "celltype" in adata.obs.columns, "'celltype' column not found in obs of anndata output" if obs_batch: - assert "batch" in adata.obs.columns + assert "batch" in adata.obs.columns, "'batch' column not found in obs of anndata output" print(">> All tests passed successfully", flush=True) diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index cd16a9de7c..b646135b0b 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -1,6 +1,5 @@ functionality: name: "openproblems_v1_multimodal" - namespace: "datasets/loaders" description: "Fetch a dataset from OpenProblems v1" argument_groups: - name: Inputs @@ -77,4 +76,7 @@ platforms: git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems + - type: python + pypi: + - pyyaml - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1_multimodal/test.py b/src/datasets/loaders/openproblems_v1_multimodal/test.py index 1f22f6732a..e925817baa 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/test.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/test.py @@ -27,12 +27,19 @@ "--dataset_description", "A couple of paragraphs worth of text.", "--dataset_organism", "homo_sapiens", ], - check=True + stderr=subprocess.STDOUT ) +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) + print(">> Checking whether files exist", flush=True) -assert path.exists(output_mod1_file) -assert path.exists(output_mod2_file) +assert path.exists(output_mod1_file), "Output mod1 file does not exist" +assert path.exists(output_mod2_file), "Output mod2 file does not exist" print(">> Read output anndata", flush=True) output_mod1 = ad.read_h5ad(output_mod1_file) @@ -42,25 +49,25 @@ print(f"output_mod2: {output_mod2}", flush=True) print(">> Check that output mod1 fits expected API", flush=True) -assert output_mod1.X is None -assert "counts" in output_mod1.layers -assert output_mod1.uns["dataset_id"] == name +assert output_mod1.X is None, ".X is not None/empty in mod 1 output" +assert "counts" in output_mod1.layers, "'counts' not found in mod 1 output layers" +assert output_mod1.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 1 output uns" if obs_celltype: - assert "celltype" in output_mod1.obs.columns + assert "celltype" in output_mod1.obs.columns, "celltype column not found in mod 1 output obs" if obs_batch: - assert "batch" in output_mod1.obs.columns + assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" if obs_tissue: - assert "tissue" in output_mod1.obs.columns + assert "tissue" in output_mod1.obs.columns, "tissue column not found in mod 1 output obs" print(">> Check that output mod2 fits expected API", flush=True) -assert output_mod2.X is None -assert "counts" in output_mod2.layers -assert output_mod2.uns["dataset_id"] == name +assert output_mod2.X is None, ".X is not None/empty in mod 2 output" +assert "counts" in output_mod2.layers, "'counts' not found in mod 2 output layers" +assert output_mod2.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 2 output uns" if obs_celltype: - assert "celltype" in output_mod2.obs.columns + assert "celltype" in output_mod2.obs.columns, "celltype column not found in mod 2 output obs" if obs_batch: - assert "batch" in output_mod2.obs.columns + assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" if obs_tissue: - assert "tissue" in output_mod2.obs.columns + assert "tissue" in output_mod2.obs.columns, "tissue column not found in mod 2 output obs" print(">> All tests passed successfully", flush=True) diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index f27cf9e0cf..a64bea9eaa 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -23,6 +23,7 @@ platforms: - scprep - "anndata~=0.8.0" - numpy + - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 19f3991fed..0e7de4cb41 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -13,6 +13,7 @@ platforms: packages: - scanpy - "anndata~=0.8.0" + - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index cdd1dadd36..71b4936b3d 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -16,7 +16,7 @@ platforms: - type: apt packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - type: python - pip: [ anndata~=0.8.0, scanpy ] + pip: [ anndata~=0.8.0, scanpy, pyyaml ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index df28ec28e3..ac360fade7 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -13,6 +13,7 @@ platforms: packages: - scanpy - "anndata~=0.8.0" + - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index d9afa0d838..a316372ea2 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -17,4 +17,5 @@ platforms: packages: - scanpy - "anndata~=0.8.0" + - pyyaml - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 20a9e8df9e..ca63a4dd1f 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -58,6 +58,7 @@ platforms: packages: - scanpy - "anndata~=0.8.0" + - pyyaml test_setup: - type: python packages: diff --git a/src/datasets/processors/subsample/test_script.py b/src/datasets/processors/subsample/test_script.py index 2e643205b5..a2e27d29a1 100644 --- a/src/datasets/processors/subsample/test_script.py +++ b/src/datasets/processors/subsample/test_script.py @@ -38,7 +38,7 @@ def test_keep_functionality(run_component): # keep_features = list(input.var_names[:10]) # use genes with high enough expression - keep_features = ["ARHGEF12", "PPM1L", "HMGB2", "NEURL4"] + keep_features = ["ANP32E", "CBX5", "HMGB2", "MAPK13"] run_component([ "--input", input_path, diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 41746677f5..e78f738649 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -39,27 +39,27 @@ viash run src/datasets/processors/subsample/config.vsh.yaml -- \ --keep_celltype_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ --keep_features "$KEEP_FEATURES" \ - --output $DATASET_DIR/temp_dataset0.h5ad \ + --output $DATASET_DIR/raw.h5ad \ --seed 123 # run log cpm normalisation viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset0.h5ad \ - --output $DATASET_DIR/temp_dataset1.h5ad + --input $DATASET_DIR/raw.h5ad \ + --output $DATASET_DIR/normalized.h5ad # run pca viash run src/datasets/processors/pca/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset1.h5ad \ - --output $DATASET_DIR/temp_dataset2.h5ad + --input $DATASET_DIR/normalized.h5ad \ + --output $DATASET_DIR/pca.h5ad # run hvg viash run src/datasets/processors/hvg/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset2.h5ad \ - --output $DATASET_DIR/temp_dataset3.h5ad + --input $DATASET_DIR/pca.h5ad \ + --output $DATASET_DIR/hvg.h5ad # run knn viash run src/datasets/processors/knn/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset3.h5ad \ + --input $DATASET_DIR/hvg.h5ad \ --output $DATASET_DIR/dataset.h5ad rm -r $DATASET_DIR/temp_* \ No newline at end of file diff --git a/src/migration/check_migration_status/test.py b/src/migration/check_migration_status/test.py index 8ea161324e..a782daece8 100644 --- a/src/migration/check_migration_status/test.py +++ b/src/migration/check_migration_status/test.py @@ -14,10 +14,17 @@ ] print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print(">> Checking whether output file exists") -assert path.exists(output_path) +assert path.exists(output_path), "Output does not exist" print(">> Reading json file") with open(output_path, 'r') as f: diff --git a/src/migration/list_git_shas/test.py b/src/migration/list_git_shas/test.py index d9db07ede6..d7bc42a5b0 100644 --- a/src/migration/list_git_shas/test.py +++ b/src/migration/list_git_shas/test.py @@ -12,10 +12,17 @@ ] print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) print(">> Checking whether output file exists") -assert path.exists(output_path) +assert path.exists(output_path), "Output path does not exist" print(">> Reading json file") with open(output_path, 'r') as f: diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/test.py b/src/tasks/dimensionality_reduction/metrics/rmse/test.py deleted file mode 100644 index eeb84c998a..0000000000 --- a/src/tasks/dimensionality_reduction/metrics/rmse/test.py +++ /dev/null @@ -1,55 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -## VIASH START -meta = { - 'executable': './target/docker/dimensionality_reduction/umap', - 'resources_dir': './resources_test/common/pancreas', -} -## VIASH END - -input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" -input_test_path = meta["resources_dir"] + "/input/test.h5ad" -output_path = "score.h5ad" -cmd = [ - meta['executable'], - "--input_reduced", input_reduced_path, - "--input_test", input_test_path, - "--output", output_path, -] - -print(">> Checking whether input files exist") -assert path.exists(input_reduced_path) -assert path.exists(input_test_path) - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input_reduced = ad.read_h5ad(input_reduced_path) -input_test = ad.read_h5ad(input_test_path) -output = ad.read_h5ad(output_path) - -print("input reduced:", input_reduced) -print("input test:", input_test) -print("output:", output) - -print(">> Checking whether metrics were added") -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert meta['functionality_name'] in output.uns["metric_ids"] - -print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'], float) - -print(">> Checking whether data from input was copied properly to output") -assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] -assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] -assert input_reduced.uns["method_id"] == output.uns["method_id"] - - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/test.py b/src/tasks/dimensionality_reduction/metrics/trustworthiness/test.py deleted file mode 100644 index eeb84c998a..0000000000 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/test.py +++ /dev/null @@ -1,55 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -## VIASH START -meta = { - 'executable': './target/docker/dimensionality_reduction/umap', - 'resources_dir': './resources_test/common/pancreas', -} -## VIASH END - -input_reduced_path = meta["resources_dir"] + "/input/reduced.h5ad" -input_test_path = meta["resources_dir"] + "/input/test.h5ad" -output_path = "score.h5ad" -cmd = [ - meta['executable'], - "--input_reduced", input_reduced_path, - "--input_test", input_test_path, - "--output", output_path, -] - -print(">> Checking whether input files exist") -assert path.exists(input_reduced_path) -assert path.exists(input_test_path) - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output file exists") -assert path.exists(output_path) - -print(">> Reading h5ad files") -input_reduced = ad.read_h5ad(input_reduced_path) -input_test = ad.read_h5ad(input_test_path) -output = ad.read_h5ad(output_path) - -print("input reduced:", input_reduced) -print("input test:", input_test) -print("output:", output) - -print(">> Checking whether metrics were added") -assert "metric_ids" in output.uns -assert "metric_values" in output.uns -assert meta['functionality_name'] in output.uns["metric_ids"] - -print(">> Checking whether metrics are float") -assert isinstance(output.uns['metric_values'], float) - -print(">> Checking whether data from input was copied properly to output") -assert input_reduced.uns["dataset_id"] == output.uns["dataset_id"] -assert input_reduced.uns["normalization_id"] == output.uns["normalization_id"] -assert input_reduced.uns["method_id"] == output.uns["method_id"] - - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/process_dataset/test.py b/src/tasks/dimensionality_reduction/process_dataset/test.py deleted file mode 100644 index ddf8e3f608..0000000000 --- a/src/tasks/dimensionality_reduction/process_dataset/test.py +++ /dev/null @@ -1,54 +0,0 @@ -import anndata as ad -import subprocess -from os import path - -## VIASH START -meta = { - 'executable': './target/docker/dimensionality_reduction/', - 'resources_dir': './resources_test/common/', -} -## VIASH END - -input_path = meta["resources_dir"] + "/input/dataset.h5ad" -output_train_path = "train.h5ad" -output_test_path = "test.h5ad" -cmd = [ - meta['executable'], - "--input", input_path, - "--output_train", output_train_path, - "--output_test", output_test_path -] - -print(">> Checking whether input file exists") -assert path.exists(input_path) - -print(">> Running script as test") -out = subprocess.run(cmd, check=True, capture_output=True, text=True) - -print(">> Checking whether output files exist") -assert path.exists(output_train_path) -assert path.exists(output_test_path) - -print(">> Reading h5ad files") -input = ad.read_h5ad(input_path) -output_train = ad.read_h5ad(output_train_path) -output_test = ad.read_h5ad(output_test_path) - -print("input:", input) -print("output_train:", output_train) -print("output_test:", output_test) - -print(">> Checking whether data from input was copied properly to output") -assert input.n_obs == output_train.n_obs -assert input.n_obs == output_test.n_obs -assert input.uns["dataset_id"] == output_train.uns["dataset_id"] -assert input.uns["dataset_id"] == output_test.uns["dataset_id"] - - -print(">> Check whether certain slots exist") -assert "counts" in output_train.layers -assert "normalized" in output_train.layers -assert 'hvg_score' in output_train.var -assert "counts" in output_test.layers - -print("All checks succeeded!") \ No newline at end of file diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index e6df0a1bb7..93b886c06c 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: reference: lotfollahi2020query documentation_url: https://docs.scvi-tools.org repository_url: https://github.com/scverse/scvi-tools - preferred_normalization: none + preferred_normalization: counts variants: scanvi_scarches: diff --git a/src/tasks/label_projection/metrics/accuracy/script.py b/src/tasks/label_projection/metrics/accuracy/script.py index 93002ee4e2..e368649828 100644 --- a/src/tasks/label_projection/metrics/accuracy/script.py +++ b/src/tasks/label_projection/metrics/accuracy/script.py @@ -17,7 +17,7 @@ input_prediction = ad.read_h5ad(par['input_prediction']) input_solution = ad.read_h5ad(par['input_solution']) -assert (input_prediction.obs_names == input_solution.obs_names).all() +assert (input_prediction.obs_names == input_solution.obs_names).all(), "obs_names not the same in prediction and solution inputs" print("Encode labels") cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) diff --git a/src/tasks/label_projection/metrics/f1/script.py b/src/tasks/label_projection/metrics/f1/script.py index 58a68341b4..856bdc9784 100644 --- a/src/tasks/label_projection/metrics/f1/script.py +++ b/src/tasks/label_projection/metrics/f1/script.py @@ -18,7 +18,7 @@ input_prediction = ad.read_h5ad(par['input_prediction']) input_solution = ad.read_h5ad(par['input_solution']) -assert (input_prediction.obs_names == input_solution.obs_names).all() +assert (input_prediction.obs_names == input_solution.obs_names).all(), "obs_names not the same in prediction and solution inputs" print("Encode labels") cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py b/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py index ca12a259dc..48cf0d26a9 100644 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py +++ b/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py @@ -26,16 +26,20 @@ # check dataset id assert "dataset_id" in adata.uns - - - print(">> Running sample_dataset with different args") -out = subprocess.check_output([ +out = subprocess.run([ "./sample_dataset", "--output", "output.h5ad", "--n_cells", "100", "--n_genes", "200" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py b/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py index ff07391c6b..34239ee5fa 100644 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py +++ b/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py @@ -14,13 +14,20 @@ print(">> Running scprep_csv") -out = subprocess.check_output([ +out = subprocess.run([ "./scprep_csv", "--id", "footest", "--input1", "adt_umi.csv.gz", "--input2", "adt_umi.csv.gz", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py index aa8324b3e5..bd4546076d 100644 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py +++ b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py @@ -5,11 +5,18 @@ import scanpy as sc print(">> Running harmonic_alignment") -out = subprocess.check_output([ +out = subprocess.run([ "./harmonic_alignment", "--input", "sample_dataset.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/methods/mnn/test.py b/src/tasks/multimodal_data_integration/methods/mnn/test.py index 00d8db5b15..cc8f323e4d 100644 --- a/src/tasks/multimodal_data_integration/methods/mnn/test.py +++ b/src/tasks/multimodal_data_integration/methods/mnn/test.py @@ -5,11 +5,18 @@ import scanpy as sc print(">> Running mnn") -out = subprocess.check_output([ +out = subprocess.run([ "./mnn", "--input", "sample_dataset.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/test.py b/src/tasks/multimodal_data_integration/methods/sample_method/test.py index 473ea8541e..441788774c 100644 --- a/src/tasks/multimodal_data_integration/methods/sample_method/test.py +++ b/src/tasks/multimodal_data_integration/methods/sample_method/test.py @@ -5,11 +5,18 @@ import scanpy as sc print(">> Running sample_method") -out = subprocess.check_output([ +out = subprocess.run([ "./sample_method", "--input", "sample_dataset.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/methods/scot/test.py b/src/tasks/multimodal_data_integration/methods/scot/test.py index 492c50743c..9d13e54dfb 100644 --- a/src/tasks/multimodal_data_integration/methods/scot/test.py +++ b/src/tasks/multimodal_data_integration/methods/scot/test.py @@ -5,11 +5,18 @@ import scanpy as sc print(">> Running scot") -out = subprocess.check_output([ +out = subprocess.run([ "./scot", "--input", "sample_dataset.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py b/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py index d4bd11a563..fe64c05c7c 100644 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py +++ b/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py @@ -6,11 +6,18 @@ import numpy as np print(">> Running knn_auc") -out = subprocess.check_output([ +out = subprocess.run([ "./knn_auc", "--input", "sample_output.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") diff --git a/src/tasks/multimodal_data_integration/metrics/mse/test.py b/src/tasks/multimodal_data_integration/metrics/mse/test.py index 3bdf2899be..557e72537f 100644 --- a/src/tasks/multimodal_data_integration/metrics/mse/test.py +++ b/src/tasks/multimodal_data_integration/metrics/mse/test.py @@ -6,11 +6,18 @@ import numpy as np print(">> Running mse") -out = subprocess.check_output([ +out = subprocess.run([ "./mse", "--input", "sample_output.h5ad", "--output", "output.h5ad" -]).decode("utf-8") +], stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.") + exit(out.returncode) print(">> Checking whether file exists") assert path.exists("output.h5ad") From 7067e2e3ba95a62c5884be4ebb909cbb54647233 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 05:00:36 +0200 Subject: [PATCH 0885/1233] Add note to viash code block (#156) * Add note to viash code block * Update script.py Former-commit-id: be91470d02c3218f339ceb051b17f44540a7db53 --- src/common/create_component/script.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index c55c03626b..143f28969b 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -274,6 +274,8 @@ def create_python_script(par, config, type): |import anndata as ad | |## VIASH START + |# Note: this section is auto-generated by viash at runtime. To edit it, make changes + |# in config.vsh.yaml and then run `viash config inject config.vsh.yaml`. |par = {{ | {par_string} |}} @@ -436,4 +438,4 @@ def main(par): if __name__ == "__main__": - main(par) \ No newline at end of file + main(par) From b8b4c20622558084482b6ffa5229427d5b6c5b5a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 05:40:12 +0200 Subject: [PATCH 0886/1233] Add type info metadata to the API files (#157) * add type info metadata to the dataset api files * add type information for tasks Former-commit-id: 29f35a777aff0d1ab31a4dbc3f82519c1e58df24 --- src/datasets/api/README.md | 8 ++++++++ src/datasets/api/README.qmd | 8 ++++++++ src/datasets/api/comp_dataset_loader.yaml | 6 ++++++ src/datasets/api/comp_normalization.yaml | 5 +++++ src/datasets/api/comp_processor_hvg.yaml | 5 +++++ src/datasets/api/comp_processor_knn.yaml | 5 +++++ src/datasets/api/comp_processor_pca.yaml | 5 +++++ src/datasets/api/comp_processor_subset.yaml | 19 +++++++++++++++++++ .../processors/subsample/config.vsh.yaml | 13 +------------ src/tasks/batch_integration/api/README.md | 8 ++++++++ src/tasks/batch_integration/api/README.qmd | 8 ++++++++ .../api/comp_method_embedding.yaml | 4 ++++ .../api/comp_method_feature.yaml | 4 ++++ .../api/comp_method_graph.yaml | 4 ++++ .../api/comp_metric_embedding.yaml | 4 ++++ .../api/comp_metric_feature.yaml | 4 ++++ .../api/comp_metric_graph.yaml | 4 ++++ .../api/comp_process_dataset.yaml | 4 ++++ src/tasks/denoising/api/README.md | 8 ++++++++ src/tasks/denoising/api/README.qmd | 8 ++++++++ .../denoising/api/comp_control_method.yaml | 9 +++++++++ src/tasks/denoising/api/comp_method.yaml | 4 ++++ src/tasks/denoising/api/comp_metric.yaml | 4 ++++ .../denoising/api/comp_process_dataset.yaml | 4 ++++ .../dimensionality_reduction/api/README.md | 8 ++++++++ .../dimensionality_reduction/api/README.qmd | 8 ++++++++ .../api/comp_control_method.yaml | 9 +++++++++ .../api/comp_method.yaml | 5 +++++ .../api/comp_metric.yaml | 4 ++++ .../api/comp_process_dataset.yaml | 4 ++++ src/tasks/label_projection/api/README.md | 8 ++++++++ src/tasks/label_projection/api/README.qmd | 8 ++++++++ .../api/comp_control_method.yaml | 9 +++++++++ .../label_projection/api/comp_method.yaml | 5 +++++ .../label_projection/api/comp_metric.yaml | 4 ++++ .../api/comp_process_dataset.yaml | 4 ++++ 36 files changed, 219 insertions(+), 12 deletions(-) create mode 100644 src/datasets/api/README.md create mode 100644 src/datasets/api/README.qmd create mode 100644 src/datasets/api/comp_processor_subset.yaml create mode 100644 src/tasks/batch_integration/api/README.md create mode 100644 src/tasks/batch_integration/api/README.qmd create mode 100644 src/tasks/denoising/api/README.md create mode 100644 src/tasks/denoising/api/README.qmd create mode 100644 src/tasks/dimensionality_reduction/api/README.md create mode 100644 src/tasks/dimensionality_reduction/api/README.qmd create mode 100644 src/tasks/label_projection/api/README.md create mode 100644 src/tasks/label_projection/api/README.qmd diff --git a/src/datasets/api/README.md b/src/datasets/api/README.md new file mode 100644 index 0000000000..7c3b9c8d87 --- /dev/null +++ b/src/datasets/api/README.md @@ -0,0 +1,8 @@ +# Component and file format specifications + +This folder contains specifications for file formats and component +interfaces. + +These are not only used for documentation (i.e. to document the file +format of inputs and outputs of a component), but also for unit testing +and validation of output files. diff --git a/src/datasets/api/README.qmd b/src/datasets/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/datasets/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index f8aa91e027..ed5c8a0552 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -1,5 +1,11 @@ functionality: namespace: "datasets/loaders" + info: + type_info: + label: Dataset loader + description: | + A component which generates a "Common dataset". A dataset loader will typically have an identifier (e.g. a GEO identifier) + or URL as input argument and additional arguments to define where the script needs to download a dataset from and how to process it. argument_groups: - name: Outputs arguments: diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index e2f27b86b3..ee748eb6ec 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,5 +1,10 @@ functionality: namespace: "datasets/normalization" + info: + type_info: + label: Dataset normalization + description: | + A normalization method which processes the raw counts output by a dataset loader. arguments: - name: "--input" __merge__: anndata_raw.yaml diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index 05e757a900..b17530d8d6 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,5 +1,10 @@ functionality: namespace: "datasets/processors" + info: + type_info: + label: HVG + description: | + Computes the highly variable genes scores. arguments: - name: "--input" __merge__: anndata_pca.yaml diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 000c167eb3..540e16824e 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -1,5 +1,10 @@ functionality: namespace: "datasets/processors" + info: + type_info: + label: KNN + description: | + Computes the k-nearest-neighbours for each cell. arguments: - name: "--input" __merge__: anndata_hvg.yaml diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index 73fbb42570..8ed4f4bc38 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -1,5 +1,10 @@ functionality: namespace: "datasets/processors" + info: + type_info: + label: PCA + description: | + Computes a PCA embedding of the normalized data. arguments: - name: "--input" __merge__: anndata_normalized.yaml diff --git a/src/datasets/api/comp_processor_subset.yaml b/src/datasets/api/comp_processor_subset.yaml new file mode 100644 index 0000000000..ef241bb635 --- /dev/null +++ b/src/datasets/api/comp_processor_subset.yaml @@ -0,0 +1,19 @@ +functionality: + namespace: "datasets/processors" + info: + type_info: + label: Subset + description: | + Subset a common dataset + arguments: + - name: "--input" + __merge__: anndata_common_dataset.yaml + - name: "--output" + __merge__: anndata_common_dataset.yaml + direction: output + test_resources: + - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index ca63a4dd1f..0083f0cc80 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -1,12 +1,8 @@ +__merge__: ../../api/comp_processor_subset.yaml functionality: name: "subsample" description: "Subsample an h5ad file" arguments: - - name: "--input" - type: "file" - description: "Input data to be resized" - required: true - example: input.h5ad - name: "--n_obs" type: integer description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. @@ -32,13 +28,6 @@ functionality: - name: "--even" type: "boolean_true" description: Subsample evenly from different batches - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - example: "output.h5ad" - description: "Output h5ad file" - required: true - name: "--seed" type: "integer" description: "A seed for the subsampling." diff --git a/src/tasks/batch_integration/api/README.md b/src/tasks/batch_integration/api/README.md new file mode 100644 index 0000000000..7c3b9c8d87 --- /dev/null +++ b/src/tasks/batch_integration/api/README.md @@ -0,0 +1,8 @@ +# Component and file format specifications + +This folder contains specifications for file formats and component +interfaces. + +These are not only used for documentation (i.e. to document the file +format of inputs and outputs of a component), but also for unit testing +and validation of output files. diff --git a/src/tasks/batch_integration/api/README.qmd b/src/tasks/batch_integration/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/tasks/batch_integration/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/batch_integration/api/comp_method_embedding.yaml b/src/tasks/batch_integration/api/comp_method_embedding.yaml index a3e2e87ff2..4bc61014f2 100644 --- a/src/tasks/batch_integration/api/comp_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_method_embedding.yaml @@ -3,6 +3,10 @@ functionality: info: type: method output_type: embedding + type_info: + label: Method (embedding) + description: | + A batch integration method which outputs a batch-corrected embedding. arguments: - name: --input __merge__: anndata_unintegrated.yaml diff --git a/src/tasks/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml index 94984233a8..e194cad097 100644 --- a/src/tasks/batch_integration/api/comp_method_feature.yaml +++ b/src/tasks/batch_integration/api/comp_method_feature.yaml @@ -3,6 +3,10 @@ functionality: info: type: method output_type: feature + type_info: + label: Method (feature) + description: | + A batch integration method which outputs a batch-corrected feature-space. arguments: - __merge__: anndata_unintegrated.yaml name: --input diff --git a/src/tasks/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml index dfb00f40e0..cefb9464e1 100644 --- a/src/tasks/batch_integration/api/comp_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_method_graph.yaml @@ -3,6 +3,10 @@ functionality: info: type: method output_type: graph + type_info: + label: Method (graph) + description: | + A batch integration method which outputs a batch-corrected cell graphs. arguments: - __merge__: anndata_unintegrated.yaml name: --input diff --git a/src/tasks/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml index 384f3abb58..586678b98a 100644 --- a/src/tasks/batch_integration/api/comp_metric_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_metric_embedding.yaml @@ -2,6 +2,10 @@ functionality: namespace: batch_integration/metrics info: type: metric + type_info: + label: Metric (embedding) + description: | + A metric for evaluating batch corrected embeddings. arguments: - name: --input_integrated __merge__: anndata_integrated_embedding.yaml diff --git a/src/tasks/batch_integration/api/comp_metric_feature.yaml b/src/tasks/batch_integration/api/comp_metric_feature.yaml index 32ac928477..bf27c747a4 100644 --- a/src/tasks/batch_integration/api/comp_metric_feature.yaml +++ b/src/tasks/batch_integration/api/comp_metric_feature.yaml @@ -2,6 +2,10 @@ functionality: namespace: batch_integration/metrics info: type: metric + type_info: + label: Metric (feature) + description: | + A metric for evaluating batch corrected feature spaces. arguments: - name: --input_integrated __merge__: anndata_integrated_feature.yaml diff --git a/src/tasks/batch_integration/api/comp_metric_graph.yaml b/src/tasks/batch_integration/api/comp_metric_graph.yaml index fbc05334e8..707c26c3e1 100644 --- a/src/tasks/batch_integration/api/comp_metric_graph.yaml +++ b/src/tasks/batch_integration/api/comp_metric_graph.yaml @@ -2,6 +2,10 @@ functionality: namespace: batch_integration/metrics info: type: metric + type_info: + label: Metric (graph) + description: | + A metric for evaluating batch corrected cell graphs. arguments: - name: --input_integrated __merge__: anndata_integrated_graph.yaml diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 5b1911f8e8..5c79ba3a56 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -2,6 +2,10 @@ functionality: namespace: batch_integration info: type: process_dataset + type_info: + label: Data processor + description: | + Prepare a common dataset for the batch integration task. arguments: - name: "--input" __merge__: /src/datasets/api/anndata_common_dataset.yaml diff --git a/src/tasks/denoising/api/README.md b/src/tasks/denoising/api/README.md new file mode 100644 index 0000000000..7c3b9c8d87 --- /dev/null +++ b/src/tasks/denoising/api/README.md @@ -0,0 +1,8 @@ +# Component and file format specifications + +This folder contains specifications for file formats and component +interfaces. + +These are not only used for documentation (i.e. to document the file +format of inputs and outputs of a component), but also for unit testing +and validation of output files. diff --git a/src/tasks/denoising/api/README.qmd b/src/tasks/denoising/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/tasks/denoising/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/denoising/api/comp_control_method.yaml b/src/tasks/denoising/api/comp_control_method.yaml index b97b38c358..bad0d9da3f 100644 --- a/src/tasks/denoising/api/comp_control_method.yaml +++ b/src/tasks/denoising/api/comp_control_method.yaml @@ -2,6 +2,15 @@ functionality: namespace: "denoising/control_methods" info: type: control_method + type_info: + label: Control method + description: | + This folder contains control components for the task. + These components have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/tasks/denoising/api/comp_method.yaml b/src/tasks/denoising/api/comp_method.yaml index 7dc5c0e4b9..288a1f4cf2 100644 --- a/src/tasks/denoising/api/comp_method.yaml +++ b/src/tasks/denoising/api/comp_method.yaml @@ -2,6 +2,10 @@ functionality: namespace: "denoising/methods" info: type: method + type_info: + label: Method + description: | + A denoising method to remove noise (i.e. technical artifacts) from a dataset. arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/tasks/denoising/api/comp_metric.yaml b/src/tasks/denoising/api/comp_metric.yaml index 8c608ae3d5..5dbe2b8241 100644 --- a/src/tasks/denoising/api/comp_metric.yaml +++ b/src/tasks/denoising/api/comp_metric.yaml @@ -2,6 +2,10 @@ functionality: namespace: "denoising/metrics" info: type: metric + type_info: + label: Metric + description: | + A metric for evaluating denoised datasets. arguments: - name: "--input_test" __merge__: anndata_test.yaml diff --git a/src/tasks/denoising/api/comp_process_dataset.yaml b/src/tasks/denoising/api/comp_process_dataset.yaml index 566537dfd6..c55115f92b 100644 --- a/src/tasks/denoising/api/comp_process_dataset.yaml +++ b/src/tasks/denoising/api/comp_process_dataset.yaml @@ -2,6 +2,10 @@ functionality: namespace: "denoising" info: type: process_dataset + type_info: + label: Data processor + description: | + Prepare a common dataset for the denoising task. arguments: - name: "--input" __merge__: /src/datasets/api/anndata_common_dataset.yaml diff --git a/src/tasks/dimensionality_reduction/api/README.md b/src/tasks/dimensionality_reduction/api/README.md new file mode 100644 index 0000000000..7c3b9c8d87 --- /dev/null +++ b/src/tasks/dimensionality_reduction/api/README.md @@ -0,0 +1,8 @@ +# Component and file format specifications + +This folder contains specifications for file formats and component +interfaces. + +These are not only used for documentation (i.e. to document the file +format of inputs and outputs of a component), but also for unit testing +and validation of output files. diff --git a/src/tasks/dimensionality_reduction/api/README.qmd b/src/tasks/dimensionality_reduction/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/tasks/dimensionality_reduction/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml index b2b2958d32..f8b04891a7 100644 --- a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml @@ -2,6 +2,15 @@ functionality: namespace: dimensionality_reduction/control_methods info: type: control_method + type_info: + label: Control method + description: | + This folder contains control components for the task. + These components have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. arguments: - name: "--input" __merge__: anndata_train.yaml diff --git a/src/tasks/dimensionality_reduction/api/comp_method.yaml b/src/tasks/dimensionality_reduction/api/comp_method.yaml index 9a7764d81b..c20650841b 100644 --- a/src/tasks/dimensionality_reduction/api/comp_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_method.yaml @@ -2,6 +2,11 @@ functionality: namespace: dimensionality_reduction/methods info: type: method + type_info: + label: Method + description: | + A dimensionality reduction method to summarise the biological information in + a dataset in as few dimensions as possible. arguments: - name: "--input" __merge__: anndata_train.yaml diff --git a/src/tasks/dimensionality_reduction/api/comp_metric.yaml b/src/tasks/dimensionality_reduction/api/comp_metric.yaml index d056eb80dc..cc8da44ac6 100644 --- a/src/tasks/dimensionality_reduction/api/comp_metric.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_metric.yaml @@ -2,6 +2,10 @@ functionality: namespace: dimensionality_reduction/metrics info: type: metric + type_info: + label: Metric + description: | + A metric for evaluating dimensionality reductions. arguments: - name: "--input_reduced" __merge__: anndata_reduced.yaml diff --git a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml index 85fadac38d..e552fadeb7 100644 --- a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml @@ -2,6 +2,10 @@ functionality: namespace: dimensionality_reduction info: type: process_dataset + type_info: + label: Data processor + description: | + Prepare a common dataset for the denoising task. arguments: - name: "--input" __merge__: /src/datasets/api/anndata_common_dataset.yaml diff --git a/src/tasks/label_projection/api/README.md b/src/tasks/label_projection/api/README.md new file mode 100644 index 0000000000..7c3b9c8d87 --- /dev/null +++ b/src/tasks/label_projection/api/README.md @@ -0,0 +1,8 @@ +# Component and file format specifications + +This folder contains specifications for file formats and component +interfaces. + +These are not only used for documentation (i.e. to document the file +format of inputs and outputs of a component), but also for unit testing +and validation of output files. diff --git a/src/tasks/label_projection/api/README.qmd b/src/tasks/label_projection/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/tasks/label_projection/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/label_projection/api/comp_control_method.yaml b/src/tasks/label_projection/api/comp_control_method.yaml index 4aa8e9b732..ebdd3ebdd5 100644 --- a/src/tasks/label_projection/api/comp_control_method.yaml +++ b/src/tasks/label_projection/api/comp_control_method.yaml @@ -2,6 +2,15 @@ functionality: namespace: "label_projection/control_methods" info: type: control_method + type_info: + label: Control method + description: | + This folder contains control components for the task. + These components have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/tasks/label_projection/api/comp_method.yaml b/src/tasks/label_projection/api/comp_method.yaml index 23e655b38a..2a7ed0f2a0 100644 --- a/src/tasks/label_projection/api/comp_method.yaml +++ b/src/tasks/label_projection/api/comp_method.yaml @@ -2,6 +2,11 @@ functionality: namespace: "label_projection/methods" info: type: method + type_info: + label: Method + description: | + A label projection method to predict the labels of a new "test" + dataset based on an annotated "training" dataset. arguments: - name: "--input_train" __merge__: anndata_train.yaml diff --git a/src/tasks/label_projection/api/comp_metric.yaml b/src/tasks/label_projection/api/comp_metric.yaml index 21ebc5534a..053e5fa15e 100644 --- a/src/tasks/label_projection/api/comp_metric.yaml +++ b/src/tasks/label_projection/api/comp_metric.yaml @@ -2,6 +2,10 @@ functionality: namespace: "label_projection/metrics" info: type: metric + type_info: + label: Metric + description: | + A metric for evaluating predicted labels. arguments: - name: "--input_solution" __merge__: anndata_solution.yaml diff --git a/src/tasks/label_projection/api/comp_process_dataset.yaml b/src/tasks/label_projection/api/comp_process_dataset.yaml index 01331774a2..2598d6d6ac 100644 --- a/src/tasks/label_projection/api/comp_process_dataset.yaml +++ b/src/tasks/label_projection/api/comp_process_dataset.yaml @@ -2,6 +2,10 @@ functionality: namespace: "label_projection" info: type: process_dataset + type_info: + label: Data processor + description: | + Prepare a common dataset for the label prediction task. arguments: - name: "--input" __merge__: /src/datasets/api/anndata_common_dataset.yaml From f8e100c32e096df18a8c536c1ff900b9b92ff3f3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 28 May 2023 06:24:07 +0200 Subject: [PATCH 0887/1233] Bump tj-actions/changed-files from 35.9.2 to 36.0.6 (#155) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 35.9.2 to 36.0.6. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v35.9.2...v36.0.6) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 9d185ef2b214a92250b3dede6716d2d5d33a91d3 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 89bb75b3f1..056773dfdc 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v35.9.2 + uses: tj-actions/changed-files@v36.0.6 with: separator: ";" diff_relative: true From fe17abfd60cd3086d6ef3a28125cdb6ff6a31015 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 28 May 2023 06:24:23 +0200 Subject: [PATCH 0888/1233] Bump nf-core/setup-nextflow from 1.2.0 to 1.3.0 (#145) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.2.0 to 1.3.0. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.2.0...v1.3.0) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 715340e8d668864d4ebb2030c5bbf4718277263d --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index acc4ed9bcc..c921cb6f31 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -129,7 +129,7 @@ jobs: - uses: viash-io/viash-actions/setup@v3 - - uses: nf-core/setup-nextflow@v1.2.0 + - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 2083e614ce..37af7046d7 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -153,7 +153,7 @@ jobs: - uses: viash-io/viash-actions/setup@v3 - - uses: nf-core/setup-nextflow@v1.2.0 + - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from release branch, hopefully these are available From edaded565433be825a49e9bcb4f58918b1508dec Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 06:27:16 +0200 Subject: [PATCH 0889/1233] fix missing backtick Former-commit-id: 94b49b8f452d5c39ffc6f41cf43a387c3ea97976 --- src/datasets/api/comp_processor_knn.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 540e16824e..c71ced7a39 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -20,7 +20,7 @@ functionality: default: "knn" description: | the neighbors data is added to `.uns[key_added]`, - distances are stored in `.obsp[key_added+'_distances'] and + distances are stored in `.obsp[key_added+'_distances']` and connectivities in `.obsp[key_added+'_connectivities']`. - name: "--num_neighbors" type: integer From e4c9eba42de8d265cb876242ef3d2db2f253001f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 06:27:34 +0200 Subject: [PATCH 0890/1233] capitalise Former-commit-id: 3f1b67e2273a3a2bf8206e80a604556ac7a8b43e --- src/datasets/api/comp_processor_knn.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index c71ced7a39..4c81440f31 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -19,7 +19,7 @@ functionality: type: string default: "knn" description: | - the neighbors data is added to `.uns[key_added]`, + The neighbors data is added to `.uns[key_added]`, distances are stored in `.obsp[key_added+'_distances']` and connectivities in `.obsp[key_added+'_connectivities']`. - name: "--num_neighbors" From 2fbed15519ba62deb9590fa24da28548bbcd1d4f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 06:32:28 +0200 Subject: [PATCH 0891/1233] make input / output args required Former-commit-id: a7f0ebb8e0e79fbd8bbfa38ccd5cc3aa8f410212 --- src/datasets/api/comp_dataset_loader.yaml | 1 + src/datasets/api/comp_normalization.yaml | 2 ++ src/datasets/api/comp_processor_hvg.yaml | 2 ++ src/datasets/api/comp_processor_knn.yaml | 2 ++ src/datasets/api/comp_processor_pca.yaml | 2 ++ src/datasets/api/comp_processor_subset.yaml | 2 ++ 6 files changed, 11 insertions(+) diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index ed5c8a0552..6f7bd814a5 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -12,3 +12,4 @@ functionality: - name: "--output" __merge__: anndata_raw.yaml direction: "output" + required: true diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index ee748eb6ec..22a1f62023 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -8,9 +8,11 @@ functionality: arguments: - name: "--input" __merge__: anndata_raw.yaml + required: true - name: "--output" direction: output __merge__: anndata_normalized.yaml + required: true - name: "--layer_output" type: string default: "normalized" diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index b17530d8d6..f29729587d 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -8,6 +8,7 @@ functionality: arguments: - name: "--input" __merge__: anndata_pca.yaml + required: true - name: "--layer_input" type: string default: "normalized" @@ -15,6 +16,7 @@ functionality: - name: "--output" direction: output __merge__: anndata_hvg.yaml + required: true - name: "--var_hvg" type: string default: "hvg" diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 4c81440f31..5d5f45226c 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -8,6 +8,7 @@ functionality: arguments: - name: "--input" __merge__: anndata_hvg.yaml + required: true - name: "--layer_input" type: string default: "normalized" @@ -15,6 +16,7 @@ functionality: - name: "--output" direction: output __merge__: anndata_knn.yaml + required: true - name: "--key_added" type: string default: "knn" diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index 8ed4f4bc38..7a1dcdd61b 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -8,6 +8,7 @@ functionality: arguments: - name: "--input" __merge__: anndata_normalized.yaml + required: true - name: "--layer_input" type: string default: "normalized" @@ -15,6 +16,7 @@ functionality: - name: "--output" direction: output __merge__: anndata_pca.yaml + required: true - name: "--obsm_embedding" type: string default: "X_pca" diff --git a/src/datasets/api/comp_processor_subset.yaml b/src/datasets/api/comp_processor_subset.yaml index ef241bb635..e3612cc366 100644 --- a/src/datasets/api/comp_processor_subset.yaml +++ b/src/datasets/api/comp_processor_subset.yaml @@ -8,9 +8,11 @@ functionality: arguments: - name: "--input" __merge__: anndata_common_dataset.yaml + required: true - name: "--output" __merge__: anndata_common_dataset.yaml direction: output + required: true test_resources: - path: /resources_test/common/pancreas dest: resources_test/common/pancreas From cc69dd7c0c598b0e04e19492e8d79ab86880fbf2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 07:42:54 +0200 Subject: [PATCH 0892/1233] move authors to task_info, remove authors from other components Former-commit-id: 1c2b2b03e591b3cf136e1b64a33a7db2f294fece --- .../sync_test_resources/config.vsh.yaml | 5 ----- src/tasks/batch_integration/api/authors.yaml | 14 ------------- .../batch_integration/api/task_info.yaml | 13 ++++++++++++ src/tasks/denoising/api/authors.yaml | 14 ------------- src/tasks/denoising/api/task_info.yaml | 13 ++++++++++++ .../dimensionality_reduction/api/authors.yaml | 20 ------------------- .../api/task_info.yaml | 19 ++++++++++++++++++ src/tasks/label_projection/api/authors.yaml | 11 ---------- src/tasks/label_projection/api/task_info.yaml | 12 ++++++++++- .../datasets/sample_dataset/config.vsh.yaml | 4 ---- .../datasets/scprep_csv/config.vsh.yaml | 4 ---- .../harmonic_alignment/config.vsh.yaml | 4 ---- .../methods/mnn/config.vsh.yaml | 4 ---- .../methods/sample_method/config.vsh.yaml | 4 ---- .../methods/scot/config.vsh.yaml | 4 ---- .../metrics/knn_auc/config.vsh.yaml | 4 ---- .../metrics/mse/config.vsh.yaml | 4 ---- 17 files changed, 56 insertions(+), 97 deletions(-) delete mode 100644 src/tasks/batch_integration/api/authors.yaml delete mode 100644 src/tasks/denoising/api/authors.yaml delete mode 100644 src/tasks/dimensionality_reduction/api/authors.yaml delete mode 100644 src/tasks/label_projection/api/authors.yaml diff --git a/src/common/sync_test_resources/config.vsh.yaml b/src/common/sync_test_resources/config.vsh.yaml index b920a9d30b..d66ce8bf74 100644 --- a/src/common/sync_test_resources/config.vsh.yaml +++ b/src/common/sync_test_resources/config.vsh.yaml @@ -6,11 +6,6 @@ functionality: usage: | sync_test_resources sync_test_resources --input s3://openproblems-data/resources_test --output resources_test - authors: - - name: Robrecht Cannoodt - email: rcannood@gmail.com - roles: [ maintainer ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } arguments: - name: "--input" alternatives: ["-i"] diff --git a/src/tasks/batch_integration/api/authors.yaml b/src/tasks/batch_integration/api/authors.yaml deleted file mode 100644 index 1b36fcea59..0000000000 --- a/src/tasks/batch_integration/api/authors.yaml +++ /dev/null @@ -1,14 +0,0 @@ -functionality: - authors: - - name: Michaela Mueller - roles: [ maintainer, author ] - props: { github: mumichae } - - name: Kai Waldrant - roles: [ contributor ] - props: { github: KaiWaldrant } - - name: Robrecht Cannoodt - roles: [ contributor ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } - - name: Daniel Strobl - roles: [ author ] - props: { github: danielStrobl } diff --git a/src/tasks/batch_integration/api/task_info.yaml b/src/tasks/batch_integration/api/task_info.yaml index 2a68e5ed9c..42255d56f9 100644 --- a/src/tasks/batch_integration/api/task_info.yaml +++ b/src/tasks/batch_integration/api/task_info.yaml @@ -22,3 +22,16 @@ description: | The batch integrated output can be a feature matrix, a low dimensional embedding and/or a neighbourhood graph. The respective batch-integrated representation is then evaluated using sets of metrics that capture how well batch effects are removed and whether biological variance is conserved. We have based this particular task on the latest, and most extensive benchmark of single-cell data integration methods [@luecken2022benchmarking]. +authors: + - name: Michaela Mueller + roles: [ maintainer, author ] + props: { github: mumichae } + - name: Kai Waldrant + roles: [ contributor ] + props: { github: KaiWaldrant } + - name: Robrecht Cannoodt + roles: [ contributor ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + - name: Daniel Strobl + roles: [ author ] + props: { github: danielStrobl } diff --git a/src/tasks/denoising/api/authors.yaml b/src/tasks/denoising/api/authors.yaml deleted file mode 100644 index 791fafbbe7..0000000000 --- a/src/tasks/denoising/api/authors.yaml +++ /dev/null @@ -1,14 +0,0 @@ -functionality: - authors: - - name: "Wesley Lewis" - roles: [ author, maintainer ] - props: { github: wes-lewis } - - name: "Scott Gigante" - roles: [ author, maintainer ] - props: { github: scottgigante } - - name: Robrecht Cannoodt - roles: [ author ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } - - name: Kai Waldrant - roles: [ author ] - props: { github: KaiWaldrant } \ No newline at end of file diff --git a/src/tasks/denoising/api/task_info.yaml b/src/tasks/denoising/api/task_info.yaml index 3cdd9fe60f..26fba03bc5 100644 --- a/src/tasks/denoising/api/task_info.yaml +++ b/src/tasks/denoising/api/task_info.yaml @@ -31,3 +31,16 @@ description: | accuracy is measured by comparing the result to the test dataset. The authors show that both in theory and in practice, the measured denoising accuracy is representative of the accuracy that would be obtained on a ground truth dataset. +authors: + - name: "Wesley Lewis" + roles: [ author, maintainer ] + props: { github: wes-lewis } + - name: "Scott Gigante" + roles: [ author, maintainer ] + props: { github: scottgigante } + - name: Robrecht Cannoodt + roles: [ author ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } + - name: Kai Waldrant + roles: [ author ] + props: { github: KaiWaldrant } \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/authors.yaml b/src/tasks/dimensionality_reduction/api/authors.yaml deleted file mode 100644 index d1a6fd6eee..0000000000 --- a/src/tasks/dimensionality_reduction/api/authors.yaml +++ /dev/null @@ -1,20 +0,0 @@ -functionality: - authors: - - name: Luke Zappia - roles: [ maintainer, author ] - props: { github: lazappi } - - name: Michal Klein - roles: [ author ] - props: { github: michalk8 } - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: Ben DeMeo - roles: [ author ] - props: { github: bendemeo } - - name: "Juan A. Cordero Varela" - roles: [ contributor ] - props: { github: jacorvar, orcid: 0000-0002-7373-5433} - - name: Robrecht Cannoodt - roles: [ contributor ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } diff --git a/src/tasks/dimensionality_reduction/api/task_info.yaml b/src/tasks/dimensionality_reduction/api/task_info.yaml index 1b7c0e739e..3c7d3cfabf 100644 --- a/src/tasks/dimensionality_reduction/api/task_info.yaml +++ b/src/tasks/dimensionality_reduction/api/task_info.yaml @@ -20,3 +20,22 @@ description: | (distances in high dimensional data don't distinguish data points well). Thus, we need to find a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data for visualization and interpretation. +authors: + - name: Luke Zappia + roles: [ maintainer, author ] + props: { github: lazappi } + - name: Michal Klein + roles: [ author ] + props: { github: michalk8 } + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: Ben DeMeo + roles: [ author ] + props: { github: bendemeo } + - name: "Juan A. Cordero Varela" + roles: [ contributor ] + props: { github: jacorvar, orcid: 0000-0002-7373-5433} + - name: Robrecht Cannoodt + roles: [ contributor ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } diff --git a/src/tasks/label_projection/api/authors.yaml b/src/tasks/label_projection/api/authors.yaml deleted file mode 100644 index 23e6587896..0000000000 --- a/src/tasks/label_projection/api/authors.yaml +++ /dev/null @@ -1,11 +0,0 @@ -functionality: - authors: - - name: "Nikolay Markov" - roles: [ author, maintainer ] - props: { github: mxposed } - - name: "Scott Gigante" - roles: [ author ] - props: { github: scottgigante } - - name: Robrecht Cannoodt - roles: [ author ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } \ No newline at end of file diff --git a/src/tasks/label_projection/api/task_info.yaml b/src/tasks/label_projection/api/task_info.yaml index 97dde85074..d5eae84715 100644 --- a/src/tasks/label_projection/api/task_info.yaml +++ b/src/tasks/label_projection/api/task_info.yaml @@ -26,4 +26,14 @@ description: | have been manually annotated with matching labels. These datasets are then split into training and test batches, and the task of each method is to train a cell type classifer on the training set and project those labels - onto the test set. \ No newline at end of file + onto the test set. +authors: + - name: "Nikolay Markov" + roles: [ author, maintainer ] + props: { github: mxposed } + - name: "Scott Gigante" + roles: [ author ] + props: { github: scottgigante } + - name: Robrecht Cannoodt + roles: [ author ] + props: { github: rcannood, orcid: "0000-0003-3641-729X" } \ No newline at end of file diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml b/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml index 524dcf0ec4..e1ad3ca0c3 100644 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/datasets" version: "dev" description: "Sample dataset for testing purposes" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } arguments: - name: "--output" alternatives: ["-o"] diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml b/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml index f46ea5bf83..0461cecdc4 100644 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/datasets" version: "dev" description: "Create a modality alignment dataset from CSV using scprep." - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } arguments: - name: "--id" type: "string" diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml index 6364f4cd35..29684dad7e 100644 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Harmonic Alignment" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } info: method_name: "Harmonic Alignment" paper_name: "Harmonic Alignment" diff --git a/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml index 1c0fb93f4c..6cbe90f7c3 100644 --- a/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Mutual Nearest Neighbours" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } info: method_label: "MNN" method_name: "Mutual Nearest Neighbors" diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml index cf367085c0..a35c59ed83 100644 --- a/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/methods" version: "dev" description: "Sample method" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } info: method_name: "Sample method" arguments: diff --git a/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml index 0b07e276f8..2cda0a5af6 100644 --- a/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/methods" version: "dev" description: "Run Single Cell Optimal Transport" - authors: - - name: "Alex Tong" - roles: [ maintainer, author ] - props: { github: atong01 } info: method_label: "SCOT" method_name: "Single Cell Optimal Transport" diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml b/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml index 02f785a343..939aa83e92 100644 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/metrics" version: "dev" description: "Compute the kNN Area Under the Curve" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } info: method_label: "KNN-AUC" metric_name: "kNN Area Under the Curve" diff --git a/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml b/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml index 881170462d..025368fbef 100644 --- a/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml +++ b/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: namespace: "multimodal_data_integration/metrics" version: "dev" description: "Compute the mean squared error" - authors: - - name: "Scott Gigante" - roles: [ maintainer, author ] - props: { github: scottgigante } info: method_label: "MSE" metric_name: "Mean Squared Error" From 5ac96ec4c392782288a7e8e6f8004767414fcaf5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 11:13:15 +0200 Subject: [PATCH 0893/1233] rename dimred objects Former-commit-id: 1f1aeecba7fc67a730ba16b4c1ba0c40cc45c99e --- ...nndata_train.yaml => anndata_dataset.yaml} | 6 ++--- ...ta_reduced.yaml => anndata_embedding.yaml} | 6 ++--- ...nndata_test.yaml => anndata_solution.yaml} | 2 +- .../api/comp_control_method.yaml | 9 +++++-- .../api/comp_method.yaml | 6 +++-- .../api/comp_metric.yaml | 11 +++++---- .../api/comp_process_dataset.yaml | 13 ++++++---- .../metrics/coranking/script.R | 18 +++++++------- .../metrics/density_preservation/script.py | 18 +++++++------- .../metrics/rmse/script.py | 20 ++++++++-------- .../metrics/trustworthiness/script.py | 18 +++++++------- .../process_dataset/script.py | 14 +++++------ .../resources_scripts/run_benchmark.sh | 6 ++--- .../resources_test_scripts/pancreas.sh | 24 +++++++++---------- 14 files changed, 92 insertions(+), 79 deletions(-) rename src/tasks/dimensionality_reduction/api/{anndata_train.yaml => anndata_dataset.yaml} (82%) rename src/tasks/dimensionality_reduction/api/{anndata_reduced.yaml => anndata_embedding.yaml} (73%) rename src/tasks/dimensionality_reduction/api/{anndata_test.yaml => anndata_solution.yaml} (91%) diff --git a/src/tasks/dimensionality_reduction/api/anndata_train.yaml b/src/tasks/dimensionality_reduction/api/anndata_dataset.yaml similarity index 82% rename from src/tasks/dimensionality_reduction/api/anndata_train.yaml rename to src/tasks/dimensionality_reduction/api/anndata_dataset.yaml index 5c0dd0fe05..bc6613a93d 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_train.yaml +++ b/src/tasks/dimensionality_reduction/api/anndata_dataset.yaml @@ -1,8 +1,8 @@ type: file -description: "The training data" -example: "resources_test/dimensionality_reduction/pancreas/train.h5ad" +description: "The dataset to pass to a method." +example: "resources_test/dimensionality_reduction/pancreas/dataset.h5ad" info: - short_description: "Training data" + short_description: "Dataset" slots: layers: - type: integer diff --git a/src/tasks/dimensionality_reduction/api/anndata_reduced.yaml b/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml similarity index 73% rename from src/tasks/dimensionality_reduction/api/anndata_reduced.yaml rename to src/tasks/dimensionality_reduction/api/anndata_embedding.yaml index efca248406..24034bdd10 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_reduced.yaml +++ b/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml @@ -1,8 +1,8 @@ type: file -description: "A dimensionally reduced dataset" -example: "resources_test/dimensionality_reduction/pancreas/reduced.h5ad" +description: "A dataset with dimensionality reduction embedding." +example: "resources_test/dimensionality_reduction/pancreas/output.h5ad" info: - short_description: "Training data" + short_description: "Embedding" slots: obsm: - type: double diff --git a/src/tasks/dimensionality_reduction/api/anndata_test.yaml b/src/tasks/dimensionality_reduction/api/anndata_solution.yaml similarity index 91% rename from src/tasks/dimensionality_reduction/api/anndata_test.yaml rename to src/tasks/dimensionality_reduction/api/anndata_solution.yaml index f51c130e8d..6292535031 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_test.yaml +++ b/src/tasks/dimensionality_reduction/api/anndata_solution.yaml @@ -1,6 +1,6 @@ type: file description: "The test data" -example: "resources_test/dimensionality_reduction/pancreas/test.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/solution.h5ad" info: short_description: "Test data" slots: diff --git a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml index f8b04891a7..443d28859c 100644 --- a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml @@ -13,10 +13,15 @@ functionality: in the task. arguments: - name: "--input" - __merge__: anndata_train.yaml + __merge__: anndata_dataset.yaml + required: true + - name: "--input_solution" + __merge__: anndata_solution.yaml + required: true - name: "--output" - __merge__: anndata_reduced.yaml + __merge__: anndata_embedding.yaml direction: output + required: true test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ dest: resources_test/dimensionality_reduction/pancreas/ diff --git a/src/tasks/dimensionality_reduction/api/comp_method.yaml b/src/tasks/dimensionality_reduction/api/comp_method.yaml index c20650841b..9fd730e65f 100644 --- a/src/tasks/dimensionality_reduction/api/comp_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_method.yaml @@ -9,10 +9,12 @@ functionality: a dataset in as few dimensions as possible. arguments: - name: "--input" - __merge__: anndata_train.yaml + __merge__: anndata_dataset.yaml + required: true - name: "--output" - __merge__: anndata_reduced.yaml + __merge__: anndata_embedding.yaml direction: output + required: true test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ dest: resources_test/dimensionality_reduction/pancreas/ diff --git a/src/tasks/dimensionality_reduction/api/comp_metric.yaml b/src/tasks/dimensionality_reduction/api/comp_metric.yaml index cc8da44ac6..114e61898e 100644 --- a/src/tasks/dimensionality_reduction/api/comp_metric.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_metric.yaml @@ -7,13 +7,16 @@ functionality: description: | A metric for evaluating dimensionality reductions. arguments: - - name: "--input_reduced" - __merge__: anndata_reduced.yaml - - name: "--input_test" - __merge__: anndata_test.yaml + - name: "--input_embedding" + __merge__: anndata_embedding.yaml + required: true + - name: "--input_solution" + __merge__: anndata_solution.yaml + required: true - name: "--output" __merge__: anndata_score.yaml direction: output + required: true test_resources: - path: /resources_test/dimensionality_reduction/pancreas/ dest: resources_test/dimensionality_reduction/pancreas/ diff --git a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml index e552fadeb7..ff7c25445f 100644 --- a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml @@ -5,16 +5,19 @@ functionality: type_info: label: Data processor description: | - Prepare a common dataset for the denoising task. + Prepare a common dataset for the dimensionality reduction task. arguments: - name: "--input" __merge__: /src/datasets/api/anndata_common_dataset.yaml - - name: "--output_train" - __merge__: anndata_train.yaml + required: true + - name: "--output_dataset" + __merge__: anndata_dataset.yaml direction: output - - name: "--output_test" - __merge__: anndata_test.yaml + required: true + - name: "--output_solution" + __merge__: anndata_solution.yaml direction: output + required: true test_resources: - path: /resources_test/common/pancreas/ dest: resources_test/common/pancreas/ diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/script.R b/src/tasks/dimensionality_reduction/metrics/coranking/script.R index 63a6b68769..7fcce8c2f8 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/script.R +++ b/src/tasks/dimensionality_reduction/metrics/coranking/script.R @@ -3,19 +3,19 @@ library(coRanking) ## VIASH START par <- list( - "input_reduced" = "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_test" = "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "input_embedding" = "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_solution" = "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output" = "score.h5ad" ) ## VIASH END cat("Read anndata objects") -input_test <- anndata::read_h5ad(par[["input_test"]]) -input_reduced <- anndata::read_h5ad(par[["input_reduced"]]) +input_solution <- anndata::read_h5ad(par[["input_solution"]]) +input_embedding <- anndata::read_h5ad(par[["input_embedding"]]) # get datasets -high_dim <- input_test$layers[["normalized"]] -X_emb <- input_reduced$obsm[["X_emb"]] +high_dim <- input_solution$layers[["normalized"]] +X_emb <- input_embedding$obsm[["X_emb"]] if (any(is.na(X_emb))) { continuity_at_k30 <- @@ -73,9 +73,9 @@ cat("construct output AnnData\n") output <- AnnData( shape = c(0L, 0L), uns = list( - dataset_id = input_test$uns[["dataset_id"]], - normalization_id = input_test$uns[["normalization_id"]], - method_id = input_reduced$uns[["method_id"]], + dataset_id = input_solution$uns[["dataset_id"]], + normalization_id = input_solution$uns[["normalization_id"]], + method_id = input_embedding$uns[["method_id"]], metric_ids = c( "continuity_at_k30", "trustworthiness_at_k30", diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py b/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py index f4a31d3caf..9cae4d1f12 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py @@ -8,8 +8,8 @@ ## VIASH START par = { - "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "input_embedding": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_solution": "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output": "score.h5ad", } ## VIASH END @@ -107,11 +107,11 @@ def compute_density_preservation( _SEED = 42 print("Load data", flush=True) -input_test = ad.read_h5ad(par["input_test"]) -input_reduced = ad.read_h5ad(par["input_reduced"]) +input_solution = ad.read_h5ad(par["input_solution"]) +input_embedding = ad.read_h5ad(par["input_embedding"]) -high_dim = input_test.layers["normalized"] -X_emb = input_reduced.obsm["X_emb"] +high_dim = input_solution.layers["normalized"] +X_emb = input_embedding.obsm["X_emb"] density_preservation = compute_density_preservation( X_emb=X_emb, @@ -123,9 +123,9 @@ def compute_density_preservation( print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": input_test.uns["dataset_id"], - "normalization_id": input_test.uns["normalization_id"], - "method_id": input_reduced.uns["method_id"], + "dataset_id": input_solution.uns["dataset_id"], + "normalization_id": input_solution.uns["normalization_id"], + "method_id": input_embedding.uns["method_id"], "metric_ids": [ "density_preservation" ], "metric_values": [ density_preservation ] } diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/script.py b/src/tasks/dimensionality_reduction/metrics/rmse/script.py index d738c95c47..4b33fe02ce 100644 --- a/src/tasks/dimensionality_reduction/metrics/rmse/script.py +++ b/src/tasks/dimensionality_reduction/metrics/rmse/script.py @@ -9,8 +9,8 @@ ## VIASH START par = { - "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "input_embedding": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_solution": "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output": "score.h5ad", } ## VIASH END @@ -24,11 +24,11 @@ def _rmse(X, X_emb): return rmse print("Load data", flush=True) -input_test = ad.read_h5ad(par["input_test"]) -input_reduced = ad.read_h5ad(par["input_reduced"]) +input_solution = ad.read_h5ad(par["input_solution"]) +input_embedding = ad.read_h5ad(par["input_embedding"]) -high_dim = input_test.layers["normalized"] -X_emb = input_reduced.obsm["X_emb"] +high_dim = input_solution.layers["normalized"] +X_emb = input_embedding.obsm["X_emb"] print("Compute NNLS residual after SVD", flush=True) n_svd = 200 @@ -36,7 +36,7 @@ def _rmse(X, X_emb): rmse = _rmse(svd_emb, X_emb) print("Compute NLSS residual after spectral embedding", flush=True) -n_comps = min(200, min(input_test.shape) - 2) +n_comps = min(200, min(input_solution.shape) - 2) umap_graph = umap.UMAP(transform_mode="graph").fit_transform(high_dim) spectral_emb = umap.spectral.spectral_layout( high_dim, umap_graph, n_comps, random_state=np.random.default_rng() @@ -46,9 +46,9 @@ def _rmse(X, X_emb): print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": input_test.uns["dataset_id"], - "normalization_id": input_test.uns["normalization_id"], - "method_id": input_reduced.uns["method_id"], + "dataset_id": input_solution.uns["dataset_id"], + "normalization_id": input_solution.uns["normalization_id"], + "method_id": input_embedding.uns["method_id"], "metric_ids": [ "rmse", "rmse_spectral" ], "metric_values": [ rmse, rmse_spectral ] } diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/script.py b/src/tasks/dimensionality_reduction/metrics/trustworthiness/script.py index 9f76a7f8ed..410a0b3263 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/script.py +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/script.py @@ -4,18 +4,18 @@ ## VIASH START par = { - "input_reduced": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_test": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "input_embedding": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", + "input_solution": "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output": "score.h5ad", } ## VIASH END print("Load data", flush=True) -input_test = ad.read_h5ad(par["input_test"]) -input_reduced = ad.read_h5ad(par["input_reduced"]) +input_solution = ad.read_h5ad(par["input_solution"]) +input_embedding = ad.read_h5ad(par["input_embedding"]) -high_dim = input_test.layers["normalized"] -X_emb = input_reduced.obsm["X_emb"] +high_dim = input_solution.layers["normalized"] +X_emb = input_embedding.obsm["X_emb"] print("Reduce dimensionality of raw data", flush=True) trustworthiness = manifold.trustworthiness( @@ -25,9 +25,9 @@ print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": input_test.uns["dataset_id"], - "normalization_id": input_test.uns["normalization_id"], - "method_id": input_reduced.uns["method_id"], + "dataset_id": input_solution.uns["dataset_id"], + "normalization_id": input_solution.uns["normalization_id"], + "method_id": input_embedding.uns["method_id"], "metric_ids": [ "trustworthiness" ], "metric_values": [ trustworthiness ] } diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index b088643f9e..9563ed56f0 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -4,12 +4,12 @@ ## VIASH START par = { "input": "resources_test/common/pancreas/dataset.h5ad", - "output_train": "train.h5ad", - "output_test": "test.h5ad", + "output_dataset": "train.h5ad", + "output_solution": "test.h5ad", } meta = { "functionality_name": "split_data", - "config": "src/dimensionality_reduction/process_dataset/.config.vsh.yaml" + "config": "src/tasks/dimensionality_reduction/process_dataset/.config.vsh.yaml" } ## VIASH END @@ -24,11 +24,11 @@ slot_info = read_config_slots_info(meta["config"]) print(">> Creating train data", flush=True) -output_train = subset_anndata(adata, slot_info["output_train"]) +output_dataset = subset_anndata(adata, slot_info["output_dataset"]) print(">> Creating test data", flush=True) -output_test = subset_anndata(adata, slot_info["output_test"]) +output_solution = subset_anndata(adata, slot_info["output_solution"]) print(">> Writing", flush=True) -output_train.write_h5ad(par["output_train"]) -output_test.write_h5ad(par["output_test"]) +output_dataset.write_h5ad(par["output_dataset"]) +output_solution.write_h5ad(par["output_solution"]) diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index 7ffc4d7995..3eecb22b2e 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -37,14 +37,14 @@ param_list = [] for dataset in datasets: id = dataset["id"] input_train = dataset_dir + "/" + id + ".train.h5ad" - input_test = dataset_dir + "/" + id + ".test.h5ad" + input_solution = dataset_dir + "/" + id + ".test.h5ad" obj = { 'id': id, 'dataset_id': dataset["dataset_id"], 'normalization_id': dataset["normalization_id"], 'input': input_train, - 'input_test': input_test + 'input_solution': input_solution } param_list.append(obj) @@ -61,7 +61,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/dimensionality_reduction/workflows/run/main.nf \ + -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ -resume \ -params-file "$params_file" \ diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index 909946635e..c208311399 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -19,21 +19,21 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/dimensionality_reduction/process_dataset/config.vsh.yaml -- \ +viash run src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ - --output_train $DATASET_DIR/train.h5ad \ - --output_test $DATASET_DIR/test.h5ad + --output_dataset $DATASET_DIR/dataset.h5ad \ + --output_solution $DATASET_DIR/solution.h5ad # run one method -viash run src/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ - --input $DATASET_DIR/train.h5ad \ - --output $DATASET_DIR/reduced.h5ad +viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset.h5ad \ + --output $DATASET_DIR/embedding.h5ad # run one metric -viash run src/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ - --input_reduced $DATASET_DIR/reduced.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ +viash run src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ + --input_embedding $DATASET_DIR/embedding.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/score.h5ad # run benchmark @@ -42,12 +42,12 @@ export NXF_VER=22.04.5 # after having added a split dataset component nextflow \ run . \ - -main-script src/dimensionality_reduction/workflows/run/main.nf \ + -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ --id pancreas \ --dataset_id pancreas \ --normalization_id log_cpm \ - --input $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ + --input $DATASET_DIR/dataset.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ \ No newline at end of file From 88d13491972d63002872e2dd41aa989c318ebf06 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 11:13:48 +0200 Subject: [PATCH 0894/1233] tasks have been moved to src/tasks Former-commit-id: d8a75c2c37d8dc9d812241f8b8d38f62064d8deb --- CHANGELOG.md | 6 +-- CONTRIBUTING.md | 26 ++++++------ CONTRIBUTING.qmd | 42 +++++++++---------- .../resource_test_scripts/pancreas_tasks.sh | 6 +-- .../resources_test_scripts/pancreas.sh | 8 ++-- .../workflows/run/nextflow.config | 2 +- .../workflows/run/run_nextflow.sh | 2 +- src/tasks/denoising/README.md | 2 +- src/tasks/denoising/process_dataset/script.py | 2 +- .../resources_scripts/run_benchmark.sh | 2 +- .../resources_test_scripts/pancreas.sh | 8 ++-- .../denoising/workflows/run/nextflow.config | 2 +- src/tasks/dimensionality_reduction/README.md | 2 +- .../workflows/run/config.vsh.yaml | 2 +- .../workflows/run/main.nf | 4 +- .../workflows/run/nextflow.config | 2 +- src/tasks/label_projection/README.md | 2 +- .../resources_scripts/run_benchmark.sh | 2 +- .../resources_test_scripts/pancreas.sh | 8 ++-- .../workflows/run/nextflow.config | 2 +- .../workflows/run/run_test.sh | 2 +- .../workflows/run/nextflow.config | 2 +- 22 files changed, 68 insertions(+), 68 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a276f1d14..129e3e9727 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -82,7 +82,7 @@ * `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. -* `resources_test/label_projection/pancreas` with `src/label_projection/resources_test_scripts/pancreas.sh`. +* `resources_test/label_projection/pancreas` with `src/tasks/label_projection/resources_test_scripts/pancreas.sh`. ### V1 MIGRATION @@ -120,7 +120,7 @@ * `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. -* `resources_test/denoising/pancreas` with `src/denoising/resources_test_scripts/pancreas.sh`. +* `resources_test/denoising/pancreas` with `src/tasks/denoising/resources_test_scripts/pancreas.sh`. ### V1 MIGRATION @@ -159,7 +159,7 @@ * `control_methods`: Added a component for baseline methods specifically. -* `resources_test/dimensionality_reduction/pancreas` with `src/dimensionality_reduction/resources_test_scripts/pancreas.sh`. +* `resources_test/dimensionality_reduction/pancreas` with `src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh`. * Added `variant` key to config files to store variants (different input parameters) of every component. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b9aae91646..198e037d70 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -113,14 +113,14 @@ The command might take a while to run, since it is building a docker container for each of the components. **Step 3, run the pipeline with nextflow.** To do so, run the bash -script located at `src/label_projection/workflows/run_nextflow.sh`: +script located at `src/tasks/label_projection/workflows/run_nextflow.sh`: ``` bash -src/label_projection/workflows/run/run_test.sh +src/tasks/label_projection/workflows/run/run_test.sh ``` N E X T F L O W ~ version 22.04.5 - Launching `src/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 + Launching `src/tasks/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 executor > local (28) [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ @@ -149,9 +149,9 @@ Executables generated by viash based on the components listed under └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. -Detailed overview of a task folder (e.g. `src/label_projection`): +Detailed overview of a task folder (e.g. `src/tasks/label_projection`): - src/label_projection/ + src/tasks/label_projection/ ├── api Specs for the components in this task. ├── control_methods Control methods which serve as quality control checks for the benchmark. ├── docs Task documentation @@ -183,7 +183,7 @@ You can start creating a new component by [creating a Viash component](https://viash.io/guide/component/creation/docker.html). For example, to create a new Python-based method named `foo`, create a -Viash config at `src/label_projection/methods/foo/config.vsh.yaml`: +Viash config at `src/tasks/label_projection/methods/foo/config.vsh.yaml`: ``` yaml __merge__: ../../api/comp_method.yaml @@ -220,7 +220,7 @@ platforms: - type: nextflow ``` -And create a script at `src/label_projection/methods/foo/script.py`: +And create a script at `src/tasks/label_projection/methods/foo/script.py`: ``` python import anndata as ad @@ -258,7 +258,7 @@ You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. ``` bash -viash run src/label_projection/methods/foo/config.vsh.yaml -- --help +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help ``` foo dev @@ -284,7 +284,7 @@ viash run src/label_projection/methods/foo/config.vsh.yaml -- --help You can **run the component** as follows: ``` bash -viash run src/label_projection/methods/foo/config.vsh.yaml -- \ +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- \ --input_train resources_test/label_projection/pancreas/train.h5ad \ --input_test resources_test/label_projection/pancreas/test.h5ad \ --output resources_test/label_projection/pancreas/prediction.h5ad @@ -309,7 +309,7 @@ and they will be able to run it, provided that they have Bash and Docker installed. ``` bash -viash build src/label_projection/methods/foo/config.vsh.yaml \ +viash build src/tasks/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` @@ -366,12 +366,12 @@ target/docker/label_projection/methods/foo/foo \ ## Unit testing a component The [method API -specifications](src/label_projection/api/comp_method.yaml) comes with a +specifications](src/tasks/label_projection/api/comp_method.yaml) comes with a generic unit test for free. This means you can unit test your component using the **`viash test`** command. ``` bash -viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011' @@ -468,7 +468,7 @@ If we now run the test, we should get an error since we didn’t create all of the required output slots. ``` bash -viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128' diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index a4d8b4c32e..f3fd25e01f 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -79,14 +79,14 @@ The flag `--setup cachedbuild` will automatically start building Docker containe The command might take a while to run, since it is building a docker container for each of the components. -**Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/label_projection/workflows/run_nextflow.sh`: +**Step 3, run the pipeline with nextflow.** To do so, run the bash script located at `src/tasks/label_projection/workflows/run_nextflow.sh`: ```bash -src/label_projection/workflows/run/run_test.sh +src/tasks/label_projection/workflows/run/run_test.sh ``` N E X T F L O W ~ version 22.04.5 - Launching `src/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 + Launching `src/tasks/label_projection/workflows/run/main.nf` [pensive_turing] DSL2 - revision: 16b7b0c332 executor > local (28) [f6/f89435] process > run_wf:run_methods:true_labels:true_labels_process (pancreas.true_labels) [100%] 1 of 1 ✔ [ed/d674a2] process > run_wf:run_methods:majority_vote:majority_vote_process (pancreas.majority_vote) [100%] 1 of 1 ✔ @@ -116,9 +116,9 @@ High level overview: ├── docker Bash executables which can be used from a terminal. └── nextflow Nextflow modules which can be used as a standalone pipeline or as part of a bigger pipeline. -Detailed overview of a task folder (e.g. `src/label_projection`): +Detailed overview of a task folder (e.g. `src/tasks/label_projection`): - src/label_projection/ + src/tasks/label_projection/ ├── api Specs for the components in this task. ├── control_methods Control methods which serve as quality control checks for the benchmark. ├── docs Task documentation @@ -152,9 +152,9 @@ You can start creating a new component by [creating a Viash component](https://v ```{bash, include=FALSE} -mkdir -p src/label_projection/methods/foo +mkdir -p src/tasks/label_projection/methods/foo -cat > src/label_projection/methods/foo/config.vsh.yaml << HERE +cat > src/tasks/label_projection/methods/foo/config.vsh.yaml << HERE __merge__: ../../api/comp_method.yaml functionality: name: "foo" @@ -189,7 +189,7 @@ platforms: - type: nextflow HERE -cat > src/label_projection/methods/foo/script.py << HERE +cat > src/tasks/label_projection/methods/foo/script.py << HERE import anndata as ad import numpy as np @@ -220,16 +220,16 @@ input_test.write_h5ad(par["output"], compression="gzip") HERE ``` -For example, to create a new Python-based method named `foo`, create a Viash config at `src/label_projection/methods/foo/config.vsh.yaml`: +For example, to create a new Python-based method named `foo`, create a Viash config at `src/tasks/label_projection/methods/foo/config.vsh.yaml`: ```{embed lang="yaml"} -src/label_projection/methods/foo/config.vsh.yaml +src/tasks/label_projection/methods/foo/config.vsh.yaml ``` -And create a script at `src/label_projection/methods/foo/script.py`: +And create a script at `src/tasks/label_projection/methods/foo/script.py`: ```{embed lang="python"} -src/label_projection/methods/foo/script.py +src/tasks/label_projection/methods/foo/script.py ``` @@ -238,13 +238,13 @@ src/label_projection/methods/foo/script.py You can view the interface of the executable by running the executable with the `-h` or `--help` parameter. ```{bash} -viash run src/label_projection/methods/foo/config.vsh.yaml -- --help +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help ``` You can **run the component** as follows: ```{bash} -viash run src/label_projection/methods/foo/config.vsh.yaml -- \ +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- \ --input_train resources_test/label_projection/pancreas/train.h5ad \ --input_test resources_test/label_projection/pancreas/test.h5ad \ --output resources_test/label_projection/pancreas/prediction.h5ad @@ -259,7 +259,7 @@ This standalone executable you can give to somebody else, and they will be able run it, provided that they have Bash and Docker installed. ```{bash} -viash build src/label_projection/methods/foo/config.vsh.yaml \ +viash build src/tasks/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` @@ -286,15 +286,15 @@ target/docker/label_projection/methods/foo/foo \ ## Unit testing a component -The [method API specifications](src/label_projection/api/comp_method.yaml) comes with a generic unit test for free. +The [method API specifications](src/tasks/label_projection/api/comp_method.yaml) comes with a generic unit test for free. This means you can unit test your component using the **`viash test`** command. ```{bash} -viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` ```{bash include=FALSE} -cat > src/label_projection/methods/foo/script.py << HERE +cat > src/tasks/label_projection/methods/foo/script.py << HERE import anndata as ad import numpy as np @@ -328,13 +328,13 @@ HERE Let's introduce a bug in the script and try running the test again. For instance: ```{embed lang="python"} -src/label_projection/methods/foo/script.py +src/tasks/label_projection/methods/foo/script.py ``` If we now run the test, we should get an error since we didn't create all of the required output slots. ```{bash error=TRUE} -viash test src/label_projection/methods/foo/config.vsh.yaml +viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` @@ -346,5 +346,5 @@ The [Viash reference docs](https://viash.io/reference/config/) page provides inf ```{bash, echo=FALSE} -rm -r src/label_projection/methods/foo target/docker/label_projection/methods/foo +rm -r src/tasks/label_projection/methods/foo target/docker/label_projection/methods/foo ``` diff --git a/src/datasets/resource_test_scripts/pancreas_tasks.sh b/src/datasets/resource_test_scripts/pancreas_tasks.sh index 1b73a2e8d7..803af8152c 100755 --- a/src/datasets/resource_test_scripts/pancreas_tasks.sh +++ b/src/datasets/resource_test_scripts/pancreas_tasks.sh @@ -1,5 +1,5 @@ #!/bin/bash -src/denoising/resources_test_scripts/pancreas.sh -src/dimensionality_reduction/resources_test_scripts/pancreas.sh -src/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file +src/tasks/denoising/resources_test_scripts/pancreas.sh +src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +src/tasks/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index 1ad7a75ede..5ca39fade0 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -18,23 +18,23 @@ mkdir -p $DATASET_DIR # process dataset echo process data... -viash run src/batch_integration/process_dataset/config.vsh.yaml -- \ +viash run src/tasks/batch_integration/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output $DATASET_DIR/unintegrated.h5ad \ --hvgs 100 echo Running BBKNN -viash run src/batch_integration/methods/bbknn/config.vsh.yaml -- \ +viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ --output $DATASET_DIR/bbknn.h5ad echo Running SCVI -viash run src/batch_integration/methods/scvi/config.vsh.yaml -- \ +viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ --output $DATASET_DIR/scvi.h5ad echo Running combat -viash run src/batch_integration/methods/combat/config.vsh.yaml -- \ +viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ --output $DATASET_DIR/combat.h5ad diff --git a/src/tasks/batch_integration/workflows/run/nextflow.config b/src/tasks/batch_integration/workflows/run/nextflow.config index 1981a33306..4fae132704 100644 --- a/src/tasks/batch_integration/workflows/run/nextflow.config +++ b/src/tasks/batch_integration/workflows/run/nextflow.config @@ -6,7 +6,7 @@ manifest { } params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() } // include common settings diff --git a/src/tasks/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run/run_nextflow.sh index 1df0c7a125..1b5a3ad108 100755 --- a/src/tasks/batch_integration/workflows/run/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run/run_nextflow.sh @@ -18,7 +18,7 @@ export NXF_VER=22.04.5 # -profile docker \ nextflow run . \ - -main-script src/batch_integration/workflows/run/main.nf \ + -main-script src/tasks/batch_integration/workflows/run/main.nf \ -profile docker \ -c src/wf_utils/labels_ci.config \ -resume \ diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 39858c3591..4c19e2d935 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -2,7 +2,7 @@ Structure of this task: - src/denoising + src/tasks/denoising ├── api Interface specifications for components and datasets in this task ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index 3c817acb63..e79a8f5074 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -12,7 +12,7 @@ } meta = { "functionality_name": "split_data", - "resources_dir": "src/denoising/process_dataset" + "resources_dir": "src/tasks/denoising/process_dataset" } ## VIASH END diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index 2e53d2b6dd..ee0557166f 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -64,7 +64,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/denoising/workflows/run/main.nf \ + -main-script src/tasks/denoising/workflows/run/main.nf \ -profile docker \ -params-file "$params_file" \ --publish_dir "$OUTPUT_DIR" \ diff --git a/src/tasks/denoising/resources_test_scripts/pancreas.sh b/src/tasks/denoising/resources_test_scripts/pancreas.sh index 50bb68e735..0096c54db3 100755 --- a/src/tasks/denoising/resources_test_scripts/pancreas.sh +++ b/src/tasks/denoising/resources_test_scripts/pancreas.sh @@ -20,19 +20,19 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/denoising/process_dataset/config.vsh.yaml -- \ +viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ --seed 123 # run one method -viash run src/denoising/methods/magic/config.vsh.yaml -- \ +viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --output $DATASET_DIR/magic.h5ad # run one metric -viash run src/denoising/metrics/poisson/config.vsh.yaml -- \ +viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ --input_denoised $DATASET_DIR/magic.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/magic_poisson.h5ad @@ -42,7 +42,7 @@ export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/denoising/workflows/run/main.nf \ + -main-script src/tasks/denoising/workflows/run/main.nf \ -profile docker \ -resume \ --id pancreas \ diff --git a/src/tasks/denoising/workflows/run/nextflow.config b/src/tasks/denoising/workflows/run/nextflow.config index e5e84e82dc..0182e7b872 100644 --- a/src/tasks/denoising/workflows/run/nextflow.config +++ b/src/tasks/denoising/workflows/run/nextflow.config @@ -6,7 +6,7 @@ manifest { } params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() } // include common settings diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index b34f1807a3..f81d55da92 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -2,7 +2,7 @@ Structure of this task: - src/dimensionality_reduction + src/tasks/dimensionality_reduction ├── api Interface specifications for components and datasets in this task ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked diff --git a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml index d8cfb4d74a..3fc4113d1d 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: - name: "--input" type: "file" required: true - - name: "--input_test" + - name: "--input_solution" type: "file" required: true - name: "--normalization_id" diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index f89ff9a7b5..8d2351e71e 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -56,7 +56,7 @@ workflow run_wf { | setWorkflowArguments( preprocess: ["dataset_id", "normalization_id"], method: ["input"], - metric: ["input_test"], + metric: ["input_solution"], output: ["output"] ) // multiply events by the number of method @@ -73,7 +73,7 @@ workflow run_wf { | run_methods // run metrics - | getWorkflowArguments(key: "metric", inputKey: "input_reduced") + | getWorkflowArguments(key: "metric", inputKey: "input_embedding") | run_metrics // convert to tsv diff --git a/src/tasks/dimensionality_reduction/workflows/run/nextflow.config b/src/tasks/dimensionality_reduction/workflows/run/nextflow.config index ed0d87ccd0..026fe3a76a 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/nextflow.config +++ b/src/tasks/dimensionality_reduction/workflows/run/nextflow.config @@ -6,7 +6,7 @@ manifest { } params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() } // include common settings diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 342fca1675..fc24c81139 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -2,7 +2,7 @@ Structure of this task: - src/label_projection + src/tasks/label_projection ├── api Interface specifications for components and datasets in this task ├── control_methods Control methods to compare methods against ├── methods Methods to be benchmarked diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 389c15ab4d..42cf975be8 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -63,7 +63,7 @@ fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/label_projection/workflows/run/main.nf \ + -main-script src/tasks/label_projection/workflows/run/main.nf \ -profile docker \ -params-file "$params_file" \ --publish_dir "$OUTPUT_DIR" \ diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index 4faf188eb5..d9780a4425 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -20,7 +20,7 @@ fi mkdir -p $DATASET_DIR # split dataset -viash run src/label_projection/process_dataset/config.vsh.yaml -- \ +viash run src/tasks/label_projection/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ @@ -28,13 +28,13 @@ viash run src/label_projection/process_dataset/config.vsh.yaml -- \ --seed 123 # run one method -viash run src/label_projection/methods/knn/config.vsh.yaml -- \ +viash run src/tasks/label_projection/methods/knn/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output $DATASET_DIR/knn.h5ad # run one metric -viash run src/label_projection/metrics/accuracy/config.vsh.yaml -- \ +viash run src/tasks/label_projection/metrics/accuracy/config.vsh.yaml -- \ --input_prediction $DATASET_DIR/knn.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/knn_accuracy.h5ad @@ -44,7 +44,7 @@ export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/label_projection/workflows/run/main.nf \ + -main-script src/tasks/label_projection/workflows/run/main.nf \ -profile docker \ -resume \ --id pancreas \ diff --git a/src/tasks/label_projection/workflows/run/nextflow.config b/src/tasks/label_projection/workflows/run/nextflow.config index a2e3947b61..3739c38969 100644 --- a/src/tasks/label_projection/workflows/run/nextflow.config +++ b/src/tasks/label_projection/workflows/run/nextflow.config @@ -6,7 +6,7 @@ manifest { } params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() } // include common settings diff --git a/src/tasks/label_projection/workflows/run/run_test.sh b/src/tasks/label_projection/workflows/run/run_test.sh index cece1a44e7..90e4a498b2 100755 --- a/src/tasks/label_projection/workflows/run/run_test.sh +++ b/src/tasks/label_projection/workflows/run/run_test.sh @@ -22,7 +22,7 @@ export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/label_projection/workflows/run/main.nf \ + -main-script src/tasks/label_projection/workflows/run/main.nf \ -profile docker \ -resume \ --id pancreas \ diff --git a/src/tasks/multimodal_data_integration/workflows/run/nextflow.config b/src/tasks/multimodal_data_integration/workflows/run/nextflow.config index 91add22b77..e2de284c42 100644 --- a/src/tasks/multimodal_data_integration/workflows/run/nextflow.config +++ b/src/tasks/multimodal_data_integration/workflows/run/nextflow.config @@ -4,7 +4,7 @@ manifest { // ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() } // set default container & default labels From f329ca3dfba166b8df866768b830ec25fe493d4c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sun, 28 May 2023 12:27:07 +0200 Subject: [PATCH 0895/1233] fix example path Former-commit-id: c1defe5981643c90a6f3edd68a7870d066a47d0b --- src/tasks/dimensionality_reduction/api/anndata_embedding.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml b/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml index 24034bdd10..31714c2eac 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml +++ b/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml @@ -1,6 +1,6 @@ type: file description: "A dataset with dimensionality reduction embedding." -example: "resources_test/dimensionality_reduction/pancreas/output.h5ad" +example: "resources_test/dimensionality_reduction/pancreas/embedding.h5ad" info: short_description: "Embedding" slots: From c46632ed50f7ab50c962bf6e6ae02fd9c25d4853 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 31 May 2023 13:10:48 +0200 Subject: [PATCH 0896/1233] Bump tj-actions/changed-files from 36.0.6 to 36.0.10 (#159) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.0.6 to 36.0.10. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.0.6...v36.0.10) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: b868cde895987e9dbaecb7ce972567c3c5d6cfce --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 056773dfdc..8d692750c3 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.0.6 + uses: tj-actions/changed-files@v36.0.10 with: separator: ";" diff_relative: true From f2490400b77be73a291790eefd10c27b670204cd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 31 May 2023 14:52:34 +0200 Subject: [PATCH 0897/1233] output more helpful error message (#161) Former-commit-id: 7a515d7993906ffa66fa7974f59da0d9fe28400a --- src/common/create_component/config.vsh.yaml | 1 + src/common/create_component/script.py | 18 +++++++++++++++++- 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index b8ce762bd0..e3495c45f3 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -40,6 +40,7 @@ functionality: Which API file to use. Defaults to `src//api/comp_.yaml`. In tasks with different subtypes of method, this location might not exist and you might need to manually specify a different API file to inherit from. + must_exist: false # required: true default: src/tasks/${VIASH_PAR_TASK}/api/comp_${VIASH_PAR_TYPE}.yaml - type: file diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 143f28969b..73b2d73edc 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -1,6 +1,7 @@ from typing import Any from ruamel.yaml import YAML from pathlib import Path +import sys import os import re import subprocess @@ -15,7 +16,8 @@ 'language': 'python', 'name': 'new_comp', 'output': 'src/tasks/denoising/methods/new_comp', - 'api_file': 'src/tasks/denoising/api/comp_method.yaml' + 'api_file': 'src/tasks/denoising/api/comp_method.yaml', + 'viash_yaml': '_viash.yaml' } ## VIASH END @@ -385,6 +387,20 @@ def main(par): pretty_name = re.sub("_", " ", par['name']).title() + ## CHECK API FILE + newline = "\n" + api_file = Path(par["api_file"]) + viash_yaml = Path(par["viash_yaml"]) + if not api_file.exists(): + api_files = [str(x.relative_to(viash_yaml.parent)) for x in api_file.parent.glob("**/comp_*.y*ml")] + list.sort(api_files) + sys.exit(strip_margin(f"""\ + |Could not find component API file at location '{par['api_file']}'. + |You might need to manually specify a value for the '--api_file' parameter. + | + |Detected component API files: + |- {(newline + "- ").join(api_files)}""")) + ####### CREATE OUTPUT DIR ####### out_dir = Path(par["output"]) out_dir.mkdir(exist_ok=True) From e292708592fc2bc72dc1990dbe4e5ccaf8035a5f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Jun 2023 07:48:23 +0200 Subject: [PATCH 0898/1233] Bump tj-actions/changed-files from 36.0.10 to 36.0.11 (#162) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.0.10 to 36.0.11. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.0.10...v36.0.11) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: b2461933775cab3be9ee406b878e002412391712 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 8d692750c3..338071d951 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.0.10 + uses: tj-actions/changed-files@v36.0.11 with: separator: ";" diff_relative: true From d816f178d466a59a50ed46c424606ebe62c44881 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Jun 2023 07:52:27 +0200 Subject: [PATCH 0899/1233] Update_create_component (#163) * output more helpful error message * add helper functions * improve create component interface Former-commit-id: 83c4a5d2e4cee93f9eb15ba91a28d48849b4f91f --- src/common/create_component/config.vsh.yaml | 1 + src/common/create_component/script.py | 68 +++++++++++-------- .../helper_functions/read_and_merge_yaml.R | 68 +++++++++++++++++++ .../helper_functions/read_and_merge_yaml.py | 49 +++++++++++++ src/common/helper_functions/strip_margin.py | 3 + 5 files changed, 161 insertions(+), 28 deletions(-) create mode 100644 src/common/helper_functions/read_and_merge_yaml.R create mode 100644 src/common/helper_functions/read_and_merge_yaml.py create mode 100644 src/common/helper_functions/strip_margin.py diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index e3495c45f3..4e927f4715 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -52,6 +52,7 @@ functionality: resources: - type: python_script path: script.py + - path: /src/common/helper_functions/read_and_merge_yaml.py test_resources: - type: python_script path: test.py diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 73b2d73edc..c7292a8bd4 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -11,18 +11,22 @@ ## VIASH START par = { - 'task': 'denoising', - 'type': 'method', - 'language': 'python', - 'name': 'new_comp', - 'output': 'src/tasks/denoising/methods/new_comp', - 'api_file': 'src/tasks/denoising/api/comp_method.yaml', - 'viash_yaml': '_viash.yaml' + "task": "denoising", + "type": "method", + "language": "python", + "name": "new_comp", + "output": "src/tasks/denoising/methods/new_comp", + "api_file": "src/tasks/denoising/api/comp_method.yaml", + "viash_yaml": "_viash.yaml" } ## VIASH END +# import helper function +sys.path.append(meta["resources_dir"]) +from read_and_merge_yaml import read_and_merge_yaml + def strip_margin(text: str) -> str: - return re.sub('(\n?)[ \t]*\|', '\\1', text) + return re.sub("(\n?)[ \t]*\|", "\\1", text) def create_config_template(par): config_template = yaml.load(strip_margin(f'''\ @@ -388,50 +392,58 @@ def main(par): pretty_name = re.sub("_", " ", par['name']).title() ## CHECK API FILE - newline = "\n" api_file = Path(par["api_file"]) viash_yaml = Path(par["viash_yaml"]) + project_dir = viash_yaml.parent if not api_file.exists(): - api_files = [str(x.relative_to(viash_yaml.parent)) for x in api_file.parent.glob("**/comp_*.y*ml")] - list.sort(api_files) + comp_types = [x.with_suffix("").name.removeprefix("comp_") for x in api_file.parent.glob("**/comp_*.y*ml")] + list.sort(comp_types) sys.exit(strip_margin(f"""\ - |Could not find component API file at location '{par['api_file']}'. - |You might need to manually specify a value for the '--api_file' parameter. - | - |Detected component API files: - |- {(newline + "- ").join(api_files)}""")) + |Error: Invalid --type argument. + | Reason: Could not find API file at '{api_file.relative_to(project_dir)}'. + | Possible values for --type: {', '.join(comp_types)}.""")) + + ## READ API FILE + api = read_and_merge_yaml(api_file) + comp_type = api.get("functionality", {}).get("info", {}).get("type", {}) + if not comp_type: + sys.exit(strip_margin(f"""\ + |Error: API file is incorrectly formatted. + | Reason: Could not find component type at `.functionality.info.type`.' + | Please fix the formatting of the API file.""")) ####### CREATE OUTPUT DIR ####### out_dir = Path(par["output"]) out_dir.mkdir(exist_ok=True) ####### CREATE CONFIG ####### - config_file = out_dir / 'config.vsh.yaml' + config_file = out_dir / "config.vsh.yaml" # get config template config_template = create_config_template(par) # Add component specific info - if par['type'] == 'metric': + # TODO: this should be based on a component type spec + if comp_type == "metric": add_metric_info(config_template, par, pretty_name) - else: + elif comp_type == "method": add_method_info(config_template, par, pretty_name) # add script to resources add_script_resource(config_template, par) # add elements depending on language - if par['language'] == 'python': + if par["language"] == "python": add_python_setup(config_template) - if par['language'] == 'r': + if par["language"] == "r": add_r_setup(config_template) - with open(config_file, 'w') as f: + with open(config_file, "w") as f: yaml.dump(config_template, f) ####### CREATE SCRIPT ####### - script_file = out_dir / config_template['functionality']['resources'][0]['path'] + script_file = out_dir / config_template["functionality"]["resources"][0]["path"] # touch file script_file.touch() @@ -442,14 +454,14 @@ def main(par): # set reasonable values set_par_values(final_config) - if par['language'] == 'python': - script_out = create_python_script(par, final_config, par['type']) + if par["language"] == "python": + script_out = create_python_script(par, final_config, comp_type) - if par['language'] == 'r': - script_out = create_r_script(par, final_config, par['type']) + if par["language"] == "r": + script_out = create_r_script(par, final_config, comp_type) # write script - with open(script_file, 'w') as f: + with open(script_file, "w") as f: f.write(script_out) diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R new file mode 100644 index 0000000000..5663630c55 --- /dev/null +++ b/src/common/helper_functions/read_and_merge_yaml.R @@ -0,0 +1,68 @@ +#' Read a Viash YAML +#' +#' If the YAML contains a "__merge__" key anywhere in the yaml, +#' the path specified in that YAML will be read and the two +#' lists will be merged. This is a recursive procedure. +#' +#' @param path Path to Viash YAML +read_and_merge_yaml <- function(path) { + data <- suppressWarnings(yaml::read_yaml(path)) + .ram_process_merge(data, path) +} + +.ram_is_named_list <- function(obj) { + is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj)))) +} + +.ram_process_merge <- function(data, path) { + if (.ram_is_named_list(data)) { + # check whether children have `__merge__` entries + processed_data <- lapply(data, function(dat) { + .ram_process_merge(dat, path) + }) + names(processed_data) <- names(data) + + # if current element has __merge__, read list2 yaml and combine with data + new_data <- + if ("__merge__" %in% names(processed_data)) { + new_data_path <- paste0(dirname(path), "/", processed_data$`__merge__`) + read_and_merge_yaml(new_data_path) + } else { + list() + } + + .ram_deep_merge(new_data, processed_data) + } else if (is.list(data)) { + lapply(data, function(dat) { + .ram_process_merge(dat, path) + }) + } else { + data + } +} + +.ram_deep_merge <- function(list1, list2) { + if (.ram_is_named_list(list1) && .ram_is_named_list(list2)) { + # if list1 and list2 are objects, recursively merge + keys <- unique(c(names(list1), names(list2))) + out <- lapply(keys, function(key) { + if (key %in% names(list1)) { + if (key %in% names(list2)) { + .ram_deep_merge(list1[[key]], list2[[key]]) + } else { + list1[[key]] + } + } else { + list2[[key]] + } + }) + names(out) <- keys + out + } else if (is.list(list1) && is.list(list2)) { + # if list1 and list2 are both lists, append + c(list1, list2) + } else { + # else override list1 with list2 + list2 + } +} \ No newline at end of file diff --git a/src/common/helper_functions/read_and_merge_yaml.py b/src/common/helper_functions/read_and_merge_yaml.py new file mode 100644 index 0000000000..7c62507fb5 --- /dev/null +++ b/src/common/helper_functions/read_and_merge_yaml.py @@ -0,0 +1,49 @@ +def read_and_merge_yaml(path): + """Read a Viash YAML + + If the YAML contains a "__merge__" key anywhere in the yaml, + the path specified in that YAML will be read and the two + lists will be merged. This is a recursive procedure. + + Arguments: + path -- Path to the Viash YAML""" + import ruamel.yaml as yaml + with open(path, 'r') as stream: + data = yaml.safe_load(stream) + return _ram_process_merge(data, path) + +def _ram_deep_merge(dict1, dict2): + if isinstance(dict1, dict) and isinstance(dict2, dict): + keys = set(list(dict1.keys()) + list(dict2.keys())) + out = {} + for key in keys: + if key in dict1: + if key in dict2: + out[key] = _ram_deep_merge(dict1[key], dict2[key]) + else: + out[key] = dict1[key] + else: + out[key] = dict2[key] + return out + elif isinstance(dict1, list) and isinstance(dict2, list): + return dict1 + dict2 + else: + return dict2 + +def _ram_process_merge(data, path): + import os + if isinstance(data, dict): + processed_data = {k: _ram_process_merge(v, path) for k, v in data.items()} + + if "__merge__" in processed_data: + new_data_path = os.path.join(os.path.dirname(path), processed_data["__merge__"]) + new_data = read_and_merge_yaml(new_data_path) + else: + new_data = {} + + return _ram_deep_merge(new_data, processed_data) + elif isinstance(data, list): + return [_ram_process_merge(dat, path) for dat in data] + else: + return data + diff --git a/src/common/helper_functions/strip_margin.py b/src/common/helper_functions/strip_margin.py new file mode 100644 index 0000000000..25a1f0426f --- /dev/null +++ b/src/common/helper_functions/strip_margin.py @@ -0,0 +1,3 @@ +def strip_margin(text: str) -> str: + import re + return re.sub('(\n?)[ \t]*\|', '\\1', text) \ No newline at end of file From 4961885316bcbf9dd9ca05b937581e8015a3f055 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Jun 2023 09:41:41 +0200 Subject: [PATCH 0900/1233] Minor_fixes (#164) * make sure python doesn't create pyc and pyo files * add helper function Former-commit-id: e0e9f1d0e38ddd39c06752f7988ab9935322ac90 --- src/common/create_component/script.py | 5 ++++- src/common/helper_functions/strip_margin.R | 3 +++ src/tasks/batch_integration/process_dataset/script.py | 3 +++ src/tasks/denoising/process_dataset/script.py | 3 +++ src/tasks/dimensionality_reduction/process_dataset/script.py | 3 +++ src/tasks/label_projection/process_dataset/script.py | 3 +++ 6 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 src/common/helper_functions/strip_margin.R diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index c7292a8bd4..476251d7d6 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -21,6 +21,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper function sys.path.append(meta["resources_dir"]) from read_and_merge_yaml import read_and_merge_yaml @@ -426,7 +429,7 @@ def main(par): # TODO: this should be based on a component type spec if comp_type == "metric": add_metric_info(config_template, par, pretty_name) - elif comp_type == "method": + elif comp_type in ["method", "control_method"]: add_method_info(config_template, par, pretty_name) # add script to resources diff --git a/src/common/helper_functions/strip_margin.R b/src/common/helper_functions/strip_margin.R new file mode 100644 index 0000000000..33356c8a9e --- /dev/null +++ b/src/common/helper_functions/strip_margin.R @@ -0,0 +1,3 @@ +strip_margin <- function(text, symbol = "\\|") { + gsub(paste0("(\n?)[ \t]*", symbol), "\\1", text) +} \ No newline at end of file diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index 34bd3f07dd..396f77684c 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -11,6 +11,9 @@ meta = {} ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index e79a8f5074..d0827b0ea0 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -16,6 +16,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # add helper scripts to path sys.path.append(meta["resources_dir"]) from helper import split_molecules diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index 9563ed56f0..d4aeca0e16 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -13,6 +13,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 71584f5d4d..55f7c75aa8 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -20,6 +20,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata From 0314f369dc4e6709606ad9df3cd419d7a1508041 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Jun 2023 14:04:27 +0200 Subject: [PATCH 0901/1233] Copy bibliography (#165) * Copied library.bib file from v1 * move batch integration bibliography to main bibliography * move bibtex * fix bibtex entry * add component for updating the bibtex, update bibtex * add unit test Former-commit-id: ceecdad3ebe6c0f2b85597a092627c9a50eee9ee --- src/common/library.bib | 1317 +++++++++++++++++++ src/migration/update_bibtex/config.vsh.yaml | 25 + src/migration/update_bibtex/script.py | 39 + src/migration/update_bibtex/test.py | 62 + src/tasks/batch_integration/library.bib | 75 -- 5 files changed, 1443 insertions(+), 75 deletions(-) create mode 100644 src/common/library.bib create mode 100644 src/migration/update_bibtex/config.vsh.yaml create mode 100644 src/migration/update_bibtex/script.py create mode 100644 src/migration/update_bibtex/test.py delete mode 100644 src/tasks/batch_integration/library.bib diff --git a/src/common/library.bib b/src/common/library.bib new file mode 100644 index 0000000000..e053f4fb6f --- /dev/null +++ b/src/common/library.bib @@ -0,0 +1,1317 @@ +@misc{10x2018pbmc, + title = {1k PBMCs from a Healthy Donor (v3 chemistry)}, + author = {{10x Genomics}}, + year = {2018}, + url = {https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0} +} + + +@misc{10x2019pbmc, + title = {5k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor with a Panel of TotalSeq-B Antibodies (v3 chemistry)}, + author = {{10x Genomics}}, + year = {2019}, + url = {https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0} +} + + +@article{agrawal2021mde, + title = {Minimum-Distortion Embedding}, + author = {Akshay Agrawal and Alnur Ali and Stephen Boyd}, + year = {2021}, + journal = {Foundations and Trends{\textregistered} in Machine Learning}, + publisher = {Now Publishers}, + volume = {14}, + number = {3}, + pages = {211--378}, + doi = {10.1561/2200000090}, + url = {https://doi.org/10.1561/2200000090} +} + + +@article{aliee2021autogenes, + title = {{AutoGeneS}: Automatic gene selection using multi-objective optimization for {RNA}-seq deconvolution}, + author = {Hananeh Aliee and Fabian J. 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name: --library + description: Path to bibtex file + type: file + default: src/common/library.bib + direction: output + - name: --library_v1 + description: Url of the v1 bibtex file + type: string + default: https://raw.githubusercontent.com/openproblems-bio/openproblems/main/main.bib + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + image: python:3.10 + setup: + - type: python + pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/migration/update_bibtex/script.py b/src/migration/update_bibtex/script.py new file mode 100644 index 0000000000..84f6a9a337 --- /dev/null +++ b/src/migration/update_bibtex/script.py @@ -0,0 +1,39 @@ +import bibtexparser +from tempfile import NamedTemporaryFile +import urllib.request + +## VIASH START +par = { + 'library': 'src/common/library.bib', + 'library_v1': 'https://raw.githubusercontent.com/openproblems-bio/openproblems/main/main.bib' +} +## VIASH END + +# Load the BibTeX file +print(">> Read input bibtex file", flush=True) +bib_input = bibtexparser.parse_file(par["library"]) + +print(" Library keys: " + ', '.join(bib_input.entries_dict.keys()), flush=True) + +# Merge with v1 library +if par["library_v1"]: + print(">> Merge with v1 library", flush=True) + with NamedTemporaryFile("w", suffix=".bib") as tempfile: + _ = urllib.request.urlretrieve(par["library_v1"], tempfile.name) + bib_v1 = bibtexparser.parse_file(tempfile.name) + + print(" Library v1 keys: " + ', '.join(bib_v1.entries_dict.keys()), flush=True) + blocks = bib_input.blocks + bib_v1.blocks +else: + blocks = bib_input.blocks + +# Remove duplicates +print(">> Remove duplicates", flush=True) +unique_blocks = {block.key : block for block in blocks if not hasattr(block, "error")} +bib_new = bibtexparser.Library(unique_blocks.values()) + +print(" New keys: " + ', '.join(bib_new.entries_dict.keys()), flush=True) + +# Save to a new BibTeX file +print(">> Write to file", flush=True) +bibtexparser.write_file(par["library"], bib_new) diff --git a/src/migration/update_bibtex/test.py b/src/migration/update_bibtex/test.py new file mode 100644 index 0000000000..2104488fa2 --- /dev/null +++ b/src/migration/update_bibtex/test.py @@ -0,0 +1,62 @@ +import subprocess + +def test_with_duplicates(exec_path): + # Create a temporary file with duplicate entries + with open("test_with_duplicates.bib", mode="w") as file: + file.write("@article{duplicate,\n author = {Duplicate, A.},\n title = {Duplicate article},\n year = {2022},\n}\n@article{duplicate,\n author = {Duplicate, A.},\n title = {Duplicate article},\n year = {2022},\n}\n") + + # Test basic functionality without merging + result = subprocess.run( + [exec_path, "--library", "test_with_duplicates.bib", "--library_v1", ""], + capture_output=True, + check=True, + text=True + ) + print(result.stdout, flush=True) + + assert "Read input bibtex file" in result.stdout, "Reading input failed" + assert not "Merge with v1 library" in result.stdout, "Merging failed" + assert "Remove duplicates" in result.stdout, "Duplicate removal failed" + assert "Write to file" in result.stdout, "Writing output failed" + + # Check the output file to make sure duplicates are removed + with open("test_with_duplicates.bib", "r") as f: + contents = f.read() + count = contents.count("article{") + assert count == 1, f"Count should be 1 but is {count}" + +def test_merge(exec_path, lib_v1_url): + # Create a temporary file with duplicate entries + with open("test_merge.bib", mode="w") as file: + file.write("@article{entry,\n author = {Duplicate, A.},\n title = {Duplicate article},\n year = {2022},\n}\n") + + # Test basic functionality without merging + result = subprocess.run( + [exec_path, "--library", "test_merge.bib", "--library_v1", lib_v1_url], + capture_output=True, + check=True, + text=True + ) + print(result.stdout, flush=True) + + assert "Read input bibtex file" in result.stdout, "Reading input failed" + assert "Merge with v1 library" in result.stdout, "Merging failed" + assert "Remove duplicates" in result.stdout, "Duplicate removal failed" + assert "Write to file" in result.stdout, "Writing output failed" + + # Check the output file to make sure duplicates are removed + with open("test_merge.bib", "r") as f: + contents = f.read() + count = contents.count("article{") + + assert count > 1, f"Count should be greater than 1 but is {count}" + +test_merge( + exec_path=meta["executable"], + lib_v1_url="https://raw.githubusercontent.com/openproblems-bio/openproblems/main/main.bib" +) +test_with_duplicates( + exec_path=meta["executable"] +) + +print("All tests passed!", flush=True) \ No newline at end of file diff --git a/src/tasks/batch_integration/library.bib b/src/tasks/batch_integration/library.bib deleted file mode 100644 index 0081cf3aa2..0000000000 --- a/src/tasks/batch_integration/library.bib +++ /dev/null @@ -1,75 +0,0 @@ -@article{hubert1985comparing, - doi = {10.1007/bf01908075}, - url = {https://doi.org/10.1007/bf01908075}, - year = {1985}, - month = dec, - publisher = {Springer Science and Business Media {LLC}}, - volume = {2}, - number = {1}, - pages = {193--218}, - author = {Lawrence Hubert and Phipps Arabie}, - title = {Comparing partitions}, - journal = {Journal of Classification} -} -@inproceedings{amelio2015normalized, - doi = {10.1145/2808797.2809344}, - url = {https://doi.org/10.1145/2808797.2809344}, - year = {2015}, - month = aug, - publisher = {{ACM}}, - author = {Alessia Amelio and Clara Pizzuti}, - title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?}, - booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015} -} -@article{zappia2018exploring, - doi = {10.1371/journal.pcbi.1006245}, - url = {https://doi.org/10.1371/journal.pcbi.1006245}, - year = {2018}, - month = jun, - publisher = {Public Library of Science ({PLoS})}, - volume = {14}, - number = {6}, - pages = {e1006245}, - author = {Luke Zappia and Belinda Phipson and Alicia Oshlack}, - editor = {Dina Schneidman}, - title = {Exploring the single-cell {RNA}-seq analysis landscape with the {scRNA}-tools database}, - journal = {{PLOS} Computational Biology} -} -@article{tran2020benchmark, - doi = {10.1186/s13059-019-1850-9}, - url = {https://doi.org/10.1186/s13059-019-1850-9}, - year = {2020}, - month = jan, - publisher = {Springer Science and Business Media {LLC}}, - volume = {21}, - number = {1}, - author = {Hoa Thi Nhu Tran and Kok Siong Ang and Marion Chevrier and Xiaomeng Zhang and Nicole Yee Shin Lee and Michelle Goh and Jinmiao Chen}, - title = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data}, - journal = {Genome Biology} -} -@article{chazarragil2021flexible, - doi = {10.1093/nar/gkab004}, - url = {https://doi.org/10.1093/nar/gkab004}, - year = {2021}, - month = feb, - publisher = {Oxford University Press ({OUP})}, - volume = {49}, - number = {7}, - pages = {e42--e42}, - author = {Ruben Chazarra-Gil and Stijn van~Dongen and Vladimir~Yu Kiselev and Martin Hemberg}, - title = {Flexible comparison of batch correction methods for single-cell {RNA}-seq using {BatchBench}}, - journal = {Nucleic Acids Research} -} -@article{mereu2020benchmarking, - doi = {10.1038/s41587-020-0469-4}, - url = {https://doi.org/10.1038/s41587-020-0469-4}, - year = {2020}, - month = apr, - publisher = {Springer Science and Business Media {LLC}}, - volume = {38}, - number = {6}, - pages = {747--755}, - author = {Elisabetta Mereu and Atefeh Lafzi and Catia Moutinho and Christoph Ziegenhain and Davis J. McCarthy and Adri{\'{a}}n {\'{A}}lvarez-Varela and Eduard Batlle and Sagar and Dominic Gr\"{u}n and Julia K. Lau and St{\'{e}}phane C. Boutet and Chad Sanada and Aik Ooi and Robert C. Jones and Kelly Kaihara and Chris Brampton and Yasha Talaga and Yohei Sasagawa and Kaori Tanaka and Tetsutaro Hayashi and Caroline Braeuning and Cornelius Fischer and Sascha Sauer and Timo Trefzer and Christian Conrad and Xian Adiconis and Lan T. Nguyen and Aviv Regev and Joshua Z. Levin and Swati Parekh and Aleksandar Janjic and Lucas E. Wange and Johannes W. Bagnoli and Wolfgang Enard and Marta Gut and Rickard Sandberg and Itoshi Nikaido and Ivo Gut and Oliver Stegle and Holger Heyn}, - title = {Benchmarking single-cell {RNA}-sequencing protocols for cell atlas projects}, - journal = {Nature Biotechnology} -} \ No newline at end of file From 016b521adb237c570315af782e0dc80bfc70c90b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Jun 2023 14:11:14 +0200 Subject: [PATCH 0902/1233] merge more bibtex entries Former-commit-id: b14493a075684d771a1d663fe05f6f429adc47e3 --- src/common/library.bib | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/src/common/library.bib b/src/common/library.bib index e053f4fb6f..e61acf4615 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1315,3 +1315,41 @@ @article{mereu2020benchmarking volume = {38}, year = {2020} } + + +@misc{cannoodt2021viashfromscripts, + doi = {10.48550/ARXIV.2110.11494}, + url = {https://arxiv.org/abs/2110.11494}, + author = {Cannoodt, Robrecht and Cannoodt, Hendrik and Van de Kerckhove, Eric and Boschmans, Andy and De Maeyer, Dries and Verbeiren, Toni}, + keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences}, + title = {Viash: from scripts to pipelines}, + publisher = {arXiv}, + year = {2021}, + copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International} +} + + +@article{donoho2017yearsdatascience, + doi = {10.1080/10618600.2017.1384734}, + url = {https://doi.org/10.1080/10618600.2017.1384734}, + year = {2017}, + month = {Oct.}, + publisher = {Informa {UK} Limited}, + volume = {26}, + number = {4}, + pages = {745--766}, + author = {David Donoho}, + title = {50 Years of Data Science}, + journal = {Journal of Computational and Graphical Statistics} +} + + +@article{virshup2021anndataannotateddata, + doi = {10.1101/2021.12.16.473007}, + url = {https://doi.org/10.1101/2021.12.16.473007}, + year = {2021}, + month = {Dec.}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Isaac Virshup and Sergei Rybakov and Fabian J. Theis and Philipp Angerer and F. Alexander Wolf}, + title = {anndata: Annotated data} +} From cbe04face7574acbba807512d73f63c1365a9db4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 1 Jun 2023 14:52:09 +0200 Subject: [PATCH 0903/1233] sort library Former-commit-id: ed13cb8d2d92747580223ab0d97b97a93b259a89 --- src/common/library.bib | 306 +++++++++++++------------- src/migration/update_bibtex/script.py | 4 +- 2 files changed, 156 insertions(+), 154 deletions(-) diff --git a/src/common/library.bib b/src/common/library.bib index e61acf4615..97b995cf1c 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -43,6 +43,18 @@ @article{aliee2021autogenes } +@inproceedings{amelio2015normalized, + doi = {10.1145/2808797.2809344}, + url = {https://doi.org/10.1145/2808797.2809344}, + year = {2015}, + month = {Aug.}, + publisher = {{ACM}}, + author = {Alessia Amelio and Clara Pizzuti}, + title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?}, + booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015} +} + + @article{andersson2020single, title = {Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography}, author = {Alma Andersson and Joseph Bergenstr{\aa}hle and Michaela Asp and Ludvig Bergenstr{\aa}hle and Aleksandra Jurek and Jos{\'{e}} Fern{\'{a}}ndez Navarro and Joakim Lundeberg}, @@ -57,6 +69,12 @@ @article{andersson2020single } +@string{apr = {Apr.}} + + +@string{aug = {Aug.}} + + @article{batson2019molecular, title = {Molecular Cross-Validation for Single-Cell RNA-seq}, author = {Batson, Joshua and Royer, Lo{\"\i}c and Webber, James}, @@ -145,6 +163,18 @@ @article{cable2021robust } +@misc{cannoodt2021viashfromscripts, + doi = {10.48550/ARXIV.2110.11494}, + url = {https://arxiv.org/abs/2110.11494}, + author = {Cannoodt, Robrecht and Cannoodt, Hendrik and Van de Kerckhove, Eric and Boschmans, Andy and De Maeyer, Dries and Verbeiren, Toni}, + keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences}, + title = {Viash: from scripts to pipelines}, + publisher = {arXiv}, + year = {2021}, + copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International} +} + + @article{cao2018joint, title = {Joint profiling of chromatin accessibility and gene expression in thousands of single cells}, author = {Junyue Cao and Darren A. Cusanovich and Vijay Ramani and Delasa Aghamirzaie and Hannah A. Pliner and Andrew J. Hill and Riza M. Daza and Jose L. McFaline-Figueroa and Jonathan S. Packer and Lena Christiansen and Frank J. Steemers and Andrew C. Adey and Cole Trapnell and Jay Shendure}, @@ -174,6 +204,21 @@ @article{cao2020human } +@article{chazarragil2021flexible, + doi = {10.1093/nar/gkab004}, + url = {https://doi.org/10.1093/nar/gkab004}, + year = {2021}, + month = {Feb.}, + publisher = {Oxford University Press ({OUP})}, + volume = {49}, + number = {7}, + pages = {e42--e42}, + author = {Ruben Chazarra-Gil and Stijn van~Dongen and Vladimir~Yu Kiselev and Martin Hemberg}, + title = {Flexible comparison of batch correction methods for single-cell {RNA}-seq using {BatchBench}}, + journal = {Nucleic Acids Research} +} + + @article{chen2009local, title = {Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis}, author = {Lisha Chen and Andreas Buja}, @@ -256,6 +301,9 @@ @inproceedings{davis2006prauc } +@string{dec = {Dec.}} + + @article{dimitrov2022comparison, title = {Comparison of methods and resources for cell-cell communication inference from single-cell {RNA}-Seq data}, author = {Daniel Dimitrov and D{\'{e}}nes T\"{u}rei and Martin Garrido-Rodriguez and Paul L. Burmedi and James S. Nagai and Charlotte Boys and Ricardo O. Ramirez Flores and Hyojin Kim and Bence Szalai and Ivan G. Costa and Alberto Valdeolivas and Aur{\'{e}}lien Dugourd and Julio Saez-Rodriguez}, @@ -270,6 +318,21 @@ @article{dimitrov2022comparison } +@article{donoho2017yearsdatascience, + doi = {10.1080/10618600.2017.1384734}, + url = {https://doi.org/10.1080/10618600.2017.1384734}, + year = {2017}, + month = {Oct.}, + publisher = {Informa {UK} Limited}, + volume = {26}, + number = {4}, + pages = {745--766}, + author = {David Donoho}, + title = {50 Years of Data Science}, + journal = {Journal of Computational and Graphical Statistics} +} + + @article{efremova2020cellphonedb, title = {{CellPhoneDB}: inferring cell{\textendash}cell communication from combined expression of multi-subunit ligand{\textendash}receptor complexes}, author = {Mirjana Efremova and Miquel Vento-Tormo and Sarah A. Teichmann and Roser Vento-Tormo}, @@ -299,6 +362,9 @@ @article{eraslan2019single } +@string{feb = {Feb.}} + + @article{gower1975generalized, title = {Generalized procrustes analysis}, author = {J. C. Gower}, @@ -472,42 +538,6 @@ @article{hou2019scmatch } -@string{jan = {Jan}} - - -@string{feb = {Feb.}} - - -@string{mar = {Mar.}} - - -@string{apr = {Apr.}} - - -@string{may = {May}} - - -@string{jun = {Jun.}} - - -@string{jul = {Jul.}} - - -@string{aug = {Aug.}} - - -@string{sep = {Sept.}} - - -@string{oct = {Oct.}} - - -@string{nov = {Nov.}} - - -@string{dec = {Dec.}} - - @article{hou2020predicting, title = {Predicting cell-to-cell communication networks using {NATMI}}, author = {Rui Hou and Elena Denisenko and Huan Ting Ong and Jordan A. Ramilowski and Alistair R. R. Forrest}, @@ -536,6 +566,30 @@ @article{hou2020systematic } +@article{hubert1985comparing, + doi = {10.1007/bf01908075}, + url = {https://doi.org/10.1007/bf01908075}, + year = {1985}, + month = {Dec.}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {2}, + number = {1}, + pages = {193--218}, + author = {Lawrence Hubert and Phipps Arabie}, + title = {Comparing partitions}, + journal = {Journal of Classification} +} + + +@string{jan = {Jan}} + + +@string{jul = {Jul.}} + + +@string{jun = {Jun.}} + + @article{kiselev2019challenges, title = {Challenges in unsupervised clustering of single-cell {RNA}-seq data}, author = {Vladimir Yu Kiselev and Tallulah S. Andrews and Martin Hemberg}, @@ -740,6 +794,12 @@ @misc{lun2019fastmnn } +@string{mar = {Mar.}} + + +@string{may = {May}} + + @article{mcinnes2018umap, title = {UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction}, author = {McInnes, Leland and Healy, John and Melville, James}, @@ -753,6 +813,19 @@ @article{mcinnes2018umap } +@article{mereu2020benchmarking, + doi = {10.1038/s41587-020-0469-4}, + author = {Mereu, Elisabetta and Lafzi, Atefeh and Moutinho, Catia and Ziegenhain, Christoph and McCarthy, Davis J and Alvarez-Varela, Adrian and Batlle, Eduard and Sagar and Gruen, Dominic and Lau, Julia K and others}, + journal = {Nature biotechnology}, + number = {6}, + pages = {747--755}, + publisher = {Nature Publishing Group US New York}, + title = {Benchmarking single-cell {RNA}-sequencing protocols for cell atlas projects}, + volume = {38}, + year = {2020} +} + + @inbook{miles2005rsquared, title = {Encyclopedia of Statistics in Behavioral Science}, author = {Jeremy Miles}, @@ -810,6 +883,12 @@ @article{nestorowa2016single } +@string{nov = {Nov.}} + + +@string{oct = {Oct.}} + + @article{olsson2016single, title = {Single-cell analysis of mixed-lineage states leading to a binary cell fate choice}, author = {Andre Olsson and Meenakshi Venkatasubramanian and Viren K. Chaudhri and Bruce J. Aronow and Nathan Salomonis and Harinder Singh and H. Leighton Grimes}, @@ -935,6 +1014,9 @@ @article{schober2018correlation } +@string{sep = {Sept.}} + + @inproceedings{stanley2020harmonic, title = {Harmonic Alignment}, author = {Jay S. Stanley and Scott Gigante and Guy Wolf and Smita Krishnaswamy}, @@ -1049,6 +1131,20 @@ @article{tian2019benchmarking } +@article{tran2020benchmark, + doi = {10.1186/s13059-019-1850-9}, + url = {https://doi.org/10.1186/s13059-019-1850-9}, + year = {2020}, + month = {Jan}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {21}, + number = {1}, + author = {Hoa Thi Nhu Tran and Kok Siong Ang and Marion Chevrier and Xiaomeng Zhang and Nicole Yee Shin Lee and Michelle Goh and Jinmiao Chen}, + title = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data}, + journal = {Genome Biology} +} + + @article{van2018recovering, title = {Recovering Gene Interactions from Single-Cell Data Using Data Diffusion}, author = {David van Dijk and Roshan Sharma and Juozas Nainys and Kristina Yim and Pooja Kathail and Ambrose J. Carr and Cassandra Burdziak and Kevin R. Moon and Christine L. Chaffer and Diwakar Pattabiraman and Brian Bierie and Linas Mazutis and Guy Wolf and Smita Krishnaswamy and Dana Pe'er}, @@ -1103,6 +1199,17 @@ @article{venna2006local } +@article{virshup2021anndataannotateddata, + doi = {10.1101/2021.12.16.473007}, + url = {https://doi.org/10.1101/2021.12.16.473007}, + year = {2021}, + month = {Dec.}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Isaac Virshup and Sergei Rybakov and Fabian J. Theis and Philipp Angerer and F. Alexander Wolf}, + title = {anndata: Annotated data} +} + + @article{wagner2018knearest, title = {K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data}, author = {Wagner, Florian and Yan, Yun and Yanai, Itai}, @@ -1217,48 +1324,6 @@ @article{xu2021probabilistic } -@article{zhang2021pydrmetrics, - title = {{pyDRMetrics} - A Python toolkit for dimensionality reduction quality assessment}, - author = {Yinsheng Zhang and Qian Shang and Guoming Zhang}, - year = {2021}, - month = {Feb.}, - journal = {Heliyon}, - publisher = {Elsevier {BV}}, - volume = {7}, - number = {2}, - pages = {e06199}, - doi = {10.1016/j.heliyon.2021.e06199}, - url = {https://doi.org/10.1016/j.heliyon.2021.e06199} -} - - -@article{hubert1985comparing, - doi = {10.1007/bf01908075}, - url = {https://doi.org/10.1007/bf01908075}, - year = {1985}, - month = {Dec.}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {2}, - number = {1}, - pages = {193--218}, - author = {Lawrence Hubert and Phipps Arabie}, - title = {Comparing partitions}, - journal = {Journal of Classification} -} - - -@inproceedings{amelio2015normalized, - doi = {10.1145/2808797.2809344}, - url = {https://doi.org/10.1145/2808797.2809344}, - year = {2015}, - month = {Aug.}, - publisher = {{ACM}}, - author = {Alessia Amelio and Clara Pizzuti}, - title = {Is Normalized Mutual Information a Fair Measure for Comparing Community Detection Methods?}, - booktitle = {Proceedings of the 2015 {IEEE}/{ACM} International Conference on Advances in Social Networks Analysis and Mining 2015} -} - - @article{zappia2018exploring, doi = {10.1371/journal.pcbi.1006245}, url = {https://doi.org/10.1371/journal.pcbi.1006245}, @@ -1275,81 +1340,16 @@ @article{zappia2018exploring } -@article{tran2020benchmark, - doi = {10.1186/s13059-019-1850-9}, - url = {https://doi.org/10.1186/s13059-019-1850-9}, - year = {2020}, - month = {Jan}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {21}, - number = {1}, - author = {Hoa Thi Nhu Tran and Kok Siong Ang and Marion Chevrier and Xiaomeng Zhang and Nicole Yee Shin Lee and Michelle Goh and Jinmiao Chen}, - title = {A benchmark of batch-effect correction methods for single-cell {RNA} sequencing data}, - journal = {Genome Biology} -} - - -@article{chazarragil2021flexible, - doi = {10.1093/nar/gkab004}, - url = {https://doi.org/10.1093/nar/gkab004}, +@article{zhang2021pydrmetrics, + title = {{pyDRMetrics} - A Python toolkit for dimensionality reduction quality assessment}, + author = {Yinsheng Zhang and Qian Shang and Guoming Zhang}, year = {2021}, month = {Feb.}, - publisher = {Oxford University Press ({OUP})}, - volume = {49}, - number = {7}, - pages = {e42--e42}, - author = {Ruben Chazarra-Gil and Stijn van~Dongen and Vladimir~Yu Kiselev and Martin Hemberg}, - title = {Flexible comparison of batch correction methods for single-cell {RNA}-seq using {BatchBench}}, - journal = {Nucleic Acids Research} -} - - -@article{mereu2020benchmarking, - doi = {10.1038/s41587-020-0469-4}, - author = {Mereu, Elisabetta and Lafzi, Atefeh and Moutinho, Catia and Ziegenhain, Christoph and McCarthy, Davis J and Alvarez-Varela, Adrian and Batlle, Eduard and Sagar and Gruen, Dominic and Lau, Julia K and others}, - journal = {Nature biotechnology}, - number = {6}, - pages = {747--755}, - publisher = {Nature Publishing Group US New York}, - title = {Benchmarking single-cell {RNA}-sequencing protocols for cell atlas projects}, - volume = {38}, - year = {2020} -} - - -@misc{cannoodt2021viashfromscripts, - doi = {10.48550/ARXIV.2110.11494}, - url = {https://arxiv.org/abs/2110.11494}, - author = {Cannoodt, Robrecht and Cannoodt, Hendrik and Van de Kerckhove, Eric and Boschmans, Andy and De Maeyer, Dries and Verbeiren, Toni}, - keywords = {Software Engineering (cs.SE), FOS: Computer and information sciences, FOS: Computer and information sciences}, - title = {Viash: from scripts to pipelines}, - publisher = {arXiv}, - year = {2021}, - copyright = {Creative Commons Attribution Non Commercial Share Alike 4.0 International} -} - - -@article{donoho2017yearsdatascience, - doi = {10.1080/10618600.2017.1384734}, - url = {https://doi.org/10.1080/10618600.2017.1384734}, - year = {2017}, - month = {Oct.}, - publisher = {Informa {UK} Limited}, - volume = {26}, - number = {4}, - pages = {745--766}, - author = {David Donoho}, - title = {50 Years of Data Science}, - journal = {Journal of Computational and Graphical Statistics} -} - - -@article{virshup2021anndataannotateddata, - doi = {10.1101/2021.12.16.473007}, - url = {https://doi.org/10.1101/2021.12.16.473007}, - year = {2021}, - month = {Dec.}, - publisher = {Cold Spring Harbor Laboratory}, - author = {Isaac Virshup and Sergei Rybakov and Fabian J. Theis and Philipp Angerer and F. Alexander Wolf}, - title = {anndata: Annotated data} + journal = {Heliyon}, + publisher = {Elsevier {BV}}, + volume = {7}, + number = {2}, + pages = {e06199}, + doi = {10.1016/j.heliyon.2021.e06199}, + url = {https://doi.org/10.1016/j.heliyon.2021.e06199} } diff --git a/src/migration/update_bibtex/script.py b/src/migration/update_bibtex/script.py index 84f6a9a337..7d2b0d516e 100644 --- a/src/migration/update_bibtex/script.py +++ b/src/migration/update_bibtex/script.py @@ -1,6 +1,7 @@ import bibtexparser from tempfile import NamedTemporaryFile import urllib.request +import collections ## VIASH START par = { @@ -30,7 +31,8 @@ # Remove duplicates print(">> Remove duplicates", flush=True) unique_blocks = {block.key : block for block in blocks if not hasattr(block, "error")} -bib_new = bibtexparser.Library(unique_blocks.values()) +unique_blocks_sorted = collections.OrderedDict(sorted(unique_blocks.items())) +bib_new = bibtexparser.Library(unique_blocks_sorted.values()) print(" New keys: " + ', '.join(bib_new.entries_dict.keys()), flush=True) From d12ceb2163bb21e4ebfe9eedecd6c3e6762e1809 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 2 Jun 2023 17:17:19 +0200 Subject: [PATCH 0904/1233] Update/docker containers (#168) * update common comp docker images * update datasets comp docker images * update migration comp docker images * update denoising comp docker images * update dim_red comp docker images * update lab_proj comp docker images * update changelog * fix lab_proj f1 Former-commit-id: 653c537cc3b0782bda58d0c73dbe3108b8d43c5b --- CHANGELOG.md | 2 ++ src/common/check_dataset_schema/config.vsh.yaml | 5 +---- src/common/extract_scores/config.vsh.yaml | 8 ++------ src/common/get_api_info/config.vsh.yaml | 5 +---- src/common/get_method_info/config.vsh.yaml | 5 +---- src/common/get_metric_info/config.vsh.yaml | 5 +---- src/common/get_results/config.vsh.yaml | 2 +- src/common/get_task_info/config.vsh.yaml | 5 +---- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 5 +---- .../loaders/openproblems_v1_multimodal/config.vsh.yaml | 5 +---- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 4 +--- src/datasets/normalization/log_cpm/config.vsh.yaml | 4 +--- .../normalization/log_scran_pooling/config.vsh.yaml | 10 +++------- src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 4 +--- src/datasets/processors/hvg/config.vsh.yaml | 4 +--- src/datasets/processors/knn/config.vsh.yaml | 4 +--- src/datasets/processors/pca/config.vsh.yaml | 4 +--- src/datasets/processors/subsample/config.vsh.yaml | 4 +--- src/migration/check_migration_status/config.vsh.yaml | 6 +----- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../control_methods/no_denoising/config.vsh.yaml | 7 +------ .../control_methods/perfect_denoising/config.vsh.yaml | 7 +------ src/tasks/denoising/methods/alra/config.vsh.yaml | 8 ++------ src/tasks/denoising/methods/dca/config.vsh.yaml | 4 +--- .../denoising/methods/knn_smoothing/config.vsh.yaml | 4 +--- src/tasks/denoising/methods/magic/config.vsh.yaml | 4 ++-- src/tasks/denoising/metrics/mse/config.vsh.yaml | 4 +--- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 7 ++----- src/tasks/denoising/process_dataset/config.vsh.yaml | 4 +--- .../control_methods/random_features/config.vsh.yaml | 7 +------ .../control_methods/true_features/config.vsh.yaml | 7 ++----- .../methods/densmap/config.vsh.yaml | 4 +--- .../methods/ivis/config.vsh.yaml | 4 +--- .../methods/neuralee/config.vsh.yaml | 4 +--- .../methods/pca/config.vsh.yaml | 7 ++----- .../methods/phate/config.vsh.yaml | 4 +--- .../methods/tsne/config.vsh.yaml | 4 +--- .../methods/umap/config.vsh.yaml | 4 +--- .../metrics/coranking/config.vsh.yaml | 8 ++------ .../metrics/density_preservation/config.vsh.yaml | 4 +--- .../metrics/rmse/config.vsh.yaml | 4 +--- .../metrics/trustworthiness/config.vsh.yaml | 4 +--- .../process_dataset/config.vsh.yaml | 7 +------ .../control_methods/majority_vote/config.vsh.yaml | 7 +------ .../control_methods/random_labels/config.vsh.yaml | 7 ++----- .../control_methods/true_labels/config.vsh.yaml | 7 +------ src/tasks/label_projection/methods/knn/config.vsh.yaml | 7 ++----- .../methods/logistic_regression/config.vsh.yaml | 7 ++----- src/tasks/label_projection/methods/mlp/config.vsh.yaml | 7 ++----- .../methods/scanvi_scarches/config.vsh.yaml | 7 ++----- .../methods/seurat_transferdata/config.vsh.yaml | 8 ++------ .../label_projection/methods/xgboost/config.vsh.yaml | 7 ++----- .../label_projection/metrics/accuracy/config.vsh.yaml | 7 ++----- src/tasks/label_projection/metrics/f1/config.vsh.yaml | 7 ++----- .../label_projection/process_dataset/config.vsh.yaml | 7 +------ 56 files changed, 75 insertions(+), 226 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 129e3e9727..25f313db12 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ * Update "baseline" to "control" (PR #146) +* Update docker images to OP pyhton/R base images (#168) + ## common ### NEW FUNCTIONALITY diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 16af1e8d46..5af98810f6 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -42,9 +42,6 @@ functionality: path: test.py platforms: - type: docker - image: python:3.10 - setup: - - type: python - pip: [anndata~=0.8.0, pyyaml] + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 124becb00a..e5bdc2d060 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,12 +26,8 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r - cran: [ anndata, tidyverse ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata~=0.8.0 ] + cran: [ tidyverse ] - type: nextflow diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index a0528d2ad6..9db89bee1d 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -8,12 +8,9 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r cran: [ tidyverse ] - test_setup: - - type: apt - packages: [ python3, python3-pip, python3-dev, python-is-python3 ] - type: nextflow - type: native diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 81e54bf45f..91cdf0a79b 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r cran: [ tidyverse ] @@ -16,8 +16,5 @@ platforms: packages: [ curl, default-jdk ] - type: docker run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" - test_setup: - - type: apt - packages: [python3, python3-pip, python3-dev, python-is-python3] - type: nextflow - type: native diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 419cd6c140..11949acbf4 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r cran: [ tidyverse ] @@ -16,8 +16,5 @@ platforms: packages: [ curl, default-jdk ] - type: docker run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" - test_setup: - - type: apt - packages: [python3, python3-pip, python3-dev, python-is-python3, git] - type: nextflow - type: native diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 97d5344348..000ae3eab3 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index 595665948e..a6b2ed3e1d 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -8,9 +8,6 @@ functionality: path: script.py platforms: - type: docker - image: python:3.10 - setup: - - type: python - pip: [ pyyaml ] + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow - type: native diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index bea378f233..a5c0762230 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -64,7 +64,7 @@ functionality: path: test.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: apt packages: git @@ -73,7 +73,4 @@ platforms: git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems - - type: python - pypi: - - pyyaml - type: nextflow diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index b646135b0b..3228877d1f 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -67,7 +67,7 @@ functionality: path: test.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: apt packages: git @@ -76,7 +76,4 @@ platforms: git clone https://github.com/openproblems-bio/openproblems.git /opt/openproblems && \ pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems - - type: python - pypi: - - pyyaml - type: nextflow diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index a64bea9eaa..0f81b1b157 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,14 +16,12 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scprep - - "anndata~=0.8.0" - numpy - - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 0e7de4cb41..7897ce6668 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -7,13 +7,11 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 71b4936b3d..f00467929a 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,16 +7,12 @@ functionality: path: script.R platforms: - type: docker - # image: eddelbuettel/r2u:22.04 - # switched to specific tag, see https://github.com/eddelbuettel/r2u/issues/29 - image: eddelbuettel/r2u@sha256:1d3a92aab5abad11787cd6b6c9479960db9f4e56dcc7f837768da2e3f3c4dfe2 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r - cran: [ Matrix, rlang, anndata, bit64, scran, BiocParallel ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] + cran: [ Matrix, rlang, bit64, scran, BiocParallel ] - type: python - pip: [ anndata~=0.8.0, scanpy, pyyaml ] + pip: scanpy - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index ac360fade7..6a3b771ca4 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -7,13 +7,11 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index ea03c68d55..8ec039ea41 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,11 +7,9 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 82742831b2..cc74bacdd7 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,11 +7,9 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index a316372ea2..6dce8d0fb3 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,11 +11,9 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 0083f0cc80..b21a2d10a8 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,13 +41,11 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml test_setup: - type: python packages: diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index 26457f3e78..9703ed4c2c 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,10 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: python:3.10 - setup: - - type: python - pip: - - pyyaml + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 20050c1007..4a7d2177cf 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 557914d197..9c1ad71a1e 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index cb8e187352..9242803f16 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,12 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - "anndata~=0.8.0" - - pyyaml + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index 68f51a8c5c..c4f5d540fb 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,12 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - "anndata~=0.8.0" - - pyyaml + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index c18a2f2945..a66057c4d2 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -31,14 +31,10 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3, git ] - - type: python - pip: [ anndata~=0.8.0, pyyaml ] - type: r - cran: [ Matrix, anndata, bit64, rsvd ] + cran: [ Matrix, bit64, rsvd ] github: KlugerLab/ALRA - type: nextflow directives: diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index c9c09bdd00..d27c2bb487 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -27,12 +27,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - - anndata~=0.8.0 - - pyyaml - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow directives: diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index d003db0b4b..d4354cfc6c 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -28,12 +28,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - - "anndata~=0.8.0" - - pyyaml - scipy github: - scottgigante-immunai/knn-smoothing@python_package diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 5824eb8dfe..92d8c5f38f 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -53,10 +53,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - pip: [ "anndata~=0.8.0", pyyaml, scprep, magic-impute, scipy, scikit-learn<1.2] + pip: [scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index f3b86c40ce..5a926f46d7 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -20,15 +20,13 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scikit-learn - - "anndata~=0.8.0" - scanpy - scprep - - pyyaml - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index f116ade916..a3aa947af4 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -22,13 +22,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - pip: - - "anndata~=0.8.0" - - scprep - - pyyaml + pip: scprep - type: nextflow directives: label: [ midmem, midcpu ] \ No newline at end of file diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 9a470c7134..6e47be922a 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,12 +26,10 @@ functionality: - path: helper.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - - "anndata~=0.8.0" - numpy - scipy - - pyyaml - type: nextflow diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 61a5f9582d..01821cdddf 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,12 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - pyyaml - - "anndata~=0.8.0" + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index a33eeae015..2bd07d2ae2 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -34,13 +34,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scanpy - - pyyaml - - "anndata~=0.8.0" + packages: scanpy - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 248995b8ec..34f68bb2fb 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -32,13 +32,11 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index b440b17fa5..eeb5549a0d 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -35,14 +35,12 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - ivis[cpu] - - pyyaml - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index dd74a3e76c..53e611af63 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -43,13 +43,11 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - torch - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 28483e00bf..5172f262d5 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -30,13 +30,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scanpy - - pyyaml - - "anndata~=0.8.0" + packages: scanpy - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 244179f574..24226db235 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -45,14 +45,12 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - - "anndata~=0.8.0" - phate==1.0.* - scprep - - pyyaml - "scikit-learn<1.2" - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 448962cdfe..e72c00466e 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: apt packages: @@ -43,8 +43,6 @@ platforms: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - MulticoreTSNE - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index c6fa67e553..fbba96436b 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -38,13 +38,11 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scanpy - - "anndata~=0.8.0" - - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 417b4ae583..6999240a65 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -91,14 +91,10 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r - cran: [ anndata, coRanking, bit64 ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata~=0.8.0, pyyaml ] + cran: [ coRanking, bit64 ] - type: nextflow directives: label: [ highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 7fe3904975..e05053582e 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -22,14 +22,12 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scipy - numpy - - "anndata~=0.8.0" - - pyyaml - umap-learn - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml index a6c1b6044b..ae42fa83c8 100644 --- a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: @@ -44,8 +44,6 @@ platforms: - scikit-learn - numpy - scipy - - pyyaml - - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 29c8bbdcd9..4a162a3a9e 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -22,14 +22,12 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python packages: - scikit-learn - numpy - - pyyaml - - "anndata~=0.8.0" - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 956fcf9cb2..dd5933fc11 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,12 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - pyyaml - - "anndata~=0.8.0" + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index c98afb822c..dcb3ff93aa 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,12 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - "anndata~=0.8.0" - - pyyaml + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index f2d33c663f..de2c83269e 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,13 +16,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scanpy - - pyyaml - - "anndata~=0.8.0" + packages: scanpy - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index 03f08e8d3a..6305bcd4b8 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -17,12 +17,7 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - pyyaml - - "anndata~=0.8.0" + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index e4d080822d..13d952c438 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -27,13 +27,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scikit-learn - - pyyaml - - "anndata~=0.8.0" + packages: scikit-learn - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 5b3899b318..40918cec25 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -24,13 +24,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scikit-learn - - pyyaml - - "anndata~=0.8.0" + packages: scikit-learn - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index cf1b855a5a..e0be583cbe 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -37,13 +37,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scikit-learn - - pyyaml - - "anndata~=0.8.0" + packages: scikit-learn - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 93b886c06c..68c5816d40 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -50,14 +50,11 @@ functionality: path: script.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest # Add custom dependencies here setup: - type: python - pypi: - - anndata~=0.8 - - pyyaml - - scvi-tools + pypi: scvi-tools - type: nextflow directives: label: [midmem, midcpu] diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 3160fe0638..fce9dfd48f 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -28,14 +28,10 @@ functionality: path: script.R platforms: - type: docker - image: eddelbuettel/r2u:22.04 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: r - cran: [ Matrix, Seurat, rlang, anndata, bit64 ] - - type: apt - packages: [ libhdf5-dev, libgeos-dev, python3, python3-pip, python3-dev, python-is-python3 ] - - type: python - pip: [ anndata~=0.8.0, pyyaml ] + cran: [ Matrix, Seurat, rlang, bit64 ] - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index b900dad81e..ee226617eb 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,13 +25,10 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - "anndata~=0.8.0" - - pyyaml - - xgboost + packages: xgboost - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 16fe6a596f..5e81c0a633 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -20,11 +20,8 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - pyyaml - - scikit-learn - - "anndata~=0.8.0" + packages: scikit-learn - type: nextflow diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index 3ba7618439..270de8be00 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -40,11 +40,8 @@ functionality: path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - packages: - - scikit-learn - - pyyaml - - "anndata~=0.8.0" + packages: scikit-learn - type: nextflow diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 0f41c7b696..f600a75680 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,10 +25,5 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: "python:3.10" - setup: - - type: python - packages: - - pyyaml - - "anndata~=0.8.0" + image: ghcr.io/openproblems-bio/base-python:latest - type: nextflow From 79ce94864b45b030dc394e6db76ec8d497a15277 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Sat, 3 Jun 2023 02:33:03 +0200 Subject: [PATCH 0905/1233] add url check to component unit test (#160) * add url check * update changelog * update url_check Former-commit-id: ad0b3df24044308339ffd03e47b6d88d6cfdec66 --- CHANGELOG.md | 2 ++ src/common/comp_tests/check_method_config.py | 10 +++++++++- src/common/comp_tests/check_metric_config.py | 14 ++++++++++++-- 3 files changed, 23 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 25f313db12..44b62cf823 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -43,6 +43,8 @@ * Refactor and standardize metric and method info fields (#99). +* Add url check to method and metric unit test (#160). + ## migration ### NEW FUNCTIONALITY diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index c953ac8ca7..ede65bb63b 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -1,6 +1,5 @@ import yaml - ## VIASH START meta = { @@ -29,7 +28,13 @@ def assert_dict(dict, functionality): for key in dict: assert key in arg_names or info, f"{key} is not a defined argument or .functionality.info field" +def check_url(url): + import requests + + get = requests.get(url) + assert get.status_code is (200 or 429), f"{url} is not reachable, {get.status_code}." # 429 rejected, too many requests + print("Load config data", flush=True) with open(meta["config"], "r") as file: @@ -56,6 +61,9 @@ def assert_dict(dict, functionality): assert "reference" in info, "reference not an info field" assert "documentation_url" in info is not None, "documentation_url not an info field or is empty" assert "repository_url" in info is not None, "repository_url not an info field or is empty" + check_url(info["documentation_url"]) + check_url(info["repository_url"]) + if "variants" in info: for key in info["variants"]: diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index d03a553f66..ba8cda41f5 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -1,7 +1,6 @@ import yaml from typing import Dict - ## VIASH START meta = { @@ -16,6 +15,13 @@ DESCRIPTION_MAXLEN = 1000 +def check_url(url): + import requests + + get = requests.get(url) + + assert get.status_code is (200 or 429), f"{url} is not reachable, {get.status_code}." # 429 rejected, too many requests + def check_metric(metric: Dict[str, str]) -> str: assert "name" in metric is not None, "name not a field or is empty" assert len(metric["name"]) <= NAME_MAXLEN, f"Component id (.functionality.info.metrics.metric.name) should not exceed {NAME_MAXLEN} characters." @@ -28,7 +34,11 @@ def check_metric(metric: Dict[str, str]) -> str: assert "FILL IN:" not in metric["description"], "description not filled in" assert "reference" in metric, "reference not a field in metric" assert "documentation_url" in metric , "documentation_url not a field in metric" - assert "repository_url" in metric , "repository_url not an info field" + assert "repository_url" in metric , "repository_url not a metric field" + if metric["documentation_url"]: + check_url(metric["documentation_url"]) + if metric["repository_url"]: + check_url(metric["repository_url"]) assert "min" in metric is not None, f"min not a field in metric or is emtpy" assert "max" in metric is not None, f"max not a field in metric or is empty" assert "maximize" in metric is not None, f"maximize not a field in metric or is emtpy" From aac14d29d5616127b4500700b7af4934374e1671 Mon Sep 17 00:00:00 2001 From: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> Date: Mon, 5 Jun 2023 02:52:45 -0400 Subject: [PATCH 0906/1233] add scottgigante orcid (#176) Former-commit-id: 336da7a69468afaefa306fe6130ea764591d16f7 --- src/tasks/denoising/api/task_info.yaml | 2 +- src/tasks/dimensionality_reduction/api/task_info.yaml | 2 +- src/tasks/label_projection/api/task_info.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/tasks/denoising/api/task_info.yaml b/src/tasks/denoising/api/task_info.yaml index 26fba03bc5..9cdb7347b6 100644 --- a/src/tasks/denoising/api/task_info.yaml +++ b/src/tasks/denoising/api/task_info.yaml @@ -37,7 +37,7 @@ authors: props: { github: wes-lewis } - name: "Scott Gigante" roles: [ author, maintainer ] - props: { github: scottgigante } + props: { github: scottgigante, orcid: "0000-0002-4544-2764" } - name: Robrecht Cannoodt roles: [ author ] props: { github: rcannood, orcid: "0000-0003-3641-729X" } diff --git a/src/tasks/dimensionality_reduction/api/task_info.yaml b/src/tasks/dimensionality_reduction/api/task_info.yaml index 3c7d3cfabf..a196dfb45f 100644 --- a/src/tasks/dimensionality_reduction/api/task_info.yaml +++ b/src/tasks/dimensionality_reduction/api/task_info.yaml @@ -29,7 +29,7 @@ authors: props: { github: michalk8 } - name: "Scott Gigante" roles: [ author ] - props: { github: scottgigante } + props: { github: scottgigante, orcid: "0000-0002-4544-2764" } - name: Ben DeMeo roles: [ author ] props: { github: bendemeo } diff --git a/src/tasks/label_projection/api/task_info.yaml b/src/tasks/label_projection/api/task_info.yaml index d5eae84715..8576d9dc79 100644 --- a/src/tasks/label_projection/api/task_info.yaml +++ b/src/tasks/label_projection/api/task_info.yaml @@ -33,7 +33,7 @@ authors: props: { github: mxposed } - name: "Scott Gigante" roles: [ author ] - props: { github: scottgigante } + props: { github: scottgigante, orcid: "0000-0002-4544-2764" } - name: Robrecht Cannoodt roles: [ author ] props: { github: rcannood, orcid: "0000-0003-3641-729X" } \ No newline at end of file From 3781b830cc141dd5c205ac2c6d52132449d17c20 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 5 Jun 2023 22:37:33 +0200 Subject: [PATCH 0907/1233] Update/bibtex ref unit test (#167) * add url check * update changelog * add bibtex check to comp unit test * add library file to test_resources * update changelog * update url_check * update changelog with PR prefix * update check_url function Former-commit-id: 00be82d9978a13cf61a4ade3633dbc6aec629ce3 --- CHANGELOG.md | 8 ++-- src/common/comp_tests/check_method_config.py | 48 +++++++++++++++++-- src/common/comp_tests/check_metric_config.py | 47 ++++++++++++++++-- .../api/comp_method_embedding.yaml | 1 + .../api/comp_method_feature.yaml | 1 + .../api/comp_method_graph.yaml | 3 +- .../api/comp_metric_embedding.yaml | 3 +- .../api/comp_metric_feature.yaml | 3 +- .../api/comp_metric_graph.yaml | 3 +- src/tasks/denoising/api/comp_method.yaml | 3 +- src/tasks/denoising/api/comp_metric.yaml | 1 + .../api/comp_method.yaml | 3 +- .../api/comp_metric.yaml | 3 +- .../label_projection/api/comp_method.yaml | 3 +- .../label_projection/api/comp_metric.yaml | 2 + 15 files changed, 112 insertions(+), 20 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44b62cf823..5493012c09 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ * Update "baseline" to "control" (PR #146) -* Update docker images to OP pyhton/R base images (#168) +* Update docker images to OP pyhton/R base images (PR #168) ## common @@ -41,9 +41,11 @@ ### MINOR CHANGES -* Refactor and standardize metric and method info fields (#99). +* Refactor and standardize metric and method info fields (PR #99). -* Add url check to method and metric unit test (#160). +* Add url check to method and metric unit test (PR #160). + +* Add library.bib file check to component unit test (PR #167) ## migration diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index ede65bb63b..8a2dabf118 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -14,6 +14,8 @@ DESCRIPTION_MAXLEN = 1000 +_MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] + def assert_dict(dict, functionality): @@ -28,13 +30,46 @@ def assert_dict(dict, functionality): for key in dict: assert key in arg_names or info, f"{key} is not a defined argument or .functionality.info field" +def _load_bib(): + bib_path = meta["resources_dir"]+"/library.bib" + with open(bib_path, "r") as file: + return file.read() + def check_url(url): import requests - get = requests.get(url) + get = requests.head(url) + + if get.ok or get.status_code == 429: # 429 rejected, too many requests + return True + else: + return False + +def search_ref_bib(reference): + import re + bib = _load_bib() + + entry_pattern = r"(@\w+{[^}]*" + reference + r"[^}]*}(.|\n)*?)(?=@)" + + bib_entry = re.search(entry_pattern, bib) + + if bib_entry: + + type_pattern = r"@(.*){" + reference + doi_pattern = r"(?=doi\s*=\s*{([^,}]+)})" + + entry_type = re.search(type_pattern, bib_entry.group(1)) + + if not (entry_type.group(1) == "misc" or reference in _MISSING_DOIS): + entry_doi = re.search(doi_pattern, bib_entry.group(1)) + assert entry_doi.group(1), "doi not found in bibtex reference" + url = f"https://doi.org/{entry_doi.group(1)}" + assert check_url(url), f"{url} is not reachable, ref= {reference}." + + return True - assert get.status_code is (200 or 429), f"{url} is not reachable, {get.status_code}." # 429 rejected, too many requests - + else: + return False print("Load config data", flush=True) with open(meta["config"], "r") as file: @@ -59,10 +94,13 @@ def check_url(url): assert len(info["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.description) should not exceed {DESCRIPTION_MAXLEN} characters." if ("control" not in info["type"]): assert "reference" in info, "reference not an info field" + bib = _load_bib() + if info["reference"]: + assert search_ref_bib(info["reference"]), f"reference {info['reference']} not added to library.bib" assert "documentation_url" in info is not None, "documentation_url not an info field or is empty" assert "repository_url" in info is not None, "repository_url not an info field or is empty" - check_url(info["documentation_url"]) - check_url(info["repository_url"]) + assert check_url(info["documentation_url"]), f"{info['documentation_url']} is not reachable" + assert check_url(info["repository_url"]), f"{info['repository_url']} is not reachable" if "variants" in info: diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index ba8cda41f5..98a588240d 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -15,12 +15,49 @@ DESCRIPTION_MAXLEN = 1000 +_MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] + + +def _load_bib(): + bib_path = meta["resources_dir"]+"/library.bib" + with open(bib_path, "r") as file: + return file.read() + def check_url(url): import requests - get = requests.get(url) + get = requests.head(url) + + if get.ok or get.status_code == 429: # 429 rejected, too many requests + return True + else: + return False + +def search_ref_bib(reference): + import re + bib = _load_bib() + + entry_pattern = r"(@\w+{[^}]*" + reference + r"[^}]*}(.|\n)*?)(?=@)" + + bib_entry = re.search(entry_pattern, bib) + + if bib_entry: + + type_pattern = r"@(.*){" + reference + doi_pattern = r"(?=doi\s*=\s*{([^,}]+)})" + + entry_type = re.search(type_pattern, bib_entry.group(1)) + + if not (entry_type.group(1) == "misc" or reference in _MISSING_DOIS): + entry_doi = re.search(doi_pattern, bib_entry.group(1)) + assert entry_doi.group(1), "doi not found in bibtex reference" + url = f"https://doi.org/{entry_doi.group(1)}" + assert check_url(url), f"{url} is not reachable, ref= {reference}." + + return True - assert get.status_code is (200 or 429), f"{url} is not reachable, {get.status_code}." # 429 rejected, too many requests + else: + return False def check_metric(metric: Dict[str, str]) -> str: assert "name" in metric is not None, "name not a field or is empty" @@ -33,12 +70,14 @@ def check_metric(metric: Dict[str, str]) -> str: assert len(metric["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.metrics.metric.description) should not exceed {DESCRIPTION_MAXLEN} characters." assert "FILL IN:" not in metric["description"], "description not filled in" assert "reference" in metric, "reference not a field in metric" + if metric["reference"]: + assert search_ref_bib(metric["reference"]), f"reference {metric['reference']} not added to library.bib" assert "documentation_url" in metric , "documentation_url not a field in metric" assert "repository_url" in metric , "repository_url not a metric field" if metric["documentation_url"]: - check_url(metric["documentation_url"]) + assert check_url(metric["documentation_url"]), f"{metric['documentation_url']} is not reachable" if metric["repository_url"]: - check_url(metric["repository_url"]) + assert check_url(metric["repository_url"]), f"{metric['repository_url']} is not reachable" assert "min" in metric is not None, f"min not a field in metric or is emtpy" assert "max" in metric is not None, f"max not a field in metric or is empty" assert "maximize" in metric is not None, f"maximize not a field in metric or is emtpy" diff --git a/src/tasks/batch_integration/api/comp_method_embedding.yaml b/src/tasks/batch_integration/api/comp_method_embedding.yaml index 4bc61014f2..dc816fe433 100644 --- a/src/tasks/batch_integration/api/comp_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_method_embedding.yaml @@ -25,3 +25,4 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml index e194cad097..20af096bda 100644 --- a/src/tasks/batch_integration/api/comp_method_feature.yaml +++ b/src/tasks/batch_integration/api/comp_method_feature.yaml @@ -25,3 +25,4 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml index cefb9464e1..8a09185863 100644 --- a/src/tasks/batch_integration/api/comp_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_method_graph.yaml @@ -24,4 +24,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml index 586678b98a..fb0fac98c2 100644 --- a/src/tasks/batch_integration/api/comp_metric_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_metric_embedding.yaml @@ -18,4 +18,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/api/comp_metric_feature.yaml b/src/tasks/batch_integration/api/comp_metric_feature.yaml index bf27c747a4..a3826b3541 100644 --- a/src/tasks/batch_integration/api/comp_metric_feature.yaml +++ b/src/tasks/batch_integration/api/comp_metric_feature.yaml @@ -18,4 +18,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/api/comp_metric_graph.yaml b/src/tasks/batch_integration/api/comp_metric_graph.yaml index 707c26c3e1..4032f3f6fd 100644 --- a/src/tasks/batch_integration/api/comp_metric_graph.yaml +++ b/src/tasks/batch_integration/api/comp_metric_graph.yaml @@ -18,4 +18,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/denoising/api/comp_method.yaml b/src/tasks/denoising/api/comp_method.yaml index 288a1f4cf2..2d6340e67f 100644 --- a/src/tasks/denoising/api/comp_method.yaml +++ b/src/tasks/denoising/api/comp_method.yaml @@ -18,4 +18,5 @@ functionality: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/denoising/pancreas - dest: resources_test/denoising/pancreas \ No newline at end of file + dest: resources_test/denoising/pancreas + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/denoising/api/comp_metric.yaml b/src/tasks/denoising/api/comp_metric.yaml index 5dbe2b8241..f2fd6aaa6e 100644 --- a/src/tasks/denoising/api/comp_metric.yaml +++ b/src/tasks/denoising/api/comp_metric.yaml @@ -21,4 +21,5 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/denoising/pancreas dest: resources_test/denoising/pancreas + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/comp_method.yaml b/src/tasks/dimensionality_reduction/api/comp_method.yaml index 9fd730e65f..5c8b1a6758 100644 --- a/src/tasks/dimensionality_reduction/api/comp_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_method.yaml @@ -21,4 +21,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/dimensionality_reduction/api/comp_metric.yaml b/src/tasks/dimensionality_reduction/api/comp_metric.yaml index 114e61898e..a0ee3ed786 100644 --- a/src/tasks/dimensionality_reduction/api/comp_metric.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_metric.yaml @@ -23,4 +23,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/label_projection/api/comp_method.yaml b/src/tasks/label_projection/api/comp_method.yaml index 2a7ed0f2a0..b218add385 100644 --- a/src/tasks/label_projection/api/comp_method.yaml +++ b/src/tasks/label_projection/api/comp_method.yaml @@ -21,4 +21,5 @@ functionality: - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py \ No newline at end of file + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib diff --git a/src/tasks/label_projection/api/comp_metric.yaml b/src/tasks/label_projection/api/comp_metric.yaml index 053e5fa15e..07766f05a7 100644 --- a/src/tasks/label_projection/api/comp_metric.yaml +++ b/src/tasks/label_projection/api/comp_metric.yaml @@ -21,3 +21,5 @@ functionality: path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib + From 6f207f82332b1d50570d044d6e044bf98c708557 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 6 Jun 2023 20:33:56 +0200 Subject: [PATCH 0908/1233] Bump tj-actions/changed-files from 36.0.11 to 36.0.17 (#178) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.0.11 to 36.0.17. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.0.11...v36.0.17) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 0d99329fd137598402f7440353d26c149185937e --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 338071d951..fae7a44d51 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.0.11 + uses: tj-actions/changed-files@v36.0.17 with: separator: ";" diff_relative: true From 6aa61ef431b5860f586b006a93de5ecb23a41118 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Jun 2023 20:39:49 +0200 Subject: [PATCH 0909/1233] update containers in create_component (#177) * update containers in create_component * fix test * refactor create component using fstrings Former-commit-id: 3f42ae000b04a0ed71d28e2612f343f2e765dacc --- src/common/comp_tests/check_method_config.py | 2 +- src/common/create_component/config.vsh.yaml | 10 +- src/common/create_component/script.py | 287 +++++++++---------- src/common/create_component/test.py | 7 +- src/common/helper_functions/strip_margin.py | 2 +- 5 files changed, 150 insertions(+), 158 deletions(-) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 8a2dabf118..642d4bce94 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -92,7 +92,7 @@ def search_ref_bib(reference): assert "description" in info is not None, "description not an info field or is empty" assert "FILL IN:" not in info["description"], "description not filled in" assert len(info["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.description) should not exceed {DESCRIPTION_MAXLEN} characters." -if ("control" not in info["type"]): +if info["type"] == "method": assert "reference" in info, "reference not an info field" bib = _load_bib() if info["reference"]: diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index 4e927f4715..5c829462ad 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -17,8 +17,7 @@ functionality: - type: string name: --type example: metric - description: The type of component to create. - choices: ['metric', 'method', 'control_method'] + description: The type of component to create. Typically must be one of 'method', 'control_method' or 'metric'. - type: string name: --language description: Which scripting language to use. Options are 'python', 'r'. @@ -64,12 +63,9 @@ platforms: - type: docker image: python:3.10-slim setup: - - type: apt - packages: [ curl, default-jre, unzip ] - - type: docker - run: [ cd /usr/bin && curl -fsSL dl.viash.io | bash ] - type: python - pip: ruamel.yaml + pypi: ruamel.yaml + - type: native - type: nextflow diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 476251d7d6..4eedf255a4 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -1,13 +1,8 @@ from typing import Any -from ruamel.yaml import YAML from pathlib import Path import sys import os import re -import subprocess - -yaml = YAML() -yaml.indent(mapping=2, sequence=4, offset=2) ## VIASH START par = { @@ -29,10 +24,14 @@ from read_and_merge_yaml import read_and_merge_yaml def strip_margin(text: str) -> str: - return re.sub("(\n?)[ \t]*\|", "\\1", text) + return re.sub("(^|\n)[ \t]*\|", "\\1", text) + +def create_config(par, component_type, pretty_name, script_path) -> str: + info_str = generate_info(par, component_type, pretty_name) + resources_str = generate_resources(par, script_path) + docker_platform = generate_docker_platform(par) -def create_config_template(par): - config_template = yaml.load(strip_margin(f'''\ + return strip_margin(f'''\ |# The API specifies which type of component this is. |# It contains specifications for: |# - The input/output files @@ -41,11 +40,13 @@ def create_config_template(par): |__merge__: {os.path.relpath(par["api_file"], par["output"])} | |functionality: + | # A unique identifier for your component (required). + | # Can contain only lowercase letters or underscores. | name: {par["name"]} | - | # Metadata for your component (required) + | # Metadata for your component | info: - | + |{info_str} | # Component-specific parameters (optional) | # arguments: | # - name: "--n_neighbors" @@ -55,101 +56,112 @@ def create_config_template(par): | | # Resources required to run the component | resources: - | # The script of your component - | - type: xx - | path: xx - | # Additional resources your script needs (optional) - | # - type: file - | # path: weights.pt - | - |# Target platforms. For more information, see . + |{resources_str} |platforms: - | - type: docker - | image: - | # Add custom dependencies here - | setup: + | # Specifications for the Docker image for this component. + |{docker_platform} + | # This platform allows running the component natively + | - type: native + | # Allows turning the component into a Nextflow module / pipeline. | - type: nextflow | directives: | label: [midmem, midcpu] |''' - )) - return config_template - -def add_method_info(conf, par, pretty_name) -> None: - """Set up the functionality info for a method.""" - conf['functionality']['info'] = { - 'pretty_name': pretty_name, - 'summary': 'FILL IN: A one sentence summary of this method.', - 'description': 'FILL IN: A (multiline) description of how this method works.', - 'reference': 'bibtex_reference_key', - 'documentation_url': 'https://url.to/the/documentation', - 'repository_url': 'https://github.com/organisation/repository', - 'preferred_normalization': 'log_cpm' - } - if par["type"] == "control_method": - del conf['functionality']['info']['reference'] - del conf['functionality']['info']['documentation_url'] - del conf['functionality']['info']['repository_url'] - -def add_metric_info(conf, par, pretty_name) -> None: - """Set up the functionality info for a metric.""" - conf['functionality']['info'] = { - 'metrics': [{ - 'name': f'{par["name"]}', - 'pretty_name': pretty_name, - 'summary': 'FILL IN: A one sentence summary of this metric.', - 'description': 'FILL IN: A (multiline) description of how this metric works.', - 'reference': 'bibtex_reference_key', - 'documentation_url': 'https://url.to/the/documentation', - 'repository_url': 'https://github.com/organisation/repository', - 'min': 0, - 'max': 1, - 'maximize': 'true', - }] - } - -def add_script_resource(conf, par) -> None: + ) + +def generate_info(par, component_type, pretty_name) -> str: + """Generate the functionality info for a component.""" + if component_type in ["method", "control_method"]: + str = strip_margin(f'''\ + | # A relatively short label, used when rendering visualisarions (required) + | pretty_name: {pretty_name} + | # A one sentence summary of how this method works (required). Used when + | # rendering summary tables. + | summary: "FILL IN: A one sentence summary of this method." + | # A multi-line description of how this component works (required). Used + | # when rendering reference documentation. + | description: | + | FILL IN: A (multi-line) description of how this method works. + | # Which normalisation method this component prefers to use (required). + | preferred_normalization: log_cpm + |''') + if component_type == "method": + str += strip_margin(f'''\ + | # A reference key from the bibtex library at src/common/library.bib (required). + | reference: bibtex_reference_key + | # URL to the documentation for this method (required). + | documentation_url: https://url.to/the/documentation + | # URL to the code repository for this method (required). + | repository_url: https://github.com/organisation/repository + |''') + return str + elif component_type == "metric": + return strip_margin(f'''\ + | metrics: + | # A unique identifier for your metric (required). + | # Can contain only lowercase letters or underscores. + | name: {par["name"]} + | # A relatively short label, used when rendering visualisarions (required) + | pretty_name: {pretty_name} + | # A one sentence summary of how this metric works (required). Used when + | # rendering summary tables. + | summary: "FILL IN: A one sentence summary of this metric." + | # A multi-line description of how this component works (required). Used + | # when rendering reference documentation. + | description: | + | FILL IN: A (multi-line) description of how this metric works. + | # A reference key from the bibtex library at src/common/library.bib (required). + | reference: bibtex_reference_key + | # URL to the documentation for this metric (required). + | documentation_url: https://url.to/the/documentation + | # URL to the code repository for this metric (required). + | repository_url: https://github.com/organisation/repository + | # The minimum possible value for this metric (required) + | min: 0 + | # The maximum possible value for this metric (required) + | max: 1 + | # Whether a higher value represents a 'better' solution (required) + | maximize: true + |''') + + +def generate_resources(par, script_path) -> str: """Add the script to the functionality resources.""" - if par['language'] == 'python': - conf['functionality']['resources'] = [{ - "type": "python_script", - "path": "script.py", - }] - if par['language'] == 'r': - conf['functionality']['resources'] = [{ - "type": "r_script", - "path": "script.R", - }] - -def add_python_setup(conf) -> None: + if par["language"] == "python": + type_str = "python_script" + elif par["language"] == "r": + type_str = "r_script" + + return strip_margin(f'''\ + | # The script of your component (required) + | - type: {type_str} + | path: {script_path} + | # Additional resources your script needs (optional) + | # - type: file + | # path: weights.pt + |''') + +def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" - conf['platforms'][0]["image"] = 'python:3.10' - conf['platforms'][0]["setup"] = [ - { - "type": "python", - "pypi": "anndata~=0.8.0" - } - ] - -def add_r_setup(conf) -> None: - """Set up the docker platform for R.""" - conf['platforms'][0]["image"] = 'eddelbuettel/r2u:22.04' - conf['platforms'][0]["setup"] = [ - { - "type": "apt", - "packages": ['libhdf5-dev', 'libgeos-dev', 'python3', 'python3-pip', 'python3-dev', 'python-is-python3'] - }, - { - "type": "python", - "pypi": "anndata~=0.8.0" - }, - { - "type": "r", - "cran": "anndata" - } - ] - -def set_par_values(config) -> dict[str, Any]: + if par["language"] == "python": + image_str = "ghcr.io/openproblems-bio/base-python:latest" + setup_type = "python" + package_example = "scanpy" + elif par["language"] == "r": + image_str = "ghcr.io/openproblems-bio/base-r:latest" + setup_type = "r" + package_example = "tidyverse" + return strip_margin(f'''\ + | - type: docker + | image: {image_str} + | # Add custom dependencies here (optional). For more information, see + | # https://viash.io/reference/config/platforms/docker/#setup . + | # setup: + | # - type: {setup_type} + | # packages: {package_example} + |''') + +def set_par_values(config) -> None: """Adds values to each of the arguments in a config file.""" args = config['functionality']['arguments'] for argi, arg in enumerate(args): @@ -158,7 +170,7 @@ def set_par_values(config) -> dict[str, Any]: # find value if arg["type"] != "file": value = arg.get("default", arg.get("example", "...")) - elif arg["direction"] == "input": + elif arg.get("direction", "input") == "input": key_strip = key.replace("input_", "") value = f'resources_test/{par["task"]}/pancreas/{key_strip}.h5ad' else: @@ -247,7 +259,7 @@ def create_python_script(par, config, type): f"{arg['key']} = ad.read_h5ad(par['{arg['key']}'])" for arg in args if arg['type'] == "file" - and arg['direction'] == "input" + and arg.get('direction', "input") == "input" ) # determine which adata to copy from @@ -258,7 +270,7 @@ def create_python_script(par, config, type): write_output_python(arg, copy_from_adata, type == "metric") for arg in args if arg["type"] == "file" - and arg["direction"] == "output" + and arg.get("direction", "input") == "output" ) if type == 'metric': @@ -314,7 +326,7 @@ def create_r_script(par, api_spec, type): f'{arg["key"]} <- anndata::read_h5ad(par[["{arg["key"]}"]])' for arg in args if arg['type'] == "file" - and arg['direction'] == "input" + and arg.get("direction", "input") == "input" ) # determine which adata to copy from @@ -325,7 +337,7 @@ def create_r_script(par, api_spec, type): write_output_r(arg, copy_from_adata, type == "metric") for arg in args if arg["type"] == "file" - and arg["direction"] == "output" + and arg.get("direction", "input") == "output" ) if type == 'metric': @@ -368,23 +380,23 @@ def create_r_script(par, api_spec, type): return script -def read_viash_config(file): - file = file.absolute() +# def read_viash_config(file): +# file = file.absolute() - # read in config - command = ["viash", "config", "view", str(file)] +# # read in config +# command = ["viash", "config", "view", str(file)] - # Execute the command and capture the output - output = subprocess.check_output( - command, - universal_newlines=True, - cwd=str(file.parent) - ) +# # Execute the command and capture the output +# output = subprocess.check_output( +# command, +# universal_newlines=True, +# cwd=str(file.parent) +# ) - # Parse the output as YAML - config = yaml.load(output) +# # Parse the output as YAML +# config = yaml.load(output) - return config +# return config def main(par): @@ -394,6 +406,14 @@ def main(par): pretty_name = re.sub("_", " ", par['name']).title() + # check language and determine script path + if par["language"] == "python": + script_path = "script.py" + elif par["language"] == "r": + script_path = "script.R" + else: + sys.exit(f"Unrecognized language parameter '{par['language']}'.") + ## CHECK API FILE api_file = Path(par["api_file"]) viash_yaml = Path(par["viash_yaml"]) @@ -423,45 +443,22 @@ def main(par): config_file = out_dir / "config.vsh.yaml" # get config template - config_template = create_config_template(par) - - # Add component specific info - # TODO: this should be based on a component type spec - if comp_type == "metric": - add_metric_info(config_template, par, pretty_name) - elif comp_type in ["method", "control_method"]: - add_method_info(config_template, par, pretty_name) - - # add script to resources - add_script_resource(config_template, par) - - # add elements depending on language - if par["language"] == "python": - add_python_setup(config_template) - - if par["language"] == "r": - add_r_setup(config_template) + config_str = create_config(par, comp_type, pretty_name, script_path) with open(config_file, "w") as f: - yaml.dump(config_template, f) + f.write(config_str) ####### CREATE SCRIPT ####### - script_file = out_dir / config_template["functionality"]["resources"][0]["path"] - - # touch file - script_file.touch() - - # read config with viash - final_config = read_viash_config(config_file) + script_file = out_dir / script_path # set reasonable values - set_par_values(final_config) + set_par_values(api) if par["language"] == "python": - script_out = create_python_script(par, final_config, comp_type) + script_out = create_python_script(par, api, comp_type) if par["language"] == "r": - script_out = create_r_script(par, final_config, comp_type) + script_out = create_r_script(par, api, comp_type) # write script with open(script_file, "w") as f: diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 2aaadfbffe..28b493bd46 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -1,7 +1,7 @@ import os import subprocess from os import path -from ruamel.yaml import YAML +import ruamel.yaml as yaml ## VIASH START meta = { @@ -40,12 +40,11 @@ assert os.path.exists(script_f), "Script file does not exist" print('>> Checking file contents', flush=True) -yaml = YAML() with open(conf_f) as f: - conf_data = yaml.load(f) + conf_data = yaml.safe_load(f) assert conf_data['functionality']['name'] == 'test_method', "Name should be equal to 'test_method'" -assert conf_data['platforms'][0]['image'] == 'python:3.10', "Python image should be equal to python:3.10" +# assert conf_data['platforms'][0]['image'] == 'python:3.10', "Python image should be equal to python:3.10" print('All checks succeeded!', flush=True) diff --git a/src/common/helper_functions/strip_margin.py b/src/common/helper_functions/strip_margin.py index 25a1f0426f..fbfb39dec9 100644 --- a/src/common/helper_functions/strip_margin.py +++ b/src/common/helper_functions/strip_margin.py @@ -1,3 +1,3 @@ def strip_margin(text: str) -> str: import re - return re.sub('(\n?)[ \t]*\|', '\\1', text) \ No newline at end of file + return re.sub("(^|\n)[ \t]*\|", "\\1", text) \ No newline at end of file From 539c31df5978ea41d5b25bc586b5a91498e0a6bd Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Jun 2023 20:57:44 +0200 Subject: [PATCH 0910/1233] update batch integration docker images (#171) * update batch integration docker images * update changelog * remove rpy2 * update changelog --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: ff31cad93d412230a25a07dc9e8558df157bca1f --- CHANGELOG.md | 11 +++++++---- .../batch_integration/methods/bbknn/config.vsh.yaml | 5 +++-- .../batch_integration/methods/combat/config.vsh.yaml | 5 +++-- .../methods/scanorama_embed/config.vsh.yaml | 5 +++-- .../methods/scanorama_feature/config.vsh.yaml | 5 +++-- .../batch_integration/methods/scvi/config.vsh.yaml | 5 +++-- .../metrics/asw_batch/config.vsh.yaml | 5 +++-- .../metrics/asw_label/config.vsh.yaml | 5 +++-- .../metrics/cell_cycle_conservation/config.vsh.yaml | 5 +++-- .../metrics/clustering_overlap/config.vsh.yaml | 5 +++-- .../batch_integration/metrics/pcr/config.vsh.yaml | 5 +++-- .../batch_integration/process_dataset/config.vsh.yaml | 6 ++++-- .../transformers/embed_to_graph/config.vsh.yaml | 6 ++---- .../transformers/feature_to_embed/config.vsh.yaml | 6 ++---- 14 files changed, 45 insertions(+), 34 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5493012c09..408c8d406b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,16 @@ * Relocate task directories to new `src/tasks/` location (PR #142). -### MINOR CHANGES +* Update Docker images to our base images; `ghcr.io/openproblems-bio/base-python` + and `ghcr.io/openproblems-bio/base-r` (PR #168). + +* Update batch integration docker images to OpenProblems base images (PR #171). -* Update test scripts (PR #143) +### MINOR CHANGES -* Update "baseline" to "control" (PR #146) +* Update test scripts (PR #143). -* Update docker images to OP pyhton/R base images (PR #168) +* Update "baseline" to "control" (PR #146). ## common diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 63a2c1d44c..1d9843840e 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -30,10 +30,11 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - bbknn - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 5479814861..fa42974027 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -33,9 +33,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index d9a06473a8..d2d03f474d 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -28,10 +28,11 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - scanorama - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 4796d527fd..e4bd9d2c7b 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -30,10 +30,11 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - scanorama - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index ca02439af7..af8bdda584 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -23,10 +23,11 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - scvi-tools - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index da3e7ec6c1..f75aee8cdd 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -22,9 +22,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 767e426304..d9dde09710 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -23,9 +23,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 5f7c03173b..a422cf0b61 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -21,9 +21,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 4fda99a7d3..8d317e2701 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -52,9 +52,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 6cd0dc37aa..6dc69b594d 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -26,9 +26,10 @@ functionality: path: script.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python pypi: - - pyyaml + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 2eb95f19f0..d30bc3a580 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -22,8 +22,10 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: mumichae/scib-base:1.1.3 + image: ghcr.io/openproblems-bio/base-r:latest setup: - type: python - pypi: pyyaml + pypi: + - scanpy + - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index b21885f3cc..c5a62176c1 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -22,10 +22,8 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - pypi: - - scanpy - - pyyaml + pypi: scanpy - type: nextflow diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 5bad68c5ac..ed2da09aa2 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -22,10 +22,8 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: python:3.10 + image: ghcr.io/openproblems-bio/base-python:latest setup: - type: python - pypi: - - pyyaml - - scanpy + pypi: scanpy - type: nextflow From 9c47ceb489e8c5661a837420036bb073fdc01622 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:35:22 +0200 Subject: [PATCH 0911/1233] Update issue templates Former-commit-id: b818b3eef244a19e03bad46bb42f6de656b40573 --- .github/ISSUE_TEMPLATE/bug_report.md | 38 +++++++++++++++++++++++ .github/ISSUE_TEMPLATE/feature_request.md | 20 ++++++++++++ .github/ISSUE_TEMPLATE/new-task.md | 32 +++++++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/ISSUE_TEMPLATE/new-task.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000000..dd84ea7824 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,38 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: '' +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Screenshots** +If applicable, add screenshots to help explain your problem. + +**Desktop (please complete the following information):** + - OS: [e.g. iOS] + - Browser [e.g. chrome, safari] + - Version [e.g. 22] + +**Smartphone (please complete the following information):** + - Device: [e.g. iPhone6] + - OS: [e.g. iOS8.1] + - Browser [e.g. stock browser, safari] + - Version [e.g. 22] + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000000..bbcbbe7d61 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/ISSUE_TEMPLATE/new-task.md b/.github/ISSUE_TEMPLATE/new-task.md new file mode 100644 index 0000000000..db2745a21d --- /dev/null +++ b/.github/ISSUE_TEMPLATE/new-task.md @@ -0,0 +1,32 @@ +--- +name: New task +about: Start creating a new benchmarking task in OpenProblems +title: "[New task] ..." +labels: New task +assignees: '' + +--- + +**Task motivation** +Explain the motivation behind your proposed task. Describe the biological or computational problem you aim to address and why it’s important. Discuss the current state of research in this area and any gaps or challenges that your task could help address. This section should convince readers of the significance and relevance of your task. + +**Task description** +Provide a clear and concise description of your task, detailing the specific problem it aims to solve. Outline the input data types, the expected output, and any assumptions or constraints. Be sure to explain any terminology or concepts that are essential for understanding the task. + +**Proposed ground-truth in datasets** +Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. + +Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. + +**Initial set of methods to implement** +List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. + +Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. + +**Proposed control methods** +Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. + +Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. + +**Proposed Metrics** +Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance. From 3ed0eafd7003a3c7c2eb072b5dd5afbf0d7fe337 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:43:29 +0200 Subject: [PATCH 0912/1233] update task issue template Former-commit-id: 040e2a4f4ef17a592453d7a41a93a448b6d53c5b --- .github/ISSUE_TEMPLATE/bug_report.md | 14 --------- .github/ISSUE_TEMPLATE/new-task.md | 32 -------------------- .github/ISSUE_TEMPLATE/new_task.md | 45 ++++++++++++++++++++++++++++ 3 files changed, 45 insertions(+), 46 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/new-task.md create mode 100644 .github/ISSUE_TEMPLATE/new_task.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index dd84ea7824..74514987e3 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -20,19 +20,5 @@ Steps to reproduce the behavior: **Expected behavior** A clear and concise description of what you expected to happen. -**Screenshots** -If applicable, add screenshots to help explain your problem. - -**Desktop (please complete the following information):** - - OS: [e.g. iOS] - - Browser [e.g. chrome, safari] - - Version [e.g. 22] - -**Smartphone (please complete the following information):** - - Device: [e.g. iPhone6] - - OS: [e.g. iOS8.1] - - Browser [e.g. stock browser, safari] - - Version [e.g. 22] - **Additional context** Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/new-task.md b/.github/ISSUE_TEMPLATE/new-task.md deleted file mode 100644 index db2745a21d..0000000000 --- a/.github/ISSUE_TEMPLATE/new-task.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -name: New task -about: Start creating a new benchmarking task in OpenProblems -title: "[New task] ..." -labels: New task -assignees: '' - ---- - -**Task motivation** -Explain the motivation behind your proposed task. Describe the biological or computational problem you aim to address and why it’s important. Discuss the current state of research in this area and any gaps or challenges that your task could help address. This section should convince readers of the significance and relevance of your task. - -**Task description** -Provide a clear and concise description of your task, detailing the specific problem it aims to solve. Outline the input data types, the expected output, and any assumptions or constraints. Be sure to explain any terminology or concepts that are essential for understanding the task. - -**Proposed ground-truth in datasets** -Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. - -Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. - -**Initial set of methods to implement** -List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. - -Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. - -**Proposed control methods** -Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. - -Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. - -**Proposed Metrics** -Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance. diff --git a/.github/ISSUE_TEMPLATE/new_task.md b/.github/ISSUE_TEMPLATE/new_task.md new file mode 100644 index 0000000000..85b837ab61 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/new_task.md @@ -0,0 +1,45 @@ +--- +name: New task +about: Start creating a new benchmarking task in OpenProblems +title: "[Task] ..." +labels: task +assignees: '' +body: + - type: markdown + attributes: + value: | + Thanks for choosing OpenProblems for hosting your benchmark. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. + - type: textarea + attributes: + label: Task motivation + description: Explain the motivation behind your proposed task. Describe the biological or computational problem you aim to address and why it’s important. Discuss the current state of research in this area and any gaps or challenges that your task could help address. This section should convince readers of the significance and relevance of your task. + - type: textarea + attributes: + label: Task description + description: Provide a clear and concise description of your task, detailing the specific problem it aims to solve. Outline the input data types, the expected output, and any assumptions or constraints. Be sure to explain any terminology or concepts that are essential for understanding the task. + - type: textarea + attributes: + label: Proposed ground-truth in datasets + description: | + Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. + + Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. + - type: textarea + attributes: + label: Initial set of methods to implement + description: | + List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. + + Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. + - type: textarea + attributes: + label: Proposed control methods + description: | + Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. + + Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. + - type: textarea + attributes: + label: Proposed Metrics + description: Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance. +--- \ No newline at end of file From ebbe738db2fb767c2d73f70c002d14d00725ba73 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:45:05 +0200 Subject: [PATCH 0913/1233] update github issue template Former-commit-id: 50936248e4591c40741aa1988af86e30f13aa4f2 --- .../{new_task.md => new_task.yml} | 20 +++++-------------- 1 file changed, 5 insertions(+), 15 deletions(-) rename .github/ISSUE_TEMPLATE/{new_task.md => new_task.yml} (74%) diff --git a/.github/ISSUE_TEMPLATE/new_task.md b/.github/ISSUE_TEMPLATE/new_task.yml similarity index 74% rename from .github/ISSUE_TEMPLATE/new_task.md rename to .github/ISSUE_TEMPLATE/new_task.yml index 85b837ab61..c193e9479e 100644 --- a/.github/ISSUE_TEMPLATE/new_task.md +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -1,9 +1,6 @@ ---- name: New task about: Start creating a new benchmarking task in OpenProblems -title: "[Task] ..." -labels: task -assignees: '' +labels: [task] body: - type: markdown attributes: @@ -21,25 +18,18 @@ body: attributes: label: Proposed ground-truth in datasets description: | - Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. - - Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. + Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. - type: textarea attributes: label: Initial set of methods to implement description: | - List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. - - Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. + List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. - type: textarea attributes: label: Proposed control methods description: | - Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. - - Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. + Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. - type: textarea attributes: label: Proposed Metrics - description: Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance. ---- \ No newline at end of file + description: Describe the metrics you propose for evaluating the performance of methods in your task. Explain the rationale for selecting these metrics and how they will accurately assess the methods’ success in addressing the task’s challenges. Consider including multiple metrics to capture different aspects of method performance. \ No newline at end of file From 07809aa40141b263df07f78190d0f8b53ce9cf43 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:48:09 +0200 Subject: [PATCH 0914/1233] update issue templates Former-commit-id: 924a8f2a53b2545a8d066d3ec46c448a6c4c77bb --- .github/ISSUE_TEMPLATE/bug_report.md | 24 ----------------------- .github/ISSUE_TEMPLATE/config.yml | 1 + .github/ISSUE_TEMPLATE/feature_request.md | 20 ------------------- .github/ISSUE_TEMPLATE/new_task.yml | 12 ++++-------- 4 files changed, 5 insertions(+), 52 deletions(-) delete mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/config.yml delete mode 100644 .github/ISSUE_TEMPLATE/feature_request.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 74514987e3..0000000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -name: Bug report -about: Create a report to help us improve -title: '' -labels: '' -assignees: '' - ---- - -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error - -**Expected behavior** -A clear and concise description of what you expected to happen. - -**Additional context** -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 0000000000..a49eab2f6b --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1 @@ +blank_issues_enabled: true \ No newline at end of file diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index bbcbbe7d61..0000000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for this project -title: '' -labels: '' -assignees: '' - ---- - -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Describe alternatives you've considered** -A clear and concise description of any alternative solutions or features you've considered. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/ISSUE_TEMPLATE/new_task.yml b/.github/ISSUE_TEMPLATE/new_task.yml index c193e9479e..5e24dea87b 100644 --- a/.github/ISSUE_TEMPLATE/new_task.yml +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -4,8 +4,7 @@ labels: [task] body: - type: markdown attributes: - value: | - Thanks for choosing OpenProblems for hosting your benchmark. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. + value: Thanks for choosing OpenProblems for hosting your benchmark. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. - type: textarea attributes: label: Task motivation @@ -17,18 +16,15 @@ body: - type: textarea attributes: label: Proposed ground-truth in datasets - description: | - Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. + description: Describe the datasets you plan to use for your task. OpenProblems offers a standard set of datasets (See [“Common datasets”](https://openproblems.bio/documentation/reference/openproblems-v2/src-datasets.html)) which you can peruse through. Explain how these datasets will provide the ground-truth for evaluating the methods implemented in your task. If possible, include references or links to the datasets to facilitate reproducibility. - type: textarea attributes: label: Initial set of methods to implement - description: | - List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. + description: List the initial set of methods you plan to implement for your task. Briefly describe each method’s core ideas and algorithms, and explain why you think they are suitable for your task. Consider including both established and cutting-edge methods to provide a comprehensive benchmarking of the state-of-the-art. - type: textarea attributes: label: Proposed control methods - description: | - Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. + description: Outline the control methods you propose for your task. These methods serve as a starting point to test the relative accuracy of new methods in the task and as quality control for the defined metrics. Include both positive controls, which are methods with known outcomes resulting in the best possible metric values, and negative controls, which are simple, naive, or random methods that do not rely on sophisticated techniques or domain knowledge. Explain the rationale for your chosen controls. - type: textarea attributes: label: Proposed Metrics From 3c0d247b1a2e7a40b3bd6870137928f1fafdcc18 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:49:01 +0200 Subject: [PATCH 0915/1233] fix github issue template Former-commit-id: 01d13c3019172538296291dcc11adc15bccfe782 --- .github/ISSUE_TEMPLATE/new_task.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/new_task.yml b/.github/ISSUE_TEMPLATE/new_task.yml index 5e24dea87b..86b9551e27 100644 --- a/.github/ISSUE_TEMPLATE/new_task.yml +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -1,5 +1,5 @@ name: New task -about: Start creating a new benchmarking task in OpenProblems +description: Start creating a new benchmarking task in OpenProblems labels: [task] body: - type: markdown From 6b567d89f5a816e6190b288d9a47d984e6517c78 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 15:50:31 +0200 Subject: [PATCH 0916/1233] update issue templates Former-commit-id: a71c9e3004fae6e82ce3f639fc5ae173bb8af0c0 --- .github/ISSUE_TEMPLATE/bug_report.md | 24 +++++++++++++++++++++++ .github/ISSUE_TEMPLATE/feature_request.md | 20 +++++++++++++++++++ .github/ISSUE_TEMPLATE/new_task.yml | 2 +- 3 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000000..74514987e3 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,24 @@ +--- +name: Bug report +about: Create a report to help us improve +title: '' +labels: '' +assignees: '' + +--- + +**Describe the bug** +A clear and concise description of what the bug is. + +**To Reproduce** +Steps to reproduce the behavior: +1. Go to '...' +2. Click on '....' +3. Scroll down to '....' +4. See error + +**Expected behavior** +A clear and concise description of what you expected to happen. + +**Additional context** +Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000000..bbcbbe7d61 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Suggest an idea for this project +title: '' +labels: '' +assignees: '' + +--- + +**Is your feature request related to a problem? Please describe.** +A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] + +**Describe the solution you'd like** +A clear and concise description of what you want to happen. + +**Describe alternatives you've considered** +A clear and concise description of any alternative solutions or features you've considered. + +**Additional context** +Add any other context or screenshots about the feature request here. diff --git a/.github/ISSUE_TEMPLATE/new_task.yml b/.github/ISSUE_TEMPLATE/new_task.yml index 86b9551e27..bd0eaf2ab7 100644 --- a/.github/ISSUE_TEMPLATE/new_task.yml +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -4,7 +4,7 @@ labels: [task] body: - type: markdown attributes: - value: Thanks for choosing OpenProblems for hosting your benchmark. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. + value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/). - type: textarea attributes: label: Task motivation From 8bed66d8bdd79b3771d22db1f27e42279ccfa746 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 7 Jun 2023 16:10:57 +0200 Subject: [PATCH 0917/1233] Bump tj-actions/changed-files from 36.0.17 to 36.0.18 (#179) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.0.17 to 36.0.18. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.0.17...v36.0.18) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 24a48f4d40638e279ff747b6a2f0c5ff0f14a3f7 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index fae7a44d51..bcad9418b2 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.0.17 + uses: tj-actions/changed-files@v36.0.18 with: separator: ";" diff_relative: true From 3986f72f5e830a141b6e94c226504a9118b41e25 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 16:30:48 +0200 Subject: [PATCH 0918/1233] fix link Former-commit-id: 16bab919fa5b61b5f3f171eb8b86800b05a875aa --- .github/ISSUE_TEMPLATE/new_task.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/ISSUE_TEMPLATE/new_task.yml b/.github/ISSUE_TEMPLATE/new_task.yml index bd0eaf2ab7..1b275f4227 100644 --- a/.github/ISSUE_TEMPLATE/new_task.yml +++ b/.github/ISSUE_TEMPLATE/new_task.yml @@ -4,7 +4,7 @@ labels: [task] body: - type: markdown attributes: - value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/labels/task) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/). + value: Thanks for choosing OpenProblems. Please check the [OpenProblems tasks](https://github.com/openproblems-bio/openproblems-v2/issues?q=label%3Atask+) to see whether a similar task has already been created. If you haven't already, please review the documentation on [how to create a new task](https://openproblems.bio/documentation/create_task/). - type: textarea attributes: label: Task motivation From 4351d3556766be72d7b381b1645357de36f57e67 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 7 Jun 2023 16:44:02 +0200 Subject: [PATCH 0919/1233] migrate more helper functions Former-commit-id: 36a9ac6e182b899cf0d1ff7fddd921b5eab09aea --- src/common/helper_functions/read_api_files.R | 206 +++++++++++++++++++ src/common/helper_functions/strip_margin.R | 2 +- 2 files changed, 207 insertions(+), 1 deletion(-) create mode 100644 src/common/helper_functions/read_api_files.R diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R new file mode 100644 index 0000000000..0653148578 --- /dev/null +++ b/src/common/helper_functions/read_api_files.R @@ -0,0 +1,206 @@ + +anndata_struct_names <- c("obs", "var", "obsm", "obsp", "varm", "varp", "layers", "uns") + +read_anndata_spec <- function(path) { + spec <- read_and_merge_yaml(path) + list( + info = read_anndata_info(spec, path), + slots = read_anndata_slots(spec, path) + ) +} +read_anndata_info <- function(spec, path) { + # TEMP: make it readable + spec$info$slots <- NULL + + df <- list_as_tibble(spec) + if (list_contains_tibble(spec$info)) { + df <- dplyr::bind_cols(df, list_as_tibble(spec$info)) + } + df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + as_tibble(df) +} +read_anndata_slots <- function(spec, path) { + map_df( + anndata_struct_names, + function(struct_name, slot) { + slot <- spec$info$slots[[struct_name]] + if (is.null(slot)) return(NULL) + df <- map_df(slot, as.data.frame) + df$struct <- struct_name + df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + df$required <- df$required %||% TRUE %|% TRUE + df$multiple <- df$multiple %||% FALSE %|% FALSE + as_tibble(df) + } + ) +} + +format_slots <- function(spec) { + example <- spec$slots %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, anndata_struct_names)) + + c(" AnnData object", paste0(" ", example$str)) +} + +format_slots_as_kable <- function(spec) { + spec$slots %>% + mutate( + tag_str = pmap_chr(lst(required), function(required) { + out <- c() + if (!required) { + out <- c(out, "Optional") + } + if (length(out) == 0) { + "" + } else { + paste0("(_", paste(out, collapse = ", "), "_) ") + } + }) + ) %>% + transmute( + Slot = paste0("`", struct, "[\"", name, "\"]`"), + # Struct = struct, + # Name = name, + Type = paste0("`", type, "`"), + # Required = ifelse(required, "yes", ""), + Description = paste0( + tag_str, + description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), + "." + ) + ) %>% + knitr::kable() +} + +list_contains_tibble <- function(li) { + is.list(li) && any(sapply(li, is.atomic)) +} + +list_as_tibble <- function(li) { + as.data.frame(li[sapply(li, is.atomic)], check.names = FALSE) +} + +read_comp_spec <- function(path) { + spec_yaml <- read_and_merge_yaml(path) + list( + info = read_comp_info(spec_yaml, path), + args = read_comp_args(spec_yaml, path) + ) +} + +read_comp_info <- function(spec_yaml, path) { + # TEMP: make it readable + spec_yaml$functionality$arguments <- NULL + spec_yaml$functionality$argument_groups <- NULL + + df <- list_as_tibble(spec_yaml$functionality) + if (list_contains_tibble(spec_yaml$functionality$info)) { + df <- dplyr::bind_cols(df, list_as_tibble(spec_yaml$functionality$info)) + } + if (list_contains_tibble(spec_yaml$functionality$info$type_info)) { + df <- dplyr::bind_cols(df, list_as_tibble(spec_yaml$functionality$info$type_info)) + } + df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + as_tibble(df) +} +read_comp_args <- function(spec_yaml, path) { + arguments <- spec_yaml$functionality$arguments + for (arg_group in spec_yaml$functionality$argument_groups) { + arguments <- c(arguments, arg_group$arguments) + } + map_df(arguments, function(arg) { + df <- list_as_tibble(arg) + if (list_contains_tibble(arg$info)) { + df <- dplyr::bind_cols(df, list_as_tibble(arg$info)) + } + df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + df$arg_name <- stringr::str_replace_all(arg$name, "^-*", "") + df$direction <- df$direction %||% "input" %|% "input" + df$parent <- df$`__merge__` %||% NA_character_ %>% basename() %>% gsub("\\.yaml", "", .) + df$required <- df$required %||% FALSE %|% FALSE + df$default <- df$default %||% NA_character_ %>% as.character + df$example <- df$example %||% NA_character_ %>% as.character + df + }) +} + +format_comp_args_as_tibble <- function(spec) { + spec$args %>% + mutate( + tag_str = pmap_chr(lst(required, direction), function(required, direction) { + out <- c() + if (!required) { + out <- c(out, "Optional") + } + if (direction == "output") { + out <- c(out, "Output") + } + if (length(out) == 0) { + "" + } else { + paste0("(_", paste(out, collapse = ", "), "_) ") + } + }) + ) %>% + transmute( + Name = paste0("`--", arg_name, "`"), + Type = paste0("`", type, "`"), + Description = paste0( + tag_str, + description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), + ".", + ifelse(!is.na(default), paste0(" Default: `", default, "`."), "") + ) + ) %>% + knitr::kable() +} + +# path <- "src/datasets/api/comp_processor_knn.yaml" +render_component <- function(path) { + spec <- read_comp_spec(path) + + cat(strip_margin(glue::glue(" + §# Component type: {spec$info$label} + § + §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{spec$info$namespace}) + § + §{spec$info$description} + § + §Arguments: + § + §:::{{.small}} + §{paste(format_comp_args_as_tibble(spec), collapse = '\n')} + §::: + § + §"), symbol = "§")) +} + +# path <- "src/datasets/api/anndata_pca.yaml" +render_file <- function(path) { + spec <- read_anndata_spec(path) + + cat(strip_margin(glue::glue(" + §# File format: {spec$info$label} + § + §Example file: `{spec$info$example %|% ''}` + § + §{spec$info$description} + § + §Format: + § + §:::{{.small}} + §{paste(format_slots(spec), collapse = '\n')} + §::: + § + §Slot description: + § + §:::{{.small}} + §{paste(format_slots_as_kable(spec), collapse = '\n')} + §::: + § + §"), symbol = "§")) +} \ No newline at end of file diff --git a/src/common/helper_functions/strip_margin.R b/src/common/helper_functions/strip_margin.R index 33356c8a9e..3830d58d79 100644 --- a/src/common/helper_functions/strip_margin.R +++ b/src/common/helper_functions/strip_margin.R @@ -1,3 +1,3 @@ strip_margin <- function(text, symbol = "\\|") { - gsub(paste0("(\n?)[ \t]*", symbol), "\\1", text) + gsub(paste0("(^|\n)[ \t]*", symbol), "\\1", text) } \ No newline at end of file From 93dfcd47bf98f256c18cd60f536d59db6935bcab Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 13 Jun 2023 09:12:41 +0200 Subject: [PATCH 0920/1233] Bump tj-actions/changed-files from 36.0.18 to 36.1.0 (#184) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.0.18 to 36.1.0. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.0.18...v36.1.0) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 18bdfdfd0184487e64b805653765452dded04a6c --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index bcad9418b2..8402d34cd1 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.0.18 + uses: tj-actions/changed-files@v36.1.0 with: separator: ";" diff_relative: true From 3e380024e11fb8cd2d55e26cac8053009e32b195 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Jun 2023 02:53:31 +0200 Subject: [PATCH 0921/1233] create schema files (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * create schema for method components * rename fields to properties * add a YAML schema validator component Co-authored-by: Michaela Müller * Rename pretty_name to label Co-authored-by: Michaela Müller * refactor test resources * update schema * commit * Rename v1_url to v1_path * refactor migration notation * update schema files * update schemas * update components * validation for urls * make urls optional for metrics * add component api schema * refactor check component * update components and apis * rename anndata_ to file_; write file schema file * fix file specs * add task info api * fix yamls * refactor dataset yamls * update schemas, unit tests and containers * fix get_api_info component * fixes to components after api changes * fix transformers * update functions * fix helper functions & dataset loader * add more defaults --------- Co-authored-by: Michaela Müller Former-commit-id: 5d9f4c83fca0b1e371eb198306a59a33c16340d8 --- .vscode/settings.json | 10 + CHANGELOG.md | 8 +- src/common/api/schema_component_api.yaml | 67 + src/common/api/schema_definitions.yaml | 277 +++ src/common/api/schema_file_api.yaml | 26 + .../api/schema_task_control_method.yaml | 70 + src/common/api/schema_task_info.yaml | 22 + src/common/api/schema_task_method.yaml | 67 + src/common/api/schema_task_metric.yaml | 88 + src/common/api/schema_viash_config.yaml | 1931 +++++++++++++++++ .../check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_dataset_schema/script.py | 2 +- src/common/check_dataset_schema/test.py | 8 +- src/common/check_yaml_schema/config.vsh.yaml | 26 + src/common/check_yaml_schema/script.py | 59 + src/common/comp_tests/check_method_config.py | 32 +- src/common/comp_tests/check_metric_config.py | 18 +- src/common/comp_tests/run_and_check_adata.py | 4 +- src/common/create_component/script.py | 8 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/common/get_api_info/config.vsh.yaml | 4 +- src/common/get_api_info/script.R | 14 +- src/common/get_method_info/config.vsh.yaml | 4 +- src/common/get_method_info/script.R | 11 +- src/common/get_metric_info/config.vsh.yaml | 4 +- src/common/get_metric_info/script.R | 19 +- src/common/get_results/config.vsh.yaml | 2 +- src/common/get_task_info/config.vsh.yaml | 2 +- src/common/helper_functions/read_api_files.R | 16 +- src/datasets/README.md | 22 +- src/datasets/README.qmd | 4 +- src/datasets/api/anndata_common_dataset.yaml | 9 - src/datasets/api/comp_dataset_loader.yaml | 17 +- src/datasets/api/comp_normalization.yaml | 12 +- src/datasets/api/comp_processor_hvg.yaml | 10 +- src/datasets/api/comp_processor_knn.yaml | 10 +- src/datasets/api/comp_processor_pca.yaml | 10 +- src/datasets/api/comp_processor_subset.yaml | 10 +- src/datasets/api/file_common_dataset.yaml | 9 + .../api/{anndata_hvg.yaml => file_hvg.yaml} | 6 +- .../api/{anndata_knn.yaml => file_knn.yaml} | 7 +- ...a_normalized.yaml => file_normalized.yaml} | 5 +- .../api/{anndata_pca.yaml => file_pca.yaml} | 4 +- .../api/{anndata_raw.yaml => file_raw.yaml} | 2 +- .../loaders/openproblems_v1/config.vsh.yaml | 8 +- .../config.vsh.yaml | 7 +- .../normalization/l1_sqrt/config.vsh.yaml | 2 +- .../normalization/log_cpm/config.vsh.yaml | 2 +- .../log_scran_pooling/config.vsh.yaml | 2 +- .../normalization/sqrt_cpm/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- .../processors/subsample/config.vsh.yaml | 2 +- .../process_openproblems_v1/config.vsh.yaml | 4 +- .../check_migration_status/config.vsh.yaml | 2 +- .../check_migration_status/script.py | 16 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../api/comp_method_embedding.yaml | 23 +- .../api/comp_method_feature.yaml | 22 +- .../api/comp_method_graph.yaml | 22 +- .../api/comp_metric_embedding.yaml | 9 +- .../api/comp_metric_feature.yaml | 9 +- .../api/comp_metric_graph.yaml | 9 +- .../api/comp_process_dataset.yaml | 10 +- ...ng.yaml => file_integrated_embedding.yaml} | 6 +- ...ture.yaml => file_integrated_feature.yaml} | 6 +- ..._graph.yaml => file_integrated_graph.yaml} | 6 +- .../{anndata_score.yaml => file_score.yaml} | 4 +- ...integrated.yaml => file_unintegrated.yaml} | 4 +- .../batch_integration/api/task_info.yaml | 30 +- .../methods/bbknn/config.vsh.yaml | 9 +- .../batch_integration/methods/bbknn/script.py | 2 +- .../methods/combat/config.vsh.yaml | 9 +- .../methods/combat/script.py | 2 +- .../methods/scanorama_embed/config.vsh.yaml | 9 +- .../methods/scanorama_embed/script.py | 2 +- .../methods/scanorama_feature/config.vsh.yaml | 11 +- .../methods/scanorama_feature/script.py | 2 +- .../methods/scvi/config.vsh.yaml | 10 +- .../batch_integration/methods/scvi/script.py | 2 +- .../metrics/asw_batch/config.vsh.yaml | 11 +- .../metrics/asw_label/config.vsh.yaml | 13 +- .../cell_cycle_conservation/config.vsh.yaml | 11 +- .../clustering_overlap/config.vsh.yaml | 21 +- .../metrics/pcr/config.vsh.yaml | 12 +- .../process_dataset/config.vsh.yaml | 2 +- .../embed_to_graph/config.vsh.yaml | 8 +- .../feature_to_embed/config.vsh.yaml | 8 +- .../denoising/api/comp_control_method.yaml | 13 +- src/tasks/denoising/api/comp_method.yaml | 11 +- src/tasks/denoising/api/comp_metric.yaml | 12 +- .../denoising/api/comp_process_dataset.yaml | 13 +- ...anndata_dataset.yaml => file_dataset.yaml} | 2 +- ...ndata_denoised.yaml => file_denoised.yaml} | 2 +- .../{anndata_score.yaml => file_score.yaml} | 2 +- .../api/{anndata_test.yaml => file_test.yaml} | 2 +- .../{anndata_train.yaml => file_train.yaml} | 2 +- src/tasks/denoising/api/task_info.yaml | 27 +- .../no_denoising/config.vsh.yaml | 10 +- .../perfect_denoising/config.vsh.yaml | 10 +- .../denoising/methods/alra/config.vsh.yaml | 9 +- .../denoising/methods/dca/config.vsh.yaml | 9 +- .../methods/knn_smoothing/config.vsh.yaml | 9 +- .../denoising/methods/magic/config.vsh.yaml | 9 +- .../denoising/metrics/mse/config.vsh.yaml | 11 +- .../denoising/metrics/poisson/config.vsh.yaml | 11 +- .../denoising/process_dataset/config.vsh.yaml | 2 +- .../api/comp_control_method.yaml | 14 +- .../api/comp_method.yaml | 10 +- .../api/comp_metric.yaml | 9 +- .../api/comp_process_dataset.yaml | 10 +- ...anndata_dataset.yaml => file_dataset.yaml} | 4 +- ...ata_embedding.yaml => file_embedding.yaml} | 7 +- .../{anndata_score.yaml => file_score.yaml} | 4 +- ...ndata_solution.yaml => file_solution.yaml} | 4 +- .../api/task_info.yaml | 34 +- .../random_features/config.vsh.yaml | 10 +- .../true_features/config.vsh.yaml | 12 +- .../methods/densmap/config.vsh.yaml | 10 +- .../methods/ivis/config.vsh.yaml | 20 +- .../methods/neuralee/config.vsh.yaml | 13 +- .../methods/pca/config.vsh.yaml | 15 +- .../methods/phate/config.vsh.yaml | 17 +- .../methods/tsne/config.vsh.yaml | 13 +- .../methods/umap/config.vsh.yaml | 13 +- .../metrics/coranking/config.vsh.yaml | 164 +- .../density_preservation/config.vsh.yaml | 11 +- .../metrics/rmse/config.vsh.yaml | 22 +- .../metrics/trustworthiness/config.vsh.yaml | 14 +- .../process_dataset/config.vsh.yaml | 2 +- .../api/comp_control_method.yaml | 16 +- .../label_projection/api/comp_method.yaml | 13 +- .../label_projection/api/comp_metric.yaml | 12 +- .../api/comp_process_dataset.yaml | 16 +- ...a_prediction.yaml => file_prediction.yaml} | 6 +- .../{anndata_score.yaml => file_score.yaml} | 4 +- ...ndata_solution.yaml => file_solution.yaml} | 8 +- .../api/{anndata_test.yaml => file_test.yaml} | 7 +- .../{anndata_train.yaml => file_train.yaml} | 8 +- src/tasks/label_projection/api/task_info.yaml | 24 +- .../majority_vote/config.vsh.yaml | 10 +- .../random_labels/config.vsh.yaml | 10 +- .../true_labels/config.vsh.yaml | 11 +- .../methods/knn/config.vsh.yaml | 15 +- .../logistic_regression/config.vsh.yaml | 13 +- .../methods/mlp/config.vsh.yaml | 13 +- .../methods/scanvi/config.vsh.yaml | 11 +- .../methods/scanvi_scarches/config.vsh.yaml | 4 +- .../seurat_transferdata/config.vsh.yaml | 18 +- .../methods/xgboost/config.vsh.yaml | 14 +- .../metrics/accuracy/config.vsh.yaml | 13 +- .../metrics/f1/config.vsh.yaml | 31 +- .../process_dataset/config.vsh.yaml | 2 +- 155 files changed, 3513 insertions(+), 665 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 src/common/api/schema_component_api.yaml create mode 100644 src/common/api/schema_definitions.yaml create mode 100644 src/common/api/schema_file_api.yaml create mode 100644 src/common/api/schema_task_control_method.yaml create mode 100644 src/common/api/schema_task_info.yaml create mode 100644 src/common/api/schema_task_method.yaml create mode 100644 src/common/api/schema_task_metric.yaml create mode 100644 src/common/api/schema_viash_config.yaml create mode 100644 src/common/check_yaml_schema/config.vsh.yaml create mode 100644 src/common/check_yaml_schema/script.py delete mode 100644 src/datasets/api/anndata_common_dataset.yaml create mode 100644 src/datasets/api/file_common_dataset.yaml rename src/datasets/api/{anndata_hvg.yaml => file_hvg.yaml} (76%) rename src/datasets/api/{anndata_knn.yaml => file_knn.yaml} (69%) rename src/datasets/api/{anndata_normalized.yaml => file_normalized.yaml} (82%) rename src/datasets/api/{anndata_pca.yaml => file_pca.yaml} (83%) rename src/datasets/api/{anndata_raw.yaml => file_raw.yaml} (95%) rename src/tasks/batch_integration/api/{anndata_integrated_embedding.yaml => file_integrated_embedding.yaml} (83%) rename src/tasks/batch_integration/api/{anndata_integrated_feature.yaml => file_integrated_feature.yaml} (83%) rename src/tasks/batch_integration/api/{anndata_integrated_graph.yaml => file_integrated_graph.yaml} (83%) rename src/tasks/batch_integration/api/{anndata_score.yaml => file_score.yaml} (94%) rename src/tasks/batch_integration/api/{anndata_unintegrated.yaml => file_unintegrated.yaml} (94%) rename src/tasks/denoising/api/{anndata_dataset.yaml => file_dataset.yaml} (87%) rename src/tasks/denoising/api/{anndata_denoised.yaml => file_denoised.yaml} (93%) rename src/tasks/denoising/api/{anndata_score.yaml => file_score.yaml} (95%) rename src/tasks/denoising/api/{anndata_test.yaml => file_test.yaml} (90%) rename src/tasks/denoising/api/{anndata_train.yaml => file_train.yaml} (89%) rename src/tasks/dimensionality_reduction/api/{anndata_dataset.yaml => file_dataset.yaml} (90%) rename src/tasks/dimensionality_reduction/api/{anndata_embedding.yaml => file_embedding.yaml} (78%) rename src/tasks/dimensionality_reduction/api/{anndata_score.yaml => file_score.yaml} (93%) rename src/tasks/dimensionality_reduction/api/{anndata_solution.yaml => file_solution.yaml} (90%) rename src/tasks/label_projection/api/{anndata_prediction.yaml => file_prediction.yaml} (84%) rename src/tasks/label_projection/api/{anndata_score.yaml => file_score.yaml} (93%) rename src/tasks/label_projection/api/{anndata_solution.yaml => file_solution.yaml} (87%) rename src/tasks/label_projection/api/{anndata_test.yaml => file_test.yaml} (88%) rename src/tasks/label_projection/api/{anndata_train.yaml => file_train.yaml} (88%) diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000000..0c9aaaaeee --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,10 @@ +{ + "yaml.schemas": { + "src/common/api/schema_component_api.yaml": "src/**/api/comp_*.yaml", + "src/common/api/schema_file_api.yaml": "src/**/api/file_*.yaml", + "src/common/api/schema_task_info.yaml": "src/**/api/task_info.yaml", + "src/common/api/schema_task_method.yaml": "src/tasks/**/methods/**/config.vsh.yaml", + "src/common/api/schema_task_control_method.yaml": "src/tasks/**/control_methods/**/config.vsh.yaml", + "src/common/api/schema_task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml" + } +} \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 408c8d406b..c6bc697f77 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,7 +38,7 @@ * `comp_tests`: Common unit tests that can be used by all tasks. -* `check_dataset_schema`: Check if the dataset used has the required fields defined in the api `anndata_*.yaml` files. +* `check_dataset_schema`: Check if the dataset used has the required fields defined in the api `file_*.yaml` files. * `Create_component`: Creates a template folder with a viash config and script file depending on the task api. @@ -85,7 +85,7 @@ ### NEW FUNCTIONALITY -* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. * `api/comp_*`: Created an api definition for the process, method and metric components. @@ -123,7 +123,7 @@ ### NEW FUNCTIONALITY -* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. * `api/comp_*`: Created an api definition for the split, method and metric components. @@ -160,7 +160,7 @@ ## Dimensionality reduction ### New functionality -* `api/anndata_*`: Created a file format specifications for the h5ad files throughout the pipeline. +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. * `api/comp_*`: Created an api definition for the split, control method, method and metric components. diff --git a/src/common/api/schema_component_api.yaml b/src/common/api/schema_component_api.yaml new file mode 100644 index 0000000000..59e5af958a --- /dev/null +++ b/src/common/api/schema_component_api.yaml @@ -0,0 +1,67 @@ +title: Component API +description: | + A component type specification file. +type: object +required: [functionality] +properties: + functionality: + type: object + description: Information regarding the functionality of the component. + required: [namespace, info, arguments, test_resources] + additionalProperties: false + properties: + namespace: + "$ref": "schema_definitions.yaml#/definitions/Namespace" + info: + type: object + description: Metadata of the component. + additionalProperties: false + required: [type, type_info] + properties: + type: + "$ref": "schema_definitions.yaml#/definitions/ComponentType" + subtype: + "$ref": "schema_definitions.yaml#/definitions/ComponentSubtype" + type_info: + type: object + description: Metadata related to the component type. + required: [label, summary, description] + properties: + label: + $ref: "schema_definitions.yaml#/definitions/Label" + summary: + $ref: "schema_definitions.yaml#/definitions/Summary" + description: + $ref: "schema_definitions.yaml#/definitions/Description" + arguments: + type: array + description: Component-specific parameters. + items: + anyOf: + - $ref: 'schema_definitions.yaml#/definitions/ComponentAPIFile' + - $ref: 'schema_viash_config.yaml#/definitions/BooleanArgument' + - $ref: 'schema_viash_config.yaml#/definitions/BooleanArgument' + - $ref: 'schema_viash_config.yaml#/definitions/BooleanTrueArgument' + - $ref: 'schema_viash_config.yaml#/definitions/BooleanFalseArgument' + - $ref: 'schema_viash_config.yaml#/definitions/DoubleArgument' + - $ref: 'schema_viash_config.yaml#/definitions/IntegerArgument' + - $ref: 'schema_viash_config.yaml#/definitions/LongArgument' + - $ref: 'schema_viash_config.yaml#/definitions/StringArgument' + resources: + type: array + description: Resources required to run the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + test_resources: + type: array + description: One or more scripts and resources used to test the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + platforms: + type: array + description: A list of platforms which Viash generates target artifacts for. + items: + anyOf: + - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" + - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" + - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_definitions.yaml b/src/common/api/schema_definitions.yaml new file mode 100644 index 0000000000..bab932a3e2 --- /dev/null +++ b/src/common/api/schema_definitions.yaml @@ -0,0 +1,277 @@ +definitions: + PlatformVdsl3: + title: VDSL3 + description: Next-gen platform for generating NextFlow VDSL3 modules. + properties: + type: + const: nextflow + description: Next-gen platform for generating NextFlow VDSL3 modules. + directives: + $ref: 'schema_viash_config.yaml#/definitions/NextflowDirectives' + # auto: + # $ref: 'schema_viash_config.yaml#/definitions/NextflowAuto' + # config: + # $ref: 'schema_viash_config.yaml#/definitions/NextflowConfig' + required: [ type ] + additionalProperties: false + PlatformDocker: + title: Docker platform + description: | + Run a Viash component on a Docker backend platform. + By specifying which dependencies your component needs, users are be able to build + a docker container from scratch using the setup flag, or pull it from a docker repository. + type: object + properties: + type: + const: docker + description: Run a Viash component on a Docker backend platform. + image: + type: string + description: The base container to start from. You can also add the tag here + if you wish. + run_args: + anyOf: + - type: string + description: Add docker run arguments. + - type: array + items: + type: string + description: Add docker run arguments. + target_image_source: + type: string + description: The source of the target image. This is used for defining labels + in the dockerfile. + setup: + type: array + items: + "$ref": "schema_viash_config.yaml#/definitions/Requirements" + test_setup: + type: array + items: + "$ref": "schema_viash_config.yaml#/definitions/Requirements" + required: [type, image] + additionalProperties: false + PlatformNative: + title: Native platform + type: object + properties: + type: + const: native + description: Specifies the type of the platform. Running a Viash component + on a native platform means that the script will be executed in your current + environment. + required: [ type ] + additionalProperties: false + PreferredNormalization: + enum: [l1_sqrt, log_cpm, log_scran_pooling, sqrt_cpm, counts] + description: | + Which normalization method a component prefers. + + Each value corresponds to a normalization component in the directory `src/datasets/normalization`. + ComponentSubtype: + type: string + description: | + A component subtype, in case the task has multiple subtypes of methods and metrics. + ComponentType: + type: string + description: | + A component subtype, in case the task has multiple subtypes of methods and metrics. + Name: + type: string + description: | + A unique identifier. Can only contain lowercase letters, numbers or underscores. + pattern: "^[a-z_][a-z0-9_]*$" + maxLength: 50 + Namespace: + type: string + description: | + The namespace a component is part of. + pattern: "^[a-z_][a-z0-9_/]*$" + Label: + type: string + description: | + A unique, human-readable, short label. Used for creating summary tables and visualisations. + maxLength: 50 + Summary: + type: string + description: | + A one sentence summary of purpose and methodology. Used for creating an overview tables. + minLength: 15 + maxLength: 180 + Description: + type: string + description: | + A longer description (one or more paragraphs). Used for creating reference documentation and supplementary information. + minLength: 30 + BibtexReference: + type: string + description: | + type: string + description: A bibtex reference key to the paper where the component is described. + DocumentationURL: + type: string + format: uri + pattern: "^https://" + description: The url to the documentation of the used software library. + RepositoryURL: + type: string + format: uri + pattern: "^https://" + description: The url to the repository of the used software library. + MigrationV1: + type: object + required: [path, commit] + properties: + additionalProperties: false + path: + type: string + description: | + If this component was migrated from the OpenProblems v1 repository, this value + represents the location of the Python file relative to the root of the repository. + commit: + type: string + description: | + If this component was migrated from the OpenProblems v1 repository, this value + is the Git commit SHA of the v1 repository corresponding to when this component + was last updated. + note: + type: string + description: | + An optional note on any changes made during the migration. + MethodVariants: + type: object + description: Alternative parameter sets which should be evaluated in the benchmark. + properties: + preferred_normalization: + "$ref": "#/definitions/PreferredNormalization" + CompAPIMerge: + type: string + description: | + The API specifies which type of component this is. + It contains specifications for: + + - The input/output files + - Common parameters + - A unit test + Merge: + type: string + description: | + Another YAML to inherit values from. + ComponentAPIFile: + description: A `file` type argument has a string value that points to a file or folder path. + type: object + properties: + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + __merge__: + type: string + description: The file format specification file. + direction: + description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. + $ref: 'schema_viash_config.yaml#/definitions/Direction' + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + required: [name, __merge__, direction, required] + additionalProperties: false + AnnDataSlots: + properties: + X: + $ref: "#/definitions/AnnDataSlot" + layers: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + var: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + varm: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + varp: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + obs: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + obsm: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + obsp: + type: array + items: + $ref: "#/definitions/AnnDataSlot" + uns: + type: array + items: + oneOf: + - $ref: "#/definitions/AnnDataSlot" + - $ref: "#/definitions/AnnDataSlotObject" + AnnDataSlot: + properties: + type: + enum: [integer, double, string, boolean] + name: + type: string + description: A unique identifier. + pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$" + description: + type: string + required: + type: boolean + required: [type, name, description, required] + AnnDataSlotObject: + properties: + type: + enum: [object] + name: + type: string + description: A unique identifier. + pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$" + description: + type: string + required: + type: boolean + required: [type, name, description, required] + Author: + description: Author metadata. + type: object + additionalProperties: false + properties: + name: + description: Full name of the author, usually in the name of FirstName MiddleName LastName. + type: string + info: + description: Additional information on the author + type: object + additionalProperties: false + properties: + github: + type: string + orcid: + type: string + email: + type: string + twitter: + type: string + linkedin: + type: string + roles: + description: | + Role of the author. Possible values: + + * `"author"`: Authors who have made substantial contributions to the component. + * `"maintainer"`: The maintainer of the component. + * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.). + type: array + items: + enum: [maintainer, author, contributor] \ No newline at end of file diff --git a/src/common/api/schema_file_api.yaml b/src/common/api/schema_file_api.yaml new file mode 100644 index 0000000000..96639dbfcd --- /dev/null +++ b/src/common/api/schema_file_api.yaml @@ -0,0 +1,26 @@ +title: File API +description: A file format specification file. +type: object +additionalProperties: false +required: [type, example, info] +properties: + type: + const: file + example: + description: A file in the `resources_test` folder which is an example of this file format. + type: string + __merge__: + $ref: "schema_definitions.yaml#/definitions/Merge" + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + required: [label, summary] + properties: + label: + $ref: "schema_definitions.yaml#/definitions/Label" + summary: + $ref: "schema_definitions.yaml#/definitions/Summary" + description: + $ref: "schema_definitions.yaml#/definitions/Description" + slots: + $ref: "schema_definitions.yaml#/definitions/AnnDataSlots" diff --git a/src/common/api/schema_task_control_method.yaml b/src/common/api/schema_task_control_method.yaml new file mode 100644 index 0000000000..e4e72b49ba --- /dev/null +++ b/src/common/api/schema_task_control_method.yaml @@ -0,0 +1,70 @@ +title: Control Method +description: | + A control method is used to test the relative performance of all other methods, + and also as a quality control for the pipeline as a whole. A control method can + either be a positive control or a negative control. The positive control and + negative control methods set a maximum and minimum threshold for performance, + so any new method should perform better than the negative control methods and + worse than the positive control method. +type: object +required: [__merge__, functionality, platforms] +properties: + __merge__: + "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + functionality: + type: object + description: Information regarding the functionality of the component. + required: [name, info, resources] + additionalProperties: false + properties: + name: + "$ref": "schema_definitions.yaml#/definitions/Name" + status: + "$ref": "schema_viash_config.yaml#/definitions/Status" + info: + type: object + description: Metadata of the component. + additionalProperties: false + required: [label, summary, description, preferred_normalization] + properties: + label: + "$ref": "schema_definitions.yaml#/definitions/Label" + summary: + "$ref": "schema_definitions.yaml#/definitions/Summary" + description: + "$ref": "schema_definitions.yaml#/definitions/Description" + preferred_normalization: + "$ref": "schema_definitions.yaml#/definitions/PreferredNormalization" + reference: + "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + documentation_url: + "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + repository_url: + "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + v1: + "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + variants: + "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + arguments: + type: array + description: Component-specific parameters. + items: + "$ref": "schema_viash_config.yaml#/definitions/Argument" + resources: + type: array + description: Resources required to run the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + test_resources: + type: array + description: One or more scripts and resources used to test the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + platforms: + type: array + description: A list of platforms which Viash generates target artifacts for. + items: + anyOf: + - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" + - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" + - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_task_info.yaml b/src/common/api/schema_task_info.yaml new file mode 100644 index 0000000000..d903aaa1fa --- /dev/null +++ b/src/common/api/schema_task_info.yaml @@ -0,0 +1,22 @@ +title: Task info +description: A file format specification file. +type: object +additionalProperties: false +required: [name, label, summary, motivation, description] +properties: + name: + $ref: "schema_definitions.yaml#/definitions/Name" + label: + $ref: "schema_definitions.yaml#/definitions/Label" + summary: + $ref: "schema_definitions.yaml#/definitions/Summary" + motivation: + $ref: "schema_definitions.yaml#/definitions/Description" + description: + $ref: "schema_definitions.yaml#/definitions/Description" + v1: + $ref: "schema_definitions.yaml#/definitions/MigrationV1" + authors: + type: array + items: + $ref: "schema_definitions.yaml#/definitions/Author" diff --git a/src/common/api/schema_task_method.yaml b/src/common/api/schema_task_method.yaml new file mode 100644 index 0000000000..a1f1a02e28 --- /dev/null +++ b/src/common/api/schema_task_method.yaml @@ -0,0 +1,67 @@ +title: Method +description: | + A method is a specific technique used to solve the task problem and is + compared to the control methods and other methods to determine the best + approach for the task depending on the type of dataset. +type: object +required: [__merge__, functionality, platforms] +properties: + __merge__: + "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + functionality: + type: object + description: Information regarding the functionality of the component. + required: [name, info, resources] + additionalProperties: false + properties: + name: + "$ref": "schema_definitions.yaml#/definitions/Name" + status: + "$ref": "schema_viash_config.yaml#/definitions/Status" + info: + type: object + description: Metadata of the component. + additionalProperties: false + required: [label, summary, description, preferred_normalization, reference, documentation_url, repository_url] + properties: + label: + "$ref": "schema_definitions.yaml#/definitions/Label" + summary: + "$ref": "schema_definitions.yaml#/definitions/Summary" + description: + "$ref": "schema_definitions.yaml#/definitions/Description" + preferred_normalization: + "$ref": "schema_definitions.yaml#/definitions/PreferredNormalization" + reference: + "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + documentation_url: + "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + repository_url: + "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + v1: + "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + variants: + "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + arguments: + type: array + description: Component-specific parameters. + items: + "$ref": "schema_viash_config.yaml#/definitions/Argument" + resources: + type: array + description: Resources required to run the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + test_resources: + type: array + description: One or more scripts and resources used to test the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + platforms: + type: array + description: A list of platforms which Viash generates target artifacts for. + items: + anyOf: + - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" + - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" + - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_task_metric.yaml b/src/common/api/schema_task_metric.yaml new file mode 100644 index 0000000000..dc36af9f1e --- /dev/null +++ b/src/common/api/schema_task_metric.yaml @@ -0,0 +1,88 @@ +title: Metric +description: | + A metric is a quantitative measure used to evaluate the performance of the + different methods in solving the specific task problem. +type: object +required: [__merge__, functionality, platforms] +properties: + __merge__: + "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + functionality: + type: object + description: Information regarding the functionality of the component. + required: [name, info, resources] + additionalProperties: false + properties: + name: + "$ref": "schema_definitions.yaml#/definitions/Name" + status: + "$ref": "schema_viash_config.yaml#/definitions/Status" + info: + type: object + description: Metadata of the component. + additionalProperties: false + required: [metrics] + properties: + metrics: + type: array + minItems: 1 + items: + type: object + description: Metadata of each metric. + additionalProperties: false + required: [label, summary, description, reference, min, max, maximize] + properties: + name: + "$ref": "schema_definitions.yaml#/definitions/Name" + label: + "$ref": "schema_definitions.yaml#/definitions/Label" + summary: + "$ref": "schema_definitions.yaml#/definitions/Summary" + description: + "$ref": "schema_definitions.yaml#/definitions/Description" + reference: + "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + documentation_url: + "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + repository_url: + "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + variants: + "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + min: + oneOf: + - type: number + description: The lowest possible value of the metric. + - const: "-.inf" + max: + oneOf: + - type: number + description: The highest possible value of the metric. + - const: "+.inf" + maximize: + type: boolean + description: Whether a higher metric value is better. + v1: + "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + arguments: + type: array + description: Component-specific parameters. + items: + "$ref": "schema_viash_config.yaml#/definitions/Argument" + resources: + type: array + description: Resources required to run the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + test_resources: + type: array + description: One or more scripts and resources used to test the component. + items: + "$ref": "schema_viash_config.yaml#/definitions/Resource" + platforms: + type: array + description: A list of platforms which Viash generates target artifacts for. + items: + anyOf: + - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" + - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" + - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_viash_config.yaml b/src/common/api/schema_viash_config.yaml new file mode 100644 index 0000000000..bad6d32a56 --- /dev/null +++ b/src/common/api/schema_viash_config.yaml @@ -0,0 +1,1931 @@ +$schema: https://json-schema.org/draft-07/schema# +description: A schema for Viash config files +definitions: + Functionality: + description: | + The functionality-part of the config file describes the behaviour of the script in terms of arguments and resources. + By specifying a few restrictions (e.g. mandatory arguments) and adding some descriptions, Viash will automatically generate a stylish command-line interface for you. + type: object + properties: + name: + description: Name of the component and the filename of the executable when built with `viash build`. + type: string + enabled: + description: Setting this to false with disable this component when using namespaces. + type: boolean + tests: + description: One or more Bash/R/Python scripts to be used to test the component behaviour when `viash test` is invoked. Additional files of type `file` will be made available only during testing. Each test script should expect no command-line inputs, be platform-independent, and return an exit code >0 when unexpected behaviour occurs during testing. + type: array + items: + $ref: '#/definitions/Resource' + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + version: + description: Version of the component. This field will be used to version the executable and the Docker container. + type: string + inputs: + description: A list of input arguments in addition to the `arguments` list. Any arguments specified here will have their `type` set to `file` and the `direction` set to `input` by default. + type: array + items: + $ref: '#/definitions/Argument' + authors: + description: "A list of @[authors](author). An author must at least have a name, but can also have a list of roles, an e-mail address, and a map of custom properties.\n\nSuggested values for roles are:\n \n| Role | Abbrev. | Description |\n|------|---------|-------------|\n| maintainer | mnt | for the maintainer of the code. Ideally, exactly one maintainer is specified. |\n| author | aut | for persons who have made substantial contributions to the software. |\n| contributor | ctb| for persons who have made smaller contributions (such as code patches).\n| datacontributor | dtc | for persons or organisations that contributed data sets for the software\n| copyrightholder | cph | for all copyright holders. This is a legal concept so should use the legal name of an institution or corporate body.\n| funder | fnd | for persons or organizations that furnished financial support for the development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html) is extremely comprehensive.\n" + type: array + items: + $ref: '#/definitions/Author' + status: + description: Allows setting a component to active, deprecated or disabled. + $ref: '#/definitions/Status' + requirements: + description: "@[Computational requirements](computational_requirements) related to running the component. \n`cpus` specifies the maximum number of (logical) cpus a component is allowed to use., whereas\n`memory` specifies the maximum amount of memory a component is allowed to allicate. Memory units must be\nin B, KB, MB, GB, TB or PB." + $ref: '#/definitions/ComputationalRequirements' + resources: + description: | + @[Resources](resources) are files that support the component. The first resource should be @[a script](scripting_languages) that will be executed when the functionality is run. Additional resources will be copied to the same directory. + + Common properties: + + * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script` / `scala_script` / `csharp_script`, specifies the type of the resource. The first resource cannot be of type `file`. When the type is not specified, the default type is simply `file`. + * dest: filename, the resulting name of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + * path: `path/to/file`, the path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + * text: ...multiline text..., the content of the resulting file specified as a string. Mutually exclusive with `path`. + * is_executable: `true` / `false`, whether the resulting resource file should be made executable. + type: array + items: + $ref: '#/definitions/Resource' + test_resources: + description: One or more @[scripts](scripting_languages) to be used to test the component behaviour when `viash test` is invoked. Additional files of type `file` will be made available only during testing. Each test script should expect no command-line inputs, be platform-independent, and return an exit code >0 when unexpected behaviour occurs during testing. See @[Unit Testing](unit_testing) for more info. + type: array + items: + $ref: '#/definitions/Resource' + argument_groups: + description: "A grouping of the @[arguments](argument), used to display the help message.\n\n - `name: foo`, the name of the argument group. \n - `description: Description of foo`, a description of the argument group. Multiline descriptions are supported.\n - `arguments: [arg1, arg2, ...]`, list of the arguments names.\n\n" + type: array + items: + $ref: '#/definitions/ArgumentGroup' + description: + description: A description of the component. This will be displayed with `--help`. + type: string + usage: + description: A description on how to use the component. This will be displayed with `--help` under the 'Usage:' section. + type: string + add_resources_to_path: + description: Adds the resources directory to the PATH variable when set to true. This is set to false by default. + type: boolean + outputs: + description: A list of output arguments in addition to the `arguments` list. Any arguments specified here will have their `type` set to `file` and thr `direction` set to `output` by default. + type: array + items: + $ref: '#/definitions/Argument' + namespace: + description: Namespace this component is a part of. See the @[Namespaces guide](namespace) for more information on namespaces. + type: string + arguments: + description: "A list of @[arguments](argument) for this component. For each argument, a type and a name must be specified. Depending on the type of argument, different properties can be set. See these reference pages per type for more information: \n\n - @[string](arg_string)\n - @[file](arg_file)\n - @[integer](arg_integer)\n - @[double](arg_double)\n - @[boolean](arg_boolean)\n - @[boolean_true](arg_boolean_true)\n - @[boolean_false](arg_boolean_false)\n" + type: array + items: + $ref: '#/definitions/Argument' + additionalProperties: false + NativePlatform: + description: | + Running a Viash component on a native platform means that the script will be executed in your current environment. + Any dependencies are assumed to have been installed by the user, so the native platform is meant for developers (who know what they're doing) or for simple bash scripts (which have no extra dependencies). + type: object + properties: + id: + description: 'As with all platforms, you can give a platform a different name. By specifying `id: foo`, you can target this platform (only) by specifying `-p foo` in any of the Viash commands.' + type: string + type: + description: | + Running a Viash component on a native platform means that the script will be executed in your current environment. + Any dependencies are assumed to have been installed by the user, so the native platform is meant for developers (who know what they're doing) or for simple bash scripts (which have no extra dependencies). + const: native + additionalProperties: false + DockerPlatform: + description: | + Run a Viash component on a Docker backend platform. + By specifying which dependencies your component needs, users will be able to build a docker container from scratch using the setup flag, or pull it from a docker repository. + type: object + properties: + organization: + description: Name of a container's [organization](https://docs.docker.com/docker-hub/orgs/). + type: string + registry: + description: The URL to the a [custom Docker registry](https://docs.docker.com/registry/) + type: string + image: + description: The base container to start from. You can also add the tag here if you wish. + type: string + tag: + description: Specify a Docker image based on its tag. + type: string + target_tag: + description: The tag the resulting image gets. Advanced usage only. + type: string + run_args: + anyOf: + - description: Add [docker run](https://docs.docker.com/engine/reference/run/) arguments. + type: string + - description: Add [docker run](https://docs.docker.com/engine/reference/run/) arguments. + type: array + items: + type: string + namespace_separator: + description: 'The separator between the namespace and the name of the component, used for determining the image name. Default: `"/"`.' + type: string + resolve_volume: + description: 'Enables or disables automatic volume mapping. Enabled when set to `Automatic` or disabled when set to `Manual`. Default: `Automatic`.' + $ref: '#/definitions/DockerResolveVolume' + port: + anyOf: + - description: A list of enabled ports. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. + type: string + - description: A list of enabled ports. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. + type: array + items: + type: string + python: + description: Specify which Python packages should be available in order to run the component. + $ref: '#/definitions/PythonRequirements' + setup: + description: | + A list of requirements for installing the following types of packages: + + - @[apt](apt_req) + - @[apk](apk_req) + - @[Docker setup instructions](docker_req) + - @[JavaScript](javascript_req) + - @[Python](python_req) + - @[R](r_req) + - @[Ruby](ruby_req) + - @[yum](yum_req) + + The order in which these dependencies are specified determines the order in which they will be installed. + type: array + items: + $ref: '#/definitions/Requirements' + workdir: + description: The working directory when starting the container. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. + type: string + apk: + description: Specify which apk packages should be available in order to run the component. + $ref: '#/definitions/ApkRequirements' + target_image: + description: If anything is specified in the setup section, running the `---setup` will result in an image with the name of `:`. If nothing is specified in the `setup` section, simply `image` will be used. Advanced usage only. + type: string + cmd: + anyOf: + - description: Set the default command being executed when running the Docker container. + type: string + - description: Set the default command being executed when running the Docker container. + type: array + items: + type: string + yum: + description: Specify which yum packages should be available in order to run the component. + $ref: '#/definitions/YumRequirements' + target_image_source: + description: The source of the target image. This is used for defining labels in the dockerfile. + type: string + test_setup: + description: Additional requirements specific for running unit tests. + type: array + items: + $ref: '#/definitions/Requirements' + entrypoint: + anyOf: + - description: Override the entrypoint of the base container. Default set `ENTRYPOINT []`. + type: string + - description: Override the entrypoint of the base container. Default set `ENTRYPOINT []`. + type: array + items: + type: string + docker: + description: Specify which Docker commands should be run during setup. + $ref: '#/definitions/DockerRequirements' + id: + description: 'As with all platforms, you can give a platform a different name. By specifying `id: foo`, you can target this platform (only) by specifying `-p foo` in any of the Viash commands.' + type: string + apt: + description: Specify which apt packages should be available in order to run the component. + $ref: '#/definitions/AptRequirements' + target_registry: + description: The URL where the resulting image will be pushed to. Advanced usage only. + type: string + privileged: + description: Adds a `privileged` flag to the docker run. + type: boolean + setup_strategy: + description: |+ + The Docker setup strategy to use when building a container. + + | Strategy | Description | + |-----|----------| + | `alwaysbuild` / `build` / `b` | Always build the image from the dockerfile. This is the default setup strategy. + | `alwayscachedbuild` / `cachedbuild` / `cb` | Always build the image from the dockerfile, with caching enabled. + | `ifneedbebuild` | Build the image if it does not exist locally. + | `ifneedbecachedbuild` | Build the image with caching enabled if it does not exist locally, with caching enabled. + | `alwayspull` / `pull` / `p` | Try to pull the container from [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry). + | `alwayspullelsebuild` / `pullelsebuild` | Try to pull the image from a registry and build it if it doesn't exist. + | `alwayspullelsecachedbuild` / `pullelsecachedbuild` | Try to pull the image from a registry and build it with caching if it doesn't exist. + | `ifneedbepull` | If the image does not exist locally, pull the image. + | `ifneedbepullelsebuild` | If the image does not exist locally, pull the image. If the image does exist, build it. + | `ifneedbepullelsecachedbuild` | If the image does not exist locally, pull the image. If the image does exist, build it with caching enabled. + | `push` | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry). + | `pushifnotpresent` | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry) if the @[tag](docker_tag) does not exist yet. + | `donothing` / `meh` | Do not build or pull anything. + + $ref: '#/definitions/DockerSetupStrategy' + r: + description: Specify which R packages should be available in order to run the component. + $ref: '#/definitions/RRequirements' + type: + description: | + Run a Viash component on a Docker backend platform. + By specifying which dependencies your component needs, users will be able to build a docker container from scratch using the setup flag, or pull it from a docker repository. + const: docker + target_organization: + description: The organization set in the resulting image. Advanced usage only. + type: string + chown: + description: 'In Linux, files created by a Docker container will be owned by `root`. With `chown: true`, Viash will automatically change the ownership of output files (arguments with `type: file` and `direction: output`) to the user running the Viash command after execution of the component. Default value: `true`.' + type: boolean + additionalProperties: false + NextflowVdsl3Platform: + description: Next-gen platform for generating NextFlow VDSL3 modules. + type: object + properties: + auto: + description: |+ + @[Automated processing flags](nextflow_auto) which can be toggled on or off: + + | Flag | Description | Default | + |---|---------|----| + | `simplifyInput` | If `true`, an input tuple only containing only a single File (e.g. `["foo", file("in.h5ad")]`) is automatically transformed to a map (i.e. `["foo", [ input: file("in.h5ad") ] ]`). | `true` | + | `simplifyOutput` | If `true`, an output tuple containing a map with a File (e.g. `["foo", [ output: file("out.h5ad") ] ]`) is automatically transformed to a map (i.e. `["foo", file("out.h5ad")]`). | `true` | + | `transcript` | If `true`, the module's transcripts from `work/` are automatically published to `params.transcriptDir`. If not defined, `params.publishDir + "/_transcripts"` will be used. Will throw an error if neither are defined. | `false` | + | `publish` | If `true`, the module's outputs are automatically published to `params.publishDir`. Will throw an error if `params.publishDir` is not defined. | `false` | + + $ref: '#/definitions/NextflowAuto' + directives: + description: "@[Directives](nextflow_directives) are optional settings that affect the execution of the process. These mostly match up with the Nextflow counterparts. \n" + $ref: '#/definitions/NextflowDirectives' + container: + description: Specifies the Docker platform id to be used to run Nextflow. + type: string + debug: + description: Whether or not to print debug messages. + type: boolean + id: + description: Every platform can be given a specific id that can later be referred to explicitly when running or building the Viash component. + type: string + type: + description: Next-gen platform for generating NextFlow VDSL3 modules. + const: nextflow + config: + description: Allows tweaking how the @[Nextflow Config](nextflow_config) file is generated. + $ref: '#/definitions/NextflowConfig' + additionalProperties: false + Platforms: + anyOf: + - $ref: '#/definitions/NativePlatform' + - $ref: '#/definitions/DockerPlatform' + - $ref: '#/definitions/NextflowVdsl3Platform' + Info: + description: Definition of meta data + type: object + properties: + config: + type: string + platform: + type: string + output: + type: string + executable: + type: string + viash_version: + type: string + git_commit: + type: string + git_remote: + type: string + git_tag: + type: string + additionalProperties: false + Author: + description: Author metadata. + type: object + properties: + name: + description: Full name of the author, usually in the name of FirstName MiddleName LastName. + type: string + email: + description: E-mail of the author. + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + roles: + anyOf: + - description: | + Role of the author. Suggested items: + + * `"author"`: Authors who have made substantial contributions to the component. + * `"maintainer"`: The maintainer of the component. + * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.). + type: string + - description: | + Role of the author. Suggested items: + + * `"author"`: Authors who have made substantial contributions to the component. + * `"maintainer"`: The maintainer of the component. + * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.). + type: array + items: + type: string + props: + description: Author properties. Must be a map of strings. + type: object + additionalProperties: + description: Author properties. Must be a map of strings. + type: string + additionalProperties: false + ComputationalRequirements: + description: Computational requirements related to running the component. + type: object + properties: + n_proc: + description: "" + type: integer + cpus: + description: The maximum number of (logical) cpus a component is allowed to use. + type: integer + commands: + description: A list of commands which should be present on the system for the script to function. + type: array + items: + type: string + memory: + description: The maximum amount of memory a component is allowed to allocate. Unit must be one of B, KB, MB, GB, TB or PB. + type: string + additionalProperties: false + ApkRequirements: + description: Specify which apk packages should be available in order to run the component. + type: object + properties: + type: + description: Specify which apk packages should be available in order to run the component. + const: apk + packages: + anyOf: + - description: Specifies which packages to install. + type: string + - description: Specifies which packages to install. + type: array + items: + type: string + additionalProperties: false + AptRequirements: + description: Specify which apt packages should be available in order to run the component. + type: object + properties: + interactive: + description: 'If `false`, the Debian frontend is set to non-interactive (recommended). Default: false.' + type: boolean + type: + description: Specify which apt packages should be available in order to run the component. + const: apt + packages: + anyOf: + - description: Specifies which packages to install. + type: string + - description: Specifies which packages to install. + type: array + items: + type: string + additionalProperties: false + DockerRequirements: + description: Specify which Docker commands should be run during setup. + type: object + properties: + run: + anyOf: + - description: Specifies which `RUN` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `RUN` entries to add to the Dockerfile while building it. + type: array + items: + type: string + label: + anyOf: + - description: Specifies which `LABEL` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `LABEL` entries to add to the Dockerfile while building it. + type: array + items: + type: string + build_args: + anyOf: + - description: Specifies which `ARG` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `ARG` entries to add to the Dockerfile while building it. + type: array + items: + type: string + type: + description: Specify which Docker commands should be run during setup. + const: docker + add: + anyOf: + - description: Specifies which `ADD` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `ADD` entries to add to the Dockerfile while building it. + type: array + items: + type: string + env: + anyOf: + - description: Specifies which `ENV` entries to add to the Dockerfile while building it. Unlike `ARG`, `ENV` entries are also accessible from inside the container. + type: string + - description: Specifies which `ENV` entries to add to the Dockerfile while building it. Unlike `ARG`, `ENV` entries are also accessible from inside the container. + type: array + items: + type: string + resources: + anyOf: + - description: Specifies which `COPY` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `COPY` entries to add to the Dockerfile while building it. + type: array + items: + type: string + copy: + anyOf: + - description: Specifies which `COPY` entries to add to the Dockerfile while building it. + type: string + - description: Specifies which `COPY` entries to add to the Dockerfile while building it. + type: array + items: + type: string + additionalProperties: false + JavascriptRequirements: + description: Specify which JavaScript packages should be available in order to run the component. + type: object + properties: + github: + anyOf: + - description: Specifies which packages to install from GitHub. + type: string + - description: Specifies which packages to install from GitHub. + type: array + items: + type: string + url: + anyOf: + - description: Specifies which packages to install using a generic URI. + type: string + - description: Specifies which packages to install using a generic URI. + type: array + items: + type: string + git: + anyOf: + - description: Specifies which packages to install using a Git URI. + type: string + - description: Specifies which packages to install using a Git URI. + type: array + items: + type: string + npm: + anyOf: + - description: Specifies which packages to install from npm. + type: string + - description: Specifies which packages to install from npm. + type: array + items: + type: string + type: + description: Specify which JavaScript packages should be available in order to run the component. + const: javascript + packages: + anyOf: + - description: Specifies which packages to install from npm. + type: string + - description: Specifies which packages to install from npm. + type: array + items: + type: string + additionalProperties: false + PythonRequirements: + description: Specify which Python packages should be available in order to run the component. + type: object + properties: + github: + anyOf: + - description: Specifies which packages to install from GitHub. + type: string + - description: Specifies which packages to install from GitHub. + type: array + items: + type: string + gitlab: + anyOf: + - description: Specifies which packages to install from GitLab. + type: string + - description: Specifies which packages to install from GitLab. + type: array + items: + type: string + pip: + anyOf: + - description: Specifies which packages to install from pip. + type: string + - description: Specifies which packages to install from pip. + type: array + items: + type: string + pypi: + anyOf: + - description: Specifies which packages to install from PyPI using pip. + type: string + - description: Specifies which packages to install from PyPI using pip. + type: array + items: + type: string + git: + anyOf: + - description: Specifies which packages to install using a Git URI. + type: string + - description: Specifies which packages to install using a Git URI. + type: array + items: + type: string + upgrade: + description: 'Sets the `--upgrade` flag when set to true. Default: true.' + type: boolean + packages: + anyOf: + - description: Specifies which packages to install from pip. + type: string + - description: Specifies which packages to install from pip. + type: array + items: + type: string + url: + anyOf: + - description: Specifies which packages to install using a generic URI. + type: string + - description: Specifies which packages to install using a generic URI. + type: array + items: + type: string + svn: + anyOf: + - description: Specifies which packages to install using an SVN URI. + type: string + - description: Specifies which packages to install using an SVN URI. + type: array + items: + type: string + bazaar: + anyOf: + - description: Specifies which packages to install using a Bazaar URI. + type: string + - description: Specifies which packages to install using a Bazaar URI. + type: array + items: + type: string + script: + anyOf: + - description: Specifies a code block to run as part of the build. + type: string + - description: Specifies a code block to run as part of the build. + type: array + items: + type: string + type: + description: Specify which Python packages should be available in order to run the component. + const: python + mercurial: + anyOf: + - description: Specifies which packages to install using a Mercurial URI. + type: string + - description: Specifies which packages to install using a Mercurial URI. + type: array + items: + type: string + user: + description: 'Sets the `--user` flag when set to true. Default: false.' + type: boolean + additionalProperties: false + RRequirements: + description: Specify which R packages should be available in order to run the component. + type: object + properties: + bioc: + anyOf: + - description: Specifies which packages to install from BioConductor. + type: string + - description: Specifies which packages to install from BioConductor. + type: array + items: + type: string + github: + anyOf: + - description: Specifies which packages to install from GitHub. + type: string + - description: Specifies which packages to install from GitHub. + type: array + items: + type: string + gitlab: + anyOf: + - description: Specifies which packages to install from GitLab. + type: string + - description: Specifies which packages to install from GitLab. + type: array + items: + type: string + url: + anyOf: + - description: Specifies which packages to install using a generic URI. + type: string + - description: Specifies which packages to install using a generic URI. + type: array + items: + type: string + bioc_force_install: + description: 'Forces packages specified in `bioc` to be reinstalled, even if they are already present in the container. Default: false.' + type: boolean + git: + anyOf: + - description: Specifies which packages to install using a Git URI. + type: string + - description: Specifies which packages to install using a Git URI. + type: array + items: + type: string + cran: + anyOf: + - description: Specifies which packages to install from CRAN. + type: string + - description: Specifies which packages to install from CRAN. + type: array + items: + type: string + bitbucket: + anyOf: + - description: Specifies which packages to install from Bitbucket. + type: string + - description: Specifies which packages to install from Bitbucket. + type: array + items: + type: string + svn: + anyOf: + - description: Specifies which packages to install using an SVN URI. + type: string + - description: Specifies which packages to install using an SVN URI. + type: array + items: + type: string + packages: + anyOf: + - description: Specifies which packages to install from CRAN. + type: string + - description: Specifies which packages to install from CRAN. + type: array + items: + type: string + script: + anyOf: + - description: Specifies a code block to run as part of the build. + type: string + - description: Specifies a code block to run as part of the build. + type: array + items: + type: string + type: + description: Specify which R packages should be available in order to run the component. + const: r + additionalProperties: false + RubyRequirements: + description: Specify which Ruby packages should be available in order to run the component. + type: object + properties: + type: + description: Specify which Ruby packages should be available in order to run the component. + const: ruby + packages: + anyOf: + - description: Specifies which packages to install. + type: string + - description: Specifies which packages to install. + type: array + items: + type: string + additionalProperties: false + YumRequirements: + description: Specify which yum packages should be available in order to run the component. + type: object + properties: + type: + description: Specify which yum packages should be available in order to run the component. + const: yum + packages: + anyOf: + - description: Specifies which packages to install. + type: string + - description: Specifies which packages to install. + type: array + items: + type: string + additionalProperties: false + Requirements: + anyOf: + - $ref: '#/definitions/ApkRequirements' + - $ref: '#/definitions/AptRequirements' + - $ref: '#/definitions/DockerRequirements' + - $ref: '#/definitions/JavascriptRequirements' + - $ref: '#/definitions/PythonRequirements' + - $ref: '#/definitions/RRequirements' + - $ref: '#/definitions/RubyRequirements' + - $ref: '#/definitions/YumRequirements' + BooleanArgument: + description: 'A `boolean` type argument has two possible values: `true` or `false`.' + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--trim`, `-t` or `trim`. The number of dashes determines how values can be passed: \n\n - `--trim` is a long option, which can be passed with `executable_name --trim`\n - `-t` is a short option, which can be passed with `executable_name -t`\n - `trim` is an argument, which can be passed with `executable_name trim` \n" + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: boolean + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: boolean + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: boolean + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: boolean + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: 'A `boolean` type argument has two possible values: `true` or `false`.' + const: boolean + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + BooleanTrueArgument: + description: An argument of the `boolean_true` type acts like a `boolean` flag with a default value of `false`. When called as an argument it sets the `boolean` to `true`. + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--silent`, `-s` or `silent`. The number of dashes determines how values can be passed: \n\n - `--silent` is a long option, which can be passed with `executable_name --silent`\n - `-s` is a short option, which can be passed with `executable_name -s`\n - `silent` is an argument, which can be passed with `executable_name silent` \n" + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + type: + description: An argument of the `boolean_true` type acts like a `boolean` flag with a default value of `false`. When called as an argument it sets the `boolean` to `true`. + const: boolean_true + additionalProperties: false + BooleanFalseArgument: + description: An argument of the `boolean_false` type acts like an inverted `boolean` flag with a default value of `true`. When called as an argument it sets the `boolean` to `false`. + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--no-log`, `-n` or `no-log`. The number of dashes determines how values can be passed: \n\n - `--no-log` is a long option, which can be passed with `executable_name --no-log`\n - `-n` is a short option, which can be passed with `executable_name -n`\n - `no-log` is an argument, which can be passed with `executable_name no-log` \n" + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + type: + description: An argument of the `boolean_false` type acts like an inverted `boolean` flag with a default value of `true`. When called as an argument it sets the `boolean` to `false`. + const: boolean_false + additionalProperties: false + DoubleArgument: + description: A `double` type argument has a numeric value with decimal points + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + max: + description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. + type: number + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: number + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: number + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: number + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: number + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + min: + description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. + type: number + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: A `double` type argument has a numeric value with decimal points + const: double + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + FileArgument: + description: A `file` type argument has a string value that points to a file or folder path. + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + create_parent: + description: 'If the output filename is a path and it does not exist, create it before executing the script (only for `direction: output`).' + type: boolean + direction: + description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. + $ref: '#/definitions/Direction' + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + must_exist: + description: Checks whether the file or folder exists. For input files, this check will happen before the execution of the script, while for output files the check will happen afterwards. + type: boolean + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: string + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: string + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: string + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: string + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: A `file` type argument has a string value that points to a file or folder path. + const: file + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + IntegerArgument: + description: An `integer` type argument has a numeric value without decimal points. + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + choices: + description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. + type: array + items: + type: integer + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + max: + description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. + type: integer + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: integer + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: integer + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: integer + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: integer + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + min: + description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. + type: integer + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: An `integer` type argument has a numeric value without decimal points. + const: integer + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + LongArgument: + description: An `long` type argument has a numeric value without decimal points. + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + choices: + description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. + type: array + items: + type: integer + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + max: + description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. + type: integer + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: integer + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: integer + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: integer + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: integer + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + min: + description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. + type: integer + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: An `long` type argument has a numeric value without decimal points. + const: long + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + StringArgument: + description: A `string` type argument has a value made up of an ordered sequences of characters, like "Hello" or "I'm a string". + type: object + properties: + alternatives: + anyOf: + - description: List of alternative format variations for this argument. + type: string + - description: List of alternative format variations for this argument. + type: array + items: + type: string + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" + type: string + choices: + description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. + type: array + items: + type: string + info: + description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' + type: object + default: + anyOf: + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: string + - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. + type: array + items: + type: string + example: + anyOf: + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: string + - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. + type: array + items: + type: string + description: + description: A description of the argument. This will be displayed with `--help`. + type: string + multiple_sep: + description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. + type: string + multiple: + description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. + type: boolean + type: + description: A `string` type argument has a value made up of an ordered sequences of characters, like "Hello" or "I'm a string". + const: string + required: + description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. + type: boolean + additionalProperties: false + Argument: + anyOf: + - $ref: '#/definitions/BooleanArgument' + - $ref: '#/definitions/BooleanTrueArgument' + - $ref: '#/definitions/BooleanFalseArgument' + - $ref: '#/definitions/DoubleArgument' + - $ref: '#/definitions/FileArgument' + - $ref: '#/definitions/IntegerArgument' + - $ref: '#/definitions/LongArgument' + - $ref: '#/definitions/StringArgument' + ArgumentGroup: + type: object + properties: + name: + description: The name of the argument group. + type: string + description: + description: A description of the argument group. Multiline descriptions are supported. + type: string + arguments: + description: List of the arguments names. + type: array + items: + $ref: '#/definitions/Argument' + required: + - name + - arguments + additionalProperties: false + BashScript: + description: |- + An executable Bash script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable Bash script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: bash_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + CSharpScript: + description: |- + An executable C# script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable C# script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: csharp_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + Executable: + description: An executable file. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: An executable file. + const: executable + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + JavaScriptScript: + description: |- + An executable JavaScript script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable JavaScript script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: javascript_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + NextflowScript: + description: A Nextflow script. Work in progress; added mainly for annotation at the moment. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + entrypoint: + description: The name of the workflow to be executed. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: A Nextflow script. Work in progress; added mainly for annotation at the moment. + const: nextflow_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + PlainFile: + description: A plain file. This can only be used as a supporting resource for the main script or unit tests. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: A plain file. This can only be used as a supporting resource for the main script or unit tests. + const: file + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + PythonScript: + description: |- + An executable Python script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable Python script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: python_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + RScript: + description: |- + An executable R script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable R script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: r_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + ScalaScript: + description: |- + An executable Scala script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + type: object + properties: + path: + description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. + type: string + text: + description: The content of the resulting file specified as a string. Mutually exclusive with `path`. + type: string + is_executable: + description: Whether the resulting resource file should be made executable. + type: boolean + type: + description: |- + An executable Scala script. + When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. + When defined in functionality.test_resources, all entries will be executed during `viash test`. + const: scala_script + dest: + description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. + type: string + additionalProperties: false + Resource: + anyOf: + - $ref: '#/definitions/BashScript' + - $ref: '#/definitions/CSharpScript' + - $ref: '#/definitions/Executable' + - $ref: '#/definitions/JavaScriptScript' + - $ref: '#/definitions/NextflowScript' + - $ref: '#/definitions/PlainFile' + - $ref: '#/definitions/PythonScript' + - $ref: '#/definitions/RScript' + - $ref: '#/definitions/ScalaScript' + NextflowDirectives: + description: | + Directives are optional settings that affect the execution of the process. + type: object + properties: + beforeScript: + description: | + The `beforeScript` directive allows you to execute a custom (Bash) snippet before the main process script is run. This may be useful to initialise the underlying cluster environment or for other custom initialisation. + + See [`beforeScript`](https://www.nextflow.io/docs/latest/process.html#beforeScript). + type: string + module: + anyOf: + - description: | + Environment Modules is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool. + + If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline. + + In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. + + See [`module`](https://www.nextflow.io/docs/latest/process.html#module). + type: string + - description: | + Environment Modules is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool. + + If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline. + + In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. + + See [`module`](https://www.nextflow.io/docs/latest/process.html#module). + type: array + items: + type: string + queue: + anyOf: + - description: | + The `queue` directory allows you to set the queue where jobs are scheduled when using a grid based executor in your pipeline. + + See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue). + type: string + - description: | + The `queue` directory allows you to set the queue where jobs are scheduled when using a grid based executor in your pipeline. + + See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue). + type: array + items: + type: string + label: + anyOf: + - description: | + The `label` directive allows the annotation of processes with mnemonic identifier of your choice. + + See [`label`](https://www.nextflow.io/docs/latest/process.html#label). + type: string + - description: | + The `label` directive allows the annotation of processes with mnemonic identifier of your choice. + + See [`label`](https://www.nextflow.io/docs/latest/process.html#label). + type: array + items: + type: string + container: + anyOf: + - description: | + The `container` directive allows you to execute the process script in a Docker container. + + It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. + + Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. + + See [`container`](https://www.nextflow.io/docs/latest/process.html#container). + type: object + additionalProperties: + description: | + The `container` directive allows you to execute the process script in a Docker container. + + It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. + + Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. + + See [`container`](https://www.nextflow.io/docs/latest/process.html#container). + type: string + - description: | + The `container` directive allows you to execute the process script in a Docker container. + + It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. + + Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. + + See [`container`](https://www.nextflow.io/docs/latest/process.html#container). + type: string + publishDir: + anyOf: + - anyOf: + - description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: string + - description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: object + additionalProperties: + description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: string + - description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: array + items: + anyOf: + - description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: string + - description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: object + additionalProperties: + description: | + The `publishDir` directive allows you to publish the process output files to a specified folder. + + Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. + The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. + + See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). + type: string + maxForks: + anyOf: + - description: | + The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1. + + If you want to execute a process in a sequential manner, set this directive to one. + + See [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks). + type: string + - description: | + The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1. + + If you want to execute a process in a sequential manner, set this directive to one. + + See [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks). + type: integer + maxErrors: + anyOf: + - description: | + The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled. + + See [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors). + type: string + - description: | + The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled. + + See [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors). + type: integer + cpus: + anyOf: + - description: | + The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. + + See [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus). + type: integer + - description: | + The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. + + See [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus). + type: string + accelerator: + description: | + The `accelerator` directive allows you to specify the hardware accelerator requirement for the task execution e.g. GPU processor. + + Viash implements this directive as a map with accepted keywords: `type`, `limit`, `request`, and `runtime`. + + See [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator). + type: object + additionalProperties: + description: | + The `accelerator` directive allows you to specify the hardware accelerator requirement for the task execution e.g. GPU processor. + + Viash implements this directive as a map with accepted keywords: `type`, `limit`, `request`, and `runtime`. + + See [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator). + type: string + time: + description: | + The `time` directive allows you to define how long a process is allowed to run. + + See [`time`](https://www.nextflow.io/docs/latest/process.html#time). + type: string + afterScript: + description: | + The `afterScript` directive allows you to execute a custom (Bash) snippet immediately after the main process has run. This may be useful to clean up your staging area. + + See [`afterScript`](https://www.nextflow.io/docs/latest/process.html#afterscript). + type: string + executor: + description: "The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the nextflow.config file.\n\nThe `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration. The following values can be used:\n\n| Name | Executor |\n|------|----------|\n| awsbatch | The process is executed using the AWS Batch service. | \n| azurebatch | The process is executed using the Azure Batch service. | \n| condor | The process is executed using the HTCondor job scheduler. | \n| google-lifesciences | The process is executed using the Google Genomics Pipelines service. | \n| ignite | The process is executed using the Apache Ignite cluster. | \n| k8s | The process is executed using the Kubernetes cluster. | \n| local | The process is executed in the computer where Nextflow is launched. | \n| lsf | The process is executed using the Platform LSF job scheduler. | \n| moab | The process is executed using the Moab job scheduler. | \n| nqsii | The process is executed using the NQSII job scheduler. | \n| oge | Alias for the sge executor. | \n| pbs | The process is executed using the PBS/Torque job scheduler. | \n| pbspro | The process is executed using the PBS Pro job scheduler. | \n| sge | The process is executed using the Sun Grid Engine / Open Grid Engine. | \n| slurm | The process is executed using the SLURM job scheduler. | \n| tes | The process is executed using the GA4GH TES service. | \n| uge | Alias for the sge executor. |\n\nSee [`executor`](https://www.nextflow.io/docs/latest/process.html#executor).\n" + type: string + containerOptions: + anyOf: + - description: | + The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path. + + See [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions). + type: string + - description: | + The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path. + + See [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions). + type: array + items: + type: string + disk: + description: | + The `disk` directive allows you to define how much local disk storage the process is allowed to use. + + See [`disk`](https://www.nextflow.io/docs/latest/process.html#disk). + type: string + tag: + description: | + The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. + + See [`tag`](https://www.nextflow.io/docs/latest/process.html#tag). + type: string + conda: + anyOf: + - description: | + The `conda` directive allows for the definition of the process dependencies using the Conda package manager. + + Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. + + See [`conda`](https://www.nextflow.io/docs/latest/process.html#conda). + type: string + - description: | + The `conda` directive allows for the definition of the process dependencies using the Conda package manager. + + Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. + + See [`conda`](https://www.nextflow.io/docs/latest/process.html#conda). + type: array + items: + type: string + machineType: + description: |2 + The `machineType` can be used to specify a predefined Google Compute Platform machine type when running using the Google Life Sciences executor. + + See [`machineType`](https://www.nextflow.io/docs/latest/process.html#machinetype). + type: string + stageInMode: + description: "The `stageInMode` directive defines how input files are staged-in to the process work directory. The following values are allowed:\n\n| Value | Description |\n|-------|-------------| \n| copy | Input files are staged in the process work directory by creating a copy. | \n| link | Input files are staged in the process work directory by creating an (hard) link for each of them. | \n| symlink | Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default). | \n| rellink | Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them. | \n\nSee [`stageInMode`](https://www.nextflow.io/docs/latest/process.html#stageinmode).\n" + type: string + cache: + anyOf: + - description: | + The `cache` directive allows you to store the process results to a local cache. When the cache is enabled and the pipeline is launched with the resume option, any following attempt to execute the process, along with the same inputs, will cause the process execution to be skipped, producing the stored data as the actual results. + + The caching feature generates a unique key by indexing the process script and inputs. This key is used to identify univocally the outputs produced by the process execution. + + The `cache` is enabled by default, you can disable it for a specific process by setting the cache directive to `false`. + + Accepted values are: `true`, `false`, `"deep"`, and `"lenient"`. + + See [`cache`](https://www.nextflow.io/docs/latest/process.html#cache). + type: boolean + - description: | + The `cache` directive allows you to store the process results to a local cache. When the cache is enabled and the pipeline is launched with the resume option, any following attempt to execute the process, along with the same inputs, will cause the process execution to be skipped, producing the stored data as the actual results. + + The caching feature generates a unique key by indexing the process script and inputs. This key is used to identify univocally the outputs produced by the process execution. + + The `cache` is enabled by default, you can disable it for a specific process by setting the cache directive to `false`. + + Accepted values are: `true`, `false`, `"deep"`, and `"lenient"`. + + See [`cache`](https://www.nextflow.io/docs/latest/process.html#cache). + type: string + pod: + anyOf: + - description: | + The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. + + See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). + type: object + additionalProperties: + description: | + The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. + + See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). + type: string + - description: | + The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. + + See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). + type: array + items: + type: object + additionalProperties: + type: string + penv: + description: | + The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the SGE resource manager. + + See [`penv`](https://www.nextflow.io/docs/latest/process.html#penv). + type: string + scratch: + anyOf: + - description: | + The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node. + + See [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch). + type: boolean + - description: | + The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node. + + See [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch). + type: string + storeDir: + description: | + The `storeDir` directive allows you to define a directory that is used as a permanent cache for your process results. + + See [`storeDir`](https://www.nextflow.io/docs/latest/process.html#storeDir). + type: string + maxRetries: + anyOf: + - description: | + The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the retry error strategy. By default only one retry is allowed. + + See [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries). + type: string + - description: | + The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the retry error strategy. By default only one retry is allowed. + + See [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries). + type: integer + echo: + anyOf: + - description: "By default the stdout produced by the commands executed in all processes is ignored. By setting the `echo` directive to true, you can forward the process stdout to the current top running process stdout file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" + type: boolean + - description: "By default the stdout produced by the commands executed in all processes is ignored. By setting the `echo` directive to true, you can forward the process stdout to the current top running process stdout file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" + type: string + errorStrategy: + description: | + The `errorStrategy` directive allows you to define how an error condition is managed by the process. By default when an error status is returned by the executed script, the process stops immediately. This in turn forces the entire pipeline to terminate. + + Table of available error strategies: + | Name | Executor | + |------|----------| + | `terminate` | Terminates the execution as soon as an error condition is reported. Pending jobs are killed (default) | + | `finish` | Initiates an orderly pipeline shutdown when an error condition is raised, waiting the completion of any submitted job. | + | `ignore` | Ignores processes execution errors. | + | `retry` | Re-submit for execution a process returning an error condition. | + + See [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy). + type: string + memory: + description: | + The `memory` directive allows you to define how much memory the process is allowed to use. + + See [`memory`](https://www.nextflow.io/docs/latest/process.html#memory). + type: string + stageOutMode: + description: "The `stageOutMode` directive defines how output files are staged-out from the scratch directory to the process work directory. The following values are allowed:\n\n| Value | Description |\n|-------|-------------| \n| copy | Output files are copied from the scratch directory to the work directory. | \n| move | Output files are moved from the scratch directory to the work directory. | \n| rsync | Output files are copied from the scratch directory to the work directory by using the rsync utility. |\n\nSee [`stageOutMode`](https://www.nextflow.io/docs/latest/process.html#stageoutmode).\n" + type: string + additionalProperties: false + NextflowAuto: + description: Automated processing flags which can be toggled on or off. + type: object + properties: + simplifyInput: + description: | + If `true`, an input tuple only containing only a single File (e.g. `["foo", file("in.h5ad")]`) is automatically transformed to a map (i.e. `["foo", [ input: file("in.h5ad") ] ]`). + + Default: `true`. + type: boolean + simplifyOutput: + description: | + If `true`, an output tuple containing a map with a File (e.g. `["foo", [ output: file("out.h5ad") ] ]`) is automatically transformed to a map (i.e. `["foo", file("out.h5ad")]`). + + Default: `true`. + type: boolean + publish: + description: | + If `true`, the module's outputs are automatically published to `params.publishDir`. + Will throw an error if `params.publishDir` is not defined. + + Default: `false`. + type: boolean + transcript: + description: | + If `true`, the module's transcripts from `work/` are automatically published to `params.transcriptDir`. + If not defined, `params.publishDir + "/_transcripts"` will be used. + Will throw an error if neither are defined. + + Default: `false`. + type: boolean + additionalProperties: false + NextflowConfig: + description: Allows tweaking how the Nextflow Config file is generated. + type: object + properties: + labels: + description: | + A series of default labels to specify memory and cpu constraints. + + The default memory labels are defined as "mem1gb", "mem2gb", "mem4gb", ... upto "mem512tb" and follows powers of 2. + The default cpu labels are defined as "cpu1", "cpu2", "cpu5", "cpu10", ... upto "cpu1000" and follows a semi logarithmic scale (1, 2, 5 per decade). + + Conceptually it is possible for a Viash Config to overwrite the full labels parameter, however likely it is more efficient to add additional labels + in the Viash Project with a config mod. + type: object + additionalProperties: + description: | + A series of default labels to specify memory and cpu constraints. + + The default memory labels are defined as "mem1gb", "mem2gb", "mem4gb", ... upto "mem512tb" and follows powers of 2. + The default cpu labels are defined as "cpu1", "cpu2", "cpu5", "cpu10", ... upto "cpu1000" and follows a semi logarithmic scale (1, 2, 5 per decade). + + Conceptually it is possible for a Viash Config to overwrite the full labels parameter, however likely it is more efficient to add additional labels + in the Viash Project with a config mod. + type: string + script: + anyOf: + - description: | + Includes a single string or list of strings into the nextflow.config file. + This can be used to add custom profiles or include an additional config file. + type: string + - description: | + Includes a single string or list of strings into the nextflow.config file. + This can be used to add custom profiles or include an additional config file. + type: array + items: + type: string + additionalProperties: false + DockerSetupStrategy: + $comment: TODO add descriptions to different strategies + enum: + - alwaysbuild + - build + - b + - alwayspull + - pull + - p + - alwayspullelsebuild + - pullelsebuild + - alwayspullelsecachedbuild + - pullelsecachedbuild + - alwayscachedbuild + - cachedbuild + - cb + - ifneedbebuild + - ifneedbecachedbuild + - ifneedbepull + - ifneedbepullelsebuild + - ifneedbepullelsecachedbuild + - donothing + - meh + - push + - forcepush + - alwayspush + - pushifnotpresent + - gentlepush + - maybepush + description: The Docker setup strategy to use when building a container. + Direction: + enum: + - input + - output + description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. + Status: + enum: + - enabled + - disabled + - deprecated + description: Allows setting a component to active, deprecated or disabled. + DockerResolveVolume: + $comment: TODO make fully case insensitive + enum: + - manual + - automatic + - auto + - Manual + - Automatic + - Auto + description: 'Enables or disables automatic volume mapping. Enabled when set to `Automatic` or disabled when set to `Manual`. Default: `Automatic`' +properties: + functionality: + description: | + The functionality-part of the config file describes the behaviour of the script in terms of arguments and resources. + By specifying a few restrictions (e.g. mandatory arguments) and adding some descriptions, Viash will automatically generate a stylish command-line interface for you. + $ref: '#/definitions/Functionality' + platforms: + description: Definition of the platforms + type: array + items: + $ref: '#/definitions/Platforms' + info: + description: Definition of meta data + $ref: '#/definitions/Info' +required: + - functionality +additionalProperties: false diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 5af98810f6..eeac1aa329 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -42,6 +42,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 64a1aec674..2f902f3fa5 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -8,7 +8,7 @@ # The following code has been auto-generated by Viash. par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'schema': 'src/tasks/denoising/api/anndata_common_dataset.yaml', + 'schema': 'src/tasks/denoising/api/file_common_dataset.yaml', 'stop_on_error': False, 'checks': 'output/error.json', 'output': 'output/output.h5ad' diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 52a0ed9891..735fc3ec01 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -3,8 +3,8 @@ import json input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -input_correct_schema = "anndata_correct.yaml" -input_error_schema = "anndata_error.yaml" +input_correct_schema = "file_correct.yaml" +input_error_schema = "file_error.yaml" output_checks = "checks.json" output_path = "output.h5ad" output_error_checks = "error_checks.json" @@ -18,7 +18,7 @@ description: "A preprocessed dataset" example: "preprocessed.h5ad" info: - short_description: "Preprocessed dataset" + label: "Preprocessed dataset" slots: layers: - type: integer @@ -37,7 +37,7 @@ description: "A preprocessed dataset" example: "preprocessed.h5ad" info: - short_description: "Preprocessed dataset" + label: "Preprocessed dataset" slots: layers: - type: integer diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml new file mode 100644 index 0000000000..66b409a7d8 --- /dev/null +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -0,0 +1,26 @@ +functionality: + name: check_yaml_schema + namespace: common + description: Checks if a YAML file adheres to a custom schema file. + argument_groups: + - name: Inputs + arguments: + - name: --input + type: file + required: true + description: A yaml file. + - name: --schema + type: file + required: true + description: A schema file for the yaml file. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.0 + setup: + - type: python + pypi: + - jsonschema + - type: nextflow diff --git a/src/common/check_yaml_schema/script.py b/src/common/check_yaml_schema/script.py new file mode 100644 index 0000000000..2058832bb2 --- /dev/null +++ b/src/common/check_yaml_schema/script.py @@ -0,0 +1,59 @@ +import jsonschema +import yaml +from pathlib import Path + +## VIASH START +par = { + 'input': 'src/tasks/batch_integration/methods/bbknn/config.vsh.yaml', + 'schema': 'src/common/api/schema_task_method.yaml' +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +def yaml_to_dict(file_path): + with open(file_path, 'r') as stream: + try: + return yaml.safe_load(stream) + except yaml.YAMLError as exc: + print(exc) + +def load_schemas(schema_dir): + schema_files = list(schema_dir.glob("./**/schema_*.yaml")) + + schemas = {} + for file in schema_files: + schema = yaml_to_dict(file) + schemas[file.absolute()] = schema + + return schemas + +def create_validator(schema_name, schemas): + schema_store = {} + for name, value in schemas.items(): + schema_store[f"file://{name}"] = value + + # Setting the first schema as the main schema + + main_schema = schemas[schema_name] + resolver = jsonschema.RefResolver( + base_uri=f"file://{schema_name}", + referrer=main_schema, + store=schema_store + ) + + return jsonschema.Draft7Validator(main_schema, resolver=resolver) + +print(">> Read input yaml", flush=True) +input_yaml_file = Path(par["input"]) +with open(input_yaml_file, 'r') as f: + input_yaml = yaml.safe_load(f) + +print(">> Read schema(s)", flush=True) +schema_yaml_file = Path(par["schema"]) +schemas = load_schemas(schema_yaml_file.parent) + +print(">> Validate input yaml against schema", flush=True) +validator = create_validator(schema_yaml_file.absolute(), schemas) +validator.validate(input_yaml) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 642d4bce94..1dea448908 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -1,13 +1,12 @@ import yaml ## VIASH START - meta = { "config" : "foo" } - ## VIASH END + NAME_MAXLEN = 50 SUMMARY_MAXLEN = 400 @@ -16,23 +15,8 @@ _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] - -def assert_dict(dict, functionality): - - arg_names = [] - args = functionality["arguments"] - - for i in args: - arg_names.append(i["name"].replace("--","")) - - info = functionality["info"] - if dict: - for key in dict: - assert key in arg_names or info, f"{key} is not a defined argument or .functionality.info field" - def _load_bib(): - bib_path = meta["resources_dir"]+"/library.bib" - with open(bib_path, "r") as file: + with open(f"{meta['resources_dir']}/library.bib", "r") as file: return file.read() def check_url(url): @@ -75,7 +59,6 @@ def search_ref_bib(reference): with open(meta["config"], "r") as file: config = yaml.safe_load(file) - print("Check general fields", flush=True) assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters." assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty" @@ -85,7 +68,7 @@ def search_ref_bib(reference): assert "type" in info, "type not an info field" info_types = ["method", "control_method"] assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" -assert "pretty_name" in info is not None, "pretty_name not an info field or is empty" +assert "label" in info is not None, "pretty_name not an info field or is empty" assert "summary" in info is not None, "summary not an info field or is empty" assert "FILL IN:" not in info["summary"], "Summary not filled in" assert len(info["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.summary) should not exceed {SUMMARY_MAXLEN} characters." @@ -102,10 +85,13 @@ def search_ref_bib(reference): assert check_url(info["documentation_url"]), f"{info['documentation_url']} is not reachable" assert check_url(info["repository_url"]), f"{info['repository_url']} is not reachable" - if "variants" in info: - for key in info["variants"]: - assert_dict(info["variants"][key], config['functionality']) + arg_names = [arg["name"].replace("--", "") for arg in config["functionality"]["arguments"]] + ["preferred_normalization"] + + for paramset_id, paramset in info["variants"].items(): + if paramset: + for arg_id in paramset: + assert arg_id in arg_names, f"Argument '{arg_id}' in `.functionality.info.variants['{paramset_id}']` is not an argument in `.functionality.arguments`." assert "preferred_normalization" in info, "preferred_normalization not an info field" norm_methods = ["log_cpm", "counts", "log_scran_pooling", "sqrt_cpm", "l1_sqrt"] diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 98a588240d..728ec710a4 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -62,27 +62,27 @@ def search_ref_bib(reference): def check_metric(metric: Dict[str, str]) -> str: assert "name" in metric is not None, "name not a field or is empty" assert len(metric["name"]) <= NAME_MAXLEN, f"Component id (.functionality.info.metrics.metric.name) should not exceed {NAME_MAXLEN} characters." - assert "pretty_name" in metric is not None, "pretty_name not a field in metric or is empty" + assert "label" in metric is not None, "pretty_name not a field in metric or is empty" assert "summary" in metric is not None, "summary not a field in metric or is empty" assert "FILL IN:" not in metric["summary"], "Summary not filled in" assert len(metric["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.metrics.metric.summary) should not exceed {SUMMARY_MAXLEN} characters." assert "description" in metric is not None, "description not a field in metric or is empty" assert len(metric["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.metrics.metric.description) should not exceed {DESCRIPTION_MAXLEN} characters." assert "FILL IN:" not in metric["description"], "description not filled in" - assert "reference" in metric, "reference not a field in metric" - if metric["reference"]: + # assert "reference" in metric, "reference not a field in metric" + if "reference" in metric: assert search_ref_bib(metric["reference"]), f"reference {metric['reference']} not added to library.bib" - assert "documentation_url" in metric , "documentation_url not a field in metric" - assert "repository_url" in metric , "repository_url not a metric field" - if metric["documentation_url"]: + # assert "documentation_url" in metric , "documentation_url not a field in metric" + # assert "repository_url" in metric , "repository_url not a metric field" + if "documentation_url" in metric: assert check_url(metric["documentation_url"]), f"{metric['documentation_url']} is not reachable" - if metric["repository_url"]: + if "repository_url" in metric: assert check_url(metric["repository_url"]), f"{metric['repository_url']} is not reachable" assert "min" in metric is not None, f"min not a field in metric or is emtpy" assert "max" in metric is not None, f"max not a field in metric or is empty" assert "maximize" in metric is not None, f"maximize not a field in metric or is emtpy" - assert isinstance(metric['min'], int), "not an int" - assert isinstance(metric['max'], (int, str)), "not an int or string (+inf)" + assert isinstance(metric['min'], (int, str)), "not an int or string (-.inf)" + assert isinstance(metric['max'], (int, str)), "not an int or string (+.inf)" assert isinstance(metric['maximize'], bool) or metric["maximize"] not in ["-inf", "+inf"], "not a bool" diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py index 1bbc11fe1b..39e8db0726 100644 --- a/src/common/comp_tests/run_and_check_adata.py +++ b/src/common/comp_tests/run_and_check_adata.py @@ -27,8 +27,8 @@ def check_slots(adata, slot_metadata): # read viash config -with open(meta["config"], "r") as stream: - config = yaml.safe_load(stream) +with open(meta["config"], "r") as file: + config = yaml.safe_load(file) # get resources arguments = [] diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 4eedf255a4..5cc04f8204 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -74,7 +74,7 @@ def generate_info(par, component_type, pretty_name) -> str: if component_type in ["method", "control_method"]: str = strip_margin(f'''\ | # A relatively short label, used when rendering visualisarions (required) - | pretty_name: {pretty_name} + | label: {pretty_name} | # A one sentence summary of how this method works (required). Used when | # rendering summary tables. | summary: "FILL IN: A one sentence summary of this method." @@ -102,7 +102,7 @@ def generate_info(par, component_type, pretty_name) -> str: | # Can contain only lowercase letters or underscores. | name: {par["name"]} | # A relatively short label, used when rendering visualisarions (required) - | pretty_name: {pretty_name} + | label: {pretty_name} | # A one sentence summary of how this metric works (required). Used when | # rendering summary tables. | summary: "FILL IN: A one sentence summary of this metric." @@ -144,11 +144,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base-python:latest" + image_str = "ghcr.io/openproblems-bio/base_python:1.0.0" setup_type = "python" package_example = "scanpy" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base-r:latest" + image_str = "ghcr.io/openproblems-bio/base_r:1.0.0" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index e5bdc2d060..4449f962e1 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 9db89bee1d..281f9897dc 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -8,9 +8,9 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r - cran: [ tidyverse ] + cran: [ purrr, dplyr, yaml, rlang, processx ] - type: nextflow - type: native diff --git a/src/common/get_api_info/script.R b/src/common/get_api_info/script.R index abaa718e84..1686dee222 100644 --- a/src/common/get_api_info/script.R +++ b/src/common/get_api_info/script.R @@ -1,4 +1,6 @@ -library(tidyverse) +library(purrr) +library(dplyr) +library(yaml) library(rlang) ## VIASH START @@ -10,7 +12,7 @@ par <- list( ## VIASH END comp_yamls <- list.files(paste(par$input, "src/tasks", par$task_id, "api", sep = "/"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste(par$input, "src/tasks", par$task_id, "api", sep = "/"), pattern = "anndata_", full.names = TRUE) +file_yamls <- list.files(paste(par$input, "src/tasks", par$task_id, "api", sep = "/"), pattern = "file_", full.names = TRUE) # list component - file args links comp_file <- map_df(comp_yamls, function(yaml_file) { @@ -19,7 +21,7 @@ comp_file <- map_df(comp_yamls, function(yaml_file) { map_df(conf$functionality$arguments, function(arg) { tibble( comp_name = basename(yaml_file) %>% gsub("\\.yaml", "", .), - arg_name = str_replace_all(arg$name, "^-*", ""), + arg_name = gsub("^-*", "", arg$name), direction = arg$direction %||% "input", file_name = basename(arg$`__merge__`) %>% gsub("\\.yaml", "", .) ) @@ -43,9 +45,9 @@ file_info <- map_df(file_yamls, function(yaml_file) { tibble( name = basename(yaml_file) %>% gsub("\\.yaml", "", .), description = arg$description, - short_description = arg$info$short_description, + label = arg$info$label, example = arg$example, - label = name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .) + clean_label = name %>% gsub("file_", "", .) %>% gsub("_", " ", .) ) }) @@ -59,7 +61,7 @@ file_slot <- map_df(file_yamls, function(yaml_file) { df$file_name <- basename(yaml_file) %>% gsub("\\.yaml", "", .) as_tibble(df) }) -}) %>% +}) %>% mutate(multiple = multiple %|% FALSE) out <- list( diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 91cdf0a79b..d89a091377 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -8,10 +8,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r - cran: [ tidyverse ] + cran: [ purrr, dplyr, yaml, rlang, processx ] - type: apt packages: [ curl, default-jdk ] - type: docker diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 01b7731956..da7936c621 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -1,4 +1,5 @@ -library(tidyverse) +library(purrr) +library(dplyr) library(rlang) ## VIASH START @@ -28,9 +29,11 @@ out <- map(configs, function(config) { info$is_baseline <- grepl("control", info$type) # rename fields to v1 format - info$method_name <- info$pretty_name - info$pretty_name <- NULL - info$method_summary <- info$description + info$method_name <- info$label + info$label <- NULL + info$method_summary <- info$summary + info$summary <- NULL + info$method_description <- info$description info$description <- NULL info$paper_reference <- info$reference info$reference <- NULL diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 11949acbf4..4bc1e03671 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,10 +8,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r - cran: [ tidyverse ] + cran: [ purrr, dplyr, yaml, rlang, processx ] - type: apt packages: [ curl, default-jdk ] - type: docker diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index c6b85b8a63..d3544ce7bd 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -1,4 +1,5 @@ -library(tidyverse) +library(purrr) +library(dplyr) library(rlang) ## VIASH START @@ -23,18 +24,14 @@ df <- map_df(configs, function(config) { info$task_id <- par$task_id info$component_id <- config$functionality$name info$namespace <- config$functionality$namespace - info$component_description <- config$functionality$description - info$v1_url <- config$functionality$info$v1_url - info$v1_commit <- config$functionality$info$v1_commit - info info }) %>% -rename( - metric_id = name, - metric_name = pretty_name, - metric_summary = description, - paper_reference = reference, -) + rename( + metric_id = name, + metric_name = label, + metric_summary = description, + paper_reference = reference, + ) jsonlite::write_json( purrr::transpose(df), diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 000ae3eab3..9560a0644c 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index a6b2ed3e1d..4c12ae0bdc 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -8,6 +8,6 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow - type: native diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index 0653148578..d8441fa0cd 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -11,7 +11,6 @@ read_anndata_spec <- function(path) { read_anndata_info <- function(spec, path) { # TEMP: make it readable spec$info$slots <- NULL - df <- list_as_tibble(spec) if (list_contains_tibble(spec$info)) { df <- dplyr::bind_cols(df, list_as_tibble(spec$info)) @@ -47,6 +46,7 @@ format_slots <- function(spec) { } format_slots_as_kable <- function(spec) { + if (nrow(spec$slots) == 0) return("") spec$slots %>% mutate( tag_str = pmap_chr(lst(required), function(required) { @@ -63,10 +63,7 @@ format_slots_as_kable <- function(spec) { ) %>% transmute( Slot = paste0("`", struct, "[\"", name, "\"]`"), - # Struct = struct, - # Name = name, Type = paste0("`", type, "`"), - # Required = ifelse(required, "yes", ""), Description = paste0( tag_str, description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), @@ -124,11 +121,14 @@ read_comp_args <- function(spec_yaml, path) { df$required <- df$required %||% FALSE %|% FALSE df$default <- df$default %||% NA_character_ %>% as.character df$example <- df$example %||% NA_character_ %>% as.character + df$description <- df$description %||% NA_character_ %>% as.character + df$summary <- df$summary %||% NA_character_ %>% as.character df }) } format_comp_args_as_tibble <- function(spec) { + if (nrow(spec$args) == 0) return("") spec$args %>% mutate( tag_str = pmap_chr(lst(required, direction), function(required, direction) { @@ -151,7 +151,7 @@ format_comp_args_as_tibble <- function(spec) { Type = paste0("`", type, "`"), Description = paste0( tag_str, - description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), + (summary %|% description) %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), ".", ifelse(!is.na(default), paste0(" Default: `", default, "`."), "") ) @@ -168,7 +168,7 @@ render_component <- function(path) { § §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{spec$info$namespace}) § - §{spec$info$description} + §{spec$info$summary} § §Arguments: § @@ -179,7 +179,7 @@ render_component <- function(path) { §"), symbol = "§")) } -# path <- "src/datasets/api/anndata_pca.yaml" +# path <- "src/datasets/api/file_pca.yaml" render_file <- function(path) { spec <- read_anndata_spec(path) @@ -188,7 +188,7 @@ render_file <- function(path) { § §Example file: `{spec$info$example %|% ''}` § - §{spec$info$description} + §{spec$info$summary} § §Format: § diff --git a/src/datasets/README.md b/src/datasets/README.md index 739febdc10..a27e061326 100644 --- a/src/datasets/README.md +++ b/src/datasets/README.md @@ -26,21 +26,21 @@ ``` mermaid %%| column: screen-inset-shaded flowchart LR - anndata_dataset(Dataset+Pca+Hvg) - anndata_normalized(Normalized Dataset) - anndata_pca(Dataset+Pca) - anndata_raw(Raw Dataset) + file_dataset(Dataset+Pca+Hvg) + file_normalized(Normalized Dataset) + file_pca(Dataset+Pca) + file_raw(Raw Dataset) comp_dataset_loader[/Dataset Loader/] comp_normalization[/Normalization/] comp_processor_hvg[/Processor Hvg/] comp_processor_pca[/Processor Pca/] - anndata_raw---comp_normalization - anndata_pca---comp_processor_hvg - anndata_normalized---comp_processor_pca - comp_dataset_loader-->anndata_raw - comp_normalization-->anndata_normalized - comp_processor_hvg-->anndata_dataset - comp_processor_pca-->anndata_pca + file_raw---comp_normalization + file_pca---comp_processor_hvg + file_normalized---comp_processor_pca + comp_dataset_loader-->file_raw + comp_normalization-->file_normalized + comp_processor_hvg-->file_dataset + comp_processor_pca-->file_pca ``` ## File format API diff --git a/src/datasets/README.qmd b/src/datasets/README.qmd index dc7db48fac..c20045fadc 100644 --- a/src/datasets/README.qmd +++ b/src/datasets/README.qmd @@ -23,7 +23,7 @@ dir <- "." ```{r data, include=FALSE} comp_yamls <- list.files(paste0(dir, "/api"), pattern = "comp_", full.names = TRUE) -file_yamls <- list.files(paste0(dir, "/api"), pattern = "anndata_", full.names = TRUE) +file_yamls <- list.files(paste0(dir, "/api"), pattern = "file_", full.names = TRUE) comp_file <- map_df(comp_yamls, function(yaml_file) { conf <- yaml::read_yaml(yaml_file) @@ -59,7 +59,7 @@ file_info <- map_df(file_yamls, function(yaml_file) { name = basename(yaml_file) %>% gsub("\\.yaml", "", .), description = arg$description, example = arg$example, - label = arg$info$label %||% (name %>% gsub("anndata_", "", .) %>% gsub("_", " ", .)) + label = arg$info$label %||% (name %>% gsub("file_", "", .) %>% gsub("_", " ", .)) ) }) diff --git a/src/datasets/api/anndata_common_dataset.yaml b/src/datasets/api/anndata_common_dataset.yaml deleted file mode 100644 index df7dba9736..0000000000 --- a/src/datasets/api/anndata_common_dataset.yaml +++ /dev/null @@ -1,9 +0,0 @@ -__merge__: anndata_knn.yaml -type: file -description: | - A dataset processed by the common dataset processing pipeline. - This dataset contains both raw counts and normalized data matrices, - as well as a PCA embedding, HVG selection and a kNN graph. -example: "resources_test/common/pancreas/dataset.h5ad" -info: - label: "Common dataset" diff --git a/src/datasets/api/comp_dataset_loader.yaml b/src/datasets/api/comp_dataset_loader.yaml index 6f7bd814a5..75909b106a 100644 --- a/src/datasets/api/comp_dataset_loader.yaml +++ b/src/datasets/api/comp_dataset_loader.yaml @@ -1,15 +1,16 @@ functionality: namespace: "datasets/loaders" info: + type: dataset_loader type_info: label: Dataset loader + summary: A component which generates a "Common dataset". description: | - A component which generates a "Common dataset". A dataset loader will typically have an identifier (e.g. a GEO identifier) + A dataset loader will typically have an identifier (e.g. a GEO identifier) or URL as input argument and additional arguments to define where the script needs to download a dataset from and how to process it. - argument_groups: - - name: Outputs - arguments: - - name: "--output" - __merge__: anndata_raw.yaml - direction: "output" - required: true + arguments: + - name: "--output" + __merge__: file_raw.yaml + direction: "output" + required: true + test_resources: [] \ No newline at end of file diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index 22a1f62023..e79534950b 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -1,17 +1,21 @@ functionality: namespace: "datasets/normalization" info: + type: dataset_normalization type_info: label: Dataset normalization - description: | - A normalization method which processes the raw counts output by a dataset loader. + summary: | + A normalization method which processes the raw counts into a normalized dataset. + description: + A component for normalizing the raw counts as output by dataset loaders into a normalized dataset. arguments: - name: "--input" - __merge__: anndata_raw.yaml + __merge__: file_raw.yaml + direction: input required: true - name: "--output" + __merge__: file_normalized.yaml direction: output - __merge__: anndata_normalized.yaml required: true - name: "--layer_output" type: string diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index f29729587d..8a1e263841 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -1,21 +1,25 @@ functionality: namespace: "datasets/processors" info: + type: dataset_processor type_info: label: HVG - description: | + summary: | Computes the highly variable genes scores. + description: | + The resulting AnnData will contain both a boolean 'hvg' column in 'var', as well as a numerical 'hvg_score' in 'var'. arguments: - name: "--input" - __merge__: anndata_pca.yaml + __merge__: file_pca.yaml required: true + direction: input - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input. - name: "--output" direction: output - __merge__: anndata_hvg.yaml + __merge__: file_hvg.yaml required: true - name: "--var_hvg" type: string diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 5d5f45226c..d432ed1d9d 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -1,21 +1,25 @@ functionality: namespace: "datasets/processors" info: + type: dataset_processor type_info: label: KNN - description: | + summary: | Computes the k-nearest-neighbours for each cell. + description: | + The resulting AnnData will contain both the knn distances and the knn connectivities in 'obsp'. arguments: - name: "--input" - __merge__: anndata_hvg.yaml + __merge__: file_hvg.yaml required: true + direction: input - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input. - name: "--output" direction: output - __merge__: anndata_knn.yaml + __merge__: file_knn.yaml required: true - name: "--key_added" type: string diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index 7a1dcdd61b..a90a3efea2 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -1,21 +1,25 @@ functionality: namespace: "datasets/processors" info: + type: dataset_processor type_info: label: PCA - description: | + summary: | Computes a PCA embedding of the normalized data. + description: + The resulting AnnData will contain an embedding in obsm, as well as optional loadings in 'varm'. arguments: - name: "--input" - __merge__: anndata_normalized.yaml + __merge__: file_normalized.yaml required: true + direction: input - name: "--layer_input" type: string default: "normalized" description: Which layer to use as input. - name: "--output" direction: output - __merge__: anndata_pca.yaml + __merge__: file_pca.yaml required: true - name: "--obsm_embedding" type: string diff --git a/src/datasets/api/comp_processor_subset.yaml b/src/datasets/api/comp_processor_subset.yaml index e3612cc366..cf50c2a940 100644 --- a/src/datasets/api/comp_processor_subset.yaml +++ b/src/datasets/api/comp_processor_subset.yaml @@ -1,16 +1,18 @@ functionality: namespace: "datasets/processors" info: + type: dataset_processor type_info: label: Subset - description: | - Subset a common dataset + summary: Sample cells and genes randomly. + description: This component subsets the layers, obs and var to create smaller test datasets. arguments: - name: "--input" - __merge__: anndata_common_dataset.yaml + __merge__: file_common_dataset.yaml required: true + direction: input - name: "--output" - __merge__: anndata_common_dataset.yaml + __merge__: file_common_dataset.yaml direction: output required: true test_resources: diff --git a/src/datasets/api/file_common_dataset.yaml b/src/datasets/api/file_common_dataset.yaml new file mode 100644 index 0000000000..ed7836bf5c --- /dev/null +++ b/src/datasets/api/file_common_dataset.yaml @@ -0,0 +1,9 @@ +__merge__: file_knn.yaml +type: file +example: "resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common dataset" + summary: A dataset processed by the common dataset processing pipeline. + description: | + This dataset contains both raw counts and normalized data matrices, + as well as a PCA embedding, HVG selection and a kNN graph. diff --git a/src/datasets/api/anndata_hvg.yaml b/src/datasets/api/file_hvg.yaml similarity index 76% rename from src/datasets/api/anndata_hvg.yaml rename to src/datasets/api/file_hvg.yaml index ef4d10ce53..81cdac966f 100644 --- a/src/datasets/api/anndata_hvg.yaml +++ b/src/datasets/api/file_hvg.yaml @@ -1,9 +1,9 @@ -__merge__: anndata_pca.yaml -type: file -description: "A normalised dataset with a PCA embedding and HVG selection." +__merge__: file_pca.yaml +type: file example: "resources_test/common/pancreas/hvg.h5ad" info: label: "Dataset+PCA+HVG" + summary: "A normalised dataset with a PCA embedding and HVG selection." slots: var: - type: boolean diff --git a/src/datasets/api/anndata_knn.yaml b/src/datasets/api/file_knn.yaml similarity index 69% rename from src/datasets/api/anndata_knn.yaml rename to src/datasets/api/file_knn.yaml index e158c837d0..80e6a69828 100644 --- a/src/datasets/api/anndata_knn.yaml +++ b/src/datasets/api/file_knn.yaml @@ -1,9 +1,9 @@ -__merge__: anndata_hvg.yaml +__merge__: file_hvg.yaml type: file -description: "A normalised data with a PCA embedding, HVG selection and a kNN graph" example: "resources_test/common/pancreas/dataset.h5ad" info: label: "Dataset+PCA+HVG+kNN" + summary: "A normalised data with a PCA embedding, HVG selection and a kNN graph" slots: obsp: - type: double @@ -17,4 +17,5 @@ info: uns: - type: object name: knn - description: Neighbors data. + description: Supplementary K nearest neighbors data. + required: true diff --git a/src/datasets/api/anndata_normalized.yaml b/src/datasets/api/file_normalized.yaml similarity index 82% rename from src/datasets/api/anndata_normalized.yaml rename to src/datasets/api/file_normalized.yaml index 4e0f9accf6..d53f5519f2 100644 --- a/src/datasets/api/anndata_normalized.yaml +++ b/src/datasets/api/file_normalized.yaml @@ -1,14 +1,15 @@ -__merge__: anndata_raw.yaml +__merge__: file_raw.yaml type: file -description: "A normalized dataset" example: "resources_test/common/pancreas/normalized.h5ad" info: label: "Normalized dataset" + summary: "A normalized dataset" slots: layers: - type: double name: normalized description: Normalised expression values + required: true obs: - type: double name: size_factors diff --git a/src/datasets/api/anndata_pca.yaml b/src/datasets/api/file_pca.yaml similarity index 83% rename from src/datasets/api/anndata_pca.yaml rename to src/datasets/api/file_pca.yaml index 9c486190e1..267f00b6a7 100644 --- a/src/datasets/api/anndata_pca.yaml +++ b/src/datasets/api/file_pca.yaml @@ -1,9 +1,9 @@ -__merge__: anndata_normalized.yaml +__merge__: file_normalized.yaml type: file -description: "A normalised dataset with a PCA embedding" example: "resources_test/common/pancreas/pca.h5ad" info: label: "Dataset+PCA" + summary: "A normalised dataset with a PCA embedding" slots: obsm: - type: double diff --git a/src/datasets/api/anndata_raw.yaml b/src/datasets/api/file_raw.yaml similarity index 95% rename from src/datasets/api/anndata_raw.yaml rename to src/datasets/api/file_raw.yaml index 0e41c8269a..877c7f2c43 100644 --- a/src/datasets/api/anndata_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -1,8 +1,8 @@ type: file -description: "An unprocessed dataset as output by a dataset loader." example: "resources_test/common/pancreas/raw.h5ad" info: label: "Raw dataset" + summary: "An unprocessed dataset as output by a dataset loader." slots: layers: - type: integer diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index a5c0762230..12f8700411 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -1,3 +1,4 @@ +__merge__: ../../api/comp_dataset_loader.yaml functionality: name: "openproblems_v1" description: "Fetch a dataset from OpenProblems v1" @@ -51,11 +52,6 @@ functionality: type: string description: The organism of the dataset. required: false - - name: Outputs - arguments: - - name: "--output" - __merge__: ../../api/anndata_raw.yaml - direction: "output" resources: - type: python_script path: script.py @@ -64,7 +60,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 3228877d1f..82b28b73dc 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -1,5 +1,6 @@ functionality: name: "openproblems_v1_multimodal" + namespace: "datasets/loaders" description: "Fetch a dataset from OpenProblems v1" argument_groups: - name: Inputs @@ -54,10 +55,10 @@ functionality: - name: Outputs arguments: - name: "--output_mod1" - __merge__: ../../api/anndata_raw.yaml + __merge__: ../../api/file_raw.yaml direction: "output" - name: "--output_mod2" - __merge__: ../../api/anndata_raw.yaml + __merge__: ../../api/file_raw.yaml direction: "output" resources: - type: python_script @@ -67,7 +68,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: apt packages: git diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 0f81b1b157..919f201d6c 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 7897ce6668..46a42824a6 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index f00467929a..171ef3c9d9 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ Matrix, rlang, bit64, scran, BiocParallel ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 6a3b771ca4..421809423b 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 8ec039ea41..295d359d4f 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index cc74bacdd7..6fc7e1929a 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 6dce8d0fb3..a277ffc00d 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index b21a2d10a8..ef9f612dfb 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 3373083b25..1000c6ba40 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -62,12 +62,12 @@ functionality: - name: "--output" direction: "output" # todo: fix inherits in nxf - # __merge__: ../../api/anndata_raw.yaml + # __merge__: ../../api/file_raw.yaml type: file description: "A raw dataset" example: "raw_dataset.h5ad" info: - short_description: "Raw dataset" + label: "Raw dataset" slots: layers: - type: integer diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index 9703ed4c2c..38db0c2485 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow - type: native diff --git a/src/migration/check_migration_status/script.py b/src/migration/check_migration_status/script.py index 30118d7fdd..86d0a2ba46 100644 --- a/src/migration/check_migration_status/script.py +++ b/src/migration/check_migration_status/script.py @@ -11,21 +11,21 @@ def check_status(comp_item: List[Dict[str, str]], git_objects: List[Dict[str, str]]) -> str: """Looks for the comp_item's matching git_object - based on the comp_item["v1_url"] and git_object["path"]. + based on the comp_item["v1"]["path"] and git_object["path"]. If found, checks whether the comp_item["v1_commit"] equals git_object["sha"].""" - v1_url = comp_item.get("v1_url") - if not v1_url: - return "v1_url missing" + v1_path = comp_item.get("v1", {}).get("path") + if not v1_path: + return "v1.path missing" - v1_commit = comp_item.get("v1_commit") + v1_commit = comp_item.get("v1", {}).get("commit") if not v1_commit: - return "v1_commit missing" + return "v1.commit missing" - git_object = [ obj for obj in git_objects if obj["path"] == v1_url ] + git_object = [ obj for obj in git_objects if obj["path"] == v1_path ] if not git_object: - return "v1_url does not exist in git repo" + return "v1.path does not exist in git repo" git_sha = git_object[0]["sha"] if git_sha == comp_item["v1_commit"]: diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 4a7d2177cf..15bb2d7757 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 9c1ad71a1e..3b70ea7517 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/api/comp_method_embedding.yaml b/src/tasks/batch_integration/api/comp_method_embedding.yaml index dc816fe433..e9ba51acb5 100644 --- a/src/tasks/batch_integration/api/comp_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_method_embedding.yaml @@ -2,27 +2,38 @@ functionality: namespace: batch_integration/methods info: type: method - output_type: embedding + subtype: embedding type_info: label: Method (embedding) + summary: A batch integration embedding method. description: | A batch integration method which outputs a batch-corrected embedding. arguments: - name: --input - __merge__: anndata_unintegrated.yaml + __merge__: file_unintegrated.yaml + direction: input + required: true - name: --output + __merge__: file_integrated_embedding.yaml direction: output - __merge__: anndata_integrated_embedding.yaml + required: true - name: --hvg type: boolean description: Whether to subset to highly variable genes default: false required: false test_resources: - - path: /resources_test/batch_integration/pancreas - dest: resources_test/batch_integration/pancreas + # check method component - type: python_script path: /src/common/comp_tests/check_method_config.py + - path: /src/common/library.bib + # auto-run component - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /src/common/library.bib + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas + # # test config against schema + # - type: python_script + # path: /src/common/check_yaml_schema/script.py + # - path: /src/common/api/schema_method.yaml + # dest: schema.yaml diff --git a/src/tasks/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml index 20af096bda..b2e34f643d 100644 --- a/src/tasks/batch_integration/api/comp_method_feature.yaml +++ b/src/tasks/batch_integration/api/comp_method_feature.yaml @@ -2,27 +2,33 @@ functionality: namespace: batch_integration/methods info: type: method - output_type: feature + subtype: feature type_info: label: Method (feature) + summary: A batch integration feature method. description: | A batch integration method which outputs a batch-corrected feature-space. arguments: - - __merge__: anndata_unintegrated.yaml - name: --input - - __merge__: anndata_integrated_feature.yaml - name: --output + - name: --input + __merge__: file_unintegrated.yaml + direction: input + required: true + - name: --output + __merge__: file_integrated_feature.yaml direction: output + required: true - name: --hvg type: boolean description: Whether to subset to highly variable genes default: false required: false test_resources: - - path: /resources_test/batch_integration/pancreas - dest: resources_test/batch_integration/pancreas + # check method component - type: python_script path: /src/common/comp_tests/check_method_config.py + - path: /src/common/library.bib + # auto-run component - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /src/common/library.bib + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml index 8a09185863..035a66d9b4 100644 --- a/src/tasks/batch_integration/api/comp_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_method_graph.yaml @@ -2,27 +2,33 @@ functionality: namespace: batch_integration/methods info: type: method - output_type: graph + subtype: graph type_info: label: Method (graph) + summary: A batch integration graph method. description: | A batch integration method which outputs a batch-corrected cell graphs. arguments: - - __merge__: anndata_unintegrated.yaml - name: --input - - __merge__: anndata_integrated_graph.yaml - name: --output + - name: --input + __merge__: file_unintegrated.yaml + direction: input + required: true + - name: --output + __merge__: file_integrated_graph.yaml direction: output + required: true - name: --hvg type: boolean description: Whether to subset to highly variable genes default: false required: false test_resources: - - path: /resources_test/batch_integration/pancreas - dest: resources_test/batch_integration/pancreas + # check method component - type: python_script path: /src/common/comp_tests/check_method_config.py + - path: /src/common/library.bib + # auto-run component - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /src/common/library.bib + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml index fb0fac98c2..d7bf03ce2a 100644 --- a/src/tasks/batch_integration/api/comp_metric_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_metric_embedding.yaml @@ -2,16 +2,21 @@ functionality: namespace: batch_integration/metrics info: type: metric + subtype: embedding type_info: label: Metric (embedding) + summary: A batch integration embedding metric. description: | A metric for evaluating batch corrected embeddings. arguments: - name: --input_integrated - __merge__: anndata_integrated_embedding.yaml + __merge__: file_integrated_embedding.yaml + direction: input + required: true - name: --output + __merge__: file_score.yaml direction: output - __merge__: anndata_score.yaml + required: true test_resources: - path: /resources_test/batch_integration/pancreas dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_metric_feature.yaml b/src/tasks/batch_integration/api/comp_metric_feature.yaml index a3826b3541..0680703a3b 100644 --- a/src/tasks/batch_integration/api/comp_metric_feature.yaml +++ b/src/tasks/batch_integration/api/comp_metric_feature.yaml @@ -2,16 +2,21 @@ functionality: namespace: batch_integration/metrics info: type: metric + subtype: feature type_info: label: Metric (feature) + summary: A batch integration feature metric. description: | A metric for evaluating batch corrected feature spaces. arguments: - name: --input_integrated - __merge__: anndata_integrated_feature.yaml + __merge__: file_integrated_feature.yaml + direction: input + required: true - name: --output + __merge__: file_score.yaml direction: output - __merge__: anndata_score.yaml + required: true test_resources: - path: /resources_test/batch_integration/pancreas dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_metric_graph.yaml b/src/tasks/batch_integration/api/comp_metric_graph.yaml index 4032f3f6fd..82805717a5 100644 --- a/src/tasks/batch_integration/api/comp_metric_graph.yaml +++ b/src/tasks/batch_integration/api/comp_metric_graph.yaml @@ -2,16 +2,21 @@ functionality: namespace: batch_integration/metrics info: type: metric + subtype: graph type_info: label: Metric (graph) + summary: A batch integration graph metric. description: | A metric for evaluating batch corrected cell graphs. arguments: - name: --input_integrated - __merge__: anndata_integrated_graph.yaml + __merge__: file_integrated_graph.yaml + direction: input + required: true - name: --output + __merge__: file_score.yaml direction: output - __merge__: anndata_score.yaml + required: true test_resources: - path: /resources_test/batch_integration/pancreas dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 5c79ba3a56..6352e41689 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -4,14 +4,18 @@ functionality: type: process_dataset type_info: label: Data processor + summary: A label projection dataset processor. description: | - Prepare a common dataset for the batch integration task. + A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_common_dataset.yaml + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_unintegrated.yaml + __merge__: file_unintegrated.yaml direction: output + required: true test_resources: - path: /resources_test/common/pancreas/ dest: resources_test/common/pancreas/ diff --git a/src/tasks/batch_integration/api/anndata_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml similarity index 83% rename from src/tasks/batch_integration/api/anndata_integrated_embedding.yaml rename to src/tasks/batch_integration/api/file_integrated_embedding.yaml index 8caacc6d16..6b49118404 100644 --- a/src/tasks/batch_integration/api/anndata_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -1,10 +1,10 @@ -__merge__: "anndata_unintegrated.yaml" +__merge__: "file_unintegrated.yaml" type: file -description: Integrated AnnData HDF5 file. example: "resources_test/batch_integration/pancreas/scvi.h5ad" info: prediction_type: embedding - short_description: "Integrated embedding" + label: "Integrated embedding" + summary: An integrated AnnData HDF5 file. slots: obsm: - type: double diff --git a/src/tasks/batch_integration/api/anndata_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml similarity index 83% rename from src/tasks/batch_integration/api/anndata_integrated_feature.yaml rename to src/tasks/batch_integration/api/file_integrated_feature.yaml index 7d71a54700..243aef9766 100644 --- a/src/tasks/batch_integration/api/anndata_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -1,10 +1,10 @@ -__merge__: "anndata_unintegrated.yaml" +__merge__: "file_unintegrated.yaml" type: file -description: Integrated AnnData HDF5 file. example: "resources_test/batch_integration/pancreas/combat.h5ad" info: prediction_type: feature - short_description: "Integrated Feature" + label: "Integrated Feature" + summary: Integrated AnnData HDF5 file. slots: layers: - type: double diff --git a/src/tasks/batch_integration/api/anndata_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml similarity index 83% rename from src/tasks/batch_integration/api/anndata_integrated_graph.yaml rename to src/tasks/batch_integration/api/file_integrated_graph.yaml index 26bb89b385..ba7e2be694 100644 --- a/src/tasks/batch_integration/api/anndata_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -1,10 +1,10 @@ -__merge__: "anndata_unintegrated.yaml" +__merge__: "file_unintegrated.yaml" type: file -description: Integrated AnnData HDF5 file. example: "resources_test/batch_integration/pancreas/bbknn.h5ad" info: prediction_type: graph - short_description: "Integrated Graph" + label: "Integrated Graph" + summary: Integrated AnnData HDF5 file. slots: obsp: - type: double diff --git a/src/tasks/batch_integration/api/anndata_score.yaml b/src/tasks/batch_integration/api/file_score.yaml similarity index 94% rename from src/tasks/batch_integration/api/anndata_score.yaml rename to src/tasks/batch_integration/api/file_score.yaml index 116694ff51..bbcdaebf98 100644 --- a/src/tasks/batch_integration/api/anndata_score.yaml +++ b/src/tasks/batch_integration/api/file_score.yaml @@ -1,8 +1,8 @@ type: file -description: "Metric score file" example: "score.h5ad" info: - short_description: "Score" + label: "Score" + summary: "Metric score file" slots: uns: - type: string diff --git a/src/tasks/batch_integration/api/anndata_unintegrated.yaml b/src/tasks/batch_integration/api/file_unintegrated.yaml similarity index 94% rename from src/tasks/batch_integration/api/anndata_unintegrated.yaml rename to src/tasks/batch_integration/api/file_unintegrated.yaml index f2e0e8f9c3..3597a43c24 100644 --- a/src/tasks/batch_integration/api/anndata_unintegrated.yaml +++ b/src/tasks/batch_integration/api/file_unintegrated.yaml @@ -1,8 +1,8 @@ type: file -description: Unintegrated AnnData HDF5 file. example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" info: - short_description: "Unintegrated" + label: "Unintegrated" + summary: Unintegrated AnnData HDF5 file. slots: layers: - type: integer diff --git a/src/tasks/batch_integration/api/task_info.yaml b/src/tasks/batch_integration/api/task_info.yaml index 42255d56f9..a41b6db605 100644 --- a/src/tasks/batch_integration/api/task_info.yaml +++ b/src/tasks/batch_integration/api/task_info.yaml @@ -1,11 +1,10 @@ -task_id: batch_integration -task_name: Batch Integration -v1_url: openproblems/tasks/batch_integration/README.md -v1_commit: 637163fba7d74ab5393c2adbee5354dcf4d46f85 +name: batch_integration +label: Batch Integration +v1: + path: openproblems/tasks/batch_integration/README.md + commit: 637163fba7d74ab5393c2adbee5354dcf4d46f85 summary: Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. -description: | - ## Motivation - +motivation: | As single-cell technologies advance, single-cell datasets are growing both in size and complexity. Especially in consortia such as the Human Cell Atlas, individual studies combine data from multiple labs, each sequencing multiple individuals possibly with different technologies. This gives rise to complex batch effects in the data that must be computationally removed to perform a joint analysis. @@ -14,9 +13,7 @@ description: | These methods balance the removal of batch effects with the conservation of nuanced biological information in different ways. This abundance of tools has complicated batch integration method choice, leading to several benchmarks on this topic [@luecken2020benchmarking; @tran2020benchmark; @chazarragil2021flexible; @mereu2020benchmarking]. Yet, benchmarks use different metrics, method implementations and datasets. Here we build a living benchmarking task for batch integration methods with the vision of improving the consistency of method evaluation. - - ## Task Description - +description: | In this task we evaluate batch integration methods on their ability to remove batch effects in the data while conserving variation attributed to biological effects. As input, methods require either normalised or unnormalised data with multiple batches and consistent cell type labels. The batch integrated output can be a feature matrix, a low dimensional embedding and/or a neighbourhood graph. @@ -25,13 +22,18 @@ description: | authors: - name: Michaela Mueller roles: [ maintainer, author ] - props: { github: mumichae } + info: + github: mumichae - name: Kai Waldrant roles: [ contributor ] - props: { github: KaiWaldrant } + info: + github: KaiWaldrant - name: Robrecht Cannoodt roles: [ contributor ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } + info: + github: rcannood + orcid: "0000-0003-3641-729X" - name: Daniel Strobl roles: [ author ] - props: { github: danielStrobl } + info: + github: danielStrobl diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 1d9843840e..1796fe5ccf 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -3,7 +3,7 @@ __merge__: ../../api/comp_method_graph.yaml functionality: name: bbknn info: - pretty_name: BBKNN + label: BBKNN summary: "BBKNN creates k nearest neighbours graph by identifying neighbours within batches, then combining and processing them with UMAP for visualization." description: | "BBKNN or batch balanced k nearest neighbours graph is built for each cell by @@ -13,8 +13,9 @@ functionality: reference: "polanski2020bbknn" repository_url: "https://github.com/Teichlab/bbknn" documentation_url: "https://github.com/Teichlab/bbknn#readme" - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm variants: bbknn_full_unscaled: @@ -30,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/bbknn/script.py b/src/tasks/batch_integration/methods/bbknn/script.py index 137b9228f1..eda4148c63 100644 --- a/src/tasks/batch_integration/methods/bbknn/script.py +++ b/src/tasks/batch_integration/methods/bbknn/script.py @@ -17,7 +17,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) input = ad.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index fa42974027..86ad9cd0be 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -3,7 +3,7 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: combat info: - pretty_name: Combat + label: Combat summary: "Adjusting batch effects in microarray expression data using empirical Bayes methods" description: | @@ -16,8 +16,9 @@ functionality: reference: "hansen2012removing" repository_url: "https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html" documentation_url: "https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html" - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm variants: combat_full_unscaled: @@ -33,7 +34,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/combat/script.py b/src/tasks/batch_integration/methods/combat/script.py index 0277493dcf..5deda4fd29 100644 --- a/src/tasks/batch_integration/methods/combat/script.py +++ b/src/tasks/batch_integration/methods/combat/script.py @@ -19,7 +19,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata = sc.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index d2d03f474d..3d4e0cb5e0 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -3,7 +3,7 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scanorama_embed info: - pretty_name: Scanorama + label: Scanorama summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" description: | @@ -11,8 +11,9 @@ functionality: reference: "hie2019efficient" repository_url: "https://github.com/brianhie/scanorama" documentation_url: "https://github.com/brianhie/scanorama#readme" - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm variants: scanorama_embed_full_unscaled: @@ -28,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py index 0bb0529fa2..9b1eb265a3 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/script.py +++ b/src/tasks/batch_integration/methods/scanorama_embed/script.py @@ -17,7 +17,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata = ad.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index e4bd9d2c7b..7a27b65745 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -2,10 +2,8 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: scanorama_feature - description: "Efficient integration of heterogeneous single-cell - transcriptomes using Scanorama" info: - pretty_name: Scanorama + label: Scanorama summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" description: | @@ -13,8 +11,9 @@ functionality: reference: "hie2019efficient" repository_url: "https://github.com/brianhie/scanorama" documentation_url: "https://github.com/brianhie/scanorama#readme" - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm variants: scanorama_feature_full_unscaled: @@ -30,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index 85a743af8d..24a904dc89 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -17,7 +17,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata = ad.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index af8bdda584..550b9676ed 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -2,17 +2,17 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scvi - description: Run scVI on adata object info: - pretty_name: scVI + label: scVI summary: "scVI combines a variational autoencoder with a hierarchical Bayesian model." description: | scVI combines a variational autoencoder with a hierarchical Bayesian model. It uses the negative binomial distribution to describe gene expression of each cell, conditioned on unobserved factors and the batch variable. ScVI is run as implemented in Luecken et al. reference: "lopez2018deep" repository_url: "https://github.com/YosefLab/scvi-tools" documentation_url: "https://github.com/YosefLab/scvi-tools#readme" - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf preferred_normalization: log_cpm variants: scvi_full_unscaled: @@ -23,7 +23,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py index f768c036e0..73af0e284f 100644 --- a/src/tasks/batch_integration/methods/scvi/script.py +++ b/src/tasks/batch_integration/methods/scvi/script.py @@ -17,7 +17,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata = ad.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index f75aee8cdd..43049c8cc6 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -3,26 +3,25 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_batch info: - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - name: asw_batch - pretty_name: ASW batch + label: ASW batch summary: Average silhouette of batches per label description: | "A batch correction metric that computes the silhouette score over all batch labels per cell type. Here, 0 indicates that batches are well mixed and any deviation from 0 indicates there remains a separation between batch labels. This is rescaled to a score between 0 and 1 by taking." reference: luecken2022benchmarking - repository_url: "" - documentation_url: "" min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index d9dde09710..33d81fdf24 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -2,28 +2,25 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: asw_label - description: Average silhouette of labels info: - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - metrics: - name: asw_label - pretty_name: ASW Label + label: ASW Label summary: "Average silhouette of labels" description: "The absolute silhouette width is computed on cell identity labels, measuring their compactness." reference: luecken2022benchmarking - repository_url: "" - documentation_url: "" min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index a422cf0b61..580332b70c 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -5,23 +5,22 @@ functionality: info: metrics: - name: cell_cycle_conservation - pretty_name: Cell Cycle Conservation + label: Cell Cycle Conservation summary: "Cell cycle conservation score based on cell cycle gene scoring" description: "The cell-cycle conservation score evaluates how well the cell-cycle effect can be captured before and after integration." reference: luecken2022benchmarking - repository_url: "" - documentation_url: "" - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 8d317e2701..7e87a0f0e7 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -2,11 +2,10 @@ __merge__: ../../api/comp_metric_graph.yaml functionality: name: clustering_overlap - description: Metrics that are based on computing the clustering overlap. info: metrics: - name: ari - pretty_name: ARI + label: ARI summary: "Adjusted Rand Index compares clustering overlap, correcting for random labels and considering correct overlaps and disagreements." description: | The Adjusted Rand Index (ARI) compares the overlap of two clusterings; @@ -19,15 +18,14 @@ functionality: respectively. We used the scikit-learn implementation of the ARI. reference: hubert1985comparing - repository_url: "" - documentation_url: "" min: 0 max: 1 maximize: true - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - name: nmi - pretty_name: NMI + label: NMI summary: "NMI compares overlap by scaling using mean entropy terms and optimizing Louvain clustering to obtain the best match between clusters and labels." description: | Normalized Mutual Information (NMI) compares the overlap of two clusterings. @@ -40,19 +38,18 @@ functionality: and the clustering output with the highest NMI with the label set was used. We the scikit-learn implementation of NMI. reference: amelio2015normalized - documentation_url: "" - repository_url: "" min: 0 max: 1 maximize: true - v1_url: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 6dc69b594d..b89bc246a0 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -2,11 +2,10 @@ __merge__: ../../api/comp_metric_embedding.yaml functionality: name: pcr - description: PCA regression info: metrics: - name: pcr - pretty_name: PCR + label: PCR summary: "The comparison of explained variance by batch before and after integration." description: | "This compares the explained variance by batch before and after integration. It @@ -14,10 +13,9 @@ functionality: contribution hasn’t changed. The larger the score, the more different the variance contributions are before and after integration." reference: luecken2022benchmarking - repository_url: "" - documentation_url: "" - v1_url: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf min: 0 max: 1 maximize: true @@ -26,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index d30bc3a580..75efbdc677 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index c5a62176c1..3b5df9aa85 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -4,12 +4,12 @@ functionality: description: "Transform an embedded integration to a graph integration" info: type: transformer - pretty_name: Embedding to Graph + label: Embedding to Graph output_type: graph arguments: - - __merge__: ../../api/anndata_integrated_embedding.yaml + - __merge__: ../../api/file_integrated_embedding.yaml name: --input - - __merge__: ../../api/anndata_integrated_graph.yaml + - __merge__: ../../api/file_integrated_graph.yaml name: --output direction: output resources: @@ -22,7 +22,7 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python pypi: scanpy diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index ed2da09aa2..4c6f4971d0 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -4,12 +4,12 @@ functionality: description: "Transform a feature integration to an embedded integration" info: type: transformer - pretty_name: Feature to Embed + label: Feature to Embed output_type: embedding arguments: - - __merge__: ../../api/anndata_integrated_feature.yaml + - __merge__: ../../api/file_integrated_feature.yaml name: --input - - __merge__: ../../api/anndata_integrated_embedding.yaml + - __merge__: ../../api/file_integrated_embedding.yaml name: --output direction: output resources: @@ -22,7 +22,7 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python pypi: scanpy diff --git a/src/tasks/denoising/api/comp_control_method.yaml b/src/tasks/denoising/api/comp_control_method.yaml index bad0d9da3f..6fe13f2a35 100644 --- a/src/tasks/denoising/api/comp_control_method.yaml +++ b/src/tasks/denoising/api/comp_control_method.yaml @@ -4,8 +4,8 @@ functionality: type: control_method type_info: label: Control method + summary: Quality control methods for verifying the pipeline. description: | - This folder contains control components for the task. These components have the same interface as the regular methods but also receive the solution object as input. It serves as a starting point to test the relative accuracy of new methods in @@ -13,12 +13,17 @@ functionality: in the task. arguments: - name: "--input_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml + direction: input + required: true - name: "--input_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_denoised.yaml + __merge__: file_denoised.yaml direction: output + required: true test_resources: - type: python_script path: /src/common/comp_tests/check_method_config.py diff --git a/src/tasks/denoising/api/comp_method.yaml b/src/tasks/denoising/api/comp_method.yaml index 2d6340e67f..9b263df2b4 100644 --- a/src/tasks/denoising/api/comp_method.yaml +++ b/src/tasks/denoising/api/comp_method.yaml @@ -4,14 +4,18 @@ functionality: type: method type_info: label: Method + summary: A denoising method. description: | A denoising method to remove noise (i.e. technical artifacts) from a dataset. arguments: - name: "--input_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_denoised.yaml + __merge__: file_denoised.yaml direction: output + required: true test_resources: - type: python_script path: /src/common/comp_tests/check_method_config.py @@ -19,4 +23,5 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/denoising/pancreas dest: resources_test/denoising/pancreas - - path: /src/common/library.bib \ No newline at end of file + - path: /src/common/library.bib + - path: /src/common/api \ No newline at end of file diff --git a/src/tasks/denoising/api/comp_metric.yaml b/src/tasks/denoising/api/comp_metric.yaml index f2fd6aaa6e..c2ef922239 100644 --- a/src/tasks/denoising/api/comp_metric.yaml +++ b/src/tasks/denoising/api/comp_metric.yaml @@ -4,16 +4,22 @@ functionality: type: metric type_info: label: Metric + summary: A denoising metric. description: | A metric for evaluating denoised datasets. arguments: - name: "--input_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml + direction: input + required: true - name: "--input_denoised" - __merge__: anndata_denoised.yaml + __merge__: file_denoised.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_score.yaml + __merge__: file_score.yaml direction: output + required: true test_resources: - type: python_script path: /src/common/comp_tests/check_metric_config.py diff --git a/src/tasks/denoising/api/comp_process_dataset.yaml b/src/tasks/denoising/api/comp_process_dataset.yaml index c55115f92b..ce6874c0ea 100644 --- a/src/tasks/denoising/api/comp_process_dataset.yaml +++ b/src/tasks/denoising/api/comp_process_dataset.yaml @@ -4,17 +4,22 @@ functionality: type: process_dataset type_info: label: Data processor + summary: A denoising dataset processor. description: | - Prepare a common dataset for the denoising task. + A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_common_dataset.yaml + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: input + required: true - name: "--output_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml direction: output + required: true - name: "--output_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml direction: output + required: true test_resources: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/tasks/denoising/api/anndata_dataset.yaml b/src/tasks/denoising/api/file_dataset.yaml similarity index 87% rename from src/tasks/denoising/api/anndata_dataset.yaml rename to src/tasks/denoising/api/file_dataset.yaml index ddaec78b4a..b0b6fd10f8 100644 --- a/src/tasks/denoising/api/anndata_dataset.yaml +++ b/src/tasks/denoising/api/file_dataset.yaml @@ -2,7 +2,7 @@ type: file description: "A preprocessed dataset" example: "resources_test/common/pancreas/dataset.h5ad" info: - short_description: "Preprocessed dataset" + label: "Preprocessed dataset" slots: layers: - type: integer diff --git a/src/tasks/denoising/api/anndata_denoised.yaml b/src/tasks/denoising/api/file_denoised.yaml similarity index 93% rename from src/tasks/denoising/api/anndata_denoised.yaml rename to src/tasks/denoising/api/file_denoised.yaml index fe0a4f3f29..c60e1564a0 100644 --- a/src/tasks/denoising/api/anndata_denoised.yaml +++ b/src/tasks/denoising/api/file_denoised.yaml @@ -2,7 +2,7 @@ type: file description: "The denoised data" example: "resources_test/denoising/pancreas/magic.h5ad" info: - short_description: "Denoised data" + label: "Denoised data" slots: layers: - type: integer diff --git a/src/tasks/denoising/api/anndata_score.yaml b/src/tasks/denoising/api/file_score.yaml similarity index 95% rename from src/tasks/denoising/api/anndata_score.yaml rename to src/tasks/denoising/api/file_score.yaml index d372473de4..04fb7a7330 100644 --- a/src/tasks/denoising/api/anndata_score.yaml +++ b/src/tasks/denoising/api/file_score.yaml @@ -2,7 +2,7 @@ type: file description: "Metric score file" example: "resources_test/denoising/pancreas/magic_poisson.h5ad" info: - short_description: "Score" + label: "Score" slots: uns: - type: string diff --git a/src/tasks/denoising/api/anndata_test.yaml b/src/tasks/denoising/api/file_test.yaml similarity index 90% rename from src/tasks/denoising/api/anndata_test.yaml rename to src/tasks/denoising/api/file_test.yaml index cf1096bf95..98567d0dae 100644 --- a/src/tasks/denoising/api/anndata_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -2,7 +2,7 @@ type: file description: "The test data" example: "resources_test/denoising/pancreas/test.h5ad" info: - short_description: "Test data" + label: "Test data" slots: layers: - type: integer diff --git a/src/tasks/denoising/api/anndata_train.yaml b/src/tasks/denoising/api/file_train.yaml similarity index 89% rename from src/tasks/denoising/api/anndata_train.yaml rename to src/tasks/denoising/api/file_train.yaml index 78a185e334..f83051a6fe 100644 --- a/src/tasks/denoising/api/anndata_train.yaml +++ b/src/tasks/denoising/api/file_train.yaml @@ -2,7 +2,7 @@ type: file description: "The training data" example: "resources_test/denoising/pancreas/train.h5ad" info: - short_description: "Training data" + label: "Training data" slots: layers: - type: integer diff --git a/src/tasks/denoising/api/task_info.yaml b/src/tasks/denoising/api/task_info.yaml index 9cdb7347b6..d093409efc 100644 --- a/src/tasks/denoising/api/task_info.yaml +++ b/src/tasks/denoising/api/task_info.yaml @@ -1,9 +1,10 @@ -task_id: denoising -task_name: Denoising -v1_url: openproblems/tasks/denoising/README.md -v1_commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb +name: denoising +label: Denoising +v1: + path: openproblems/tasks/denoising/README.md + commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb summary: "Removing noise in sparse single-cell RNA-sequencing count data" -description: | +motivation: | Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present in each cell. As a result, the measurements (UMI counts) observed for each gene and each cell are associated with generally high levels of technical noise ([Grün et al., @@ -14,7 +15,7 @@ description: | "missing data", and "technical zeros", this terminology can create confusion about the underlying measurement process ([Sarkar and Stephens, 2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). - +description: | A key challenge in evaluating denoising methods is the general lack of a ground truth. A recent benchmark study ([Hou et al., 2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) @@ -34,13 +35,19 @@ description: | authors: - name: "Wesley Lewis" roles: [ author, maintainer ] - props: { github: wes-lewis } + info: + github: wes-lewis - name: "Scott Gigante" roles: [ author, maintainer ] - props: { github: scottgigante, orcid: "0000-0002-4544-2764" } + info: + github: scottgigante + orcid: "0000-0002-4544-2764" - name: Robrecht Cannoodt roles: [ author ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } + info: + github: rcannood + orcid: "0000-0003-3641-729X" - name: Kai Waldrant roles: [ author ] - props: { github: KaiWaldrant } \ No newline at end of file + info: + github: KaiWaldrant \ No newline at end of file diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index 9242803f16..0423eb2ee6 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "no_denoising" info: - subtype: negative_control - pretty_name: No Denoising + label: No Denoising summary: "negative control by copying train counts" description: "This method serves as a negative control, where the denoised data is a copy of the unaltered training data. This represents the scoring threshold if denoising was not performed on the data." - v1_url: openproblems/tasks/denoising/methods/baseline.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/baseline.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: no_denoising: preferred_normalization: counts @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index c4f5d540fb..0934f3becf 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "perfect_denoising" info: - subtype: positive_control - pretty_name: Perfect Denoising + label: Perfect Denoising summary: "Positive control by copying the test counts" description: "This method serves as a positive control, where the test data is copied 1-to-1 to the denoised data. This makes it seem as if the data is perfectly denoised as it will be compared to the test data in the metrics." - v1_url: openproblems/tasks/denoising/methods/baseline.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/baseline.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: perfect_denoising: preferred_normalization: counts @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index a66057c4d2..6f89ccd57f 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "alra" info: - pretty_name: ALRA + label: ALRA summary: "ALRA imputes missing values in scRNA-seq data by computing rank-k approximation, thresholding by gene, and rescaling the matrix." description: | "Adaptively-thresholded Low Rank Approximation (ALRA). @@ -16,8 +16,9 @@ functionality: reference: "linderman2018zero" repository_url: "https://github.com/KlugerLab/ALRA" documentation_url: https://github.com/KlugerLab/ALRA/blob/master/README.md - v1_url: openproblems/tasks/denoising/methods/alra.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/alra.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: alra: preferred_normalization: counts @@ -31,7 +32,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ Matrix, bit64, rsvd ] diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index d27c2bb487..4f60b1f6f4 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "dca" info: - pretty_name: DCA + label: DCA summary: "A deep autoencoder with ZINB loss function to address the dropout effect in count data" description: | "Deep Count Autoencoder @@ -12,8 +12,9 @@ functionality: reference: "eraslan2019single" documentation_url: "https://github.com/theislab/dca#readme" repository_url: "https://github.com/theislab/dca" - v1_url: openproblems/tasks/denoising/methods/dca.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/dca.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: dca: preferred_normalization: counts @@ -27,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index d4354cfc6c..ce5978893e 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn_smoothing" info: - pretty_name: KNN Smoothing + label: KNN Smoothing summary: "Iterative kNN-smoothing denoises scRNA-seq data by iteratively increasing the size of neighbourhoods for smoothing until a maximum k value is reached." description: "Iterative kNN-smoothing is a method to repair or denoise noisy scRNA-seq expression matrices. Given a scRNA-seq expression matrix, KNN-smoothing first @@ -18,8 +18,9 @@ functionality: reference: "wagner2018knearest" documentation_url: "https://github.com/yanailab/knn-smoothing#readme" repository_url: "https://github.com/yanailab/knn-smoothing" - v1_url: openproblems/tasks/denoising/methods/knn_smoothing.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/knn_smoothing.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: knn_smoothing: preferred_normalization: counts @@ -28,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 92d8c5f38f..886694ed25 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -2,7 +2,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "magic" info: - pretty_name: MAGIC + label: MAGIC summary: "MAGIC imputes and denoises scRNA-seq data using Euclidean distances and a Gaussian kernel to calculate the affinity matrix, followed by a Markov process and multiplication with the normalised data to obtain imputed values." description: "MAGIC (Markov Affinity-based Graph Imputation of Cells) is a method for imputation and denoising of noisy or dropout-prone single cell RNA-sequencing @@ -18,8 +18,9 @@ functionality: reference: "van2018recovering" documentation_url: "https://github.com/KrishnaswamyLab/MAGIC#readme" repository_url: "https://github.com/KrishnaswamyLab/MAGIC" - v1_url: openproblems/tasks/denoising/methods/magic.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/methods/magic.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf variants: magic: magic_approx: @@ -53,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 5a926f46d7..1530f50b68 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -4,14 +4,13 @@ functionality: info: metrics: - name: mse - pretty_name: Mean-squared error + label: Mean-squared error summary: "The mean squared error between the denoised counts and the true counts." description: "The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio" reference: batson2019molecular - documentation_url: "" - repository_url: "" - v1_url: openproblems/tasks/denoising/metrics/mse.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/metrics/mse.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf maximize: false min: 0 max: +inf @@ -20,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index a3aa947af4..6b204d8685 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -5,15 +5,14 @@ functionality: reference: "batson2019molecular" metrics: - name: poisson - pretty_name: Poisson Loss + label: Poisson Loss summary: "The Poisson log lieklihood of the true counts observed in the distribution of denoised counts" description: "The Poisson log likelihood of observing the true counts of the test dataset given the distribution given in the denoised dataset." reference: batson2019molecular - documentation_url: "" - repository_url: "" - v1_url: openproblems/tasks/denoising/metrics/poisson.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + v1: + path: openproblems/tasks/denoising/metrics/poisson.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf maximize: false min: 0 max: +inf @@ -22,7 +21,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python pip: scprep diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 6e47be922a..bc6a083717 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml index 443d28859c..dfa346752f 100644 --- a/src/tasks/dimensionality_reduction/api/comp_control_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_control_method.yaml @@ -4,22 +4,24 @@ functionality: type: control_method type_info: label: Control method + summary: Quality control methods for verifying the pipeline. description: | - This folder contains control components for the task. - These components have the same interface as the regular methods + Control methods have the same interface as the regular methods but also receive the solution object as input. It serves as a starting point to test the relative accuracy of new methods in the task, and also as a quality control for the metrics defined - in the task. + in the task. arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: file_dataset.yaml + direction: input required: true - name: "--input_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml + direction: input required: true - name: "--output" - __merge__: anndata_embedding.yaml + __merge__: file_embedding.yaml direction: output required: true test_resources: diff --git a/src/tasks/dimensionality_reduction/api/comp_method.yaml b/src/tasks/dimensionality_reduction/api/comp_method.yaml index 5c8b1a6758..34d63607a4 100644 --- a/src/tasks/dimensionality_reduction/api/comp_method.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_method.yaml @@ -4,15 +4,17 @@ functionality: type: method type_info: label: Method + summary: A dimensionality reduction method. description: | - A dimensionality reduction method to summarise the biological information in - a dataset in as few dimensions as possible. + A dimensionality reduction method to summarise the biological + information in a dataset in as few dimensions as possible. arguments: - name: "--input" - __merge__: anndata_dataset.yaml + __merge__: file_dataset.yaml + direction: input required: true - name: "--output" - __merge__: anndata_embedding.yaml + __merge__: file_embedding.yaml direction: output required: true test_resources: diff --git a/src/tasks/dimensionality_reduction/api/comp_metric.yaml b/src/tasks/dimensionality_reduction/api/comp_metric.yaml index a0ee3ed786..8cd90e4ca1 100644 --- a/src/tasks/dimensionality_reduction/api/comp_metric.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_metric.yaml @@ -4,17 +4,20 @@ functionality: type: metric type_info: label: Metric + summary: A dimensionality reduction metric. description: | A metric for evaluating dimensionality reductions. arguments: - name: "--input_embedding" - __merge__: anndata_embedding.yaml + direction: input + __merge__: file_embedding.yaml required: true - name: "--input_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml + direction: input required: true - name: "--output" - __merge__: anndata_score.yaml + __merge__: file_score.yaml direction: output required: true test_resources: diff --git a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml index ff7c25445f..1f7b150871 100644 --- a/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/comp_process_dataset.yaml @@ -4,18 +4,20 @@ functionality: type: process_dataset type_info: label: Data processor + summary: A dimensionality reduction dataset processor. description: | - Prepare a common dataset for the dimensionality reduction task. + A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_common_dataset.yaml + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: input required: true - name: "--output_dataset" - __merge__: anndata_dataset.yaml + __merge__: file_dataset.yaml direction: output required: true - name: "--output_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml direction: output required: true test_resources: diff --git a/src/tasks/dimensionality_reduction/api/anndata_dataset.yaml b/src/tasks/dimensionality_reduction/api/file_dataset.yaml similarity index 90% rename from src/tasks/dimensionality_reduction/api/anndata_dataset.yaml rename to src/tasks/dimensionality_reduction/api/file_dataset.yaml index bc6613a93d..8061f8f0c5 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/file_dataset.yaml @@ -1,8 +1,8 @@ type: file -description: "The dataset to pass to a method." example: "resources_test/dimensionality_reduction/pancreas/dataset.h5ad" info: - short_description: "Dataset" + label: "Dataset" + summary: "The dataset to pass to a method." slots: layers: - type: integer diff --git a/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml b/src/tasks/dimensionality_reduction/api/file_embedding.yaml similarity index 78% rename from src/tasks/dimensionality_reduction/api/anndata_embedding.yaml rename to src/tasks/dimensionality_reduction/api/file_embedding.yaml index 31714c2eac..c33d76ae8f 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_embedding.yaml +++ b/src/tasks/dimensionality_reduction/api/file_embedding.yaml @@ -1,20 +1,23 @@ type: file -description: "A dataset with dimensionality reduction embedding." example: "resources_test/dimensionality_reduction/pancreas/embedding.h5ad" info: - short_description: "Embedding" + label: "Embedding" + summary: "A dataset with dimensionality reduction embedding." slots: obsm: - type: double name: X_emb description: The dimensionally reduced embedding. + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true - type: string name: method_id description: "A unique identifier for the method" + required: true - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/dimensionality_reduction/api/anndata_score.yaml b/src/tasks/dimensionality_reduction/api/file_score.yaml similarity index 93% rename from src/tasks/dimensionality_reduction/api/anndata_score.yaml rename to src/tasks/dimensionality_reduction/api/file_score.yaml index 4e0c848e38..71200ef9e1 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_score.yaml +++ b/src/tasks/dimensionality_reduction/api/file_score.yaml @@ -1,8 +1,8 @@ type: file -description: "Metric score file" example: "resources_test/dimensionality_reduction/pancreas/score.h5ad" info: - short_description: "Score" + label: "Score" + summary: "Metric score file" slots: uns: - type: string diff --git a/src/tasks/dimensionality_reduction/api/anndata_solution.yaml b/src/tasks/dimensionality_reduction/api/file_solution.yaml similarity index 90% rename from src/tasks/dimensionality_reduction/api/anndata_solution.yaml rename to src/tasks/dimensionality_reduction/api/file_solution.yaml index 6292535031..02b376a78b 100644 --- a/src/tasks/dimensionality_reduction/api/anndata_solution.yaml +++ b/src/tasks/dimensionality_reduction/api/file_solution.yaml @@ -1,8 +1,8 @@ type: file -description: "The test data" example: "resources_test/dimensionality_reduction/pancreas/solution.h5ad" info: - short_description: "Test data" + label: "Test data" + summary: "The data for evaluating a dimensionality reduction." slots: layers: - type: integer diff --git a/src/tasks/dimensionality_reduction/api/task_info.yaml b/src/tasks/dimensionality_reduction/api/task_info.yaml index a196dfb45f..e22c15910e 100644 --- a/src/tasks/dimensionality_reduction/api/task_info.yaml +++ b/src/tasks/dimensionality_reduction/api/task_info.yaml @@ -1,9 +1,10 @@ -task_id: dimensionality_reduction -task_name: "Dimensionality reduction for visualization" -v1_url: openproblems/tasks/dimensionality_reduction/README.md -v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b +name: dimensionality_reduction +label: "Dimensionality reduction for visualization" +v1: + path: openproblems/tasks/dimensionality_reduction/README.md + commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b summary: Reduction of high-dimensional datasets to 2D for visualization & interpretation -description: | +motivation: | Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional @@ -12,7 +13,7 @@ description: | experiments would yield a few hundred cells, at best. Now, it is not uncommon to see experiments that yield over [100,000 cells]() or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). - +description: | Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 dimensions measured in each cell contribute to an underlying data structure, the overall structure of the data is challenging to display in few dimensions due to data sparsity @@ -23,19 +24,28 @@ description: | authors: - name: Luke Zappia roles: [ maintainer, author ] - props: { github: lazappi } + info: + github: lazappi - name: Michal Klein roles: [ author ] - props: { github: michalk8 } + info: + github: michalk8 - name: "Scott Gigante" roles: [ author ] - props: { github: scottgigante, orcid: "0000-0002-4544-2764" } + info: + github: scottgigante + orcid: "0000-0002-4544-2764" - name: Ben DeMeo roles: [ author ] - props: { github: bendemeo } + info: + github: bendemeo - name: "Juan A. Cordero Varela" roles: [ contributor ] - props: { github: jacorvar, orcid: 0000-0002-7373-5433} + info: + github: jacorvar + orcid: 0000-0002-7373-5433 - name: Robrecht Cannoodt roles: [ contributor ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } + info: + github: rcannood + orcid: "0000-0003-3641-729X" diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 01821cdddf..f809954aeb 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_features" info: - subtype: negative_control - pretty_name: Random Features + label: Random Features summary: "Negative control by randomly embedding into a 2D space." description: "This method serves as a negative control, where the data is randomly embedded into a two-dimensional space, with no attempt to preserve the original structure." - v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/baseline.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: counts variants: random_features: @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 2bd07d2ae2..f094ef8208 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -1,15 +1,13 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "true_features" - description: "Positive control method which generates high-dimensional (full data) embedding" info: - subtype: positive_control - pretty_name: True Features + label: True Features summary: "Positive control by retaining the dimensionality without loss of information." description: "This serves as a positive control since the original high-dimensional data is retained as is, without any loss of information" - v1_url: openproblems/tasks/dimensionality_reduction/methods/baseline.py - v1_comp_id: "True Features" - v1_commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 + v1: + path: openproblems/tasks/dimensionality_reduction/methods/baseline.py + commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 preferred_normalization: counts variants: true_features: @@ -34,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 34f68bb2fb..8429584e45 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -2,14 +2,15 @@ __merge__: ../../api/comp_method.yaml functionality: name: "densmap" info: - pretty_name: densMAP + label: densMAP summary: "Modified UMAP with preservation of local density information" description: "A modification of UMAP that adds an extra cost term in order to preserve information about the relative local density of the data. It is performed on the same inputs as UMAP." reference: "narayan2021assessing" repository_url: https://github.com/lmcinnes/umap documentation_url: https://github.com/lmcinnes/umap#readme - v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/umap.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: densmap_logCPM: @@ -32,12 +33,13 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: - scanpy - umap-learn + - type: native - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index eeb5549a0d..b9fc0587bd 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -6,18 +6,18 @@ functionality: status: disabled name: "ivis" info: - pretty_name: "ivis" - summary: "" + label: "ivis" + summary: "Structure-preserving dimensionality reduction using a siamese neural network trained on triplets." description: | - "ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. + ivis is a machine learning library for reducing dimensionality of very large datasets using Siamese Neural Networks. ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using - a parametric mapping function, and scales linearly to millions of observations." - reference: szubert2019structurepreserving + a parametric mapping function, and scales linearly to millions of observations. + reference: szubert2019structurepreserving repository_url: "https://github.com/beringresearch/ivis" documentation_url: "https://github.com/beringresearch/ivis#readme" - reference: "" - v1_url: openproblems/tasks/dimensionality_reduction/methods/ivis.py - v1_commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc + v1: + path: openproblems/tasks/dimensionality_reduction/methods/ivis.py + commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc preferred_normalization: log_cpm variants: ivis_logCPM_1kHVG: @@ -35,12 +35,12 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: - scanpy - ivis[cpu] - type: nextflow - directives: + directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 53e611af63..ae946ea497 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -2,22 +2,23 @@ __merge__: ../../api/comp_method.yaml functionality: name: "neuralee" info: - pretty_name: NeuralEE + label: NeuralEE summary: "Non-linear method that uses a neural network to preserve pairwise distances between data points in a high-dimensional space." description: | - "A neural network implementation of elastic embedding. It is a + A neural network implementation of elastic embedding. It is a non-linear method that preserves pairwise distances between data points. NeuralEE uses a neural network to optimize an objective function that measures the difference between pairwise distances in the original high-dimensional space and the two-dimensional space. It is computed on both the recommended input from the package authors of 500 HVGs selected from a logged expression matrix (without sequencing depth scaling) and the default - logCPM matrix with 1000 HVGs." + logCPM matrix with 1000 HVGs. reference: "xiong2020neuralee" repository_url: "https://github.com/HiBearME/NeuralEE" documentation_url: "https://github.com/HiBearME/NeuralEE#readme" - v1_url: openproblems/tasks/dimensionality_reduction/methods/neuralee.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/neuralee.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: neuralee_default: @@ -43,7 +44,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 5172f262d5..d97081cb14 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -2,20 +2,21 @@ __merge__: ../../api/comp_method.yaml functionality: name: "pca" info: - pretty_name: "PCA" - summary: "A linear method that finds orthogonal directions to compute the two-dimensional embedding, capturing maximum variance from logCPM expression matrix with/without selecting 1000 HVGs." + label: "PCA" + summary: A linear method that finds orthogonal directions to compute the two-dimensional embedding. description: | - 'Principal Component Analysis is a linear method that finds orthogonal + Principal Component Analysis is a linear method that finds orthogonal directions in the data that capture the most variance. The first two principal components are chosen as the two-dimensional embedding. We select only the first two principal components as the two-dimensional embedding. PCA is calculated on the logCPM expression matrix with and without selecting 1000 - HVGs.' + HVGs. reference: pearson1901pca repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" - v1_url: openproblems/tasks/dimensionality_reduction/methods/pca.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/pca.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: pca_logCPM: @@ -30,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 24226db235..31bfde4e29 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -2,22 +2,23 @@ __merge__: ../../api/comp_method.yaml functionality: name: "phate" info: - pretty_name: PHATE - summary: "Preservating trajectories in a dataset by using heat diffusion potential via an affinity-based method that creates an embedding from dominant eigenvalues of a Markov transition matrix." + label: PHATE + summary: Preservating trajectories in a dataset by using heat diffusion potential. description: | - "PHATE or “Potential of Heat - diffusion for Affinity - based Transition - Embedding” uses the potential of heat diffusion to preserve trajectories in a + PHATE or "Potential of Heat - diffusion for Affinity - based Transition + Embedding" uses the potential of heat diffusion to preserve trajectories in a dataset via a diffusion process. It is an affinity - based method that creates an embedding by finding the dominant eigenvalues of a Markov transition matrix. We evaluate several variants including using the recommended square - root transformed CPM matrix as input, this input with the gamma parameter set to zero and the normal logCPM transformed matrix with - and without HVG selection." + and without HVG selection. reference: "moon2019visualizing" repository_url: "https://github.com/KrishnaswamyLab/PHATE" documentation_url: "https://github.com/KrishnaswamyLab/PHATE#readme" - v1_url: openproblems/tasks/dimensionality_reduction/methods/phate.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/phate.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: sqrt_cpm variants: phate_default: @@ -45,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index e72c00466e..2764dbe010 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -2,20 +2,21 @@ __merge__: ../../api/comp_method.yaml functionality: name: "tsne" info: - pretty_name: t-SNE + label: t-SNE summary: "Minimizing Kullback-Leibler divergence by converting similarities into joint probabilities between data points and the low/high dimensional embedding." description: | - "t-distributed Stochastic Neighbor Embedding converts similarities + t-distributed Stochastic Neighbor Embedding converts similarities between data points to joint probabilities and tries to minimize the Kullback-Leibler divergence between the joint probabilities of the low-dimensional embedding and the high-dimensional data. We use the implementation in the scanpy package with the result of PCA on the logCPM - expression matrix (with and without HVG selection)." + expression matrix (with and without HVG selection). reference: vandermaaten2008visualizing repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE" documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE" - v1_url: openproblems/tasks/dimensionality_reduction/methods/tsne.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/tsne.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: tsne_logCPM: @@ -34,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: apt packages: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index fbba96436b..b8508657ec 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -2,19 +2,20 @@ __merge__: ../../api/comp_method.yaml functionality: name: "umap" info: - pretty_name: UMAP + label: UMAP summary: "A manifold learning algorithm that utilizes topological data analysis for dimension reduction." description: | - "Uniform Manifold Approximation and Projection is an algorithm for + Uniform Manifold Approximation and Projection is an algorithm for dimension reduction based on manifold learning techniques and ideas from topological data analysis. We perform UMAP on the logCPM expression matrix before and after HVG selection and with and without PCA as a pre-processing - step." + step. reference : "mcinnes2018umap" repository_url: "https://github.com/lmcinnes/umap" documentation_url: "https://github.com/lmcinnes/umap#readme" - v1_url: openproblems/tasks/dimensionality_reduction/methods/umap.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf + v1: + path: openproblems/tasks/dimensionality_reduction/methods/umap.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf preferred_normalization: log_cpm variants: umap_logCPM: @@ -38,7 +39,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 6999240a65..59a1d9aeeb 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -1,97 +1,163 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "coranking" - description: | - This is a set of metrics which all use a co-ranking matrix as the basis of the metric. + # description: | + # This is a set of metrics which all use a co-ranking matrix as the basis of the metric. info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - v1_commit: 14d70b330cae09527a6d4c4e552db240601e31cf - v1_note: | - The original v1 implementations consisted of a lot of helper functions which were - derived from the pyDRMetrics package. This version uses the coRanking package - to avoid reimplementing and potentially introducing a lot of bugs in how - the various metrics are computed. - - In addition, the references for each of the metrics were looked up to - properly attribute the original authors of each of the metrics. - reference: kraemer2018dimred metrics: - name: continuity_at_k30 - pretty_name: Continuity at k=30 + label: Continuity at k=30 reference: venna2006local - summary: "" - description: "" - repository_url: "" - documentation_url: "" + summary: "The continuity metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + description: "The continuity metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: trustworthiness_at_k30 - pretty_name: Trustworthiness at k=30 - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: Trustworthiness at k=30 + summary: "The trustworthiness metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + description: "The trustworthiness metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: venna2006local min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: qnx_at_k30 - pretty_name: The value for QNX at k=30 - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: The value for QNX at k=30 + summary: "The QNX metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + description: "The QNX metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: lee2009quality min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: lcmc_at_k30 - pretty_name: The value for LCMC at k=30 - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: The value for LCMC at k=30 + summary: "The LCMC metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + description: "The LCMC metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: chen2009local min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: qnx_auc - pretty_name: Area under the QNX curve - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: Area under the QNX curve + summary: "The AU-QNX metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + description: "The AU-QNX metric at k=30 computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: lueks2011evaluate min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: qlocal - pretty_name: Local quality measure - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: Local quality measure + summary: "The local quality metric computed on the co-ranking matrix between expression matrix and embedding." + description: "The local quality metric computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: lueks2011evaluate min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. - name: qglobal - pretty_name: Global quality measure - summary: "" - description: "" - repository_url: "" - documentation_url: "" + label: Global quality measure + summary: "The Global quality metric computed on the co-ranking matrix between expression matrix and embedding." + description: "The Global quality metric computed on the co-ranking matrix between expression matrix and embedding." + repository_url: https://github.com/gdkrmr/coRanking/ + documentation_url: https://coranking.guido-kraemer.com/ reference: lueks2011evaluate min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py + commit: 14d70b330cae09527a6d4c4e552db240601e31cf + note: | + The original v1 implementations consisted of a lot of helper functions which were + derived from the pyDRMetrics package. This version uses the coRanking package + to avoid reimplementing and potentially introducing a lot of bugs in how + the various metrics are computed. + + In addition, the references for each of the metrics were looked up to + properly attribute the original authors of each of the metrics. resources: - type: r_script path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ coRanking, bit64 ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index e05053582e..f9e40482d0 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -2,27 +2,26 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "density_preservation" info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/density.py - v1_commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf metrics: - name: density_preservation - pretty_name: Density preservation + label: Density preservation summary: "Similarity between local densities in the high-dimensional data and the reduced data." description: | "Similarity between local densities in the high-dimensional data and the reduced data. This is computed as the pearson correlation of local radii with the local radii in the original data space." - repository_url: "" - documentation_url: "" reference: narayan2021assessing min: -1 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/density.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml index ae42fa83c8..08879e3599 100644 --- a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -1,32 +1,28 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "rmse" - description: The root mean squared error between the full (or processed) data matrix and a list of dimensionally-reduced matrices info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py - v1_commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b - v1_note: This metric was ported but will probably be removed soon. metrics: - name: rmse - pretty_name: RMSE + label: RMSE summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." reference: kruskal1964mds - repository_url: "" - documentation_url: "" min: 0 - max: +inf + max: "+.inf" maximize: false - name: rmse_spectral - pretty_name: RMSE Spectral + label: RMSE Spectral summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." reference: coifman2006diffusion - repository_url: "" - documentation_url: "" min: 0 - max: +inf + max: "+.inf" maximize: false + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py + commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b + note: This metric was ported but will probably be removed soon. arguments: - name: "--spectral" type: boolean_true @@ -36,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 4a162a3a9e..a67250fd79 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -1,28 +1,26 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "trustworthiness" - description: "To what extent the local structure is retained in a low-dimensional embedding in a value between 0 and 1." info: - v1_url: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - v1_note: This metric is already included in the 'coranking' component and can be removed. metrics: - name: trustworthiness - pretty_name: Trustworthiness at k=15 + label: Trustworthiness at k=15 summary: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." description: "A measurement of similarity between the rank of each point's nearest neighbors in the high-dimensional data and the reduced data." reference: venna2006local - repository_url: "" - documentation_url: "" min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py + commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + note: This metric is already included in the 'coranking' component and can be removed. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index dd5933fc11..8a1e9f3fbf 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/label_projection/api/comp_control_method.yaml b/src/tasks/label_projection/api/comp_control_method.yaml index ebdd3ebdd5..d32de4ab2c 100644 --- a/src/tasks/label_projection/api/comp_control_method.yaml +++ b/src/tasks/label_projection/api/comp_control_method.yaml @@ -4,6 +4,7 @@ functionality: type: control_method type_info: label: Control method + summary: Quality control methods for verifying the pipeline. description: | This folder contains control components for the task. These components have the same interface as the regular methods @@ -13,14 +14,21 @@ functionality: in the task. arguments: - name: "--input_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml + direction: input + required: true - name: "--input_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml + direction: input + required: true - name: "--input_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_prediction.yaml + __merge__: file_prediction.yaml direction: output + required: true test_resources: - path: /resources_test/label_projection/pancreas dest: resources_test/label_projection/pancreas diff --git a/src/tasks/label_projection/api/comp_method.yaml b/src/tasks/label_projection/api/comp_method.yaml index b218add385..2650f839ac 100644 --- a/src/tasks/label_projection/api/comp_method.yaml +++ b/src/tasks/label_projection/api/comp_method.yaml @@ -4,17 +4,23 @@ functionality: type: method type_info: label: Method + summary: A label projection method. description: | A label projection method to predict the labels of a new "test" dataset based on an annotated "training" dataset. arguments: - name: "--input_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml + direction: input + required: true - name: "--input_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_prediction.yaml + __merge__: file_prediction.yaml direction: output + required: true test_resources: - path: /resources_test/label_projection/pancreas dest: resources_test/label_projection/pancreas @@ -23,3 +29,4 @@ functionality: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - path: /src/common/library.bib + - path: /src/common/api diff --git a/src/tasks/label_projection/api/comp_metric.yaml b/src/tasks/label_projection/api/comp_metric.yaml index 07766f05a7..ce81b0f89f 100644 --- a/src/tasks/label_projection/api/comp_metric.yaml +++ b/src/tasks/label_projection/api/comp_metric.yaml @@ -4,15 +4,21 @@ functionality: type: metric type_info: label: Metric + summary: A label projection metric. description: | A metric for evaluating predicted labels. arguments: - name: "--input_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml + direction: input + required: true - name: "--input_prediction" - __merge__: anndata_prediction.yaml + __merge__: file_prediction.yaml + direction: input + required: true - name: "--output" - __merge__: anndata_score.yaml + __merge__: file_score.yaml + required: true direction: output test_resources: - path: /resources_test/label_projection/pancreas diff --git a/src/tasks/label_projection/api/comp_process_dataset.yaml b/src/tasks/label_projection/api/comp_process_dataset.yaml index 2598d6d6ac..13adb6ec84 100644 --- a/src/tasks/label_projection/api/comp_process_dataset.yaml +++ b/src/tasks/label_projection/api/comp_process_dataset.yaml @@ -4,20 +4,26 @@ functionality: type: process_dataset type_info: label: Data processor + summary: A label projection dataset processor. description: | - Prepare a common dataset for the label prediction task. + A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/anndata_common_dataset.yaml + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: input + required: true - name: "--output_train" - __merge__: anndata_train.yaml + __merge__: file_train.yaml direction: output + required: true - name: "--output_test" - __merge__: anndata_test.yaml + __merge__: file_test.yaml direction: output + required: true - name: "--output_solution" - __merge__: anndata_solution.yaml + __merge__: file_solution.yaml direction: output + required: true test_resources: - path: /resources_test/common/pancreas dest: resources_test/common/pancreas diff --git a/src/tasks/label_projection/api/anndata_prediction.yaml b/src/tasks/label_projection/api/file_prediction.yaml similarity index 84% rename from src/tasks/label_projection/api/anndata_prediction.yaml rename to src/tasks/label_projection/api/file_prediction.yaml index bc305cd04d..adbb0327fe 100644 --- a/src/tasks/label_projection/api/anndata_prediction.yaml +++ b/src/tasks/label_projection/api/file_prediction.yaml @@ -1,13 +1,14 @@ type: file -description: "The prediction file" example: "resources_test/label_projection/pancreas/knn.h5ad" info: - short_description: "Prediction" + label: "Prediction" + summary: "The prediction file" slots: obs: - type: string name: label_pred description: Predicted labels for the test cells. + required: true uns: - type: string name: dataset_id @@ -20,3 +21,4 @@ info: - type: string name: method_id description: "A unique identifier for the method" + required: true diff --git a/src/tasks/label_projection/api/anndata_score.yaml b/src/tasks/label_projection/api/file_score.yaml similarity index 93% rename from src/tasks/label_projection/api/anndata_score.yaml rename to src/tasks/label_projection/api/file_score.yaml index 34801c5396..997bdda587 100644 --- a/src/tasks/label_projection/api/anndata_score.yaml +++ b/src/tasks/label_projection/api/file_score.yaml @@ -1,8 +1,8 @@ type: file -description: "Metric score file" example: "resources_test/label_projection/pancreas/knn_accuracy.h5ad" info: - short_description: "Score" + label: "Score" + summary: "Metric score file" slots: uns: - type: string diff --git a/src/tasks/label_projection/api/anndata_solution.yaml b/src/tasks/label_projection/api/file_solution.yaml similarity index 87% rename from src/tasks/label_projection/api/anndata_solution.yaml rename to src/tasks/label_projection/api/file_solution.yaml index 69468001d1..78bc3243f6 100644 --- a/src/tasks/label_projection/api/anndata_solution.yaml +++ b/src/tasks/label_projection/api/file_solution.yaml @@ -1,23 +1,27 @@ type: file -description: "The solution for the test data" example: "resources_test/label_projection/pancreas/solution.h5ad" info: - short_description: "Solution" + label: "Solution" + summary: "The solution for the test data" slots: layers: - type: integer name: counts description: Raw counts + required: true - type: double name: normalized description: Normalized counts + required: true obs: - type: string name: label description: Ground truth cell type labels + required: true - type: string name: batch description: Batch information + required: true var: - type: boolean name: hvg diff --git a/src/tasks/label_projection/api/anndata_test.yaml b/src/tasks/label_projection/api/file_test.yaml similarity index 88% rename from src/tasks/label_projection/api/anndata_test.yaml rename to src/tasks/label_projection/api/file_test.yaml index d82811f356..48eb3d98c5 100644 --- a/src/tasks/label_projection/api/anndata_test.yaml +++ b/src/tasks/label_projection/api/file_test.yaml @@ -1,20 +1,23 @@ type: file -description: "The test data (without labels)" example: "resources_test/label_projection/pancreas/test.h5ad" info: - short_description: "Test data" + label: "Test data" + summary: "The test data (without labels)" slots: layers: - type: integer name: counts description: Raw counts + required: true - type: double name: normalized description: Normalized counts + required: true obs: - type: string name: batch description: Batch information + required: true var: - type: boolean name: hvg diff --git a/src/tasks/label_projection/api/anndata_train.yaml b/src/tasks/label_projection/api/file_train.yaml similarity index 88% rename from src/tasks/label_projection/api/anndata_train.yaml rename to src/tasks/label_projection/api/file_train.yaml index 83fb4deb66..7f87e63e7d 100644 --- a/src/tasks/label_projection/api/anndata_train.yaml +++ b/src/tasks/label_projection/api/file_train.yaml @@ -1,23 +1,27 @@ type: file -description: "The training data" example: "resources_test/label_projection/pancreas/train.h5ad" info: - short_description: "Training data" + label: "Training data" + summary: "The training data" slots: layers: - type: integer name: counts description: Raw counts + required: true - type: double name: normalized description: Normalized counts + required: true obs: - type: string name: label description: Ground truth cell type labels + required: true - type: string name: batch description: Batch information + required: true var: - type: boolean name: hvg diff --git a/src/tasks/label_projection/api/task_info.yaml b/src/tasks/label_projection/api/task_info.yaml index 8576d9dc79..8ee865a131 100644 --- a/src/tasks/label_projection/api/task_info.yaml +++ b/src/tasks/label_projection/api/task_info.yaml @@ -1,9 +1,10 @@ -task_id: label_projection -task_name: Label projection -v1_url: openproblems/tasks/label_projection/README.md -v1_commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 +name: label_projection +label: Label projection +v1: + path: openproblems/tasks/label_projection/README.md + commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 summary: Automated cell type annotation from rich, labeled reference data -description: | +motivation: | A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for annotating cell types is referred to as @@ -15,7 +16,7 @@ description: | [known marker genes](https://www.nature.com/articles/s41592-019-0535-3). However, these strategies pose a difficulty for integrating atlas-scale datasets as the particular annotations may not match. - +description: | To ensure that the cell type labels in newly generated datasets match existing reference datasets, some methods align cells to a previously annotated [reference dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) @@ -30,10 +31,15 @@ description: | authors: - name: "Nikolay Markov" roles: [ author, maintainer ] - props: { github: mxposed } + info: + github: mxposed - name: "Scott Gigante" roles: [ author ] - props: { github: scottgigante, orcid: "0000-0002-4544-2764" } + info: + github: scottgigante + orcid: "0000-0002-4544-2764" - name: Robrecht Cannoodt roles: [ author ] - props: { github: rcannood, orcid: "0000-0003-3641-729X" } \ No newline at end of file + info: + github: rcannood + orcid: "0000-0003-3641-729X" \ No newline at end of file diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index dcb3ff93aa..ac66f99216 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "majority_vote" info: - subtype: negative_control - pretty_name: Majority Vote + label: Majority Vote summary: "A control-type method that predicts all cells to belong to the most abundant cell type in the dataset" description: "A control-type method that predicts all cells to belong to the most abundant cell type in the dataset" - v1_url: openproblems/tasks/label_projection/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1: + path: openproblems/tasks/label_projection/methods/baseline.py + commit: b460ecb183328c857cbbf653488f522a4034a61c variants: majority_vote: preferred_normalization: counts @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index de2c83269e..9b408e83fa 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -2,12 +2,12 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "random_labels" info: - subtype: negative_control - pretty_name: Random Labels + label: Random Labels summary: "a negative control, where the labels are randomly predicted." description: "A negative control, where the labels are randomly predicted without training the data." - v1_url: openproblems/tasks/label_projection/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1: + path: openproblems/tasks/label_projection/methods/baseline.py + commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts variants: random_labels: @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scanpy diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index 6305bcd4b8..c2ec2b3d5b 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -1,14 +1,13 @@ __merge__: ../../api/comp_control_method.yaml functionality: name: "true_labels" - description: "Positive control method by returning the true labels" info: - subtype: positive_control - pretty_name: True labels + label: True labels summary: "a positive control, solution labels are copied 1 to 1 to the predicted data." description: "A positive control, where the solution labels are copied 1 to 1 to the predicted data." - v1_url: openproblems/tasks/label_projection/methods/baseline.py - v1_commit: b460ecb183328c857cbbf653488f522a4034a61c + v1: + path: openproblems/tasks/label_projection/methods/baseline.py + commit: b460ecb183328c857cbbf653488f522a4034a61c preferred_normalization: counts variants: true_labels: @@ -17,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index 13d952c438..d9971e602a 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -2,21 +2,22 @@ __merge__: ../../api/comp_method.yaml functionality: name: "knn" info: - pretty_name: KNN + label: KNN summary: "Assumes cells with similar gene expression belong to the same cell type, and assigns an unlabelled cell the most common cell type among its k nearest neighbors in PCA space." description: | - 'Using the "k-nearest neighbours" approach, which is a + Using the "k-nearest neighbours" approach, which is a popular machine learning algorithm for classification and regression tasks. The assumption underlying KNN in this context is that cells with similar gene expression profiles tend to belong to the same cell type. For each unlabelled cell, this method computes the $k$ labelled cells (in this case, 5) with the smallest distance in PCA space, and assigns that cell the most common cell - type among its $k$ nearest neighbors.' + type among its $k$ nearest neighbors. reference : "cover1967nearest" repository_url: https://github.com/scikit-learn/scikit-learn documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" - v1_url: openproblems/tasks/label_projection/methods/knn_classifier.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1: + path: openproblems/tasks/label_projection/methods/knn_classifier.py + commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm variants: knn_classifier_log_cpm: @@ -27,10 +28,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python - packages: scikit-learn + packages: [scikit-learn, jsonschema] - type: nextflow directives: label: [ midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 40918cec25..a6c20757a0 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -2,18 +2,19 @@ __merge__: ../../api/comp_method.yaml functionality: name: "logistic_regression" info: - pretty_name: Logistic Regression + label: Logistic Regression summary: "Logistic Regression with 100-dimensional PCA coordinates estimates parameters for multivariate classification by minimizing cross entropy loss over cell type classes." description: | - "Logistic Regression estimates parameters of a logistic function for + Logistic Regression estimates parameters of a logistic function for multivariate classification tasks. Here, we use 100-dimensional whitened PCA coordinates as independent variables, and the model minimises the cross - entropy loss over all cell type classes." + entropy loss over all cell type classes. reference: "hosmer2013applied" repository_url: https://github.com/scikit-learn/scikit-learn documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" - v1_url: openproblems/tasks/label_projection/methods/logistic_regression.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1: + path: openproblems/tasks/label_projection/methods/logistic_regression.py + commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm variants: logistic_regression_log_cpm: @@ -24,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index e0be583cbe..a6fe991468 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -2,21 +2,22 @@ __merge__: ../../api/comp_method.yaml functionality: name: "mlp" info: - pretty_name: Multilayer perceptron + label: Multilayer perceptron summary: "A neural network with 100-dimensional PCA input, two hidden layers, and gradient descent weight updates to minimize cross entropy loss." description: | - "Multi-Layer Perceptron is a type of artificial neural network that + Multi-Layer Perceptron is a type of artificial neural network that consists of multiple layers of interconnected neurons. Each neuron computes a weighted sum of all neurons in the previous layer and transforms it with nonlinear activation function. The output layer provides the final prediction, and network weights are updated by gradient descent to minimize the cross entropy loss. Here, the input data is 100-dimensional whitened PCA - coordinates for each cell, and we use two hidden layers of 100 neurons each." + coordinates for each cell, and we use two hidden layers of 100 neurons each. reference: "hinton1989connectionist" repository_url: https://github.com/scikit-learn/scikit-learn documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" - v1_url: openproblems/tasks/label_projection/methods/mlp.py - v1_commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + v1: + path: openproblems/tasks/label_projection/methods/mlp.py + commit: c2470ce02e6f196267cec1c554ba7ae389c0956a preferred_normalization: log_cpm variants: mlp_log_cpm: @@ -37,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index ddcfedc2b9..f765b07c98 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -2,21 +2,22 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" info: - pretty_name: SCANVI + label: SCANVI summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." description: | - "single-cell ANnotation using Variational Inference is a + single-cell ANnotation using Variational Inference is a semi-supervised variant of the scVI(Lopez et al. 2018) algorithm. Like scVI, scANVI uses deep neural networks and stochastic optimization to model uncertainty caused by technical noise and bias in single - cell transcriptomics measurements. However, scANVI also leverages cell type labels in the generative modelling. In this approach, scANVI is used to predict the - cell type labels of the unlabelled test data." + cell type labels of the unlabelled test data. reference: "lotfollahi2020query" repository_url: "https://github.com/YosefLab/scvi-tools" documentation_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html - v1_url: openproblems/tasks/label_projection/methods/scvi_tools.py - v1_commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 + v1: + path: openproblems/tasks/label_projection/methods/scvi_tools.py + commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 preferred_normalization: log_cpm variants: scanvi_all_genes: diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 68c5816d40..5057ca0b58 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: # Metadata for your component (required) info: - pretty_name: scANVI+scArches + label: scANVI+scArches summary: 'Query to reference single-cell integration with transfer learning with scANVI and scArches' description: 'scArches+scANVI or "Single-cell architecture surgery" is a deep learning method for mapping new datasets onto a pre-existing reference model, using transfer learning and parameter optimization. It first uses scANVI to build a reference model from the training data, and then apply scArches to map the test data onto the reference model and make predictions.' reference: lotfollahi2020query @@ -50,7 +50,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 # Add custom dependencies here setup: - type: python diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index fce9dfd48f..52b94f9f41 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -1,25 +1,23 @@ __merge__: ../../api/comp_method.yaml functionality: name: "seurat_transferdata" - description: | - The Seurat v3 anchoring procedure is designed to integrate - diverse single-cell datasets across technologies and modalities. info: - pretty_name: Seurat TransferData + label: Seurat TransferData summary: "Seurat reference mapping predicts cell types for unlabelled cells using PCA distances, labelled anchors, and transfer anchors from Seurat, with SCTransform normalization." description: | - "Seurat reference mapping is a cell type label transfer method provided by the + Seurat reference mapping is a cell type label transfer method provided by the Seurat package. Gene expression counts are first normalised by SCTransform before computing PCA. Then it finds mutual nearest neighbours, known as transfer anchors, between the labelled and unlabelled part of the data in PCA - space, and computes each cell’s distance to each of the anchor pairs. + space, and computes each cell's distance to each of the anchor pairs. Finally, it uses the labelled anchors to predict cell types for unlabelled - cells based on these distances." + cells based on these distances. reference: "hao2021integrated" repository_url: "https://github.com/satijalab/seurat" documentation_url: "https://satijalab.org/seurat/articles/integration_mapping.html" - v1_url: openproblems/tasks/label_projection/methods/seurat.py - v1_commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 + v1: + path: openproblems/tasks/label_projection/methods/seurat.py + commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 preferred_normalization: log_cpm variants: seurat: @@ -28,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base-r:latest + image: ghcr.io/openproblems-bio/base_r:1.0.0 setup: - type: r cran: [ Matrix, Seurat, rlang, bit64 ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index ee226617eb..c28d5a64ff 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -1,20 +1,20 @@ __merge__: ../../api/comp_method.yaml functionality: name: "xgboost" - description: "XGBoost: A Scalable Tree Boosting System" info: - pretty_name: XGBoost + label: XGBoost summary: "XGBoost is a decision tree model that averages multiple trees with gradient boosting." description: | - "XGBoost is a gradient boosting decision tree model that learns multiple tree + XGBoost is a gradient boosting decision tree model that learns multiple tree structures in the form of a series of input features and their values, leading to a prediction decision, and averages predictions from all its - trees. Here, input features are normalised gene expression values." + trees. Here, input features are normalised gene expression values. reference: "chen2016xgboost" repository_url: "https://github.com/dmlc/xgboost" documentation_url: "https://xgboost.readthedocs.io/en/stable/index.html" - v1_url: openproblems/tasks/label_projection/methods/xgboost.py - v1_commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c + v1: + path: openproblems/tasks/label_projection/methods/xgboost.py + commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c preferred_normalization: log_cpm variants: xgboost_log_cpm: @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: xgboost diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 5e81c0a633..b9bd67454d 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -2,25 +2,24 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "accuracy" info: - v1_url: openproblems/tasks/label_projection/metrics/accuracy.py - v1_commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 metrics: - name: accuracy - pretty_name: Accuracy + label: Accuracy summary: "The percentage of correctly predicted labels." description: "The percentage of correctly predicted labels." - reference: "" - repository_url: "" - documentation_url: "" min: 0 max: 1 maximize: true + reference: grandini2020metrics + v1: + path: openproblems/tasks/label_projection/metrics/accuracy.py + commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index 270de8be00..64746259de 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -2,45 +2,46 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "f1" info: - v1_url: openproblems/tasks/label_projection/metrics/f1.py - v1_commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 metrics: - name: f1_weighted - pretty_name: F1 weighted + label: F1 weighted summary: "Average weigthed support between each labels F1 score" description: "Calculates the F1 score for each label, and find their average weighted by support (the number of true instances for each label). This alters 'macro' to account for label imbalance; it can result in an F-score that is not between precision and recall." - reference: "" - repository_url: "" - documentation_url: "" + reference: grandini2020metrics min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/label_projection/metrics/f1.py + commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 - name: f1_macro - pretty_name: F1 macro + label: F1 macro summary: "Unweighted mean of each label F1-score" description: "Calculates the F1 score for each label, and find their unweighted mean. This does not take label imbalance into account." - reference: "" - repository_url: "" - documentation_url: "" + reference: grandini2020metrics min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/label_projection/metrics/f1.py + commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 - name: f1_micro - pretty_name: F1 micro + label: F1 micro summary: "Calculation of TP, FN and FP." description: "Calculates the F1 score globally by counting the total true positives, false negatives and false positives." - reference: "" - repository_url: "" - documentation_url: "" + reference: grandini2020metrics min: 0 max: 1 maximize: true + v1: + path: openproblems/tasks/label_projection/metrics/f1.py + commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index f600a75680..09bcd9fddf 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,5 +25,5 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base-python:latest + image: ghcr.io/openproblems-bio/base_python:1.0.0 - type: nextflow From e7e4d08fed7b1bdf4637eb189b02e314f336d6f5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Jun 2023 13:50:11 +0200 Subject: [PATCH 0922/1233] Refactor schemas (#185) * rename schemas * move schema files * rename once more Former-commit-id: 1f8c45e1c7da12e9673cc62da87ae78e95cb833a --- .vscode/settings.json | 12 +- src/common/api/schema_component_api.yaml | 67 - src/common/api/schema_task_info.yaml | 22 - src/common/api/schema_viash_config.yaml | 1931 -------------- src/common/schemas/api_component.yaml | 67 + .../api_file.yaml} | 10 +- .../defs_common.yaml} | 12 +- src/common/schemas/defs_viash.yaml | 2252 +++++++++++++++++ .../task_control_method.yaml} | 36 +- src/common/schemas/task_info.yaml | 22 + .../task_method.yaml} | 36 +- .../task_metric.yaml} | 36 +- 12 files changed, 2410 insertions(+), 2093 deletions(-) delete mode 100644 src/common/api/schema_component_api.yaml delete mode 100644 src/common/api/schema_task_info.yaml delete mode 100644 src/common/api/schema_viash_config.yaml create mode 100644 src/common/schemas/api_component.yaml rename src/common/{api/schema_file_api.yaml => schemas/api_file.yaml} (64%) rename src/common/{api/schema_definitions.yaml => schemas/defs_common.yaml} (95%) create mode 100644 src/common/schemas/defs_viash.yaml rename src/common/{api/schema_task_control_method.yaml => schemas/task_control_method.yaml} (57%) create mode 100644 src/common/schemas/task_info.yaml rename src/common/{api/schema_task_method.yaml => schemas/task_method.yaml} (54%) rename src/common/{api/schema_task_metric.yaml => schemas/task_metric.yaml} (63%) diff --git a/.vscode/settings.json b/.vscode/settings.json index 0c9aaaaeee..e662fc6472 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,10 +1,10 @@ { "yaml.schemas": { - "src/common/api/schema_component_api.yaml": "src/**/api/comp_*.yaml", - "src/common/api/schema_file_api.yaml": "src/**/api/file_*.yaml", - "src/common/api/schema_task_info.yaml": "src/**/api/task_info.yaml", - "src/common/api/schema_task_method.yaml": "src/tasks/**/methods/**/config.vsh.yaml", - "src/common/api/schema_task_control_method.yaml": "src/tasks/**/control_methods/**/config.vsh.yaml", - "src/common/api/schema_task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml" + "src/common/schemas/api_component.yaml": "src/**/api/comp_*.yaml", + "src/common/schemas/api_file.yaml": "src/**/api/file_*.yaml", + "src/common/schemas/task_info.yaml": "src/**/api/task_info.yaml", + "src/common/schemas/task_method.yaml": "src/tasks/**/methods/**/config.vsh.yaml", + "src/common/schemas/task_control_method.yaml": "src/tasks/**/control_methods/**/config.vsh.yaml", + "src/common/schemas/task_metric.yaml": "src/tasks/**/metrics/**/config.vsh.yaml" } } \ No newline at end of file diff --git a/src/common/api/schema_component_api.yaml b/src/common/api/schema_component_api.yaml deleted file mode 100644 index 59e5af958a..0000000000 --- a/src/common/api/schema_component_api.yaml +++ /dev/null @@ -1,67 +0,0 @@ -title: Component API -description: | - A component type specification file. -type: object -required: [functionality] -properties: - functionality: - type: object - description: Information regarding the functionality of the component. - required: [namespace, info, arguments, test_resources] - additionalProperties: false - properties: - namespace: - "$ref": "schema_definitions.yaml#/definitions/Namespace" - info: - type: object - description: Metadata of the component. - additionalProperties: false - required: [type, type_info] - properties: - type: - "$ref": "schema_definitions.yaml#/definitions/ComponentType" - subtype: - "$ref": "schema_definitions.yaml#/definitions/ComponentSubtype" - type_info: - type: object - description: Metadata related to the component type. - required: [label, summary, description] - properties: - label: - $ref: "schema_definitions.yaml#/definitions/Label" - summary: - $ref: "schema_definitions.yaml#/definitions/Summary" - description: - $ref: "schema_definitions.yaml#/definitions/Description" - arguments: - type: array - description: Component-specific parameters. - items: - anyOf: - - $ref: 'schema_definitions.yaml#/definitions/ComponentAPIFile' - - $ref: 'schema_viash_config.yaml#/definitions/BooleanArgument' - - $ref: 'schema_viash_config.yaml#/definitions/BooleanArgument' - - $ref: 'schema_viash_config.yaml#/definitions/BooleanTrueArgument' - - $ref: 'schema_viash_config.yaml#/definitions/BooleanFalseArgument' - - $ref: 'schema_viash_config.yaml#/definitions/DoubleArgument' - - $ref: 'schema_viash_config.yaml#/definitions/IntegerArgument' - - $ref: 'schema_viash_config.yaml#/definitions/LongArgument' - - $ref: 'schema_viash_config.yaml#/definitions/StringArgument' - resources: - type: array - description: Resources required to run the component. - items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" - test_resources: - type: array - description: One or more scripts and resources used to test the component. - items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" - platforms: - type: array - description: A list of platforms which Viash generates target artifacts for. - items: - anyOf: - - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" - - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" - - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_task_info.yaml b/src/common/api/schema_task_info.yaml deleted file mode 100644 index d903aaa1fa..0000000000 --- a/src/common/api/schema_task_info.yaml +++ /dev/null @@ -1,22 +0,0 @@ -title: Task info -description: A file format specification file. -type: object -additionalProperties: false -required: [name, label, summary, motivation, description] -properties: - name: - $ref: "schema_definitions.yaml#/definitions/Name" - label: - $ref: "schema_definitions.yaml#/definitions/Label" - summary: - $ref: "schema_definitions.yaml#/definitions/Summary" - motivation: - $ref: "schema_definitions.yaml#/definitions/Description" - description: - $ref: "schema_definitions.yaml#/definitions/Description" - v1: - $ref: "schema_definitions.yaml#/definitions/MigrationV1" - authors: - type: array - items: - $ref: "schema_definitions.yaml#/definitions/Author" diff --git a/src/common/api/schema_viash_config.yaml b/src/common/api/schema_viash_config.yaml deleted file mode 100644 index bad6d32a56..0000000000 --- a/src/common/api/schema_viash_config.yaml +++ /dev/null @@ -1,1931 +0,0 @@ -$schema: https://json-schema.org/draft-07/schema# -description: A schema for Viash config files -definitions: - Functionality: - description: | - The functionality-part of the config file describes the behaviour of the script in terms of arguments and resources. - By specifying a few restrictions (e.g. mandatory arguments) and adding some descriptions, Viash will automatically generate a stylish command-line interface for you. - type: object - properties: - name: - description: Name of the component and the filename of the executable when built with `viash build`. - type: string - enabled: - description: Setting this to false with disable this component when using namespaces. - type: boolean - tests: - description: One or more Bash/R/Python scripts to be used to test the component behaviour when `viash test` is invoked. Additional files of type `file` will be made available only during testing. Each test script should expect no command-line inputs, be platform-independent, and return an exit code >0 when unexpected behaviour occurs during testing. - type: array - items: - $ref: '#/definitions/Resource' - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - version: - description: Version of the component. This field will be used to version the executable and the Docker container. - type: string - inputs: - description: A list of input arguments in addition to the `arguments` list. Any arguments specified here will have their `type` set to `file` and the `direction` set to `input` by default. - type: array - items: - $ref: '#/definitions/Argument' - authors: - description: "A list of @[authors](author). An author must at least have a name, but can also have a list of roles, an e-mail address, and a map of custom properties.\n\nSuggested values for roles are:\n \n| Role | Abbrev. | Description |\n|------|---------|-------------|\n| maintainer | mnt | for the maintainer of the code. Ideally, exactly one maintainer is specified. |\n| author | aut | for persons who have made substantial contributions to the software. |\n| contributor | ctb| for persons who have made smaller contributions (such as code patches).\n| datacontributor | dtc | for persons or organisations that contributed data sets for the software\n| copyrightholder | cph | for all copyright holders. This is a legal concept so should use the legal name of an institution or corporate body.\n| funder | fnd | for persons or organizations that furnished financial support for the development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html) is extremely comprehensive.\n" - type: array - items: - $ref: '#/definitions/Author' - status: - description: Allows setting a component to active, deprecated or disabled. - $ref: '#/definitions/Status' - requirements: - description: "@[Computational requirements](computational_requirements) related to running the component. \n`cpus` specifies the maximum number of (logical) cpus a component is allowed to use., whereas\n`memory` specifies the maximum amount of memory a component is allowed to allicate. Memory units must be\nin B, KB, MB, GB, TB or PB." - $ref: '#/definitions/ComputationalRequirements' - resources: - description: | - @[Resources](resources) are files that support the component. The first resource should be @[a script](scripting_languages) that will be executed when the functionality is run. Additional resources will be copied to the same directory. - - Common properties: - - * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script` / `scala_script` / `csharp_script`, specifies the type of the resource. The first resource cannot be of type `file`. When the type is not specified, the default type is simply `file`. - * dest: filename, the resulting name of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - * path: `path/to/file`, the path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - * text: ...multiline text..., the content of the resulting file specified as a string. Mutually exclusive with `path`. - * is_executable: `true` / `false`, whether the resulting resource file should be made executable. - type: array - items: - $ref: '#/definitions/Resource' - test_resources: - description: One or more @[scripts](scripting_languages) to be used to test the component behaviour when `viash test` is invoked. Additional files of type `file` will be made available only during testing. Each test script should expect no command-line inputs, be platform-independent, and return an exit code >0 when unexpected behaviour occurs during testing. See @[Unit Testing](unit_testing) for more info. - type: array - items: - $ref: '#/definitions/Resource' - argument_groups: - description: "A grouping of the @[arguments](argument), used to display the help message.\n\n - `name: foo`, the name of the argument group. \n - `description: Description of foo`, a description of the argument group. Multiline descriptions are supported.\n - `arguments: [arg1, arg2, ...]`, list of the arguments names.\n\n" - type: array - items: - $ref: '#/definitions/ArgumentGroup' - description: - description: A description of the component. This will be displayed with `--help`. - type: string - usage: - description: A description on how to use the component. This will be displayed with `--help` under the 'Usage:' section. - type: string - add_resources_to_path: - description: Adds the resources directory to the PATH variable when set to true. This is set to false by default. - type: boolean - outputs: - description: A list of output arguments in addition to the `arguments` list. Any arguments specified here will have their `type` set to `file` and thr `direction` set to `output` by default. - type: array - items: - $ref: '#/definitions/Argument' - namespace: - description: Namespace this component is a part of. See the @[Namespaces guide](namespace) for more information on namespaces. - type: string - arguments: - description: "A list of @[arguments](argument) for this component. For each argument, a type and a name must be specified. Depending on the type of argument, different properties can be set. See these reference pages per type for more information: \n\n - @[string](arg_string)\n - @[file](arg_file)\n - @[integer](arg_integer)\n - @[double](arg_double)\n - @[boolean](arg_boolean)\n - @[boolean_true](arg_boolean_true)\n - @[boolean_false](arg_boolean_false)\n" - type: array - items: - $ref: '#/definitions/Argument' - additionalProperties: false - NativePlatform: - description: | - Running a Viash component on a native platform means that the script will be executed in your current environment. - Any dependencies are assumed to have been installed by the user, so the native platform is meant for developers (who know what they're doing) or for simple bash scripts (which have no extra dependencies). - type: object - properties: - id: - description: 'As with all platforms, you can give a platform a different name. By specifying `id: foo`, you can target this platform (only) by specifying `-p foo` in any of the Viash commands.' - type: string - type: - description: | - Running a Viash component on a native platform means that the script will be executed in your current environment. - Any dependencies are assumed to have been installed by the user, so the native platform is meant for developers (who know what they're doing) or for simple bash scripts (which have no extra dependencies). - const: native - additionalProperties: false - DockerPlatform: - description: | - Run a Viash component on a Docker backend platform. - By specifying which dependencies your component needs, users will be able to build a docker container from scratch using the setup flag, or pull it from a docker repository. - type: object - properties: - organization: - description: Name of a container's [organization](https://docs.docker.com/docker-hub/orgs/). - type: string - registry: - description: The URL to the a [custom Docker registry](https://docs.docker.com/registry/) - type: string - image: - description: The base container to start from. You can also add the tag here if you wish. - type: string - tag: - description: Specify a Docker image based on its tag. - type: string - target_tag: - description: The tag the resulting image gets. Advanced usage only. - type: string - run_args: - anyOf: - - description: Add [docker run](https://docs.docker.com/engine/reference/run/) arguments. - type: string - - description: Add [docker run](https://docs.docker.com/engine/reference/run/) arguments. - type: array - items: - type: string - namespace_separator: - description: 'The separator between the namespace and the name of the component, used for determining the image name. Default: `"/"`.' - type: string - resolve_volume: - description: 'Enables or disables automatic volume mapping. Enabled when set to `Automatic` or disabled when set to `Manual`. Default: `Automatic`.' - $ref: '#/definitions/DockerResolveVolume' - port: - anyOf: - - description: A list of enabled ports. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. - type: string - - description: A list of enabled ports. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. - type: array - items: - type: string - python: - description: Specify which Python packages should be available in order to run the component. - $ref: '#/definitions/PythonRequirements' - setup: - description: | - A list of requirements for installing the following types of packages: - - - @[apt](apt_req) - - @[apk](apk_req) - - @[Docker setup instructions](docker_req) - - @[JavaScript](javascript_req) - - @[Python](python_req) - - @[R](r_req) - - @[Ruby](ruby_req) - - @[yum](yum_req) - - The order in which these dependencies are specified determines the order in which they will be installed. - type: array - items: - $ref: '#/definitions/Requirements' - workdir: - description: The working directory when starting the container. This doesn't change the Dockerfile but gets added as a command-line argument at runtime. - type: string - apk: - description: Specify which apk packages should be available in order to run the component. - $ref: '#/definitions/ApkRequirements' - target_image: - description: If anything is specified in the setup section, running the `---setup` will result in an image with the name of `:`. If nothing is specified in the `setup` section, simply `image` will be used. Advanced usage only. - type: string - cmd: - anyOf: - - description: Set the default command being executed when running the Docker container. - type: string - - description: Set the default command being executed when running the Docker container. - type: array - items: - type: string - yum: - description: Specify which yum packages should be available in order to run the component. - $ref: '#/definitions/YumRequirements' - target_image_source: - description: The source of the target image. This is used for defining labels in the dockerfile. - type: string - test_setup: - description: Additional requirements specific for running unit tests. - type: array - items: - $ref: '#/definitions/Requirements' - entrypoint: - anyOf: - - description: Override the entrypoint of the base container. Default set `ENTRYPOINT []`. - type: string - - description: Override the entrypoint of the base container. Default set `ENTRYPOINT []`. - type: array - items: - type: string - docker: - description: Specify which Docker commands should be run during setup. - $ref: '#/definitions/DockerRequirements' - id: - description: 'As with all platforms, you can give a platform a different name. By specifying `id: foo`, you can target this platform (only) by specifying `-p foo` in any of the Viash commands.' - type: string - apt: - description: Specify which apt packages should be available in order to run the component. - $ref: '#/definitions/AptRequirements' - target_registry: - description: The URL where the resulting image will be pushed to. Advanced usage only. - type: string - privileged: - description: Adds a `privileged` flag to the docker run. - type: boolean - setup_strategy: - description: |+ - The Docker setup strategy to use when building a container. - - | Strategy | Description | - |-----|----------| - | `alwaysbuild` / `build` / `b` | Always build the image from the dockerfile. This is the default setup strategy. - | `alwayscachedbuild` / `cachedbuild` / `cb` | Always build the image from the dockerfile, with caching enabled. - | `ifneedbebuild` | Build the image if it does not exist locally. - | `ifneedbecachedbuild` | Build the image with caching enabled if it does not exist locally, with caching enabled. - | `alwayspull` / `pull` / `p` | Try to pull the container from [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry). - | `alwayspullelsebuild` / `pullelsebuild` | Try to pull the image from a registry and build it if it doesn't exist. - | `alwayspullelsecachedbuild` / `pullelsecachedbuild` | Try to pull the image from a registry and build it with caching if it doesn't exist. - | `ifneedbepull` | If the image does not exist locally, pull the image. - | `ifneedbepullelsebuild` | If the image does not exist locally, pull the image. If the image does exist, build it. - | `ifneedbepullelsecachedbuild` | If the image does not exist locally, pull the image. If the image does exist, build it with caching enabled. - | `push` | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry). - | `pushifnotpresent` | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry) if the @[tag](docker_tag) does not exist yet. - | `donothing` / `meh` | Do not build or pull anything. - - $ref: '#/definitions/DockerSetupStrategy' - r: - description: Specify which R packages should be available in order to run the component. - $ref: '#/definitions/RRequirements' - type: - description: | - Run a Viash component on a Docker backend platform. - By specifying which dependencies your component needs, users will be able to build a docker container from scratch using the setup flag, or pull it from a docker repository. - const: docker - target_organization: - description: The organization set in the resulting image. Advanced usage only. - type: string - chown: - description: 'In Linux, files created by a Docker container will be owned by `root`. With `chown: true`, Viash will automatically change the ownership of output files (arguments with `type: file` and `direction: output`) to the user running the Viash command after execution of the component. Default value: `true`.' - type: boolean - additionalProperties: false - NextflowVdsl3Platform: - description: Next-gen platform for generating NextFlow VDSL3 modules. - type: object - properties: - auto: - description: |+ - @[Automated processing flags](nextflow_auto) which can be toggled on or off: - - | Flag | Description | Default | - |---|---------|----| - | `simplifyInput` | If `true`, an input tuple only containing only a single File (e.g. `["foo", file("in.h5ad")]`) is automatically transformed to a map (i.e. `["foo", [ input: file("in.h5ad") ] ]`). | `true` | - | `simplifyOutput` | If `true`, an output tuple containing a map with a File (e.g. `["foo", [ output: file("out.h5ad") ] ]`) is automatically transformed to a map (i.e. `["foo", file("out.h5ad")]`). | `true` | - | `transcript` | If `true`, the module's transcripts from `work/` are automatically published to `params.transcriptDir`. If not defined, `params.publishDir + "/_transcripts"` will be used. Will throw an error if neither are defined. | `false` | - | `publish` | If `true`, the module's outputs are automatically published to `params.publishDir`. Will throw an error if `params.publishDir` is not defined. | `false` | - - $ref: '#/definitions/NextflowAuto' - directives: - description: "@[Directives](nextflow_directives) are optional settings that affect the execution of the process. These mostly match up with the Nextflow counterparts. \n" - $ref: '#/definitions/NextflowDirectives' - container: - description: Specifies the Docker platform id to be used to run Nextflow. - type: string - debug: - description: Whether or not to print debug messages. - type: boolean - id: - description: Every platform can be given a specific id that can later be referred to explicitly when running or building the Viash component. - type: string - type: - description: Next-gen platform for generating NextFlow VDSL3 modules. - const: nextflow - config: - description: Allows tweaking how the @[Nextflow Config](nextflow_config) file is generated. - $ref: '#/definitions/NextflowConfig' - additionalProperties: false - Platforms: - anyOf: - - $ref: '#/definitions/NativePlatform' - - $ref: '#/definitions/DockerPlatform' - - $ref: '#/definitions/NextflowVdsl3Platform' - Info: - description: Definition of meta data - type: object - properties: - config: - type: string - platform: - type: string - output: - type: string - executable: - type: string - viash_version: - type: string - git_commit: - type: string - git_remote: - type: string - git_tag: - type: string - additionalProperties: false - Author: - description: Author metadata. - type: object - properties: - name: - description: Full name of the author, usually in the name of FirstName MiddleName LastName. - type: string - email: - description: E-mail of the author. - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - roles: - anyOf: - - description: | - Role of the author. Suggested items: - - * `"author"`: Authors who have made substantial contributions to the component. - * `"maintainer"`: The maintainer of the component. - * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.). - type: string - - description: | - Role of the author. Suggested items: - - * `"author"`: Authors who have made substantial contributions to the component. - * `"maintainer"`: The maintainer of the component. - * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.). - type: array - items: - type: string - props: - description: Author properties. Must be a map of strings. - type: object - additionalProperties: - description: Author properties. Must be a map of strings. - type: string - additionalProperties: false - ComputationalRequirements: - description: Computational requirements related to running the component. - type: object - properties: - n_proc: - description: "" - type: integer - cpus: - description: The maximum number of (logical) cpus a component is allowed to use. - type: integer - commands: - description: A list of commands which should be present on the system for the script to function. - type: array - items: - type: string - memory: - description: The maximum amount of memory a component is allowed to allocate. Unit must be one of B, KB, MB, GB, TB or PB. - type: string - additionalProperties: false - ApkRequirements: - description: Specify which apk packages should be available in order to run the component. - type: object - properties: - type: - description: Specify which apk packages should be available in order to run the component. - const: apk - packages: - anyOf: - - description: Specifies which packages to install. - type: string - - description: Specifies which packages to install. - type: array - items: - type: string - additionalProperties: false - AptRequirements: - description: Specify which apt packages should be available in order to run the component. - type: object - properties: - interactive: - description: 'If `false`, the Debian frontend is set to non-interactive (recommended). Default: false.' - type: boolean - type: - description: Specify which apt packages should be available in order to run the component. - const: apt - packages: - anyOf: - - description: Specifies which packages to install. - type: string - - description: Specifies which packages to install. - type: array - items: - type: string - additionalProperties: false - DockerRequirements: - description: Specify which Docker commands should be run during setup. - type: object - properties: - run: - anyOf: - - description: Specifies which `RUN` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `RUN` entries to add to the Dockerfile while building it. - type: array - items: - type: string - label: - anyOf: - - description: Specifies which `LABEL` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `LABEL` entries to add to the Dockerfile while building it. - type: array - items: - type: string - build_args: - anyOf: - - description: Specifies which `ARG` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `ARG` entries to add to the Dockerfile while building it. - type: array - items: - type: string - type: - description: Specify which Docker commands should be run during setup. - const: docker - add: - anyOf: - - description: Specifies which `ADD` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `ADD` entries to add to the Dockerfile while building it. - type: array - items: - type: string - env: - anyOf: - - description: Specifies which `ENV` entries to add to the Dockerfile while building it. Unlike `ARG`, `ENV` entries are also accessible from inside the container. - type: string - - description: Specifies which `ENV` entries to add to the Dockerfile while building it. Unlike `ARG`, `ENV` entries are also accessible from inside the container. - type: array - items: - type: string - resources: - anyOf: - - description: Specifies which `COPY` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `COPY` entries to add to the Dockerfile while building it. - type: array - items: - type: string - copy: - anyOf: - - description: Specifies which `COPY` entries to add to the Dockerfile while building it. - type: string - - description: Specifies which `COPY` entries to add to the Dockerfile while building it. - type: array - items: - type: string - additionalProperties: false - JavascriptRequirements: - description: Specify which JavaScript packages should be available in order to run the component. - type: object - properties: - github: - anyOf: - - description: Specifies which packages to install from GitHub. - type: string - - description: Specifies which packages to install from GitHub. - type: array - items: - type: string - url: - anyOf: - - description: Specifies which packages to install using a generic URI. - type: string - - description: Specifies which packages to install using a generic URI. - type: array - items: - type: string - git: - anyOf: - - description: Specifies which packages to install using a Git URI. - type: string - - description: Specifies which packages to install using a Git URI. - type: array - items: - type: string - npm: - anyOf: - - description: Specifies which packages to install from npm. - type: string - - description: Specifies which packages to install from npm. - type: array - items: - type: string - type: - description: Specify which JavaScript packages should be available in order to run the component. - const: javascript - packages: - anyOf: - - description: Specifies which packages to install from npm. - type: string - - description: Specifies which packages to install from npm. - type: array - items: - type: string - additionalProperties: false - PythonRequirements: - description: Specify which Python packages should be available in order to run the component. - type: object - properties: - github: - anyOf: - - description: Specifies which packages to install from GitHub. - type: string - - description: Specifies which packages to install from GitHub. - type: array - items: - type: string - gitlab: - anyOf: - - description: Specifies which packages to install from GitLab. - type: string - - description: Specifies which packages to install from GitLab. - type: array - items: - type: string - pip: - anyOf: - - description: Specifies which packages to install from pip. - type: string - - description: Specifies which packages to install from pip. - type: array - items: - type: string - pypi: - anyOf: - - description: Specifies which packages to install from PyPI using pip. - type: string - - description: Specifies which packages to install from PyPI using pip. - type: array - items: - type: string - git: - anyOf: - - description: Specifies which packages to install using a Git URI. - type: string - - description: Specifies which packages to install using a Git URI. - type: array - items: - type: string - upgrade: - description: 'Sets the `--upgrade` flag when set to true. Default: true.' - type: boolean - packages: - anyOf: - - description: Specifies which packages to install from pip. - type: string - - description: Specifies which packages to install from pip. - type: array - items: - type: string - url: - anyOf: - - description: Specifies which packages to install using a generic URI. - type: string - - description: Specifies which packages to install using a generic URI. - type: array - items: - type: string - svn: - anyOf: - - description: Specifies which packages to install using an SVN URI. - type: string - - description: Specifies which packages to install using an SVN URI. - type: array - items: - type: string - bazaar: - anyOf: - - description: Specifies which packages to install using a Bazaar URI. - type: string - - description: Specifies which packages to install using a Bazaar URI. - type: array - items: - type: string - script: - anyOf: - - description: Specifies a code block to run as part of the build. - type: string - - description: Specifies a code block to run as part of the build. - type: array - items: - type: string - type: - description: Specify which Python packages should be available in order to run the component. - const: python - mercurial: - anyOf: - - description: Specifies which packages to install using a Mercurial URI. - type: string - - description: Specifies which packages to install using a Mercurial URI. - type: array - items: - type: string - user: - description: 'Sets the `--user` flag when set to true. Default: false.' - type: boolean - additionalProperties: false - RRequirements: - description: Specify which R packages should be available in order to run the component. - type: object - properties: - bioc: - anyOf: - - description: Specifies which packages to install from BioConductor. - type: string - - description: Specifies which packages to install from BioConductor. - type: array - items: - type: string - github: - anyOf: - - description: Specifies which packages to install from GitHub. - type: string - - description: Specifies which packages to install from GitHub. - type: array - items: - type: string - gitlab: - anyOf: - - description: Specifies which packages to install from GitLab. - type: string - - description: Specifies which packages to install from GitLab. - type: array - items: - type: string - url: - anyOf: - - description: Specifies which packages to install using a generic URI. - type: string - - description: Specifies which packages to install using a generic URI. - type: array - items: - type: string - bioc_force_install: - description: 'Forces packages specified in `bioc` to be reinstalled, even if they are already present in the container. Default: false.' - type: boolean - git: - anyOf: - - description: Specifies which packages to install using a Git URI. - type: string - - description: Specifies which packages to install using a Git URI. - type: array - items: - type: string - cran: - anyOf: - - description: Specifies which packages to install from CRAN. - type: string - - description: Specifies which packages to install from CRAN. - type: array - items: - type: string - bitbucket: - anyOf: - - description: Specifies which packages to install from Bitbucket. - type: string - - description: Specifies which packages to install from Bitbucket. - type: array - items: - type: string - svn: - anyOf: - - description: Specifies which packages to install using an SVN URI. - type: string - - description: Specifies which packages to install using an SVN URI. - type: array - items: - type: string - packages: - anyOf: - - description: Specifies which packages to install from CRAN. - type: string - - description: Specifies which packages to install from CRAN. - type: array - items: - type: string - script: - anyOf: - - description: Specifies a code block to run as part of the build. - type: string - - description: Specifies a code block to run as part of the build. - type: array - items: - type: string - type: - description: Specify which R packages should be available in order to run the component. - const: r - additionalProperties: false - RubyRequirements: - description: Specify which Ruby packages should be available in order to run the component. - type: object - properties: - type: - description: Specify which Ruby packages should be available in order to run the component. - const: ruby - packages: - anyOf: - - description: Specifies which packages to install. - type: string - - description: Specifies which packages to install. - type: array - items: - type: string - additionalProperties: false - YumRequirements: - description: Specify which yum packages should be available in order to run the component. - type: object - properties: - type: - description: Specify which yum packages should be available in order to run the component. - const: yum - packages: - anyOf: - - description: Specifies which packages to install. - type: string - - description: Specifies which packages to install. - type: array - items: - type: string - additionalProperties: false - Requirements: - anyOf: - - $ref: '#/definitions/ApkRequirements' - - $ref: '#/definitions/AptRequirements' - - $ref: '#/definitions/DockerRequirements' - - $ref: '#/definitions/JavascriptRequirements' - - $ref: '#/definitions/PythonRequirements' - - $ref: '#/definitions/RRequirements' - - $ref: '#/definitions/RubyRequirements' - - $ref: '#/definitions/YumRequirements' - BooleanArgument: - description: 'A `boolean` type argument has two possible values: `true` or `false`.' - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--trim`, `-t` or `trim`. The number of dashes determines how values can be passed: \n\n - `--trim` is a long option, which can be passed with `executable_name --trim`\n - `-t` is a short option, which can be passed with `executable_name -t`\n - `trim` is an argument, which can be passed with `executable_name trim` \n" - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: boolean - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: boolean - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: boolean - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: boolean - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: 'A `boolean` type argument has two possible values: `true` or `false`.' - const: boolean - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - BooleanTrueArgument: - description: An argument of the `boolean_true` type acts like a `boolean` flag with a default value of `false`. When called as an argument it sets the `boolean` to `true`. - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--silent`, `-s` or `silent`. The number of dashes determines how values can be passed: \n\n - `--silent` is a long option, which can be passed with `executable_name --silent`\n - `-s` is a short option, which can be passed with `executable_name -s`\n - `silent` is an argument, which can be passed with `executable_name silent` \n" - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - type: - description: An argument of the `boolean_true` type acts like a `boolean` flag with a default value of `false`. When called as an argument it sets the `boolean` to `true`. - const: boolean_true - additionalProperties: false - BooleanFalseArgument: - description: An argument of the `boolean_false` type acts like an inverted `boolean` flag with a default value of `true`. When called as an argument it sets the `boolean` to `false`. - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--no-log`, `-n` or `no-log`. The number of dashes determines how values can be passed: \n\n - `--no-log` is a long option, which can be passed with `executable_name --no-log`\n - `-n` is a short option, which can be passed with `executable_name -n`\n - `no-log` is an argument, which can be passed with `executable_name no-log` \n" - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - type: - description: An argument of the `boolean_false` type acts like an inverted `boolean` flag with a default value of `true`. When called as an argument it sets the `boolean` to `false`. - const: boolean_false - additionalProperties: false - DoubleArgument: - description: A `double` type argument has a numeric value with decimal points - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - max: - description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. - type: number - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: number - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: number - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: number - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: number - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - min: - description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. - type: number - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: A `double` type argument has a numeric value with decimal points - const: double - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - FileArgument: - description: A `file` type argument has a string value that points to a file or folder path. - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" - type: string - create_parent: - description: 'If the output filename is a path and it does not exist, create it before executing the script (only for `direction: output`).' - type: boolean - direction: - description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. - $ref: '#/definitions/Direction' - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - must_exist: - description: Checks whether the file or folder exists. For input files, this check will happen before the execution of the script, while for output files the check will happen afterwards. - type: boolean - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: string - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: string - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: string - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: string - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: A `file` type argument has a string value that points to a file or folder path. - const: file - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - IntegerArgument: - description: An `integer` type argument has a numeric value without decimal points. - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" - type: string - choices: - description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. - type: array - items: - type: integer - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - max: - description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. - type: integer - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: integer - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: integer - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: integer - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: integer - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - min: - description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. - type: integer - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: An `integer` type argument has a numeric value without decimal points. - const: integer - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - LongArgument: - description: An `long` type argument has a numeric value without decimal points. - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" - type: string - choices: - description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. - type: array - items: - type: integer - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - max: - description: Maximum allowed value for this argument. If set and the provided value is higher than the maximum, an error will be produced. Can be combined with [`min`](#min) to clamp values. - type: integer - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: integer - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: integer - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: integer - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: integer - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - min: - description: Minimum allowed value for this argument. If set and the provided value is lower than the minimum, an error will be produced. Can be combined with [`max`](#max) to clamp values. - type: integer - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: An `long` type argument has a numeric value without decimal points. - const: long - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - StringArgument: - description: A `string` type argument has a value made up of an ordered sequences of characters, like "Hello" or "I'm a string". - type: object - properties: - alternatives: - anyOf: - - description: List of alternative format variations for this argument. - type: string - - description: List of alternative format variations for this argument. - type: array - items: - type: string - name: - description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed: \n\n - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n - `-f` is a short option, which can be passed with `executable_name -f value`\n - `foo` is an argument, which can be passed with `executable_name value` \n" - type: string - choices: - description: Limit the amount of valid values for this argument to those set in this list. When set and a value not present in the list is provided, an error will be produced. - type: array - items: - type: string - info: - description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' - type: object - default: - anyOf: - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: string - - description: The default value when no argument value is provided. This will not work if the [`required`](#required) property is enabled. - type: array - items: - type: string - example: - anyOf: - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: string - - description: An example value for this argument. If no [`default`](#default) property was specified, this will be used for that purpose. - type: array - items: - type: string - description: - description: A description of the argument. This will be displayed with `--help`. - type: string - multiple_sep: - description: The delimiter character for providing [`multiple`](#multiple) values. `:` by default. - type: string - multiple: - description: Treat the argument value as an array. Arrays can be passed using the delimiter `--foo=1:2:3` or by providing the same argument multiple times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep) property. `false` by default. - type: boolean - type: - description: A `string` type argument has a value made up of an ordered sequences of characters, like "Hello" or "I'm a string". - const: string - required: - description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default. - type: boolean - additionalProperties: false - Argument: - anyOf: - - $ref: '#/definitions/BooleanArgument' - - $ref: '#/definitions/BooleanTrueArgument' - - $ref: '#/definitions/BooleanFalseArgument' - - $ref: '#/definitions/DoubleArgument' - - $ref: '#/definitions/FileArgument' - - $ref: '#/definitions/IntegerArgument' - - $ref: '#/definitions/LongArgument' - - $ref: '#/definitions/StringArgument' - ArgumentGroup: - type: object - properties: - name: - description: The name of the argument group. - type: string - description: - description: A description of the argument group. Multiline descriptions are supported. - type: string - arguments: - description: List of the arguments names. - type: array - items: - $ref: '#/definitions/Argument' - required: - - name - - arguments - additionalProperties: false - BashScript: - description: |- - An executable Bash script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable Bash script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: bash_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - CSharpScript: - description: |- - An executable C# script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable C# script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: csharp_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - Executable: - description: An executable file. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: An executable file. - const: executable - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - JavaScriptScript: - description: |- - An executable JavaScript script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable JavaScript script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: javascript_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - NextflowScript: - description: A Nextflow script. Work in progress; added mainly for annotation at the moment. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - entrypoint: - description: The name of the workflow to be executed. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: A Nextflow script. Work in progress; added mainly for annotation at the moment. - const: nextflow_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - PlainFile: - description: A plain file. This can only be used as a supporting resource for the main script or unit tests. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: A plain file. This can only be used as a supporting resource for the main script or unit tests. - const: file - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - PythonScript: - description: |- - An executable Python script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable Python script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: python_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - RScript: - description: |- - An executable R script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable R script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: r_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - ScalaScript: - description: |- - An executable Scala script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - type: object - properties: - path: - description: The path of the input file. Can be a relative or an absolute path, or a URI. Mutually exclusive with `text`. - type: string - text: - description: The content of the resulting file specified as a string. Mutually exclusive with `path`. - type: string - is_executable: - description: Whether the resulting resource file should be made executable. - type: boolean - type: - description: |- - An executable Scala script. - When defined in functionality.resources, only the first entry will be executed when running the built component or when running `viash run`. - When defined in functionality.test_resources, all entries will be executed during `viash test`. - const: scala_script - dest: - description: Resulting filename of the resource. From within a script, the file can be accessed at `meta["resources_dir"] + "/" + dest`. If unspecified, `dest` will be set to the basename of the `path` parameter. - type: string - additionalProperties: false - Resource: - anyOf: - - $ref: '#/definitions/BashScript' - - $ref: '#/definitions/CSharpScript' - - $ref: '#/definitions/Executable' - - $ref: '#/definitions/JavaScriptScript' - - $ref: '#/definitions/NextflowScript' - - $ref: '#/definitions/PlainFile' - - $ref: '#/definitions/PythonScript' - - $ref: '#/definitions/RScript' - - $ref: '#/definitions/ScalaScript' - NextflowDirectives: - description: | - Directives are optional settings that affect the execution of the process. - type: object - properties: - beforeScript: - description: | - The `beforeScript` directive allows you to execute a custom (Bash) snippet before the main process script is run. This may be useful to initialise the underlying cluster environment or for other custom initialisation. - - See [`beforeScript`](https://www.nextflow.io/docs/latest/process.html#beforeScript). - type: string - module: - anyOf: - - description: | - Environment Modules is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool. - - If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline. - - In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. - - See [`module`](https://www.nextflow.io/docs/latest/process.html#module). - type: string - - description: | - Environment Modules is a package manager that allows you to dynamically configure your execution environment and easily switch between multiple versions of the same software tool. - - If it is available in your system you can use it with Nextflow in order to configure the processes execution environment in your pipeline. - - In a process definition you can use the `module` directive to load a specific module version to be used in the process execution environment. - - See [`module`](https://www.nextflow.io/docs/latest/process.html#module). - type: array - items: - type: string - queue: - anyOf: - - description: | - The `queue` directory allows you to set the queue where jobs are scheduled when using a grid based executor in your pipeline. - - See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue). - type: string - - description: | - The `queue` directory allows you to set the queue where jobs are scheduled when using a grid based executor in your pipeline. - - See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue). - type: array - items: - type: string - label: - anyOf: - - description: | - The `label` directive allows the annotation of processes with mnemonic identifier of your choice. - - See [`label`](https://www.nextflow.io/docs/latest/process.html#label). - type: string - - description: | - The `label` directive allows the annotation of processes with mnemonic identifier of your choice. - - See [`label`](https://www.nextflow.io/docs/latest/process.html#label). - type: array - items: - type: string - container: - anyOf: - - description: | - The `container` directive allows you to execute the process script in a Docker container. - - It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. - - Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. - - See [`container`](https://www.nextflow.io/docs/latest/process.html#container). - type: object - additionalProperties: - description: | - The `container` directive allows you to execute the process script in a Docker container. - - It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. - - Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. - - See [`container`](https://www.nextflow.io/docs/latest/process.html#container). - type: string - - description: | - The `container` directive allows you to execute the process script in a Docker container. - - It requires the Docker daemon to be running in machine where the pipeline is executed, i.e. the local machine when using the local executor or the cluster nodes when the pipeline is deployed through a grid executor. - - Viash implements allows either a string value or a map. In case a map is used, the allowed keys are: `registry`, `image`, and `tag`. The `image` value must be specified. - - See [`container`](https://www.nextflow.io/docs/latest/process.html#container). - type: string - publishDir: - anyOf: - - anyOf: - - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: string - - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: object - additionalProperties: - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: string - - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: array - items: - anyOf: - - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: string - - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: object - additionalProperties: - description: | - The `publishDir` directive allows you to publish the process output files to a specified folder. - - Viash implements this directive as a plain string or a map. The allowed keywords for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key and value are required. - The allowed values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. - - See [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir). - type: string - maxForks: - anyOf: - - description: | - The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1. - - If you want to execute a process in a sequential manner, set this directive to one. - - See [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks). - type: string - - description: | - The `maxForks` directive allows you to define the maximum number of process instances that can be executed in parallel. By default this value is equals to the number of CPU cores available minus 1. - - If you want to execute a process in a sequential manner, set this directive to one. - - See [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks). - type: integer - maxErrors: - anyOf: - - description: | - The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled. - - See [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors). - type: string - - description: | - The `maxErrors` directive allows you to specify the maximum number of times a process can fail when using the `retry` error strategy. By default this directive is disabled. - - See [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors). - type: integer - cpus: - anyOf: - - description: | - The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. - - See [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus). - type: integer - - description: | - The `cpus` directive allows you to define the number of (logical) CPU required by the process' task. - - See [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus). - type: string - accelerator: - description: | - The `accelerator` directive allows you to specify the hardware accelerator requirement for the task execution e.g. GPU processor. - - Viash implements this directive as a map with accepted keywords: `type`, `limit`, `request`, and `runtime`. - - See [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator). - type: object - additionalProperties: - description: | - The `accelerator` directive allows you to specify the hardware accelerator requirement for the task execution e.g. GPU processor. - - Viash implements this directive as a map with accepted keywords: `type`, `limit`, `request`, and `runtime`. - - See [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator). - type: string - time: - description: | - The `time` directive allows you to define how long a process is allowed to run. - - See [`time`](https://www.nextflow.io/docs/latest/process.html#time). - type: string - afterScript: - description: | - The `afterScript` directive allows you to execute a custom (Bash) snippet immediately after the main process has run. This may be useful to clean up your staging area. - - See [`afterScript`](https://www.nextflow.io/docs/latest/process.html#afterscript). - type: string - executor: - description: "The `executor` defines the underlying system where processes are executed. By default a process uses the executor defined globally in the nextflow.config file.\n\nThe `executor` directive allows you to configure what executor has to be used by the process, overriding the default configuration. The following values can be used:\n\n| Name | Executor |\n|------|----------|\n| awsbatch | The process is executed using the AWS Batch service. | \n| azurebatch | The process is executed using the Azure Batch service. | \n| condor | The process is executed using the HTCondor job scheduler. | \n| google-lifesciences | The process is executed using the Google Genomics Pipelines service. | \n| ignite | The process is executed using the Apache Ignite cluster. | \n| k8s | The process is executed using the Kubernetes cluster. | \n| local | The process is executed in the computer where Nextflow is launched. | \n| lsf | The process is executed using the Platform LSF job scheduler. | \n| moab | The process is executed using the Moab job scheduler. | \n| nqsii | The process is executed using the NQSII job scheduler. | \n| oge | Alias for the sge executor. | \n| pbs | The process is executed using the PBS/Torque job scheduler. | \n| pbspro | The process is executed using the PBS Pro job scheduler. | \n| sge | The process is executed using the Sun Grid Engine / Open Grid Engine. | \n| slurm | The process is executed using the SLURM job scheduler. | \n| tes | The process is executed using the GA4GH TES service. | \n| uge | Alias for the sge executor. |\n\nSee [`executor`](https://www.nextflow.io/docs/latest/process.html#executor).\n" - type: string - containerOptions: - anyOf: - - description: | - The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path. - - See [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions). - type: string - - description: | - The `containerOptions` directive allows you to specify any container execution option supported by the underlying container engine (ie. Docker, Singularity, etc). This can be useful to provide container settings only for a specific process e.g. mount a custom path. - - See [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions). - type: array - items: - type: string - disk: - description: | - The `disk` directive allows you to define how much local disk storage the process is allowed to use. - - See [`disk`](https://www.nextflow.io/docs/latest/process.html#disk). - type: string - tag: - description: | - The `tag` directive allows you to associate each process execution with a custom label, so that it will be easier to identify them in the log file or in the trace execution report. - - See [`tag`](https://www.nextflow.io/docs/latest/process.html#tag). - type: string - conda: - anyOf: - - description: | - The `conda` directive allows for the definition of the process dependencies using the Conda package manager. - - Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. - - See [`conda`](https://www.nextflow.io/docs/latest/process.html#conda). - type: string - - description: | - The `conda` directive allows for the definition of the process dependencies using the Conda package manager. - - Nextflow automatically sets up an environment for the given package names listed by in the `conda` directive. - - See [`conda`](https://www.nextflow.io/docs/latest/process.html#conda). - type: array - items: - type: string - machineType: - description: |2 - The `machineType` can be used to specify a predefined Google Compute Platform machine type when running using the Google Life Sciences executor. - - See [`machineType`](https://www.nextflow.io/docs/latest/process.html#machinetype). - type: string - stageInMode: - description: "The `stageInMode` directive defines how input files are staged-in to the process work directory. The following values are allowed:\n\n| Value | Description |\n|-------|-------------| \n| copy | Input files are staged in the process work directory by creating a copy. | \n| link | Input files are staged in the process work directory by creating an (hard) link for each of them. | \n| symlink | Input files are staged in the process work directory by creating a symbolic link with an absolute path for each of them (default). | \n| rellink | Input files are staged in the process work directory by creating a symbolic link with a relative path for each of them. | \n\nSee [`stageInMode`](https://www.nextflow.io/docs/latest/process.html#stageinmode).\n" - type: string - cache: - anyOf: - - description: | - The `cache` directive allows you to store the process results to a local cache. When the cache is enabled and the pipeline is launched with the resume option, any following attempt to execute the process, along with the same inputs, will cause the process execution to be skipped, producing the stored data as the actual results. - - The caching feature generates a unique key by indexing the process script and inputs. This key is used to identify univocally the outputs produced by the process execution. - - The `cache` is enabled by default, you can disable it for a specific process by setting the cache directive to `false`. - - Accepted values are: `true`, `false`, `"deep"`, and `"lenient"`. - - See [`cache`](https://www.nextflow.io/docs/latest/process.html#cache). - type: boolean - - description: | - The `cache` directive allows you to store the process results to a local cache. When the cache is enabled and the pipeline is launched with the resume option, any following attempt to execute the process, along with the same inputs, will cause the process execution to be skipped, producing the stored data as the actual results. - - The caching feature generates a unique key by indexing the process script and inputs. This key is used to identify univocally the outputs produced by the process execution. - - The `cache` is enabled by default, you can disable it for a specific process by setting the cache directive to `false`. - - Accepted values are: `true`, `false`, `"deep"`, and `"lenient"`. - - See [`cache`](https://www.nextflow.io/docs/latest/process.html#cache). - type: string - pod: - anyOf: - - description: | - The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. - - See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). - type: object - additionalProperties: - description: | - The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. - - See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). - type: string - - description: | - The `pod` directive allows the definition of pods specific settings, such as environment variables, secrets and config maps when using the Kubernetes executor. - - See [`pod`](https://www.nextflow.io/docs/latest/process.html#pod). - type: array - items: - type: object - additionalProperties: - type: string - penv: - description: | - The `penv` directive allows you to define the parallel environment to be used when submitting a parallel task to the SGE resource manager. - - See [`penv`](https://www.nextflow.io/docs/latest/process.html#penv). - type: string - scratch: - anyOf: - - description: | - The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node. - - See [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch). - type: boolean - - description: | - The `scratch` directive allows you to execute the process in a temporary folder that is local to the execution node. - - See [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch). - type: string - storeDir: - description: | - The `storeDir` directive allows you to define a directory that is used as a permanent cache for your process results. - - See [`storeDir`](https://www.nextflow.io/docs/latest/process.html#storeDir). - type: string - maxRetries: - anyOf: - - description: | - The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the retry error strategy. By default only one retry is allowed. - - See [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries). - type: string - - description: | - The `maxRetries` directive allows you to define the maximum number of times a process instance can be re-submitted in case of failure. This value is applied only when using the retry error strategy. By default only one retry is allowed. - - See [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries). - type: integer - echo: - anyOf: - - description: "By default the stdout produced by the commands executed in all processes is ignored. By setting the `echo` directive to true, you can forward the process stdout to the current top running process stdout file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" - type: boolean - - description: "By default the stdout produced by the commands executed in all processes is ignored. By setting the `echo` directive to true, you can forward the process stdout to the current top running process stdout file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" - type: string - errorStrategy: - description: | - The `errorStrategy` directive allows you to define how an error condition is managed by the process. By default when an error status is returned by the executed script, the process stops immediately. This in turn forces the entire pipeline to terminate. - - Table of available error strategies: - | Name | Executor | - |------|----------| - | `terminate` | Terminates the execution as soon as an error condition is reported. Pending jobs are killed (default) | - | `finish` | Initiates an orderly pipeline shutdown when an error condition is raised, waiting the completion of any submitted job. | - | `ignore` | Ignores processes execution errors. | - | `retry` | Re-submit for execution a process returning an error condition. | - - See [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy). - type: string - memory: - description: | - The `memory` directive allows you to define how much memory the process is allowed to use. - - See [`memory`](https://www.nextflow.io/docs/latest/process.html#memory). - type: string - stageOutMode: - description: "The `stageOutMode` directive defines how output files are staged-out from the scratch directory to the process work directory. The following values are allowed:\n\n| Value | Description |\n|-------|-------------| \n| copy | Output files are copied from the scratch directory to the work directory. | \n| move | Output files are moved from the scratch directory to the work directory. | \n| rsync | Output files are copied from the scratch directory to the work directory by using the rsync utility. |\n\nSee [`stageOutMode`](https://www.nextflow.io/docs/latest/process.html#stageoutmode).\n" - type: string - additionalProperties: false - NextflowAuto: - description: Automated processing flags which can be toggled on or off. - type: object - properties: - simplifyInput: - description: | - If `true`, an input tuple only containing only a single File (e.g. `["foo", file("in.h5ad")]`) is automatically transformed to a map (i.e. `["foo", [ input: file("in.h5ad") ] ]`). - - Default: `true`. - type: boolean - simplifyOutput: - description: | - If `true`, an output tuple containing a map with a File (e.g. `["foo", [ output: file("out.h5ad") ] ]`) is automatically transformed to a map (i.e. `["foo", file("out.h5ad")]`). - - Default: `true`. - type: boolean - publish: - description: | - If `true`, the module's outputs are automatically published to `params.publishDir`. - Will throw an error if `params.publishDir` is not defined. - - Default: `false`. - type: boolean - transcript: - description: | - If `true`, the module's transcripts from `work/` are automatically published to `params.transcriptDir`. - If not defined, `params.publishDir + "/_transcripts"` will be used. - Will throw an error if neither are defined. - - Default: `false`. - type: boolean - additionalProperties: false - NextflowConfig: - description: Allows tweaking how the Nextflow Config file is generated. - type: object - properties: - labels: - description: | - A series of default labels to specify memory and cpu constraints. - - The default memory labels are defined as "mem1gb", "mem2gb", "mem4gb", ... upto "mem512tb" and follows powers of 2. - The default cpu labels are defined as "cpu1", "cpu2", "cpu5", "cpu10", ... upto "cpu1000" and follows a semi logarithmic scale (1, 2, 5 per decade). - - Conceptually it is possible for a Viash Config to overwrite the full labels parameter, however likely it is more efficient to add additional labels - in the Viash Project with a config mod. - type: object - additionalProperties: - description: | - A series of default labels to specify memory and cpu constraints. - - The default memory labels are defined as "mem1gb", "mem2gb", "mem4gb", ... upto "mem512tb" and follows powers of 2. - The default cpu labels are defined as "cpu1", "cpu2", "cpu5", "cpu10", ... upto "cpu1000" and follows a semi logarithmic scale (1, 2, 5 per decade). - - Conceptually it is possible for a Viash Config to overwrite the full labels parameter, however likely it is more efficient to add additional labels - in the Viash Project with a config mod. - type: string - script: - anyOf: - - description: | - Includes a single string or list of strings into the nextflow.config file. - This can be used to add custom profiles or include an additional config file. - type: string - - description: | - Includes a single string or list of strings into the nextflow.config file. - This can be used to add custom profiles or include an additional config file. - type: array - items: - type: string - additionalProperties: false - DockerSetupStrategy: - $comment: TODO add descriptions to different strategies - enum: - - alwaysbuild - - build - - b - - alwayspull - - pull - - p - - alwayspullelsebuild - - pullelsebuild - - alwayspullelsecachedbuild - - pullelsecachedbuild - - alwayscachedbuild - - cachedbuild - - cb - - ifneedbebuild - - ifneedbecachedbuild - - ifneedbepull - - ifneedbepullelsebuild - - ifneedbepullelsecachedbuild - - donothing - - meh - - push - - forcepush - - alwayspush - - pushifnotpresent - - gentlepush - - maybepush - description: The Docker setup strategy to use when building a container. - Direction: - enum: - - input - - output - description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. - Status: - enum: - - enabled - - disabled - - deprecated - description: Allows setting a component to active, deprecated or disabled. - DockerResolveVolume: - $comment: TODO make fully case insensitive - enum: - - manual - - automatic - - auto - - Manual - - Automatic - - Auto - description: 'Enables or disables automatic volume mapping. Enabled when set to `Automatic` or disabled when set to `Manual`. Default: `Automatic`' -properties: - functionality: - description: | - The functionality-part of the config file describes the behaviour of the script in terms of arguments and resources. - By specifying a few restrictions (e.g. mandatory arguments) and adding some descriptions, Viash will automatically generate a stylish command-line interface for you. - $ref: '#/definitions/Functionality' - platforms: - description: Definition of the platforms - type: array - items: - $ref: '#/definitions/Platforms' - info: - description: Definition of meta data - $ref: '#/definitions/Info' -required: - - functionality -additionalProperties: false diff --git a/src/common/schemas/api_component.yaml b/src/common/schemas/api_component.yaml new file mode 100644 index 0000000000..b197e2e367 --- /dev/null +++ b/src/common/schemas/api_component.yaml @@ -0,0 +1,67 @@ +title: Component API +description: | + A component type specification file. +type: object +required: [functionality] +properties: + functionality: + type: object + description: Information regarding the functionality of the component. + required: [namespace, info, arguments, test_resources] + additionalProperties: false + properties: + namespace: + "$ref": "defs_common.yaml#/definitions/Namespace" + info: + type: object + description: Metadata of the component. + additionalProperties: false + required: [type, type_info] + properties: + type: + "$ref": "defs_common.yaml#/definitions/ComponentType" + subtype: + "$ref": "defs_common.yaml#/definitions/ComponentSubtype" + type_info: + type: object + description: Metadata related to the component type. + required: [label, summary, description] + properties: + label: + $ref: "defs_common.yaml#/definitions/Label" + summary: + $ref: "defs_common.yaml#/definitions/Summary" + description: + $ref: "defs_common.yaml#/definitions/Description" + arguments: + type: array + description: Component-specific parameters. + items: + anyOf: + - $ref: 'defs_common.yaml#/definitions/ComponentAPIFile' + - $ref: 'defs_viash.yaml#/definitions/BooleanArgument' + - $ref: 'defs_viash.yaml#/definitions/BooleanArgument' + - $ref: 'defs_viash.yaml#/definitions/BooleanTrueArgument' + - $ref: 'defs_viash.yaml#/definitions/BooleanFalseArgument' + - $ref: 'defs_viash.yaml#/definitions/DoubleArgument' + - $ref: 'defs_viash.yaml#/definitions/IntegerArgument' + - $ref: 'defs_viash.yaml#/definitions/LongArgument' + - $ref: 'defs_viash.yaml#/definitions/StringArgument' + resources: + type: array + description: Resources required to run the component. + items: + "$ref": "defs_viash.yaml#/definitions/Resource" + test_resources: + type: array + description: One or more scripts and resources used to test the component. + items: + "$ref": "defs_viash.yaml#/definitions/Resource" + platforms: + type: array + description: A list of platforms which Viash generates target artifacts for. + items: + anyOf: + - "$ref": "defs_common.yaml#/definitions/PlatformDocker" + - "$ref": "defs_common.yaml#/definitions/PlatformNative" + - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_file_api.yaml b/src/common/schemas/api_file.yaml similarity index 64% rename from src/common/api/schema_file_api.yaml rename to src/common/schemas/api_file.yaml index 96639dbfcd..6294439eda 100644 --- a/src/common/api/schema_file_api.yaml +++ b/src/common/schemas/api_file.yaml @@ -10,17 +10,17 @@ properties: description: A file in the `resources_test` folder which is an example of this file format. type: string __merge__: - $ref: "schema_definitions.yaml#/definitions/Merge" + $ref: "defs_common.yaml#/definitions/Merge" info: description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' type: object required: [label, summary] properties: label: - $ref: "schema_definitions.yaml#/definitions/Label" + $ref: "defs_common.yaml#/definitions/Label" summary: - $ref: "schema_definitions.yaml#/definitions/Summary" + $ref: "defs_common.yaml#/definitions/Summary" description: - $ref: "schema_definitions.yaml#/definitions/Description" + $ref: "defs_common.yaml#/definitions/Description" slots: - $ref: "schema_definitions.yaml#/definitions/AnnDataSlots" + $ref: "defs_common.yaml#/definitions/AnnDataSlots" diff --git a/src/common/api/schema_definitions.yaml b/src/common/schemas/defs_common.yaml similarity index 95% rename from src/common/api/schema_definitions.yaml rename to src/common/schemas/defs_common.yaml index bab932a3e2..740c066784 100644 --- a/src/common/api/schema_definitions.yaml +++ b/src/common/schemas/defs_common.yaml @@ -7,11 +7,7 @@ definitions: const: nextflow description: Next-gen platform for generating NextFlow VDSL3 modules. directives: - $ref: 'schema_viash_config.yaml#/definitions/NextflowDirectives' - # auto: - # $ref: 'schema_viash_config.yaml#/definitions/NextflowAuto' - # config: - # $ref: 'schema_viash_config.yaml#/definitions/NextflowConfig' + $ref: 'defs_viash.yaml#/definitions/NextflowDirectives' required: [ type ] additionalProperties: false PlatformDocker: @@ -44,11 +40,11 @@ definitions: setup: type: array items: - "$ref": "schema_viash_config.yaml#/definitions/Requirements" + "$ref": "defs_viash.yaml#/definitions/Requirements" test_setup: type: array items: - "$ref": "schema_viash_config.yaml#/definitions/Requirements" + "$ref": "defs_viash.yaml#/definitions/Requirements" required: [type, image] additionalProperties: false PlatformNative: @@ -169,7 +165,7 @@ definitions: description: The file format specification file. direction: description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default. - $ref: 'schema_viash_config.yaml#/definitions/Direction' + $ref: 'defs_viash.yaml#/definitions/Direction' info: description: 'Structured information. Can be any shape: a string, vector, map or even nested map.' type: object diff --git a/src/common/schemas/defs_viash.yaml b/src/common/schemas/defs_viash.yaml new file mode 100644 index 0000000000..fff25ab382 --- /dev/null +++ b/src/common/schemas/defs_viash.yaml @@ -0,0 +1,2252 @@ +$schema: "https://json-schema.org/draft-07/schema#" +title: Viash config schema definitions. +oneOf: + - $ref: "#/definitions/Config" +definitions: + Config: + description: "A Viash Config" + properties: + functionality: + description: "The functionality-part of the config file describes the behaviour\ + \ of the script in terms of arguments and resources.\nBy specifying a few restrictions\ + \ (e.g. mandatory arguments) and adding some descriptions, Viash will automatically\ + \ generate a stylish command-line interface for you.\n" + $ref: "#/definitions/Functionality" + platforms: + description: "Definition of the platforms" + type: "array" + items: + $ref: "#/definitions/Platforms" + info: + description: "Definition of meta data" + $ref: "#/definitions/Info" + required: + - "functionality" + additionalProperties: false + NativePlatform: + description: "Running a Viash component on a native platform means that the script\ + \ will be executed in your current environment.\nAny dependencies are assumed\ + \ to have been installed by the user, so the native platform is meant for developers\ + \ (who know what they're doing) or for simple bash scripts (which have no extra\ + \ dependencies).\n" + type: "object" + properties: + id: + description: "As with all platforms, you can give a platform a different name.\ + \ By specifying `id: foo`, you can target this platform (only) by specifying\ + \ `-p foo` in any of the Viash commands." + type: "string" + type: + description: "Running a Viash component on a native platform means that the\ + \ script will be executed in your current environment.\nAny dependencies\ + \ are assumed to have been installed by the user, so the native platform\ + \ is meant for developers (who know what they're doing) or for simple bash\ + \ scripts (which have no extra dependencies).\n" + const: "native" + required: + - "type" + additionalProperties: false + DockerPlatform: + description: "Run a Viash component on a Docker backend platform.\nBy specifying\ + \ which dependencies your component needs, users will be able to build a docker\ + \ container from scratch using the setup flag, or pull it from a docker repository.\n" + type: "object" + properties: + organization: + description: "Name of a container's [organization](https://docs.docker.com/docker-hub/orgs/)." + type: "string" + registry: + description: "The URL to the a [custom Docker registry](https://docs.docker.com/registry/)" + type: "string" + image: + description: "The base container to start from. You can also add the tag here\ + \ if you wish." + type: "string" + tag: + description: "Specify a Docker image based on its tag." + type: "string" + target_tag: + description: "The tag the resulting image gets. Advanced usage only." + type: "string" + run_args: + anyOf: + - description: "Add [docker run](https://docs.docker.com/engine/reference/run/)\ + \ arguments." + type: "string" + - description: "Add [docker run](https://docs.docker.com/engine/reference/run/)\ + \ arguments." + type: "array" + items: + type: "string" + namespace_separator: + description: "The separator between the namespace and the name of the component,\ + \ used for determining the image name. Default: `\"/\"`." + type: "string" + resolve_volume: + description: "Enables or disables automatic volume mapping. Enabled when set\ + \ to `Automatic` or disabled when set to `Manual`. Default: `Automatic`." + $ref: "#/definitions/DockerResolveVolume" + port: + anyOf: + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "string" + - description: "A list of enabled ports. This doesn't change the Dockerfile\ + \ but gets added as a command-line argument at runtime." + type: "array" + items: + type: "string" + setup: + description: "A list of requirements for installing the following types of\ + \ packages:\n\n - @[apt](apt_req)\n - @[apk](apk_req)\n - @[Docker setup\ + \ instructions](docker_req)\n - @[JavaScript](javascript_req)\n - @[Python](python_req)\n\ + \ - @[R](r_req)\n - @[Ruby](ruby_req)\n - @[yum](yum_req)\n\nThe order in\ + \ which these dependencies are specified determines the order in which they\ + \ will be installed.\n" + type: "array" + items: + $ref: "#/definitions/Requirements" + workdir: + description: "The working directory when starting the container. This doesn't\ + \ change the Dockerfile but gets added as a command-line argument at runtime." + type: "string" + target_image: + description: "If anything is specified in the setup section, running the `---setup`\ + \ will result in an image with the name of `:`. If\ + \ nothing is specified in the `setup` section, simply `image` will be used.\ + \ Advanced usage only." + type: "string" + cmd: + anyOf: + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "string" + - description: "Set the default command being executed when running the Docker\ + \ container." + type: "array" + items: + type: "string" + target_image_source: + description: "The source of the target image. This is used for defining labels\ + \ in the dockerfile." + type: "string" + test_setup: + description: "Additional requirements specific for running unit tests." + type: "array" + items: + $ref: "#/definitions/Requirements" + entrypoint: + anyOf: + - description: "Override the entrypoint of the base container. Default set\ + \ `ENTRYPOINT []`." + type: "string" + - description: "Override the entrypoint of the base container. Default set\ + \ `ENTRYPOINT []`." + type: "array" + items: + type: "string" + id: + description: "As with all platforms, you can give a platform a different name.\ + \ By specifying `id: foo`, you can target this platform (only) by specifying\ + \ `-p foo` in any of the Viash commands." + type: "string" + target_registry: + description: "The URL where the resulting image will be pushed to. Advanced\ + \ usage only." + type: "string" + setup_strategy: + description: "The Docker setup strategy to use when building a container.\n\ + \n| Strategy | Description |\n|-----|----------|\n| `alwaysbuild` / `build`\ + \ / `b` | Always build the image from the dockerfile. This is the default\ + \ setup strategy.\n| `alwayscachedbuild` / `cachedbuild` / `cb` | Always\ + \ build the image from the dockerfile, with caching enabled.\n| `ifneedbebuild`\ + \ | Build the image if it does not exist locally.\n| `ifneedbecachedbuild`\ + \ | Build the image with caching enabled if it does not exist locally, with\ + \ caching enabled.\n| `alwayspull` / `pull` / `p` | Try to pull the container\ + \ from [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry).\n\ + | `alwayspullelsebuild` / `pullelsebuild` | Try to pull the image from\ + \ a registry and build it if it doesn't exist.\n| `alwayspullelsecachedbuild`\ + \ / `pullelsecachedbuild` | Try to pull the image from a registry and build\ + \ it with caching if it doesn't exist.\n| `ifneedbepull` | If the image\ + \ does not exist locally, pull the image.\n| `ifneedbepullelsebuild` | \ + \ If the image does not exist locally, pull the image. If the image does\ + \ exist, build it.\n| `ifneedbepullelsecachedbuild` | If the image does\ + \ not exist locally, pull the image. If the image does exist, build it with\ + \ caching enabled.\n| `push` | Push the container to [Docker Hub](https://hub.docker.com)\ + \ or the @[specified docker registry](docker_registry).\n| `pushifnotpresent`\ + \ | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified\ + \ docker registry](docker_registry) if the @[tag](docker_tag) does not exist\ + \ yet.\n| `donothing` / `meh` | Do not build or pull anything.\n\n" + $ref: "#/definitions/DockerSetupStrategy" + type: + description: "Run a Viash component on a Docker backend platform.\nBy specifying\ + \ which dependencies your component needs, users will be able to build a\ + \ docker container from scratch using the setup flag, or pull it from a\ + \ docker repository.\n" + const: "docker" + target_organization: + description: "The organization set in the resulting image. Advanced usage\ + \ only." + type: "string" + chown: + description: "In Linux, files created by a Docker container will be owned\ + \ by `root`. With `chown: true`, Viash will automatically change the ownership\ + \ of output files (arguments with `type: file` and `direction: output`)\ + \ to the user running the Viash command after execution of the component.\ + \ Default value: `true`." + type: "boolean" + required: + - "image" + - "type" + additionalProperties: false + NextflowVdsl3Platform: + description: "Next-gen platform for generating NextFlow VDSL3 modules." + type: "object" + properties: + auto: + description: "@[Automated processing flags](nextflow_auto) which can be toggled\ + \ on or off:\n\n| Flag | Description | Default |\n|---|---------|----|\n\ + | `simplifyInput` | If `true`, an input tuple only containing only a single\ + \ File (e.g. `[\"foo\", file(\"in.h5ad\")]`) is automatically transformed\ + \ to a map (i.e. `[\"foo\", [ input: file(\"in.h5ad\") ] ]`). | `true` |\n\ + | `simplifyOutput` | If `true`, an output tuple containing a map with a\ + \ File (e.g. `[\"foo\", [ output: file(\"out.h5ad\") ] ]`) is automatically\ + \ transformed to a map (i.e. `[\"foo\", file(\"out.h5ad\")]`). | `true`\ + \ |\n| `transcript` | If `true`, the module's transcripts from `work/` are\ + \ automatically published to `params.transcriptDir`. If not defined, `params.publishDir\ + \ + \"/_transcripts\"` will be used. Will throw an error if neither are\ + \ defined. | `false` |\n| `publish` | If `true`, the module's outputs are\ + \ automatically published to `params.publishDir`. Will throw an error if\ + \ `params.publishDir` is not defined. | `false` |\n\n" + $ref: "#/definitions/NextflowAuto" + directives: + description: "@[Directives](nextflow_directives) are optional settings that\ + \ affect the execution of the process. These mostly match up with the Nextflow\ + \ counterparts. \n" + $ref: "#/definitions/NextflowDirectives" + container: + description: "Specifies the Docker platform id to be used to run Nextflow." + type: "string" + debug: + description: "Whether or not to print debug messages." + type: "boolean" + id: + description: "Every platform can be given a specific id that can later be\ + \ referred to explicitly when running or building the Viash component." + type: "string" + type: + description: "Next-gen platform for generating NextFlow VDSL3 modules." + const: "nextflow" + config: + description: "Allows tweaking how the @[Nextflow Config](nextflow_config)\ + \ file is generated." + $ref: "#/definitions/NextflowConfig" + required: + - "type" + additionalProperties: false + Platforms: + anyOf: + - $ref: "#/definitions/NativePlatform" + - $ref: "#/definitions/DockerPlatform" + - $ref: "#/definitions/NextflowVdsl3Platform" + Info: + description: "Meta information fields filled in by Viash during build." + type: "object" + properties: + git_tag: + description: "Git tag." + type: "string" + git_remote: + description: "Git remote name." + type: "string" + viash_version: + description: "The Viash version that was used to build the component." + type: "string" + config: + description: "Path to the config used during build." + type: "string" + output: + description: "Folder path to the build artifacts." + type: "string" + platform: + description: "The platform id used during build." + type: "string" + git_commit: + description: "Git commit hash." + type: "string" + executable: + description: "Output folder with main executable path." + type: "string" + required: + - "config" + additionalProperties: false + Functionality: + description: "The functionality-part of the config file describes the behaviour\ + \ of the script in terms of arguments and resources.\nBy specifying a few restrictions\ + \ (e.g. mandatory arguments) and adding some descriptions, Viash will automatically\ + \ generate a stylish command-line interface for you.\n" + type: "object" + properties: + name: + description: "Name of the component and the filename of the executable when\ + \ built with `viash build`." + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + version: + description: "Version of the component. This field will be used to version\ + \ the executable and the Docker container." + type: "string" + authors: + description: "A list of @[authors](author). An author must at least have a\ + \ name, but can also have a list of roles, an e-mail address, and a map\ + \ of custom properties.\n\nSuggested values for roles are:\n \n| Role |\ + \ Abbrev. | Description |\n|------|---------|-------------|\n| maintainer\ + \ | mnt | for the maintainer of the code. Ideally, exactly one maintainer\ + \ is specified. |\n| author | aut | for persons who have made substantial\ + \ contributions to the software. |\n| contributor | ctb| for persons who\ + \ have made smaller contributions (such as code patches).\n| datacontributor\ + \ | dtc | for persons or organisations that contributed data sets for the\ + \ software\n| copyrightholder | cph | for all copyright holders. This is\ + \ a legal concept so should use the legal name of an institution or corporate\ + \ body.\n| funder | fnd | for persons or organizations that furnished financial\ + \ support for the development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html)\ + \ is extremely comprehensive.\n" + type: "array" + items: + $ref: "#/definitions/Author" + status: + description: "Allows setting a component to active, deprecated or disabled." + $ref: "#/definitions/Status" + requirements: + description: "@[Computational requirements](computational_requirements) related\ + \ to running the component. \n`cpus` specifies the maximum number of (logical)\ + \ cpus a component is allowed to use., whereas\n`memory` specifies the maximum\ + \ amount of memory a component is allowed to allicate. Memory units must\ + \ be\nin B, KB, MB, GB, TB or PB." + $ref: "#/definitions/ComputationalRequirements" + resources: + description: "@[Resources](resources) are files that support the component.\ + \ The first resource should be @[a script](scripting_languages) that will\ + \ be executed when the functionality is run. Additional resources will be\ + \ copied to the same directory.\n\nCommon properties:\n\n * type: `file`\ + \ / `r_script` / `python_script` / `bash_script` / `javascript_script` /\ + \ `scala_script` / `csharp_script`, specifies the type of the resource.\ + \ The first resource cannot be of type `file`. When the type is not specified,\ + \ the default type is simply `file`.\n * dest: filename, the resulting name\ + \ of the resource. From within a script, the file can be accessed at `meta[\"\ + resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\ + \ the basename of the `path` parameter.\n * path: `path/to/file`, the path\ + \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\ + \ exclusive with `text`.\n * text: ...multiline text..., the content of\ + \ the resulting file specified as a string. Mutually exclusive with `path`.\n\ + \ * is_executable: `true` / `false`, whether the resulting resource file\ + \ should be made executable.\n" + type: "array" + items: + $ref: "#/definitions/Resource" + test_resources: + description: "One or more @[scripts](scripting_languages) to be used to test\ + \ the component behaviour when `viash test` is invoked. Additional files\ + \ of type `file` will be made available only during testing. Each test script\ + \ should expect no command-line inputs, be platform-independent, and return\ + \ an exit code >0 when unexpected behaviour occurs during testing. See @[Unit\ + \ Testing](unit_testing) for more info." + type: "array" + items: + $ref: "#/definitions/Resource" + argument_groups: + description: "A grouping of the @[arguments](argument), used to display the\ + \ help message.\n\n - `name: foo`, the name of the argument group. \n -\ + \ `description: Description of foo`, a description of the argument group.\ + \ Multiline descriptions are supported.\n - `arguments: [arg1, arg2, ...]`,\ + \ list of the arguments names.\n\n" + type: "array" + items: + $ref: "#/definitions/ArgumentGroup" + description: + description: "A description of the component. This will be displayed with\ + \ `--help`." + type: "string" + usage: + description: "A description on how to use the component. This will be displayed\ + \ with `--help` under the 'Usage:' section." + type: "string" + namespace: + description: "Namespace this component is a part of. See the @[Namespaces\ + \ guide](namespace) for more information on namespaces." + type: "string" + arguments: + description: "A list of @[arguments](argument) for this component. For each\ + \ argument, a type and a name must be specified. Depending on the type of\ + \ argument, different properties can be set. See these reference pages per\ + \ type for more information: \n\n - @[string](arg_string)\n - @[file](arg_file)\n\ + \ - @[integer](arg_integer)\n - @[double](arg_double)\n - @[boolean](arg_boolean)\n\ + \ - @[boolean_true](arg_boolean_true)\n - @[boolean_false](arg_boolean_false)\n" + type: "array" + items: + $ref: "#/definitions/Argument" + required: + - "name" + additionalProperties: false + Author: + description: "Author metadata." + type: "object" + properties: + name: + description: "Full name of the author, usually in the name of FirstName MiddleName\ + \ LastName." + type: "string" + email: + description: "E-mail of the author." + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + roles: + anyOf: + - description: "Role of the author. Suggested items:\n\n* `\"author\"`: Authors\ + \ who have made substantial contributions to the component.\n* `\"maintainer\"\ + `: The maintainer of the component.\n* `\"contributor\"`: Authors who\ + \ have made smaller contributions (such as code patches etc.).\n" + type: "string" + - description: "Role of the author. Suggested items:\n\n* `\"author\"`: Authors\ + \ who have made substantial contributions to the component.\n* `\"maintainer\"\ + `: The maintainer of the component.\n* `\"contributor\"`: Authors who\ + \ have made smaller contributions (such as code patches etc.).\n" + type: "array" + items: + type: "string" + props: + description: "Author properties. Must be a map of strings." + type: "object" + additionalProperties: + description: "Author properties. Must be a map of strings." + type: "string" + required: + - "name" + additionalProperties: false + ComputationalRequirements: + description: "Computational requirements related to running the component." + type: "object" + properties: + cpus: + description: "The maximum number of (logical) cpus a component is allowed\ + \ to use." + type: "integer" + commands: + description: "A list of commands which should be present on the system for\ + \ the script to function." + type: "array" + items: + type: "string" + memory: + description: "The maximum amount of memory a component is allowed to allocate.\ + \ Unit must be one of B, KB, MB, GB, TB or PB." + type: "string" + required: [] + additionalProperties: false + RubyRequirements: + description: "Specify which Ruby packages should be available in order to run\ + \ the component." + type: "object" + properties: + type: + description: "Specify which Ruby packages should be available in order to\ + \ run the component." + const: "ruby" + packages: + anyOf: + - description: "Specifies which packages to install." + type: "string" + - description: "Specifies which packages to install." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + YumRequirements: + description: "Specify which yum packages should be available in order to run the\ + \ component." + type: "object" + properties: + type: + description: "Specify which yum packages should be available in order to run\ + \ the component." + const: "yum" + packages: + anyOf: + - description: "Specifies which packages to install." + type: "string" + - description: "Specifies which packages to install." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + JavascriptRequirements: + description: "Specify which JavaScript packages should be available in order to\ + \ run the component." + type: "object" + properties: + github: + anyOf: + - description: "Specifies which packages to install from GitHub." + type: "string" + - description: "Specifies which packages to install from GitHub." + type: "array" + items: + type: "string" + url: + anyOf: + - description: "Specifies which packages to install using a generic URI." + type: "string" + - description: "Specifies which packages to install using a generic URI." + type: "array" + items: + type: "string" + git: + anyOf: + - description: "Specifies which packages to install using a Git URI." + type: "string" + - description: "Specifies which packages to install using a Git URI." + type: "array" + items: + type: "string" + npm: + anyOf: + - description: "Specifies which packages to install from npm." + type: "string" + - description: "Specifies which packages to install from npm." + type: "array" + items: + type: "string" + type: + description: "Specify which JavaScript packages should be available in order\ + \ to run the component." + const: "javascript" + packages: + anyOf: + - description: "Specifies which packages to install from npm." + type: "string" + - description: "Specifies which packages to install from npm." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + DockerRequirements: + description: "Specify which Docker commands should be run during setup." + type: "object" + properties: + run: + anyOf: + - description: "Specifies which `RUN` entries to add to the Dockerfile while\ + \ building it." + type: "string" + - description: "Specifies which `RUN` entries to add to the Dockerfile while\ + \ building it." + type: "array" + items: + type: "string" + label: + anyOf: + - description: "Specifies which `LABEL` entries to add to the Dockerfile while\ + \ building it." + type: "string" + - description: "Specifies which `LABEL` entries to add to the Dockerfile while\ + \ building it." + type: "array" + items: + type: "string" + build_args: + anyOf: + - description: "Specifies which `ARG` entries to add to the Dockerfile while\ + \ building it." + type: "string" + - description: "Specifies which `ARG` entries to add to the Dockerfile while\ + \ building it." + type: "array" + items: + type: "string" + type: + description: "Specify which Docker commands should be run during setup." + const: "docker" + add: + anyOf: + - description: "Specifies which `ADD` entries to add to the Dockerfile while\ + \ building it." + type: "string" + - description: "Specifies which `ADD` entries to add to the Dockerfile while\ + \ building it." + type: "array" + items: + type: "string" + env: + anyOf: + - description: "Specifies which `ENV` entries to add to the Dockerfile while\ + \ building it. Unlike `ARG`, `ENV` entries are also accessible from inside\ + \ the container." + type: "string" + - description: "Specifies which `ENV` entries to add to the Dockerfile while\ + \ building it. Unlike `ARG`, `ENV` entries are also accessible from inside\ + \ the container." + type: "array" + items: + type: "string" + copy: + anyOf: + - description: "Specifies which `COPY` entries to add to the Dockerfile while\ + \ building it." + type: "string" + - description: "Specifies which `COPY` entries to add to the Dockerfile while\ + \ building it." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + RRequirements: + description: "Specify which R packages should be available in order to run the\ + \ component." + type: "object" + properties: + bioc: + anyOf: + - description: "Specifies which packages to install from BioConductor." + type: "string" + - description: "Specifies which packages to install from BioConductor." + type: "array" + items: + type: "string" + github: + anyOf: + - description: "Specifies which packages to install from GitHub." + type: "string" + - description: "Specifies which packages to install from GitHub." + type: "array" + items: + type: "string" + gitlab: + anyOf: + - description: "Specifies which packages to install from GitLab." + type: "string" + - description: "Specifies which packages to install from GitLab." + type: "array" + items: + type: "string" + url: + anyOf: + - description: "Specifies which packages to install using a generic URI." + type: "string" + - description: "Specifies which packages to install using a generic URI." + type: "array" + items: + type: "string" + bioc_force_install: + description: "Forces packages specified in `bioc` to be reinstalled, even\ + \ if they are already present in the container. Default: false." + type: "boolean" + git: + anyOf: + - description: "Specifies which packages to install using a Git URI." + type: "string" + - description: "Specifies which packages to install using a Git URI." + type: "array" + items: + type: "string" + cran: + anyOf: + - description: "Specifies which packages to install from CRAN." + type: "string" + - description: "Specifies which packages to install from CRAN." + type: "array" + items: + type: "string" + bitbucket: + anyOf: + - description: "Specifies which packages to install from Bitbucket." + type: "string" + - description: "Specifies which packages to install from Bitbucket." + type: "array" + items: + type: "string" + svn: + anyOf: + - description: "Specifies which packages to install using an SVN URI." + type: "string" + - description: "Specifies which packages to install using an SVN URI." + type: "array" + items: + type: "string" + packages: + anyOf: + - description: "Specifies which packages to install from CRAN." + type: "string" + - description: "Specifies which packages to install from CRAN." + type: "array" + items: + type: "string" + script: + anyOf: + - description: "Specifies a code block to run as part of the build." + type: "string" + - description: "Specifies a code block to run as part of the build." + type: "array" + items: + type: "string" + type: + description: "Specify which R packages should be available in order to run\ + \ the component." + const: "r" + required: + - "type" + additionalProperties: false + ApkRequirements: + description: "Specify which apk packages should be available in order to run the\ + \ component." + type: "object" + properties: + type: + description: "Specify which apk packages should be available in order to run\ + \ the component." + const: "apk" + packages: + anyOf: + - description: "Specifies which packages to install." + type: "string" + - description: "Specifies which packages to install." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + PythonRequirements: + description: "Specify which Python packages should be available in order to run\ + \ the component." + type: "object" + properties: + github: + anyOf: + - description: "Specifies which packages to install from GitHub." + type: "string" + - description: "Specifies which packages to install from GitHub." + type: "array" + items: + type: "string" + gitlab: + anyOf: + - description: "Specifies which packages to install from GitLab." + type: "string" + - description: "Specifies which packages to install from GitLab." + type: "array" + items: + type: "string" + pip: + anyOf: + - description: "Specifies which packages to install from pip." + type: "string" + - description: "Specifies which packages to install from pip." + type: "array" + items: + type: "string" + pypi: + anyOf: + - description: "Specifies which packages to install from PyPI using pip." + type: "string" + - description: "Specifies which packages to install from PyPI using pip." + type: "array" + items: + type: "string" + git: + anyOf: + - description: "Specifies which packages to install using a Git URI." + type: "string" + - description: "Specifies which packages to install using a Git URI." + type: "array" + items: + type: "string" + upgrade: + description: "Sets the `--upgrade` flag when set to true. Default: true." + type: "boolean" + packages: + anyOf: + - description: "Specifies which packages to install from pip." + type: "string" + - description: "Specifies which packages to install from pip." + type: "array" + items: + type: "string" + url: + anyOf: + - description: "Specifies which packages to install using a generic URI." + type: "string" + - description: "Specifies which packages to install using a generic URI." + type: "array" + items: + type: "string" + svn: + anyOf: + - description: "Specifies which packages to install using an SVN URI." + type: "string" + - description: "Specifies which packages to install using an SVN URI." + type: "array" + items: + type: "string" + bazaar: + anyOf: + - description: "Specifies which packages to install using a Bazaar URI." + type: "string" + - description: "Specifies which packages to install using a Bazaar URI." + type: "array" + items: + type: "string" + script: + anyOf: + - description: "Specifies a code block to run as part of the build." + type: "string" + - description: "Specifies a code block to run as part of the build." + type: "array" + items: + type: "string" + type: + description: "Specify which Python packages should be available in order to\ + \ run the component." + const: "python" + mercurial: + anyOf: + - description: "Specifies which packages to install using a Mercurial URI." + type: "string" + - description: "Specifies which packages to install using a Mercurial URI." + type: "array" + items: + type: "string" + user: + description: "Sets the `--user` flag when set to true. Default: false." + type: "boolean" + required: + - "type" + additionalProperties: false + AptRequirements: + description: "Specify which apt packages should be available in order to run the\ + \ component." + type: "object" + properties: + interactive: + description: "If `false`, the Debian frontend is set to non-interactive (recommended).\ + \ Default: false." + type: "boolean" + type: + description: "Specify which apt packages should be available in order to run\ + \ the component." + const: "apt" + packages: + anyOf: + - description: "Specifies which packages to install." + type: "string" + - description: "Specifies which packages to install." + type: "array" + items: + type: "string" + required: + - "type" + additionalProperties: false + Requirements: + anyOf: + - $ref: "#/definitions/RubyRequirements" + - $ref: "#/definitions/YumRequirements" + - $ref: "#/definitions/JavascriptRequirements" + - $ref: "#/definitions/DockerRequirements" + - $ref: "#/definitions/RRequirements" + - $ref: "#/definitions/ApkRequirements" + - $ref: "#/definitions/PythonRequirements" + - $ref: "#/definitions/AptRequirements" + StringArgument: + description: "A `string` type argument has a value made up of an ordered sequences\ + \ of characters, like \"Hello\" or \"I'm a string\"." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f`\ + \ or `foo`. The number of dashes determines how values can be passed: \n\ + \n - `--foo` is a long option, which can be passed with `executable_name\ + \ --foo=value` or `executable_name --foo value`\n - `-f` is a short option,\ + \ which can be passed with `executable_name -f value`\n - `foo` is an argument,\ + \ which can be passed with `executable_name value` \n" + type: "string" + choices: + description: "Limit the amount of valid values for this argument to those\ + \ set in this list. When set and a value not present in the list is provided,\ + \ an error will be produced." + type: "array" + items: + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "string" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "string" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "string" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "string" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "A `string` type argument has a value made up of an ordered sequences\ + \ of characters, like \"Hello\" or \"I'm a string\"." + const: "string" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + BooleanArgument: + description: "A `boolean` type argument has two possible values: `true` or `false`." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--trim`, `-t`\ + \ or `trim`. The number of dashes determines how values can be passed: \ + \ \n\n - `--trim` is a long option, which can be passed with `executable_name\ + \ --trim`\n - `-t` is a short option, which can be passed with `executable_name\ + \ -t`\n - `trim` is an argument, which can be passed with `executable_name\ + \ trim` \n" + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "boolean" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "boolean" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "boolean" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "boolean" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "A `boolean` type argument has two possible values: `true` or\ + \ `false`." + const: "boolean" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + BooleanTrueArgument: + description: "An argument of the `boolean_true` type acts like a `boolean` flag\ + \ with a default value of `false`. When called as an argument it sets the `boolean`\ + \ to `true`." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--silent`,\ + \ `-s` or `silent`. The number of dashes determines how values can be passed:\ + \ \n\n - `--silent` is a long option, which can be passed with `executable_name\ + \ --silent`\n - `-s` is a short option, which can be passed with `executable_name\ + \ -s`\n - `silent` is an argument, which can be passed with `executable_name\ + \ silent` \n" + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + type: + description: "An argument of the `boolean_true` type acts like a `boolean`\ + \ flag with a default value of `false`. When called as an argument it sets\ + \ the `boolean` to `true`." + const: "boolean_true" + required: + - "name" + - "type" + additionalProperties: false + IntegerArgument: + description: "An `integer` type argument has a numeric value without decimal points." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f`\ + \ or `foo`. The number of dashes determines how values can be passed: \n\ + \n - `--foo` is a long option, which can be passed with `executable_name\ + \ --foo=value` or `executable_name --foo value`\n - `-f` is a short option,\ + \ which can be passed with `executable_name -f value`\n - `foo` is an argument,\ + \ which can be passed with `executable_name value` \n" + type: "string" + choices: + description: "Limit the amount of valid values for this argument to those\ + \ set in this list. When set and a value not present in the list is provided,\ + \ an error will be produced." + type: "array" + items: + type: "integer" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + max: + description: "Maximum allowed value for this argument. If set and the provided\ + \ value is higher than the maximum, an error will be produced. Can be combined\ + \ with [`min`](#min) to clamp values." + type: "integer" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "integer" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "integer" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "integer" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "integer" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + min: + description: "Minimum allowed value for this argument. If set and the provided\ + \ value is lower than the minimum, an error will be produced. Can be combined\ + \ with [`max`](#max) to clamp values." + type: "integer" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "An `integer` type argument has a numeric value without decimal\ + \ points." + const: "integer" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + LongArgument: + description: "An `long` type argument has a numeric value without decimal points." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f`\ + \ or `foo`. The number of dashes determines how values can be passed: \n\ + \n - `--foo` is a long option, which can be passed with `executable_name\ + \ --foo=value` or `executable_name --foo value`\n - `-f` is a short option,\ + \ which can be passed with `executable_name -f value`\n - `foo` is an argument,\ + \ which can be passed with `executable_name value` \n" + type: "string" + choices: + description: "Limit the amount of valid values for this argument to those\ + \ set in this list. When set and a value not present in the list is provided,\ + \ an error will be produced." + type: "array" + items: + type: "integer" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + max: + description: "Maximum allowed value for this argument. If set and the provided\ + \ value is higher than the maximum, an error will be produced. Can be combined\ + \ with [`min`](#min) to clamp values." + type: "integer" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "integer" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "integer" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "integer" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "integer" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + min: + description: "Minimum allowed value for this argument. If set and the provided\ + \ value is lower than the minimum, an error will be produced. Can be combined\ + \ with [`max`](#max) to clamp values." + type: "integer" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "An `long` type argument has a numeric value without decimal\ + \ points." + const: "long" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + BooleanFalseArgument: + description: "An argument of the `boolean_false` type acts like an inverted `boolean`\ + \ flag with a default value of `true`. When called as an argument it sets the\ + \ `boolean` to `false`." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--no-log`,\ + \ `-n` or `no-log`. The number of dashes determines how values can be passed:\ + \ \n\n - `--no-log` is a long option, which can be passed with `executable_name\ + \ --no-log`\n - `-n` is a short option, which can be passed with `executable_name\ + \ -n`\n - `no-log` is an argument, which can be passed with `executable_name\ + \ no-log` \n" + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + type: + description: "An argument of the `boolean_false` type acts like an inverted\ + \ `boolean` flag with a default value of `true`. When called as an argument\ + \ it sets the `boolean` to `false`." + const: "boolean_false" + required: + - "name" + - "type" + additionalProperties: false + DoubleArgument: + description: "A `double` type argument has a numeric value with decimal points" + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f`\ + \ or `foo`. The number of dashes determines how values can be passed: \n\ + \n - `--foo` is a long option, which can be passed with `executable_name\ + \ --foo=value` or `executable_name --foo value`\n - `-f` is a short option,\ + \ which can be passed with `executable_name -f value`\n - `foo` is an argument,\ + \ which can be passed with `executable_name value` \n" + type: "string" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + max: + description: "Maximum allowed value for this argument. If set and the provided\ + \ value is higher than the maximum, an error will be produced. Can be combined\ + \ with [`min`](#min) to clamp values." + type: "number" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "number" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "number" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "number" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "number" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + min: + description: "Minimum allowed value for this argument. If set and the provided\ + \ value is lower than the minimum, an error will be produced. Can be combined\ + \ with [`max`](#max) to clamp values." + type: "number" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "A `double` type argument has a numeric value with decimal points" + const: "double" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + FileArgument: + description: "A `file` type argument has a string value that points to a file\ + \ or folder path." + type: "object" + properties: + alternatives: + anyOf: + - description: "List of alternative format variations for this argument." + type: "string" + - description: "List of alternative format variations for this argument." + type: "array" + items: + type: "string" + name: + description: "The name of the argument. Can be in the formats `--foo`, `-f`\ + \ or `foo`. The number of dashes determines how values can be passed: \n\ + \n - `--foo` is a long option, which can be passed with `executable_name\ + \ --foo=value` or `executable_name --foo value`\n - `-f` is a short option,\ + \ which can be passed with `executable_name -f value`\n - `foo` is an argument,\ + \ which can be passed with `executable_name value` \n" + type: "string" + create_parent: + description: "If the output filename is a path and it does not exist, create\ + \ it before executing the script (only for `direction: output`)." + type: "boolean" + direction: + description: "Makes this argument an `input` or an `output`, as in does the\ + \ file/folder needs to be read or written. `input` by default." + $ref: "#/definitions/Direction" + info: + description: "Structured information. Can be any shape: a string, vector,\ + \ map or even nested map." + type: "object" + must_exist: + description: "Checks whether the file or folder exists. For input files, this\ + \ check will happen before the execution of the script, while for output\ + \ files the check will happen afterwards." + type: "boolean" + default: + anyOf: + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "string" + - description: "The default value when no argument value is provided. This\ + \ will not work if the [`required`](#required) property is enabled." + type: "array" + items: + type: "string" + example: + anyOf: + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "string" + - description: "An example value for this argument. If no [`default`](#default)\ + \ property was specified, this will be used for that purpose." + type: "array" + items: + type: "string" + description: + description: "A description of the argument. This will be displayed with `--help`." + type: "string" + multiple_sep: + description: "The delimiter character for providing [`multiple`](#multiple)\ + \ values. `:` by default." + type: "string" + multiple: + description: "Treat the argument value as an array. Arrays can be passed using\ + \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\ + \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\ + \ property. `false` by default." + type: "boolean" + type: + description: "A `file` type argument has a string value that points to a file\ + \ or folder path." + const: "file" + required: + description: "Make the value for this argument required. If set to `true`,\ + \ an error will be produced if no value was provided. `false` by default." + type: "boolean" + required: + - "name" + - "type" + additionalProperties: false + Argument: + anyOf: + - $ref: "#/definitions/StringArgument" + - $ref: "#/definitions/BooleanArgument" + - $ref: "#/definitions/BooleanTrueArgument" + - $ref: "#/definitions/IntegerArgument" + - $ref: "#/definitions/LongArgument" + - $ref: "#/definitions/BooleanFalseArgument" + - $ref: "#/definitions/DoubleArgument" + - $ref: "#/definitions/FileArgument" + ArgumentGroup: + type: "object" + properties: + name: + description: "The name of the argument group." + type: "string" + description: + description: "A description of the argument group. Multiline descriptions\ + \ are supported." + type: "string" + arguments: + description: "List of the arguments names." + type: "array" + items: + $ref: "#/definitions/Argument" + required: + - "name" + - "arguments" + additionalProperties: false + JavaScriptScript: + description: "An executable JavaScript script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable JavaScript script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "javascript_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + CSharpScript: + description: "An executable C# script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable C# script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "csharp_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + Executable: + description: "An executable file." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable file." + const: "executable" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + ScalaScript: + description: "An executable Scala script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable Scala script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "scala_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + NextflowScript: + description: "A Nextflow script. Work in progress; added mainly for annotation\ + \ at the moment." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + entrypoint: + description: "The name of the workflow to be executed." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "A Nextflow script. Work in progress; added mainly for annotation\ + \ at the moment." + const: "nextflow_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + PlainFile: + description: "A plain file. This can only be used as a supporting resource for\ + \ the main script or unit tests." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "A plain file. This can only be used as a supporting resource\ + \ for the main script or unit tests." + const: "file" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "path" + additionalProperties: false + BashScript: + description: "An executable Bash script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable Bash script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "bash_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + PythonScript: + description: "An executable Python script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable Python script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "python_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + RScript: + description: "An executable R script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component or\ + \ when running `viash run`.\nWhen defined in functionality.test_resources, all\ + \ entries will be executed during `viash test`." + type: "object" + properties: + path: + description: "The path of the input file. Can be a relative or an absolute\ + \ path, or a URI. Mutually exclusive with `text`." + type: "string" + text: + description: "The content of the resulting file specified as a string. Mutually\ + \ exclusive with `path`." + type: "string" + is_executable: + description: "Whether the resulting resource file should be made executable." + type: "boolean" + type: + description: "An executable R script.\nWhen defined in functionality.resources,\ + \ only the first entry will be executed when running the built component\ + \ or when running `viash run`.\nWhen defined in functionality.test_resources,\ + \ all entries will be executed during `viash test`." + const: "r_script" + dest: + description: "Resulting filename of the resource. From within a script, the\ + \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\ + \ `dest` will be set to the basename of the `path` parameter." + type: "string" + required: + - "type" + additionalProperties: false + Resource: + anyOf: + - $ref: "#/definitions/JavaScriptScript" + - $ref: "#/definitions/CSharpScript" + - $ref: "#/definitions/Executable" + - $ref: "#/definitions/ScalaScript" + - $ref: "#/definitions/NextflowScript" + - $ref: "#/definitions/PlainFile" + - $ref: "#/definitions/BashScript" + - $ref: "#/definitions/PythonScript" + - $ref: "#/definitions/RScript" + NextflowDirectives: + description: "Directives are optional settings that affect the execution of the\ + \ process.\n" + type: "object" + properties: + beforeScript: + description: "The `beforeScript` directive allows you to execute a custom\ + \ (Bash) snippet before the main process script is run. This may be useful\ + \ to initialise the underlying cluster environment or for other custom initialisation.\n\ + \nSee [`beforeScript`](https://www.nextflow.io/docs/latest/process.html#beforeScript).\n" + type: "string" + module: + anyOf: + - description: "Environment Modules is a package manager that allows you to\ + \ dynamically configure your execution environment and easily switch between\ + \ multiple versions of the same software tool.\n\nIf it is available in\ + \ your system you can use it with Nextflow in order to configure the processes\ + \ execution environment in your pipeline.\n\nIn a process definition you\ + \ can use the `module` directive to load a specific module version to\ + \ be used in the process execution environment.\n\nSee [`module`](https://www.nextflow.io/docs/latest/process.html#module).\n" + type: "string" + - description: "Environment Modules is a package manager that allows you to\ + \ dynamically configure your execution environment and easily switch between\ + \ multiple versions of the same software tool.\n\nIf it is available in\ + \ your system you can use it with Nextflow in order to configure the processes\ + \ execution environment in your pipeline.\n\nIn a process definition you\ + \ can use the `module` directive to load a specific module version to\ + \ be used in the process execution environment.\n\nSee [`module`](https://www.nextflow.io/docs/latest/process.html#module).\n" + type: "array" + items: + type: "string" + queue: + anyOf: + - description: "The `queue` directory allows you to set the queue where jobs\ + \ are scheduled when using a grid based executor in your pipeline.\n\n\ + See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue).\n" + type: "string" + - description: "The `queue` directory allows you to set the queue where jobs\ + \ are scheduled when using a grid based executor in your pipeline.\n\n\ + See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue).\n" + type: "array" + items: + type: "string" + label: + anyOf: + - description: "The `label` directive allows the annotation of processes with\ + \ mnemonic identifier of your choice.\n\nSee [`label`](https://www.nextflow.io/docs/latest/process.html#label).\n" + type: "string" + - description: "The `label` directive allows the annotation of processes with\ + \ mnemonic identifier of your choice.\n\nSee [`label`](https://www.nextflow.io/docs/latest/process.html#label).\n" + type: "array" + items: + type: "string" + container: + anyOf: + - description: "The `container` directive allows you to execute the process\ + \ script in a Docker container.\n\nIt requires the Docker daemon to be\ + \ running in machine where the pipeline is executed, i.e. the local machine\ + \ when using the local executor or the cluster nodes when the pipeline\ + \ is deployed through a grid executor.\n\nViash implements allows either\ + \ a string value or a map. In case a map is used, the allowed keys are:\ + \ `registry`, `image`, and `tag`. The `image` value must be specified.\n\ + \nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n" + type: "object" + additionalProperties: + description: "The `container` directive allows you to execute the process\ + \ script in a Docker container.\n\nIt requires the Docker daemon to\ + \ be running in machine where the pipeline is executed, i.e. the local\ + \ machine when using the local executor or the cluster nodes when the\ + \ pipeline is deployed through a grid executor.\n\nViash implements\ + \ allows either a string value or a map. In case a map is used, the\ + \ allowed keys are: `registry`, `image`, and `tag`. The `image` value\ + \ must be specified.\n\nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n" + type: "string" + - description: "The `container` directive allows you to execute the process\ + \ script in a Docker container.\n\nIt requires the Docker daemon to be\ + \ running in machine where the pipeline is executed, i.e. the local machine\ + \ when using the local executor or the cluster nodes when the pipeline\ + \ is deployed through a grid executor.\n\nViash implements allows either\ + \ a string value or a map. In case a map is used, the allowed keys are:\ + \ `registry`, `image`, and `tag`. The `image` value must be specified.\n\ + \nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n" + type: "string" + publishDir: + anyOf: + - anyOf: + - description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are:\ + \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path`\ + \ key and value are required.\nThe allowed values for `mode` are: `symlink`,\ + \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "string" + - description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are:\ + \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path`\ + \ key and value are required.\nThe allowed values for `mode` are: `symlink`,\ + \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "object" + additionalProperties: + description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are:\ + \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\ + \ `path` key and value are required.\nThe allowed values for `mode`\ + \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\ + \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "string" + - description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are: `path`,\ + \ `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key\ + \ and value are required.\nThe allowed values for `mode` are: `symlink`,\ + \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "array" + items: + anyOf: + - description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are:\ + \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\ + \ `path` key and value are required.\nThe allowed values for `mode`\ + \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\ + \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "string" + - description: "The `publishDir` directive allows you to publish the process\ + \ output files to a specified folder.\n\nViash implements this directive\ + \ as a plain string or a map. The allowed keywords for the map are:\ + \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\ + \ `path` key and value are required.\nThe allowed values for `mode`\ + \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\ + \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "object" + additionalProperties: + description: "The `publishDir` directive allows you to publish the\ + \ process output files to a specified folder.\n\nViash implements\ + \ this directive as a plain string or a map. The allowed keywords\ + \ for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`,\ + \ `enabled`. The `path` key and value are required.\nThe allowed\ + \ values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`,\ + \ `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n" + type: "string" + maxForks: + anyOf: + - description: "The `maxForks` directive allows you to define the maximum\ + \ number of process instances that can be executed in parallel. By default\ + \ this value is equals to the number of CPU cores available minus 1.\n\ + \nIf you want to execute a process in a sequential manner, set this directive\ + \ to one.\n\nSee [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks).\n" + type: "string" + - description: "The `maxForks` directive allows you to define the maximum\ + \ number of process instances that can be executed in parallel. By default\ + \ this value is equals to the number of CPU cores available minus 1.\n\ + \nIf you want to execute a process in a sequential manner, set this directive\ + \ to one.\n\nSee [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks).\n" + type: "integer" + maxErrors: + anyOf: + - description: "The `maxErrors` directive allows you to specify the maximum\ + \ number of times a process can fail when using the `retry` error strategy.\ + \ By default this directive is disabled.\n\nSee [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors).\n" + type: "string" + - description: "The `maxErrors` directive allows you to specify the maximum\ + \ number of times a process can fail when using the `retry` error strategy.\ + \ By default this directive is disabled.\n\nSee [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors).\n" + type: "integer" + cpus: + anyOf: + - description: "The `cpus` directive allows you to define the number of (logical)\ + \ CPU required by the process' task.\n\nSee [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus).\n" + type: "integer" + - description: "The `cpus` directive allows you to define the number of (logical)\ + \ CPU required by the process' task.\n\nSee [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus).\n" + type: "string" + accelerator: + description: "The `accelerator` directive allows you to specify the hardware\ + \ accelerator requirement for the task execution e.g. GPU processor.\n\n\ + Viash implements this directive as a map with accepted keywords: `type`,\ + \ `limit`, `request`, and `runtime`.\n\nSee [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator).\n" + type: "object" + additionalProperties: + description: "The `accelerator` directive allows you to specify the hardware\ + \ accelerator requirement for the task execution e.g. GPU processor.\n\ + \nViash implements this directive as a map with accepted keywords: `type`,\ + \ `limit`, `request`, and `runtime`.\n\nSee [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator).\n" + type: "string" + time: + description: "The `time` directive allows you to define how long a process\ + \ is allowed to run.\n\nSee [`time`](https://www.nextflow.io/docs/latest/process.html#time).\n" + type: "string" + afterScript: + description: "The `afterScript` directive allows you to execute a custom (Bash)\ + \ snippet immediately after the main process has run. This may be useful\ + \ to clean up your staging area.\n\nSee [`afterScript`](https://www.nextflow.io/docs/latest/process.html#afterscript).\n" + type: "string" + executor: + description: "The `executor` defines the underlying system where processes\ + \ are executed. By default a process uses the executor defined globally\ + \ in the nextflow.config file.\n\nThe `executor` directive allows you to\ + \ configure what executor has to be used by the process, overriding the\ + \ default configuration. The following values can be used:\n\n| Name | Executor\ + \ |\n|------|----------|\n| awsbatch | The process is executed using the\ + \ AWS Batch service. | \n| azurebatch | The process is executed using the\ + \ Azure Batch service. | \n| condor | The process is executed using the\ + \ HTCondor job scheduler. | \n| google-lifesciences | The process is executed\ + \ using the Google Genomics Pipelines service. | \n| ignite | The process\ + \ is executed using the Apache Ignite cluster. | \n| k8s | The process is\ + \ executed using the Kubernetes cluster. | \n| local | The process is executed\ + \ in the computer where Nextflow is launched. | \n| lsf | The process is\ + \ executed using the Platform LSF job scheduler. | \n| moab | The process\ + \ is executed using the Moab job scheduler. | \n| nqsii | The process is\ + \ executed using the NQSII job scheduler. | \n| oge | Alias for the sge\ + \ executor. | \n| pbs | The process is executed using the PBS/Torque job\ + \ scheduler. | \n| pbspro | The process is executed using the PBS Pro job\ + \ scheduler. | \n| sge | The process is executed using the Sun Grid Engine\ + \ / Open Grid Engine. | \n| slurm | The process is executed using the SLURM\ + \ job scheduler. | \n| tes | The process is executed using the GA4GH TES\ + \ service. | \n| uge | Alias for the sge executor. |\n\nSee [`executor`](https://www.nextflow.io/docs/latest/process.html#executor).\n" + type: "string" + containerOptions: + anyOf: + - description: "The `containerOptions` directive allows you to specify any\ + \ container execution option supported by the underlying container engine\ + \ (ie. Docker, Singularity, etc). This can be useful to provide container\ + \ settings only for a specific process e.g. mount a custom path.\n\nSee\ + \ [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions).\n" + type: "string" + - description: "The `containerOptions` directive allows you to specify any\ + \ container execution option supported by the underlying container engine\ + \ (ie. Docker, Singularity, etc). This can be useful to provide container\ + \ settings only for a specific process e.g. mount a custom path.\n\nSee\ + \ [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions).\n" + type: "array" + items: + type: "string" + disk: + description: "The `disk` directive allows you to define how much local disk\ + \ storage the process is allowed to use.\n\nSee [`disk`](https://www.nextflow.io/docs/latest/process.html#disk).\n" + type: "string" + tag: + description: "The `tag` directive allows you to associate each process execution\ + \ with a custom label, so that it will be easier to identify them in the\ + \ log file or in the trace execution report.\n\nSee [`tag`](https://www.nextflow.io/docs/latest/process.html#tag).\n" + type: "string" + conda: + anyOf: + - description: "The `conda` directive allows for the definition of the process\ + \ dependencies using the Conda package manager.\n\nNextflow automatically\ + \ sets up an environment for the given package names listed by in the\ + \ `conda` directive.\n\nSee [`conda`](https://www.nextflow.io/docs/latest/process.html#conda).\n" + type: "string" + - description: "The `conda` directive allows for the definition of the process\ + \ dependencies using the Conda package manager.\n\nNextflow automatically\ + \ sets up an environment for the given package names listed by in the\ + \ `conda` directive.\n\nSee [`conda`](https://www.nextflow.io/docs/latest/process.html#conda).\n" + type: "array" + items: + type: "string" + machineType: + description: " The `machineType` can be used to specify a predefined Google\ + \ Compute Platform machine type when running using the Google Life Sciences\ + \ executor.\n\nSee [`machineType`](https://www.nextflow.io/docs/latest/process.html#machinetype).\n" + type: "string" + stageInMode: + description: "The `stageInMode` directive defines how input files are staged-in\ + \ to the process work directory. The following values are allowed:\n\n|\ + \ Value | Description |\n|-------|-------------| \n| copy | Input files\ + \ are staged in the process work directory by creating a copy. | \n| link\ + \ | Input files are staged in the process work directory by creating an\ + \ (hard) link for each of them. | \n| symlink | Input files are staged in\ + \ the process work directory by creating a symbolic link with an absolute\ + \ path for each of them (default). | \n| rellink | Input files are staged\ + \ in the process work directory by creating a symbolic link with a relative\ + \ path for each of them. | \n\nSee [`stageInMode`](https://www.nextflow.io/docs/latest/process.html#stageinmode).\n" + type: "string" + cache: + anyOf: + - description: "The `cache` directive allows you to store the process results\ + \ to a local cache. When the cache is enabled and the pipeline is launched\ + \ with the resume option, any following attempt to execute the process,\ + \ along with the same inputs, will cause the process execution to be skipped,\ + \ producing the stored data as the actual results.\n\nThe caching feature\ + \ generates a unique key by indexing the process script and inputs. This\ + \ key is used to identify univocally the outputs produced by the process\ + \ execution.\n\nThe `cache` is enabled by default, you can disable it\ + \ for a specific process by setting the cache directive to `false`.\n\n\ + Accepted values are: `true`, `false`, `\"deep\"`, and `\"lenient\"`.\n\ + \nSee [`cache`](https://www.nextflow.io/docs/latest/process.html#cache).\n" + type: "boolean" + - description: "The `cache` directive allows you to store the process results\ + \ to a local cache. When the cache is enabled and the pipeline is launched\ + \ with the resume option, any following attempt to execute the process,\ + \ along with the same inputs, will cause the process execution to be skipped,\ + \ producing the stored data as the actual results.\n\nThe caching feature\ + \ generates a unique key by indexing the process script and inputs. This\ + \ key is used to identify univocally the outputs produced by the process\ + \ execution.\n\nThe `cache` is enabled by default, you can disable it\ + \ for a specific process by setting the cache directive to `false`.\n\n\ + Accepted values are: `true`, `false`, `\"deep\"`, and `\"lenient\"`.\n\ + \nSee [`cache`](https://www.nextflow.io/docs/latest/process.html#cache).\n" + type: "string" + pod: + anyOf: + - description: "The `pod` directive allows the definition of pods specific\ + \ settings, such as environment variables, secrets and config maps when\ + \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n" + type: "object" + additionalProperties: + description: "The `pod` directive allows the definition of pods specific\ + \ settings, such as environment variables, secrets and config maps when\ + \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n" + type: "string" + - description: "The `pod` directive allows the definition of pods specific\ + \ settings, such as environment variables, secrets and config maps when\ + \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n" + type: "array" + items: + type: "object" + additionalProperties: + type: "string" + penv: + description: "The `penv` directive allows you to define the parallel environment\ + \ to be used when submitting a parallel task to the SGE resource manager.\n\ + \nSee [`penv`](https://www.nextflow.io/docs/latest/process.html#penv).\n" + type: "string" + scratch: + anyOf: + - description: "The `scratch` directive allows you to execute the process\ + \ in a temporary folder that is local to the execution node.\n\nSee [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch).\n" + type: "boolean" + - description: "The `scratch` directive allows you to execute the process\ + \ in a temporary folder that is local to the execution node.\n\nSee [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch).\n" + type: "string" + storeDir: + description: "The `storeDir` directive allows you to define a directory that\ + \ is used as a permanent cache for your process results.\n\nSee [`storeDir`](https://www.nextflow.io/docs/latest/process.html#storeDir).\n" + type: "string" + maxRetries: + anyOf: + - description: "The `maxRetries` directive allows you to define the maximum\ + \ number of times a process instance can be re-submitted in case of failure.\ + \ This value is applied only when using the retry error strategy. By default\ + \ only one retry is allowed.\n\nSee [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries).\n" + type: "string" + - description: "The `maxRetries` directive allows you to define the maximum\ + \ number of times a process instance can be re-submitted in case of failure.\ + \ This value is applied only when using the retry error strategy. By default\ + \ only one retry is allowed.\n\nSee [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries).\n" + type: "integer" + echo: + anyOf: + - description: "By default the stdout produced by the commands executed in\ + \ all processes is ignored. By setting the `echo` directive to true, you\ + \ can forward the process stdout to the current top running process stdout\ + \ file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" + type: "boolean" + - description: "By default the stdout produced by the commands executed in\ + \ all processes is ignored. By setting the `echo` directive to true, you\ + \ can forward the process stdout to the current top running process stdout\ + \ file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n" + type: "string" + errorStrategy: + description: "The `errorStrategy` directive allows you to define how an error\ + \ condition is managed by the process. By default when an error status is\ + \ returned by the executed script, the process stops immediately. This in\ + \ turn forces the entire pipeline to terminate.\n\nTable of available error\ + \ strategies:\n| Name | Executor |\n|------|----------|\n| `terminate` |\ + \ Terminates the execution as soon as an error condition is reported. Pending\ + \ jobs are killed (default) |\n| `finish` | Initiates an orderly pipeline\ + \ shutdown when an error condition is raised, waiting the completion of\ + \ any submitted job. |\n| `ignore` | Ignores processes execution errors.\ + \ |\n| `retry` | Re-submit for execution a process returning an error condition.\ + \ |\n\nSee [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy).\n" + type: "string" + memory: + description: "The `memory` directive allows you to define how much memory\ + \ the process is allowed to use.\n\nSee [`memory`](https://www.nextflow.io/docs/latest/process.html#memory).\n" + type: "string" + stageOutMode: + description: "The `stageOutMode` directive defines how output files are staged-out\ + \ from the scratch directory to the process work directory. The following\ + \ values are allowed:\n\n| Value | Description |\n|-------|-------------|\ + \ \n| copy | Output files are copied from the scratch directory to the work\ + \ directory. | \n| move | Output files are moved from the scratch directory\ + \ to the work directory. | \n| rsync | Output files are copied from the\ + \ scratch directory to the work directory by using the rsync utility. |\n\ + \nSee [`stageOutMode`](https://www.nextflow.io/docs/latest/process.html#stageoutmode).\n" + type: "string" + required: [] + additionalProperties: false + NextflowAuto: + description: "Automated processing flags which can be toggled on or off." + type: "object" + properties: + simplifyInput: + description: "If `true`, an input tuple only containing only a single File\ + \ (e.g. `[\"foo\", file(\"in.h5ad\")]`) is automatically transformed to\ + \ a map (i.e. `[\"foo\", [ input: file(\"in.h5ad\") ] ]`).\n\nDefault: `true`.\n" + type: "boolean" + simplifyOutput: + description: "If `true`, an output tuple containing a map with a File (e.g.\ + \ `[\"foo\", [ output: file(\"out.h5ad\") ] ]`) is automatically transformed\ + \ to a map (i.e. `[\"foo\", file(\"out.h5ad\")]`).\n\nDefault: `true`.\n" + type: "boolean" + publish: + description: "If `true`, the module's outputs are automatically published\ + \ to `params.publishDir`.\nWill throw an error if `params.publishDir` is\ + \ not defined.\n\nDefault: `false`.\n" + type: "boolean" + transcript: + description: "If `true`, the module's transcripts from `work/` are automatically\ + \ published to `params.transcriptDir`.\nIf not defined, `params.publishDir\ + \ + \"/_transcripts\"` will be used.\nWill throw an error if neither are\ + \ defined.\n\nDefault: `false`.\n" + type: "boolean" + required: [] + additionalProperties: false + NextflowConfig: + description: "Allows tweaking how the Nextflow Config file is generated." + type: "object" + properties: + labels: + description: "A series of default labels to specify memory and cpu constraints.\n\ + \nThe default memory labels are defined as \"mem1gb\", \"mem2gb\", \"mem4gb\"\ + , ... upto \"mem512tb\" and follows powers of 2.\nThe default cpu labels\ + \ are defined as \"cpu1\", \"cpu2\", \"cpu5\", \"cpu10\", ... upto \"cpu1000\"\ + \ and follows a semi logarithmic scale (1, 2, 5 per decade).\n\nConceptually\ + \ it is possible for a Viash Config to overwrite the full labels parameter,\ + \ however likely it is more efficient to add additional labels\nin the Viash\ + \ Project with a config mod.\n" + type: "object" + additionalProperties: + description: "A series of default labels to specify memory and cpu constraints.\n\ + \nThe default memory labels are defined as \"mem1gb\", \"mem2gb\", \"\ + mem4gb\", ... upto \"mem512tb\" and follows powers of 2.\nThe default\ + \ cpu labels are defined as \"cpu1\", \"cpu2\", \"cpu5\", \"cpu10\", ...\ + \ upto \"cpu1000\" and follows a semi logarithmic scale (1, 2, 5 per decade).\n\ + \nConceptually it is possible for a Viash Config to overwrite the full\ + \ labels parameter, however likely it is more efficient to add additional\ + \ labels\nin the Viash Project with a config mod.\n" + type: "string" + script: + anyOf: + - description: "Includes a single string or list of strings into the nextflow.config\ + \ file.\nThis can be used to add custom profiles or include an additional\ + \ config file.\n" + type: "string" + - description: "Includes a single string or list of strings into the nextflow.config\ + \ file.\nThis can be used to add custom profiles or include an additional\ + \ config file.\n" + type: "array" + items: + type: "string" + required: [] + additionalProperties: false + DockerSetupStrategy: + $comment: "TODO add descriptions to different strategies" + enum: + - "cb" + - "ifneedbepullelsecachedbuild" + - "donothing" + - "gentlepush" + - "alwayspullelsebuild" + - "build" + - "alwayspull" + - "alwaysbuild" + - "ifneedbebuild" + - "pullelsebuild" + - "p" + - "alwayspullelsecachedbuild" + - "pull" + - "maybepush" + - "ifneedbepullelsebuild" + - "cachedbuild" + - "pullelsecachedbuild" + - "push" + - "forcepush" + - "alwayspush" + - "b" + - "pushifnotpresent" + - "alwayscachedbuild" + - "meh" + - "ifneedbepull" + - "ifneedbecachedbuild" + description: "The Docker setup strategy to use when building a container." + Direction: + enum: + - "input" + - "output" + description: "Makes this argument an `input` or an `output`, as in does the file/folder\ + \ needs to be read or written. `input` by default." + Status: + enum: + - "enabled" + - "disabled" + - "deprecated" + description: "Allows setting a component to active, deprecated or disabled." + DockerResolveVolume: + $comment: "TODO make fully case insensitive" + enum: + - "manual" + - "automatic" + - "auto" + - "Manual" + - "Automatic" + - "Auto" + description: "Enables or disables automatic volume mapping. Enabled when set to\ + \ `Automatic` or disabled when set to `Manual`. Default: `Automatic`" diff --git a/src/common/api/schema_task_control_method.yaml b/src/common/schemas/task_control_method.yaml similarity index 57% rename from src/common/api/schema_task_control_method.yaml rename to src/common/schemas/task_control_method.yaml index e4e72b49ba..f4e760db50 100644 --- a/src/common/api/schema_task_control_method.yaml +++ b/src/common/schemas/task_control_method.yaml @@ -10,7 +10,7 @@ type: object required: [__merge__, functionality, platforms] properties: __merge__: - "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + "$ref": "defs_common.yaml#/definitions/CompAPIMerge" functionality: type: object description: Information regarding the functionality of the component. @@ -18,9 +18,9 @@ properties: additionalProperties: false properties: name: - "$ref": "schema_definitions.yaml#/definitions/Name" + "$ref": "defs_common.yaml#/definitions/Name" status: - "$ref": "schema_viash_config.yaml#/definitions/Status" + "$ref": "defs_viash.yaml#/definitions/Status" info: type: object description: Metadata of the component. @@ -28,43 +28,43 @@ properties: required: [label, summary, description, preferred_normalization] properties: label: - "$ref": "schema_definitions.yaml#/definitions/Label" + "$ref": "defs_common.yaml#/definitions/Label" summary: - "$ref": "schema_definitions.yaml#/definitions/Summary" + "$ref": "defs_common.yaml#/definitions/Summary" description: - "$ref": "schema_definitions.yaml#/definitions/Description" + "$ref": "defs_common.yaml#/definitions/Description" preferred_normalization: - "$ref": "schema_definitions.yaml#/definitions/PreferredNormalization" + "$ref": "defs_common.yaml#/definitions/PreferredNormalization" reference: - "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + "$ref": "defs_common.yaml#/definitions/BibtexReference" documentation_url: - "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + "$ref": "defs_common.yaml#/definitions/DocumentationURL" repository_url: - "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + "$ref": "defs_common.yaml#/definitions/RepositoryURL" v1: - "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + "$ref": "defs_common.yaml#/definitions/MigrationV1" variants: - "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + "$ref": "defs_common.yaml#/definitions/MethodVariants" arguments: type: array description: Component-specific parameters. items: - "$ref": "schema_viash_config.yaml#/definitions/Argument" + "$ref": "defs_viash.yaml#/definitions/Argument" resources: type: array description: Resources required to run the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" test_resources: type: array description: One or more scripts and resources used to test the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" platforms: type: array description: A list of platforms which Viash generates target artifacts for. items: anyOf: - - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" - - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" - - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" + - "$ref": "defs_common.yaml#/definitions/PlatformDocker" + - "$ref": "defs_common.yaml#/definitions/PlatformNative" + - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/schemas/task_info.yaml b/src/common/schemas/task_info.yaml new file mode 100644 index 0000000000..3f3da8f822 --- /dev/null +++ b/src/common/schemas/task_info.yaml @@ -0,0 +1,22 @@ +title: Task info +description: A file format specification file. +type: object +additionalProperties: false +required: [name, label, summary, motivation, description] +properties: + name: + $ref: "defs_common.yaml#/definitions/Name" + label: + $ref: "defs_common.yaml#/definitions/Label" + summary: + $ref: "defs_common.yaml#/definitions/Summary" + motivation: + $ref: "defs_common.yaml#/definitions/Description" + description: + $ref: "defs_common.yaml#/definitions/Description" + v1: + $ref: "defs_common.yaml#/definitions/MigrationV1" + authors: + type: array + items: + $ref: "defs_common.yaml#/definitions/Author" diff --git a/src/common/api/schema_task_method.yaml b/src/common/schemas/task_method.yaml similarity index 54% rename from src/common/api/schema_task_method.yaml rename to src/common/schemas/task_method.yaml index a1f1a02e28..c74d8b762c 100644 --- a/src/common/api/schema_task_method.yaml +++ b/src/common/schemas/task_method.yaml @@ -7,7 +7,7 @@ type: object required: [__merge__, functionality, platforms] properties: __merge__: - "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + "$ref": "defs_common.yaml#/definitions/CompAPIMerge" functionality: type: object description: Information regarding the functionality of the component. @@ -15,9 +15,9 @@ properties: additionalProperties: false properties: name: - "$ref": "schema_definitions.yaml#/definitions/Name" + "$ref": "defs_common.yaml#/definitions/Name" status: - "$ref": "schema_viash_config.yaml#/definitions/Status" + "$ref": "defs_viash.yaml#/definitions/Status" info: type: object description: Metadata of the component. @@ -25,43 +25,43 @@ properties: required: [label, summary, description, preferred_normalization, reference, documentation_url, repository_url] properties: label: - "$ref": "schema_definitions.yaml#/definitions/Label" + "$ref": "defs_common.yaml#/definitions/Label" summary: - "$ref": "schema_definitions.yaml#/definitions/Summary" + "$ref": "defs_common.yaml#/definitions/Summary" description: - "$ref": "schema_definitions.yaml#/definitions/Description" + "$ref": "defs_common.yaml#/definitions/Description" preferred_normalization: - "$ref": "schema_definitions.yaml#/definitions/PreferredNormalization" + "$ref": "defs_common.yaml#/definitions/PreferredNormalization" reference: - "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + "$ref": "defs_common.yaml#/definitions/BibtexReference" documentation_url: - "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + "$ref": "defs_common.yaml#/definitions/DocumentationURL" repository_url: - "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + "$ref": "defs_common.yaml#/definitions/RepositoryURL" v1: - "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + "$ref": "defs_common.yaml#/definitions/MigrationV1" variants: - "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + "$ref": "defs_common.yaml#/definitions/MethodVariants" arguments: type: array description: Component-specific parameters. items: - "$ref": "schema_viash_config.yaml#/definitions/Argument" + "$ref": "defs_viash.yaml#/definitions/Argument" resources: type: array description: Resources required to run the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" test_resources: type: array description: One or more scripts and resources used to test the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" platforms: type: array description: A list of platforms which Viash generates target artifacts for. items: anyOf: - - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" - - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" - - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" + - "$ref": "defs_common.yaml#/definitions/PlatformDocker" + - "$ref": "defs_common.yaml#/definitions/PlatformNative" + - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3" diff --git a/src/common/api/schema_task_metric.yaml b/src/common/schemas/task_metric.yaml similarity index 63% rename from src/common/api/schema_task_metric.yaml rename to src/common/schemas/task_metric.yaml index dc36af9f1e..31a687b49a 100644 --- a/src/common/api/schema_task_metric.yaml +++ b/src/common/schemas/task_metric.yaml @@ -6,7 +6,7 @@ type: object required: [__merge__, functionality, platforms] properties: __merge__: - "$ref": "schema_definitions.yaml#/definitions/CompAPIMerge" + "$ref": "defs_common.yaml#/definitions/CompAPIMerge" functionality: type: object description: Information regarding the functionality of the component. @@ -14,9 +14,9 @@ properties: additionalProperties: false properties: name: - "$ref": "schema_definitions.yaml#/definitions/Name" + "$ref": "defs_common.yaml#/definitions/Name" status: - "$ref": "schema_viash_config.yaml#/definitions/Status" + "$ref": "defs_viash.yaml#/definitions/Status" info: type: object description: Metadata of the component. @@ -33,21 +33,21 @@ properties: required: [label, summary, description, reference, min, max, maximize] properties: name: - "$ref": "schema_definitions.yaml#/definitions/Name" + "$ref": "defs_common.yaml#/definitions/Name" label: - "$ref": "schema_definitions.yaml#/definitions/Label" + "$ref": "defs_common.yaml#/definitions/Label" summary: - "$ref": "schema_definitions.yaml#/definitions/Summary" + "$ref": "defs_common.yaml#/definitions/Summary" description: - "$ref": "schema_definitions.yaml#/definitions/Description" + "$ref": "defs_common.yaml#/definitions/Description" reference: - "$ref": "schema_definitions.yaml#/definitions/BibtexReference" + "$ref": "defs_common.yaml#/definitions/BibtexReference" documentation_url: - "$ref": "schema_definitions.yaml#/definitions/DocumentationURL" + "$ref": "defs_common.yaml#/definitions/DocumentationURL" repository_url: - "$ref": "schema_definitions.yaml#/definitions/RepositoryURL" + "$ref": "defs_common.yaml#/definitions/RepositoryURL" variants: - "$ref": "schema_definitions.yaml#/definitions/MethodVariants" + "$ref": "defs_common.yaml#/definitions/MethodVariants" min: oneOf: - type: number @@ -62,27 +62,27 @@ properties: type: boolean description: Whether a higher metric value is better. v1: - "$ref": "schema_definitions.yaml#/definitions/MigrationV1" + "$ref": "defs_common.yaml#/definitions/MigrationV1" arguments: type: array description: Component-specific parameters. items: - "$ref": "schema_viash_config.yaml#/definitions/Argument" + "$ref": "defs_viash.yaml#/definitions/Argument" resources: type: array description: Resources required to run the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" test_resources: type: array description: One or more scripts and resources used to test the component. items: - "$ref": "schema_viash_config.yaml#/definitions/Resource" + "$ref": "defs_viash.yaml#/definitions/Resource" platforms: type: array description: A list of platforms which Viash generates target artifacts for. items: anyOf: - - "$ref": "schema_definitions.yaml#/definitions/PlatformDocker" - - "$ref": "schema_definitions.yaml#/definitions/PlatformNative" - - "$ref": "schema_definitions.yaml#/definitions/PlatformVdsl3" + - "$ref": "defs_common.yaml#/definitions/PlatformDocker" + - "$ref": "defs_common.yaml#/definitions/PlatformNative" + - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3" From bd0076d5e993f9ca0feb3f319239fa0fcb50a4f3 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Jun 2023 17:16:20 +0200 Subject: [PATCH 0923/1233] Create component for rendering the readme from the task api (#182) * WIP version of create_task_readme component * update denoising readme * add label_projection readme * update component based on new task info format * update readmes * fix readme * add quotes * workaround for 'graph' in mermaid * fix config * fix create task readme component * fix component & output Former-commit-id: 0e19901bcc2eb41799e2b4926c876871ff87614a --- src/common/create_task_readme/config.vsh.yaml | 54 ++ src/common/create_task_readme/render_all.sh | 8 + src/common/create_task_readme/script.R | 102 ++++ src/common/create_task_readme/test.R | 29 ++ .../helper_functions/read_and_merge_yaml.R | 47 +- src/common/helper_functions/read_api_files.R | 149 +++++- src/tasks/batch_integration/README.md | 490 +++++++++++++++++- src/tasks/denoising/README.md | 345 +++++++++++- src/tasks/dimensionality_reduction/README.md | 352 ++++++++++++- src/tasks/label_projection/README.md | 405 ++++++++++++++- 10 files changed, 1905 insertions(+), 76 deletions(-) create mode 100644 src/common/create_task_readme/config.vsh.yaml create mode 100755 src/common/create_task_readme/render_all.sh create mode 100644 src/common/create_task_readme/script.R create mode 100644 src/common/create_task_readme/test.R diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml new file mode 100644 index 0000000000..6f41273616 --- /dev/null +++ b/src/common/create_task_readme/config.vsh.yaml @@ -0,0 +1,54 @@ +functionality: + name: create_task_readme + namespace: common + description: | + Create a README for the task. + arguments: + - type: string + name: --task + description: Which task the component will be added to. + example: denoising + - type: file + name: --output + direction: output + description: Path to the component directory. Suggested location is `src//README.md`. + default: src/tasks/${VIASH_PAR_TASK}/README.md + - type: file + name: --viash_yaml + description: | + Path to the project config file. Needed for knowing the relative location of a file to the project root. + default: "_viash.yaml" + resources: + - type: r_script + path: script.R + - path: /src/common/helper_functions/read_and_merge_yaml.R + - path: /src/common/helper_functions/read_api_files.R + - path: /src/common/helper_functions/strip_margin.R + test_resources: + - type: r_script + path: test.R + - path: /src + dest: openproblems-v2/src + - path: /_viash.yaml + dest: openproblems-v2/_viash.yaml +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.0 + setup: + - type: r + packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64] + - type: apt + packages: [jq, curl] + - type: docker + # download and install quarto-*-linux-amd64.deb from latest release + run: | + release_info=$(curl -s https://api.github.com/repos/quarto-dev/quarto-cli/releases/latest) && \ + download_url=$(echo "$release_info" | jq -r '.assets[] | select(.name | test("quarto-.*-linux-amd64.deb")) | .browser_download_url') && \ + curl -sL "$download_url" -o /opt/quarto.deb && \ + dpkg -i /opt/quarto.deb && \ + rm /opt/quarto.deb + - type: native + - type: nextflow + directives: + label: [ lowmem, lowcpu ] + diff --git a/src/common/create_task_readme/render_all.sh b/src/common/create_task_readme/render_all.sh new file mode 100755 index 0000000000..00dc2a8db0 --- /dev/null +++ b/src/common/create_task_readme/render_all.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +TASK_IDS=`ls src/tasks` + +for task_id in $TASK_IDS; do + echo ">> Processing $task_id" + viash run src/common/create_task_readme/config.vsh.yaml -- --task $task_id +done \ No newline at end of file diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R new file mode 100644 index 0000000000..ef3ac2d466 --- /dev/null +++ b/src/common/create_task_readme/script.R @@ -0,0 +1,102 @@ +library(rlang, quietly = TRUE, warn.conflicts = FALSE) +library(purrr, quietly = TRUE, warn.conflicts = FALSE) +library(dplyr, quietly = TRUE, warn.conflicts = FALSE) + +## VIASH START +par <- list( + "task" = "batch_integration", + "output" = "src/tasks/batch_integration/README.md", + "viash_yaml" = "_viash.yaml" +) +meta <- list( + "resources_dir" = "src/common/helper_functions", + "temp_dir" = "temp/" +) +## VIASH END + +# import helper function +source(paste0(meta["resources_dir"], "/read_and_merge_yaml.R")) +source(paste0(meta["resources_dir"], "/strip_margin.R")) +source(paste0(meta["resources_dir"], "/read_api_files.R")) + +cat("Read task info\n") +task_dir <- paste0(dirname(par[["viash_yaml"]]), "/src/tasks/", par[["task"]]) %>% + gsub("^\\./", "", .) +task_api <- read_task_api(task_dir) + +r_graph <- render_task_graph(task_api) + +# todo: fix hard coded node +order <- names(igraph::bfs(task_api$task_graph, "file_common_dataset")$order) + +cat("Render API details\n") +r_details <- map_chr( + order, + function(file_name) { + if (file_name %in% names(task_api$comp_specs)) { + render_component(task_api$comp_specs[[file_name]]) + } else { + render_file(task_api$file_specs[[file_name]]) + } + } +) + +cat("Render authors\n") +authors_str <- + if (nrow(task_api$authors) > 0) { + paste0( + "\n## Authors & contributors\n\n", + task_api$authors %>% knitr::kable() %>% paste(collapse = "\n"), + "\n" + ) + } else { + "" + } + +cat("Generate qmd content\n") +qmd_content <- strip_margin(glue::glue(" + §--- + §title: \"{task_api$task_info$label}\" + §format: gfm + §--- + § + §{task_api$task_info$summary} + § + §Path: [`{task_dir}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{task_dir}) + § + §## Motivation + § + §{task_api$task_info$motivation} + § + §## Description + § + §{task_api$task_info$description} + §{authors_str} + §## API + § + §{r_graph} + § + §{paste(r_details, collapse = '\n\n')} + § + §"), symbol = "§") + +cat("Write README.qmd to file\n") +qmd_file <- tempfile( + pattern = "README_", + fileext = ".qmd", + tmpdir = meta$temp_dir +) + +if (!dir.exists(meta$temp_dir)) { + dir.create(meta$temp_dir, recursive = TRUE) +} +writeLines(qmd_content, qmd_file) + +cat("Render README.qmd to README.md\n") +md_content <- system( + paste0("quarto render ", qmd_file, " --output -"), + ignore.stderr = TRUE, + intern = TRUE +) + +writeLines(md_content, par$output) \ No newline at end of file diff --git a/src/common/create_task_readme/test.R b/src/common/create_task_readme/test.R new file mode 100644 index 0000000000..abf3f4521f --- /dev/null +++ b/src/common/create_task_readme/test.R @@ -0,0 +1,29 @@ + +## VIASH START + +## VIASH END + +opv2 <- paste0(meta$resources_dir, "/openproblems-v2") +output_path <- "output.md" + +cat(">> Running the script as test\n") +system(paste( + meta["executable"], + "--task", "label_projection", + "--output", output_path, + "--viash_yaml", paste0(opv2, "/_viash.yaml") +)) + +cat(">> Checking whether output files exist\n") +assertthat::assert_that(file.exists(output_path)) + +cat(">> Checking file contents\n") +lines <- readLines(output_path) +assertthat::assert_that(any(grepl("# Label projection", lines))) +assertthat::assert_that(any(grepl("# Description", lines))) +assertthat::assert_that(any(grepl("# Motivation", lines))) +assertthat::assert_that(any(grepl("# Authors", lines))) +assertthat::assert_that(any(grepl("flowchart LR", lines))) +assertthat::assert_that(any(grepl("# File format:", lines))) + +cat("All checks succeeded!\n") diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R index 5663630c55..f5e96d8cc0 100644 --- a/src/common/helper_functions/read_and_merge_yaml.R +++ b/src/common/helper_functions/read_and_merge_yaml.R @@ -5,28 +5,49 @@ #' lists will be merged. This is a recursive procedure. #' #' @param path Path to Viash YAML -read_and_merge_yaml <- function(path) { - data <- suppressWarnings(yaml::read_yaml(path)) - .ram_process_merge(data, path) +read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { + path <- normalizePath(path, mustWork = FALSE) + data <- tryCatch({ + suppressWarnings(yaml::read_yaml(path)) + }, error = function(e) { + stop("Could not read ", path, ". Error: ", e) + }) + .ram_process_merge(data, path, project_path) +} + +.ram_find_project <- function(path) { + path <- normalizePath(path, mustWork = FALSE) + check <- paste0(dirname(path), "/_viash.yaml") + if (file.exists(check)) { + dirname(check) + } else if (check == "//_viash.yaml") { + NULL + } else { + .ram_find_project(dirname(check)) + } } .ram_is_named_list <- function(obj) { is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj)))) } -.ram_process_merge <- function(data, path) { +.ram_process_merge <- function(data, path, project_path) { if (.ram_is_named_list(data)) { # check whether children have `__merge__` entries processed_data <- lapply(data, function(dat) { - .ram_process_merge(dat, path) + .ram_process_merge(dat, path, project_path) }) names(processed_data) <- names(data) # if current element has __merge__, read list2 yaml and combine with data - new_data <- + new_data <- if ("__merge__" %in% names(processed_data)) { - new_data_path <- paste0(dirname(path), "/", processed_data$`__merge__`) - read_and_merge_yaml(new_data_path) + new_data_path <- .ram_resolve_path( + path = processed_data$`__merge__`, + project_path = project_path, + parent_path = dirname(path) + ) + read_and_merge_yaml(new_data_path, project_path) } else { list() } @@ -34,13 +55,21 @@ read_and_merge_yaml <- function(path) { .ram_deep_merge(new_data, processed_data) } else if (is.list(data)) { lapply(data, function(dat) { - .ram_process_merge(dat, path) + .ram_process_merge(dat, path, project_path) }) } else { data } } +.ram_resolve_path <- function(path, project_path, parent_path) { + ifelse( + grepl("^/", path), + paste0(project_path, "/", path), + fs::path_abs(path, parent_path) + ) +} + .ram_deep_merge <- function(list1, list2) { if (.ram_is_named_list(list1) && .ram_is_named_list(list2)) { # if list1 and list2 are objects, recursively merge diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index d8441fa0cd..c7c5a9fc5d 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -16,6 +16,8 @@ read_anndata_info <- function(spec, path) { df <- dplyr::bind_cols(df, list_as_tibble(spec$info)) } df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + df$description <- df$description %||% NA_character_ %>% as.character + df$summary <- df$summary %||% NA_character_ %>% as.character as_tibble(df) } read_anndata_slots <- function(spec, path) { @@ -104,6 +106,7 @@ read_comp_info <- function(spec_yaml, path) { df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) as_tibble(df) } + read_comp_args <- function(spec_yaml, path) { arguments <- spec_yaml$functionality$arguments for (arg_group in spec_yaml$functionality$argument_groups) { @@ -115,7 +118,7 @@ read_comp_args <- function(spec_yaml, path) { df <- dplyr::bind_cols(df, list_as_tibble(arg$info)) } df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) - df$arg_name <- stringr::str_replace_all(arg$name, "^-*", "") + df$arg_name <- gsub("^-*", "", arg$name) df$direction <- df$direction %||% "input" %|% "input" df$parent <- df$`__merge__` %||% NA_character_ %>% basename() %>% gsub("\\.yaml", "", .) df$required <- df$required %||% FALSE %|% FALSE @@ -160,11 +163,13 @@ format_comp_args_as_tibble <- function(spec) { } # path <- "src/datasets/api/comp_processor_knn.yaml" -render_component <- function(path) { - spec <- read_comp_spec(path) +render_component <- function(spec) { + if (is.character(spec)) { + spec <- read_comp_spec(spec) + } - cat(strip_margin(glue::glue(" - §# Component type: {spec$info$label} + strip_margin(glue::glue(" + §## Component type: {spec$info$label} § §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{spec$info$namespace}) § @@ -176,19 +181,29 @@ render_component <- function(path) { §{paste(format_comp_args_as_tibble(spec), collapse = '\n')} §::: § - §"), symbol = "§")) + §"), symbol = "§") } # path <- "src/datasets/api/file_pca.yaml" -render_file <- function(path) { - spec <- read_anndata_spec(path) +render_file <- function(spec) { + if (is.character(spec)) { + spec <- read_anndata_spec(spec) + } + + if (!"label" %in% names(spec$info)) { + spec$info$label <- basename(spec$info$example) + } - cat(strip_margin(glue::glue(" - §# File format: {spec$info$label} + strip_margin(glue::glue(" + §## File format: {spec$info$label} + § + §{spec$info$summary %||% ''} § §Example file: `{spec$info$example %|% ''}` § - §{spec$info$summary} + §Description: + § + §{spec$info$description %||% ''} § §Format: § @@ -202,5 +217,113 @@ render_file <- function(path) { §{paste(format_slots_as_kable(spec), collapse = '\n')} §::: § - §"), symbol = "§")) -} \ No newline at end of file + §"), symbol = "§") +} + +# path <- "src/tasks/denoising" +read_task_api <- function(path) { + cli::cli_inform("Looking for project root") + project_path <- .ram_find_project(path) + api_dir <- paste0(path, "/api") + + cli::cli_inform("Reading task info") + task_info_yaml <- list.files(api_dir, pattern = "task_info.ya?ml", full.names = TRUE) + assertthat::assert_that(length(task_info_yaml) == 1) + task_info <- read_and_merge_yaml(task_info_yaml, project_path) + + cli::cli_inform("Reading task authors") + authors <- map_df(task_info$authors, function(aut) { + aut$roles <- paste(aut$roles, collapse = ", ") + list_as_tibble(aut) + }) + + cli::cli_inform("Reading component yamls") + comp_yamls <- list.files(api_dir, pattern = "comp_.*\\.ya?ml", full.names = TRUE) + comps <- map(comp_yamls, read_comp_spec) + comp_info <- map_df(comps, "info") + comp_args <- map_df(comps, "args") + names(comps) <- basename(comp_yamls) %>% gsub("\\..*$", "", .) + + cli::cli_inform("Reading file yamls") + file_yamls <- .ram_resolve_path( + path = na.omit(unique(comp_args$`__merge__`)), + project_path = project_path, + parent_path = api_dir + ) + files <- map(file_yamls, read_anndata_spec) + names(files) <- basename(file_yamls) %>% gsub("\\..*$", "", .) + file_info <- map_df(files, "info") + file_slots <- map_df(files, "slots") + + cli::cli_inform("Generating task graph") + task_graph <- create_task_graph(file_info, comp_info, comp_args) + + list( + task_info = task_info, + file_specs = files, + file_info = file_info, + file_slots = file_slots, + comp_specs = comps, + comp_info = comp_info, + comp_args = comp_args, + task_graph = task_graph, + authors = authors + ) +} + + +create_task_graph <- function(file_info, comp_info, comp_args) { + clean_id <- function(id) { + gsub("graph", "graaf", id) + } + nodes <- + bind_rows( + file_info %>% + mutate(id = file_name, label = label, is_comp = FALSE), + comp_info %>% + mutate(id = file_name, label = label, is_comp = TRUE) + ) %>% + select(id, label, everything()) %>% + mutate(str = paste0( + " ", + clean_id(id), + ifelse(is_comp, "[/\"", "(\""), + label, + ifelse(is_comp, "\"/]", "\")") + )) + edges <- bind_rows( + comp_args %>% + filter(type == "file", direction == "input") %>% + mutate( + from = parent, + to = file_name, + arrow = "---" + ), + comp_args %>% + filter(type == "file", direction == "output") %>% + mutate( + from = file_name, + to = parent, + arrow = "-->" + ) + ) %>% + select(from, to, everything()) %>% + mutate(str = paste0(" ", clean_id(from), arrow, clean_id(to))) + + igraph::graph_from_data_frame( + edges, + vertices = nodes, + directed = TRUE + ) +} + +render_task_graph <- function(task_api) { + strip_margin(glue::glue(" + §```{{mermaid}} + §%%| column: screen-inset-shaded + §flowchart LR + §{paste(igraph::V(task_api$task_graph)$str, collapse = '\n')} + §{paste(igraph::E(task_api$task_graph)$str, collapse = '\n')} + §``` + §"), symbol = "§") +} diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 56a4500c51..d43f432205 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -1,9 +1,489 @@ -# Batch integration +# Batch Integration -Batch (or data) integration methods integrate datasets across batches that arise from various biological (e.g., tissue, location, individual, species) and technical (e.g., ambient RNA, lab, protocol) sources. The goal of a batch integration method is to remove unwanted batch effects in the data, while retaining biologically-meaningful variation that can help us to detect cell identities, fit cellular trajectories, or understand patterns of gene or pathway activity. +Remove unwanted batch effects from scRNA data while retaining +biologically meaningful variation. -Methods that integrate batches typically have one of three different types of output: a corrected feature matrix, a joint embedding across batches, and/or an integrated cell-cell similarity graph (e.g., a kNN graph). In order to define a consistent input and output for each method and metric, we have created separate component subtypes for each of the three method types: "graph", "embedding" and "feature". +Path: +[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/batch_integration) -These subtypes collate methods that have the same data output type and metrics that evaluate this output. As corrected feature matrices can be turned into embeddings, which in turn can be processed into integrated graphs, methods overlap between the tasks. All methods are added to the graph subtask and imported into other subtasks from there. +## Motivation -Metrics for this task either assess the removal of batch effects or assess the conservation of biological variation. This can be a helpful distinction when devising new metrics. This task, including the subtask structure, was taken from a [benchmarking study of data integration methods](https://www.biorxiv.org/content/10.1101/2020.05.22.111161v2), which is a useful reference for more background reading on this task and the above concepts. +As single-cell technologies advance, single-cell datasets are growing +both in size and complexity. Especially in consortia such as the Human +Cell Atlas, individual studies combine data from multiple labs, each +sequencing multiple individuals possibly with different technologies. +This gives rise to complex batch effects in the data that must be +computationally removed to perform a joint analysis. These batch +integration methods must remove the batch effect while not removing +relevant biological information. Currently, over 200 tools exist that +aim to remove batch effects scRNA-seq datasets \[@zappia2018exploring\]. +These methods balance the removal of batch effects with the conservation +of nuanced biological information in different ways. This abundance of +tools has complicated batch integration method choice, leading to +several benchmarks on this topic \[@luecken2020benchmarking; +@tran2020benchmark; @chazarragil2021flexible; @mereu2020benchmarking\]. +Yet, benchmarks use different metrics, method implementations and +datasets. Here we build a living benchmarking task for batch integration +methods with the vision of improving the consistency of method +evaluation. + +## Description + +In this task we evaluate batch integration methods on their ability to +remove batch effects in the data while conserving variation attributed +to biological effects. As input, methods require either normalised or +unnormalised data with multiple batches and consistent cell type labels. +The batch integrated output can be a feature matrix, a low dimensional +embedding and/or a neighbourhood graph. The respective batch-integrated +representation is then evaluated using sets of metrics that capture how +well batch effects are removed and whether biological variance is +conserved. We have based this particular task on the latest, and most +extensive benchmark of single-cell data integration methods +\[@luecken2022benchmarking\]. + +## Authors & contributors + +| name | roles | +|:------------------|:-------------------| +| Michaela Mueller | maintainer, author | +| Kai Waldrant | contributor | +| Robrecht Cannoodt | contributor | +| Daniel Strobl | author | + +## API + +``` mermaid +flowchart LR + file_unintegrated("Unintegrated") + file_integrated_embedding("Integrated embedding") + file_integrated_feature("Integrated Feature") + file_integrated_graaf("Integrated Graph") + file_score("Score") + file_common_dataset("Common dataset") + comp_method_embedding[/"Method (embedding)"/] + comp_method_feature[/"Method (feature)"/] + comp_method_graaf[/"Method (graph)"/] + comp_metric_embedding[/"Metric (embedding)"/] + comp_metric_feature[/"Metric (feature)"/] + comp_metric_graaf[/"Metric (graph)"/] + comp_process_dataset[/"Data processor"/] + file_unintegrated---comp_method_embedding + file_unintegrated---comp_method_feature + file_unintegrated---comp_method_graaf + file_integrated_embedding---comp_metric_embedding + file_integrated_feature---comp_metric_feature + file_integrated_graaf---comp_metric_graaf + file_common_dataset---comp_process_dataset + comp_method_embedding-->file_integrated_embedding + comp_method_feature-->file_integrated_feature + comp_method_graaf-->file_integrated_graaf + comp_metric_embedding-->file_score + comp_metric_feature-->file_score + comp_metric_graaf-->file_score + comp_process_dataset-->file_unintegrated +``` + +## File format: Common dataset + +A dataset processed by the common dataset processing pipeline. + +Example file: `resources_test/common/pancreas/dataset.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + obsp: 'knn_distances', 'knn_connectivities' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | +| `obs["batch"]` | `string` | (*Optional*) Batch information. | +| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + +
+ +## Component type: Data processor + +Path: +[`src/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration) + +A label projection dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:-------|:---------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | + +
+ +## File format: Unintegrated + +Unintegrated AnnData HDF5 file. + +Example file: +`resources_test/batch_integration/pancreas/unintegrated.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'label' + var: 'hvg' + obsm: 'X_pca' + obsp: 'knn_connectivities' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id', 'dataset_organism' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | Which normalization was used. | + +
+ +## Component type: Method (embedding) + +Path: +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) + +A batch integration embedding method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | +| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | + +
+ +## Component type: Method (feature) + +Path: +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) + +A batch integration feature method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | +| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | + +
+ +## Component type: Method (graph) + +Path: +[`src/batch_integration/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/methods) + +A batch integration graph method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | +| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | + +
+ +## File format: Integrated embedding + +An integrated AnnData HDF5 file. + +Example file: `resources_test/batch_integration/pancreas/scvi.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'label' + var: 'hvg' + obsm: 'X_pca', 'X_emb' + obsp: 'knn_connectivities' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsm["X_emb"]` | `double` | integration embedding prediction. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | +| `uns["output_type"]` | `string` | what kind of output has been generated. | + +
+ +## File format: Integrated Feature + +Integrated AnnData HDF5 file. + +Example file: `resources_test/batch_integration/pancreas/combat.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'label' + var: 'hvg' + obsm: 'X_pca' + obsp: 'knn_connectivities' + layers: 'counts', 'normalized', 'corrected_counts' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `layers["corrected_counts"]` | `double` | Corrected counts after integration. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | +| `uns["output_type"]` | `string` | what kind of output has been generated. | + +
+ +## File format: Integrated Graph + +Integrated AnnData HDF5 file. + +Example file: `resources_test/batch_integration/pancreas/bbknn.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'label' + var: 'hvg' + obsm: 'X_pca' + obsp: 'knn_connectivities', 'connectivities' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | +| `uns["output_type"]` | `string` | what kind of output has been generated. | + +
+ +## Component type: Metric (embedding) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration embedding metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:---------------------------------| +| `--input_integrated` | `file` | An integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## Component type: Metric (feature) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration feature metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:------------------------------| +| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## Component type: Metric (graph) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration graph metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:------------------------------| +| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Score + +Metric score file + +Example file: `score.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values', 'hvg', 'output_type' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | +| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | +| `uns["output_type"]` | `string` | what kind of output has been generated. | + +
diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 4c19e2d935..a89ccef627 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -1,23 +1,336 @@ # Denoising -Structure of this task: +Removing noise in sparse single-cell RNA-sequencing count data - src/tasks/denoising - ├── api Interface specifications for components and datasets in this task - ├── control_methods Control methods to compare methods against - ├── methods Methods to be benchmarked - ├── metrics Metrics used to quantify performance of methods - ├── README.md This file - ├── resources_scripts Scripts to process the datasets - ├── resources_test_scripts Scripts to process the test resources - ├── process_dataset Component to prepare common datasets - └── workflows Pipelines to run the full benchmark +Path: +[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/denoising) -Relevant links: +## Motivation -* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/denoising/) +Single-cell RNA-Seq protocols only detect a fraction of the mRNA +molecules present in each cell. As a result, the measurements (UMI +counts) observed for each gene and each cell are associated with +generally high levels of technical noise ([Grün et al., +2014](https://www.nature.com/articles/nmeth.2930)). Denoising describes +the task of estimating the true expression level of each gene in each +cell. In the single-cell literature, this task is also referred to as +*imputation*, a term which is typically used for missing data problems +in statistics. Similar to the use of the terms “dropout”, “missing +data”, and “technical zeros”, this terminology can create confusion +about the underlying measurement process ([Sarkar and Stephens, +2020](https://www.biorxiv.org/content/10.1101/2020.04.07.030007v2)). -* [Experimental results](https://openproblems-experimental.netlify.app/results/denoising/) +## Description - -* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) +A key challenge in evaluating denoising methods is the general lack of a +ground truth. A recent benchmark study ([Hou et al., +2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02132-x)) +relied on flow-sorted datasets, mixture control experiments ([Tian et +al., 2019](https://www.nature.com/articles/s41592-019-0425-8)), and +comparisons with bulk RNA-Seq data. Since each of these approaches +suffers from specific limitations, it is difficult to combine these +different approaches into a single quantitative measure of denoising +accuracy. Here, we instead rely on an approach termed molecular +cross-validation (MCV), which was specifically developed to quantify +denoising accuracy in the absence of a ground truth ([Batson et al., +2019](https://www.biorxiv.org/content/10.1101/786269v1)). In MCV, the +observed molecules in a given scRNA-Seq dataset are first partitioned +between a *training* and a *test* dataset. Next, a denoising method is +applied to the training dataset. Finally, denoising accuracy is measured +by comparing the result to the test dataset. The authors show that both +in theory and in practice, the measured denoising accuracy is +representative of the accuracy that would be obtained on a ground truth +dataset. + +## Authors & contributors + +| name | roles | +|:------------------|:-------------------| +| Wesley Lewis | author, maintainer | +| Scott Gigante | author, maintainer | +| Robrecht Cannoodt | author | +| Kai Waldrant | author | + +## API + +``` mermaid +flowchart LR + file_train("Training data") + file_test("Test data") + file_denoised("Denoised data") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] + file_train---comp_control_method + file_test---comp_control_method + file_train---comp_method + file_test---comp_metric + file_denoised---comp_metric + file_common_dataset---comp_process_dataset + comp_control_method-->file_denoised + comp_method-->file_denoised + comp_metric-->file_score + comp_process_dataset-->file_train + comp_process_dataset-->file_test +``` + +## File format: Common dataset + +A dataset processed by the common dataset processing pipeline. + +Example file: `resources_test/common/pancreas/dataset.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + obsp: 'knn_distances', 'knn_connectivities' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | +| `obs["batch"]` | `string` | (*Optional*) Batch information. | +| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + +
+ +## Component type: Data processor + +Path: +[`src/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising) + +A denoising dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------------|:-------|:---------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output_train` | `file` | (*Output*) The training data. | +| `--output_test` | `file` | (*Output*) The test data. | + +
+ +## File format: Training data + +NA + +Example file: `resources_test/denoising/pancreas/train.h5ad` + +Description: + +The training data + +Format: + +
+ + AnnData object + layers: 'counts' + uns: 'dataset_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------|:----------|:-------------------------------------| +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | + +
+ +## File format: Test data + +NA + +Example file: `resources_test/denoising/pancreas/test.h5ad` + +Description: + +The test data + +Format: + +
+ + AnnData object + layers: 'counts' + uns: 'dataset_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------|:----------|:-------------------------------------| +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | + +
+ +## Component type: Control method + +Path: +[`src/denoising/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/control_methods) + +Quality control methods for verifying the pipeline. + +Arguments: + +
+ +| Name | Type | Description | +|:----------------|:-------|:------------------------------| +| `--input_train` | `file` | The training data. | +| `--input_test` | `file` | The test data. | +| `--output` | `file` | (*Output*) The denoised data. | + +
+ +## Component type: Method + +Path: +[`src/denoising/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/methods) + +A denoising method. + +Arguments: + +
+ +| Name | Type | Description | +|:----------------|:-------|:------------------------------| +| `--input_train` | `file` | The training data. | +| `--output` | `file` | (*Output*) The denoised data. | + +
+ +## Component type: Metric + +Path: +[`src/denoising/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/denoising/metrics) + +A denoising metric. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------|:-------|:------------------------------| +| `--input_test` | `file` | The test data. | +| `--input_denoised` | `file` | The denoised data. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Denoised data + +NA + +Example file: `resources_test/denoising/pancreas/magic.h5ad` + +Description: + +The denoised data + +Format: + +
+ + AnnData object + layers: 'counts', 'denoised' + uns: 'dataset_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------|:----------|:-------------------------------------| +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["denoised"]` | `integer` | denoised data. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | + +
+ +## File format: Score + +NA + +Example file: `resources_test/denoising/pancreas/magic_poisson.h5ad` + +Description: + +Metric score file + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index f81d55da92..07321d1bbd 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -1,23 +1,341 @@ -# Dimensionality reduction +# Dimensionality reduction for visualization -Structure of this task: +Reduction of high-dimensional datasets to 2D for visualization & +interpretation - src/tasks/dimensionality_reduction - ├── api Interface specifications for components and datasets in this task - ├── control_methods Control methods to compare methods against - ├── methods Methods to be benchmarked - ├── metrics Metrics used to quantify performance of methods - ├── README.md This file - ├── resources_scripts Scripts to process the datasets - ├── resources_test_scripts Scripts to process the test resources - ├── process_dataset Component to prepare common datasets - └── workflows Pipelines to run the full benchmark +Path: +[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/dimensionality_reduction) -Relevant links: +## Motivation -* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/dimensionality_reduction/) +Dimensionality reduction is one of the key challenges in single-cell +data representation. Routine single-cell RNA sequencing (scRNA-seq) +experiments measure cells in roughly 20,000-30,000 dimensions (i.e., +features - mostly gene transcripts but also other functional elements +encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq +experiments have been growing in terms of the number of cells measured. +Originally, cutting-edge SmartSeq experiments would yield a few hundred +cells, at best. Now, it is not uncommon to see experiments that yield +over [100,000 cells](https://www.nature.com/articles/s41586-018-0590-4) +or even [\> 1 million cells](https://doi.org/10.1126/science.aba7721). -* [Experimental results](https://openproblems-experimental.netlify.app/results/dimensionality_reduction/) +## Description - -* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) +Each *feature* in a dataset functions as a single dimension. While each +of the ~30,000 dimensions measured in each cell contribute to an +underlying data structure, the overall structure of the data is +challenging to display in few dimensions due to data sparsity and the +[*“curse of +dimensionality”*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) +(distances in high dimensional data don’t distinguish data points well). +Thus, we need to find a way to [dimensionally +reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data +for visualization and interpretation. + +## Authors & contributors + +| name | roles | +|:-----------------------|:-------------------| +| Luke Zappia | maintainer, author | +| Michal Klein | author | +| Scott Gigante | author | +| Ben DeMeo | author | +| Juan A. Cordero Varela | contributor | +| Robrecht Cannoodt | contributor | + +## API + +``` mermaid +flowchart LR + file_dataset("Dataset") + file_solution("Test data") + file_embedding("Embedding") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] + file_dataset---comp_control_method + file_solution---comp_control_method + file_dataset---comp_method + file_embedding---comp_metric + file_solution---comp_metric + file_common_dataset---comp_process_dataset + comp_control_method-->file_embedding + comp_method-->file_embedding + comp_metric-->file_score + comp_process_dataset-->file_dataset + comp_process_dataset-->file_solution +``` + +## File format: Common dataset + +A dataset processed by the common dataset processing pipeline. + +Example file: `resources_test/common/pancreas/dataset.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + obsp: 'knn_distances', 'knn_connectivities' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | +| `obs["batch"]` | `string` | (*Optional*) Batch information. | +| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + +
+ +## Component type: Data processor + +Path: +[`src/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction) + +A dimensionality reduction dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:--------------------|:-------|:---------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output_dataset` | `file` | (*Output*) The dataset to pass to a method. | +| `--output_solution` | `file` | (*Output*) The data for evaluating a dimensionality reduction. | + +
+ +## File format: Dataset + +The dataset to pass to a method. + +Example file: +`resources_test/dimensionality_reduction/pancreas/dataset.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + var: 'hvg_score' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------------------| +| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Test data + +The data for evaluating a dimensionality reduction. + +Example file: +`resources_test/dimensionality_reduction/pancreas/solution.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + var: 'hvg_score' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------------------| +| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## Component type: Control method + +Path: +[`src/dimensionality_reduction/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/control_methods) + +Quality control methods for verifying the pipeline. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------|:-------|:--------------------------------------------------------------| +| `--input` | `file` | The dataset to pass to a method. | +| `--input_solution` | `file` | The data for evaluating a dimensionality reduction. | +| `--output` | `file` | (*Output*) A dataset with dimensionality reduction embedding. | + +
+ +## Component type: Method + +Path: +[`src/dimensionality_reduction/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/methods) + +A dimensionality reduction method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:-------|:--------------------------------------------------------------| +| `--input` | `file` | The dataset to pass to a method. | +| `--output` | `file` | (*Output*) A dataset with dimensionality reduction embedding. | + +
+ +## Component type: Metric + +Path: +[`src/dimensionality_reduction/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/dimensionality_reduction/metrics) + +A dimensionality reduction metric. + +Arguments: + +
+ +| Name | Type | Description | +|:--------------------|:-------|:----------------------------------------------------| +| `--input_embedding` | `file` | A dataset with dimensionality reduction embedding. | +| `--input_solution` | `file` | The data for evaluating a dimensionality reduction. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Embedding + +A dataset with dimensionality reduction embedding. + +Example file: +`resources_test/dimensionality_reduction/pancreas/embedding.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obsm: 'X_emb' + uns: 'dataset_id', 'method_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:-------------------------------------| +| `obsm["X_emb"]` | `double` | The dimensionally reduced embedding. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Score + +Metric score file + +Example file: +`resources_test/dimensionality_reduction/pancreas/score.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index fc24c81139..cfc1d2a88a 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -1,23 +1,396 @@ # Label projection -Structure of this task: +Automated cell type annotation from rich, labeled reference data - src/tasks/label_projection - ├── api Interface specifications for components and datasets in this task - ├── control_methods Control methods to compare methods against - ├── methods Methods to be benchmarked - ├── metrics Metrics used to quantify performance of methods - ├── README.md This file - ├── resources_scripts Scripts to process the datasets - ├── resources_test_scripts Scripts to process the test resources - ├── process_dataset Component to prepare common datasets - └── workflows Pipelines to run the full benchmark +Path: +[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/label_projection) -Relevant links: +## Motivation -* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/label_projection/) +A major challenge for integrating single cell datasets is creating +matching cell type annotations for each cell. One of the most common +strategies for annotating cell types is referred to as +[“cluster-then-annotate”](https://www.nature.com/articles/s41576-018-0088-9) +whereby cells are aggregated into clusters based on feature similarity +and then manually characterized based on differential gene expression or +previously identified marker genes. Recently, methods have emerged to +build on this strategy and annotate cells using [known marker +genes](https://www.nature.com/articles/s41592-019-0535-3). However, +these strategies pose a difficulty for integrating atlas-scale datasets +as the particular annotations may not match. -* [Experimental results](https://openproblems-experimental.netlify.app/results/label_projection/) +## Description - -* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) +To ensure that the cell type labels in newly generated datasets match +existing reference datasets, some methods align cells to a previously +annotated [reference +dataset](https://academic.oup.com/bioinformatics/article/35/22/4688/54802990) +and then *project* labels from the reference to the new dataset. + +Here, we compare methods for annotation based on a reference dataset. +The datasets consist of two or more samples of single cell profiles that +have been manually annotated with matching labels. These datasets are +then split into training and test batches, and the task of each method +is to train a cell type classifer on the training set and project those +labels onto the test set. + +## Authors & contributors + +| name | roles | +|:------------------|:-------------------| +| Nikolay Markov | author, maintainer | +| Scott Gigante | author | +| Robrecht Cannoodt | author | + +## API + +``` mermaid +flowchart LR + file_train("Training data") + file_test("Test data") + file_solution("Solution") + file_prediction("Prediction") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] + file_train---comp_control_method + file_test---comp_control_method + file_solution---comp_control_method + file_train---comp_method + file_test---comp_method + file_solution---comp_metric + file_prediction---comp_metric + file_common_dataset---comp_process_dataset + comp_control_method-->file_prediction + comp_method-->file_prediction + comp_metric-->file_score + comp_process_dataset-->file_train + comp_process_dataset-->file_test + comp_process_dataset-->file_solution +``` + +## File format: Common dataset + +A dataset processed by the common dataset processing pipeline. + +Example file: `resources_test/common/pancreas/dataset.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obs: 'celltype', 'batch', 'tissue', 'size_factors' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + obsp: 'knn_distances', 'knn_connectivities' + varm: 'pca_loadings' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | +| `obs["batch"]` | `string` | (*Optional*) Batch information. | +| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + +
+ +## Component type: Data processor + +Path: +[`src/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection) + +A label projection dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:--------------------|:-------|:---------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output_train` | `file` | (*Output*) The training data. | +| `--output_test` | `file` | (*Output*) The test data (without labels). | +| `--output_solution` | `file` | (*Output*) The solution for the test data. | + +
+ +## File format: Training data + +The training data + +Example file: `resources_test/label_projection/pancreas/train.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'label', 'batch' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["label"]` | `string` | Ground truth cell type labels. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Test data + +The test data (without labels) + +Example file: `resources_test/label_projection/pancreas/test.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Solution + +The solution for the test data + +Example file: `resources_test/label_projection/pancreas/solution.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'label', 'batch' + var: 'hvg', 'hvg_score' + obsm: 'X_pca' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["label"]` | `string` | Ground truth cell type labels. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## Component type: Control method + +Path: +[`src/label_projection/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/control_methods) + +Quality control methods for verifying the pipeline. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------|:-------|:--------------------------------| +| `--input_train` | `file` | The training data. | +| `--input_test` | `file` | The test data (without labels). | +| `--input_solution` | `file` | The solution for the test data. | +| `--output` | `file` | (*Output*) The prediction file. | + +
+ +## Component type: Method + +Path: +[`src/label_projection/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/methods) + +A label projection method. + +Arguments: + +
+ +| Name | Type | Description | +|:----------------|:-------|:--------------------------------| +| `--input_train` | `file` | The training data. | +| `--input_test` | `file` | The test data (without labels). | +| `--output` | `file` | (*Output*) The prediction file. | + +
+ +## Component type: Metric + +Path: +[`src/label_projection/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/label_projection/metrics) + +A label projection metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:--------------------------------| +| `--input_solution` | `file` | The solution for the test data. | +| `--input_prediction` | `file` | The prediction file. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Prediction + +The prediction file + +Example file: `resources_test/label_projection/pancreas/knn.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'label_pred' + uns: 'dataset_id', 'normalization_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:-------------------------------------| +| `obs["label_pred"]` | `string` | Predicted labels for the test cells. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | + +
+ +## File format: Score + +Metric score file + +Example file: +`resources_test/label_projection/pancreas/knn_accuracy.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
From d9e3e28a549b7528c1050c707ae7b865ee92562d Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 14 Jun 2023 23:11:30 +0200 Subject: [PATCH 0924/1233] change "label" assert message (#186) Former-commit-id: 8d1ea8e6d444c05888357ef5aa85bee4eb0af88d --- src/common/comp_tests/check_method_config.py | 2 +- src/common/comp_tests/check_metric_config.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 1dea448908..dd460b9b6c 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -68,7 +68,7 @@ def search_ref_bib(reference): assert "type" in info, "type not an info field" info_types = ["method", "control_method"] assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}" -assert "label" in info is not None, "pretty_name not an info field or is empty" +assert "label" in info is not None, "label not an info field or is empty" assert "summary" in info is not None, "summary not an info field or is empty" assert "FILL IN:" not in info["summary"], "Summary not filled in" assert len(info["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.summary) should not exceed {SUMMARY_MAXLEN} characters." diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 728ec710a4..732e7aa69a 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -62,7 +62,7 @@ def search_ref_bib(reference): def check_metric(metric: Dict[str, str]) -> str: assert "name" in metric is not None, "name not a field or is empty" assert len(metric["name"]) <= NAME_MAXLEN, f"Component id (.functionality.info.metrics.metric.name) should not exceed {NAME_MAXLEN} characters." - assert "label" in metric is not None, "pretty_name not a field in metric or is empty" + assert "label" in metric is not None, "label not a field in metric or is empty" assert "summary" in metric is not None, "summary not a field in metric or is empty" assert "FILL IN:" not in metric["summary"], "Summary not filled in" assert len(metric["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.metrics.metric.summary) should not exceed {SUMMARY_MAXLEN} characters." From 2e8670031019ec65500b1578959109575e71a0c5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Jun 2023 15:55:20 +0200 Subject: [PATCH 0925/1233] fix links Former-commit-id: 180fedc793e44ea09c4de0e7766f49cf5663b9ad --- src/common/create_task_readme/script.R | 3 ++- src/common/helper_functions/read_api_files.R | 4 +-- src/tasks/batch_integration/README.md | 28 ++++++++++---------- src/tasks/denoising/README.md | 20 +++++++------- src/tasks/dimensionality_reduction/README.md | 20 +++++++------- src/tasks/label_projection/README.md | 22 +++++++-------- 6 files changed, 49 insertions(+), 48 deletions(-) diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index ef3ac2d466..8e5df6f6a5 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -54,6 +54,7 @@ authors_str <- } cat("Generate qmd content\n") +task_dir_short <- gsub(".*openproblems-v2/", "", task_dir) qmd_content <- strip_margin(glue::glue(" §--- §title: \"{task_api$task_info$label}\" @@ -62,7 +63,7 @@ qmd_content <- strip_margin(glue::glue(" § §{task_api$task_info$summary} § - §Path: [`{task_dir}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/{task_dir}) + §Path: [`{task_dir_short}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/{task_dir_short}) § §## Motivation § diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index c7c5a9fc5d..e59ca1e9ed 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -287,9 +287,9 @@ create_task_graph <- function(file_info, comp_info, comp_args) { mutate(str = paste0( " ", clean_id(id), - ifelse(is_comp, "[/\"", "(\""), + ifelse(is_comp, "[/", "("), label, - ifelse(is_comp, "\"/]", "\")") + ifelse(is_comp, "/]", ")") )) edges <- bind_rows( comp_args %>% diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index d43f432205..e6587abf70 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -4,7 +4,7 @@ Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. Path: -[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/batch_integration) +[`src/tasks/batch_integration`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/batch_integration) ## Motivation @@ -54,19 +54,19 @@ extensive benchmark of single-cell data integration methods ``` mermaid flowchart LR - file_unintegrated("Unintegrated") - file_integrated_embedding("Integrated embedding") - file_integrated_feature("Integrated Feature") - file_integrated_graaf("Integrated Graph") - file_score("Score") - file_common_dataset("Common dataset") - comp_method_embedding[/"Method (embedding)"/] - comp_method_feature[/"Method (feature)"/] - comp_method_graaf[/"Method (graph)"/] - comp_metric_embedding[/"Metric (embedding)"/] - comp_metric_feature[/"Metric (feature)"/] - comp_metric_graaf[/"Metric (graph)"/] - comp_process_dataset[/"Data processor"/] + file_unintegrated(Unintegrated) + file_integrated_embedding(Integrated embedding) + file_integrated_feature(Integrated Feature) + file_integrated_graaf(Integrated Graph) + file_score(Score) + file_common_dataset(Common dataset) + comp_method_embedding[/Method (embedding)/] + comp_method_feature[/Method (feature)/] + comp_method_graaf[/Method (graph)/] + comp_metric_embedding[/Metric (embedding)/] + comp_metric_feature[/Metric (feature)/] + comp_metric_graaf[/Metric (graph)/] + comp_process_dataset[/Data processor/] file_unintegrated---comp_method_embedding file_unintegrated---comp_method_feature file_unintegrated---comp_method_graaf diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index a89ccef627..fcb0e7e8e1 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -3,7 +3,7 @@ Removing noise in sparse single-cell RNA-sequencing count data Path: -[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/denoising) +[`src/tasks/denoising`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/denoising) ## Motivation @@ -55,15 +55,15 @@ dataset. ``` mermaid flowchart LR - file_train("Training data") - file_test("Test data") - file_denoised("Denoised data") - file_score("Score") - file_common_dataset("Common dataset") - comp_control_method[/"Control method"/] - comp_method[/"Method"/] - comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_train(Training data) + file_test(Test data) + file_denoised(Denoised data) + file_score(Score) + file_common_dataset(Common dataset) + comp_control_method[/Control method/] + comp_method[/Method/] + comp_metric[/Metric/] + comp_process_dataset[/Data processor/] file_train---comp_control_method file_test---comp_control_method file_train---comp_method diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 07321d1bbd..a4295badd1 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -4,7 +4,7 @@ Reduction of high-dimensional datasets to 2D for visualization & interpretation Path: -[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/dimensionality_reduction) +[`src/tasks/dimensionality_reduction`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/dimensionality_reduction) ## Motivation @@ -47,15 +47,15 @@ for visualization and interpretation. ``` mermaid flowchart LR - file_dataset("Dataset") - file_solution("Test data") - file_embedding("Embedding") - file_score("Score") - file_common_dataset("Common dataset") - comp_control_method[/"Control method"/] - comp_method[/"Method"/] - comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_dataset(Dataset) + file_solution(Test data) + file_embedding(Embedding) + file_score(Score) + file_common_dataset(Common dataset) + comp_control_method[/Control method/] + comp_method[/Method/] + comp_metric[/Metric/] + comp_process_dataset[/Data processor/] file_dataset---comp_control_method file_solution---comp_control_method file_dataset---comp_method diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index cfc1d2a88a..2f88fcf74c 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -3,7 +3,7 @@ Automated cell type annotation from rich, labeled reference data Path: -[`/viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src//viash_automount/home/rcannood/workspace/openproblems/openproblems-v2/src/tasks/label_projection) +[`src/tasks/label_projection`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/label_projection) ## Motivation @@ -46,16 +46,16 @@ labels onto the test set. ``` mermaid flowchart LR - file_train("Training data") - file_test("Test data") - file_solution("Solution") - file_prediction("Prediction") - file_score("Score") - file_common_dataset("Common dataset") - comp_control_method[/"Control method"/] - comp_method[/"Method"/] - comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_train(Training data) + file_test(Test data) + file_solution(Solution) + file_prediction(Prediction) + file_score(Score) + file_common_dataset(Common dataset) + comp_control_method[/Control method/] + comp_method[/Method/] + comp_metric[/Metric/] + comp_process_dataset[/Data processor/] file_train---comp_control_method file_test---comp_control_method file_solution---comp_control_method From 6430b1296f4f47fde09274e1d4e05eb4ff652853 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Jun 2023 15:59:55 +0200 Subject: [PATCH 0926/1233] fix readmes Former-commit-id: 2cba3af7210916466feeb69a164bef578580059c --- src/common/helper_functions/read_api_files.R | 3 +-- src/tasks/batch_integration/README.md | 14 +++++++------- src/tasks/denoising/README.md | 10 +++++----- src/tasks/dimensionality_reduction/README.md | 10 +++++----- src/tasks/label_projection/README.md | 12 ++++++------ 5 files changed, 24 insertions(+), 25 deletions(-) diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index e59ca1e9ed..6fc4700e6c 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -319,8 +319,7 @@ create_task_graph <- function(file_info, comp_info, comp_args) { render_task_graph <- function(task_api) { strip_margin(glue::glue(" - §```{{mermaid}} - §%%| column: screen-inset-shaded + §```mermaid §flowchart LR §{paste(igraph::V(task_api$task_graph)$str, collapse = '\n')} §{paste(igraph::E(task_api$task_graph)$str, collapse = '\n')} diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index e6587abf70..6a3be5a869 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -74,13 +74,13 @@ flowchart LR file_integrated_feature---comp_metric_feature file_integrated_graaf---comp_metric_graaf file_common_dataset---comp_process_dataset - comp_method_embedding-->file_integrated_embedding - comp_method_feature-->file_integrated_feature - comp_method_graaf-->file_integrated_graaf - comp_metric_embedding-->file_score - comp_metric_feature-->file_score - comp_metric_graaf-->file_score - comp_process_dataset-->file_unintegrated + comp_method_embedding-->file_integrated_embedding + comp_method_feature-->file_integrated_feature + comp_method_graaf-->file_integrated_graaf + comp_metric_embedding-->file_score + comp_metric_feature-->file_score + comp_metric_graaf-->file_score + comp_process_dataset-->file_unintegrated ``` ## File format: Common dataset diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index fcb0e7e8e1..ad3d7c19a4 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -70,11 +70,11 @@ flowchart LR file_test---comp_metric file_denoised---comp_metric file_common_dataset---comp_process_dataset - comp_control_method-->file_denoised - comp_method-->file_denoised - comp_metric-->file_score - comp_process_dataset-->file_train - comp_process_dataset-->file_test + comp_control_method-->file_denoised + comp_method-->file_denoised + comp_metric-->file_score + comp_process_dataset-->file_train + comp_process_dataset-->file_test ``` ## File format: Common dataset diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index a4295badd1..1930a4f4fd 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -62,11 +62,11 @@ flowchart LR file_embedding---comp_metric file_solution---comp_metric file_common_dataset---comp_process_dataset - comp_control_method-->file_embedding - comp_method-->file_embedding - comp_metric-->file_score - comp_process_dataset-->file_dataset - comp_process_dataset-->file_solution + comp_control_method-->file_embedding + comp_method-->file_embedding + comp_metric-->file_score + comp_process_dataset-->file_dataset + comp_process_dataset-->file_solution ``` ## File format: Common dataset diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 2f88fcf74c..e815839c7d 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -64,12 +64,12 @@ flowchart LR file_solution---comp_metric file_prediction---comp_metric file_common_dataset---comp_process_dataset - comp_control_method-->file_prediction - comp_method-->file_prediction - comp_metric-->file_score - comp_process_dataset-->file_train - comp_process_dataset-->file_test - comp_process_dataset-->file_solution + comp_control_method-->file_prediction + comp_method-->file_prediction + comp_metric-->file_score + comp_process_dataset-->file_train + comp_process_dataset-->file_test + comp_process_dataset-->file_solution ``` ## File format: Common dataset From 62e68440653a76eed41e95a3ce101c8a5dcb9ca1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 16 Jun 2023 16:01:41 +0200 Subject: [PATCH 0927/1233] update graph Former-commit-id: 9ced3d3e6ec10e78b7f574feebb3bf41d568ec3e --- src/common/helper_functions/read_api_files.R | 4 +-- src/tasks/batch_integration/README.md | 26 ++++++++++---------- src/tasks/denoising/README.md | 18 +++++++------- src/tasks/dimensionality_reduction/README.md | 18 +++++++------- src/tasks/label_projection/README.md | 20 +++++++-------- 5 files changed, 43 insertions(+), 43 deletions(-) diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index 6fc4700e6c..fe19c5f033 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -287,9 +287,9 @@ create_task_graph <- function(file_info, comp_info, comp_args) { mutate(str = paste0( " ", clean_id(id), - ifelse(is_comp, "[/", "("), + ifelse(is_comp, "[/\"", "(\""), label, - ifelse(is_comp, "/]", ")") + ifelse(is_comp, "\"/]", "\")") )) edges <- bind_rows( comp_args %>% diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 6a3be5a869..0c35c109f0 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -54,19 +54,19 @@ extensive benchmark of single-cell data integration methods ``` mermaid flowchart LR - file_unintegrated(Unintegrated) - file_integrated_embedding(Integrated embedding) - file_integrated_feature(Integrated Feature) - file_integrated_graaf(Integrated Graph) - file_score(Score) - file_common_dataset(Common dataset) - comp_method_embedding[/Method (embedding)/] - comp_method_feature[/Method (feature)/] - comp_method_graaf[/Method (graph)/] - comp_metric_embedding[/Metric (embedding)/] - comp_metric_feature[/Metric (feature)/] - comp_metric_graaf[/Metric (graph)/] - comp_process_dataset[/Data processor/] + file_unintegrated("Unintegrated") + file_integrated_embedding("Integrated embedding") + file_integrated_feature("Integrated Feature") + file_integrated_graaf("Integrated Graph") + file_score("Score") + file_common_dataset("Common dataset") + comp_method_embedding[/"Method (embedding)"/] + comp_method_feature[/"Method (feature)"/] + comp_method_graaf[/"Method (graph)"/] + comp_metric_embedding[/"Metric (embedding)"/] + comp_metric_feature[/"Metric (feature)"/] + comp_metric_graaf[/"Metric (graph)"/] + comp_process_dataset[/"Data processor"/] file_unintegrated---comp_method_embedding file_unintegrated---comp_method_feature file_unintegrated---comp_method_graaf diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index ad3d7c19a4..d5a3f78058 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -55,15 +55,15 @@ dataset. ``` mermaid flowchart LR - file_train(Training data) - file_test(Test data) - file_denoised(Denoised data) - file_score(Score) - file_common_dataset(Common dataset) - comp_control_method[/Control method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_process_dataset[/Data processor/] + file_train("Training data") + file_test("Test data") + file_denoised("Denoised data") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] file_train---comp_control_method file_test---comp_control_method file_train---comp_method diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 1930a4f4fd..d5d1c70cab 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -47,15 +47,15 @@ for visualization and interpretation. ``` mermaid flowchart LR - file_dataset(Dataset) - file_solution(Test data) - file_embedding(Embedding) - file_score(Score) - file_common_dataset(Common dataset) - comp_control_method[/Control method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_process_dataset[/Data processor/] + file_dataset("Dataset") + file_solution("Test data") + file_embedding("Embedding") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] file_dataset---comp_control_method file_solution---comp_control_method file_dataset---comp_method diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index e815839c7d..5dd13651f9 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -46,16 +46,16 @@ labels onto the test set. ``` mermaid flowchart LR - file_train(Training data) - file_test(Test data) - file_solution(Solution) - file_prediction(Prediction) - file_score(Score) - file_common_dataset(Common dataset) - comp_control_method[/Control method/] - comp_method[/Method/] - comp_metric[/Metric/] - comp_process_dataset[/Data processor/] + file_train("Training data") + file_test("Test data") + file_solution("Solution") + file_prediction("Prediction") + file_score("Score") + file_common_dataset("Common dataset") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + comp_process_dataset[/"Data processor"/] file_train---comp_control_method file_test---comp_control_method file_solution---comp_control_method From 856786f9edb1c44a89a4956069a9db894b94458e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 21 Jun 2023 15:47:20 +0200 Subject: [PATCH 0928/1233] switch base containers in batch integration from python to r (#190) * switch base containers in batch integration from python to r * add scanpy to the base_ images Former-commit-id: 116ef177583a56d4d4b833fa95e15d098fa2ace8 --- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 6 +++--- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/common/get_api_info/config.vsh.yaml | 2 +- src/common/get_method_info/config.vsh.yaml | 2 +- src/common/get_metric_info/config.vsh.yaml | 2 +- src/common/get_results/config.vsh.yaml | 2 +- src/common/get_task_info/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- .../loaders/openproblems_v1_multimodal/config.vsh.yaml | 2 +- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 2 +- src/datasets/normalization/log_cpm/config.vsh.yaml | 6 +----- .../normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cpm/config.vsh.yaml | 6 +----- src/datasets/processors/hvg/config.vsh.yaml | 6 +----- src/datasets/processors/knn/config.vsh.yaml | 6 +----- src/datasets/processors/pca/config.vsh.yaml | 6 +----- src/datasets/processors/subsample/config.vsh.yaml | 6 +----- src/migration/check_migration_status/config.vsh.yaml | 2 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 5 ++--- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 3 +-- .../methods/scanorama_embed/config.vsh.yaml | 3 +-- .../methods/scanorama_feature/config.vsh.yaml | 3 +-- src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 3 +-- .../batch_integration/metrics/asw_batch/config.vsh.yaml | 5 ++--- .../batch_integration/metrics/asw_label/config.vsh.yaml | 5 ++--- .../metrics/cell_cycle_conservation/config.vsh.yaml | 5 ++--- .../metrics/clustering_overlap/config.vsh.yaml | 5 ++--- src/tasks/batch_integration/metrics/pcr/config.vsh.yaml | 5 ++--- src/tasks/batch_integration/process_dataset/config.vsh.yaml | 5 ++--- .../transformers/embed_to_graph/config.vsh.yaml | 2 +- .../transformers/feature_to_embed/config.vsh.yaml | 2 +- .../denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- .../control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/tasks/denoising/methods/alra/config.vsh.yaml | 2 +- src/tasks/denoising/methods/dca/config.vsh.yaml | 2 +- src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/tasks/denoising/methods/magic/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/mse/config.vsh.yaml | 3 +-- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 2 +- src/tasks/denoising/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../methods/densmap/config.vsh.yaml | 3 +-- .../dimensionality_reduction/methods/ivis/config.vsh.yaml | 3 +-- .../methods/neuralee/config.vsh.yaml | 3 +-- .../dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 3 +-- .../dimensionality_reduction/methods/umap/config.vsh.yaml | 3 +-- .../metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 2 +- .../dimensionality_reduction/metrics/rmse/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/mlp/config.vsh.yaml | 2 +- .../methods/scanvi_scarches/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/xgboost/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/tasks/label_projection/process_dataset/config.vsh.yaml | 2 +- 71 files changed, 80 insertions(+), 121 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index eeac1aa329..274f2885b6 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -42,6 +42,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml index 66b409a7d8..7c78fd9d94 100644 --- a/src/common/check_yaml_schema/config.vsh.yaml +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 5cc04f8204..b56ce924c0 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -144,11 +144,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base_python:1.0.0" + image_str = "ghcr.io/openproblems-bio/base_python:1.0.1" setup_type = "python" - package_example = "scanpy" + package_example = "scib==1.1.3" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base_r:1.0.0" + image_str = "ghcr.io/openproblems-bio/base_r:1.0.1" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index 6f41273616..dc4b5dbc21 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 4449f962e1..a7c65412e1 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 281f9897dc..03a8958d7b 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index d89a091377..8c322e5cd7 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 4bc1e03671..775a78232e 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 9560a0644c..3bc4f93974 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index 4c12ae0bdc..924fceadfc 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -8,6 +8,6 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow - type: native diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 12f8700411..6e4fa0e20d 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 82b28b73dc..dc2db19f50 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: apt packages: git diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 919f201d6c..2f4e422c4a 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml index 46a42824a6..631bdbae10 100644 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ b/src/datasets/normalization/log_cpm/config.vsh.yaml @@ -7,11 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 171ef3c9d9..9fbf3bf670 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ Matrix, rlang, bit64, scran, BiocParallel ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml index 421809423b..dcf0b36b64 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cpm/config.vsh.yaml @@ -7,11 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 295d359d4f..376009359c 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,9 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 6fc7e1929a..8626769323 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,9 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index a277ffc00d..1d6cd05a51 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,9 +11,5 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index ef9f612dfb..9a80d32143 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,11 +41,7 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 - setup: - - type: python - packages: - - scanpy + image: ghcr.io/openproblems-bio/base_python:1.0.1 test_setup: - type: python packages: diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index 38db0c2485..f41f58a353 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 15bb2d7757..6a0ba6a5ac 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 3b70ea7517..8214a5925c 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 1796fe5ccf..7aa1d14fdf 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -31,11 +31,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: - - bbknn - - scanpy - scib==1.1.3 + - bbknn - type: nextflow diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 86ad9cd0be..1b2a312fba 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -34,10 +34,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: - - scanpy - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 3d4e0cb5e0..38a7781518 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -29,11 +29,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: - scanorama - - scanpy - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 7a27b65745..3ace46a181 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -29,11 +29,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: - scanorama - - scanpy - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 550b9676ed..c857066d88 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -23,11 +23,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: - scvi-tools - - scanpy - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index 43049c8cc6..392547e522 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -21,10 +21,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 33d81fdf24..01b744879b 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -20,10 +20,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 580332b70c..b7ebce1162 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -20,10 +20,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 7e87a0f0e7..dcb91e807e 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -49,10 +49,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index b89bc246a0..47a76a4ac3 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -24,10 +24,9 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 75efbdc677..59af760ac1 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -22,10 +22,9 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python - pypi: - - scanpy + pypi: - scib==1.1.3 - type: nextflow diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 3b5df9aa85..650417d813 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: scanpy diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 4c6f4971d0..9826aead39 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -22,7 +22,7 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: scanpy diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index 0423eb2ee6..f5267b9a22 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index 0934f3becf..b4d7f84cfe 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ midmem, midcpu ] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 6f89ccd57f..96bf990a7d 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ Matrix, bit64, rsvd ] diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index 4f60b1f6f4..125ee0e4a1 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index ce5978893e..92f35e3240 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 886694ed25..48c6044fef 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 1530f50b68..89dc75d285 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -19,12 +19,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: - scikit-learn - - scanpy - scprep - type: nextflow directives: diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index 6b204d8685..1ef35f9d76 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -21,7 +21,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pip: scprep diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index bc6a083717..747733efe3 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index f809954aeb..9cbb060c57 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index f094ef8208..37fb6bac0e 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 8429584e45..cfb1ccd926 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -33,11 +33,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: - - scanpy - umap-learn - type: native - type: nextflow diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index b9fc0587bd..4d57c4df9d 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -35,11 +35,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: - - scanpy - ivis[cpu] - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index ae946ea497..6911b450a2 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -44,11 +44,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: - - scanpy - torch - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index d97081cb14..7ae19d13e9 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 31bfde4e29..d69b8cc6f2 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 2764dbe010..7ec1899577 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: apt packages: @@ -43,7 +43,6 @@ platforms: - gcc - type: python packages: - - scanpy - MulticoreTSNE - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index b8508657ec..1aff2d0c2c 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,11 +39,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: - - scanpy - umap-learn - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 59a1d9aeeb..552b50fd04 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -157,7 +157,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ coRanking, bit64 ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index f9e40482d0..91d10dcf43 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -21,7 +21,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml index 08879e3599..5874ffb3c1 100644 --- a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index a67250fd79..ce65fc8b60 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 8a1e9f3fbf..17f7eaa2b1 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index ac66f99216..6cd01534c4 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 9b408e83fa..014ee5249d 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scanpy diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index c2ec2b3d5b..ef313a16ee 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: label: [ lowmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index d9971e602a..0841b7ebe4 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: [scikit-learn, jsonschema] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index a6c20757a0..8deac18a99 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index a6fe991468..8ec1f9cbf0 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 5057ca0b58..56662a542c 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -50,7 +50,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 # Add custom dependencies here setup: - type: python diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 52b94f9f41..50eef997cb 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.0 + image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r cran: [ Matrix, Seurat, rlang, bit64 ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index c28d5a64ff..2234967a79 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: xgboost diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index b9bd67454d..9414a5eaad 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index 64746259de..f78f4c8bba 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 09bcd9fddf..eb5a564cdb 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,5 +25,5 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow From c344bb51ae0f5588b4c1db8d1d6df95137c536b1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 21 Jun 2023 15:47:35 +0200 Subject: [PATCH 0929/1233] Bump tj-actions/changed-files from 36.1.0 to 36.4.1 (#189) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.1.0 to 36.4.1. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.1.0...v36.4.1) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 4079e18fe8200ae19246a228c6e0ca9ab465819c --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 8402d34cd1..f05aa1b380 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.1.0 + uses: tj-actions/changed-files@v36.4.1 with: separator: ";" diff_relative: true From 5be6c11471dfdf199d1a135b42638ce3f1c44cc9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 21 Jun 2023 16:37:09 +0200 Subject: [PATCH 0930/1233] add transformers to the api (#192) * add transformers to the api * fix trafo components Former-commit-id: 541c06b309f92c23a63b982010ae009845c8f764 --- src/tasks/batch_integration/README.md | 42 +++++++++++++++++++ .../comp_transformer_embedding_to_graph.yaml | 25 +++++++++++ ...comp_transformer_feature_to_embedding.yaml | 25 +++++++++++ .../embed_to_graph/config.vsh.yaml | 19 ++------- .../transformers/embed_to_graph/script.py | 2 +- .../feature_to_embed/config.vsh.yaml | 20 +++------ .../transformers/feature_to_embed/script.py | 2 +- 7 files changed, 103 insertions(+), 32 deletions(-) create mode 100644 src/tasks/batch_integration/api/comp_transformer_embedding_to_graph.yaml create mode 100644 src/tasks/batch_integration/api/comp_transformer_feature_to_embedding.yaml diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 0c35c109f0..d02a73be07 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -67,6 +67,8 @@ flowchart LR comp_metric_feature[/"Metric (feature)"/] comp_metric_graaf[/"Metric (graph)"/] comp_process_dataset[/"Data processor"/] + comp_transformer_embedding_to_graaf[/"Embedding to Graph"/] + comp_transformer_feature_to_embedding[/"Feature to Embedding"/] file_unintegrated---comp_method_embedding file_unintegrated---comp_method_feature file_unintegrated---comp_method_graaf @@ -74,6 +76,8 @@ flowchart LR file_integrated_feature---comp_metric_feature file_integrated_graaf---comp_metric_graaf file_common_dataset---comp_process_dataset + file_integrated_embedding---comp_transformer_embedding_to_graaf + file_integrated_feature---comp_transformer_feature_to_embedding comp_method_embedding-->file_integrated_embedding comp_method_feature-->file_integrated_feature comp_method_graaf-->file_integrated_graaf @@ -81,6 +85,8 @@ flowchart LR comp_metric_feature-->file_score comp_metric_graaf-->file_score comp_process_dataset-->file_unintegrated + comp_transformer_embedding_to_graaf-->file_integrated_graaf + comp_transformer_feature_to_embedding-->file_integrated_embedding ``` ## File format: Common dataset @@ -417,6 +423,24 @@ Arguments:

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+## Component type: Embedding to Graph + +Path: +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) + +Transform an embedding to a graph output. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:-------|:-----------------------------------------| +| `--input` | `file` | An integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | + +
+ ## Component type: Metric (feature) Path: @@ -435,6 +459,24 @@ Arguments: +## Component type: Feature to Embedding + +Path: +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) + +Transform a feature output to an embedding. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:-------|:--------------------------------------------| +| `--input` | `file` | Integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | + +
+ ## Component type: Metric (graph) Path: diff --git a/src/tasks/batch_integration/api/comp_transformer_embedding_to_graph.yaml b/src/tasks/batch_integration/api/comp_transformer_embedding_to_graph.yaml new file mode 100644 index 0000000000..d8e815dad5 --- /dev/null +++ b/src/tasks/batch_integration/api/comp_transformer_embedding_to_graph.yaml @@ -0,0 +1,25 @@ +functionality: + namespace: batch_integration/transformers + info: + type: transformer + subtype: graph + type_info: + label: Embedding to Graph + summary: Transform an embedding to a graph output. + description: | + Transform an embedding to a graph output by applying the k nearest neighbors algorithm. + arguments: + - name: --input + __merge__: file_integrated_embedding.yaml + direction: input + required: true + - name: --output + __merge__: file_integrated_graph.yaml + direction: output + required: true + test_resources: + # auto-run component + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas \ No newline at end of file diff --git a/src/tasks/batch_integration/api/comp_transformer_feature_to_embedding.yaml b/src/tasks/batch_integration/api/comp_transformer_feature_to_embedding.yaml new file mode 100644 index 0000000000..788e4b965a --- /dev/null +++ b/src/tasks/batch_integration/api/comp_transformer_feature_to_embedding.yaml @@ -0,0 +1,25 @@ +functionality: + namespace: batch_integration/transformers + info: + type: transformer + subtype: embedding + type_info: + label: Feature to Embedding + summary: Transform a feature output to an embedding. + description: | + Transform a feature output to an embedding by computing a PCA on the corrected counts. + arguments: + - name: --input + __merge__: file_integrated_feature.yaml + direction: input + required: true + - name: --output + __merge__: file_integrated_embedding.yaml + direction: output + required: true + test_resources: + # auto-run component + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas \ No newline at end of file diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 650417d813..cbcea84eeb 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -1,25 +1,14 @@ +__merge__: ../../api/comp_transformer_embedding_to_graph.yaml functionality: name: embed_to_graph - namespace: batch_integration/transformers - description: "Transform an embedded integration to a graph integration" info: - type: transformer label: Embedding to Graph - output_type: graph - arguments: - - __merge__: ../../api/file_integrated_embedding.yaml - name: --input - - __merge__: ../../api/file_integrated_graph.yaml - name: --output - direction: output + summary: Transform an embedding to a graph output. + description: | + Transform an embedding to a graph output by applying the k nearest neighbors algorithm. resources: - type: python_script path: script.py - test_resources: - - path: /resources_test/batch_integration/pancreas/ - dest: resources_test/batch_integration/pancreas/ - - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/script.py b/src/tasks/batch_integration/transformers/embed_to_graph/script.py index eae49d968e..d68a4e1574 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/script.py +++ b/src/tasks/batch_integration/transformers/embed_to_graph/script.py @@ -11,7 +11,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata = sc.read_h5ad(par['input']) diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 9826aead39..3f1f5986cf 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -1,25 +1,15 @@ +__merge__: ../../api/comp_transformer_feature_to_embedding.yaml functionality: name: feature_to_embed - namespace: batch_integration/transformers - description: "Transform a feature integration to an embedded integration" info: type: transformer - label: Feature to Embed - output_type: embedding - arguments: - - __merge__: ../../api/file_integrated_feature.yaml - name: --input - - __merge__: ../../api/file_integrated_embedding.yaml - name: --output - direction: output + label: Feature to Embedding + summary: Transform a feature output to an embedding. + description: | + Transform a feature output to an embedding by computing a PCA on the corrected counts. resources: - type: python_script path: script.py - test_resources: - - path: /resources_test/batch_integration/pancreas/ - dest: resources_test/batch_integration/pancreas/ - - type: python_script - path: /src/common/comp_tests/run_and_check_adata.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/script.py b/src/tasks/batch_integration/transformers/feature_to_embed/script.py index 7c61d3e67e..68ee83f72f 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/script.py +++ b/src/tasks/batch_integration/transformers/feature_to_embed/script.py @@ -11,7 +11,7 @@ with open(meta['config'], 'r', encoding="utf8") as file: config = yaml.safe_load(file) -output_type = config["functionality"]["info"]["output_type"] +output_type = config["functionality"]["info"]["subtype"] print('Read input', flush=True) adata= sc.read_h5ad(par['input']) From cb7672946f642d6f8d0494d022bc62ac282bc7fd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 22 Jun 2023 09:51:07 +0200 Subject: [PATCH 0931/1233] fix ordering (#193) Former-commit-id: 19a67c2cac07b74e644ffa43d20520b04a9e42dc --- src/common/create_task_readme/script.R | 7 ++-- src/common/helper_functions/read_api_files.R | 24 ++++++++++++-- src/tasks/batch_integration/README.md | 34 ++++++++++---------- src/tasks/denoising/README.md | 18 +++++------ src/tasks/dimensionality_reduction/README.md | 18 +++++------ src/tasks/label_projection/README.md | 22 ++++++------- 6 files changed, 71 insertions(+), 52 deletions(-) diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 8e5df6f6a5..4645020ea5 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -24,12 +24,13 @@ task_dir <- paste0(dirname(par[["viash_yaml"]]), "/src/tasks/", par[["task"]]) % gsub("^\\./", "", .) task_api <- read_task_api(task_dir) -r_graph <- render_task_graph(task_api) +# determine ordering +root <- .task_graph_get_root(task_api) -# todo: fix hard coded node -order <- names(igraph::bfs(task_api$task_graph, "file_common_dataset")$order) +r_graph <- render_task_graph(task_api, root) cat("Render API details\n") +order <- names(igraph::bfs(task_api$task_graph, root)$order) r_details <- map_chr( order, function(file_name) { diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index fe19c5f033..54f93792e2 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -317,12 +317,30 @@ create_task_graph <- function(file_info, comp_info, comp_args) { ) } -render_task_graph <- function(task_api) { +.task_graph_get_root <- function(task_api) { + root <- names(which(igraph::degree(task_api$task_graph, mode = "in") == 0)) + if (length(root) > 1) { + stop( + "There should only be one node with in-degree equal to 0.\n", + " Nodes with in-degree == 0: ", paste(root, collapse = ", ") + ) + } + root +} + +render_task_graph <- function(task_api, root = .task_graph_get_root(task_api)) { + order <- names(igraph::bfs(task_api$task_graph, root)$order) + + vdf <- igraph::as_data_frame(task_api$task_graph, "vertices") %>% + arrange(match(name, order)) + edf <- igraph::as_data_frame(task_api$task_graph, "edges") %>% + arrange(match(from, order), match(to, order)) + strip_margin(glue::glue(" §```mermaid §flowchart LR - §{paste(igraph::V(task_api$task_graph)$str, collapse = '\n')} - §{paste(igraph::E(task_api$task_graph)$str, collapse = '\n')} + §{paste(vdf$str, collapse = '\n')} + §{paste(edf$str, collapse = '\n')} §``` §"), symbol = "§") } diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index d02a73be07..1ce7960b5e 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -54,39 +54,39 @@ extensive benchmark of single-cell data integration methods ``` mermaid flowchart LR - file_unintegrated("Unintegrated") - file_integrated_embedding("Integrated embedding") - file_integrated_feature("Integrated Feature") - file_integrated_graaf("Integrated Graph") - file_score("Score") file_common_dataset("Common dataset") + comp_process_dataset[/"Data processor"/] + file_unintegrated("Unintegrated") comp_method_embedding[/"Method (embedding)"/] comp_method_feature[/"Method (feature)"/] comp_method_graaf[/"Method (graph)"/] + file_integrated_embedding("Integrated embedding") + file_integrated_feature("Integrated Feature") + file_integrated_graaf("Integrated Graph") comp_metric_embedding[/"Metric (embedding)"/] - comp_metric_feature[/"Metric (feature)"/] - comp_metric_graaf[/"Metric (graph)"/] - comp_process_dataset[/"Data processor"/] comp_transformer_embedding_to_graaf[/"Embedding to Graph"/] + comp_metric_feature[/"Metric (feature)"/] comp_transformer_feature_to_embedding[/"Feature to Embedding"/] + comp_metric_graaf[/"Metric (graph)"/] + file_score("Score") + file_common_dataset---comp_process_dataset + comp_process_dataset-->file_unintegrated file_unintegrated---comp_method_embedding file_unintegrated---comp_method_feature file_unintegrated---comp_method_graaf - file_integrated_embedding---comp_metric_embedding - file_integrated_feature---comp_metric_feature - file_integrated_graaf---comp_metric_graaf - file_common_dataset---comp_process_dataset - file_integrated_embedding---comp_transformer_embedding_to_graaf - file_integrated_feature---comp_transformer_feature_to_embedding comp_method_embedding-->file_integrated_embedding comp_method_feature-->file_integrated_feature comp_method_graaf-->file_integrated_graaf + file_integrated_embedding---comp_metric_embedding + file_integrated_embedding---comp_transformer_embedding_to_graaf + file_integrated_feature---comp_metric_feature + file_integrated_feature---comp_transformer_feature_to_embedding + file_integrated_graaf---comp_metric_graaf comp_metric_embedding-->file_score - comp_metric_feature-->file_score - comp_metric_graaf-->file_score - comp_process_dataset-->file_unintegrated comp_transformer_embedding_to_graaf-->file_integrated_graaf + comp_metric_feature-->file_score comp_transformer_feature_to_embedding-->file_integrated_embedding + comp_metric_graaf-->file_score ``` ## File format: Common dataset diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index d5a3f78058..ab51f3e5a9 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -55,26 +55,26 @@ dataset. ``` mermaid flowchart LR + file_common_dataset("Common dataset") + comp_process_dataset[/"Data processor"/] file_train("Training data") file_test("Test data") - file_denoised("Denoised data") - file_score("Score") - file_common_dataset("Common dataset") comp_control_method[/"Control method"/] comp_method[/"Method"/] comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_denoised("Denoised data") + file_score("Score") + file_common_dataset---comp_process_dataset + comp_process_dataset-->file_train + comp_process_dataset-->file_test file_train---comp_control_method - file_test---comp_control_method file_train---comp_method + file_test---comp_control_method file_test---comp_metric - file_denoised---comp_metric - file_common_dataset---comp_process_dataset comp_control_method-->file_denoised comp_method-->file_denoised comp_metric-->file_score - comp_process_dataset-->file_train - comp_process_dataset-->file_test + file_denoised---comp_metric ``` ## File format: Common dataset diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index d5d1c70cab..01f7b4e15f 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -47,26 +47,26 @@ for visualization and interpretation. ``` mermaid flowchart LR + file_common_dataset("Common dataset") + comp_process_dataset[/"Data processor"/] file_dataset("Dataset") file_solution("Test data") - file_embedding("Embedding") - file_score("Score") - file_common_dataset("Common dataset") comp_control_method[/"Control method"/] comp_method[/"Method"/] comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_embedding("Embedding") + file_score("Score") + file_common_dataset---comp_process_dataset + comp_process_dataset-->file_dataset + comp_process_dataset-->file_solution file_dataset---comp_control_method - file_solution---comp_control_method file_dataset---comp_method - file_embedding---comp_metric + file_solution---comp_control_method file_solution---comp_metric - file_common_dataset---comp_process_dataset comp_control_method-->file_embedding comp_method-->file_embedding comp_metric-->file_score - comp_process_dataset-->file_dataset - comp_process_dataset-->file_solution + file_embedding---comp_metric ``` ## File format: Common dataset diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 5dd13651f9..ffc7ec4f67 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -46,30 +46,30 @@ labels onto the test set. ``` mermaid flowchart LR + file_common_dataset("Common dataset") + comp_process_dataset[/"Data processor"/] file_train("Training data") file_test("Test data") file_solution("Solution") - file_prediction("Prediction") - file_score("Score") - file_common_dataset("Common dataset") comp_control_method[/"Control method"/] comp_method[/"Method"/] comp_metric[/"Metric"/] - comp_process_dataset[/"Data processor"/] + file_prediction("Prediction") + file_score("Score") + file_common_dataset---comp_process_dataset + comp_process_dataset-->file_train + comp_process_dataset-->file_test + comp_process_dataset-->file_solution file_train---comp_control_method - file_test---comp_control_method - file_solution---comp_control_method file_train---comp_method + file_test---comp_control_method file_test---comp_method + file_solution---comp_control_method file_solution---comp_metric - file_prediction---comp_metric - file_common_dataset---comp_process_dataset comp_control_method-->file_prediction comp_method-->file_prediction comp_metric-->file_score - comp_process_dataset-->file_train - comp_process_dataset-->file_test - comp_process_dataset-->file_solution + file_prediction---comp_metric ``` ## File format: Common dataset From 02d72d245de74593cfd27abd330406d6b8018be3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 23 Jun 2023 09:36:17 +0200 Subject: [PATCH 0932/1233] Bump viash-io/viash-actions from 3 to 4 (#194) Bumps [viash-io/viash-actions](https://github.com/viash-io/viash-actions) from 3 to 4. - [Release notes](https://github.com/viash-io/viash-actions/releases) - [Changelog](https://github.com/viash-io/viash-actions/blob/main/CHANGELOG.md) - [Commits](https://github.com/viash-io/viash-actions/compare/v3...v4) --- updated-dependencies: - dependency-name: viash-io/viash-actions dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 1aeb36230a16344098335003ed252316093cf6f4 --- .github/workflows/integration-test.yml | 20 ++++++++++---------- .github/workflows/main-build.yml | 16 ++++++++-------- .github/workflows/release-build.yml | 26 +++++++++++++------------- .github/workflows/viash-test.yml | 10 +++++----- 4 files changed, 36 insertions(+), 36 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index c921cb6f31..80429759ff 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -17,9 +17,9 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 id: cache with: s3_bucket: $s3_bucket @@ -31,7 +31,7 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v3 + - uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'integration_build' parallel: true @@ -44,14 +44,14 @@ jobs: publish_branch: integration_build - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: platform: docker src: src format: json - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: src: workflows format: json @@ -87,10 +87,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - name: Build container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'integration_build' setup: build @@ -104,7 +104,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'integration_build' platform: docker @@ -127,14 +127,14 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from integration_build branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: ".functionality.version := 'integration_build'" parallel: true diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 76768ab031..f1d3820486 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -16,20 +16,20 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v3 + - uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'main_build' parallel: true - name: Build nextflow schemas - uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 + uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: workflows: src components: src @@ -37,7 +37,7 @@ jobs: tools_version: 'main_build' - name: Build parameter files - uses: viash-io/viash-actions/pro/build-nextflow-params@v3 + uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: workflows: src components: src @@ -52,7 +52,7 @@ jobs: publish_branch: main_build - id: ns_list - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: platform: docker src: src @@ -81,10 +81,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - name: Build container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -99,7 +99,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'main_build' platform: docker diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 37af7046d7..e6ec3ac4b3 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -22,9 +22,9 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 id: cache with: s3_bucket: $s3_bucket @@ -36,13 +36,13 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v3 + - uses: viash-io/viash-actions/ns-build@v4 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true - name: Build nextflow schemas - uses: viash-io/viash-actions/pro/build-nextflow-schemas@v3 + uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 with: workflows: src components: src @@ -50,7 +50,7 @@ jobs: tools_version: 'main_build' - name: Build parameter files - uses: viash-io/viash-actions/pro/build-nextflow-params@v3 + uses: viash-io/viash-actions/pro/build-nextflow-params@v4 with: workflows: src components: src @@ -66,14 +66,14 @@ jobs: full_commit_message: "Deploy for release ${{ github.event.inputs.version_tag }} from ${{ github.sha }}" - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: platform: docker src: src format: json - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: src: workflows format: json @@ -110,10 +110,10 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - name: Build container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -128,7 +128,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: .functionality.version := '${{ github.event.inputs.version_tag }}' platform: docker @@ -151,14 +151,14 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - uses: nf-core/setup-nextflow@v1.3.0 # build target dir # use containers from release branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v3 + uses: viash-io/viash-actions/ns-build@v4 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true @@ -197,7 +197,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 # use cache - name: Cache resources data diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index f05aa1b380..7a6e4408fb 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -41,9 +41,9 @@ jobs: with: fetch-depth: 0 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v3 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 id: cache with: s3_bucket: $s3_bucket @@ -58,13 +58,13 @@ jobs: diff_relative: true - id: ns_list - uses: viash-io/viash-actions/ns-list@v3 + uses: viash-io/viash-actions/ns-list@v4 with: platform: docker format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@v3 + uses: viash-io/viash-actions/project/detect-changed-components@v4 with: input_file: "${{ steps.ns_list.outputs.output_file }}" @@ -91,7 +91,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: viash-io/viash-actions/setup@v3 + - uses: viash-io/viash-actions/setup@v4 # use cache - name: Cache resources data From ae4a22be4ea86f973dfe7724d16a7452c492b1d4 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 23 Jun 2023 12:05:24 +0200 Subject: [PATCH 0933/1233] add several control methods for batch integration (#141) * add random embedding * update description * add no_integration_batch * [wip] graph baseline * update api to match schemas * move control_methods to new task structure * update config files to match schemas * update docker images * update output type * update random_int to use knn fields * update api to use file i.o. anndata * add test_resources * Rename test resources in batch integration Co-authored-by: Kai Waldrant * remove hvg from required fields * add comment for output_type requirement * remove hvg field from output * update changelog --------- Co-authored-by: Robrecht Cannoodt Co-authored-by: Kai Waldrant Former-commit-id: bd2a128ccedc6749a54edda47aa5b576a0979db1 --- CHANGELOG.md | 44 +++++++++++++ src/tasks/batch_integration/README.md | 6 +- .../api/comp_control_method_embedding.yaml | 31 +++++++++ .../api/comp_control_method_graph.yaml | 31 +++++++++ .../api/file_integrated_embedding.yaml | 8 +-- .../api/file_integrated_feature.yaml | 8 +-- .../api/file_integrated_graph.yaml | 8 +-- .../api/file_unintegrated.yaml | 9 +++ .../no_integration_batch/config.vsh.yaml | 24 +++++++ .../no_integration_batch/script.py | 45 +++++++++++++ .../random_embed_cell/config.vsh.yaml | 23 +++++++ .../random_embed_cell/script.py | 38 +++++++++++ .../random_embed_cell_jitter/config.vsh.yaml | 29 +++++++++ .../random_embed_cell_jitter/script.py | 43 ++++++++++++ .../random_integration/config.vsh.yaml | 23 +++++++ .../random_integration/script.py | 65 +++++++++++++++++++ .../batch_integration/methods/bbknn/script.py | 1 - .../methods/combat/script.py | 1 - .../methods/scanorama_embed/script.py | 1 - .../methods/scanorama_feature/script.py | 1 - .../batch_integration/methods/scvi/script.py | 1 - .../metrics/asw_batch/script.py | 2 +- .../metrics/asw_label/script.py | 2 +- .../metrics/cell_cycle_conservation/script.py | 2 +- .../metrics/clustering_overlap/script.py | 2 +- .../batch_integration/metrics/pcr/script.py | 2 +- .../resources_test_scripts/pancreas.sh | 6 +- .../transformers/embed_to_graph/script.py | 2 +- .../transformers/feature_to_embed/script.py | 2 +- 29 files changed, 427 insertions(+), 33 deletions(-) create mode 100644 src/tasks/batch_integration/api/comp_control_method_embedding.yaml create mode 100644 src/tasks/batch_integration/api/comp_control_method_graph.yaml create mode 100644 src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/no_integration_batch/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/script.py diff --git a/CHANGELOG.md b/CHANGELOG.md index c6bc697f77..16ec26f108 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -81,6 +81,50 @@ * `loaders/openproblems_v1_multimodal`: Fetch a multimodal dataset from OpenProblems v1, whilst adding extra information to the `.uns`. +## batch_integration + +### NEW FUNCTIONALITY + +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the process, method and metric components. + +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. + +* `resources_test/label_projection/pancreas` with `src/tasks/label_projection/resources_test_scripts/pancreas.sh`. + +### V1 MIGRATION + +* Removed the separate subtask specific subfolders. The "subtask" is added to the config. + +* `control_methods/no_integration_batch`: Migrated from v1 embedding. + +* `control_methods/random_embed_cell`: Migrated from v1 embedding. + +* `control_methods/random_embed_cel_jitter`: Migrated from v1 embedding. + +* `control_methods/random_integration`: Migrated from v1 graph. + +* `methods/bbknn`: Migrated from v1 graph. + +* `methods/combat`: Migrated from v1 feature. + +* `methods/scanorama_embed`: Migrated from v1 embedding. + +* `methods/scanorama_feature`: Migrated from v1 feature. + +* `methods/scvi`: Migrated from v1 embedding. + +* `metrics/asw_batch`: Migrated from v1 embedding. + +* `metrics/asw_label`: Migrated from v1 embedding. + +* `metrics/cell_cycle_conservation`: Migrated from v1 embedding. + +* `metrics/clustering_overlap`: Migrated from v1 graph NMI & ARI. + +* `metrics/pcr`: Migrated from v1 embedding. + ## label_projection ### NEW FUNCTIONALITY diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 1ce7960b5e..bf764e6fde 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -268,7 +268,7 @@ Arguments: An integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/scvi.h5ad` +Example file: `resources_test/batch_integration/pancreas/integrated_embedding.h5ad` Description: @@ -315,7 +315,7 @@ Slot description: Integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/combat.h5ad` +Example file: `resources_test/batch_integration/pancreas/integrated_feature.h5ad` Description: @@ -362,7 +362,7 @@ Slot description: Integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/bbknn.h5ad` +Example file: `resources_test/batch_integration/pancreas/integrated_graph.h5ad` Description: diff --git a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml new file mode 100644 index 0000000000..8e01b9210b --- /dev/null +++ b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml @@ -0,0 +1,31 @@ +functionality: + namespace: batch_integration/control_methods + info: + type: control_method + subtype: embedding + type_info: + label: control method (embedding) + summary: A batch integration embedding control method. + description: | + A batch integration control method which outputs a batch-corrected embedding. + arguments: + - name: --input + __merge__: file_unintegrated.yaml + direction: input + required: true + - name: --output + direction: output + __merge__: file_integrated_embedding.yaml + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/comp_control_method_graph.yaml b/src/tasks/batch_integration/api/comp_control_method_graph.yaml new file mode 100644 index 0000000000..ab317ddca9 --- /dev/null +++ b/src/tasks/batch_integration/api/comp_control_method_graph.yaml @@ -0,0 +1,31 @@ +functionality: + namespace: batch_integration/control_methods + info: + type: control_method + subtype: graph + type_info: + label: control method (graph) + summary: A batch integration graph control method. + description: | + A batch integration control method which outputs a batch-corrected cell graphs. + arguments: + - __merge__: file_unintegrated.yaml + name: --input + direction: input + required: true + - __merge__: file_integrated_graph.yaml + name: --output + direction: output + required: true + - name: --hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/api/file_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml index 6b49118404..b5e4734516 100644 --- a/src/tasks/batch_integration/api/file_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -1,6 +1,6 @@ __merge__: "file_unintegrated.yaml" type: file -example: "resources_test/batch_integration/pancreas/scvi.h5ad" +example: "resources_test/batch_integration/pancreas/integrated_embedding.h5ad" info: prediction_type: embedding label: "Integrated embedding" @@ -16,10 +16,8 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: boolean - name: hvg - description: If the method was done on hvg or full - required: true + + #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml index 243aef9766..94fd9dbd6f 100644 --- a/src/tasks/batch_integration/api/file_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -1,6 +1,6 @@ __merge__: "file_unintegrated.yaml" type: file -example: "resources_test/batch_integration/pancreas/combat.h5ad" +example: "resources_test/batch_integration/pancreas/integrated_feature.h5ad" info: prediction_type: feature label: "Integrated Feature" @@ -16,10 +16,8 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: boolean - name: hvg - description: If the method was done on hvg or full - required: true + + #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml index ba7e2be694..f3013cbc28 100644 --- a/src/tasks/batch_integration/api/file_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -1,6 +1,6 @@ __merge__: "file_unintegrated.yaml" type: file -example: "resources_test/batch_integration/pancreas/bbknn.h5ad" +example: "resources_test/batch_integration/pancreas/integrated_graph.h5ad" info: prediction_type: graph label: "Integrated Graph" @@ -16,10 +16,8 @@ info: name: method_id description: "A unique identifier for the method" required: true - - type: boolean - name: hvg - description: If the method was done on hvg or full - required: true + + #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_unintegrated.yaml b/src/tasks/batch_integration/api/file_unintegrated.yaml index 3597a43c24..0b3ea56305 100644 --- a/src/tasks/batch_integration/api/file_unintegrated.yaml +++ b/src/tasks/batch_integration/api/file_unintegrated.yaml @@ -33,6 +33,10 @@ info: description: The resulting PCA embedding. required: true obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true - type: double name: knn_connectivities description: K nearest neighbors connectivities matrix. @@ -50,3 +54,8 @@ info: name: dataset_organism description: "Which normalization was used" required: true + - type: object + name: knn + description: Supplementary K nearest neighbors data. + required: true + diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml new file mode 100644 index 0000000000..da3013e908 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -0,0 +1,24 @@ +# use method api spec +__merge__: ../../api/comp_control_method_embedding.yaml +functionality: + name: no_integration_batch + info: + label: No integration by Batch + summary: "Cells are embedded by computing PCA independently on each batch" + description: "Cells are embedded by computing PCA independently on each batch" + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.0 + setup: + - type: python + pypi: + - scanpy + - numpy + - type: nextflow diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/script.py b/src/tasks/batch_integration/control_methods/no_integration_batch/script.py new file mode 100644 index 0000000000..7fb811892c --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/script.py @@ -0,0 +1,45 @@ +import scanpy as sc +import numpy as np +import yaml + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["subtype"] + +print('Read input', flush=True) +input = sc.read_h5ad(par['input']) + +print("process dataset", flush=True) +input.obsm["X_emb"] = np.zeros((input.shape[0], 50), dtype=float) +for batch in input.obs["batch"].unique(): + batch_idx = input.obs["batch"] == batch + n_comps = min(50, np.sum(batch_idx)) + solver = "full" if n_comps == np.sum(batch_idx) else "arpack" + # input.obsm["X_emb"][batch_idx, :n_comps] = sc.tl.pca( + # input[batch_idx], + # n_comps=n_comps, + # use_highly_variable=False, + # svd_solver=solver, + # copy=True, + # ).obsm["X_pca"] + +print("Store outputs", flush=True) +input.uns['output_type'] = output_type +input.uns['method_id'] = meta['functionality_name'] + +input.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml new file mode 100644 index 0000000000..f6f6e89a56 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../api/comp_control_method_embedding.yaml +functionality: + name: random_embed_cell + info: + label: Random Embedding by Celltype + summary: "Cells are embedded as a one-hot encoding of celltype labels" + description: "Cells are embedded as a one-hot encoding of celltype labels" + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.0 + setup: + - type: python + pypi: + - scikit-learn + - type: nextflow diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py new file mode 100644 index 0000000000..f3765ef36f --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py @@ -0,0 +1,38 @@ +from sklearn.preprocessing import LabelEncoder +from sklearn.preprocessing import OneHotEncoder +import anndata as ad +import yaml + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["subtype"] + +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) + + +print('processing data', flush=True) +input.obsm['X_emb'] = OneHotEncoder().fit_transform( + LabelEncoder().fit_transform(input.obs["label"])[:, None] +) + +print("Store outputs", flush=True) +input.uns['output_type'] = output_type +input.uns['hvg'] = par['hvg'] +input.uns['method_id'] = meta['functionality_name'] +input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml new file mode 100644 index 0000000000..3e4a0fc924 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -0,0 +1,29 @@ +# use method api spec +__merge__: ../../api/comp_control_method_embedding.yaml +functionality: + name: random_embed_cell_jitter + info: + label: Random Embedding by Celltype with jitter + summary: "Cells are embedded as a one-hot encoding of celltype labels, with a small amount of random noise added to the embedding" + description: "Cells are embedded as a one-hot encoding of celltype labels, with a small amount of random noise added to the embedding" + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + arguments: + - name: "--jitter" + type: double + default: 0.01 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.0 + setup: + - type: python + pypi: + - scikit-learn + - numpy + - scipy + - type: nextflow diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py new file mode 100644 index 0000000000..7c20bb83dd --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py @@ -0,0 +1,43 @@ +from sklearn.preprocessing import LabelEncoder +from sklearn.preprocessing import OneHotEncoder +import numpy as np +import anndata as ad +import yaml +from scipy.sparse import csr_matrix + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'jitter': 0.01 +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["subtype"] + +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) + + +print('processing data', flush=True) +embedding = OneHotEncoder().fit_transform( + LabelEncoder().fit_transform(input.obs["label"])[:, None] +) + +input.obsm['X_emb'] = csr_matrix(embedding + np.random.uniform(-1 * par['jitter'], par['jitter'], embedding.shape)) + +print("Store outputs", flush=True) +input.uns['output_type'] = output_type +input.uns['hvg'] = par['hvg'] +input.uns['method_id'] = meta['functionality_name'] +input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml new file mode 100644 index 0000000000..a9e0884ca5 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../api/comp_control_method_graph.yaml +functionality: + name: random_integration + info: + label: Random integration + summary: "Feature values, embedding coordinates, and graph connectivity are all randomly permuted." + description: "Feature values, embedding coordinates, and graph connectivity are all randomly permuted." + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.0 + setup: + - type: python + pypi: + - numpy + - type: nextflow diff --git a/src/tasks/batch_integration/control_methods/random_integration/script.py b/src/tasks/batch_integration/control_methods/random_integration/script.py new file mode 100644 index 0000000000..b9191a294d --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/script.py @@ -0,0 +1,65 @@ +import anndata as ad +import numpy as np +import yaml + + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar', +} + +## VIASH END + +def _set_uns(adata): + adata.uns["neighbors"] = adata.uns["knn"] + adata.uns["neighbors"]["connectivities_key"] = "connectivities" + adata.uns["neighbors"]["distances_key"] = "distances" + +def _randomize_features(X, partition=None): + X_out = X.copy() + if partition is None: + partition = np.full(X.shape[0], 0) + else: + partition = np.asarray(partition) + for partition_name in np.unique(partition): + partition_idx = np.argwhere(partition == partition_name).flatten() + X_out[partition_idx] = X[np.random.permutation(partition_idx)] + return X_out + +def _randomize_graph(adata, partition=None): + distances, connectivities = ( + adata.obsp["knn_distances"], + adata.obsp["knn_connectivities"], + ) + new_idx = _randomize_features(np.arange(distances.shape[0]), partition=partition) + adata.obsp["distances"] = distances[new_idx][:, new_idx] + adata.obsp["connectivities"] = connectivities[new_idx][:, new_idx] + _set_uns(adata) + return adata + +with open(meta['config'], 'r', encoding="utf8") as file: + config = yaml.safe_load(file) + +output_type = config["functionality"]["info"]["subtype"] + +print('Read input', flush=True) +input = ad.read_h5ad(par['input']) +input.X = input.layers["normalized"] + +input.X = _randomize_features(input.X) +input.obsm["X_emb"] = _randomize_features(input.obsm["X_pca"]) +input = _randomize_graph(input) +del input.X + +print("Store outputs", flush=True) +input.uns['output_type'] = output_type +input.uns['method_id'] = meta['functionality_name'] + +input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/bbknn/script.py b/src/tasks/batch_integration/methods/bbknn/script.py index eda4148c63..0f2deece55 100644 --- a/src/tasks/batch_integration/methods/bbknn/script.py +++ b/src/tasks/batch_integration/methods/bbknn/script.py @@ -33,6 +33,5 @@ print("Store outputs", flush=True) input.uns['output_type'] = output_type -input.uns['hvg'] = par['hvg'] input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/combat/script.py b/src/tasks/batch_integration/methods/combat/script.py index 5deda4fd29..a92d0616cc 100644 --- a/src/tasks/batch_integration/methods/combat/script.py +++ b/src/tasks/batch_integration/methods/combat/script.py @@ -37,6 +37,5 @@ print("Store outputs", flush=True) adata.uns['output_type'] = output_type -adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py index 9b1eb265a3..88d14f058c 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/script.py +++ b/src/tasks/batch_integration/methods/scanorama_embed/script.py @@ -33,6 +33,5 @@ print("Store outputs", flush=True) adata.uns['output_type'] = output_type -adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index 24a904dc89..59cc5df88c 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -44,6 +44,5 @@ print("Store outputs", flush=True) adata.uns['output_type'] = output_type -adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py index 73af0e284f..aca51dd4c4 100644 --- a/src/tasks/batch_integration/methods/scvi/script.py +++ b/src/tasks/batch_integration/methods/scvi/script.py @@ -33,6 +33,5 @@ print("Store outputs", flush=True) adata.uns['output_type'] = output_type -adata.uns['hvg'] = par['hvg'] adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/metrics/asw_batch/script.py b/src/tasks/batch_integration/metrics/asw_batch/script.py index 82860ccc24..cdb3057c49 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/script.py +++ b/src/tasks/batch_integration/metrics/asw_batch/script.py @@ -4,7 +4,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', 'output': 'output.h5ad', } meta = { diff --git a/src/tasks/batch_integration/metrics/asw_label/script.py b/src/tasks/batch_integration/metrics/asw_label/script.py index be878f105b..fe089f517d 100644 --- a/src/tasks/batch_integration/metrics/asw_label/script.py +++ b/src/tasks/batch_integration/metrics/asw_label/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', 'output': 'output.h5ad', } diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index 54df10fd9e..2740c26fea 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', 'output': 'output.h5ad' } diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/script.py b/src/tasks/batch_integration/metrics/clustering_overlap/script.py index 9e57be8496..2617cc7136 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/script.py +++ b/src/tasks/batch_integration/metrics/clustering_overlap/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/pancreas/bbknn.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_graph.h5ad', 'output': 'output.h5ad', } diff --git a/src/tasks/batch_integration/metrics/pcr/script.py b/src/tasks/batch_integration/metrics/pcr/script.py index 6750c22349..3fc9c483ed 100644 --- a/src/tasks/batch_integration/metrics/pcr/script.py +++ b/src/tasks/batch_integration/metrics/pcr/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input_integrated': 'resources_test/batch_integration/pancreas/scvi.h5ad', + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', 'output': 'output.h5ad', } diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index 5ca39fade0..3a4dddda5e 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -26,17 +26,17 @@ viash run src/tasks/batch_integration/process_dataset/config.vsh.yaml -- \ echo Running BBKNN viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ - --output $DATASET_DIR/bbknn.h5ad + --output $DATASET_DIR/integrated_graph.h5ad echo Running SCVI viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ - --output $DATASET_DIR/scvi.h5ad + --output $DATASET_DIR/integrated_embedding.h5ad echo Running combat viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ --input $DATASET_DIR/unintegrated.h5ad \ - --output $DATASET_DIR/combat.h5ad + --output $DATASET_DIR/integrated_feature.h5ad # run one metric echo run metrics... diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/script.py b/src/tasks/batch_integration/transformers/embed_to_graph/script.py index d68a4e1574..7881291a42 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/script.py +++ b/src/tasks/batch_integration/transformers/embed_to_graph/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/scvi.h5ad', + 'input': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', 'ouput': 'output.h5ad' } ## VIASH END diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/script.py b/src/tasks/batch_integration/transformers/feature_to_embed/script.py index 68ee83f72f..b067afc3f3 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/script.py +++ b/src/tasks/batch_integration/transformers/feature_to_embed/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/combat.h5ad', + 'input': 'resources_test/batch_integration/pancreas/integrated_feature.h5ad', 'ouput': 'output.h5ad' } ## VIASH END From c54165592b593c91e564362e9448d8a4c7d60908 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 10 Jul 2023 13:24:40 +0200 Subject: [PATCH 0934/1233] Bump tj-actions/changed-files from 36.4.1 to 37.0.5 (#199) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 36.4.1 to 37.0.5. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v36.4.1...v37.0.5) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 0bd28d2c89cdd003edf75e24f9a7f290d9dd938e --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 7a6e4408fb..2406939a9d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v36.4.1 + uses: tj-actions/changed-files@v37.0.5 with: separator: ";" diff_relative: true From 1671c16fcb73ec6b038591dddd2ac333c5629b75 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 12 Jul 2023 13:13:22 +0200 Subject: [PATCH 0935/1233] Bump tj-actions/changed-files from 37.0.5 to 37.1.1 (#203) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 37.0.5 to 37.1.1. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v37.0.5...v37.1.1) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: ce13b7faef119978953cc9b839387a27a7153116 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 2406939a9d..263ed2cc8d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v37.0.5 + uses: tj-actions/changed-files@v37.1.1 with: separator: ";" diff_relative: true From ec05ee2c478467de49fe94921e96cee6bd44c3c6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 12 Jul 2023 16:31:41 +0200 Subject: [PATCH 0936/1233] Refactor Nextflow workflows (#196) * wip * improve wip * improve implementation * fix dimred workflow * refactor state management helper functions * improvements * update * update benchmarking workflows * fix benchmarkhelper * Let dataset schema return the metadata stored in the uns * add more comments * refactor v1 datasets pipeline * refactor denoising nxf wf * set up pipeline to latest standard * working pipeline for cluster overlap scores on scanorama_feature * add resource scripts * add directive labels to methods and metrics * extend batch integration wf * update api files * remove hvg & output type when not relevant * no need to store copy of input * fix test script * update api * capitalize * add control methods --------- Co-authored-by: Kai Waldrant Co-authored-by: Michaela Mueller Former-commit-id: 8874ba94c0cf07dd139379e9025b38a90b9cda8e --- .../check_dataset_schema/config.vsh.yaml | 8 +- src/common/check_dataset_schema/script.py | 83 +++-- .../resource_scripts/openproblems_v1.sh | 5 +- .../process_openproblems_v1/config.vsh.yaml | 9 +- .../workflows/process_openproblems_v1/main.nf | 99 ++++-- src/tasks/batch_integration/README.md | 150 +++++--- .../api/comp_control_method_embedding.yaml | 2 +- .../api/comp_control_method_graph.yaml | 2 +- .../api/file_integrated_embedding.yaml | 1 - .../api/file_integrated_feature.yaml | 1 - .../api/file_integrated_graph.yaml | 1 - .../batch_integration/api/file_score.yaml | 8 - .../random_embed_cell/script.py | 1 - .../random_embed_cell_jitter/script.py | 1 - .../methods/bbknn/config.vsh.yaml | 2 + .../methods/combat/config.vsh.yaml | 2 + .../methods/scanorama_embed/config.vsh.yaml | 2 + .../methods/scanorama_feature/config.vsh.yaml | 2 + .../methods/scvi/config.vsh.yaml | 2 + .../metrics/asw_batch/config.vsh.yaml | 2 + .../metrics/asw_batch/script.py | 4 +- .../metrics/asw_label/config.vsh.yaml | 2 + .../metrics/asw_label/script.py | 2 - .../cell_cycle_conservation/config.vsh.yaml | 2 + .../metrics/cell_cycle_conservation/script.py | 4 +- .../clustering_overlap/config.vsh.yaml | 2 + .../metrics/clustering_overlap/script.py | 4 +- .../metrics/pcr/config.vsh.yaml | 2 + .../batch_integration/metrics/pcr/script.py | 4 +- .../resources_scripts/process_datasets.sh | 61 ++++ .../resources_scripts/run_benchmark.sh | 66 ++++ .../batch_integration/workflows/run/main.nf | 329 +++++++++--------- .../workflows/run/run_nextflow.sh | 4 +- .../denoising/workflows/run/config.vsh.yaml | 8 + src/tasks/denoising/workflows/run/main.nf | 221 +++++------- src/tasks/denoising/workflows/run/run_test.sh | 28 ++ .../workflows/run/main.nf | 245 ++++++------- .../workflows/run/run_test.sh | 28 ++ .../workflows/run/config.vsh.yaml | 15 +- .../label_projection/workflows/run/main.nf | 239 +++++++------ .../workflows/run/run_test.sh | 10 +- src/wf_utils/BenchmarkHelper.nf | 152 ++++++++ 42 files changed, 1105 insertions(+), 710 deletions(-) create mode 100755 src/tasks/batch_integration/resources_scripts/process_datasets.sh create mode 100755 src/tasks/batch_integration/resources_scripts/run_benchmark.sh create mode 100755 src/tasks/denoising/workflows/run/run_test.sh create mode 100755 src/tasks/dimensionality_reduction/workflows/run/run_test.sh create mode 100644 src/wf_utils/BenchmarkHelper.nf diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 274f2885b6..dfd1baebe8 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: description: A h5ad file. - name: --schema type: file - required: true + required: false description: A schema file for the h5ad object. - name: Arguments arguments: @@ -33,6 +33,12 @@ functionality: description: If specified, the output file will be a copy of the input file. example: output.h5ad direction: output + - name: --meta + type: file + required: false + description: If specified, the output file will contain metadata of the dataset. + example: output_meta.yaml + direction: output resources: - type: python_script path: script.py diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 2f902f3fa5..727d3bf59f 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -3,62 +3,79 @@ import shutil import json - ## VIASH START -# The following code has been auto-generated by Viash. par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', 'schema': 'src/tasks/denoising/api/file_common_dataset.yaml', 'stop_on_error': False, 'checks': 'output/error.json', - 'output': 'output/output.h5ad' -} -meta = { - 'functionality_name': 'foo', - + 'output': 'output/output.h5ad', + 'meta': 'output/meta.json', } - ## VIASH END -def check_structure (slot_info, adata_slot): - missing=[] +def check_structure(slot_info, adata_slot): + missing = [] for obj in slot_info: - if obj['name'] not in adata_slot: - missing.append(obj['name']) - + if obj['name'] not in adata_slot: + missing.append(obj['name']) return missing - print('Load data', flush=True) adata = ad.read_h5ad(par['input']) -with open(par['schema'], 'r') as f: - data_struct = yaml.safe_load(f) +# create data structure +out = { + "exit_code": 0, + "error": {} +} + +def is_atomic(obj): + return isinstance(obj, str) or isinstance(obj, int) or isinstance(obj, bool) + +def is_list_of_atomics(obj): + if not isinstance(obj, list): + return False + return all(is_atomic(elem) for elem in obj) +def is_dict_of_atomics(obj): + if not isinstance(obj, dict): + return False + return all(is_atomic(elem) for key, elem in obj.items()) -def_slots = data_struct['info']['slots'] -out={ - 'exit_code' : 0, - 'data_schema': 'ok', - 'error': { - +if par['meta'] is not None: + print("Extract metadata from object", flush=True) + meta = { + key: val + for key, val in adata.uns.items() + if is_atomic(val) or is_list_of_atomics(val) or is_dict_of_atomics(val) } -} + with open(par["meta"], "w") as f: + yaml.dump(meta, f, indent=2) + +if par['schema'] is not None: + print("Check AnnData against schema", flush=True) + with open(par["schema"], "r") as f: + data_struct = yaml.safe_load(f) -for slot in def_slots: - check = check_structure(def_slots[slot], getattr(adata, slot)) - if bool(check): - out['exit_code'] = 1 - out['data_schema'] = 'not ok' - out['error'][slot] = check + def_slots = data_struct['info']['slots'] -if par['checks'] is not None: - with open(par["checks"], "w") as f: - json.dump(out, f, indent=2) + out["data_schema"] = "ok" + + for slot in def_slots: + check = check_structure(def_slots[slot], getattr(adata, slot)) + if bool(check): + out['exit_code'] = 1 + out['data_schema'] = 'not ok' + out['error'][slot] = check + + if par['checks'] is not None: + with open(par["checks"], "w") as f: + json.dump(out, f, indent=2) if par['output'] is not None: shutil.copyfile(par["input"], par["output"]) - + if par['stop_on_error']: exit(out['exit_code']) diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 89f4888555..5fa3ab2d22 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -145,11 +145,12 @@ param_list: dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio -output: '$id.h5ad' +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_meta.yaml' HERE fi -export NXF_VER=22.04.5 +export NXF_VER=23.04.2 nextflow \ run . \ -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 1000c6ba40..b82f448ed8 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -59,13 +59,13 @@ functionality: required: false - name: Outputs arguments: - - name: "--output" + - name: "--output_dataset" direction: "output" # todo: fix inherits in nxf # __merge__: ../../api/file_raw.yaml type: file description: "A raw dataset" - example: "raw_dataset.h5ad" + example: "dataset.h5ad" info: label: "Raw dataset" slots: @@ -92,6 +92,11 @@ functionality: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: "--output_meta" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_meta.yaml" resources: - type: nextflow_script path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index edbcfa8bd7..aa6e0f4243 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -3,23 +3,37 @@ nextflow.enable.dsl=2 sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +// dataset loaders include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/main.nf" + +// normalization methods include { log_cpm } from "$targetDir/datasets/normalization/log_cpm/main.nf" include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" +include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" + +// dataset processors include { pca } from "$targetDir/datasets/processors/pca/main.nf" include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" include { knn } from "$targetDir/datasets/processors/knn/main.nf" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" -include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" +// helper functions +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// normalization_methods = [log_cpm, log_scran_pooling, sqrt_cpm, l1_sqrt +normalization_methods = [log_cpm, sqrt_cpm, l1_sqrt] + workflow { helpMessage(config) - viashChannel(params, config) + channelFromParams(params, config) | run_wf } @@ -29,42 +43,69 @@ workflow run_wf { main: output_ch = input_ch + | preprocessInputs(config: config) - // split params for downstream components - | setWorkflowArguments( - loader: [ + // fetch data from legacy openproblems + | run_components( + components: openproblems_v1, + from_state: [ "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse", "dataset_name", "data_url", "data_reference", "dataset_summary", "dataset_description", "dataset_organism" ], - output: [ "output" ] + to_state: [ dataset: "output" ] ) - // fetch data from legacy openproblems - | getWorkflowArguments(key: "loader") - | openproblems_v1 - // run normalization methods - | (log_cpm & log_scran_pooling & sqrt_cpm) - | mix - - // make id unique again - | pmap{ id, file -> - // derive unique ids from output filenames - def newId = file.getName().replaceAll(".output.*", "") - [ newId, file ] - } - - | pca - | hvg - - | getWorkflowArguments(key: "output") - | knn.run( - auto: [ publish: true ] + | run_components( + components: normalization_methods, + id: { id, state, config -> id + "/" + config.functionality.name }, + from_state: [ input: "dataset" ], + to_state: [ + normalization_id: config.functionality.name, + output_normalization: "output" + ] ) - // clean up channel - | pmap{id, data, passthrough -> [id, data]} + | run_components( + components: pca, + from_state: [ input: "output_normalization" ], + to_state: [ pca: "output" ] + ) + + | run_components( + components: hvg, + from_state: [ input: "pca" ], + to_state: [ hvg: "output" ] + ) + + | run_components( + components: knn, + from_state: [ input: "hvg" ], + to_state: [ knn: "output" ] + ) + + | run_components( + components: check_dataset_schema, + from_state: {id, state, config -> + [ + input: state.knn, + meta: state.output_meta, + output: state.output_dataset, + checks: null + ] + }, + to_state: [], + auto: [publish: true] + ) emit: output_ch +} + +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() + + write_json(traces, file("$publish_dir/traces.json")) + write_json(normalization_methods.collect{it.config}, file("$publish_dir/normalization_methods.json")) } \ No newline at end of file diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index bf764e6fde..8fbcdccbb6 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -57,36 +57,42 @@ flowchart LR file_common_dataset("Common dataset") comp_process_dataset[/"Data processor"/] file_unintegrated("Unintegrated") + comp_control_method_embedding[/"Control method (embedding)"/] + comp_control_method_graaf[/"Control method (graph)"/] comp_method_embedding[/"Method (embedding)"/] comp_method_feature[/"Method (feature)"/] comp_method_graaf[/"Method (graph)"/] file_integrated_embedding("Integrated embedding") - file_integrated_feature("Integrated Feature") file_integrated_graaf("Integrated Graph") + file_integrated_feature("Integrated Feature") comp_metric_embedding[/"Metric (embedding)"/] comp_transformer_embedding_to_graaf[/"Embedding to Graph"/] + comp_metric_graaf[/"Metric (graph)"/] comp_metric_feature[/"Metric (feature)"/] comp_transformer_feature_to_embedding[/"Feature to Embedding"/] - comp_metric_graaf[/"Metric (graph)"/] file_score("Score") file_common_dataset---comp_process_dataset comp_process_dataset-->file_unintegrated + file_unintegrated---comp_control_method_embedding + file_unintegrated---comp_control_method_graaf file_unintegrated---comp_method_embedding file_unintegrated---comp_method_feature file_unintegrated---comp_method_graaf + comp_control_method_embedding-->file_integrated_embedding + comp_control_method_graaf-->file_integrated_graaf comp_method_embedding-->file_integrated_embedding comp_method_feature-->file_integrated_feature comp_method_graaf-->file_integrated_graaf file_integrated_embedding---comp_metric_embedding file_integrated_embedding---comp_transformer_embedding_to_graaf + file_integrated_graaf---comp_metric_graaf file_integrated_feature---comp_metric_feature file_integrated_feature---comp_transformer_feature_to_embedding - file_integrated_graaf---comp_metric_graaf comp_metric_embedding-->file_score comp_transformer_embedding_to_graaf-->file_integrated_graaf + comp_metric_graaf-->file_score comp_metric_feature-->file_score comp_transformer_feature_to_embedding-->file_integrated_embedding - comp_metric_graaf-->file_score ``` ## File format: Common dataset @@ -182,9 +188,9 @@ Format: obs: 'batch', 'label' var: 'hvg' obsm: 'X_pca' - obsp: 'knn_connectivities' + obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn' @@ -198,12 +204,52 @@ Slot description: | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | | `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + + + +## Component type: Control method (embedding) + +Path: +[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/control_methods) + +A batch integration embedding control method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | +| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | + +
+ +## Component type: Control method (graph) + +Path: +[`src/batch_integration/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/control_methods) + +A batch integration graph control method. + +Arguments: + +
+ +| Name | Type | Description | +|:-----------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | +| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. |
@@ -268,7 +314,8 @@ Arguments: An integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/integrated_embedding.h5ad` +Example file: +`resources_test/batch_integration/pancreas/integrated_embedding.h5ad` Description: @@ -282,9 +329,9 @@ Format: obs: 'batch', 'label' var: 'hvg' obsm: 'X_pca', 'X_emb' - obsp: 'knn_connectivities' + obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' @@ -299,23 +346,25 @@ Slot description: | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsm["X_emb"]` | `double` | integration embedding prediction. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | | `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | | `uns["output_type"]` | `string` | what kind of output has been generated. | -## File format: Integrated Feature +## File format: Integrated Graph Integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/integrated_feature.h5ad` +Example file: +`resources_test/batch_integration/pancreas/integrated_graph.h5ad` Description: @@ -329,9 +378,9 @@ Format: obs: 'batch', 'label' var: 'hvg' obsm: 'X_pca' - obsp: 'knn_connectivities' - layers: 'counts', 'normalized', 'corrected_counts' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + obsp: 'knn_distances', 'knn_connectivities', 'connectivities' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' @@ -345,24 +394,26 @@ Slot description: | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | -| `layers["corrected_counts"]` | `double` | Corrected counts after integration. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | | `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | | `uns["output_type"]` | `string` | what kind of output has been generated. | -## File format: Integrated Graph +## File format: Integrated Feature Integrated AnnData HDF5 file. -Example file: `resources_test/batch_integration/pancreas/integrated_graph.h5ad` +Example file: +`resources_test/batch_integration/pancreas/integrated_feature.h5ad` Description: @@ -376,9 +427,9 @@ Format: obs: 'batch', 'label' var: 'hvg' obsm: 'X_pca' - obsp: 'knn_connectivities', 'connectivities' - layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'hvg', 'output_type' + obsp: 'knn_distances', 'knn_connectivities' + layers: 'counts', 'normalized', 'corrected_counts' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' @@ -392,15 +443,16 @@ Slot description: | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | +| `layers["corrected_counts"]` | `double` | Corrected counts after integration. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | | `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | | `uns["output_type"]` | `string` | what kind of output has been generated. | @@ -441,12 +493,12 @@ Arguments: -## Component type: Metric (feature) +## Component type: Metric (graph) Path: [`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) -A batch integration feature metric. +A batch integration graph metric. Arguments: @@ -459,39 +511,39 @@ Arguments: -## Component type: Feature to Embedding +## Component type: Metric (feature) Path: -[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) -Transform a feature output to an embedding. +A batch integration feature metric. Arguments:
-| Name | Type | Description | -|:-----------|:-------|:--------------------------------------------| -| `--input` | `file` | Integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | +| Name | Type | Description | +|:---------------------|:-------|:------------------------------| +| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Metric score file. |
-## Component type: Metric (graph) +## Component type: Feature to Embedding Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) -A batch integration graph metric. +Transform a feature output to an embedding. Arguments:
-| Name | Type | Description | -|:---------------------|:-------|:------------------------------| -| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Metric score file. | +| Name | Type | Description | +|:-----------|:-------|:--------------------------------------------| +| `--input` | `file` | Integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. |
@@ -510,7 +562,7 @@ Format:
AnnData object - uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values', 'hvg', 'output_type' + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values'
@@ -518,14 +570,12 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:---------------------------------------------------------------------------------------------| -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | -| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | -| `uns["hvg"]` | `boolean` | If the method was done on hvg or full. | -| `uns["output_type"]` | `string` | what kind of output has been generated. | +| Slot | Type | Description | +|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |
diff --git a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml index 8e01b9210b..802c7c040d 100644 --- a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml @@ -4,7 +4,7 @@ functionality: type: control_method subtype: embedding type_info: - label: control method (embedding) + label: Control method (embedding) summary: A batch integration embedding control method. description: | A batch integration control method which outputs a batch-corrected embedding. diff --git a/src/tasks/batch_integration/api/comp_control_method_graph.yaml b/src/tasks/batch_integration/api/comp_control_method_graph.yaml index ab317ddca9..902937f270 100644 --- a/src/tasks/batch_integration/api/comp_control_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_graph.yaml @@ -4,7 +4,7 @@ functionality: type: control_method subtype: graph type_info: - label: control method (graph) + label: Control method (graph) summary: A batch integration graph control method. description: | A batch integration control method which outputs a batch-corrected cell graphs. diff --git a/src/tasks/batch_integration/api/file_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml index b5e4734516..09816eeebb 100644 --- a/src/tasks/batch_integration/api/file_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -17,7 +17,6 @@ info: description: "A unique identifier for the method" required: true - #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml index 94fd9dbd6f..cfbff9ed5f 100644 --- a/src/tasks/batch_integration/api/file_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -17,7 +17,6 @@ info: description: "A unique identifier for the method" required: true - #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml index f3013cbc28..a174fb82ee 100644 --- a/src/tasks/batch_integration/api/file_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -17,7 +17,6 @@ info: description: "A unique identifier for the method" required: true - #? Still required ? info can be extracted from config (initialy added to check which metric should be run on the h5ad) - type: string name: output_type description: what kind of output has been generated diff --git a/src/tasks/batch_integration/api/file_score.yaml b/src/tasks/batch_integration/api/file_score.yaml index bbcdaebf98..9b4dac654f 100644 --- a/src/tasks/batch_integration/api/file_score.yaml +++ b/src/tasks/batch_integration/api/file_score.yaml @@ -26,12 +26,4 @@ info: name: metric_values description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." multiple: true - required: true - - type: boolean - name: hvg - description: If the method was done on hvg or full - required: true - - type: string - name: output_type - description: what kind of output has been generated required: true \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py index f3765ef36f..29491726fd 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py @@ -33,6 +33,5 @@ print("Store outputs", flush=True) input.uns['output_type'] = output_type -input.uns['hvg'] = par['hvg'] input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py index 7c20bb83dd..50622f60b4 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py @@ -38,6 +38,5 @@ print("Store outputs", flush=True) input.uns['output_type'] = output_type -input.uns['hvg'] = par['hvg'] input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 7aa1d14fdf..7588b7504f 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -38,3 +38,5 @@ platforms: - scib==1.1.3 - bbknn - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 1b2a312fba..8f6c527cf1 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -40,3 +40,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 38a7781518..21056ecbdc 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -36,3 +36,5 @@ platforms: - scanorama - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 3ace46a181..ca7edd0983 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -36,3 +36,5 @@ platforms: - scanorama - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index c857066d88..a917f6ecaa 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -30,3 +30,5 @@ platforms: - scvi-tools - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index 392547e522..99271d5752 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_batch/script.py b/src/tasks/batch_integration/metrics/asw_batch/script.py index cdb3057c49..cb0fc92b54 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/script.py +++ b/src/tasks/batch_integration/metrics/asw_batch/script.py @@ -30,9 +30,7 @@ 'normalization_id': adata.uns['normalization_id'], 'method_id': adata.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], - 'metric_values': [ score ], - 'hvg': adata.uns['hvg'], - 'output_type': adata.uns['output_type'], + 'metric_values': [ score ] } ) diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 01b744879b..5eac779cb5 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -26,3 +26,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_label/script.py b/src/tasks/batch_integration/metrics/asw_label/script.py index fe089f517d..be069fe0de 100644 --- a/src/tasks/batch_integration/metrics/asw_label/script.py +++ b/src/tasks/batch_integration/metrics/asw_label/script.py @@ -28,8 +28,6 @@ "dataset_id": adata.uns['dataset_id'], 'normalization_id': adata.uns['normalization_id'], "method_id": adata.uns['method_id'], - "hvg": adata.uns['hvg'], - "output_type": adata.uns['output_type'], "metric_ids": [meta['functionality_name']], "metric_values": [score] } diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index b7ebce1162..252625ef4a 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -26,3 +26,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index 2740c26fea..296155df97 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -40,9 +40,7 @@ 'normalization_id': adata.uns['normalization_id'], 'method_id': adata.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], - 'metric_values': [ score ], - 'hvg': adata.uns['hvg'], - 'output_type': adata.uns['output_type'], + 'metric_values': [ score ] } ) diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index dcb91e807e..edf8ee14fe 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -55,3 +55,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/script.py b/src/tasks/batch_integration/metrics/clustering_overlap/script.py index 2617cc7136..11420782ea 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/script.py +++ b/src/tasks/batch_integration/metrics/clustering_overlap/script.py @@ -38,9 +38,7 @@ 'normalization_id': input.uns['normalization_id'], "method_id": input.uns['method_id'], "metric_ids": [ "ari", "nmi" ], - "metric_values": [ ari_score, nmi_score ], - "hvg": input.uns['hvg'], - 'output_type': input.uns['output_type'], + "metric_values": [ ari_score, nmi_score ] } ) diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 47a76a4ac3..2e0c306411 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -30,3 +30,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/pcr/script.py b/src/tasks/batch_integration/metrics/pcr/script.py index 3fc9c483ed..5e5d7edce6 100644 --- a/src/tasks/batch_integration/metrics/pcr/script.py +++ b/src/tasks/batch_integration/metrics/pcr/script.py @@ -36,9 +36,7 @@ 'normalization_id': adata.uns['normalization_id'], 'method_id': adata.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], - 'metric_values': [ score ], - 'hvg': adata.uns['hvg'], - 'output_type': adata.uns['output_type'], + 'metric_values': [ score ] } ) diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh new file mode 100755 index 0000000000..bdf8413fab --- /dev/null +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -0,0 +1,61 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +COMMON_DATASETS="resources/datasets/openproblems_v1" +OUTPUT_DIR="resources/batch_integration/datasets/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import anndata as ad +import glob +import yaml + +h5ad_files = glob.glob("$COMMON_DATASETS/**/*.h5ad", recursive=True) + +param_list = [] + +for h5ad_file in h5ad_files: + print(f"Checking {h5ad_file}") + adata = ad.read_h5ad(h5ad_file, backed=True) + + if "batch" in adata.obs and "celltype" in adata.obs: + dataset_id = adata.uns["dataset_id"].replace("/", ".") + normalization_id = adata.uns["normalization_id"] + id = dataset_id + "." + normalization_id + obj = { + 'id': id, + 'input': h5ad_file + } + param_list.append(obj) + +output = { + "param_list": param_list, + "obs_label": "celltype", + "obs_batch": "batch", + "output": "\$id.h5ad" +} + +with open("$params_file", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +nextflow \ + run . \ + -main-script target/nextflow/batch_integration/process_dataset/main.nf \ + -profile docker \ + -resume \ + -params-file $params_file \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..1f92a7e227 --- /dev/null +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -0,0 +1,66 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources/batch_integration/datasets/openproblems_v1" +OUTPUT_DIR="resources/batch_integration/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="$OUTPUT_DIR/params.yaml" + +if [ ! -f $params_file ]; then + python << HERE +import anndata as ad +import glob +import yaml + +h5ad_files = glob.glob("$DATASETS_DIR/**/*.h5ad", recursive=True) + +# figure out where dataset files are stored +param_list = [] + +for h5ad_file in h5ad_files: + print(f"Checking {h5ad_file}") + adata = ad.read_h5ad(h5ad_file, backed=True) + + dataset_id = adata.uns["dataset_id"].replace("/", ".") + normalization_id = adata.uns["normalization_id"] + id = dataset_id + "." + normalization_id + + obj = { + 'id': id, + 'input': h5ad_file, + # 'dataset_id': dataset_id, + # 'normalization_id': normalization_id + } + param_list.append(obj) + +# write as output file +output = { + "param_list": param_list, +} + +with open("$params_file", "w") as file: + yaml.dump(output, file) +HERE +fi + +export NXF_VER=22.04.5 +nextflow \ + run . \ + -main-script src/tasks/batch_integration/workflows/run/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" diff --git a/src/tasks/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run/main.nf index f88d77c7f3..11bbd2e733 100644 --- a/src/tasks/batch_integration/workflows/run/main.nf +++ b/src/tasks/batch_integration/workflows/run/main.nf @@ -3,214 +3,201 @@ nextflow.enable.dsl=2 sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + +// import preprocessing +include { process_dataset } from "$targetDir/batch_integration/process_dataset/main.nf" + // import methods -include { bbknn } from "$targetDir/batch_integration/methods_graph/bbknn/main.nf" -include { combat } from "$targetDir/batch_integration/methods_feature/combat/main.nf" -include { scanorama_embed } from "$targetDir/batch_integration/methods_embedding/scanorama_embed/main.nf" -include { scanorama_feature } from "$targetDir/batch_integration/methods_feature/scanorama_feature/main.nf" -include { scvi } from "$targetDir/batch_integration/methods_graph/scvi/main.nf" +include { bbknn } from "$targetDir/batch_integration/methods/bbknn/main.nf" +include { combat } from "$targetDir/batch_integration/methods/combat/main.nf" +include { scanorama_embed } from "$targetDir/batch_integration/methods/scanorama_embed/main.nf" +include { scanorama_feature } from "$targetDir/batch_integration/methods/scanorama_feature/main.nf" +include { scvi } from "$targetDir/batch_integration/methods/scvi/main.nf" + +// import control methods +include { no_integration_batch } from "$targetDir/batch_integration/control_methods/no_integration_batch/main.nf" +include { random_embed_cell } from "$targetDir/batch_integration/control_methods/random_embed_cell/main.nf" +include { random_embed_cell_jitter } from "$targetDir/batch_integration/control_methods/random_embed_cell_jitter/main.nf" +include { random_integration } from "$targetDir/batch_integration/control_methods/random_integration/main.nf" // import transformers -include ( feature_to_embed ) from "$targetDir/batch_integration/methods_feature/feature_to_embed/main.nf" -include ( embed_to_graph ) from "$targetDir/batch_integration/methods_graph/embed_to_graph/main.nf" +include { feature_to_embed } from "$targetDir/batch_integration/transformers/feature_to_embed/main.nf" +include { embed_to_graph } from "$targetDir/batch_integration/transformers/embed_to_graph/main.nf" // import metrics -include { clustering_overlap } from "$targetDir/batch_integration/metrics_graph/clustering_overlap/main.nf" -include { asw_batch } from "$targetDir/batch_integration/metrics_embedding/asw_batch/main.nf" -include { asw_label } from "$targetDir/batch_integration/metrics_embedding/asw_label/main.nf" -include { ccc } from "$targetDir/batch_integration/metrics_embedding/cel_cycle_conservation/main.nf" -include { pcr } from "$targetDir/batch_integration/metrics_embedding/pcr/main.nf" +include { clustering_overlap } from "$targetDir/batch_integration/metrics/clustering_overlap/main.nf" +include { asw_batch } from "$targetDir/batch_integration/metrics/asw_batch/main.nf" +include { asw_label } from "$targetDir/batch_integration/metrics/asw_label/main.nf" +include { cell_cycle_conservation } from "$targetDir/batch_integration/metrics/cell_cycle_conservation/main.nf" +include { pcr } from "$targetDir/batch_integration/metrics/pcr/main.nf" // tsv generation component include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" +include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// collect method list +methods = [ + bbknn, + combat, + scanorama_embed, + scanorama_feature, + scvi, + no_integration_batch, + random_embed_cell, + random_embed_cell_jitter, + random_integration +] + +// collect metric list +metrics = [ + asw_batch, + asw_label, + cell_cycle_conservation, + clustering_overlap, + pcr +] -// construct a map of methods (id -> method_module) -methods = [ bbknn, combat, scanorama_embed, scanorama_feature, scvi] - .collectEntries{method -> - [method.config.functionality.name, method] - } workflow { helpMessage(config) - viashChannel(params, config) + channelFromParams(params, config) | run_wf } -/******************************************************* -* Main workflow * -*******************************************************/ - workflow run_wf { take: input_ch main: - output_ch = input_ch + // process input parameter channel + dataset_ch = input_ch + | preprocessInputs(config: config) - // split params for downstream components - | setWorkflowArguments( - preprocess: ["normalization_id", "dataset_id"], - method: ["input"], - output: ["output"] + // extract the dataset metadata + | run_components( + components: check_dataset_schema, + from_state: ["input"], + to_state: { id, output, config -> + new org.yaml.snakeyaml.Yaml().load(output.meta) + } ) - // multiply events by the number of method - | getWorkflowArguments(key: "preprocess") - | add_methods - - // filter the normalization methods that a method actually prefers - | check_filtered_normalization_id - - // run methods - | getWorkflowArguments(key: "method") - | run_methods - // run feature methods - meth_feature = input_ch - | (combat & scanorama_feature) - | mix - // run embed methods - meth_embed = input_ch - | (scanorama_embed & scvi) - | mix - // run graph methods - meth_graph = input_ch - | (bbknn) - - // apply feature metrics on feature outputs - // metr_feat = meth_feature - // | (asw_batch & asw_label & cell_cycle_conservation & pcr) - - // convert feature outputs to embedding outputs - meth_feat_to_embed = meth_feature - | feature_to_embed - - // apply embedding metrics to embedding outputs - metr_embed = meth_embed - | mix(meth_feat_to_embed) - | (asw_batch & asw_label & cell_cycle_conservation & pcr) - | mix - - // convert embedding outputs to graph outputs - meth_embed_to_graph = meth_embed - | mix(meth_feat_to_embed) - | embed_to_graph - - // apply graph metrics to graph outputs - metr_graph = meth_graph - | mix(meth_embed_to_graph) - | (clustering_overlap) - + method_out_ch1 = dataset_ch + | run_components( + components: methods, + + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, config -> + def norm = state.normalization_id + def pref = config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cpm" && pref == "counts") || norm == pref + }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: ["input"], + + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + method_id: config.functionality.name, + method_output: output.output, + method_subtype: config.functionality.info.subtype + ] + } + ) - output_ch = metr_embed.mix(metr_graph) - - // convert to tsv - | aggregate_results - - emit: - output_ch -/* - | (bbknn & combat & scvi & scanorama_embed & scanorama_feature) - | mix - | toSortedList - | view { "toSortedList $it" } -/* - | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - | (ari & nmi) - | extract_scores.run( - auto: [ publish: true ] - ) -*/ -} - -/******************************************************* -* Sub workflows * -*******************************************************/ - - - -workflow add_methods { - take: input_ch - main: - output_ch = Channel.fromList(methods.keySet()) - | combine(input_ch) - - // generate combined id for method_id and dataset_id - | pmap{method_id, dataset_id, data -> - def new_id = dataset_id + "." + method_id - def new_data = data.clone() + [method_id: method_id] - new_data.remove("id") - [new_id, new_data] - } - emit: output_ch -} - -workflow check_filtered_normalization_id { - take: input_ch - main: - output_ch = input_ch - | pfilter{id, data -> - data = data.clone() - def method = methods[data.method_id] - def preferred = method.config.functionality.info.preferred_normalization - // if a method is just using the counts, we can use any normalization method - if (preferred == "counts") { - preferred = "log_cpm" + // append feature->embed transformations + method_out_ch2 = method_out_ch1 + | run_components( + components: feature_to_embed, + filter: { id, state, config -> state.method_subtype == "feature"}, + from_state: [ input: "method_output" ], + to_state: { id, output, config -> + [ + method_output: output.output, + method_subtype: config.functionality.info.subtype + ] } - data.normalization_id == preferred - } - emit: output_ch -} - -workflow run_methods { - take: input_ch - main: - // generate one channel per method - method_chs = methods.collect { method_id, method_module -> - input_ch - | filter{it[1].method_id == method_id} - | method_module + ) + | mix(method_out_ch1) + + // append embed->graph transformations + method_out_ch3 = method_out_ch2 + | run_components( + components: embed_to_graph, + filter: { id, state, config -> state.method_subtype == "embedding"}, + from_state: [ input: "method_output" ], + to_state: { id, output, config -> + [ + method_output: output.output, + method_subtype: config.functionality.info.subtype + ] } - // mix all results - output_ch = method_chs[0].mix(*method_chs.drop(1)) - - emit: output_ch -} + ) + | mix(method_out_ch2) + + // run metrics + output_ch = method_out_ch3 + | run_components( + components: metrics, + filter: { id, state, config -> + state.method_subtype == config.functionality.info.subtype + }, + from_state: [input_integrated: "method_output"], + to_state: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] + } + ) -workflow run_metrics { - take: input_ch - main: + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] + } - output_ch = input_ch - | (ari & nmi) - | mix + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) - emit: output_ch + emit: + output_ch } -workflow aggregate_results { - take: input_ch - main: +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ it -> - [ "combined", it.collect{ it[1] } ] + it[0].drop(2) - } - | getWorkflowArguments(key: "output") - | extract_scores.run( - auto: [ publish: true ] - ) - - emit: output_ch -} + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) +} \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run/run_nextflow.sh index 1b5a3ad108..09ceb8c11d 100755 --- a/src/tasks/batch_integration/workflows/run/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run/run_nextflow.sh @@ -25,6 +25,6 @@ nextflow run . \ --id pancreas \ --dataset_id pancreas \ --normalization_id log_cpm \ - --input $DATASET_DIR/processed.h5ad \ + --input $DATASET_DIR/unintegrated.h5ad \ --output scores.tsv \ - --publish_dir $DATASET_DIR/ + --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run/config.vsh.yaml index e093719368..05ce8f8889 100644 --- a/src/tasks/denoising/workflows/run/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run/config.vsh.yaml @@ -8,6 +8,14 @@ functionality: type: "string" description: "The ID of the dataset" required: true + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--normalization_id" + type: "string" + description: "The ID of the normalization used" + required: true - name: "--input_train" type: "file" # todo: replace with includes - name: "--input_test" diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf index e596a2e707..4b98ec7698 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run/main.nf @@ -21,21 +21,36 @@ include { poisson } from "$targetDir/denoising/metrics/poisson/main.nf" include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap } from sourceDir + "/wf_utils/DataflowHelper.nf" +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + // construct a map of methods (id -> method_module) -methods = [ no_denoising, perfect_denoising, alra, dca, knn_smoothing, magic] - .collectEntries{method -> - [method.config.functionality.name, method] - } +methods = [ + no_denoising, + perfect_denoising, + alra, + dca, + knn_smoothing, + magic +] + +metrics = [ + mse, + poisson +] + workflow { helpMessage(config) - viashChannel(params, config) + // create channel from input parameters with + // arguments as defined in the config + channelFromParams(params, config) | run_wf } @@ -45,133 +60,89 @@ workflow run_wf { main: output_ch = input_ch - - // split params for downstream components - | setWorkflowArguments( - method: ["input_train"], - metric: ["input_test"], - output: ["output"] + | preprocessInputs(config: config) + + /// run all methods + | run_components( + components: methods, + + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, config -> + def norm = state.normalization_id + def pref = config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cpm" && pref == "counts") || norm == pref + }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: { id, state, config -> + def new_args = [ + input_train: state.input_train, + input_test: state.input_test + ] + new_args + }, + + + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + method_id: config.functionality.name, + method_output: output.output + ] + } ) - // multiply events by the number of method - | add_methods - - // add input_solution to data for the positive controls - | controls_can_cheat - - // run methods - | getWorkflowArguments(key: "method") - | run_methods + // run all metrics + | run_components( + components: metrics, + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: [ + input_test: "input_test", + input_denoised: "method_output" + ], + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] + } + ) - // construct tuples for metrics - | pmap{ id, file, passthrough -> - // derive unique ids from output filenames - def newId = file.getName().replaceAll(".output.*", "") - // combine prediction with solution - def newData = [ input_denoised: file, input_test: passthrough.metric.input_test ] - [ newId, newData, passthrough ] + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] } - // run metrics - | getWorkflowArguments(key: "metric") - | run_metrics - - // convert to tsv - | aggregate_results + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) emit: output_ch } -workflow add_methods { - take: input_ch - main: - output_ch = Channel.fromList(methods.keySet()) - | combine(input_ch) - - // generate combined id for method_id and dataset_id - | pmap{method_id, dataset_id, data -> - def new_id = dataset_id + "." + method_id - def new_data = data.clone() + [method_id: method_id] - new_data.remove("id") - [new_id, new_data] - } - emit: output_ch -} - -// workflow check_filtered_normalization_id { -// take: input_ch -// main: -// output_ch = input_ch -// | pfilter{id, data -> -// data = data.clone() -// def method = methods[data.method_id] -// def preferred = method.config.functionality.info.preferred_normalization -// // if a method is just using the counts, we can use any normalization method -// if (preferred == "counts") { -// preferred = "log_cpm" -// } -// data.normalization_id == preferred -// } -// emit: output_ch -// } - -workflow controls_can_cheat { - take: input_ch - main: - output_ch = input_ch - | pmap{id, data, passthrough -> - def method = methods[data.method_id] - def method_type = method.config.functionality.info.method_type - def new_data = data.clone() - if (method_type != "method") { - new_data = new_data + [input_test: passthrough.metric.input_test] - } - [id, new_data, passthrough] - } - emit: output_ch -} - -workflow run_methods { - take: input_ch - main: - // generate one channel per method - method_chs = methods.collect { method_id, method_module -> - input_ch - | filter{it[1].method_id == method_id} - | method_module - } - // mix all results - output_ch = method_chs[0].mix(*method_chs.drop(1)) - - emit: output_ch -} - -workflow run_metrics { - take: input_ch - main: - - output_ch = input_ch - | (mse & poisson) - | mix - - emit: output_ch -} - -workflow aggregate_results { - take: input_ch - main: - - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ it -> - [ "combined", it.collect{ it[1] } ] + it[0].drop(2) - } - | getWorkflowArguments(key: "output") - | extract_scores.run( - auto: [ publish: true ] - ) +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() - emit: output_ch + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/run_test.sh b/src/tasks/denoising/workflows/run/run_test.sh new file mode 100755 index 0000000000..bdfc09dd19 --- /dev/null +++ b/src/tasks/denoising/workflows/run/run_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash ns build -q 'denoising|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/denoising/pancreas + +# run benchmark +export NXF_VER=23.04.2 + +nextflow \ + run . \ + -main-script src/tasks/denoising/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ + --input_train $DATASET_DIR/train.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output scores.tsv \ + --publish_dir output/denoising/ \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index 8d2351e71e..c50efda401 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -1,46 +1,61 @@ -nextflow.enable.dsl=2 - sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" // import control methods -include { true_features } from "$targetDir/dimensionality_reduction/control_methods/true_features/main.nf" include { random_features } from "$targetDir/dimensionality_reduction/control_methods/random_features/main.nf" +include { true_features } from "$targetDir/dimensionality_reduction/control_methods/true_features/main.nf" // import methods -include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" include { densmap } from "$targetDir/dimensionality_reduction/methods/densmap/main.nf" +// include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" +include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" +include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" -include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" -include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" -// include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" +include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" // import metrics -include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" include { coranking } from "$targetDir/dimensionality_reduction/metrics/coranking/main.nf" +include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" -// tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/wf_utils/DataflowHelper.nf" +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +// read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") -// construct a map of methods (id -> method_module) -methods = [ random_features, true_features, umap, densmap, phate, tsne, pca, neuralee ] - .collectEntries{method -> - [method.config.functionality.name, method] - } +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// collect method list +methods = [ + random_features, + true_features, + densmap, + neuralee, + pca, + phate, + tsne, + umap +] + +// collect metric list +metrics = [ + coranking, + density_preservation, + rmse, + trustworthiness +] workflow { helpMessage(config) - viashChannel(params, config) + // create channel from input parameters with + // arguments as defined in the config + channelFromParams(params, config) | run_wf } @@ -50,128 +65,92 @@ workflow run_wf { main: output_ch = input_ch - - // split params for downstream components - | view{"step 0: $it"} - | setWorkflowArguments( - preprocess: ["dataset_id", "normalization_id"], - method: ["input"], - metric: ["input_solution"], - output: ["output"] + | preprocessInputs(config: config) + + // run all methods + | run_components( + components: methods, + + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, config -> + def norm = state.normalization_id + def pref = config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cpm" && pref == "counts") || norm == pref + }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: { id, state, config -> + def new_args = [ + input: state.input + ] + if (config.functionality.info.type == "control_method") { + new_args.input_solution = state.input_solution + } + new_args + }, + + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + method_id: config.functionality.name, + method_output: output.output + ] + } ) - // multiply events by the number of method - | getWorkflowArguments(key: "preprocess") - | add_methods - - // filter the normalization methods that a method actually prefers - | check_filtered_normalization_id - // add input_solution to data for the positive controls - | controls_can_cheat - - // run methods - | getWorkflowArguments(key: "method") - | run_methods - - // run metrics - | getWorkflowArguments(key: "metric", inputKey: "input_embedding") - | run_metrics - - // convert to tsv - | aggregate_results - - emit: - output_ch -} - -workflow add_methods { - take: input_ch - main: - output_ch = Channel.fromList(methods.keySet()) - | combine(input_ch) - - // generate combined id for method_id and dataset_id - | pmap{method_id, dataset_id, data -> - def new_id = dataset_id + "." + method_id - def new_data = data.clone() + [method_id: method_id] - new_data.remove("id") - [new_id, new_data] - } - emit: output_ch -} -workflow check_filtered_normalization_id { - take: input_ch - main: - output_ch = input_ch - | pfilter{id, data -> - data = data.clone() - def method = methods[data.method_id] - def preferred = method.config.functionality.info.preferred_normalization - // if a method is just using the counts, we can use any normalization method - if (preferred == "counts") { - preferred = "log_cpm" + // run all metrics + | run_components( + components: metrics, + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: { id, state, config -> + [ + input_solution: state.input_solution, + input_embedding: state.method_output + ] + }, + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] } - data.normalization_id == preferred - } - emit: output_ch -} - -workflow controls_can_cheat { - take: input_ch - main: - output_ch = input_ch - | pmap{id, data, passthrough -> - def method = methods[data.method_id] - def method_type = method.config.functionality.info.method_type - def new_data = data.clone() - // if (method_type != "method") { - // new_data = new_data + [input_solution: passthrough.metric.input_solution] - // } - [id, new_data, passthrough] - } - emit: output_ch -} + ) -workflow run_methods { - take: input_ch - main: - // generate one channel per method - method_chs = methods.collect { method_id, method_module -> - input_ch - | filter{it[1].method_id == method_id} - | method_module + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states( + apply: { ids, states -> + ["output", [ + input: states.collect{it.metric_output}, + output: states[0].output + ]] } - // mix all results - output_ch = method_chs[0].mix(*method_chs.drop(1)) - - emit: output_ch -} - -workflow run_metrics { - take: input_ch - main: + ) - output_ch = input_ch - | (density_preservation & coranking & rmse & trustworthiness) - | mix + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) - emit: output_ch + emit: + output_ch } -workflow aggregate_results { - take: input_ch - main: - - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ it -> - [ "combined", it.collect{ it[1] } ] + it[0].drop(2) - } - | getWorkflowArguments(key: "output") - | extract_scores.run( - auto: [ publish: true ] - ) +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() - emit: output_ch + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run/run_test.sh new file mode 100755 index 0000000000..3aeeb58baa --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/run/run_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/dimensionality_reduction/pancreas + +# run benchmark +export NXF_VER=23.04.2 + +nextflow \ + run . \ + -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --dataset_id pancreas \ + --normalization_id log_cpm \ + --input $DATASET_DIR/dataset.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output scores.tsv \ + --publish_dir output/dimensionality_reduction/ \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/config.vsh.yaml b/src/tasks/label_projection/workflows/run/config.vsh.yaml index 395a3333ba..5ac96b82f2 100644 --- a/src/tasks/label_projection/workflows/run/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run/config.vsh.yaml @@ -17,11 +17,20 @@ functionality: description: "The ID of the normalization used" required: true - name: "--input_train" - type: "file" # todo: replace with includes + # __merge__: ../../api/file_train.yaml + type: file + direction: input + required: true - name: "--input_test" - type: "file" # todo: replace with includes + # __merge__: ../../api/file_test.yaml + type: file + direction: input + required: true - name: "--input_solution" - type: "file" # todo: replace with includes + # __merge__: ../../api/file_solution.yaml + type: file + direction: input + required: true - name: Outputs arguments: - name: "--output" diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index ec9089d88b..fda1c42e33 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -1,5 +1,3 @@ -nextflow.enable.dsl=2 - sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" @@ -10,9 +8,10 @@ include { random_labels } from "$targetDir/label_projection/control_methods/rand // import methods include { knn } from "$targetDir/label_projection/methods/knn/main.nf" -include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" +include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" +include { scanvi_scarches } from "$targetDir/label_projection/methods/scanvi_scarches/main.nf" include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" include { xgboost } from "$targetDir/label_projection/methods/xgboost/main.nf" @@ -20,25 +19,45 @@ include { xgboost } from "$targetDir/label_projection/methods/xgboost/main.nf" include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" -// tsv generation component +// convert scores to tsv include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions -include { readConfig; viashChannel; helpMessage } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { setWorkflowArguments; getWorkflowArguments; passthroughMap as pmap; passthroughFilter as pfilter } from sourceDir + "/wf_utils/DataflowHelper.nf" +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +// read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") -// construct a map of methods (id -> method_module) -methods = [ true_labels, majority_vote, random_labels, knn, mlp, logistic_regression, scanvi, seurat_transferdata, xgboost ] - .collectEntries{method -> - [method.config.functionality.name, method] - } +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// collect method list +methods = [ + true_labels, + majority_vote, + random_labels, + knn, + logistic_regression, + mlp, + scanvi, + scanvi_scarches, + seurat_transferdata, + xgboost +] + +// collect metric list +metrics = [ + accuracy, + f1 +] workflow { helpMessage(config) - viashChannel(params, config) + // create channel from input parameters with + // arguments as defined in the config + channelFromParams(params, config) | run_wf } @@ -48,129 +67,105 @@ workflow run_wf { main: output_ch = input_ch - - // split params for downstream components - | setWorkflowArguments( - preprocess: ["normalization_id", "dataset_id"], - method: ["input_train", "input_test"], - metric: ["input_solution"], - output: ["output"] - ) - - // multiply events by the number of method - | getWorkflowArguments(key: "preprocess") - | add_methods - - // filter the normalization methods that a method actually prefers - | check_filtered_normalization_id - - // add input_solution to data for the positive controls - | controls_can_cheat + // based on the config file (config.vsh.yaml), run assertions on parameter sets + // and fill in default values + | preprocessInputs(config: config) - // run methods - | getWorkflowArguments(key: "method") - | run_methods - - // run metrics - | getWorkflowArguments(key: "metric", inputKey: "input_prediction") - | run_metrics - - // convert to tsv - | aggregate_results - - emit: - output_ch -} - -workflow add_methods { - take: input_ch - main: - output_ch = Channel.fromList(methods.keySet()) - | combine(input_ch) - - // generate combined id for method_id and dataset_id - | pmap{method_id, dataset_id, data -> - def new_id = dataset_id + "." + method_id - def new_data = data.clone() + [method_id: method_id] - new_data.remove("id") - [new_id, new_data] + | view{ id, state -> + "input event: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, ...]" } - emit: output_ch -} -workflow check_filtered_normalization_id { - take: input_ch - main: - output_ch = input_ch - | pfilter{id, data -> - data = data.clone() - def method = methods[data.method_id] - def preferred = method.config.functionality.info.preferred_normalization - // if a method is just using the counts, we can use any normalization method - if (preferred == "counts") { - preferred = "log_cpm" + // run all methods + | run_components( + components: methods, + + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, config -> + def norm = state.normalization_id + def pref = config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cpm" && pref == "counts") || norm == pref + }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: { id, state, config -> + def new_args = [ + input_train: state.input_train, + input_test: state.input_test + ] + if (config.functionality.info.type == "control_method") { + new_args.input_solution = state.input_solution + } + new_args + }, + + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + method_id: config.functionality.name, + method_output: output.output + ] } - data.normalization_id == preferred - } - emit: output_ch -} + ) -workflow controls_can_cheat { - take: input_ch - main: - output_ch = input_ch - | pmap{id, data, passthrough -> - def method = methods[data.method_id] - def method_type = method.config.functionality.info.method_type - def new_data = data.clone() - if (method_type != "method") { - new_data = new_data + [input_solution: passthrough.metric.input_solution] - } - [id, new_data, passthrough] + | view{ id, state -> + "after method: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, method_id: $state.method_id, ...]" } - emit: output_ch -} -workflow run_methods { - take: input_ch - main: - // generate one channel per method - method_chs = methods.collect { method_id, method_module -> - input_ch - | filter{it[1].method_id == method_id} - | method_module + // run all metrics + | run_components( + components: metrics, + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: [ + input_solution: "input_solution", + input_prediction: "method_output" + ], + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] } - // mix all results - output_ch = method_chs[0].mix(*method_chs.drop(1)) + ) - emit: output_ch -} + | view{ id, state -> + "after metric: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, method_id: $state.method_id, metric_id: $state.metric_id, ...]" + } -workflow run_metrics { - take: input_ch - main: + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] + } - output_ch = input_ch - | (accuracy & f1) - | mix + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) - emit: output_ch + emit: + output_ch } -workflow aggregate_results { - take: input_ch - main: - - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ it -> - [ "combined", it.collect{ it[1] } ] + it[0].drop(2) - } - | getWorkflowArguments(key: "output") - | extract_scores.run( - auto: [ publish: true ] - ) +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() - emit: output_ch + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/run_test.sh b/src/tasks/label_projection/workflows/run/run_test.sh index 90e4a498b2..b31c9ae4ac 100755 --- a/src/tasks/label_projection/workflows/run/run_test.sh +++ b/src/tasks/label_projection/workflows/run/run_test.sh @@ -9,16 +9,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/label_projection/pancreas -if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 -fi - # run benchmark -export NXF_VER=22.04.5 +export NXF_VER=23.04.2 nextflow \ run . \ @@ -32,4 +26,4 @@ nextflow \ --input_test $DATASET_DIR/test.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ - --publish_dir output/ \ No newline at end of file + --publish_dir output/label_projection/ \ No newline at end of file diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf new file mode 100644 index 0000000000..42b1da4e61 --- /dev/null +++ b/src/wf_utils/BenchmarkHelper.nf @@ -0,0 +1,152 @@ +def run_components(Map args) { + assert args.components: "run_components should be passed a list of components to run" + + def components_ = args.components + if (components_ !instanceof List) { + components_ = [ components_ ] + } + assert components_.size() > 0: "pass at least one component to run_components" + + def from_state_ = args.from_state + def to_state_ = args.to_state + def filter_ = args.filter + def id_ = args.id + + workflow run_components_wf { + take: input_ch + main: + + // generate one channel per method + out_chs = components_.collect{ comp_ -> + def comp_config = comp_.config + + filter_ch = filter_ + ? input_ch | filter{tup -> + filter_(tup[0], tup[1], comp_config) + } + : input_ch + id_ch = id_ + ? filter_ch | map{tup -> + // def new_id = id_(tup[0], tup[1], comp_config) + def new_id = tup[0] + if (id_ instanceof String) { + new_id = id_ + } else if (id_ instanceof Closure) { + new_id = id_(new_id, tup[1], comp_config) + } + [new_id] + tup.drop(1) + } + : filter_ch + data_ch = id_ch | map{tup -> + def new_data = tup[1] + if (from_state_ instanceof Map) { + new_data = from_state_.collectEntries{ key0, key1 -> + [key0, new_data[key1]] + } + } else if (from_state_ instanceof List) { + new_data = from_state_.collectEntries{ key -> + [key, new_data[key]] + } + } else if (from_state_ instanceof Closure) { + new_data = from_state_(tup[0], new_data, comp_config) + } + tup.take(1) + [new_data] + tup.drop(1) + } + out_ch = data_ch + | comp_.run( + auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] + ) + post_ch = to_state_ + ? out_ch | map{tup -> + def new_outputs = tup[1] + if (to_state_ instanceof Map) { + new_outputs = to_state_.collectEntries{ key0, key1 -> + [key0, new_outputs[key1]] + } + } else if (to_state_ instanceof List) { + new_outputs = to_state_.collectEntries{ key -> + [key, new_outputs[key]] + } + } else if (to_state_ instanceof Closure) { + new_outputs = to_state_(tup[0], new_outputs, comp_config) + } + [tup[0], tup[2] + new_outputs] + tup.drop(3) + } + : out_ch + + post_ch + } + + // mix all results + output_ch = + (out_chs.size == 1) + ? out_chs[0] + : out_chs[0].mix(*out_chs.drop(1)) + + emit: output_ch + } + + return run_components_wf +} + +def join_states(Closure apply_) { + workflow join_states_wf { + take: input_ch + main: + output_ch = input_ch + | toSortedList + | filter{ it.size() > 0 } + | map{ tups -> + def ids = tups.collect{it[0]} + def states = tups.collect{it[1]} + apply_(ids, states) + } + + emit: output_ch + } + return join_states_wf +} + + +class CustomTraceObserver implements nextflow.trace.TraceObserver { + List traces + + CustomTraceObserver(List traces) { + this.traces = traces + } + + @Override + void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } + + @Override + void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } +} + +def initialize_tracer() { + def traces = Collections.synchronizedList([]) + + // add custom trace observer which stores traces in the traces object + session.observers.add(new CustomTraceObserver(traces)) + + traces +} + +def write_json(data, file) { + assert data: "write_json: data should not be null" + assert file: "write_json: file should not be null" + file.write(groovy.json.JsonOutput.toJson(data)) +} + +def get_publish_dir() { + return params.containsKey("publish_dir") ? params.publish_dir : + params.containsKey("publishDir") ? params.publishDir : + null +} \ No newline at end of file From cb9837bf75f9609eace1c9ab23c668e77d93e79b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Jul 2023 04:27:55 +0200 Subject: [PATCH 0937/1233] clean up Former-commit-id: dc35c4350a6982d381df05af0aa64a1588b5c07c --- main.nf | 2 -- nextflow.config | 29 ------------------- .../workflows/run/run_nextflow.sh | 2 -- 3 files changed, 33 deletions(-) diff --git a/main.nf b/main.nf index 28839dad42..fd40518830 100644 --- a/main.nf +++ b/main.nf @@ -1,5 +1,3 @@ -nextflow.enable.dsl=2 - workflow { print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.") } diff --git a/nextflow.config b/nextflow.config index ab0869fbae..ac14c601b7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,32 +1,3 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } - -// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT -rootDir = "$projectDir" -targetDir = "$rootDir/target/nextflow" - -// INSERT CUSTOM IMPORTS HERE - -// END INSERT - -docker { - runOptions = "-v $rootDir:$rootDir" -} - -process { - maxForks = 30 - cpus = 2 - errorStrategy='ignore' - container = 'nextflow/bash:latest' - - pod = [ [ nodeSelector: 'worker-group = m5s' ] ] - - withLabel: highmem { memory = 50.Gb } - withLabel: highcpu { cpus = 20 } - withLabel: highmem_highcpu { - cpus = 20 - memory = 128.Gb - } -} - diff --git a/src/tasks/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run/run_nextflow.sh index 09ceb8c11d..2d5a9a1688 100755 --- a/src/tasks/batch_integration/workflows/run/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run/run_nextflow.sh @@ -23,8 +23,6 @@ nextflow run . \ -c src/wf_utils/labels_ci.config \ -resume \ --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cpm \ --input $DATASET_DIR/unintegrated.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ \ No newline at end of file From b8ccfc3575bb1e5061c30e45839854bb36b86cc5 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 13 Jul 2023 07:40:29 +0200 Subject: [PATCH 0938/1233] Update/add multimodal test resources (#200) * create multimodal test_resource script * update subsample config * update subsample script * add norm, pca and knn to test script * update comment test resources * update changelog * update subsample mod2 check * add svd processor * replace pca to svd in test_resources script * update svd processor * refactor subsample * update subsample config * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 863c0082f730e18fb85afd77e0293c0e99fb8aae --- CHANGELOG.md | 2 + src/datasets/api/comp_processor_subset.yaml | 8 ++ src/datasets/api/comp_processor_svd.yaml | 45 +++++++++ src/datasets/api/file_svd.yaml | 12 +++ src/datasets/processors/hvg/script.py | 2 +- src/datasets/processors/subsample/script.py | 99 +++++++++++++++---- src/datasets/processors/svd/config.vsh.yaml | 14 +++ src/datasets/processors/svd/script.py | 45 +++++++++ .../resource_test_scripts/multimodal.sh | 71 +++++++++++++ 9 files changed, 277 insertions(+), 21 deletions(-) create mode 100644 src/datasets/api/comp_processor_svd.yaml create mode 100644 src/datasets/api/file_svd.yaml create mode 100644 src/datasets/processors/svd/config.vsh.yaml create mode 100644 src/datasets/processors/svd/script.py create mode 100644 src/datasets/resource_test_scripts/multimodal.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 16ec26f108..44625dad77 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,6 +75,8 @@ * `subsample`: Subsample an h5ad file. Allows keeping observations from specific batches and celltypes, also allows keeping certain features. +* `resources_test_scripts`: Scripts to create test_resources for local development with "pancreas", "pancreas_tasks" and "multimodal". + ### V1 MIGRATION * `loaders/openproblems_v1`: Fetch a dataset from OpenProblems v1, whilst adding extra information to the `.uns`. diff --git a/src/datasets/api/comp_processor_subset.yaml b/src/datasets/api/comp_processor_subset.yaml index cf50c2a940..bad64a6762 100644 --- a/src/datasets/api/comp_processor_subset.yaml +++ b/src/datasets/api/comp_processor_subset.yaml @@ -11,10 +11,18 @@ functionality: __merge__: file_common_dataset.yaml required: true direction: input + - name: "--input_mod2" + __merge__: file_common_dataset.yaml + direction: input + required: false - name: "--output" __merge__: file_common_dataset.yaml direction: output required: true + - name: "--output_mod2" + __merge__: file_common_dataset.yaml + direction: output + required: false test_resources: - path: /resources_test/common/pancreas dest: resources_test/common/pancreas diff --git a/src/datasets/api/comp_processor_svd.yaml b/src/datasets/api/comp_processor_svd.yaml new file mode 100644 index 0000000000..3f92376f8a --- /dev/null +++ b/src/datasets/api/comp_processor_svd.yaml @@ -0,0 +1,45 @@ +functionality: + namespace: "datasets/processors" + info: + type: dataset_processor + type_info: + label: SVD + summary: | + Computes a SVD PCA embedding of the normalized data. + description: + The resulting AnnData will contain an embedding in obsm. + arguments: + - name: "--input" + __merge__: file_normalized.yaml + required: true + direction: input + - name: "--input_mod2" + __merge__: file_normalized.yaml + required: false + direction: input + - name: "--layer_input" + type: string + default: "normalized" + description: Which layer to use as input. + - name: "--output" + direction: output + __merge__: file_svd.yaml + required: true + - name: "--output_mod2" + direction: output + __merge__: file_svd.yaml + required: false + - name: "--obsm_embedding" + type: string + default: "X_svd" + description: "In which .obsm slot to store the resulting embedding." + - name: "--num_components" + type: integer + default: 100 + description: Number of principal components to compute. Defaults to 100, or 1 - minimum dimension size of selected representation. + test_resources: + - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + diff --git a/src/datasets/api/file_svd.yaml b/src/datasets/api/file_svd.yaml new file mode 100644 index 0000000000..2a727369e3 --- /dev/null +++ b/src/datasets/api/file_svd.yaml @@ -0,0 +1,12 @@ +__merge__: file_normalized.yaml +type: file +example: "resources_test/common/pancreas/svd.h5ad" +info: + label: "Dataset+SVD" + summary: "A normalised dataset with a SVD embedding" + slots: + obsm: + - type: double + name: X_svd + description: The resulting SVD embedding. + required: true \ No newline at end of file diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index 1163a158db..23632da9fc 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -18,7 +18,7 @@ print(">> Look for layer") layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] -print(">> Run PCA") +print(">> Run HVG") out = sc.pp.highly_variable_genes( adata, layer=par["layer_input"], diff --git a/src/datasets/processors/subsample/script.py b/src/datasets/processors/subsample/script.py index fd73d54b4d..a5b3102c5b 100644 --- a/src/datasets/processors/subsample/script.py +++ b/src/datasets/processors/subsample/script.py @@ -4,16 +4,18 @@ ### VIASH START par = { - "input": "resources_test/common/pancreas/dataset.h5ad", - "n_obs": 500, - "n_vars": 500, + "input": "resources_test/common/multimodal/temp_mod1_full.h5ad", + "input_mod2": "resources_test/common/multimodal/temp_mod2_full.h5ad", + "n_obs": 600, + "n_vars": 1500, "keep_celltype_categories": None, "keep_batch_categories": None, - "keep_features": ["HMGB2", "CDK1", "NUSAP1", "UBE2C"], - "keep_celltype_categories": ["acinar", "beta"], - "keep_batch_categories": ["celseq", "inDrop4", "smarter"], - "even": True, - "output": "toy_data.h5ad", + "keep_features": None, + "keep_celltype_categories": None, + "keep_batch_categories": None, + "even": False, + "output": "subsample_mod1.h5ad", + "output_mod2": "subsample_mod2.h5ad", "seed": 123 } ### VIASH END @@ -25,12 +27,24 @@ print(">> Load data", flush=True) adata_input = sc.read_h5ad(par["input"]) +if par["input_mod2"] is not None: + adata_mod2 = sc.read_h5ad(par["input_mod2"]) + # copy counts to .X because otherwise filter_genes and filter_cells won't work adata_input.X = adata_input.layers["counts"] +if par["input_mod2"] is not None: + adata_mod2.X = adata_mod2.layers["counts"] print(">> Determining output shape", flush=True) -n_obs = min(par["n_obs"], adata_input.shape[0]) -n_vars = min(par["n_vars"], adata_input.shape[1]) +min_obs_list = [par["n_obs"], adata_input.shape[0]] +if par["input_mod2"] is not None: + min_obs_list.append(adata_mod2.shape[0]) +n_obs = min(min_obs_list) + +min_vars_list = [par["n_vars"], adata_input.shape[1]] +if par["input_mod2"] is not None: + min_vars_list.append(adata_mod2.shape[1]) +n_vars = min(min_vars_list) print(">> Subsampling the observations", flush=True) obs_filt = np.ones(dtype=np.bool_, shape=adata_input.n_obs) @@ -56,31 +70,76 @@ choice_probs = [ probs[batch] for batch in choice_batch ] obs_index = np.random.choice(choice_ix, size=n_obs, replace=False, p=choice_probs) else: - obs_index = np.random.choice(np.where(obs_filt)[0], n_vars, replace=False) + obs_index = np.random.choice(np.where(obs_filt)[0], n_obs, replace=False) + +# subsample obs +adata_output = adata_input[obs_index].copy() +if par["input_mod2"] is not None: + adata_output_mod2 = adata_mod2[obs_index].copy() + +# filter cells and genes +if par["input_mod2"] is not None: + n_cells = adata_output.X.sum(axis=1).A.flatten() + n_cells_mod2 = adata_output_mod2.X.sum(axis=1).A.flatten() + keep_cells = np.minimum(n_cells, n_cells_mod2) > 1 + adata_output = adata_output[keep_cells, :].copy() + adata_output_mod2 = adata_output_mod2[keep_cells, :].copy() + + sc.pp.filter_genes(adata_output, min_cells=1) + sc.pp.filter_genes(adata_output_mod2, min_cells=1) + +else: + # todo: this should not remove features in keep_features! + print(">> Remove empty observations and features", flush=True) + sc.pp.filter_genes(adata_output, min_cells=1) + sc.pp.filter_cells(adata_output, min_counts=2) print(">> Subsampling the features", flush=True) if par.get("keep_features"): - initial_filt = adata_input.var_names.isin(par["keep_features"]) + initial_filt = adata_output.var_names.isin(par["keep_features"]) initial_idx, *_ = initial_filt.nonzero() remaining_idx, *_ = (~initial_filt).nonzero() rest_idx = remaining_idx[np.random.choice(len(remaining_idx), n_vars - len(initial_idx), replace=False)] var_ix = np.concatenate([initial_idx, rest_idx]) else: - var_ix = np.random.choice(adata_input.shape[1], n_vars, replace=False) - - -adata_output = adata_input[obs_index, var_ix].copy() + var_ix = np.random.choice(adata_output.shape[1], n_vars, replace=False) + if par["input_mod2"] is not None: + var_ix_mod2 = np.random.choice(adata_output_mod2.shape[1], n_vars, replace=False) + +# subsample vars +adata_output = adata_output[:, var_ix].copy() +if par["input_mod2"] is not None: + adata_output_mod2 = adata_output_mod2[:, var_ix_mod2].copy() + +# filter cells and genes +if par["input_mod2"] is not None: + n_cells = adata_output.X.sum(axis=1).A.flatten() + n_cells_mod2 = adata_output_mod2.X.sum(axis=1).A.flatten() + keep_cells = np.minimum(n_cells, n_cells_mod2) > 1 + adata_output = adata_output[keep_cells, :].copy() + adata_output_mod2 = adata_output_mod2[keep_cells, :].copy() + + sc.pp.filter_genes(adata_output, min_cells=1) + sc.pp.filter_genes(adata_output_mod2, min_cells=1) + -# todo: this should not remove features in keep_features! -print(">> Remove empty observations and features", flush=True) -sc.pp.filter_genes(adata_output, min_cells=1) -sc.pp.filter_cells(adata_output, min_counts=2) +else: + # todo: this should not remove features in keep_features! + print(">> Remove empty observations and features", flush=True) + sc.pp.filter_genes(adata_output, min_cells=1) + sc.pp.filter_cells(adata_output, min_counts=2) print(">> Update dataset_id", flush=True) adata_output.uns["dataset_id"] = adata_output.uns["dataset_id"] + "_subsample" +if par["input_mod2"] is not None: + adata_output_mod2.uns["dataset_id"] = adata_output_mod2.uns["dataset_id"] + "_subsample" # remove previously copied .X del adata_output.X +if par["input_mod2"] is not None: + del adata_output_mod2.X print(">> Writing data") adata_output.write_h5ad(par["output"]) +if par["output_mod2"] is not None: + adata_output_mod2.write_h5ad(par["output_mod2"]) diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml new file mode 100644 index 0000000000..550d540e1d --- /dev/null +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -0,0 +1,14 @@ +__merge__: ../../api/comp_processor_svd.yaml +functionality: + name: "svd" + description: "Compute SVD pca reduction" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: [scikit-learn] + - type: nextflow diff --git a/src/datasets/processors/svd/script.py b/src/datasets/processors/svd/script.py new file mode 100644 index 0000000000..c359615c60 --- /dev/null +++ b/src/datasets/processors/svd/script.py @@ -0,0 +1,45 @@ +import anndata as ad +import sklearn.decomposition + + +## VIASH START +par = { + "input": "resources_test/common/multimodal/normalized_mod1.h5ad", + "input_mod2": "resources_test/common/multimodal/normalized_mod2.h5ad", + "output": "output.h5ad", + "layer_input": "normalized", + "obsm_embedding": "X_svd", + "num_components": 100, +} +## VIASH END + +print(">> Load data", flush=True) +adata = ad.read(par["input"]) +if par["input_mod2"] is not None: + adata2 = ad.read(par["input_mod2"]) + +print(">> check parameters", flush=True) +min_list = [par["num_components"], min(adata.layers[par["layer_input"]].shape) - 1] + +if par["input_mod2"] is not None: + min_list.append(min(adata2.layers[par["layer_input"]].shape) - 1) + +n_svd = min(min_list) + + +print(">> Run SVD", flush=True) +svd1 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.layers[par["layer_input"]]) +if par["input_mod2"] is not None: + svd2 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata2.layers[par["layer_input"]]) + +print(">> Storing output", flush=True) +adata.obsm[par["obsm_embedding"]] = svd1 +if par["input_mod2"] is not None: + adata2.obsm[par["obsm_embedding"]] = svd2 + + +print(">> Writing data", flush=True) +adata.write_h5ad(par["output"]) +if par["input_mod2"] is not None: + adata2.write_h5ad(par["output_mod2"]) + diff --git a/src/datasets/resource_test_scripts/multimodal.sh b/src/datasets/resource_test_scripts/multimodal.sh new file mode 100644 index 0000000000..fe0e9c472b --- /dev/null +++ b/src/datasets/resource_test_scripts/multimodal.sh @@ -0,0 +1,71 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash ns build -q 'datasets|common' --parallel --setup cb + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/common/multimodal + +set -e + +mkdir -p $DATASET_DIR + +# download dataset +viash run src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml -- \ + --obs_tissue "source" \ + --layer_counts "counts" \ + --obs_celltype "cell_name" \ + --dataset_id scicar_cell_lines \ + --dataset_name "sci-CAR cell lines" \ + --data_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ + --data_reference "cao2018joint" \ + --dataset_summary "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells" \ + --dataset_description "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells. Here, we use two sciCAR datasets that were obtained from the same study. The first dataset contains 4,825 cells from three cell lines (HEK293T cells, NIH/3T3 cells, and A549 cells) at multiple timepoints (0, 1 hour, 3 hours) after dexamethasone treatment. The second dataset contains 11,233 cells from wild-type adult mouse kidney." \ + --dataset_organism "[homo_sapiens, mus_musculus]" \ + --output_mod1 $DATASET_DIR/temp_mod1_full.h5ad \ + --output_mod2 $DATASET_DIR/temp_mod2_full.h5ad + + +# subsample +viash run src/datasets/processors/subsample/config.vsh.yaml -- \ + --input $DATASET_DIR/temp_mod1_full.h5ad \ + --input_mod2 $DATASET_DIR/temp_mod2_full.h5ad \ + --n_obs 600 \ + --n_vars 1500 \ + --output $DATASET_DIR/raw_mod1.h5ad \ + --output_mod2 $DATASET_DIR/raw_mod2.h5ad \ + --seed 123 + + +# run sqrt cpm normalisation on mod 1 file +viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/raw_mod1.h5ad \ + --output $DATASET_DIR/normalized_mod1.h5ad + +# run log cpm normalisation on mod 2 file +viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ + --input $DATASET_DIR/raw_mod2.h5ad \ + --output $DATASET_DIR/normalized_mod2.h5ad + +# run svd +viash run src/datasets/processors/svd/config.vsh.yaml -- \ + --input $DATASET_DIR/normalized_mod1.h5ad \ + --input_mod2 $DATASET_DIR/normalized_mod2.h5ad \ + --output $DATASET_DIR/svd_mod1.h5ad \ + --output_mod2 $DATASET_DIR/svd_mod2.h5ad + +# run hvg +viash run src/datasets/processors/hvg/config.vsh.yaml -- \ + --input $DATASET_DIR/svd_mod1.h5ad \ + --output $DATASET_DIR/dataset_mod1.h5ad + +viash run src/datasets/processors/hvg/config.vsh.yaml -- \ + --input $DATASET_DIR/svd_mod2.h5ad \ + --output $DATASET_DIR/dataset_mod2.h5ad + +rm -r $DATASET_DIR/temp_* \ No newline at end of file From c1a401bd821fb8c1dad853b6478a27c1affcfe81 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 07:02:17 +0200 Subject: [PATCH 0939/1233] Migrate the Neurips 2021 predict modality task (#70) This PR migrates the NeurIPS 2021 task from https://github.com/openproblems-bio/neurips2021_multimodal_viash/tree/main/src/predict_modality to this repo. Note that this task still needs to be extended with the competitions top methods in https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods. Commits: * add mask_dataset component * add meanpergene control method * add random control_method * add solution control_method * add zeros control_method * add correct solution file * add knnr_py method * add knnr_r method * add lm method * add newwave_knnr method * add random_forest method * add correlation metrics * add mse metric * add mse script * update resurces test script * update authors * add babel method (not working) * update random control_method config * add NF workflow * rename random control to random_predict * fix NF workflow errors * add task info * add readme * use +inf instead of 9999 in metric * move task * safeguard info field * remove redundant space * update api * update process dataset * remove babel * fix method scripts * fix control method scripts * fix metrics code * add references * fix random forest * add metadata * fix api files * fix more api files * update readme * add doi * update files * more test resources --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: afb06fe00dd38c5ddefc760447a7312eb8d1e7e8 --- src/common/comp_tests/run_and_check_adata.py | 18 +- src/common/helper_functions/read_api_files.R | 6 +- src/common/library.bib | 97 ++++ .../process_openproblems_v1/nextflow.config | 2 + .../api/file_unintegrated.yaml | 10 +- .../workflows/run/nextflow.config | 2 + .../denoising/workflows/run/nextflow.config | 4 +- .../workflows/run/nextflow.config | 2 + .../workflows/run/nextflow.config | 2 + src/tasks/predict_modality/README.md | 481 ++++++++++++++++++ .../api/comp_control_method.yaml | 42 ++ .../predict_modality/api/comp_method.yaml | 36 ++ .../predict_modality/api/comp_metric.yaml | 30 ++ .../api/comp_process_dataset.yaml | 43 ++ .../api/file_dataset_other_mod.yaml | 43 ++ .../api/file_dataset_rna.yaml | 43 ++ .../predict_modality/api/file_prediction.yaml | 20 + .../predict_modality/api/file_score.yaml | 25 + .../predict_modality/api/file_test_mod1.yaml | 47 ++ .../predict_modality/api/file_test_mod2.yaml | 47 ++ .../predict_modality/api/file_train_mod1.yaml | 47 ++ .../predict_modality/api/file_train_mod2.yaml | 47 ++ src/tasks/predict_modality/api/task_info.yaml | 49 ++ .../meanpergene/config.vsh.yaml | 17 + .../control_methods/meanpergene/script.py | 37 ++ .../random_predict/config.vsh.yaml | 19 + .../control_methods/random_predict/script.R | 34 ++ .../control_methods/solution/config.vsh.yaml | 19 + .../control_methods/solution/script.R | 20 + .../control_methods/zeros/config.vsh.yaml | 16 + .../control_methods/zeros/script.py | 37 ++ .../methods/knnr_py/config.vsh.yaml | 32 ++ .../methods/knnr_py/script.py | 67 +++ .../methods/knnr_r/config.vsh.yaml | 35 ++ .../predict_modality/methods/knnr_r/script.R | 81 +++ .../methods/lm/config.vsh.yaml | 31 ++ .../predict_modality/methods/lm/script.R | 74 +++ .../methods/newwave_knnr/config.vsh.yaml | 42 ++ .../methods/newwave_knnr/script.R | 100 ++++ .../methods/random_forest/config.vsh.yaml | 35 ++ .../methods/random_forest/script.R | 83 +++ .../metrics/correlation/config.vsh.yaml | 66 +++ .../metrics/correlation/script.R | 85 ++++ .../metrics/mse/config.vsh.yaml | 30 ++ .../predict_modality/metrics/mse/script.py | 43 ++ .../process_dataset/config.vsh.yaml | 20 + .../predict_modality/process_dataset/script.R | 138 +++++ .../resources_test_scripts/bmmc_x_starter.sh | 95 ++++ .../workflows/run/config.vsh.yaml | 28 + .../predict_modality/workflows/run/main.nf | 159 ++++++ .../workflows/run/nextflow.config | 16 + .../workflows/run/run_test.sh | 37 ++ 52 files changed, 2624 insertions(+), 15 deletions(-) create mode 100644 src/tasks/predict_modality/README.md create mode 100644 src/tasks/predict_modality/api/comp_control_method.yaml create mode 100644 src/tasks/predict_modality/api/comp_method.yaml create mode 100644 src/tasks/predict_modality/api/comp_metric.yaml create mode 100644 src/tasks/predict_modality/api/comp_process_dataset.yaml create mode 100644 src/tasks/predict_modality/api/file_dataset_other_mod.yaml create mode 100644 src/tasks/predict_modality/api/file_dataset_rna.yaml create mode 100644 src/tasks/predict_modality/api/file_prediction.yaml create mode 100644 src/tasks/predict_modality/api/file_score.yaml create mode 100644 src/tasks/predict_modality/api/file_test_mod1.yaml create mode 100644 src/tasks/predict_modality/api/file_test_mod2.yaml create mode 100644 src/tasks/predict_modality/api/file_train_mod1.yaml create mode 100644 src/tasks/predict_modality/api/file_train_mod2.yaml create mode 100644 src/tasks/predict_modality/api/task_info.yaml create mode 100644 src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml create mode 100644 src/tasks/predict_modality/control_methods/meanpergene/script.py create mode 100644 src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml create mode 100644 src/tasks/predict_modality/control_methods/random_predict/script.R create mode 100644 src/tasks/predict_modality/control_methods/solution/config.vsh.yaml create mode 100644 src/tasks/predict_modality/control_methods/solution/script.R create mode 100644 src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml create mode 100644 src/tasks/predict_modality/control_methods/zeros/script.py create mode 100644 src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/knnr_py/script.py create mode 100644 src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/knnr_r/script.R create mode 100644 src/tasks/predict_modality/methods/lm/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/lm/script.R create mode 100644 src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/newwave_knnr/script.R create mode 100644 src/tasks/predict_modality/methods/random_forest/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/random_forest/script.R create mode 100644 src/tasks/predict_modality/metrics/correlation/config.vsh.yaml create mode 100644 src/tasks/predict_modality/metrics/correlation/script.R create mode 100644 src/tasks/predict_modality/metrics/mse/config.vsh.yaml create mode 100644 src/tasks/predict_modality/metrics/mse/script.py create mode 100644 src/tasks/predict_modality/process_dataset/config.vsh.yaml create mode 100644 src/tasks/predict_modality/process_dataset/script.R create mode 100755 src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh create mode 100644 src/tasks/predict_modality/workflows/run/config.vsh.yaml create mode 100644 src/tasks/predict_modality/workflows/run/main.nf create mode 100644 src/tasks/predict_modality/workflows/run/nextflow.config create mode 100755 src/tasks/predict_modality/workflows/run/run_test.sh diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py index 39e8db0726..224c767694 100644 --- a/src/common/comp_tests/run_and_check_adata.py +++ b/src/common/comp_tests/run_and_check_adata.py @@ -18,12 +18,18 @@ def check_slots(adata, slot_metadata): slots in the corresponding .info.slots field. """ for struc_name, slot_items in slot_metadata.items(): - struc_dict = getattr(adata, struc_name) + struc_x = getattr(adata, struc_name) - for slot_item in slot_items: - if slot_item.get("required", True): - assert slot_item["name"] in struc_dict,\ - f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']" + if struc_name == "X": + if slot_items.get("required", True): + assert struc_x is not None,\ + f"File '{arg['value']}' is missing slot .{struc_name}" + + else: + for slot_item in slot_items: + if slot_item.get("required", True): + assert slot_item["name"] in struc_x,\ + f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']" # read viash config @@ -83,7 +89,7 @@ def check_slots(adata, slot_metadata): if arg["type"] == "file": print(f"Reading and checking {arg['clean_name']}", flush=True) adata = ad.read_h5ad(arg["value"]) - slots = arg["info"]["slots"] + slots = arg["info"].get("slots") or {} print(f" {adata}") diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index 54f93792e2..67f5a1c550 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -320,12 +320,12 @@ create_task_graph <- function(file_info, comp_info, comp_args) { .task_graph_get_root <- function(task_api) { root <- names(which(igraph::degree(task_api$task_graph, mode = "in") == 0)) if (length(root) > 1) { - stop( - "There should only be one node with in-degree equal to 0.\n", + warning( + "There should probably only be one node with in-degree equal to 0.\n", " Nodes with in-degree == 0: ", paste(root, collapse = ", ") ) } - root + root[[1]] } render_task_graph <- function(task_api, root = .task_graph_get_root(task_api)) { diff --git a/src/common/library.bib b/src/common/library.bib index 97b995cf1c..abfcd7164c 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -14,6 +14,22 @@ @misc{10x2019pbmc } +@article{agostinis2022newwave, + doi = {10.1093/bioinformatics/btac149}, + url = {https://doi.org/10.1093/bioinformatics/btac149}, + year = {2022}, + month = {Mar.}, + publisher = {Oxford University Press ({OUP})}, + volume = {38}, + number = {9}, + pages = {2648--2650}, + author = {Federico Agostinis and Chiara Romualdi and Gabriele Sales and Davide Risso}, + editor = {Yann Ponty}, + title = {NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell {RNA}-seq data}, + journal = {Bioinformatics} +} + + @article{agrawal2021mde, title = {Minimum-Distortion Embedding}, author = {Akshay Agrawal and Alnur Ali and Stephen Boyd}, @@ -118,6 +134,19 @@ @article{bland2000odds } +@article{breiman2001random, + doi = {10.1023/a:1010933404324}, + url = {https://doi.org/10.1023/a:1010933404324}, + year = {2001}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {45}, + number = {1}, + pages = {5--32}, + author = {Leo Breiman}, + journal = {Machine Learning} +} + + @article{bttner2018test, title = {A test metric for assessing single-cell {RNA}-seq batch correction}, author = {Maren B\"{u}ttner and Zhichao Miao and F. Alexander Wolf and Sarah A. Teichmann and Fabian J. Theis}, @@ -204,6 +233,17 @@ @article{cao2020human } +@article{chai2014root, + doi = {10.5194/gmdd-7-1525-2014}, + url = {https://doi.org/10.5194/gmdd-7-1525-2014}, + year = {2014}, + month = {Feb.}, + publisher = {Copernicus {GmbH}}, + author = {T. Chai and R. R. Draxler}, + title = {Root mean square error ({RMSE}) or mean absolute error ({MAE})?} +} + + @article{chazarragil2021flexible, doi = {10.1093/nar/gkab004}, url = {https://doi.org/10.1093/nar/gkab004}, @@ -365,6 +405,21 @@ @article{eraslan2019single @string{feb = {Feb.}} +@article{fix1989discriminatory, + doi = {10.2307/1403797}, + url = {https://doi.org/10.2307/1403797}, + year = {1989}, + month = {Dec.}, + publisher = {{JSTOR}}, + volume = {57}, + number = {3}, + pages = {238}, + author = {Evelyn Fix and J. L. Hodges}, + title = {Discriminatory Analysis. Nonparametric Discrimination: Consistency Properties}, + journal = {International Statistical Review / Revue Internationale de Statistique} +} + + @article{gower1975generalized, title = {Generalized procrustes analysis}, author = {J. C. Gower}, @@ -590,6 +645,21 @@ @string{jul @string{jun = {Jun.}} +@article{kendall1938new, + doi = {10.1093/biomet/30.1-2.81}, + url = {https://doi.org/10.1093/biomet/30.1-2.81}, + year = {1938}, + month = {Jun.}, + publisher = {Oxford University Press ({OUP})}, + volume = {30}, + number = {1-2}, + pages = {81--93}, + author = {M. G. KENDALL}, + title = {A new measure of rank correlation}, + journal = {Biometrika} +} + + @article{kiselev2019challenges, title = {Challenges in unsupervised clustering of single-cell {RNA}-seq data}, author = {Vladimir Yu Kiselev and Tallulah S. Andrews and Martin Hemberg}, @@ -912,6 +982,19 @@ @misc{openproblems } +@article{pearson1895regression, + doi = {10.1098/rspl.1895.0041}, + title = {VII. Note on regression and inheritance in the case of two parents}, + author = {Pearson, Karl}, + journal = {proceedings of the royal society of London}, + volume = {58}, + number = {347-352}, + pages = {240--242}, + year = {1895}, + publisher = {The Royal Society London} +} + + @article{pearson1901pca, title = {On lines and planes of closest fit to systems of points in space}, author = {Karl Pearson}, @@ -1268,6 +1351,20 @@ @article{welch2019single } +@article{wilkinson1973symbolic, + doi = {10.2307/2346786}, + url = {https://doi.org/10.2307/2346786}, + year = {1973}, + publisher = {{JSTOR}}, + volume = {22}, + number = {3}, + pages = {392}, + author = {G. N. Wilkinson and C. E. Rogers}, + title = {Symbolic Description of Factorial Models for Analysis of Variance}, + journal = {Applied Statistics} +} + + @article{wu2021single, title = {A single-cell and spatially resolved atlas of human breast cancers}, author = {Sunny Z. Wu and Ghamdan Al-Eryani and Daniel Lee Roden and Simon Junankar and Kate Harvey and Alma Andersson and Aatish Thennavan and Chenfei Wang and James R. Torpy and Nenad Bartonicek and Taopeng Wang and Ludvig Larsson and Dominik Kaczorowski and Neil I. Weisenfeld and Cedric R. Uytingco and Jennifer G. Chew and Zachary W. Bent and Chia-Ling Chan and Vikkitharan Gnanasambandapillai and Charles-Antoine Dutertre and Laurence Gluch and Mun N. Hui and Jane Beith and Andrew Parker and Elizabeth Robbins and Davendra Segara and Caroline Cooper and Cindy Mak and Belinda Chan and Sanjay Warrier and Florent Ginhoux and Ewan Millar and Joseph E. Powell and Stephen R. Williams and X. Shirley Liu and Sandra O'Toole and Elgene Lim and Joakim Lundeberg and Charles M. Perou and Alexander Swarbrick}, diff --git a/src/datasets/workflows/process_openproblems_v1/nextflow.config b/src/datasets/workflows/process_openproblems_v1/nextflow.config index 3527df50c8..7b8ddab87d 100644 --- a/src/datasets/workflows/process_openproblems_v1/nextflow.config +++ b/src/datasets/workflows/process_openproblems_v1/nextflow.config @@ -12,3 +12,5 @@ params { // include common settings includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/batch_integration/api/file_unintegrated.yaml b/src/tasks/batch_integration/api/file_unintegrated.yaml index 0b3ea56305..1ef3c09007 100644 --- a/src/tasks/batch_integration/api/file_unintegrated.yaml +++ b/src/tasks/batch_integration/api/file_unintegrated.yaml @@ -4,7 +4,7 @@ info: label: "Unintegrated" summary: Unintegrated AnnData HDF5 file. slots: - layers: + layers: - type: integer name: counts description: Raw counts @@ -50,10 +50,10 @@ info: name: normalization_id description: "Which normalization was used" required: true - - type: string - name: dataset_organism - description: "Which normalization was used" - required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: object name: knn description: Supplementary K nearest neighbors data. diff --git a/src/tasks/batch_integration/workflows/run/nextflow.config b/src/tasks/batch_integration/workflows/run/nextflow.config index 4fae132704..150119dfa2 100644 --- a/src/tasks/batch_integration/workflows/run/nextflow.config +++ b/src/tasks/batch_integration/workflows/run/nextflow.config @@ -12,3 +12,5 @@ params { // include common settings includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/denoising/workflows/run/nextflow.config b/src/tasks/denoising/workflows/run/nextflow.config index 0182e7b872..2e537df35c 100644 --- a/src/tasks/denoising/workflows/run/nextflow.config +++ b/src/tasks/denoising/workflows/run/nextflow.config @@ -11,4 +11,6 @@ params { // include common settings includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") \ No newline at end of file +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/nextflow.config b/src/tasks/dimensionality_reduction/workflows/run/nextflow.config index 026fe3a76a..eadd1bd660 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/nextflow.config +++ b/src/tasks/dimensionality_reduction/workflows/run/nextflow.config @@ -12,3 +12,5 @@ params { // include common settings includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/label_projection/workflows/run/nextflow.config b/src/tasks/label_projection/workflows/run/nextflow.config index 3739c38969..826337a8b1 100644 --- a/src/tasks/label_projection/workflows/run/nextflow.config +++ b/src/tasks/label_projection/workflows/run/nextflow.config @@ -12,3 +12,5 @@ params { // include common settings includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md new file mode 100644 index 0000000000..37da76b8ec --- /dev/null +++ b/src/tasks/predict_modality/README.md @@ -0,0 +1,481 @@ +# Predict Modality + +Predicting the profiles of one modality (e.g. protein abundance) from +another (e.g. mRNA expression). + +Path: +[`src/tasks/predict_modality`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/predict_modality) + +## Motivation + +Experimental techniques to measure multiple modalities within the same +single cell are increasingly becoming available. The demand for these +measurements is driven by the promise to provide a deeper insight into +the state of a cell. Yet, the modalities are also intrinsically linked. +We know that DNA must be accessible (ATAC data) to produce mRNA +(expression data), and mRNA in turn is used as a template to produce +protein (protein abundance). These processes are regulated often by the +same molecules that they produce: for example, a protein may bind DNA to +prevent the production of more mRNA. Understanding these regulatory +processes would be transformative for synthetic biology and drug target +discovery. Any method that can predict a modality from another must have +accounted for these regulatory processes, but the demand for multi-modal +data shows that this is not trivial. + +## Description + +In this task, the goal is to take one modality and predict the other +modality for all features in each cell. This task requires translating +information between multiple layers of gene regulation. In some ways, +this is similar to the task of machine translation. In machine +translation, the same sentiment is expressed in multiple languages and +the goal is to train a model to represent the same meaning in a +different language. In this context, the same cellular state is measured +in two different feature sets and the goal of this task is to translate +the information about cellular state from one modality to the other. + +## Authors & contributors + +| name | roles | +|:-------------------|:-------------------| +| Robrecht Cannoodt | author, maintainer | +| Kai Waldrant | contributor | +| Louise Deconinck | author | +| Alex Tong | author | +| Bastian Rieck | author | +| Daniel Burkhardt | author | +| Alejandro Granados | author | + +## API + +``` mermaid +flowchart LR + file_dataset_rna("Raw dataset RNA") + comp_process_dataset[/"Data processor"/] + file_train_mod1("Train mod1") + file_train_mod2("Train mod2") + file_test_mod1("Test mod1") + file_test_mod2("Test mod2") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + file_prediction("Prediction") + file_score("Score") + file_dataset_other_mod("Raw dataset mod2") + file_dataset_rna---comp_process_dataset + comp_process_dataset-->file_train_mod1 + comp_process_dataset-->file_train_mod2 + comp_process_dataset-->file_test_mod1 + comp_process_dataset-->file_test_mod2 + file_train_mod1---comp_control_method + file_train_mod1---comp_method + file_train_mod2---comp_control_method + file_train_mod2---comp_method + file_test_mod1---comp_control_method + file_test_mod1---comp_method + file_test_mod2---comp_control_method + file_test_mod2---comp_metric + comp_control_method-->file_prediction + comp_method-->file_prediction + comp_metric-->file_score + file_prediction---comp_metric + file_dataset_other_mod---comp_process_dataset +``` + +## File format: Raw dataset RNA + +The RNA modality of the raw dataset. + +Example file: +`resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts' + uns: 'dataset_id', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
+ +## Component type: Data processor + +Path: +[`src/predict_modality`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality) + +A predict modality dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:----------------------|:----------|:---------------------------------------------------------------------------| +| `--input_rna` | `file` | The RNA modality of the raw dataset. | +| `--input_other_mod` | `file` | The second modality of the raw dataset. Must be an ADT or an ATAC dataset. | +| `--output_train_mod1` | `file` | (*Output*) The mod1 expression values of the train cells. | +| `--output_train_mod2` | `file` | (*Output*) The mod2 expression values of the train cells. | +| `--output_test_mod1` | `file` | (*Output*) The mod1 expression values of the test cells. | +| `--output_test_mod2` | `file` | (*Output*) The mod2 expression values of the test cells. | +| `--seed` | `integer` | (*Optional*) The seed for determining the train/test split. Default: `1`. | + +
+ +## File format: Train mod1 + +The mod1 expression values of the train cells. + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
+ +## File format: Train mod2 + +The mod2 expression values of the train cells. + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
+ +## File format: Test mod1 + +The mod1 expression values of the test cells. + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
+ +## File format: Test mod2 + +The mod2 expression values of the test cells. + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
+ +## Component type: Control method + +Path: +[`src/predict_modality/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/control_methods) + +Quality control methods for verifying the pipeline. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:-------------------------------------------------------------------------| +| `--input_train_mod1` | `file` | The mod1 expression values of the train cells. | +| `--input_train_mod2` | `file` | The mod2 expression values of the train cells. | +| `--input_test_mod1` | `file` | The mod1 expression values of the test cells. | +| `--input_test_mod2` | `file` | The mod2 expression values of the test cells. | +| `--output` | `file` | (*Output*) A prediction of the mod2 expression values of the test cells. | + +
+ +## Component type: Method + +Path: +[`src/predict_modality/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/methods) + +A regression method. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:-------------------------------------------------------------------------| +| `--input_train_mod1` | `file` | The mod1 expression values of the train cells. | +| `--input_train_mod2` | `file` | The mod2 expression values of the train cells. | +| `--input_test_mod1` | `file` | The mod1 expression values of the test cells. | +| `--output` | `file` | (*Output*) A prediction of the mod2 expression values of the test cells. | + +
+ +## Component type: Metric + +Path: +[`src/predict_modality/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/predict_modality/metrics) + +A predict modality metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:--------------------------------------------------------------| +| `--input_prediction` | `file` | A prediction of the mod2 expression values of the test cells. | +| `--input_test_mod2` | `file` | The mod2 expression values of the test cells. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Prediction + +A prediction of the mod2 expression values of the test cells + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/prediction.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + layers: 'normalized' + uns: 'dataset_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------|:---------|:----------------------------------------| +| `layers["normalized"]` | `double` | Predicted normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | + +
+ +## File format: Score + +Metric score file + +Example file: +`resources_test/predict_modality/bmmc_cite_starter/score.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
+ +## File format: Raw dataset mod2 + +The second modality of the raw dataset. Must be an ADT or an ATAC +dataset + +Example file: +`resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'size_factors' + var: 'gene_ids' + obsm: 'gene_activity' + layers: 'counts' + uns: 'dataset_id', 'gene_activity_var_names' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | + +
diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml new file mode 100644 index 0000000000..1adf1c18b1 --- /dev/null +++ b/src/tasks/predict_modality/api/comp_control_method.yaml @@ -0,0 +1,42 @@ +functionality: + namespace: "predict_modality/control_methods" + info: + type: control_method + preferred_normalization: counts # there is currently only one type of normalization + type_info: + label: Control method + summary: Quality control methods for verifying the pipeline. + description: | + These components have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. + arguments: + - name: "--input_train_mod1" + __merge__: file_train_mod1.yaml + direction: input + required: true + - name: "--input_train_mod2" + __merge__: file_train_mod2.yaml + direction: input + required: true + - name: "--input_test_mod1" + __merge__: file_test_mod1.yaml + direction: input + required: true + - name: "--input_test_mod2" + __merge__: file_test_mod2.yaml + direction: input + required: true + - name: "--output" + __merge__: file_prediction.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/predict_modality/bmmc_cite_starter + dest: resources_test/predict_modality/bmmc_cite_starter \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml new file mode 100644 index 0000000000..59fe99ec28 --- /dev/null +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -0,0 +1,36 @@ +functionality: + namespace: "predict_modality/methods" + info: + type: method + preferred_normalization: counts # there is currently only one type of normalization + type_info: + label: Method + summary: A regression method. + description: | + A regression method to predict the expression of one modality from another. + arguments: + - name: "--input_train_mod1" + __merge__: file_train_mod1.yaml + direction: input + required: true + - name: "--input_train_mod2" + __merge__: file_train_mod2.yaml + direction: input + required: true + - name: "--input_test_mod1" + __merge__: file_test_mod1.yaml + direction: input + required: true + - name: "--output" + __merge__: file_prediction.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/predict_modality/bmmc_cite_starter + dest: resources_test/predict_modality/bmmc_cite_starter + - path: /src/common/library.bib + - path: /src/common/api \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml new file mode 100644 index 0000000000..d7abb273c5 --- /dev/null +++ b/src/tasks/predict_modality/api/comp_metric.yaml @@ -0,0 +1,30 @@ +functionality: + namespace: "predict_modality/metrics" + info: + type: metric + type_info: + label: Metric + summary: A predict modality metric. + description: | + A metric for evaluating predicted expression. + arguments: + - name: --input_prediction + __merge__: file_prediction.yaml + direction: input + required: true + - name: --input_test_mod2 + __merge__: file_test_mod2.yaml + direction: input + required: true + - name: --output + __merge__: file_score.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_metric_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/predict_modality/bmmc_cite_starter + dest: resources_test/predict_modality/bmmc_cite_starter + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_process_dataset.yaml b/src/tasks/predict_modality/api/comp_process_dataset.yaml new file mode 100644 index 0000000000..844cf61c9f --- /dev/null +++ b/src/tasks/predict_modality/api/comp_process_dataset.yaml @@ -0,0 +1,43 @@ +functionality: + namespace: "predict_modality" + info: + type: process_dataset + type_info: + label: Data processor + summary: A predict modality dataset processor. + description: | + A component for processing a Common Dataset into a task-specific dataset. + arguments: + - name: "--input_rna" + __merge__: file_dataset_rna.yaml + direction: input + required: true + - name: "--input_other_mod" + __merge__: file_dataset_other_mod.yaml + direction: input + required: true + - name: "--output_train_mod1" + __merge__: file_train_mod1.yaml + direction: output + required: true + - name: "--output_train_mod2" + __merge__: file_train_mod2.yaml + direction: output + required: true + - name: "--output_test_mod1" + __merge__: file_test_mod1.yaml + direction: "output" + required: true + - name: "--output_test_mod2" + __merge__: file_test_mod2.yaml + direction: output + required: true + - name: "--seed" + type: integer + default: 1 + description: "The seed for determining the train/test split." + test_resources: + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/common/bmmc_cite_starter + dest: resources_test/common/bmmc_cite_starter \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml new file mode 100644 index 0000000000..d1b2c8714b --- /dev/null +++ b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml @@ -0,0 +1,43 @@ +type: file +example: "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad" +info: + label: "Raw dataset mod2" + summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" + slots: + X: + type: double + description: Normalized expression values + required: true + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_dataset_rna.yaml b/src/tasks/predict_modality/api/file_dataset_rna.yaml new file mode 100644 index 0000000000..c8c68478fd --- /dev/null +++ b/src/tasks/predict_modality/api/file_dataset_rna.yaml @@ -0,0 +1,43 @@ +type: file +example: "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" +info: + label: "Raw dataset RNA" + summary: "The RNA modality of the raw dataset." + slots: + X: + type: double + description: Normalized expression values + required: true + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml new file mode 100644 index 0000000000..3e27bc5822 --- /dev/null +++ b/src/tasks/predict_modality/api/file_prediction.yaml @@ -0,0 +1,20 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/prediction.h5ad" +info: + label: "Prediction" + summary: "A prediction of the mod2 expression values of the test cells" + slots: + layers: + - type: double + name: normalized + description: Predicted normalized expression values + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml new file mode 100644 index 0000000000..e7ef707e58 --- /dev/null +++ b/src/tasks/predict_modality/api/file_score.yaml @@ -0,0 +1,25 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/score.h5ad" +info: + label: "Score" + summary: "Metric score file" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + required: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true + required: true diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml new file mode 100644 index 0000000000..f0be88a16f --- /dev/null +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -0,0 +1,47 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad" +info: + label: "Test mod1" + summary: "The mod1 expression values of the test cells." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml new file mode 100644 index 0000000000..217dfd8d61 --- /dev/null +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -0,0 +1,47 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad" +info: + label: "Test mod2" + summary: "The mod2 expression values of the test cells." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml new file mode 100644 index 0000000000..c71332ed3c --- /dev/null +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -0,0 +1,47 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad" +info: + label: "Train mod1" + summary: "The mod1 expression values of the train cells." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml new file mode 100644 index 0000000000..fa5c73c0aa --- /dev/null +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -0,0 +1,47 @@ +type: file +example: "resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad" +info: + label: "Train mod2" + summary: "The mod2 expression values of the train cells." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/task_info.yaml b/src/tasks/predict_modality/api/task_info.yaml new file mode 100644 index 0000000000..5ba57f5529 --- /dev/null +++ b/src/tasks/predict_modality/api/task_info.yaml @@ -0,0 +1,49 @@ +name: predict_modality +label: Predict Modality +summary: "Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression)." +motivation: | + Experimental techniques to measure multiple modalities within the same single cell are increasingly becoming available. + The demand for these measurements is driven by the promise to provide a deeper insight into the state of a cell. + Yet, the modalities are also intrinsically linked. We know that DNA must be accessible (ATAC data) to produce mRNA + (expression data), and mRNA in turn is used as a template to produce protein (protein abundance). These processes + are regulated often by the same molecules that they produce: for example, a protein may bind DNA to prevent the production + of more mRNA. Understanding these regulatory processes would be transformative for synthetic biology and drug target discovery. + Any method that can predict a modality from another must have accounted for these regulatory processes, but the demand for + multi-modal data shows that this is not trivial. +description: | + In this task, the goal is to take one modality and predict the other modality for all + features in each cell. This task requires translating information between multiple layers of + gene regulation. In some ways, this is similar to the task of machine translation. In machine translation, the same + sentiment is expressed in multiple languages and the goal is to train a model to represent the same meaning in a different + language. In this context, the same cellular state is measured in two different feature sets and the goal of this task + is to translate the information about cellular state from one modality to the other. +authors: + - name: Robrecht Cannoodt + roles: [ author, maintainer ] + info: + github: rcannood + orcid: "0000-0003-3641-729X" + - name: Kai Waldrant + roles: [ contributor ] + info: + github: KaiWaldrant + - name: Louise Deconinck + roles: [ author ] + info: + github: LouiseDck + - name: Alex Tong + roles: [ author ] + info: + github: atong01 + - name: Bastian Rieck + roles: [ author ] + info: + github: Pseudomanifold + - name: Daniel Burkhardt + roles: [ author ] + info: + github: dburkhardt + - name: Alejandro Granados + roles: [ author ] + info: + github: agranado diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml new file mode 100644 index 0000000000..74e11e78f4 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -0,0 +1,17 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: meanpergene + info: + label: Mean per gene + summary: Returns the mean expression value per gene. + description: Returns the mean expression value per gene. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] + \ No newline at end of file diff --git a/src/tasks/predict_modality/control_methods/meanpergene/script.py b/src/tasks/predict_modality/control_methods/meanpergene/script.py new file mode 100644 index 0000000000..038e6db9f6 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/meanpergene/script.py @@ -0,0 +1,37 @@ +import anndata as ad +from scipy.sparse import csc_matrix +import numpy as np + +# VIASH START +par = { + "input_train_mod1": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", + "input_test_mod1": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", + "input_train_mod2": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", + "output": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", +} + +meta = { + "functionality_name": "foo" +} +# VIASH END + +input_test_mod1 = ad.read_h5ad(par["input_test_mod1"]) +input_train_mod2 = ad.read_h5ad(par["input_train_mod2"]) + + +# Find the correct shape +mean = np.array(input_train_mod2.layers["normalized"].mean(axis=0)).flatten() +prediction = csc_matrix(np.tile(mean, (input_test_mod1.shape[0], 1))) + +# Write out prediction +out = ad.AnnData( + layers={"normalized": prediction}, + shape=prediction.shape, + obs=input_test_mod1.obs, + var=input_train_mod2.var, + uns={ + "dataset_id": input_test_mod1.uns["dataset_id"], + "method_id": meta["functionality_name"], + } +) +out.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml new file mode 100644 index 0000000000..973f13ec46 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -0,0 +1,19 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: random_predict + info: + label: Random predictions + summary: Returns random training profiles. + description: Returns random training profiles. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ bit64] + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/random_predict/script.R b/src/tasks/predict_modality/control_methods/random_predict/script.R new file mode 100644 index 0000000000..b044ea2f08 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/random_predict/script.R @@ -0,0 +1,34 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) + +## VIASH START +par <- list( + input_train_mod1 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", + input_test_mod1 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", + input_train_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", + output = "output.h5ad" +) +meta <- list(functionality_name = "foo") +## VIASH END + +cat("Reading h5ad files\n") +input_train_mod2 <- anndata::read_h5ad(par$input_train_mod2) +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) + +cat("Creating outputs object\n") +sample_ix <- sample.int(nrow(input_train_mod2), nrow(input_test_mod1), replace = TRUE) +prediction <- input_train_mod2$layers[["normalized"]][sample_ix, , drop = FALSE] +rownames(prediction) <- rownames(input_test_mod1) + +out <- anndata::AnnData( + layers = list(normalized = prediction), + shape = dim(prediction), + uns = list( + dataset_id = input_train_mod2$uns[["dataset_id"]], + method_id = meta[["functionality_name"]] + ) +) + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml new file mode 100644 index 0000000000..9e9419b385 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -0,0 +1,19 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: solution + info: + label: Solution + summary: Returns the ground-truth solution. + description: Returns the ground-truth solution. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ bit64] + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/solution/script.R b/src/tasks/predict_modality/control_methods/solution/script.R new file mode 100644 index 0000000000..fda1769695 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/solution/script.R @@ -0,0 +1,20 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) + +## VIASH START +par <- list( + input_test_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", + output = "output.h5ad" +) + +meta <- list( + functionality_name = "foo" +) +## VIASH END + +cat("Reading h5ad files\n") +ad2_test <- anndata::read_h5ad(par$input_test_mod2) +ad2_test$uns[["method_id"]] <- meta$functionality_name + +cat("Writing predictions to file\n") +zzz <- ad2_test$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml new file mode 100644 index 0000000000..9819b74835 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -0,0 +1,16 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: zeros + info: + label: Zeros + summary: Returns a prediction consisting of all zeros. + description: Returns a prediction consisting of all zeros. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/zeros/script.py b/src/tasks/predict_modality/control_methods/zeros/script.py new file mode 100644 index 0000000000..827a292b81 --- /dev/null +++ b/src/tasks/predict_modality/control_methods/zeros/script.py @@ -0,0 +1,37 @@ +import anndata +from scipy.sparse import csc_matrix +import numpy as np + +# VIASH START +par = { + "input_train_mod1": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", + "input_test_mod1": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", + "input_train_mod2": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", + "output": "output.h5ad", +} + +meta = { + "functionality_name": "foo" +} +# VIASH END + +print("Reading h5ad files", flush=True) +ad_mod1_test = anndata.read_h5ad(par["input_test_mod1"]) +ad_mod2 = anndata.read_h5ad(par["input_train_mod2"]) + +print("create output objects", flush=True) +prediction = csc_matrix((ad_mod1_test.n_obs, ad_mod2.n_vars), dtype = np.float32) + +out = anndata.AnnData( + layers={"normalized": prediction}, + shape=prediction.shape, + obs=ad_mod1_test.obs, + var=ad_mod2.var, + uns={ + "dataset_id": ad_mod2.uns["dataset_id"], + "method_id": meta["functionality_name"], + } +) + +print("write predictions to file", flush=True) +out.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml new file mode 100644 index 0000000000..1d188d18d2 --- /dev/null +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -0,0 +1,32 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: knnr_py + info: + label: KNNR (Py) + summary: K-nearest neighbor regression in Python. + description: K-nearest neighbor regression in Python. + reference: fix1989discriminatory + documentation_url: https://scikit-learn.org/stable/modules/neighbors.html + repository_url: https://github.com/scikit-learn/scikit-learn + arguments: + - name: "--distance_method" + type: "string" + default: "minkowski" + description: The distance metric to use. Possible values include `euclidean` and `minkowski`. + - name: "--n_pcs" + type: "integer" + default: 50 + description: Number of components to use for dimensionality reduction. + - name: "--n_neighbors" + type: "integer" + default: 100 + description: Number of neighbors to use. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_py/script.py b/src/tasks/predict_modality/methods/knnr_py/script.py new file mode 100644 index 0000000000..3ba132d1b9 --- /dev/null +++ b/src/tasks/predict_modality/methods/knnr_py/script.py @@ -0,0 +1,67 @@ +import anndata as ad +from scipy.sparse import csc_matrix +from sklearn.decomposition import TruncatedSVD +from sklearn.neighbors import KNeighborsRegressor + +## VIASH START +par = { + 'input_train_mod1': 'resources_test/predict_modality/bmmc_cite_starter/cite_train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/bmmc_cite_starter/cite_train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/bmmc_cite_starter/cite_test_mod1.h5ad', + 'distance_method': 'minkowski', + 'output': 'output.h5ad', + 'n_pcs': 4, + 'n_neighbors': 5, +} +meta = { 'functionality_name': 'foo' } +## VIASH END + +print('Reading `h5ad` files...', flush=True) +input_train_mod1 = ad.read_h5ad(par['input_train_mod1']) +input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) +input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) + +input_train = ad.concat( + {"train": input_train_mod1, "test": input_test_mod1}, + axis=0, + join="outer", + label="group", + fill_value=0, + index_unique="-" +) + +print('Performing dimensionality reduction on modality 1 values...', flush=True) +embedder = TruncatedSVD(n_components=par['n_pcs']) +X = embedder.fit_transform(input_train.layers["normalized"]) + +# split dimred back up +X_train = X[input_train.obs['group'] == 'train'] +X_test = X[input_train.obs['group'] == 'test'] +y_train = input_train_mod2.layers["normalized"].toarray() + +assert len(X_train) + len(X_test) == len(X) + +print('Running KNN regression...', flush=True) + +reg = KNeighborsRegressor( + n_neighbors=par['n_neighbors'], + metric=par['distance_method'] +) + +reg.fit(X_train, y_train) +y_pred = reg.predict(X_test) + +y_pred = csc_matrix(y_pred) + +adata = ad.AnnData( + layers={"normalized": y_pred}, + obs=input_test_mod1.obs, + var=input_train_mod2.var, + uns={ + 'dataset_id': input_train_mod1.uns['dataset_id'], + 'method_id': meta["functionality_name"], + }, +) + +print('Storing annotated data...', flush=True) +adata.write_h5ad(par['output'], compression = "gzip") diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml new file mode 100644 index 0000000000..cd70569e15 --- /dev/null +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -0,0 +1,35 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: knnr_r + info: + label: KNNR (R) + summary: K-nearest neighbor regression in R. + description: K-nearest neighbor regression in R. + reference: fix1989discriminatory + documentation_url: https://cran.r-project.org/package=FNN + repository_url: https://github.com/cran/FNN + arguments: + - name: "--distance_method" + type: "string" + default: "spearman" + description: The distance method to use. Possible values are euclidean, pearson, spearman and others. + - name: "--n_pcs" + type: "integer" + default: 50 + description: Number of principal components to use. + - name: "--n_neighbors" + type: "integer" + default: 20 + description: Number of neighbors to use in the knn regression. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ lmds, FNN, proxyC, bit64 ] + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_r/script.R b/src/tasks/predict_modality/methods/knnr_r/script.R new file mode 100644 index 0000000000..b7c20f6596 --- /dev/null +++ b/src/tasks/predict_modality/methods/knnr_r/script.R @@ -0,0 +1,81 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) + +## VIASH START +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +par <- list( + input_train_mod1 = paste0(path, "train_mod1.h5ad"), + input_test_mod1 = paste0(path, "test_mod1.h5ad"), + input_train_mod2 = paste0(path, "train_mod2.h5ad"), + output = "output.h5ad", + n_pcs = 4L, + n_neighbors = 3, + distance_method = "pearson" +) +## VIASH END + +cat("Reading mod1 h5ad files\n") +input_train_mod1 <- anndata::read_h5ad(par$input_train_mod1) +dataset_id <- input_train_mod1$uns[["dataset_id"]] + +# subset to HVG to reduce memory consumption +train_mod1_sd <- proxyC::colSds(input_train_mod1$layers[["normalized"]]) +ix <- order(train_mod1_sd, decreasing = TRUE)[seq_len(min(1000, length(train_mod1_sd)))] +input_train_mod1 <- input_train_mod1[,ix]$copy() +gc() + +# subset to HVG to reduce memory consumption +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) +input_test_mod1 <- input_test_mod1[,ix]$copy() +gc() + +cat("Performing DR on the mod1 values\n") +# LMDS is more efficient than regular MDS because +# it does not compure a square distance matrix. +dr_mod1 <- lmds::lmds( + rbind(input_train_mod1$layers[["normalized"]], input_test_mod1$layers[["normalized"]]), + ndim = par$n_pcs, + distance_method = par$distance_method +) + +ix <- seq_len(nrow(input_train_mod1)) +dr_mod1_train <- dr_mod1[ix, , drop = FALSE] +dr_mod1_test <- dr_mod1[-ix, , drop = FALSE] + +# remove previous objects to save memory +rm(input_train_mod1, input_test_mod1) +gc() + +cat("Reading mod2 h5ad files\n") +input_train_mod2 <- anndata::read_h5ad(par$input_train_mod2) + +cat("Predicting for each column in modality 2\n") +# precompute knn indices +knn_ix <- FNN::get.knnx( + dr_mod1_train, + dr_mod1_test, + k = par$n_neighbors +)$nn.index + +# perform knn regression. +pred <- input_train_mod2$layers[["normalized"]][knn_ix[, 1], , drop = FALSE] +if (par$n_neighbors > 1) { + for (k in seq(2, par$n_neighbors)) { + pred <- pred + input_train_mod2$layers[["normalized"]][knn_ix[, k], , drop = FALSE] + } +} +pred <- pred / par$n_neighbors +rownames(pred) <- rownames(dr_mod1_test) + +out <- anndata::AnnData( + layers = list(normalized = pred), + shape = dim(pred), + uns = list( + dataset_id = dataset_id, + method_id = meta$functionality_name + ) +) + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml new file mode 100644 index 0000000000..f244e8f806 --- /dev/null +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -0,0 +1,31 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: lm + info: + label: Linear Model + summary: Linear model regression. + description: A linear model regression method. + reference: wilkinson1973symbolic + repository_url: https://github.com/RcppCore/RcppArmadillo + documentation_url: https://cran.r-project.org/package=RcppArmadillo + arguments: + - name: "--distance_method" + type: "string" + default: "spearman" + description: The distance method to use. Possible values are euclidean, pearson, spearman and others. + - name: "--n_pcs" + type: "integer" + default: 50 + description: Number of principal components to use. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ lmds, RcppArmadillo, pbapply, bit64] + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/lm/script.R b/src/tasks/predict_modality/methods/lm/script.R new file mode 100644 index 0000000000..410b47f803 --- /dev/null +++ b/src/tasks/predict_modality/methods/lm/script.R @@ -0,0 +1,74 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +requireNamespace("pbapply", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) + +## VIASH START +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +par <- list( + input_train_mod1 = paste0(path, "train_mod1.h5ad"), + input_test_mod1 = paste0(path, "test_mod1.h5ad"), + input_train_mod2 = paste0(path, "train_mod2.h5ad"), + output = "output.h5ad", + n_pcs = 4L +) +meta <- list(functionality_name = "foo") +## VIASH END + +n_cores <- parallel::detectCores(all.tests = FALSE, logical = TRUE) + +cat("Reading mod1 files\n") +input_train_mod1 <- anndata::read_h5ad(par$input_train_mod1) +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) + + +cat("Performing DR on the mod1 values\n") +dr <- lmds::lmds( + rbind(input_train_mod1$layers[["normalized"]], input_test_mod1$layers[["normalized"]]), + ndim = par$n_pcs, + distance_method = par$distance_method +) + +ix <- seq_len(nrow(input_train_mod1)) +dr_train <- dr[ix, , drop = FALSE] +dr_test <- dr[-ix, , drop = FALSE] + +rm(input_test_mod1) +gc() + + +cat("Reading mod2 files\n") +X_mod2 <- anndata::read_h5ad(par$input_train_mod2)$layers[["normalized"]] + +cat("Predicting for each column in modality 2\n") +preds <- pbapply::pblapply( + seq_len(ncol(X_mod2)), + function(i) { + y <- X_mod2[, i] + uy <- unique(y) + if (length(uy) > 1) { + fit <- RcppArmadillo::fastLm(dr_train, y) + # fit <- lm(y ~ ., dr_train) + stats::predict(fit, dr_test) + } else { + rep(uy, nrow(dr_test)) + } + } +) + +cat("Creating outputs object\n") +prediction <- Matrix::Matrix(do.call(cbind, preds), sparse = TRUE) +rownames(prediction) <- rownames(dr_test) +colnames(prediction) <- colnames(X_mod2) + +out <- anndata::AnnData( + layers = list(normalized = prediction), + shape = dim(prediction), + uns = list( + dataset_id = input_train_mod1$uns[["dataset_id"]], + method_id = meta$functionality_name + ) +) + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml new file mode 100644 index 0000000000..e3ba765967 --- /dev/null +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -0,0 +1,42 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: newwave_knnr + info: + label: NewWave+KNNR + summary: Perform DR with NewWave, predict modality with KNN regression. + description: Perform DR with NewWave, predict modality with KNN regression. + reference: agostinis2022newwave + repository_url: https://github.com/fedeago/NewWave + documentation_url: https://bioconductor.org/packages/release/bioc/html/NewWave.html + arguments: + - name: "--newwave_maxiter" + type: "integer" + default: 40 + description: Maximum number of NewWave iterations. + - name: "--newwave_ngene" + type: "integer" + default: 200 + description: Setting of the n_gene_par NewWave parameter. + - name: "--newwave_ncell" + type: "integer" + default: 200 + description: Setting of the n_cell_par NewWave parameter. + - name: "--n_neighbors" + type: "integer" + default: 20 + description: Number of neighbors to use in the knn regression. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ lmds, FNN, proxy, proxyC, bit64 ] + bioc: [ SingleCellExperiment, NewWave ] + - type: r + github: [Jiefei-Wang/SharedObject, fedeago/NewWave] + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/script.R b/src/tasks/predict_modality/methods/newwave_knnr/script.R new file mode 100644 index 0000000000..2f1c7a36e0 --- /dev/null +++ b/src/tasks/predict_modality/methods/newwave_knnr/script.R @@ -0,0 +1,100 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) +requireNamespace("NewWave", quietly = TRUE) +requireNamespace("FNN", quietly = TRUE) +requireNamespace("SingleCellExperiment", quietly = TRUE) + +## VIASH START +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +path <- "resources_test/predict_modality/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter." +path <- "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter." +par <- list( + input_train_mod1 = paste0(path, "train_mod1.h5ad"), + input_test_mod1 = paste0(path, "test_mod1.h5ad"), + input_train_mod2 = paste0(path, "train_mod2.h5ad"), + output = "output.h5ad", + newwave_maxiter = 40L, + newwave_ngene = 200L, + newwave_ncell = 200L, + n_neighbors = 20L +) +meta <- list(functionality_name = "foo") +## VIASH END + +print(par) + +n_cores <- parallel::detectCores(all.tests = FALSE, logical = TRUE) + +method_id <- meta$functionality_name + +cat("Reading h5ad files\n") +input_train_mod1 <- anndata::read_h5ad(par$input_train_mod1) +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) + +# fetch batch labels +batch1 <- c(as.character(input_train_mod1$obs$batch), as.character(input_test_mod1$obs$batch)) +batch2 <- as.character(input_train_mod1$obs$batch) + +data1 <- SummarizedExperiment::SummarizedExperiment( + assays = list(counts = cbind(t(input_train_mod1$layers[["counts"]]), t(input_test_mod1$layers[["counts"]]))), + colData = data.frame(batch = factor(batch1)) +) +data1 <- data1[Matrix::rowSums(SummarizedExperiment::assay(data1)) > 0, ] +rm(input_train_mod1, input_test_mod1) +gc() + +cat("Running NewWave on mod1\n") +res1 <- NewWave::newWave( + data1, + X = "~batch", + verbose = TRUE, + K = 10, + maxiter_optimize = par$newwave_maxiter, + n_gene_par = min(par$newwave_ngene, nrow(data1)), + n_cell_par = min(par$newwave_ncell, ncol(data1)), + commondispersion = FALSE +) +dr_mod1 <- SingleCellExperiment::reducedDim(res1) +colnames(dr_mod1) <- paste0("comp_", seq_len(ncol(dr_mod1))) +rm(data1) +gc() + +# split DR matrices +train_ix <- seq_along(batch2) +dr_mod1_train <- dr_mod1[train_ix, , drop = FALSE] +dr_mod1_test <- dr_mod1[-train_ix, , drop = FALSE] + + +cat("Predicting for each column in modality 2\n") +input_train_mod2 <- anndata::read_h5ad(par$input_train_mod2) + +# precompute knn indices +knn_ix <- FNN::get.knnx( + dr_mod1_train, + dr_mod1_test, + k = min(nrow(dr_mod1_train), par$n_neighbors) +)$nn.index + +# perform knn regression. +pred <- input_train_mod2$layers[["normalized"]][knn_ix[, 1], , drop = FALSE] +if (par$n_neighbors > 1) { + for (k in seq(2, par$n_neighbors)) { + pred <- pred + input_train_mod2$layers[["normalized"]][knn_ix[, k], , drop = FALSE] + } +} +pred <- pred / par$n_neighbors +rownames(pred) <- rownames(dr_mod1_test) + +cat("Creating outputs object\n") +out <- anndata::AnnData( + layers = list(normalized = pred), + shape = dim(pred), + uns = list( + dataset_id = input_train_mod2$uns[["dataset_id"]], + method_id = meta$functionality_name + ) +) + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml new file mode 100644 index 0000000000..3862c13ba8 --- /dev/null +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -0,0 +1,35 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: random_forest + info: + label: Random Forests + summary: Random forest regression. + description: A random forest regression method. + reference: breiman2001random + documentation_url: https://www.stat.berkeley.edu/~breiman/RandomForests/reg_home.htm + repository_url: https://github.com/cran/randomForest + arguments: + - name: "--distance_method" + type: "string" + default: "pearson" + description: The distance method to use. Possible values are euclidean, pearson, spearman and others. + - name: "--n_pcs" + type: "integer" + default: 20 + description: Number of principal components to use. + - name: "--n_trees" + type: "integer" + default: 50 + description: Number of trees to use. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ lmds, ranger, pbapply, bit64 ] + - type: nextflow + directives: + label: [ highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/random_forest/script.R b/src/tasks/predict_modality/methods/random_forest/script.R new file mode 100644 index 0000000000..91612bbd48 --- /dev/null +++ b/src/tasks/predict_modality/methods/random_forest/script.R @@ -0,0 +1,83 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +requireNamespace("pbapply", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) + +## VIASH START +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +par <- list( + input_train_mod1 = paste0(path, "train_mod1.h5ad"), + input_test_mod1 = paste0(path, "test_mod1.h5ad"), + input_train_mod2 = paste0(path, "train_mod2.h5ad"), + output = "output.h5ad", + n_pcs = 20L, + n_trees = 50L +) +meta <- list(functionality_name = "foo") +## VIASH END + +n_cores <- parallel::detectCores(all.tests = FALSE, logical = TRUE) + +cat("Reading mod1 files\n") +input_train_mod1 <- anndata::read_h5ad(par$input_train_mod1) +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) + +dataset_id <- input_train_mod1$uns[["dataset_id"]] + +cat("Performing DR on the mod1 values\n") +dr <- lmds::lmds( + rbind(input_train_mod1$layers[["normalized"]], input_test_mod1$layers[["normalized"]]), + ndim = par$n_pcs, + distance_method = par$distance_method +) + +ix <- seq_len(nrow(input_train_mod1)) +dr_train <- as.data.frame(dr[ix, , drop = FALSE]) +dr_test <- as.data.frame(dr[-ix, , drop = FALSE]) +dr_train <- dr[ix, , drop = FALSE] +dr_test <- dr[-ix, , drop = FALSE] + +rm(input_train_mod1, input_test_mod1) +gc() + + +cat("Reading mod2 files\n") +X_mod2 <- anndata::read_h5ad(par$input_train_mod2)$layers[["normalized"]] + +cat("Predicting for each column in modality 2\n") +preds <- pbapply::pblapply( + seq_len(ncol(X_mod2)), + cl = n_cores, + function(i) { + y <- X_mod2[, i] + uy <- unique(y) + if (length(uy) > 1) { + rf <- ranger::ranger( + x = dr_train, + y = y, + num.trees = par$n_trees + ) + stats::predict(rf, dr_test)$prediction + } else { + rep(uy, nrow(dr_test)) + } + } +) + +cat("Creating outputs object\n") +prediction <- Matrix::Matrix(do.call(cbind, preds), sparse = TRUE) +rownames(prediction) <- rownames(dr_test) +colnames(prediction) <- colnames(X_mod2) + +out <- anndata::AnnData( + layers = list(normalized = prediction), + shape = dim(prediction), + uns = list( + dataset_id = dataset_id, + method_id = meta$functionality_name + ) +) + + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml new file mode 100644 index 0000000000..8130364eba --- /dev/null +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -0,0 +1,66 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: correlation + info: + metrics: + - name: mean_pearson_per_cell + label: Mean pearson per cell + summary: The mean of the pearson values of per-cell expression value vectors. + description: The mean of the pearson values of per-cell expression value vectors. + min: -1 + max: 1 + maximize: true + reference: pearson1895regression + - name: mean_spearman_per_cell + label: Mean spearman per cell + summary: The mean of the spearman values of per-cell expression value vectors. + description: The mean of the spearman values of per-cell expression value vectors. + min: -1 + max: 1 + maximize: true + reference: kendall1938new + - name: mean_pearson_per_gene + label: Mean pearson per gene + summary: The mean of the pearson values of per-gene expression value vectors. + description: The mean of the pearson values of per-gene expression value vectors. + min: -1 + max: 1 + maximize: true + reference: pearson1895regression + - name: mean_spearman_per_gene + label: Mean spearman per gene + summary: The mean of the spearman values of per-gene expression value vectors. + description: The mean of the spearman values of per-gene expression value vectors. + min: -1 + max: 1 + maximize: true + reference: kendall1938new + - name: overall_pearson + label: Overall pearson + summary: The mean of the pearson values of vectorized expression matrices. + description: The mean of the pearson values of vectorized expression matrices. + min: -1 + max: 1 + maximize: true + reference: pearson1895regression + - name: overall_spearman + label: Overall spearman + summary: The mean of the spearman values of vectorized expression matrices. + description: The mean of the spearman values of vectorized expression matrices. + min: -1 + max: 1 + maximize: true + reference: kendall1938new + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ proxyC, testthat, bit64 ] + github: dynverse/dynutils + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/metrics/correlation/script.R b/src/tasks/predict_modality/metrics/correlation/script.R new file mode 100644 index 0000000000..1fe6c31af0 --- /dev/null +++ b/src/tasks/predict_modality/metrics/correlation/script.R @@ -0,0 +1,85 @@ +cat("Load dependencies\n") +library(testthat, quietly = TRUE, warn.conflicts = FALSE) +library(Matrix, quietly = TRUE, warn.conflicts = FALSE) +requireNamespace("anndata", quietly = TRUE) + +## VIASH START +par <- list( + input_test_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", + input_prediction = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", + output = "openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.scores.h5ad" +) +#/home/rcannood/workspace/openproblems/neurips2021_multimodal_viash/work/29/320fe1e10fcd323020345bcc8969c2/openproblems_bmmc_cite_mod2_dummy_meanpergene.correlation.output.h5ad +## VIASH END + +cat("Reading solution file\n") +ad_sol <- anndata::read_h5ad(par$input_test_mod2) + +cat("Reading prediction file\n") +ad_pred <- anndata::read_h5ad(par$input_prediction) + +cat("Check prediction format\n") +expect_equal( + ad_sol$uns$dataset_id, ad_pred$uns$dataset_id, + info = "Prediction and solution have differing dataset_ids" +) + +expect_true( + isTRUE(all.equal(dim(ad_sol), dim(ad_pred))), + info = "Dataset and prediction anndata objects should have the same shape / dimensions." +) + +cat("Computing correlation metrics\n") +# Wrangle data +tv <- ad_sol$layers[["normalized"]] +pv <- ad_pred$layers[["normalized"]] + +# precompute sds +tv_sd2 <- proxyC::colSds(tv) +pv_sd2 <- proxyC::colSds(pv) +tv_sd1 <- proxyC::rowSds(tv) +pv_sd1 <- proxyC::rowSds(pv) + +# Compute metrics +pearson_vec_1 <- diag(dynutils::calculate_similarity(tv, pv, method = "pearson", margin = 1, diag = TRUE, drop0 = TRUE)) +spearman_vec_1 <- diag(dynutils::calculate_similarity(tv, pv, method = "spearman", margin = 1, diag = TRUE, drop0 = TRUE)) + +pearson_vec_1[tv_sd1 == 0 | pv_sd1 == 0] <- 0 +spearman_vec_1[tv_sd1 == 0 | pv_sd1 == 0] <- 0 +# pearson_vec_1[!is.finite(pearson_vec_1) | pearson_vec_1 > 10] <- 0 +# spearman_vec_1[!is.finite(spearman_vec_1) | spearman_vec_1 > 10] <- 0 + +mean_pearson_per_cell <- mean(pearson_vec_1) +mean_spearman_per_cell <- mean(spearman_vec_1) + +pearson_vec_2 <- diag(dynutils::calculate_similarity(tv, pv, method = "pearson", margin = 2, diag = TRUE, drop0 = TRUE)) +spearman_vec_2 <- diag(dynutils::calculate_similarity(tv, pv, method = "spearman", margin = 2, diag = TRUE, drop0 = TRUE)) + +pearson_vec_2[tv_sd2 == 0 | pv_sd2 == 0] <- 0 +spearman_vec_2[tv_sd2 == 0 | pv_sd2 == 0] <- 0 +# pearson_vec_2[!is.finite(pearson_vec_2) | pearson_vec_2 > 10] <- 0 +# spearman_vec_2[!is.finite(spearman_vec_2) | spearman_vec_2 > 10] <- 0 + +mean_pearson_per_gene <- mean(pearson_vec_2) +mean_spearman_per_gene <- mean(spearman_vec_2) + +overall_pearson <- cor(as.vector(tv), as.vector(pv), method = "pearson") +overall_spearman <- cor(as.vector(tv), as.vector(pv), method = "spearman") + +metric_ids <- c("mean_pearson_per_cell", "mean_spearman_per_cell", "mean_pearson_per_gene", "mean_spearman_per_gene", "overall_pearson", "overall_spearman") +metric_values <- c(mean_pearson_per_cell, mean_spearman_per_cell, mean_pearson_per_gene, mean_spearman_per_gene, overall_pearson, overall_spearman) + +cat("Create output object\n") +out <- anndata::AnnData( + obs = data.frame(row.names = rownames(ad_sol), pearson = pearson_vec_1, spearman = spearman_vec_1), + var = data.frame(row.names = colnames(ad_sol), pearson = pearson_vec_2, spearman = spearman_vec_2), + uns = list( + dataset_id = ad_pred$uns$dataset_id, + method_id = ad_pred$uns$method_id, + metric_ids = metric_ids, + metric_values = metric_values + ) +) + +cat("Write output to h5ad file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml new file mode 100644 index 0000000000..052268beaf --- /dev/null +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -0,0 +1,30 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: mse + info: + metrics: + - name: rmse + label: RMSE + summary: The root mean squared error. + description: The square root of the mean of the square of all of the error. + min: 0 + max: "+inf" + maximize: false + reference: chai2014root + - name: mae + label: MAE + summary: The mean absolute error. + description: The average difference between the expression values and the predicted expression values. + min: 0 + max: "+inf" + maximize: false + reference: chai2014root + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/metrics/mse/script.py b/src/tasks/predict_modality/metrics/mse/script.py new file mode 100644 index 0000000000..449b4970cb --- /dev/null +++ b/src/tasks/predict_modality/metrics/mse/script.py @@ -0,0 +1,43 @@ +import anndata as ad +import logging +import numpy as np + +## VIASH START +par = { + "input_test_mod2" : "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", + "input_prediction" : "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", + "output" : "openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.scores.h5ad" +} +## VIASH END + +logging.info("Reading solution file") +ad_sol = ad.read_h5ad(par["input_test_mod2"]) + +logging.info("Reading prediction file") +ad_pred = ad.read_h5ad(par["input_prediction"]) + +logging.info("Check prediction format") +if ad_sol.uns["dataset_id"] != ad_pred.uns["dataset_id"]: + raise ValueError("Prediction and solution have differing dataset_ids") + +if ad_sol.shape != ad_pred.shape: + raise ValueError("Dataset and prediction anndata objects should have the same shape / dimensions.") + +logging.info("Computing MSE metrics") + +tmp = ad_sol.layers["normalized"] - ad_pred.layers["normalized"] +rmse = np.sqrt(tmp.power(2).mean()) +mae = np.abs(tmp).mean() + +logging.info("Create output object") +out = ad.AnnData( + uns = { + "dataset_id" : ad_pred.uns["dataset_id"], + "method_id" : ad_pred.uns["method_id"], + "metric_ids" : ["rmse", "mae"], + "metric_values" : [rmse, mae], + } +) + +logging.info("Write output to h5ad file") +out.write_h5ad(par["output"], compression=9) diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml new file mode 100644 index 0000000000..fef6c2b40b --- /dev/null +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -0,0 +1,20 @@ +__merge__: ../api/comp_process_dataset.yaml +functionality: + name: "process_dataset" + arguments: + - name: "--swap" + type: "boolean" + description: "Swap mod1 and mod2" + default: true + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: [ bit64 ] + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R new file mode 100644 index 0000000000..171bc4a9c9 --- /dev/null +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -0,0 +1,138 @@ +cat("Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input_rna = "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad", + input_other_mod = "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad", + output_train_mod1 = "resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad", + output_train_mod2 = "resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad", + output_test_mod1 = "resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad", + output_test_mod2 = "resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad", + swap = TRUE, + seed = 1L +) +# par <- list( +# input_rna = "resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad", +# input_other_mod = "resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad", +# output_train_mod1 = "resources_test/predict_modality/bmmc_multiome_starter/train_mod1.h5ad", +# output_train_mod2 = "resources_test/predict_modality/bmmc_multiome_starter/train_mod2.h5ad", +# output_test_mod1 = "resources_test/predict_modality/bmmc_multiome_starter/test_mod1.h5ad", +# output_test_mod2 = "resources_test/predict_modality/bmmc_multiome_starter/test_mod2.h5ad", +# swap = TRUE, +# seed = 1L +# ) +## VIASH END + +cat("Using seed ", par$seed, "\n", sep = "") +set.seed(par$seed) + +cat("Reading input data\n") +ad1 <- anndata::read_h5ad(if (!par$swap) par$input_rna else par$input_other_mod) +ad2 <- anndata::read_h5ad(if (!par$swap) par$input_other_mod else par$input_rna) + +# figure out modality types +ad1_mod <- unique(ad1$var[["feature_types"]]) +ad2_mod <- unique(ad2$var[["feature_types"]]) + +# determine new dataset id +new_dataset_id <- paste0(ad1$uns[["dataset_id"]], "_", tolower(ad1_mod), "2", tolower(ad2_mod)) + +# determine new uns +ad1_uns <- ad2_uns <- list( + dataset_id = new_dataset_id, + # TODO: this should already be part of the source dataset + dataset_organism = "homo_sapiens" +) +ad1_uns$modality <- ad1_mod +ad2_uns$modality <- ad2_mod + +# determine new obsm +ad1_obsm <- ad2_obsm <- list() + +# determine new varm +ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids")), drop = FALSE] +ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids")), drop = FALSE] + +if (ad1_mod == "ATAC") { + ad1$X@x <- (ad1$X@x > 0) + 0 + # copy gene activity in new object + ad1_uns$gene_activity_var_names <- ad1$uns$gene_activity_var_names + ad1_obsm$gene_activity <- as(ad1$obsm$gene_activity, "CsparseMatrix") +} + +if (ad2_mod == "ATAC") { + # subset to make the task computationally feasible + if (ncol(ad2) > 10000) { + poss_ix <- which(Matrix::colSums(ad2$X) > 0) + sel_ix <- sort(sample(poss_ix, 10000)) + ad2 <- ad2[, sel_ix]$copy() + ad2_var <- ad2_var[sel_ix, , drop = FALSE] + } + ad2$X@x <- (ad2$X@x > 0) + 0 + + # copy gene activity in new object + ad2_uns$gene_activity_var_names <- ad2$uns$gene_activity_var_names + ad2_obsm$gene_activity <- as(ad2$obsm$gene_activity, "CsparseMatrix") +} + +cat("Creating train/test split\n") +is_train <- which(ad1$obs[["is_train"]]) +is_test <- which(!ad1$obs[["is_train"]]) + +# sample cells +if (length(is_test) > 1000) { + ct <- as.character(ad1$obs[["cell_type"]][is_test]) + ct_tab <- table(ct) + ct_freq <- setNames(as.vector(ct_tab) / sum(ct_tab), names(ct_tab)) + is_test <- sample(is_test, 1000, prob = sqrt(1 / ct_freq[ct])) +} + +train_obs <- ad1$obs[is_train, intersect(colnames(ad1$obs), c("batch", "size_factors")), drop = FALSE] +test_obs <- ad1$obs[is_test, intersect(colnames(ad1$obs), c("batch", "size_factors")), drop = FALSE] +subset_mats <- function(li, obs_filt) { + out <- list() + for (n in names(li)) { + out[[n]] <- li[[n]][obs_filt, , drop = FALSE] + } + out +} + +cat("Create train objects\n") +output_train_mod1 <- anndata::AnnData( + layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$X), is_train), + obsm = subset_mats(ad1_obsm, is_train), + obs = train_obs, + var = ad1_var, + uns = ad1_uns +) +output_train_mod2 <- anndata::AnnData( + layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$X), is_train), + obsm = subset_mats(ad2_obsm, is_train), + obs = train_obs, + var = ad2_var, + uns = ad2_uns +) + +cat("Create test objects\n") +output_test_mod1 <- anndata::AnnData( + layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$X), is_test), + obsm = subset_mats(ad1_obsm, is_test), + obs = test_obs, + var = ad1_var, + uns = ad1_uns +) +output_test_mod2 <- anndata::AnnData( + layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$X), is_test), + obsm = subset_mats(ad2_obsm, is_test), + obs = test_obs, + var = ad2_var, + uns = ad2_uns +) + +cat("Saving output files as h5ad\n") +zzz <- output_train_mod1$write_h5ad(par$output_train_mod1, compression = "gzip") +zzz <- output_train_mod2$write_h5ad(par$output_train_mod2, compression = "gzip") +zzz <- output_test_mod1$write_h5ad(par$output_test_mod1, compression = "gzip") +zzz <- output_test_mod2$write_h5ad(par$output_test_mod2, compression = "gzip") diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh new file mode 100755 index 0000000000..5753a22fa4 --- /dev/null +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -0,0 +1,95 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash ns build -q 'predict_modality|common' --parallel --setup cb + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e +# TODO: Download the starter datasets from the source repository +# TODO TODO: Generate the datasets from the source GEO dataset + +generate_pm_test_resources () { + DATASET_ID="$1" + MOD_1_DATA="$2" + MOD_2_DATA="$3" + DATASET_DIR="$4" + FLAGS="$5" + + if [ ! -f $MOD_1_DATA ]; then + echo "Error! Could not find raw data" + exit 1 + fi + + mkdir -p $DATASET_DIR + + + # process_dataset + viash run src/tasks/predict_modality/process_dataset/config.vsh.yaml -- \ + --input_rna $MOD_1_DATA \ + --input_other_mod $MOD_2_DATA \ + --output_train_mod1 $DATASET_DIR/train_mod1.h5ad \ + --output_train_mod2 $DATASET_DIR/train_mod2.h5ad \ + --output_test_mod1 $DATASET_DIR/test_mod1.h5ad \ + --output_test_mod2 $DATASET_DIR/test_mod2.h5ad $FLAGS + + # run one method + viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ + --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ + --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ + --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ + --output $DATASET_DIR/prediction.h5ad + + # run one metric + viash run src/tasks/predict_modality/metrics/mse/config.vsh.yaml -- \ + --input_prediction $DATASET_DIR/prediction.h5ad \ + --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ + --output $DATASET_DIR/score.h5ad + + # run benchmark on test data + export NXF_VER=22.04.5 + + nextflow run . \ + -main-script src/tasks/predict_modality/workflows/run/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + --id "$DATASET_ID" \ + --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ + --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ + --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ + --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ + --output scores.tsv \ + --publish_dir $DATASET_DIR/ +} + +generate_pm_test_resources \ + bmmc_cite_starter \ + resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad \ + resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad \ + resources_test/predict_modality/bmmc_cite_starter \ + "" + +generate_pm_test_resources \ + bmmc_cite_starter_swapped \ + resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad \ + resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad \ + resources_test/predict_modality/bmmc_cite_starter_swapped \ + "--swap true" + +generate_pm_test_resources \ + bmmc_multiome_starter \ + resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad \ + resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad \ + resources_test/predict_modality/bmmc_multiome_starter \ + "" + +generate_pm_test_resources \ + bmmc_multiome_starter_swapped \ + resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad \ + resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad \ + resources_test/predict_modality/bmmc_multiome_starter_swapped \ + "--swap true" \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/config.vsh.yaml b/src/tasks/predict_modality/workflows/run/config.vsh.yaml new file mode 100644 index 0000000000..70c4356a0e --- /dev/null +++ b/src/tasks/predict_modality/workflows/run/config.vsh.yaml @@ -0,0 +1,28 @@ +functionality: + name: "run_benchmark" + namespace: "predict_modality/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input_train_mod1" + type: "file" # todo: replace with includes + - name: "--input_train_mod2" + type: "file" + - name: "--input_test_mod1" + type: "file" # todo: replace with includes + - name: "--input_test_mod2" + type: "file" # todo: replace with includes + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + resources: + - type: nextflow_script + path: main.nf +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run/main.nf new file mode 100644 index 0000000000..1521194017 --- /dev/null +++ b/src/tasks/predict_modality/workflows/run/main.nf @@ -0,0 +1,159 @@ +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +// import control methods +include { meanpergene } from "$targetDir/predict_modality/control_methods/meanpergene/main.nf" +include { random_predict } from "$targetDir/predict_modality/control_methods/random_predict/main.nf" +include { zeros } from "$targetDir/predict_modality/control_methods/zeros/main.nf" +include { solution } from "$targetDir/predict_modality/control_methods/solution/main.nf" + +// import methods +include { knnr_py } from "$targetDir/predict_modality/methods/knnr_py/main.nf" +include { knnr_r } from "$targetDir/predict_modality/methods/knnr_r/main.nf" +include { lm } from "$targetDir/predict_modality/methods/lm/main.nf" +include { newwave_knnr } from "$targetDir/predict_modality/methods/newwave_knnr/main.nf" +include { random_forest } from "$targetDir/predict_modality/methods/random_forest/main.nf" + + +// import metrics +include { correlation } from "$targetDir/predict_modality/metrics/correlation/main.nf" +include { mse } from "$targetDir/predict_modality/metrics/mse/main.nf" + +// tsv generation component +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" + +// import helper functions +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" + +// read in pipeline config +config = readConfig("$projectDir/config.vsh.yaml") + +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// collect method list +methods = [ + meanpergene, + random_predict, + zeros, + solution, + knnr_py, + knnr_r, + lm, + newwave_knnr, + random_forest +] + +// collect metric list +metrics = [ + correlation, + mse +] + +workflow { + helpMessage(config) + + // create channel from input parameters with + // arguments as defined in the config + channelFromParams(params, config) + | run_wf +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + // based on the config file (config.vsh.yaml), run assertions on parameter sets + // and fill in default values + | preprocessInputs(config: config) + + // run all methods + | run_components( + components: methods, + + // // use the 'filter' argument to only run a method on the normalisation the component is asking for + // filter: { id, state, config -> + // def norm = state.normalization_id + // def pref = config.functionality.info.preferred_normalization + // // if the preferred normalisation is none at all, + // // we can pass whichever dataset we want + // (norm == "log_cpm" && pref == "counts") || norm == pref + // }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: { id, state, config -> + def new_args = [ + input_train_mod1: state.input_train_mod1, + input_train_mod2: state.input_train_mod2, + input_test_mod1: state.input_test_mod1 + ] + if (config.functionality.info.type == "control_method") { + new_args.input_test_mod2 = state.input_test_mod2 + } + new_args + }, + + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + method_id: config.functionality.name, + method_output: output.output + ] + } + ) + + // run all metrics + | run_components( + components: metrics, + // use 'from_state' to fetch the arguments the component requires from the overall state + from_state: [ + input_test_mod2: "input_test_mod2", + input_prediction: "method_output" + ], + // use 'to_state' to publish that component's outputs to the overall state + to_state: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] + } + ) + + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] + } + + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) + + emit: + output_ch +} + +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() + + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) +} \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/nextflow.config b/src/tasks/predict_modality/workflows/run/nextflow.config new file mode 100644 index 0000000000..d0feacc62f --- /dev/null +++ b/src/tasks/predict_modality/workflows/run/nextflow.config @@ -0,0 +1,16 @@ +manifest { + name = 'predict_modality/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Predict modality' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/run_test.sh b/src/tasks/predict_modality/workflows/run/run_test.sh new file mode 100755 index 0000000000..2aa603e738 --- /dev/null +++ b/src/tasks/predict_modality/workflows/run/run_test.sh @@ -0,0 +1,37 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash_build -q 'label_projection|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +# run benchmark +export NXF_VER=23.04.2 + +cat > /tmp/params.yaml << HERE +param_list: +HERE + +# for id in bmmc_cite_starter bmmc_cite_starter_swapped bmmc_multiome_starter bmmc_multiome_starter_swapped; do +for id in `ls resources_test/predict_modality/`; do +cat >> /tmp/params.yaml << HERE + - id: $id + input_train_mod1: resources_test/predict_modality/$id/train_mod1.h5ad + input_train_mod2: resources_test/predict_modality/$id/train_mod2.h5ad + input_test_mod1: resources_test/predict_modality/$id/test_mod1.h5ad + input_test_mod2: resources_test/predict_modality/$id/test_mod2.h5ad +HERE +done + +nextflow \ + run . \ + -main-script src/tasks/predict_modality/workflows/run/main.nf \ + -profile docker \ + -resume \ + -params-file /tmp/params.yaml \ + --output scores.tsv \ + --publish_dir output/predict_modality/ \ No newline at end of file From e608bc9540e0bfdb70d41d24d445110351897a9e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 07:03:57 +0200 Subject: [PATCH 0940/1233] update readme Former-commit-id: 5fead5d0b377cacd043edfb2ed1f7c395c201fcc --- src/tasks/batch_integration/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 8fbcdccbb6..e4c4a642dc 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -210,7 +210,7 @@ Slot description: | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | @@ -352,7 +352,7 @@ Slot description: | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | | `uns["output_type"]` | `string` | what kind of output has been generated. | @@ -401,7 +401,7 @@ Slot description: | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | | `uns["output_type"]` | `string` | what kind of output has been generated. | @@ -450,7 +450,7 @@ Slot description: | `layers["corrected_counts"]` | `double` | Corrected counts after integration. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | | `uns["output_type"]` | `string` | what kind of output has been generated. | From b6b81e7ecaf673f836dd8ff191e4e14ed4d5fa15 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 07:04:07 +0200 Subject: [PATCH 0941/1233] try to switch to a major release for changed-files Former-commit-id: f5d1871df0006b952176a2a6baccae2f5babc631 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 263ed2cc8d..6a839ee094 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v37.1.1 + uses: tj-actions/changed-files@v37 with: separator: ";" diff_relative: true From 8fe5324a81bc5c50b089658eab93f57f00e5f3b1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 07:05:25 +0200 Subject: [PATCH 0942/1233] rename PM control method Former-commit-id: e4fabb019a9aeae50db5e5758d633edf7e346745 --- .../control_methods/meanpergene/config.vsh.yaml | 2 +- src/tasks/predict_modality/metrics/correlation/script.R | 2 +- src/tasks/predict_modality/workflows/run/main.nf | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 74e11e78f4..950b09c86b 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -1,6 +1,6 @@ __merge__: ../../api/comp_control_method.yaml functionality: - name: meanpergene + name: mean_per_gene info: label: Mean per gene summary: Returns the mean expression value per gene. diff --git a/src/tasks/predict_modality/metrics/correlation/script.R b/src/tasks/predict_modality/metrics/correlation/script.R index 1fe6c31af0..a79620a350 100644 --- a/src/tasks/predict_modality/metrics/correlation/script.R +++ b/src/tasks/predict_modality/metrics/correlation/script.R @@ -9,7 +9,7 @@ par <- list( input_prediction = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", output = "openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.scores.h5ad" ) -#/home/rcannood/workspace/openproblems/neurips2021_multimodal_viash/work/29/320fe1e10fcd323020345bcc8969c2/openproblems_bmmc_cite_mod2_dummy_meanpergene.correlation.output.h5ad +#/home/rcannood/workspace/openproblems/neurips2021_multimodal_viash/work/29/320fe1e10fcd323020345bcc8969c2/openproblems_bmmc_cite_mod2_dummy_mean_per_gene.correlation.output.h5ad ## VIASH END cat("Reading solution file\n") diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run/main.nf index 1521194017..fc5bc3c346 100644 --- a/src/tasks/predict_modality/workflows/run/main.nf +++ b/src/tasks/predict_modality/workflows/run/main.nf @@ -2,7 +2,7 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" // import control methods -include { meanpergene } from "$targetDir/predict_modality/control_methods/meanpergene/main.nf" +include { mean_per_gene } from "$targetDir/predict_modality/control_methods/mean_per_gene/main.nf" include { random_predict } from "$targetDir/predict_modality/control_methods/random_predict/main.nf" include { zeros } from "$targetDir/predict_modality/control_methods/zeros/main.nf" include { solution } from "$targetDir/predict_modality/control_methods/solution/main.nf" @@ -34,7 +34,7 @@ traces = initialize_tracer() // collect method list methods = [ - meanpergene, + mean_per_gene, random_predict, zeros, solution, From b82eecf59640bd224ce13297d1a440de7480c84d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 08:30:53 +0200 Subject: [PATCH 0943/1233] free up space Former-commit-id: 12ab8d3012fb939c70b4a282ec21230983094587 --- .github/workflows/integration-test.yml | 6 ++++++ .github/workflows/main-build.yml | 3 +++ .github/workflows/release-build.yml | 6 ++++++ .github/workflows/viash-test.yml | 3 +++ 4 files changed, 18 insertions(+) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 80429759ff..4575580c62 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -85,6 +85,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 @@ -125,6 +128,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index f1d3820486..d78bfe880c 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -79,6 +79,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index e6ec3ac4b3..9daa016c2d 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -108,6 +108,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 @@ -149,6 +152,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.workflow_matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 6a839ee094..8726c9cb97 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -89,6 +89,9 @@ jobs: component: ${{ fromJson(needs.list.outputs.matrix) }} steps: + # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' + - uses: data-intuitive/reclaim-the-bytes@v2 + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 From bb8818c1b1312bbe5c7400a6007f5a842b1bee1c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 13:58:43 +0200 Subject: [PATCH 0944/1233] update integration test Former-commit-id: 18606b55ffaeeaac2097ad8e9e00c20c578baa80 --- .github/workflows/integration-test.yml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 4575580c62..5c7985356e 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -42,6 +42,7 @@ jobs: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . publish_branch: integration_build + exclude_assets: '' - id: ns_list_components uses: viash-io/viash-actions/ns-list@v4 @@ -60,18 +61,20 @@ jobs: run: | echo "components=$(jq -c '[ .[] | { - "name": (.functionality.namespace + "/" + .functionality.name), + "name": (.functionality.namespace + (.platforms | map(select(.type == "docker"))[0].namespace_separator) + .functionality.name), + "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT - echo "workflows=$(jq -c '[ .[] | + echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | { - "name": (.functionality.namespace + "/" + .functionality.name), - "main_script": (.info.config | capture("^(?.*\/)").dir + "/" + .functionality.test_resources[].path), - "entry": .functionality.test_resources[].entrypoint + "name": ($config.functionality.namespace + "/" + $config.functionality.name), + "main_script": (($config.info.config | capture("^(?.*\/)").dir) + "/" + .path), + "entry": .entrypoint, + "config": $config.info.config } - ]' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT + ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT # phase 2 build: @@ -87,7 +90,7 @@ jobs: steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 @@ -130,7 +133,7 @@ jobs: steps: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - + - uses: actions/checkout@v3 - uses: viash-io/viash-actions/setup@v4 @@ -152,6 +155,7 @@ jobs: with: path: resources_test key: ${{ needs.list.outputs.cache_key }} + fail-on-cache-miss: true - name: Run integration test timeout-minutes: 45 From e84f730e1135b9d730818a9d6e8c2dd7d5620148 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 14:43:45 +0200 Subject: [PATCH 0945/1233] also allow `read_and_merge_yaml.R` to read in json schemas Former-commit-id: 33e609e1fa6ab35f9367c7a271540ed366b664ef --- .../helper_functions/read_and_merge_yaml.R | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R index f5e96d8cc0..2bc9a14ecb 100644 --- a/src/common/helper_functions/read_and_merge_yaml.R +++ b/src/common/helper_functions/read_and_merge_yaml.R @@ -48,6 +48,39 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { parent_path = dirname(path) ) read_and_merge_yaml(new_data_path, project_path) + } else if ("$ref" %in% names(processed_data)) { + ref_parts <- strsplit(processed_data$`$ref`, "#")[[1]] + + # resolve the path in $ref + new_data_path <- .ram_resolve_path( + path = ref_parts[[1]], + project_path = project_path, + parent_path = dirname(path) + ) + new_data_path <- normalizePath(new_data_path, mustWork = FALSE) + + # read in the new data + x <- + tryCatch({ + suppressWarnings(yaml::read_yaml(new_data_path)) + }, error = function(e) { + stop("Could not read ", new_data_path, ". Error: ", e) + }) + + # Navigate the path and retrieve the referenced data + ref_path_parts <- unlist(strsplit(ref_parts[[2]], "/")) + for (part in ref_path_parts) { + if (part == "") { + next + } else if (part %in% names(x)) { + x <- x[[part]] + } else { + stop("Could not find ", part, " in ", new_data_path, "#", ref_parts[[2]]) + } + } + + # postprocess the new data + .ram_process_merge(x, new_data_path, project_path) } else { list() } From 3d94bc78d852557ada4f9018dfba9340fce5e9e2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:06:25 +0200 Subject: [PATCH 0946/1233] add nf-tower test for denoising Former-commit-id: 35e48e31906ddc310396109a39f87928c47467f7 --- src/tasks/denoising/workflows/run/run_test.sh | 1 + .../workflows/run/run_test_on_tower.sh | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+) create mode 100644 src/tasks/denoising/workflows/run/run_test_on_tower.sh diff --git a/src/tasks/denoising/workflows/run/run_test.sh b/src/tasks/denoising/workflows/run/run_test.sh index bdfc09dd19..e671b93965 100755 --- a/src/tasks/denoising/workflows/run/run_test.sh +++ b/src/tasks/denoising/workflows/run/run_test.sh @@ -19,6 +19,7 @@ nextflow \ -main-script src/tasks/denoising/workflows/run/main.nf \ -profile docker \ -resume \ + -c src/wf_utils/labels_ci.config \ --id pancreas \ --dataset_id pancreas \ --normalization_id log_cpm \ diff --git a/src/tasks/denoising/workflows/run/run_test_on_tower.sh b/src/tasks/denoising/workflows/run/run_test_on_tower.sh new file mode 100644 index 0000000000..5634670594 --- /dev/null +++ b/src/tasks/denoising/workflows/run/run_test_on_tower.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +DATASET_DIR=resources_test/denoising/pancreas + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: pancreas_subsample +input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad +input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad +dataset_id: pancreas +normalization_id: log_cpm +output: scores.tsv +publish_dir: s3://openproblems-nextflow/output_test/v2/denoising +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script src/tasks/denoising/workflows/run/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file From e602a430bc33fff3a5bce7f313bdd2ab51411571 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:07:38 +0200 Subject: [PATCH 0947/1233] add nf-tower sript for batch_integration Former-commit-id: d4b60da9ccdd70c104d0072ff95d0ad899f94549 --- .../workflows/run/run_test_on_tower.sh | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 src/tasks/batch_integration/workflows/run/run_test_on_tower.sh diff --git a/src/tasks/batch_integration/workflows/run/run_test_on_tower.sh b/src/tasks/batch_integration/workflows/run/run_test_on_tower.sh new file mode 100644 index 0000000000..e769eb77e1 --- /dev/null +++ b/src/tasks/batch_integration/workflows/run/run_test_on_tower.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +DATASET_DIR=resources_test/batch_integration/pancreas + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: pancreas_subsample +input: s3://openproblems-data/$DATASET_DIR/unintegrated.h5ad +output: scores.tsv +publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script src/tasks/batch_integration/workflows/run/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file From e44abbe005e0cbd4586b4fd51efe4614a8f88d87 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:08:33 +0200 Subject: [PATCH 0948/1233] remove input_type storage from batch_int scripts Former-commit-id: 1fd12b724a761e98ec4be52954f622e196f3ff80 --- .../control_methods/no_integration_batch/script.py | 7 ------- .../control_methods/random_embed_cell/script.py | 6 ------ .../control_methods/random_embed_cell_jitter/script.py | 6 ------ .../control_methods/random_integration/script.py | 6 ------ src/tasks/batch_integration/methods/bbknn/script.py | 6 ------ src/tasks/batch_integration/methods/combat/script.py | 6 ------ .../batch_integration/methods/scanorama_embed/script.py | 6 ------ .../batch_integration/methods/scanorama_feature/script.py | 6 ------ src/tasks/batch_integration/methods/scvi/script.py | 6 ------ .../transformers/embed_to_graph/script.py | 6 ------ .../transformers/feature_to_embed/script.py | 6 ------ 11 files changed, 67 deletions(-) diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/script.py b/src/tasks/batch_integration/control_methods/no_integration_batch/script.py index 7fb811892c..c47dd1d8fc 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/script.py +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/script.py @@ -16,11 +16,6 @@ ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) input = sc.read_h5ad(par['input']) @@ -39,7 +34,5 @@ # ).obsm["X_pca"] print("Store outputs", flush=True) -input.uns['output_type'] = output_type input.uns['method_id'] = meta['functionality_name'] - input.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py index 29491726fd..5c7c87da87 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py @@ -17,11 +17,6 @@ ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) input = ad.read_h5ad(par['input']) @@ -32,6 +27,5 @@ ) print("Store outputs", flush=True) -input.uns['output_type'] = output_type input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py index 50622f60b4..a99f5c14cd 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py @@ -20,11 +20,6 @@ ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) input = ad.read_h5ad(par['input']) @@ -37,6 +32,5 @@ input.obsm['X_emb'] = csr_matrix(embedding + np.random.uniform(-1 * par['jitter'], par['jitter'], embedding.shape)) print("Store outputs", flush=True) -input.uns['output_type'] = output_type input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/script.py b/src/tasks/batch_integration/control_methods/random_integration/script.py index b9191a294d..7b7cf45e69 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/script.py +++ b/src/tasks/batch_integration/control_methods/random_integration/script.py @@ -44,11 +44,6 @@ def _randomize_graph(adata, partition=None): _set_uns(adata) return adata -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) input = ad.read_h5ad(par['input']) input.X = input.layers["normalized"] @@ -59,7 +54,6 @@ def _randomize_graph(adata, partition=None): del input.X print("Store outputs", flush=True) -input.uns['output_type'] = output_type input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/bbknn/script.py b/src/tasks/batch_integration/methods/bbknn/script.py index 0f2deece55..0647e6f2c0 100644 --- a/src/tasks/batch_integration/methods/bbknn/script.py +++ b/src/tasks/batch_integration/methods/bbknn/script.py @@ -14,11 +14,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) input = ad.read_h5ad(par['input']) @@ -32,6 +27,5 @@ del input.X print("Store outputs", flush=True) -input.uns['output_type'] = output_type input.uns['method_id'] = meta['functionality_name'] input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/combat/script.py b/src/tasks/batch_integration/methods/combat/script.py index a92d0616cc..44bf56468c 100644 --- a/src/tasks/batch_integration/methods/combat/script.py +++ b/src/tasks/batch_integration/methods/combat/script.py @@ -16,11 +16,6 @@ ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata = sc.read_h5ad(par['input']) @@ -36,6 +31,5 @@ del(adata.X) print("Store outputs", flush=True) -adata.uns['output_type'] = output_type adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py index 88d14f058c..c1dfb46aa4 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/script.py +++ b/src/tasks/batch_integration/methods/scanorama_embed/script.py @@ -14,11 +14,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) @@ -32,6 +27,5 @@ del adata.X print("Store outputs", flush=True) -adata.uns['output_type'] = output_type adata.uns['method_id'] = meta['functionality_name'] adata.write(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index 59cc5df88c..c914d6f7bc 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -14,11 +14,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) @@ -43,6 +38,5 @@ # ) print("Store outputs", flush=True) -adata.uns['output_type'] = output_type adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py index aca51dd4c4..1b0738dd95 100644 --- a/src/tasks/batch_integration/methods/scvi/script.py +++ b/src/tasks/batch_integration/methods/scvi/script.py @@ -14,11 +14,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) @@ -32,6 +27,5 @@ del adata.X print("Store outputs", flush=True) -adata.uns['output_type'] = output_type adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/script.py b/src/tasks/batch_integration/transformers/embed_to_graph/script.py index 7881291a42..1731e82066 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/script.py +++ b/src/tasks/batch_integration/transformers/embed_to_graph/script.py @@ -8,11 +8,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata = sc.read_h5ad(par['input']) @@ -20,5 +15,4 @@ sc.pp.neighbors(adata, use_rep='X_emb') print("Store outputs", flush=True) -adata.uns['output_type'] = output_type adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/script.py b/src/tasks/batch_integration/transformers/feature_to_embed/script.py index b067afc3f3..f7793bb153 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/script.py +++ b/src/tasks/batch_integration/transformers/feature_to_embed/script.py @@ -8,11 +8,6 @@ } ## VIASH END -with open(meta['config'], 'r', encoding="utf8") as file: - config = yaml.safe_load(file) - -output_type = config["functionality"]["info"]["subtype"] - print('Read input', flush=True) adata= sc.read_h5ad(par['input']) @@ -27,5 +22,4 @@ ) print('Store outputs', flush=True) -adata.uns['output_type'] = output_type adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file From eab58366450b12ff96c8df6971e59de97d39bf77 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:09:29 +0200 Subject: [PATCH 0949/1233] add nf-tower script for lab_proj Former-commit-id: 866335292a97f2ada56e4619ae21554b9aa0f7be --- .../workflows/run/run_test_on_tower.sh | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 src/tasks/label_projection/workflows/run/run_test_on_tower.sh diff --git a/src/tasks/label_projection/workflows/run/run_test_on_tower.sh b/src/tasks/label_projection/workflows/run/run_test_on_tower.sh new file mode 100644 index 0000000000..27c7ee8e3d --- /dev/null +++ b/src/tasks/label_projection/workflows/run/run_test_on_tower.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +DATASET_DIR=resources_test/label_projection/pancreas + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: pancreas_subsample +input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad +input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad +input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad +dataset_id: pancreas +normalization_id: log_cpm +output: scores.tsv +publish_dir: s3://openproblems-nextflow/output_test/v2/label_projection +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script src/tasks/label_projection/workflows/run/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file From 0c3acbce1bdc64eec9f8d472daa2ceacb53ef0b1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:12:09 +0200 Subject: [PATCH 0950/1233] update Matrix to at least 1.5.3 to fix nf-tower error Former-commit-id: fb71a7bdbc3814bfc388352b3af0c702211cec31 --- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 50eef997cb..867a741593 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -29,7 +29,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.1 setup: - type: r - cran: [ Matrix, Seurat, rlang, bit64 ] + cran: [ Matrix>=1.5.3, Seurat, rlang, bit64 ] - type: nextflow directives: label: [ highmem, highcpu ] From 3a24db72145a8b799e41ad8288564310f6f73b22 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 14 Jul 2023 15:31:44 +0200 Subject: [PATCH 0951/1233] update ram_yaml Former-commit-id: ae31ddbf2c7511b389d234a0797ac7375906251b --- .../helper_functions/read_and_merge_yaml.R | 56 ++++++++++++------- 1 file changed, 35 insertions(+), 21 deletions(-) diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R index 2bc9a14ecb..932d3feb92 100644 --- a/src/common/helper_functions/read_and_merge_yaml.R +++ b/src/common/helper_functions/read_and_merge_yaml.R @@ -12,7 +12,7 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { }, error = function(e) { stop("Could not read ", path, ". Error: ", e) }) - .ram_process_merge(data, path, project_path) + .ram_process_merge(data, data, path, project_path) } .ram_find_project <- function(path) { @@ -31,41 +31,51 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj)))) } -.ram_process_merge <- function(data, path, project_path) { +.ram_process_merge <- function(data, root_data, path, project_path) { if (.ram_is_named_list(data)) { # check whether children have `__merge__` entries processed_data <- lapply(data, function(dat) { - .ram_process_merge(dat, path, project_path) + .ram_process_merge(dat, root_data, path, project_path) + }) + processed_data <- lapply(names(data), function(nm) { + dat <- data[[nm]] + .ram_process_merge(dat, root_data, path, project_path) }) names(processed_data) <- names(data) # if current element has __merge__, read list2 yaml and combine with data new_data <- - if ("__merge__" %in% names(processed_data)) { + if ("__merge__" %in% names(processed_data) && !.ram_is_named_list(processed_data$`__merge__`)) { new_data_path <- .ram_resolve_path( path = processed_data$`__merge__`, project_path = project_path, parent_path = dirname(path) ) read_and_merge_yaml(new_data_path, project_path) - } else if ("$ref" %in% names(processed_data)) { + } else if ("$ref" %in% names(processed_data) && !.ram_is_named_list(processed_data$`$ref`)) { ref_parts <- strsplit(processed_data$`$ref`, "#")[[1]] # resolve the path in $ref - new_data_path <- .ram_resolve_path( - path = ref_parts[[1]], - project_path = project_path, - parent_path = dirname(path) - ) - new_data_path <- normalizePath(new_data_path, mustWork = FALSE) - - # read in the new data x <- - tryCatch({ - suppressWarnings(yaml::read_yaml(new_data_path)) - }, error = function(e) { - stop("Could not read ", new_data_path, ". Error: ", e) - }) + if (ref_parts[[1]] == "") { + root_data + } else { + new_data_path <- .ram_resolve_path( + path = ref_parts[[1]], + project_path = project_path, + parent_path = dirname(path) + ) + new_data_path <- normalizePath(new_data_path, mustWork = FALSE) + + # read in the new data + tryCatch({ + suppressWarnings(yaml::read_yaml(new_data_path)) + }, error = function(e) { + stop("Could not read ", new_data_path, ". Error: ", e) + }) + } + x_root <- x + # Navigate the path and retrieve the referenced data ref_path_parts <- unlist(strsplit(ref_parts[[2]], "/")) @@ -75,12 +85,16 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { } else if (part %in% names(x)) { x <- x[[part]] } else { - stop("Could not find ", part, " in ", new_data_path, "#", ref_parts[[2]]) + stop("Could not find ", processed_data$`$ref`, " in ", path) } } # postprocess the new data - .ram_process_merge(x, new_data_path, project_path) + if (ref_parts[[1]] == "") { + x + } else { + .ram_process_merge(x, x_root, new_data_path, project_path) + } } else { list() } @@ -88,7 +102,7 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) { .ram_deep_merge(new_data, processed_data) } else if (is.list(data)) { lapply(data, function(dat) { - .ram_process_merge(dat, path, project_path) + .ram_process_merge(dat, root_data, path, project_path) }) } else { data From 57dc8a5063731fa4165cc2f85b2e885cc00afbb2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 14 Jul 2023 15:35:25 +0200 Subject: [PATCH 0952/1233] remove required uns field output_type Former-commit-id: eccdc2464699e8a7e33c06f41d1f31e07667b675 --- .../batch_integration/api/file_integrated_embedding.yaml | 5 ----- src/tasks/batch_integration/api/file_integrated_feature.yaml | 5 ----- src/tasks/batch_integration/api/file_integrated_graph.yaml | 5 ----- 3 files changed, 15 deletions(-) diff --git a/src/tasks/batch_integration/api/file_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml index 09816eeebb..c2c0c668ff 100644 --- a/src/tasks/batch_integration/api/file_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -16,8 +16,3 @@ info: name: method_id description: "A unique identifier for the method" required: true - - - type: string - name: output_type - description: what kind of output has been generated - required: true diff --git a/src/tasks/batch_integration/api/file_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml index cfbff9ed5f..bdb0a3bdb0 100644 --- a/src/tasks/batch_integration/api/file_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -15,9 +15,4 @@ info: - type: string name: method_id description: "A unique identifier for the method" - required: true - - - type: string - name: output_type - description: what kind of output has been generated required: true \ No newline at end of file diff --git a/src/tasks/batch_integration/api/file_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml index a174fb82ee..54b60d7720 100644 --- a/src/tasks/batch_integration/api/file_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -16,8 +16,3 @@ info: name: method_id description: "A unique identifier for the method" required: true - - - type: string - name: output_type - description: what kind of output has been generated - required: true From 197592ee1b8d84ec29cc409a1edb575afef50fb0 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 19 Jul 2023 11:25:04 +0200 Subject: [PATCH 0953/1233] temp add debug message Former-commit-id: 81df12409c4265cce4cf6b68ab15654083457a32 --- .../label_projection/methods/seurat_transferdata/script.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/tasks/label_projection/methods/seurat_transferdata/script.R b/src/tasks/label_projection/methods/seurat_transferdata/script.R index d7539cdbc4..999eb769ce 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/script.R +++ b/src/tasks/label_projection/methods/seurat_transferdata/script.R @@ -1,7 +1,7 @@ cat(">> Loading dependencies\n") +library(Matrix, warn.conflicts = FALSE) library(anndata, warn.conflicts = FALSE) requireNamespace("Seurat", quietly = TRUE) -library(Matrix, warn.conflicts = FALSE) library(magrittr, warn.conflicts = FALSE) ## VIASH START @@ -12,6 +12,8 @@ par <- list( ) ## VIASH END +packageVersion("Matrix") + cat(">> Load input data\n") input_train <- read_h5ad(par$input_train) input_test <- read_h5ad(par$input_test) From 18f35ea1b325e5f812cd662512247d307ed18457 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 19 Jul 2023 13:22:07 +0200 Subject: [PATCH 0954/1233] fix dim_red tsne Former-commit-id: 60fa337aa9ff08388dfbce602bd728ade69d64e7 --- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 7ec1899577..0da62a6a83 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -42,8 +42,8 @@ platforms: - cmake - gcc - type: python - packages: - - MulticoreTSNE + github: + - DmitryUlyanov/Multicore-TSNE - type: nextflow directives: label: [ highmem, highcpu ] From b255dc0e3062ada1edd7b7d2b6940db9f48ddec9 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:11:03 +0200 Subject: [PATCH 0955/1233] disable seurat_transferdata Former-commit-id: c52a86c2288e9fa604a8e07420e3cee6dec14a8c --- .../label_projection/methods/seurat_transferdata/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 50eef997cb..c8f5eadeb6 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -1,5 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: + status: disabled name: "seurat_transferdata" info: label: Seurat TransferData From b60c81f09bfff6da82531df3f363a6be2467d0c3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:16:41 +0200 Subject: [PATCH 0956/1233] update changelog Former-commit-id: e9a6b0c27a6233537856cb99c54cb76d69705c75 --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44625dad77..c5e1b60be6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,10 @@ * Update "baseline" to "control" (PR #146). +### BUG FIXES + +* fix dim_red and temp disbale label_projection test scripts (PR #206). + ## common ### NEW FUNCTIONALITY From b716d66ccbd16434394db1600d091fa6f1a0a2a3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:33:46 +0200 Subject: [PATCH 0957/1233] remove ns-list workflows Former-commit-id: 30dc7ccdaf2a72836339a80e37dc3080f6858ee1 --- .github/workflows/integration-test.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 5c7985356e..90cb9dc5a4 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -51,11 +51,11 @@ jobs: src: src format: json - - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v4 - with: - src: workflows - format: json + # - id: ns_list_workflows + # uses: viash-io/viash-actions/ns-list@v4 + # with: + # src: workflows + # format: json - id: set_matrix run: | From ba4e0113c4c4f63ebd9a78280e35fb70c834597c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 20 Jul 2023 16:40:04 +0200 Subject: [PATCH 0958/1233] update changelog Former-commit-id: a1ee7892f54ce32db7ce33cc550068bc0bb7facd --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44625dad77..b769bf160e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,10 @@ * Update "baseline" to "control" (PR #146). +### BUG FIXES + +* Remove the ns-list action for worklfows in integration test (PR #208) + ## common ### NEW FUNCTIONALITY From 51d4bae7905d4269733dba6f31c8191f5d422671 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Jul 2023 06:08:53 +0200 Subject: [PATCH 0959/1233] fix set_matrix Former-commit-id: a908df60eb45199b7cc3a89ec6a97be1252b5a16 --- .github/workflows/integration-test.yml | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 90cb9dc5a4..02abaa3513 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -44,19 +44,13 @@ jobs: publish_branch: integration_build exclude_assets: '' - - id: ns_list_components + - id: ns_list uses: viash-io/viash-actions/ns-list@v4 with: platform: docker src: src format: json - # - id: ns_list_workflows - # uses: viash-io/viash-actions/ns-list@v4 - # with: - # src: workflows - # format: json - - id: set_matrix run: | echo "components=$(jq -c '[ .[] | @@ -65,7 +59,7 @@ jobs: "config": .info.config, "dir": .info.config | capture("^(?.*\/)").dir } - ]' ${{ steps.ns_list_components.outputs.output_file }} )" >> $GITHUB_OUTPUT + ]' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT echo "workflows=$(jq -c '[ .[] | . as $config | (.functionality.test_resources // [])[] | select(.type == "nextflow_script", .entrypoint) | { @@ -74,7 +68,7 @@ jobs: "entry": .entrypoint, "config": $config.info.config } - ] | unique' ${{ steps.ns_list_workflows.outputs.output_file }} )" >> $GITHUB_OUTPUT + ] | unique' ${{ steps.ns_list.outputs.output_file }} )" >> $GITHUB_OUTPUT # phase 2 build: From 9e01fcba68fa3aa99a35acf0a3d2d0a471ee7323 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 21 Jul 2023 06:09:19 +0200 Subject: [PATCH 0960/1233] Fix typo Former-commit-id: 9cdc29b7474c224658f3011e22216df90f1bedee --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b769bf160e..92ccfddc34 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,7 @@ ### BUG FIXES -* Remove the ns-list action for worklfows in integration test (PR #208) +* Remove the ns-list action for workflows in integration test (PR #208) ## common From f5c0be49d7b27b0c993add63257b10023e796bd1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 08:26:00 +0200 Subject: [PATCH 0961/1233] ci force Former-commit-id: eb31c65b93b8390a420f0f3425e026fdc4d003fc From cc55eca7fb4eeafd9ae8d1946d0a72e348ff3183 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 08:28:15 +0200 Subject: [PATCH 0962/1233] ci force Former-commit-id: ea00a93c1855e7e978039fa7426f06e93a7211c7 From 237379d317e984430a177c09da6626f99701cfc2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 10:42:58 +0200 Subject: [PATCH 0963/1233] Update CHANGELOG.md Co-authored-by: Robrecht Cannoodt Former-commit-id: 6a1139b5ce6a1d0b0ec08ef574897c2faada0c21 --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c5e1b60be6..af546e7ef3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,8 @@ ### BUG FIXES -* fix dim_red and temp disbale label_projection test scripts (PR #206). +* `dimensionality_reduction/methods/tsne`: Use GitHub version of MulticoreTSNE. +* `label_projection/methods/seurat_transferdata`: Temporarily disable component as it appears to not be working (PR #206). ## common From dfa656e8e797a73093bfb0afe8e22453b98b802c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 15:02:54 +0200 Subject: [PATCH 0964/1233] disable seurat in lab_proj Former-commit-id: 58bd1d964a702978abf55775465b57ff49a1ee16 --- src/tasks/label_projection/workflows/run/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index fda1c42e33..bd54498e0c 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -12,7 +12,7 @@ include { logistic_regression } from "$targetDir/label_projection/methods/logist include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" include { scanvi_scarches } from "$targetDir/label_projection/methods/scanvi_scarches/main.nf" -include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" +// include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" include { xgboost } from "$targetDir/label_projection/methods/xgboost/main.nf" // import metrics @@ -42,7 +42,7 @@ methods = [ mlp, scanvi, scanvi_scarches, - seurat_transferdata, + // seurat_transferdata, xgboost ] From e28e8e60faeea6dcc79bfe3d830e233f7e351fdb Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 24 Jul 2023 16:04:31 +0200 Subject: [PATCH 0965/1233] update nx-wf dim_red Former-commit-id: 18428d8aa6a145058e7a4ee47242af3facbb271e --- .../workflows/run/main.nf | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index c50efda401..9dd5b10231 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -20,6 +20,9 @@ include { density_preservation } from "$targetDir/dimensionality_reduction/metri include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" +// convert scores to tsv +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" + // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" @@ -127,14 +130,14 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states( - apply: { ids, states -> - ["output", [ - input: states.collect{it.metric_output}, - output: states[0].output - ]] - } - ) + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] + } // convert to tsv and publish | extract_scores.run( From 8b2828a4f53f12a287e9b7a455e5312d7d6029d6 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 25 Jul 2023 09:56:34 +0200 Subject: [PATCH 0966/1233] add nf test to dim_red Former-commit-id: ad278f2caf8cbd6c21a5a0fc03c76a9e119efeca --- .../workflows/run/run_test_on_tower.sh | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh b/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh new file mode 100644 index 0000000000..befcde4d49 --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +DATASET_DIR=resources_test/dimensionality_reduction/pancreas + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: pancreas_subsample +input: s3://openproblems-data/$DATASET_DIR/dataset.h5ad +input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad +dataset_id: pancreas +normalization_id: log_cpm +output: scores.tsv +publish_dir: s3://openproblems-nextflow/output_test/v2/dimensionality_reduction +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision integration_build \ + --pull-latest \ + --main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file From 0edcd3c0a42fd39e087173bc38e3dab181299bd5 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 25 Jul 2023 10:05:49 +0200 Subject: [PATCH 0967/1233] update CHANGELOG.md Former-commit-id: 54ef82f32c2a6307f3e3a2aa793ee3b16a8a1082 --- CHANGELOG.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e4aa806f..4e037fae86 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -104,6 +104,8 @@ * `resources_test/label_projection/pancreas` with `src/tasks/label_projection/resources_test_scripts/pancreas.sh`. +* `workflows/run`: Added nf-tower test script. (PR #205) + ### V1 MIGRATION * Removed the separate subtask specific subfolders. The "subtask" is added to the config. @@ -136,6 +138,10 @@ * `metrics/pcr`: Migrated from v1 embedding. +### MINOR CHANGES + +* Removed the `.uns["output_type"]` field from output anndata in methods and control methods. (PR #205) + ## label_projection ### NEW FUNCTIONALITY @@ -148,6 +154,8 @@ * `resources_test/label_projection/pancreas` with `src/tasks/label_projection/resources_test_scripts/pancreas.sh`. +* * `workflows/run`: Added nf-tower test script. (PR #205) + ### V1 MIGRATION * `methods/knn`: Migrated from v1. @@ -185,6 +193,8 @@ * `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. * `resources_test/denoising/pancreas` with `src/tasks/denoising/resources_test_scripts/pancreas.sh`. + +* `workflows/run`: Added nf-tower test script. (PR #205) ### V1 MIGRATION @@ -226,6 +236,8 @@ * `resources_test/dimensionality_reduction/pancreas` with `src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh`. * Added `variant` key to config files to store variants (different input parameters) of every component. + +* `workflows/run`: Added nf-tower test script. (PR #205) ### V1 migration * `control_methods/true_features`: Migrated from v1. Extracted from baseline method `True Features`. From 1176c3ae707c522317faf70ec79c79c018f54640 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 27 Jul 2023 19:21:56 +0200 Subject: [PATCH 0968/1233] update schemas Former-commit-id: a4d7f99ac9e67f4889e60deb1192bf00679944f5 --- src/common/schemas/defs_common.yaml | 3 +-- src/common/schemas/task_metric.yaml | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/common/schemas/defs_common.yaml b/src/common/schemas/defs_common.yaml index 740c066784..0032c0e1c6 100644 --- a/src/common/schemas/defs_common.yaml +++ b/src/common/schemas/defs_common.yaml @@ -102,8 +102,7 @@ definitions: BibtexReference: type: string description: | - type: string - description: A bibtex reference key to the paper where the component is described. + A bibtex reference key to the paper where the component is described. DocumentationURL: type: string format: uri diff --git a/src/common/schemas/task_metric.yaml b/src/common/schemas/task_metric.yaml index 31a687b49a..198646fc48 100644 --- a/src/common/schemas/task_metric.yaml +++ b/src/common/schemas/task_metric.yaml @@ -49,14 +49,14 @@ properties: variants: "$ref": "defs_common.yaml#/definitions/MethodVariants" min: + description: The lowest possible value of the metric. oneOf: - type: number - description: The lowest possible value of the metric. - const: "-.inf" max: + description: The highest possible value of the metric. oneOf: - type: number - description: The highest possible value of the metric. - const: "+.inf" maximize: type: boolean From e77b73a911cb9ab9d80ffa8d0921b4abd86ba596 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 27 Jul 2023 19:30:29 +0200 Subject: [PATCH 0969/1233] update CHANGELOG.md Former-commit-id: 573ccc81836a2e232750dbdcbb4a576d19715531 --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 84e4aa806f..8dda454af9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -59,6 +59,10 @@ * Add library.bib file check to component unit test (PR #167) +### BUG FIXES + +* fix typos in metric and common defenition schemas (PR #212) + ## migration ### NEW FUNCTIONALITY From ec3dda02a66ebcdd0709d5a96a8a7bcee7feb1d9 Mon Sep 17 00:00:00 2001 From: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Date: Mon, 7 Aug 2023 12:22:11 +0200 Subject: [PATCH 0970/1233] add scanvi (#191) * add scanvi * Update config.vsh.yaml add description * Apply suggestions from code review --------- Co-authored-by: Kai Waldrant Former-commit-id: 6a1f3890b63b68b6bd77738516daac73cfca6013 --- .../methods/scanvi/config.vsh.yaml | 46 +++++++++++++++++++ .../methods/scanvi/script.py | 33 +++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 src/tasks/batch_integration/methods/scanvi/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/scanvi/script.py diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml new file mode 100644 index 0000000000..530adec675 --- /dev/null +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -0,0 +1,46 @@ +# The API specifies which type of component this is. +# It contains specifications for: +# - The input/output files +# - Common parameters +# - A unit test +__merge__: ../../api/comp_method_embedding.yaml + +functionality: + # A unique identifier for your component (required). + # Can contain only lowercase letters or underscores. + name: scanvi + + # Metadata for your component + info: + # A relatively short label, used when rendering visualisarions (required) + label: ScanVI + # A one sentence summary of how this method works (required). Used when + # rendering summary tables. + summary: "ScanVI is a deep learning method that considers cell type labels." + description : | + scANVI (single-cell ANnotation using Variational Inference; Python class SCANVI) is a semi-supervised model for single-cell transcriptomics data. In a sense, it can be seen as a scVI extension that can leverage the cell type knowledge for a subset of the cells present in the data sets to infer the states of the rest of the cells. + reference: "lopez2018deep" + repository_url: "https://github.com/YosefLab/scvi-tools" + documentation_url: "https://github.com/YosefLab/scvi-tools#readme" + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + scanvi_full_unscaled: + scanvi_hvg_unscaled: + hvg: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: python + pypi: + - scvi-tools + - scib==1.1.3 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scanvi/script.py b/src/tasks/batch_integration/methods/scanvi/script.py new file mode 100644 index 0000000000..5b3c8cd1d9 --- /dev/null +++ b/src/tasks/batch_integration/methods/scanvi/script.py @@ -0,0 +1,33 @@ +import yaml +import anndata as ad +from scib.integration import scanvi + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'hvg': True, +} +meta = { + 'functionality_name' : 'foo', + 'config': 'bar' +} +## VIASH END + + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']].copy() + +print('Run scanvi', flush=True) +adata.X = adata.layers['normalized'] +adata = scanvi(adata, batch='batch', labels='label') +del adata.X + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') From 9164b8a8d1ee850eb24b218922235d0c23d511d4 Mon Sep 17 00:00:00 2001 From: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Date: Wed, 9 Aug 2023 14:15:45 +0200 Subject: [PATCH 0971/1233] add mnn (#210) * add mnn * Update config.vsh.yaml add documentation * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review see PR https://github.com/chriscainx/mnnpy#48 * process comments * Update src/tasks/batch_integration/methods/mnn/script.py Co-authored-by: Robrecht Cannoodt * rename method * update descriptions --------- Co-authored-by: Kai Waldrant Co-authored-by: Robrecht Cannoodt Former-commit-id: febb220b9bf3df79dd8daaee35f8026a602fd8f0 --- .../methods/mnnpy/config.vsh.yaml | 52 +++++++++++++++++++ .../batch_integration/methods/mnnpy/script.py | 31 +++++++++++ 2 files changed, 83 insertions(+) create mode 100644 src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/mnnpy/script.py diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml new file mode 100644 index 0000000000..e41aa393a7 --- /dev/null +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -0,0 +1,52 @@ +# use method api spec +__merge__: ../../api/comp_method_feature.yaml +functionality: + name: mnnpy + info: + label: mnnpy + summary: "Batch effect correction by matching mutual nearest neighbors, Python implementation." + description: | + An implementation of MNN correct in python featuring low memory usage, full multicore support and compatibility with the scanpy framework. + + Batch effect correction by matching mutual nearest neighbors (Haghverdi et al, 2018) has been implemented as a function 'mnnCorrect' in the R package scran. Sadly it's extremely slow for big datasets and doesn't make full use of the parallel architecture of modern CPUs. + + This project is a python implementation of the MNN correct algorithm which takes advantage of python's extendability and hackability. It seamlessly integrates with the scanpy framework and has multicore support in its bones. + reference: "hie2019efficient" + repository_url: "https://github.com/chriscainx/mnnpy" + documentation_url: "https://github.com/chriscainx/mnnpy#readme" + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py + commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + preferred_normalization: log_cpm + variants: + mnn_full_unscaled: + mnn_hvg_unscaled: + hvg: true + mnn_hvg_scaled: + hvg: true + preferred_normalization: log_cpm_scaled + mnn_full_scaled: + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: python:3.8 + setup: + - type: apt + packages: + - procps + - type: python + pypi: + - anndata~=0.8.0 + - scanpy + - pyyaml + - requests + - jsonschema + - scib==1.1.3 + github: + - chriscainx/mnnpy + - type: nextflow + directives: + label: [ lowcpu, lowmem ] diff --git a/src/tasks/batch_integration/methods/mnnpy/script.py b/src/tasks/batch_integration/methods/mnnpy/script.py new file mode 100644 index 0000000000..d50ce3b742 --- /dev/null +++ b/src/tasks/batch_integration/methods/mnnpy/script.py @@ -0,0 +1,31 @@ +import anndata as ad +from scib.integration import mnn + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'hvg': True, +} +meta = { + 'functionality_name': 'foo', + 'config': 'bar' +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +if par['hvg']: + print('Select HVGs', flush=True) + adata = adata[:, adata.var['hvg']] + +print('Run mnn', flush=True) +adata.X = adata.layers['normalized'] +adata.layers['corrected_counts'] = mnn(adata, batch='batch').X + +del adata.X + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') From 8ef545d43aa838e0084862be11ceec4c50ff2231 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Aug 2023 14:10:28 +0200 Subject: [PATCH 0972/1233] update to viash 0.7.5 #ci force Former-commit-id: 2c53b0261bb2a597ccee887814fce1f3c2bb9e22 --- _viash.yaml | 2 +- src/common/create_component/script.py | 3 --- src/tasks/denoising/process_dataset/script.py | 3 --- src/tasks/dimensionality_reduction/process_dataset/script.py | 3 --- src/tasks/label_projection/process_dataset/script.py | 3 --- 5 files changed, 1 insertion(+), 13 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index f116ef6c2e..12c157deb6 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.3 +viash_version: 0.7.5 source: src target: target diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index b56ce924c0..1bc6d97cc5 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -16,9 +16,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper function sys.path.append(meta["resources_dir"]) from read_and_merge_yaml import read_and_merge_yaml diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index d0827b0ea0..e79a8f5074 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -16,9 +16,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # add helper scripts to path sys.path.append(meta["resources_dir"]) from helper import split_molecules diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index d4aeca0e16..9563ed56f0 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -13,9 +13,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 55f7c75aa8..71584f5d4d 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -20,9 +20,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata From 1024e95f38acec8f84fe017dbde46be374be9771 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Aug 2023 14:11:37 +0200 Subject: [PATCH 0973/1233] Revert "update to viash 0.7.5 #ci force" This reverts commit 8ef545d43aa838e0084862be11ceec4c50ff2231 [formerly 2c53b0261bb2a597ccee887814fce1f3c2bb9e22]. Former-commit-id: 4f1d8d8a587621411b9df9a5c56d6707c37d898b --- _viash.yaml | 2 +- src/common/create_component/script.py | 3 +++ src/tasks/denoising/process_dataset/script.py | 3 +++ src/tasks/dimensionality_reduction/process_dataset/script.py | 3 +++ src/tasks/label_projection/process_dataset/script.py | 3 +++ 5 files changed, 13 insertions(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 12c157deb6..f116ef6c2e 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.5 +viash_version: 0.7.3 source: src target: target diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 1bc6d97cc5..b56ce924c0 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -16,6 +16,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper function sys.path.append(meta["resources_dir"]) from read_and_merge_yaml import read_and_merge_yaml diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index e79a8f5074..d0827b0ea0 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -16,6 +16,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # add helper scripts to path sys.path.append(meta["resources_dir"]) from helper import split_molecules diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index 9563ed56f0..d4aeca0e16 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -13,6 +13,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 71584f5d4d..55f7c75aa8 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -20,6 +20,9 @@ } ## VIASH END +# Remove this after upgrading to Viash 0.7.5 +sys.dont_write_bytecode = True + # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata From c5f34acdd59a777a386130e5a6693d64766e40d4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Aug 2023 14:43:13 +0200 Subject: [PATCH 0974/1233] Update to Viash 0.7.5 (#217) * Revert "Revert "update to viash 0.7.5 #ci force"" This reverts commit 1024e95f38acec8f84fe017dbde46be374be9771 [formerly 4f1d8d8a587621411b9df9a5c56d6707c37d898b]. * fix config Former-commit-id: d86505da74adf67ee8be8c6380c9c93a800904ac --- _viash.yaml | 2 +- src/common/create_component/script.py | 3 --- src/common/sync_test_resources/config.vsh.yaml | 1 - src/tasks/denoising/process_dataset/script.py | 3 --- src/tasks/dimensionality_reduction/process_dataset/script.py | 3 --- src/tasks/label_projection/process_dataset/script.py | 3 --- 6 files changed, 1 insertion(+), 14 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index f116ef6c2e..12c157deb6 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.3 +viash_version: 0.7.5 source: src target: target diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index b56ce924c0..1bc6d97cc5 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -16,9 +16,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper function sys.path.append(meta["resources_dir"]) from read_and_merge_yaml import read_and_merge_yaml diff --git a/src/common/sync_test_resources/config.vsh.yaml b/src/common/sync_test_resources/config.vsh.yaml index d66ce8bf74..f443d634e8 100644 --- a/src/common/sync_test_resources/config.vsh.yaml +++ b/src/common/sync_test_resources/config.vsh.yaml @@ -42,4 +42,3 @@ platforms: image: "amazon/aws-cli:2.7.12" - type: native - type: nextflow - variant: vdsl3 diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index d0827b0ea0..e79a8f5074 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -16,9 +16,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # add helper scripts to path sys.path.append(meta["resources_dir"]) from helper import split_molecules diff --git a/src/tasks/dimensionality_reduction/process_dataset/script.py b/src/tasks/dimensionality_reduction/process_dataset/script.py index d4aeca0e16..9563ed56f0 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/script.py +++ b/src/tasks/dimensionality_reduction/process_dataset/script.py @@ -13,9 +13,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 55f7c75aa8..71584f5d4d 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -20,9 +20,6 @@ } ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata From 70a1550146ce6c52153d6872ce5ff464d74bf8ed Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 16 Aug 2023 16:53:48 +0200 Subject: [PATCH 0975/1233] add mnn_correct method (#215) * add mnn_correct method * update script * disable fastmnn_feature for now * update description Former-commit-id: dcecd3775790cc5bc9768c388f2c8b8b53dddd25 --- .../methods/fastmnn/config.vsh.yaml | 37 +++++++++++++ .../methods/fastmnn/script.R | 54 +++++++++++++++++++ .../methods/mnn_correct/config.vsh.yaml | 31 +++++++++++ .../methods/mnn_correct/script.R | 40 ++++++++++++++ .../methods/scanorama_feature/script.py | 10 ---- 5 files changed, 162 insertions(+), 10 deletions(-) create mode 100644 src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/fastmnn/script.R create mode 100644 src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/mnn_correct/script.R diff --git a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml new file mode 100644 index 0000000000..45ba50afbc --- /dev/null +++ b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml @@ -0,0 +1,37 @@ +# use method api spec +__merge__: ../../api/comp_method_embedding.yaml +functionality: + name: fastmnn + info: + label: fastMnn + summary: "A simpler version of the original mnnCorrect algorithm." + description: | + The fastMNN() approach is much simpler than the original mnnCorrect() algorithm, and proceeds in several steps. + + 1. Perform a multi-sample PCA on the (cosine-)normalized expression values to reduce dimensionality. + 2. Identify MNN pairs in the low-dimensional space between a reference batch and a target batch. + 3. Remove variation along the average batch vector in both reference and target batches. + 4. Correct the cells in the target batch towards the reference, using locally weighted correction vectors. + 5. Merge the corrected target batch with the reference, and repeat with the next target batch. + + reference: "haghverdi2018batch" + repository_url: "https://code.bioconductor.org/browse/batchelor/" + documentation_url: "https://bioconductor.org/packages/batchelor/" + preferred_normalization: log_cpm + variants: + mnn_full_unscaled: + mnn_hvg_unscaled: + hvg: true + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + bioc: + - batchelor + - type: nextflow + directives: + label: [ lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/fastmnn/script.R b/src/tasks/batch_integration/methods/fastmnn/script.R new file mode 100644 index 0000000000..f951c3979d --- /dev/null +++ b/src/tasks/batch_integration/methods/fastmnn/script.R @@ -0,0 +1,54 @@ +cat("Loading dependencies\n") +suppressPackageStartupMessages({ + requireNamespace("anndata", quietly = TRUE) + library(Matrix, warn.conflicts = FALSE) + requireNamespace("batchelor", quietly = TRUE) + library(SingleCellExperiment, warn.conflicts = FALSE) +}) +## VIASH START +par <- list( + input = 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + output = 'output.h5ad', + hvg = FALSE +) +meta <- list( + functionality_name = "mnn_correct_feature" +) +## VIASH END + +cat("Read input\n") +adata <- anndata::read_h5ad(par$input) + +# don't subset when return_type is not "feature" +if ("hvg" %in% names(par) && par$hvg) { + cat("Select HVGs\n") + adata <- adata[, adata$var[["hvg"]]] +} + +# TODO: pass output of 'multiBatchNorm' to fastMNN + +cat("Run mnn\n") +out <- suppressWarnings(batchelor::fastMNN( + t(adata$layers[["normalized"]]), + batch = adata$obs[["batch"]] +)) + +cat("Reformat output\n") +obsm <- SingleCellExperiment::reducedDim(out, "corrected") +adata$obsm[["X_emb"]] <- obsm +# return_type == "feature" is currently not working in fastMNN + +# # reusing the same script for mnn_correct and mnn_correct_feature +# return_type <- gsub("mnn_correct_", "", meta[["functionality_name"]]) + +# if (return_type == "feature") { +# layer <- SummarizedExperiment::assay(out, "corrected") +# adata$layers[["corrected_counts"]] <- as(t(layer), "sparseMatrix") +# } else if (return_type == "embedding") { +# obsm <- SingleCellExperiment::reducedDim(out, "corrected") +# adata$obsm[["X_emb"]] <- obsm +# } + +cat("Store outputs\n") +adata$uns[["method_id"]] <- meta$functionality_name +zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml new file mode 100644 index 0000000000..2121d8b972 --- /dev/null +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -0,0 +1,31 @@ +# use method api spec +__merge__: ../../api/comp_method_feature.yaml +functionality: + name: mnn_correct + info: + label: mnnCorrect + summary: "Correct for batch effects in single-cell expression data using the mutual nearest neighbors method." + description: | + We present a strategy for batch correction based on the detection of mutual nearest neighbors (MNNs) in the high-dimensional expression space. + Our approach does not rely on predefined or equal population compositions across batches; instead, it requires only that a subset of the population be shared between batches. + reference: "haghverdi2018batch" + repository_url: "https://code.bioconductor.org/browse/batchelor/" + documentation_url: "https://bioconductor.org/packages/batchelor/" + preferred_normalization: log_cpm + variants: + mnn_full_unscaled: + mnn_hvg_unscaled: + hvg: true + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + bioc: + - batchelor + - type: nextflow + directives: + label: [ lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/mnn_correct/script.R b/src/tasks/batch_integration/methods/mnn_correct/script.R new file mode 100644 index 0000000000..e012e48a57 --- /dev/null +++ b/src/tasks/batch_integration/methods/mnn_correct/script.R @@ -0,0 +1,40 @@ +cat("Loading dependencies\n") +suppressPackageStartupMessages({ + requireNamespace("anndata", quietly = TRUE) + library(Matrix, warn.conflicts = FALSE) + requireNamespace("batchelor", quietly = TRUE) + library(SingleCellExperiment, warn.conflicts = FALSE) +}) +## VIASH START +par <- list( + input = 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + output = 'output.h5ad', + hvg = FALSE +) +meta <- list( + functionality_name = "mnn_correct_feature" +) +## VIASH END + +cat("Read input\n") +adata <- anndata::read_h5ad(par$input) + +# don't subset when return_type is not "feature" +if ("hvg" %in% names(par) && par$hvg) { + cat("Select HVGs\n") + adata <- adata[, adata$var[["hvg"]]] +} + +cat("Run mnn\n") +out <- suppressWarnings(batchelor::mnnCorrect( + t(adata$layers[["normalized"]]), + batch = adata$obs[["batch"]] +)) + +cat("Reformat output\n") +layer <- SummarizedExperiment::assay(out, "corrected") +adata$layers[["corrected_counts"]] <- as(t(layer), "sparseMatrix") + +cat("Store outputs\n") +adata$uns[["method_id"]] <- meta$functionality_name +zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index c914d6f7bc..af66a5219e 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -27,16 +27,6 @@ del adata.X -# ? Create new comp feature_to_graph? -# print("Run PCA", flush=True) -# sc.pp.pca( -# adata, -# n_comps=50, -# use_highly_variable=False, -# svd_solver='arpack', -# return_info=True -# ) - print("Store outputs", flush=True) adata.uns['method_id'] = meta['functionality_name'] adata.write_h5ad(par['output'], compression='gzip') From cd8f5f27420c6bb800b8391b5ebe3f114ea8e7f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michaela=20M=C3=BCller?= <51025211+mumichae@users.noreply.github.com> Date: Wed, 23 Aug 2023 13:46:44 +0200 Subject: [PATCH 0976/1233] Batch integration - add more metrics (#213) * add graph connectivity * add LISI scores * update LISI description * add isolated label scores * install scib from git * add kBET metric * add HVG overlap metric * add new metrics to workflow * update CHANGELOG * update metric documentations * update unit test * fix unit tests --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: dd975cd8d28443ccc438087a48a7182f2ffac505 --- CHANGELOG.md | 14 +++- src/common/comp_tests/check_method_config.py | 8 ++- src/common/comp_tests/check_metric_config.py | 8 ++- .../metrics/asw_batch/config.vsh.yaml | 21 +++++- .../metrics/asw_label/config.vsh.yaml | 10 ++- .../cell_cycle_conservation/config.vsh.yaml | 19 +++++- .../clustering_overlap/config.vsh.yaml | 14 ++-- .../graph_connectivity/config.vsh.yaml | 45 +++++++++++++ .../metrics/graph_connectivity/script.py | 35 ++++++++++ .../metrics/hvg_overlap/config.vsh.yaml | 44 +++++++++++++ .../metrics/hvg_overlap/script.py | 43 ++++++++++++ .../isolated_label_asw/config.vsh.yaml | 38 +++++++++++ .../metrics/isolated_label_asw/script.py | 46 +++++++++++++ .../metrics/isolated_label_f1/config.vsh.yaml | 50 ++++++++++++++ .../metrics/isolated_label_f1/script.py | 46 +++++++++++++ .../metrics/kbet/config.vsh.yaml | 54 +++++++++++++++ .../batch_integration/metrics/kbet/script.py | 43 ++++++++++++ .../metrics/lisi/config.vsh.yaml | 53 +++++++++++++++ .../batch_integration/metrics/lisi/script.py | 65 +++++++++++++++++++ .../metrics/pcr/config.vsh.yaml | 18 +++-- .../batch_integration/workflows/run/main.nf | 19 +++++- .../workflows/run/run_nextflow.sh | 3 +- 22 files changed, 669 insertions(+), 27 deletions(-) create mode 100644 src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/graph_connectivity/script.py create mode 100644 src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/hvg_overlap/script.py create mode 100644 src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/isolated_label_asw/script.py create mode 100644 src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/isolated_label_f1/script.py create mode 100644 src/tasks/batch_integration/metrics/kbet/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/kbet/script.py create mode 100644 src/tasks/batch_integration/metrics/lisi/config.vsh.yaml create mode 100644 src/tasks/batch_integration/metrics/lisi/script.py diff --git a/CHANGELOG.md b/CHANGELOG.md index eb10c3cf7d..c63820536b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -108,7 +108,9 @@ * `resources_test/label_projection/pancreas` with `src/tasks/label_projection/resources_test_scripts/pancreas.sh`. -* `workflows/run`: Added nf-tower test script. (PR #205) +* `workflows/run`: Added nf-tower test script (PR #205). + +* `metrics/lisi`: Added a component for cLISI and iLISI graph metrics from scib (PR #213). ### V1 MIGRATION @@ -140,6 +142,16 @@ * `metrics/clustering_overlap`: Migrated from v1 graph NMI & ARI. +* `metrics/graph_connectivity`: Migrated from v1 graph. + +* `metrics/hvg_overlap`: Migrated from v1 feature. + +* `metrics/isolated_label_asw`: Migrated from v1 embedding. + +* `metrics/isolated_label_f1`: Migrated from v1 graph. + +* `metrics/kbet`: Migrated from v1 embedding. + * `metrics/pcr`: Migrated from v1 embedding. ### MINOR CHANGES diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index dd460b9b6c..ecbb2dbaf2 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -11,7 +11,7 @@ SUMMARY_MAXLEN = 400 -DESCRIPTION_MAXLEN = 1000 +DESCRIPTION_MAXLEN = 5000 _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] @@ -79,7 +79,11 @@ def search_ref_bib(reference): assert "reference" in info, "reference not an info field" bib = _load_bib() if info["reference"]: - assert search_ref_bib(info["reference"]), f"reference {info['reference']} not added to library.bib" + reference = info["reference"] + if not isinstance(reference, list): + reference = [reference] + for ref in reference: + assert search_ref_bib(ref), f"reference {ref} not added to library.bib" assert "documentation_url" in info is not None, "documentation_url not an info field or is empty" assert "repository_url" in info is not None, "repository_url not an info field or is empty" assert check_url(info["documentation_url"]), f"{info['documentation_url']} is not reachable" diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 732e7aa69a..e8ff523dda 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -13,7 +13,7 @@ SUMMARY_MAXLEN = 400 -DESCRIPTION_MAXLEN = 1000 +DESCRIPTION_MAXLEN = 5000 _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] @@ -71,7 +71,11 @@ def check_metric(metric: Dict[str, str]) -> str: assert "FILL IN:" not in metric["description"], "description not filled in" # assert "reference" in metric, "reference not a field in metric" if "reference" in metric: - assert search_ref_bib(metric["reference"]), f"reference {metric['reference']} not added to library.bib" + reference = metric["reference"] + if not isinstance(reference, list): + reference = [reference] + for ref in reference: + assert search_ref_bib(ref), f"reference {ref} not added to library.bib" # assert "documentation_url" in metric , "documentation_url not a field in metric" # assert "repository_url" in metric , "repository_url not a metric field" if "documentation_url" in metric: diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index 99271d5752..dbf6d97f4d 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -6,9 +6,26 @@ functionality: metrics: - name: asw_batch label: ASW batch - summary: Average silhouette of batches per label + summary: Average silhouette of batches per cell identity label (cell type) description: | - "A batch correction metric that computes the silhouette score over all batch labels per cell type. Here, 0 indicates that batches are well mixed and any deviation from 0 indicates there remains a separation between batch labels. This is rescaled to a score between 0 and 1 by taking." + We consider the absolute silhouette width, s(i), on + batch labels per cell i. Here, 0 indicates that batches are well mixed, and any + deviation from 0 indicates a batch effect: + 𝑠batch(𝑖)=|𝑠(𝑖)|. + + To ensure higher scores indicate better batch mixing, these scores are scaled by + subtracting them from 1. As we expect batches to integrate within cell identity + clusters, we compute the batchASWj score for each cell label j separately, + using the equation: + batchASW𝑗=1|𝐶𝑗|∑𝑖∈𝐶𝑗1−𝑠batch(𝑖), + + where Cj is the set of cells with the cell label j and |Cj| denotes the number of cells + in that set. + + To obtain the final batchASW score, the label-specific batchASWj scores are averaged: + batchASW=1|𝑀|∑𝑗∈𝑀batchASW𝑗. + + Here, M is the set of unique cell labels. reference: luecken2022benchmarking min: 0 max: 1 diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 5eac779cb5..50435d3ce6 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -6,8 +6,14 @@ functionality: metrics: - name: asw_label label: ASW Label - summary: "Average silhouette of labels" - description: "The absolute silhouette width is computed on cell identity labels, measuring their compactness." + summary: Average silhouette of cell identity labels (cell types) + description: | + For the bio-conservation score, the ASW was computed on cell identity labels and + scaled to a value between 0 and 1 using the equation: + celltypeASW=(ASW_C+1)/2, + + where C denotes the set of all cell identity labels. + For information about the batch silhouette score, check sil_batch. reference: luecken2022benchmarking min: 0 max: 1 diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 252625ef4a..95fb0804d4 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -6,8 +6,23 @@ functionality: metrics: - name: cell_cycle_conservation label: Cell Cycle Conservation - summary: "Cell cycle conservation score based on cell cycle gene scoring" - description: "The cell-cycle conservation score evaluates how well the cell-cycle effect can be captured before and after integration." + summary: Cell cycle conservation score based on principle component regression on cell cycle gene scores + description: | + The cell-cycle conservation score evaluates how well the cell-cycle effect can be + captured before and after integration. We computed cell-cycle scores using Scanpy’s + score_cell_cycle function with a reference gene set from Tirosh et al for the + respective cell-cycle phases. We used the same set of cell-cycle genes for mouse and + human data (using capitalization to convert between the gene symbols). We then computed + the variance contribution of the resulting S and G2/M phase scores using principal + component regression (Principal component regression), which was performed for each + batch separately. The differences in variance before, Varbefore, and after, Varafter, + integration were aggregated into a final score between 0 and 1, using the equation: + CCconservation=1−|Varafter−Varbefore|/Varbefore. + + In this equation, values close to 0 indicate lower conservation and 1 indicates complete + conservation of the variance explained by cell cycle. In other words, the variance + remains unchanged within each batch for complete conservation, while any deviation from + the preintegration variance contribution reduces the score. reference: luecken2022benchmarking min: 0 max: 1 diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index edf8ee14fe..9e6558df6a 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -6,7 +6,7 @@ functionality: metrics: - name: ari label: ARI - summary: "Adjusted Rand Index compares clustering overlap, correcting for random labels and considering correct overlaps and disagreements." + summary: Adjusted Rand Index compares clustering overlap, correcting for random labels and considering correct overlaps and disagreements. description: | The Adjusted Rand Index (ARI) compares the overlap of two clusterings; it considers both correct clustering overlaps while also counting correct @@ -16,8 +16,9 @@ functionality: The adjustment of the Rand index corrects for randomly correct labels. An ARI of 0 or 1 corresponds to random labeling or a perfect match, respectively. - We used the scikit-learn implementation of the ARI. - reference: hubert1985comparing + reference: + - hubert1985comparing + - luecken2022benchmarking min: 0 max: 1 maximize: true @@ -34,10 +35,9 @@ functionality: for cell-type and cluster labels. Thus, NMI scores of 0 or 1 correspond to uncorrelated clustering or a perfect match, respectively. We performed optimized Louvain clustering for this metric to obtain the best match between clusters and labels. - Louvain clustering was performed at a resolution range of 0.1 to 2 in steps of 0.1, - and the clustering output with the highest NMI with the label set was used. We - the scikit-learn implementation of NMI. - reference: amelio2015normalized + reference: + - amelio2015normalized + - luecken2022benchmarking min: 0 max: 1 maximize: true diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml new file mode 100644 index 0000000000..4e6b0642bf --- /dev/null +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -0,0 +1,45 @@ +# use metric api spec +__merge__: ../../api/comp_metric_graph.yaml +functionality: + name: graph_connectivity + info: + metrics: + - name: graph_connectivity + label: Graph Connectivity + summary: Connectivity of the subgraph per cell type label + description: | + The graph connectivity metric assesses whether the kNN graph representation, + G, of the integrated data directly connects all cells with the same cell + identity label. For each cell identity label c, we created the subset kNN + graph G(Nc;Ec) to contain only cells from a given label. Using these subset + kNN graphs, we computed the graph connectivity score using the equation: + + gc =1/|C| Σc∈C |LCC(G(Nc;Ec))|/|Nc|. + + Here, C represents the set of cell identity labels, |LCC()| is the number + of nodes in the largest connected component of the graph, and |Nc| is the + number of nodes with cell identity c. The resultant score has a range + of (0;1], where 1 indicates that all cells with the same cell identity + are connected in the integrated kNN graph, and the lowest possible score + indicates a graph where no cell is connected. As this score is computed + on the kNN graph, it can be used to evaluate all integration outputs. + reference: luecken2022benchmarking + min: 0 + max: 1 + maximize: true + v1: + path: https://github.com/openproblems-bio/openproblems/blob/main/openproblems/tasks/_batch_integration/batch_integration_graph/metrics/graph_connectivity.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scib==1.1.4 + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/script.py b/src/tasks/batch_integration/metrics/graph_connectivity/script.py new file mode 100644 index 0000000000..581caab941 --- /dev/null +++ b/src/tasks/batch_integration/metrics/graph_connectivity/script.py @@ -0,0 +1,35 @@ +import anndata as ad +import scib + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + +print('compute score', flush=True) +score = scib.metrics.graph_connectivity( + adata, + label_key='label', +) + +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ] + } +) + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml new file mode 100644 index 0000000000..32d09ce523 --- /dev/null +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -0,0 +1,44 @@ +# use metric api spec +__merge__: ../../api/comp_metric_feature.yaml +functionality: + name: hvg_overlap + info: + metrics: + - name: hvg_overlap + label: HVG overlap + summary: Overlap of highly variable genes per batch before and after integration. + description: | + The HVG conservation score is a proxy for the preservation of + the biological signal. If the data integration method returned + a corrected data matrix, we computed the number of HVGs before + and after correction for each batch via Scanpy’s + highly_variable_genes function (using the ‘cell ranger’ flavor). + If available, we computed 500 HVGs per batch. If fewer than 500 + genes were present in the integrated object for a batch, + the number of HVGs was set to half the total genes in that batch. + The overlap coefficient is as follows: + overlap(𝑋,𝑌)=|𝑋∩𝑌|/min(|𝑋|,|𝑌|), + + where X and Y denote the fraction of preserved informative genes. + The overall HVG score is the mean of the per-batch HVG overlap + coefficients. + reference: luecken2022benchmarking + min: 0 + max: 1 + maximize: true + v1: + path: openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scib==1.1.4 + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/script.py b/src/tasks/batch_integration/metrics/hvg_overlap/script.py new file mode 100644 index 0000000000..dca69ab4bb --- /dev/null +++ b/src/tasks/batch_integration/metrics/hvg_overlap/script.py @@ -0,0 +1,43 @@ +import anndata as ad +from scib.metrics import hvg_overlap + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + +print('prepare data') +adata_unint = adata.copy() +adata_unint.X = adata_unint.layers["normalized"] +adata.X = adata.layers["corrected_counts"] + +print('compute score') + +score = hvg_overlap( + adata_unint, + adata, + batch_key="batch" +) + +print("Create output AnnData object") +output = ad.AnnData( + uns={ + "dataset_id": adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + "method_id": adata.uns['method_id'], + "metric_ids": [meta['functionality_name']], + "metric_values": [score] + } +) + +print("Write data to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml new file mode 100644 index 0000000000..45de30b5db --- /dev/null +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -0,0 +1,38 @@ +# use metric api spec +__merge__: ../../api/comp_metric_embedding.yaml +functionality: + name: isolated_label_asw + info: + metrics: + - name: isolated_label_asw + label: Isolated label ASW + summary: Evaluate how well isolated labels separate by average silhouette width + description: | + Isolated cell labels are defined as the labels present in the least number + of batches in the integration task. The score evaluates how well these isolated labels + separate from other cell identities. + + The isolated label ASW score is obtained by computing the + ASW of isolated versus non-isolated labels on the PCA embedding (ASW metric above) and + scaling this score to be between 0 and 1. The final score for each metric version + consists of the mean isolated score of all isolated labels. + reference: luecken2022benchmarking + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_sil.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + min: 0 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scib==1.1.4 + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/script.py b/src/tasks/batch_integration/metrics/isolated_label_asw/script.py new file mode 100644 index 0000000000..1613230a8f --- /dev/null +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/script.py @@ -0,0 +1,46 @@ +import anndata as ad +from scib.metrics import isolated_labels_asw + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + +print('preprocess data', flush=True) +adata.X = adata.layers['normalized'] +adata_int = adata.copy() + +print('compute score') + +score = isolated_labels_asw( + adata, + label_key='label', + batch_key='batch', + embed='X_emb', + iso_threshold=None, + verbose=True, +) +print(score, flush=True) + +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ] + } +) + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml new file mode 100644 index 0000000000..08db06865d --- /dev/null +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -0,0 +1,50 @@ +# use metric api spec +__merge__: ../../api/comp_metric_graph.yaml +functionality: + name: isolated_label_f1 + info: + metrics: + - name: isolated_label_f1 + label: Isolated label F1 score + summary: Evaluate how well isolated labels coincide with clusters + description: | + We developed two isolated label scores to evaluate how well the data integration methods + dealt with cell identity labels shared by few batches. Specifically, we identified + isolated cell labels as the labels present in the least number of batches in the + integration task. + The score evaluates how well these isolated labels separate from other cell identities. + We implemented the isolated label metric in two versions: + (1) the best clustering of the isolated label (F1 score) and + (2) the global ASW of the isolated label. For the cluster-based score, + we first optimize the cluster assignment of the isolated label using the F1 score˚ + across louvain clustering resolutions ranging from 0.1 to 2 in resolution steps of 0.1. + The optimal F1 score for the isolated label is then used as the metric score. + The F1 score is a weighted mean of precision and recall given by the equation: + 𝐹1=2×(precision×recall)/(precision+recall). + + It returns a value between 0 and 1, + where 1 shows that all of the isolated label cells and no others are captured in + the cluster. For the isolated label ASW score, we compute the ASW of isolated + versus nonisolated labels on the PCA embedding (ASW metric above) and scale this + score to be between 0 and 1. The final score for each metric version consists of + the mean isolated score of all isolated labels. + reference: luecken2022benchmarking + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/iso_label_f1.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + min: 0 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scib==1.1.4 + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/script.py b/src/tasks/batch_integration/metrics/isolated_label_f1/script.py new file mode 100644 index 0000000000..f32167ed44 --- /dev/null +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/script.py @@ -0,0 +1,46 @@ +import anndata as ad +from scib.metrics import isolated_labels_f1 + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + + +print('preprocess data', flush=True) +adata.X = adata.layers['normalized'] +adata_int = adata.copy() + +print('compute score') +score = isolated_labels_f1( + adata, + label_key='label', + batch_key='batch', + embed=None, + iso_threshold=None, + verbose=True, +) +print(score, flush=True) + +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ] + } +) + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml new file mode 100644 index 0000000000..161ba1802f --- /dev/null +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -0,0 +1,54 @@ +# use metric api spec +__merge__: ../../api/comp_metric_embedding.yaml +functionality: + name: kbet + info: + metrics: + - name: kbet + label: kBET + summary: kBET algorithm to determine how well batches are mixed within a cell type + description: | + The kBET algorithm (v.0.99.6, release 4c9dafa) determines whether the label composition + of a k nearest neighborhood of a cell is similar to the expected (global) label + composition (Buettner et al., Nat Meth 2019). The test is repeated for a random subset + of cells, and the results are summarized as a rejection rate over all tested + neighborhoods. Thus, kBET works on a kNN graph. + + We compute kNN graphs where k = 50 for joint embeddings and corrected feature outputs + via Scanpy preprocessing steps. To test for technical effects and to account for + cell-type frequency shifts across datasets, we applied kBET + separately on the batch variable for each cell identity label. Using the kBET defaults, + a k equal to the median of the number of cells per batch within each label is used for + this computation. Additionally, we set the minimum and maximum thresholds of k to 10 and + 100, respectively. As kNN graphs that have been subset by cell identity labels may no + longer be connected, we compute kBET per connected component. If >25% of cells were + assigned to connected components too small for kBET computation (smaller than k × 3), + we assigned a kBET score of 1 to denote poor batch removal. Subsequently, kBET scores + for each label were averaged and subtracted from 1 to give a final kBET score. + + In Open Problems we do not run kBET on graph outputs to avoid computation-intensive + diffusion processes being run. + reference: luecken2022benchmarking + v1: + path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/kBET.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + min: 0 + max: 1 + maximize: true + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + github: theislab/kBET + - type: python + pypi: + - scib==1.1.4 + - rpy2>=3 + - anndata2ri + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/kbet/script.py b/src/tasks/batch_integration/metrics/kbet/script.py new file mode 100644 index 0000000000..cdbf4029f8 --- /dev/null +++ b/src/tasks/batch_integration/metrics/kbet/script.py @@ -0,0 +1,43 @@ +import anndata as ad +from scib.metrics import kBET + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + +print('compute score', flush=True) + +score = kBET( + adata, + batch_key="batch", + label_key="label", + type_="embed", + embed="X_emb", + scaled=True, + verbose=False, +) +print(score, flush=True) + +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ meta['functionality_name'] ], + 'metric_values': [ score ] + } +) + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml new file mode 100644 index 0000000000..73edbfd341 --- /dev/null +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -0,0 +1,53 @@ +# use metric api spec +__merge__: ../../api/comp_metric_graph.yaml +functionality: + name: lisi + info: + metrics: + - name: ilisi + label: iLISI + summary: Local inverse Simpson's Index + description: | + Local Inverse Simpson's Index metrics adapted from Korsunsky et al. 2019 to run on + all full feature, embedding and kNN integration outputs via shortest path-based + distance computation on single-cell kNN graphs. The metric assesses whether clusters + of cells in a single-cell RNA-seq dataset are well-mixed across a categorical batch + variable. + + The original LISI score ranges from 0 to the number of categories, with the latter + indicating good cell mixing. This is rescaled to a score between 0 and 1. + reference: luecken2022benchmarking + min: 0 + max: 1 + maximize: true + repository_url: https://github.com/theislab/scib/blob/ed3e2846414ca1e3dc07552c0eef1e68d82230d4/scib/metrics/lisi.py + documentation_url: https://scib.readthedocs.io/en/latest/api/scib.metrics.ilisi_graph.html + - name: clisi + label: cLISI + summary: Local inverse Simpson's Index + description: | + Local Inverse Simpson's Index metrics adapted from Korsunsky et al. 2019 to run on + all full feature, embedding and kNN integration outputs via shortest path-based + distance computation on single-cell kNN graphs. The metric assesses whether clusters + of cells in a single-cell RNA-seq dataset are well-mixed across a categorical cell type variable. + + The original LISI score ranges from 0 to the number of categories, with the latter indicating good cell mixing. This is rescaled to a score between 0 and 1. + reference: luecken2022benchmarking + min: 0 + max: 1 + maximize: true + repository_url: https://github.com/theislab/scib/blob/ed3e2846414ca1e3dc07552c0eef1e68d82230d4/scib/metrics/lisi.py + documentation_url: https://scib.readthedocs.io/en/latest/api/scib.metrics.clisi_graph.html + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - git+https://github.com/theislab/scib.git@v1.1.4 + - type: nextflow + directives: + label: [ midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/lisi/script.py b/src/tasks/batch_integration/metrics/lisi/script.py new file mode 100644 index 0000000000..10e1aefce3 --- /dev/null +++ b/src/tasks/batch_integration/metrics/lisi/script.py @@ -0,0 +1,65 @@ +import numpy as np +import anndata as ad +from scib.metrics.lisi import recompute_knn, lisi_graph_py + +## VIASH START +par = { + 'input_integrated': 'resources_test/batch_integration/pancreas/integrated_embedding.h5ad', + 'output': 'output.h5ad', +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input_integrated']) + +print('recompute kNN graph..', flush=True) +output_type = adata.uns['output_type'] +adata_tmp = recompute_knn( + adata, + type_=output_type, + use_rep= "X_emb" if output_type == 'embed' else "X_pca", +) + +print('compute iLISI score...', flush=True) +ilisi_scores = lisi_graph_py( + adata=adata_tmp, + obs_key='batch', + n_neighbors=90, + perplexity=None, + subsample=None, + n_cores=1, + verbose=False, +) +ilisi = np.nanmedian(ilisi_scores) +ilisi = (ilisi - 1) / (adata.obs['batch'].nunique() - 1) + +print('compute cLISI scores...', flush=True) +clisi_scores = lisi_graph_py( + adata=adata_tmp, + obs_key='label', + n_neighbors=90, + perplexity=None, + subsample=None, + n_cores=1, + verbose=False, +) +clisi = np.nanmedian(clisi_scores) +nlabs = adata.obs['label'].nunique() +clisi = (nlabs - clisi) / (nlabs - 1) + +print('Create output AnnData object', flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': adata.uns['method_id'], + 'metric_ids': [ 'ilisi_graph', 'clisi_graph' ], + 'metric_values': [ ilisi, clisi ] + } +) + +print('Write data to file', flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 2e0c306411..68704855a0 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -6,12 +6,20 @@ functionality: metrics: - name: pcr label: PCR - summary: "The comparison of explained variance by batch before and after integration." + summary: Compare explained variance by batch before and after integration description: | - "This compares the explained variance by batch before and after integration. It - returns a score between 0 and 1 (scaled=True) with 0 if the variance - contribution hasn’t changed. The larger the score, the more different the - variance contributions are before and after integration." + Principal component regression, derived from PCA, has previously been used to quantify + batch removal. Briefly, the R2 was calculated from a linear regression of the + covariate of interest (for example, the batch variable B) onto each principal component. + The variance contribution of the batch effect per principal component was then + calculated as the product of the variance explained by the ith principal component (PC) + and the corresponding R2(PCi|B). The sum across all variance contributions by the batch + effects in all principal components gives the total variance explained by the batch + variable as follows: + Var(𝐶|𝐵)=∑𝑖=1𝐺Var(𝐶|PC𝑖)×𝑅2(PC𝑖|𝐵), + + where Var(C|PCi) is the variance of the data matrix C explained by the ith principal + component. reference: luecken2022benchmarking v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py diff --git a/src/tasks/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run/main.nf index 11bbd2e733..d79e51a705 100644 --- a/src/tasks/batch_integration/workflows/run/main.nf +++ b/src/tasks/batch_integration/workflows/run/main.nf @@ -26,10 +26,17 @@ include { feature_to_embed } from "$targetDir/batch_integration/transformers/fea include { embed_to_graph } from "$targetDir/batch_integration/transformers/embed_to_graph/main.nf" // import metrics -include { clustering_overlap } from "$targetDir/batch_integration/metrics/clustering_overlap/main.nf" include { asw_batch } from "$targetDir/batch_integration/metrics/asw_batch/main.nf" include { asw_label } from "$targetDir/batch_integration/metrics/asw_label/main.nf" include { cell_cycle_conservation } from "$targetDir/batch_integration/metrics/cell_cycle_conservation/main.nf" +include { clustering_overlap } from "$targetDir/batch_integration/metrics/clustering_overlap/main.nf" +include { graph_connectivity } from "$targetDir/batch_integration/metrics/graph_connectivity/main.nf" +include { lisi } from "$targetDir/batch_integration/metrics/lisi/main.nf" +include { hvg_overlap } from "$targetDir/batch_integration/metrics/hvg_overlap/main.nf" +include { isolated_label_asw } from "$targetDir/batch_integration/metrics/isolated_label_asw/main.nf" +include { isolated_label_f1 } from "$targetDir/batch_integration/metrics/isolated_label_f1/main.nf" +include { kbet } from "$targetDir/batch_integration/metrics/kbet/main.nf" +include { lisi } from "$targetDir/batch_integration/metrics/lisi/main.nf" include { pcr } from "$targetDir/batch_integration/metrics/pcr/main.nf" // tsv generation component @@ -63,7 +70,13 @@ metrics = [ asw_label, cell_cycle_conservation, clustering_overlap, - pcr + graph_connectivity, + hvg_overlap, + isolated_label_asw, + isolated_label_f1, + kbet, + lisi, + pcr, ] @@ -93,7 +106,7 @@ workflow run_wf { } ) - // run feature methods + // run all methods method_out_ch1 = dataset_ch | run_components( components: methods, diff --git a/src/tasks/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run/run_nextflow.sh index 2d5a9a1688..dd7108da30 100755 --- a/src/tasks/batch_integration/workflows/run/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run/run_nextflow.sh @@ -25,4 +25,5 @@ nextflow run . \ --id pancreas \ --input $DATASET_DIR/unintegrated.h5ad \ --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ No newline at end of file + --publish_dir $DATASET_DIR/ \ + $@ \ No newline at end of file From f847cc5de54f426d2dda07483fa6845a65811a5c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Aug 2023 14:07:16 +0200 Subject: [PATCH 0977/1233] Remove --hvg from methods (#216) * Remove --hvg from methods * commit scanvi changes * remove hvg related code Former-commit-id: 488e40df01346015a7bfde21e69aa08e91bae669 --- .../api/comp_control_method_embedding.yaml | 5 ----- .../api/comp_control_method_graph.yaml | 5 ----- .../api/comp_method_embedding.yaml | 10 ---------- .../api/comp_method_feature.yaml | 5 ----- .../api/comp_method_graph.yaml | 5 ----- .../api/comp_process_dataset.yaml | 18 ++++++++++++++++++ .../methods/bbknn/config.vsh.yaml | 5 ----- .../batch_integration/methods/bbknn/script.py | 4 ---- .../methods/combat/config.vsh.yaml | 5 ----- .../batch_integration/methods/combat/script.py | 4 ---- .../methods/mnnpy/config.vsh.yaml | 5 ----- .../batch_integration/methods/mnnpy/script.py | 4 ---- .../methods/scanorama_embed/config.vsh.yaml | 5 ----- .../methods/scanorama_embed/script.py | 4 ---- .../methods/scanorama_feature/config.vsh.yaml | 5 ----- .../methods/scanorama_feature/script.py | 4 ---- .../methods/scanvi/config.vsh.yaml | 2 -- .../batch_integration/methods/scanvi/script.py | 3 --- .../methods/scvi/config.vsh.yaml | 2 -- .../batch_integration/methods/scvi/script.py | 4 ---- .../process_dataset/config.vsh.yaml | 14 -------------- .../process_dataset/script.py | 4 ++++ 22 files changed, 22 insertions(+), 100 deletions(-) diff --git a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml index 802c7c040d..09ecf0531b 100644 --- a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml @@ -17,11 +17,6 @@ functionality: direction: output __merge__: file_integrated_embedding.yaml required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false test_resources: - type: python_script path: /src/common/comp_tests/check_method_config.py diff --git a/src/tasks/batch_integration/api/comp_control_method_graph.yaml b/src/tasks/batch_integration/api/comp_control_method_graph.yaml index 902937f270..d855391c82 100644 --- a/src/tasks/batch_integration/api/comp_control_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_graph.yaml @@ -17,11 +17,6 @@ functionality: name: --output direction: output required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false test_resources: - type: python_script path: /src/common/comp_tests/check_method_config.py diff --git a/src/tasks/batch_integration/api/comp_method_embedding.yaml b/src/tasks/batch_integration/api/comp_method_embedding.yaml index e9ba51acb5..9f9c661beb 100644 --- a/src/tasks/batch_integration/api/comp_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_method_embedding.yaml @@ -17,11 +17,6 @@ functionality: __merge__: file_integrated_embedding.yaml direction: output required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false test_resources: # check method component - type: python_script @@ -32,8 +27,3 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/batch_integration/pancreas dest: resources_test/batch_integration/pancreas - # # test config against schema - # - type: python_script - # path: /src/common/check_yaml_schema/script.py - # - path: /src/common/api/schema_method.yaml - # dest: schema.yaml diff --git a/src/tasks/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml index b2e34f643d..cab7baf02d 100644 --- a/src/tasks/batch_integration/api/comp_method_feature.yaml +++ b/src/tasks/batch_integration/api/comp_method_feature.yaml @@ -17,11 +17,6 @@ functionality: __merge__: file_integrated_feature.yaml direction: output required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false test_resources: # check method component - type: python_script diff --git a/src/tasks/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml index 035a66d9b4..e6adb287a3 100644 --- a/src/tasks/batch_integration/api/comp_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_method_graph.yaml @@ -17,11 +17,6 @@ functionality: __merge__: file_integrated_graph.yaml direction: output required: true - - name: --hvg - type: boolean - description: Whether to subset to highly variable genes - default: false - required: false test_resources: # check method component - type: python_script diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 6352e41689..775155cbea 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -16,6 +16,24 @@ functionality: __merge__: file_unintegrated.yaml direction: output required: true + - name: "--obs_label" + type: "string" + description: "Which .obs slot to use as label." + default: "celltype" + - name: "--obs_batch" + type: "string" + description: "Which .obs slot to use as batch covariate." + default: "batch" + - name: --hvgs + type: integer + description: Number of highly variable genes + default: 2000 + required: false + - name: --subset_hvg + type: boolean + description: Whether to subset to highly variable genes + default: false + required: false test_resources: - path: /resources_test/common/pancreas/ dest: resources_test/common/pancreas/ diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 7588b7504f..129bac5cbf 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -19,12 +19,7 @@ functionality: preferred_normalization: log_cpm variants: bbknn_full_unscaled: - bbknn_hvg_unscaled: - hvg: true - bbknn_hvg_scaled: - preferred_normalization: log_cpm_scaled bbknn_full_scaled: - hvg: true preferred_normalization: log_cpm_scaled resources: - type: python_script diff --git a/src/tasks/batch_integration/methods/bbknn/script.py b/src/tasks/batch_integration/methods/bbknn/script.py index 0647e6f2c0..e47655a87e 100644 --- a/src/tasks/batch_integration/methods/bbknn/script.py +++ b/src/tasks/batch_integration/methods/bbknn/script.py @@ -17,10 +17,6 @@ print('Read input', flush=True) input = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - input = input[:, input.var['hvg']].copy() - print('Run BBKNN', flush=True) input.X = input.layers['normalized'] input = bbknn(input, batch='batch') diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 8f6c527cf1..4e01dfb1ec 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -22,13 +22,8 @@ functionality: preferred_normalization: log_cpm variants: combat_full_unscaled: - combat_hvg_unscaled: - hvg: true combat_full_scaled: preferred_normalization: log_cpm_scaled - combat_hvg_scaled: - hvg: true - preferred_normalization: log_cpm_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/combat/script.py b/src/tasks/batch_integration/methods/combat/script.py index 44bf56468c..6cd90fc28f 100644 --- a/src/tasks/batch_integration/methods/combat/script.py +++ b/src/tasks/batch_integration/methods/combat/script.py @@ -19,10 +19,6 @@ print('Read input', flush=True) adata = sc.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']].copy() - print('Run Combat', flush=True) adata.X = adata.layers['normalized'] adata.X = sc.pp.combat(adata, key='batch', inplace=False) diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index e41aa393a7..47123c7372 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -20,11 +20,6 @@ functionality: preferred_normalization: log_cpm variants: mnn_full_unscaled: - mnn_hvg_unscaled: - hvg: true - mnn_hvg_scaled: - hvg: true - preferred_normalization: log_cpm_scaled mnn_full_scaled: preferred_normalization: log_cpm_scaled resources: diff --git a/src/tasks/batch_integration/methods/mnnpy/script.py b/src/tasks/batch_integration/methods/mnnpy/script.py index d50ce3b742..0fdae66a0a 100644 --- a/src/tasks/batch_integration/methods/mnnpy/script.py +++ b/src/tasks/batch_integration/methods/mnnpy/script.py @@ -16,10 +16,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']] - print('Run mnn', flush=True) adata.X = adata.layers['normalized'] adata.layers['corrected_counts'] = mnn(adata, batch='batch').X diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 21056ecbdc..ae4de238f1 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -17,11 +17,6 @@ functionality: preferred_normalization: log_cpm variants: scanorama_embed_full_unscaled: - scanorama_embed_hvg_unscaled: - hvg: true - scanorama_embed_hvg_scaled: - hvg: true - preferred_normalization: log_cpm_scaled scanorama_embed_full_scaled: preferred_normalization: log_cpm_scaled resources: diff --git a/src/tasks/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py index c1dfb46aa4..321d3163fb 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/script.py +++ b/src/tasks/batch_integration/methods/scanorama_embed/script.py @@ -17,10 +17,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']].copy() - print('Run scanorama', flush=True) adata.X = adata.layers['normalized'] adata.obsm['X_emb'] = scanorama(adata, batch='batch').obsm['X_emb'] diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index ca7edd0983..43b5e10062 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -17,11 +17,6 @@ functionality: preferred_normalization: log_cpm variants: scanorama_feature_full_unscaled: - scanorama_feature_hvg_unscaled: - hvg: true - scanorama_feature_hvg_scaled: - hvg: true - preferred_normalization: log_cpm_scaled scanorama_feature_full_scaled: preferred_normalization: log_cpm_scaled resources: diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index af66a5219e..b7ad5a8a08 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -17,10 +17,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']] - print('Run scanorama', flush=True) adata.X = adata.layers['normalized'] adata.layers['corrected_counts'] = scanorama(adata, batch='batch').X diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 530adec675..82f75714b8 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -28,8 +28,6 @@ functionality: preferred_normalization: log_cpm variants: scanvi_full_unscaled: - scanvi_hvg_unscaled: - hvg: true resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scanvi/script.py b/src/tasks/batch_integration/methods/scanvi/script.py index 5b3c8cd1d9..e812191e6e 100644 --- a/src/tasks/batch_integration/methods/scanvi/script.py +++ b/src/tasks/batch_integration/methods/scanvi/script.py @@ -19,9 +19,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']].copy() print('Run scanvi', flush=True) adata.X = adata.layers['normalized'] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index a917f6ecaa..75f1bcf6e5 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -16,8 +16,6 @@ functionality: preferred_normalization: log_cpm variants: scvi_full_unscaled: - scvi_hvg_unscaled: - hvg: true resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py index 1b0738dd95..f9811c10ac 100644 --- a/src/tasks/batch_integration/methods/scvi/script.py +++ b/src/tasks/batch_integration/methods/scvi/script.py @@ -17,10 +17,6 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -if par['hvg']: - print('Select HVGs', flush=True) - adata = adata[:, adata.var['hvg']].copy() - print('Run scvi', flush=True) adata.X = adata.layers['normalized'] adata = scvi(adata, batch='batch') diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 59af760ac1..c463d416a6 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -2,20 +2,6 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: process_dataset description: Preprocess adata object for data integration - arguments: - - name: "--obs_label" - type: "string" - description: "Which .obs slot to use as label." - default: "celltype" - - name: "--obs_batch" - type: "string" - description: "Which .obs slot to use as batch covariate." - default: "batch" - - name: --hvgs - type: integer - description: Number of highly variable genes - default: 2000 - required: false resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index 396f77684c..8faf3f7bf6 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -40,6 +40,10 @@ def compute_batched_hvg(adata, n_hvgs): print(f'Select {par["hvgs"]} highly variable genes', flush=True) adata_with_hvg = compute_batched_hvg(input, n_hvgs=par['hvgs']) +if par['subset_hvg']: + print('Subsetting to HVG dimensions', flush=True) + adata_with_hvg = adata_with_hvg[:, adata_with_hvg.var['hvg']].copy() + print(">> Figuring out which data needs to be copied to which output file", flush=True) # use par arguments to look for label and batch value in different slots slot_mapping = { From 5e7db1067040d2bba44aa9c4d18e43df9e9ac628 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 23 Aug 2023 15:23:39 +0200 Subject: [PATCH 0978/1233] fix removed hvg parameter after pr merge (#221) Former-commit-id: dafa63242e01d970c186a1365dbdfc378ce867a3 --- .../batch_integration/methods/fastmnn/config.vsh.yaml | 4 ---- src/tasks/batch_integration/methods/fastmnn/script.R | 9 +-------- .../methods/mnn_correct/config.vsh.yaml | 4 ---- src/tasks/batch_integration/methods/mnn_correct/script.R | 9 +-------- 4 files changed, 2 insertions(+), 24 deletions(-) diff --git a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml index 45ba50afbc..a20640b119 100644 --- a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml @@ -18,10 +18,6 @@ functionality: repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" preferred_normalization: log_cpm - variants: - mnn_full_unscaled: - mnn_hvg_unscaled: - hvg: true resources: - type: r_script path: script.R diff --git a/src/tasks/batch_integration/methods/fastmnn/script.R b/src/tasks/batch_integration/methods/fastmnn/script.R index f951c3979d..6ae1ab84fe 100644 --- a/src/tasks/batch_integration/methods/fastmnn/script.R +++ b/src/tasks/batch_integration/methods/fastmnn/script.R @@ -8,8 +8,7 @@ suppressPackageStartupMessages({ ## VIASH START par <- list( input = 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - output = 'output.h5ad', - hvg = FALSE + output = 'output.h5ad' ) meta <- list( functionality_name = "mnn_correct_feature" @@ -19,12 +18,6 @@ meta <- list( cat("Read input\n") adata <- anndata::read_h5ad(par$input) -# don't subset when return_type is not "feature" -if ("hvg" %in% names(par) && par$hvg) { - cat("Select HVGs\n") - adata <- adata[, adata$var[["hvg"]]] -} - # TODO: pass output of 'multiBatchNorm' to fastMNN cat("Run mnn\n") diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 2121d8b972..12c3b5ef52 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -12,10 +12,6 @@ functionality: repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" preferred_normalization: log_cpm - variants: - mnn_full_unscaled: - mnn_hvg_unscaled: - hvg: true resources: - type: r_script path: script.R diff --git a/src/tasks/batch_integration/methods/mnn_correct/script.R b/src/tasks/batch_integration/methods/mnn_correct/script.R index e012e48a57..3f3476d7d4 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/script.R +++ b/src/tasks/batch_integration/methods/mnn_correct/script.R @@ -8,8 +8,7 @@ suppressPackageStartupMessages({ ## VIASH START par <- list( input = 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - output = 'output.h5ad', - hvg = FALSE + output = 'output.h5ad' ) meta <- list( functionality_name = "mnn_correct_feature" @@ -19,12 +18,6 @@ meta <- list( cat("Read input\n") adata <- anndata::read_h5ad(par$input) -# don't subset when return_type is not "feature" -if ("hvg" %in% names(par) && par$hvg) { - cat("Select HVGs\n") - adata <- adata[, adata$var[["hvg"]]] -} - cat("Run mnn\n") out <- suppressWarnings(batchelor::mnnCorrect( t(adata$layers[["normalized"]]), From 8e1254c9ab7b91c3dcfb1ab4efbbd46190342526 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 24 Aug 2023 09:50:27 +0200 Subject: [PATCH 0979/1233] Bump tj-actions/changed-files from 37 to 38 (#222) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 37 to 38. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v37...v38) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: c5542aea744b0b1d9bd8b7cc2a0d80478ea100b9 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 8726c9cb97..452c54e3f2 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v37 + uses: tj-actions/changed-files@v38 with: separator: ";" diff_relative: true From e1a96368a5c59f1ee85a4a164b0b28c8b9bb0b30 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 24 Aug 2023 09:50:42 +0200 Subject: [PATCH 0980/1233] flush when printing (#220) Former-commit-id: 995ca846a87f8799cba3eca51480a3db7a4e107d --- CONTRIBUTING.md | 16 +++++++-------- CONTRIBUTING.qmd | 16 +++++++-------- src/common/check_dataset_schema/test.py | 2 +- src/datasets/normalization/l1_sqrt/script.py | 8 ++++---- src/datasets/normalization/log_cpm/script.py | 8 ++++---- src/datasets/normalization/sqrt_cpm/script.py | 8 ++++---- src/datasets/processors/hvg/script.py | 10 +++++----- src/datasets/processors/knn/script.py | 8 ++++---- src/datasets/processors/pca/script.py | 10 +++++----- src/datasets/processors/subsample/script.py | 2 +- src/migration/check_migration_status/test.py | 8 ++++---- src/migration/list_git_shas/test.py | 8 ++++---- .../control_methods/no_denoising/script.py | 6 +++--- .../perfect_denoising/script.py | 6 +++--- src/tasks/denoising/methods/dca/script.py | 10 +++++----- .../denoising/methods/knn_smoothing/script.py | 6 +++--- src/tasks/denoising/methods/magic/script.py | 6 +++--- src/tasks/denoising/metrics/mse/script.py | 10 +++++----- src/tasks/denoising/metrics/poisson/script.py | 8 ++++---- src/tasks/denoising/process_dataset/script.py | 6 +++--- .../methods/ivis/script.py | 2 +- .../control_methods/majority_vote/script.py | 8 ++++---- .../control_methods/random_labels/script.py | 8 ++++---- .../control_methods/true_labels/script.py | 6 +++--- .../label_projection/methods/knn/script.py | 8 ++++---- .../methods/logistic_regression/script.py | 8 ++++---- .../label_projection/methods/mlp/script.py | 8 ++++---- .../metrics/accuracy/script.py | 10 +++++----- .../label_projection/metrics/f1/script.py | 10 +++++----- .../process_dataset/script.py | 12 +++++------ .../datasets/sample_dataset/script.py | 12 +++++------ .../datasets/sample_dataset/test.py | 14 ++++++------- .../datasets/scprep_csv/script.py | 10 +++++----- .../datasets/scprep_csv/test.py | 10 +++++----- .../methods/harmonic_alignment/script.py | 18 ++++++++--------- .../methods/harmonic_alignment/test.py | 8 ++++---- .../methods/mnn/test.py | 8 ++++---- .../methods/sample_method/script.py | 8 ++++---- .../methods/sample_method/test.py | 8 ++++---- .../methods/scot/script.py | 16 +++++++-------- .../methods/scot/test.py | 8 ++++---- .../metrics/knn_auc/script.py | 20 +++++++++---------- .../metrics/knn_auc/test.py | 8 ++++---- .../metrics/mse/script.py | 10 +++++----- .../metrics/mse/test.py | 8 ++++---- 45 files changed, 204 insertions(+), 204 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 198e037d70..d21edceda4 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -238,17 +238,17 @@ meta = { } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Create predictions") +print("Create predictions", flush=True) input_test.obs["label_pred"] = "foo" -print("Add method name to uns") +print("Add method name to uns", flush=True) input_test.uns["method_id"] = meta["functionality_name"] -print("Write output to file") +print("Write output to file", flush=True) input_test.write_h5ad(par["output"], compression="gzip") ``` @@ -450,17 +450,17 @@ meta = { } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Not creating any predictions!!!") +print("Not creating any predictions!!!", flush=True) # input_test.obs["label_pred"] = "foo" -print("Not adding method name to uns!!!") +print("Not adding method name to uns!!!", flush=True) # input_test.uns["method_id"] = meta["functionality_name"] -print("Write output to file") +print("Write output to file", flush=True) input_test.write_h5ad(par["output"], compression="gzip") ``` diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index f3fd25e01f..4543aa8ec8 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -205,17 +205,17 @@ meta = { } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Create predictions") +print("Create predictions", flush=True) input_test.obs["label_pred"] = "foo" -print("Add method name to uns") +print("Add method name to uns", flush=True) input_test.uns["method_id"] = meta["functionality_name"] -print("Write output to file") +print("Write output to file", flush=True) input_test.write_h5ad(par["output"], compression="gzip") HERE ``` @@ -310,17 +310,17 @@ meta = { } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Not creating any predictions!!!") +print("Not creating any predictions!!!", flush=True) # input_test.obs["label_pred"] = "foo" -print("Not adding method name to uns!!!") +print("Not adding method name to uns!!!", flush=True) # input_test.uns["method_id"] = meta["functionality_name"] -print("Write output to file") +print("Write output to file", flush=True) input_test.write_h5ad(par["output"], compression="gzip") HERE ``` diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 735fc3ec01..aaba49c11e 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -106,4 +106,4 @@ print(out) -print("All checks succeeded!") +print("All checks succeeded!", flush=True) diff --git a/src/datasets/normalization/l1_sqrt/script.py b/src/datasets/normalization/l1_sqrt/script.py index 33243e14c0..e3e5d04a81 100644 --- a/src/datasets/normalization/l1_sqrt/script.py +++ b/src/datasets/normalization/l1_sqrt/script.py @@ -12,18 +12,18 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) adata = ad.read_h5ad(par['input']) -print("Normalize data") +print("Normalize data", flush=True) # libsize and sqrt L1 norm sqrt_data = scprep.utils.matrix_transform(adata.layers['counts'], np.sqrt) l1_sqrt, libsize = scprep.normalize.library_size_normalize(sqrt_data, rescale=1, return_library_size=True) l1_sqrt = l1_sqrt.tocsr() -print("Store output in adata") +print("Store output in adata", flush=True) adata.layers[par["layer_output"]] = l1_sqrt adata.uns["normalization_id"] = meta['functionality_name'] -print("Write data") +print("Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_cpm/script.py b/src/datasets/normalization/log_cpm/script.py index 98034b3fa9..6a28cbcc22 100644 --- a/src/datasets/normalization/log_cpm/script.py +++ b/src/datasets/normalization/log_cpm/script.py @@ -12,10 +12,10 @@ } ## VIASH END -print(">> Load data") +print(">> Load data", flush=True) adata = sc.read_h5ad(par['input']) -print(">> Normalize data") +print(">> Normalize data", flush=True) norm = sc.pp.normalize_total( adata, target_sum=1e6, @@ -24,10 +24,10 @@ ) lognorm = sc.pp.log1p(norm["X"]) -print(">> Store output in adata") +print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] adata.uns["normalization_id"] = meta["functionality_name"] -print(">> Write data") +print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/sqrt_cpm/script.py b/src/datasets/normalization/sqrt_cpm/script.py index f8e96952bf..f99227f3c9 100644 --- a/src/datasets/normalization/sqrt_cpm/script.py +++ b/src/datasets/normalization/sqrt_cpm/script.py @@ -13,10 +13,10 @@ } ## VIASH END -print(">> Load data") +print(">> Load data", flush=True) adata = sc.read_h5ad(par['input']) -print(">> Normalize data") +print(">> Normalize data", flush=True) norm = sc.pp.normalize_total( adata, target_sum=1e6, @@ -25,10 +25,10 @@ ) lognorm = np.sqrt(norm["X"]) -print(">> Store output in adata") +print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] adata.uns["normalization_id"] = meta["functionality_name"] -print(">> Write data") +print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index 23632da9fc..dd16f41cf1 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -12,13 +12,13 @@ } ### VIASH END -print(">> Load data") +print(">> Load data", flush=True) adata = sc.read_h5ad(par['input']) -print(">> Look for layer") +print(">> Look for layer", flush=True) layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] -print(">> Run HVG") +print(">> Run HVG", flush=True) out = sc.pp.highly_variable_genes( adata, layer=par["layer_input"], @@ -27,10 +27,10 @@ inplace=False ) -print(">> Storing output") +print(">> Storing output", flush=True) adata.var[par["var_hvg"]] = out['highly_variable'].values adata.var[par["var_hvg_score"]] = out['dispersions_norm'].values -print(">> Writing data") +print(">> Writing data", flush=True) adata.write_h5ad(par['output']) diff --git a/src/datasets/processors/knn/script.py b/src/datasets/processors/knn/script.py index d2f2f7f52b..370c8ca2a8 100644 --- a/src/datasets/processors/knn/script.py +++ b/src/datasets/processors/knn/script.py @@ -11,13 +11,13 @@ } ### VIASH END -print(">> Load data") +print(">> Load data", flush=True) adata = sc.read(par['input']) -print(">> Look for layer") +print(">> Look for layer", flush=True) adata.X = adata.layers[par['layer_input']] -print(">> Run kNN") +print(">> Run kNN", flush=True) sc.pp.neighbors( adata, use_rep='X_pca', @@ -27,6 +27,6 @@ del adata.X -print(">> Writing data") +print(">> Writing data", flush=True) adata.write_h5ad(par['output']) diff --git a/src/datasets/processors/pca/script.py b/src/datasets/processors/pca/script.py index ca0bd5ed10..ffc89c34c0 100644 --- a/src/datasets/processors/pca/script.py +++ b/src/datasets/processors/pca/script.py @@ -13,20 +13,20 @@ } ### VIASH END -print(">> Load data") +print(">> Load data", flush=True) adata = sc.read(par['input']) -print(">> Look for layer") +print(">> Look for layer", flush=True) layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] -print(">> Run PCA") +print(">> Run PCA", flush=True) X_pca, loadings, variance, variance_ratio = sc.tl.pca( layer, n_comps=par["num_components"], return_info=True ) -print(">> Storing output") +print(">> Storing output", flush=True) adata.obsm[par["obsm_embedding"]] = X_pca adata.varm[par["varm_loadings"]] = loadings.T adata.uns[par["uns_variance"]] = { @@ -34,6 +34,6 @@ "variance_ratio": variance_ratio } -print(">> Writing data") +print(">> Writing data", flush=True) adata.write_h5ad(par['output']) diff --git a/src/datasets/processors/subsample/script.py b/src/datasets/processors/subsample/script.py index a5b3102c5b..1b5d1b3992 100644 --- a/src/datasets/processors/subsample/script.py +++ b/src/datasets/processors/subsample/script.py @@ -139,7 +139,7 @@ if par["input_mod2"] is not None: del adata_output_mod2.X -print(">> Writing data") +print(">> Writing data", flush=True) adata_output.write_h5ad(par["output"]) if par["output_mod2"] is not None: adata_output_mod2.write_h5ad(par["output_mod2"]) diff --git a/src/migration/check_migration_status/test.py b/src/migration/check_migration_status/test.py index a782daece8..a202a77b98 100644 --- a/src/migration/check_migration_status/test.py +++ b/src/migration/check_migration_status/test.py @@ -13,7 +13,7 @@ "--output", output_path, ] -print(">> Running script as test") +print(">> Running script as test", flush=True) out = subprocess.run(cmd, stderr=subprocess.STDOUT) if out.stdout: @@ -23,12 +23,12 @@ print(f"script: '{cmd}' exited with an error.") exit(out.returncode) -print(">> Checking whether output file exists") +print(">> Checking whether output file exists", flush=True) assert path.exists(output_path), "Output does not exist" -print(">> Reading json file") +print(">> Reading json file", flush=True) with open(output_path, 'r') as f: out = json.load(f) print(out) -print("All checks succeeded!") +print("All checks succeeded!", flush=True) diff --git a/src/migration/list_git_shas/test.py b/src/migration/list_git_shas/test.py index d7bc42a5b0..5b8d44906a 100644 --- a/src/migration/list_git_shas/test.py +++ b/src/migration/list_git_shas/test.py @@ -11,7 +11,7 @@ "--output", output_path ] -print(">> Running script as test") +print(">> Running script as test", flush=True) out = subprocess.run(cmd, stderr=subprocess.STDOUT) if out.stdout: @@ -21,12 +21,12 @@ print(f"script: '{cmd}' exited with an error.") exit(out.returncode) -print(">> Checking whether output file exists") +print(">> Checking whether output file exists", flush=True) assert path.exists(output_path), "Output path does not exist" -print(">> Reading json file") +print(">> Reading json file", flush=True) with open(output_path, 'r') as f: out = json.load(f) print(out[0]) -print("All checks succeeded!") \ No newline at end of file +print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/tasks/denoising/control_methods/no_denoising/script.py b/src/tasks/denoising/control_methods/no_denoising/script.py index f99452c094..97c9a4184c 100644 --- a/src/tasks/denoising/control_methods/no_denoising/script.py +++ b/src/tasks/denoising/control_methods/no_denoising/script.py @@ -10,13 +10,13 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) -print("Process data") +print("Process data", flush=True) input_train.layers["denoised"] = input_train.layers['counts'] input_train.uns["method_id"] = meta['functionality_name'] -print("Write Data") +print("Write Data", flush=True) input_train.write_h5ad(par['output'],compression="gzip") diff --git a/src/tasks/denoising/control_methods/perfect_denoising/script.py b/src/tasks/denoising/control_methods/perfect_denoising/script.py index 97223c965a..c280a4a3bc 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/script.py +++ b/src/tasks/denoising/control_methods/perfect_denoising/script.py @@ -11,14 +11,14 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Process data") +print("Process data", flush=True) input_train.layers["denoised"] = input_test.layers['counts'] input_train.uns["method_id"] = meta['functionality_name'] -print("Write Data") +print("Write Data", flush=True) input_train.write_h5ad(par['output'],compression="gzip") diff --git a/src/tasks/denoising/methods/dca/script.py b/src/tasks/denoising/methods/dca/script.py index 2de2e8b236..2604f41574 100644 --- a/src/tasks/denoising/methods/dca/script.py +++ b/src/tasks/denoising/methods/dca/script.py @@ -13,19 +13,19 @@ } ## VIASH END -print("load input data") +print("load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) -print("move layer to X") +print("move layer to X", flush=True) input_train.X = input_train.layers["counts"] -print("running dca") +print("running dca", flush=True) dca(input_train, epochs=par["epochs"]) -print("moving X back to layer") +print("moving X back to layer", flush=True) input_train.layers["denoised"] = scipy.sparse.csr_matrix(input_train.X) del input_train.X -print("Writing data") +print("Writing data", flush=True) input_train.uns["method_id"] = meta["functionality_name"] input_train.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/denoising/methods/knn_smoothing/script.py b/src/tasks/denoising/methods/knn_smoothing/script.py index 7d1fca3a0f..ec65960f42 100644 --- a/src/tasks/denoising/methods/knn_smoothing/script.py +++ b/src/tasks/denoising/methods/knn_smoothing/script.py @@ -13,13 +13,13 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par["input_train"]) -print("process data") +print("process data", flush=True) X = input_train.layers["counts"].transpose().toarray() input_train.layers["denoised"] = scipy.sparse.csr_matrix((knn_smooth.knn_smoothing(X, k=10)).transpose()) -print("Writing data") +print("Writing data", flush=True) input_train.uns["method_id"] = meta["functionality_name"] input_train.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/denoising/methods/magic/script.py b/src/tasks/denoising/methods/magic/script.py index 059f5fe4a5..8f2ed4e566 100644 --- a/src/tasks/denoising/methods/magic/script.py +++ b/src/tasks/denoising/methods/magic/script.py @@ -20,7 +20,7 @@ ## VIASH END -print("load data") +print("load data", flush=True) input_train = ad.read_h5ad(par['input_train']) normtype = par['norm'] @@ -32,7 +32,7 @@ norm_fn = np.log1p denorm_fn = np.expm1 -print("processing data") +print("processing data", flush=True) X, libsize = scprep.normalize.library_size_normalize( input_train.layers['counts'], rescale=1, return_library_size=True @@ -50,6 +50,6 @@ output_denoised.uns["method_id"] = meta["functionality_name"] output_denoised.layers["denoised"] = scipy.sparse.csr_matrix(Y) -print("Writing Data") +print("Writing Data", flush=True) output_denoised.write_h5ad(par['output'],compression="gzip") diff --git a/src/tasks/denoising/metrics/mse/script.py b/src/tasks/denoising/metrics/mse/script.py index 4f217ff305..4635a8065a 100644 --- a/src/tasks/denoising/metrics/mse/script.py +++ b/src/tasks/denoising/metrics/mse/script.py @@ -15,7 +15,7 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_denoised = ad.read_h5ad(par['input_denoised']) input_test = ad.read_h5ad(par['input_test']) @@ -23,7 +23,7 @@ test_data = ad.AnnData(X=input_test.layers["counts"].toarray(), dtype="float") denoised_data = ad.AnnData( X=input_denoised.layers["denoised"].toarray(), dtype="float") -print("Normalize data") +print("Normalize data", flush=True) # scaling and transformation target_sum = 10000 @@ -34,12 +34,12 @@ sc.pp.normalize_total(denoised_data, target_sum) sc.pp.log1p(denoised_data) -print("Compute mse value") +print("Compute mse value", flush=True) error = sklearn.metrics.mean_squared_error( scprep.utils.toarray(test_data.X), denoised_data.X ) -print("Store mse value") +print("Store mse value", flush=True) output_metric = ad.AnnData( layers={}, obs=input_denoised.obs[[]], @@ -53,6 +53,6 @@ output_metric.uns["metric_ids"] = meta['functionality_name'] output_metric.uns["metric_values"] = error -print("Write adata to file") +print("Write adata to file", flush=True) output_metric.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/denoising/metrics/poisson/script.py b/src/tasks/denoising/metrics/poisson/script.py index f85c1d751b..98049825c7 100644 --- a/src/tasks/denoising/metrics/poisson/script.py +++ b/src/tasks/denoising/metrics/poisson/script.py @@ -13,14 +13,14 @@ } ## VIASH END -print("Load Data") +print("Load Data", flush=True) input_denoised = ad.read_h5ad(par['input_denoised']) input_test = ad.read_h5ad(par['input_test']) test_data = input_test.layers["counts"].toarray() denoised_data = input_denoised.layers["denoised"].toarray() -print("Compute metric value") +print("Compute metric value", flush=True) # scaling initial_sum = input_denoised.layers["counts"].sum() target_sum = test_data.sum() @@ -33,7 +33,7 @@ def poisson_nll_loss(y_pred: np.ndarray, y_true: np.ndarray) -> float: error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) -print("Store poisson value") +print("Store poisson value", flush=True) output_metric = ad.AnnData( layers={}, obs=input_denoised.obs[[]], @@ -47,5 +47,5 @@ def poisson_nll_loss(y_pred: np.ndarray, y_true: np.ndarray) -> float: output_metric.uns["metric_ids"] = meta['functionality_name'] output_metric.uns["metric_values"] = error -print("Write adata to file") +print("Write adata to file", flush=True) output_metric.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index e79a8f5074..7f097490bf 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -23,7 +23,7 @@ # set random state random_state = np.random.RandomState(par['seed']) -print(">> Load Data") +print(">> Load Data", flush=True) adata = ad.read_h5ad(par["input"]) # remove all layers except for counts @@ -34,7 +34,7 @@ # round counts and convert to int counts = np.array(adata.layers["counts"]).round().astype(int) -print(">> process and split data") +print(">> process and split data", flush=True) train_data, test_data = split_molecules( counts.data, par["train_frac"], 0.0, random_state ) @@ -66,6 +66,6 @@ output_train = output_train[:, ~is_missing.flatten()] output_test = output_test[:, ~is_missing.flatten()] -print(">> Write to file") +print(">> Write to file", flush=True) output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) diff --git a/src/tasks/dimensionality_reduction/methods/ivis/script.py b/src/tasks/dimensionality_reduction/methods/ivis/script.py index 8af3b8e242..704e56be6e 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/script.py +++ b/src/tasks/dimensionality_reduction/methods/ivis/script.py @@ -28,7 +28,7 @@ print(f"Running PCA with {par['n_pca_dims']} dimensions", flush=True) X_pca = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack")[:, :2] -print("Run ivis") +print("Run ivis", flush=True) # parameters taken from: # https://bering-ivis.readthedocs.io/en/latest/scanpy_singlecell.html#reducing-dimensionality-using-ivis ivis = Ivis( diff --git a/src/tasks/label_projection/control_methods/majority_vote/script.py b/src/tasks/label_projection/control_methods/majority_vote/script.py index 2a29fdaa80..0fc6446f0d 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/script.py +++ b/src/tasks/label_projection/control_methods/majority_vote/script.py @@ -11,16 +11,16 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Compute majority vote") +print("Compute majority vote", flush=True) majority = input_train.obs.label.value_counts().index[0] -print("Create prediction object") +print("Create prediction object", flush=True) input_test.obs["label_pred"] = majority -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/label_projection/control_methods/random_labels/script.py b/src/tasks/label_projection/control_methods/random_labels/script.py index 6733c4957d..a57a9d37f2 100644 --- a/src/tasks/label_projection/control_methods/random_labels/script.py +++ b/src/tasks/label_projection/control_methods/random_labels/script.py @@ -12,15 +12,15 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Compute label distribution") +print("Compute label distribution", flush=True) label_distribution = input_train.obs.label.value_counts() label_distribution = label_distribution / label_distribution.sum() -print("Create prediction object") +print("Create prediction object", flush=True) input_test.obs["label_pred"] = np.random.choice( label_distribution.index, size=input_test.n_obs, @@ -28,6 +28,6 @@ p=label_distribution ) -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/label_projection/control_methods/true_labels/script.py b/src/tasks/label_projection/control_methods/true_labels/script.py index b0f205b2fe..dc9354c290 100644 --- a/src/tasks/label_projection/control_methods/true_labels/script.py +++ b/src/tasks/label_projection/control_methods/true_labels/script.py @@ -12,14 +12,14 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) # input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) input_solution = ad.read_h5ad(par['input_solution']) -print("Create prediction object") +print("Create prediction object", flush=True) input_test.obs["label_pred"] = input_solution.obs["label"] -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/label_projection/methods/knn/script.py b/src/tasks/label_projection/methods/knn/script.py index e714e01736..44b8b6f4de 100644 --- a/src/tasks/label_projection/methods/knn/script.py +++ b/src/tasks/label_projection/methods/knn/script.py @@ -12,17 +12,17 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Fit to train data") +print("Fit to train data", flush=True) classifier = sklearn.neighbors.KNeighborsClassifier() classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) -print("Predict on test data") +print("Predict on test data", flush=True) input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/label_projection/methods/logistic_regression/script.py b/src/tasks/label_projection/methods/logistic_regression/script.py index 2973e7ecfd..e8796c1b75 100644 --- a/src/tasks/label_projection/methods/logistic_regression/script.py +++ b/src/tasks/label_projection/methods/logistic_regression/script.py @@ -12,17 +12,17 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Fit to train data") +print("Fit to train data", flush=True) classifier = sklearn.linear_model.LogisticRegression() classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) -print("Predict on test data") +print("Predict on test data", flush=True) input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/tasks/label_projection/methods/mlp/script.py b/src/tasks/label_projection/methods/mlp/script.py index 1a7d924b77..c98fba3954 100644 --- a/src/tasks/label_projection/methods/mlp/script.py +++ b/src/tasks/label_projection/methods/mlp/script.py @@ -12,20 +12,20 @@ } ## VIASH END -print("Load input data") +print("Load input data", flush=True) input_train = ad.read_h5ad(par['input_train']) input_test = ad.read_h5ad(par['input_test']) -print("Fit to train data") +print("Fit to train data", flush=True) classifier = MLPClassifier( max_iter=par["max_iter"], hidden_layer_sizes=tuple(par["hidden_layer_sizes"]) ) classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) -print("Predict on test data") +print("Predict on test data", flush=True) input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) -print("Write output to file") +print("Write output to file", flush=True) input_test.uns["method_id"] = meta["functionality_name"] input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file diff --git a/src/tasks/label_projection/metrics/accuracy/script.py b/src/tasks/label_projection/metrics/accuracy/script.py index e368649828..80795111d5 100644 --- a/src/tasks/label_projection/metrics/accuracy/script.py +++ b/src/tasks/label_projection/metrics/accuracy/script.py @@ -13,24 +13,24 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_prediction = ad.read_h5ad(par['input_prediction']) input_solution = ad.read_h5ad(par['input_solution']) assert (input_prediction.obs_names == input_solution.obs_names).all(), "obs_names not the same in prediction and solution inputs" -print("Encode labels") +print("Encode labels", flush=True) cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) encoder = sklearn.preprocessing.LabelEncoder().fit(cats) input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) -print("Compute prediction accuracy") +print("Compute prediction accuracy", flush=True) accuracy = np.mean(input_solution.obs["label"] == input_prediction.obs["label_pred"]) -print("Store metric value") +print("Store metric value", flush=True) input_prediction.uns["metric_ids"] = "accuracy" input_prediction.uns["metric_values"] = accuracy -print("Writing adata to file") +print("Writing adata to file", flush=True) input_prediction.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/label_projection/metrics/f1/script.py b/src/tasks/label_projection/metrics/f1/script.py index 856bdc9784..4d4b1a2395 100644 --- a/src/tasks/label_projection/metrics/f1/script.py +++ b/src/tasks/label_projection/metrics/f1/script.py @@ -14,19 +14,19 @@ } ## VIASH END -print("Load data") +print("Load data", flush=True) input_prediction = ad.read_h5ad(par['input_prediction']) input_solution = ad.read_h5ad(par['input_solution']) assert (input_prediction.obs_names == input_solution.obs_names).all(), "obs_names not the same in prediction and solution inputs" -print("Encode labels") +print("Encode labels", flush=True) cats = list(input_solution.obs["label"].dtype.categories) + list(input_prediction.obs["label_pred"].dtype.categories) encoder = sklearn.preprocessing.LabelEncoder().fit(cats) input_solution.obs["label"] = encoder.transform(input_solution.obs["label"]) input_prediction.obs["label_pred"] = encoder.transform(input_prediction.obs["label_pred"]) -print("Compute F1 score") +print("Compute F1 score", flush=True) metric_type = [ "macro", "micro", "weighted" ] metric_id = [ "f1_" + x for x in metric_type] metric_value = [ f1_score( @@ -35,9 +35,9 @@ average=x ) for x in metric_type ] -print("Store metric value") +print("Store metric value", flush=True) input_prediction.uns["metric_ids"] = metric_id input_prediction.uns["metric_values"] = metric_value -print("Writing adata to file") +print("Writing adata to file", flush=True) input_prediction.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 71584f5d4d..6f1459da86 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -29,7 +29,7 @@ print(f">> Setting seed to {par['seed']}") random.seed(par["seed"]) -print(">> Load data") +print(">> Load data", flush=True) adata = ad.read_h5ad(par["input"]) print("input:", adata) @@ -44,7 +44,7 @@ is_test = [ not x in train_ix for x in range(0, adata.n_obs) ] # subset the different adatas -print(">> Figuring which data needs to be copied to which output file") +print(">> Figuring which data needs to be copied to which output file", flush=True) # use par arguments to look for label and batch value in different slots slot_mapping = { "obs": { @@ -54,25 +54,25 @@ } slot_info = read_config_slots_info(meta["config"], slot_mapping) -print(">> Creating train data") +print(">> Creating train data", flush=True) output_train = subset_anndata( adata[[not x for x in is_test]], slot_info["output_train"] ) -print(">> Creating test data") +print(">> Creating test data", flush=True) output_test = subset_anndata( adata[is_test], slot_info["output_test"] ) -print(">> Creating solution data") +print(">> Creating solution data", flush=True) output_solution = subset_anndata( adata[is_test], slot_info['output_solution'] ) -print(">> Writing data") +print(">> Writing data", flush=True) output_train.write_h5ad(par["output_train"]) output_test.write_h5ad(par["output_test"]) output_solution.write_h5ad(par["output_solution"]) diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py b/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py index 1d0a3cdefc..ec85442fd9 100644 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py +++ b/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py @@ -1,4 +1,4 @@ -print("Importing libraries") +print("Importing libraries", flush=True) import scprep import pandas as pd import numpy as np @@ -33,14 +33,14 @@ "&format=file&file=GSM3271045%5FATAC%5Fmouse%5Fkidney%5Fpeak.txt.gz" ) -print("Downloading input files") +print("Downloading input files", flush=True) sys.stdout.flush() rna_genes = pd.read_csv(rna_genes_url, low_memory=False, index_col=0) atac_genes = pd.read_csv(atac_genes_url, low_memory=False, index_col=1) rna_cells = pd.read_csv(rna_cells_url, low_memory=False, index_col=0) atac_cells = pd.read_csv(atac_cells_url, low_memory=False, index_col=0) -print("Creating joint adata object") +print("Creating joint adata object", flush=True) keep_cells = np.intersect1d(rna_cells.index, atac_cells.index)[:200] rna_cells = rna_cells.loc[keep_cells] atac_cells = atac_cells.loc[keep_cells] @@ -57,7 +57,7 @@ Y_columns=atac_genes.index, ) -print("Merging obs and var") +print("Merging obs and var", flush=True) adata.obs = rna_cells.loc[adata.obs.index] adata.var = rna_genes for key in atac_cells.columns: @@ -75,10 +75,10 @@ adata = filter_joint_data_empty_cells(adata) -print("Subsetting dataset") +print("Subsetting dataset", flush=True) adata = subset_joint_data(adata, n_cells = par["n_cells"], n_genes = par["n_genes"]) adata.uns["dataset_id"] = "sample_dataset_test" -print("Writing adata to file") +print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py b/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py index 48cf0d26a9..43d47be23e 100644 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py +++ b/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py @@ -6,16 +6,16 @@ import pandas import numpy as np -print(">> Running sample_dataset") +print(">> Running sample_dataset", flush=True) out = subprocess.check_output([ "./sample_dataset", "--output", "output.h5ad" ]).decode("utf-8") -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns @@ -26,7 +26,7 @@ # check dataset id assert "dataset_id" in adata.uns -print(">> Running sample_dataset with different args") +print(">> Running sample_dataset with different args", flush=True) out = subprocess.run([ "./sample_dataset", "--output", "output.h5ad", @@ -41,10 +41,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns @@ -60,4 +60,4 @@ -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py b/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py index c6d4fef450..1ad363d1b7 100644 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py +++ b/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py @@ -12,7 +12,7 @@ resources_dir = "../../utils/" ## VIASH END -print("Importing libraries") +print("Importing libraries", flush=True) import scprep # adding resources dir to system path @@ -26,7 +26,7 @@ from utils import filter_joint_data_empty_cells from utils import subset_joint_data -print("Downloading expression datasets from GEO (this might take a while)") +print("Downloading expression datasets from GEO (this might take a while)", flush=True) sys.stdout.flush() # par["input1"] can be the path to a local file, or a url @@ -37,16 +37,16 @@ par["input2"], cell_axis="col", compression=par["compression"], sparse=True, chunksize=1000 ) -print("Transforming into adata") +print("Transforming into adata", flush=True) adata = create_joint_adata(adata1, adata2) adata = filter_joint_data_empty_cells(adata) adata.uns["dataset_id"] = par["id"] if par["test"]: - print("Subsetting dataset") + print("Subsetting dataset", flush=True) adata = subset_joint_data(adata) adata.uns["dataset_id"] = par["id"] + "_test" -print("Writing adata to file") +print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py b/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py index 34239ee5fa..c9776ca640 100644 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py +++ b/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py @@ -8,11 +8,11 @@ import urllib.request -print(">> Downloading input file") +print(">> Downloading input file", flush=True) # need to download file manually for now; viash docker platform tries to auto-mount them urllib.request.urlretrieve("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100866/suppl/GSE100866%5FCD8%5Fmerged%2DADT%5Fumi%2Ecsv%2Egz", "adt_umi.csv.gz") -print(">> Running scprep_csv") +print(">> Running scprep_csv", flush=True) out = subprocess.run([ "./scprep_csv", @@ -29,10 +29,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "mode2" in adata.obsm assert "mode2_obs" in adata.uns @@ -47,4 +47,4 @@ assert "dataset_id" in adata.uns assert adata.uns["dataset_id"] == "footest" -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py index 5ae4c08db2..4a0de1d6c1 100644 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py +++ b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py @@ -1,4 +1,4 @@ -print("Loading dependencies") +print("Loading dependencies", flush=True) import scanpy as sc import harmonicalignment import sklearn.decomposition @@ -20,10 +20,10 @@ from preprocessing import log_cpm from preprocessing import sqrt_cpm -print("Reading input h5ad file") +print("Reading input h5ad file", flush=True) adata = sc.read_h5ad(par["input"]) -print("Check parameters") +print("Check parameters", flush=True) n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) n_eigenvectors = par["n_eigenvectors"] n_pca_XY = par["n_pca_XY"] @@ -33,27 +33,27 @@ if adata.X.shape[0] <= n_pca_XY: n_pca_XY = None -print("Normalising mode 1") +print("Normalising mode 1", flush=True) sqrt_cpm(adata) -print("Normalising mode 2") +print("Normalising mode 2", flush=True) log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") -print("Performing PCA reduction") +print("Performing PCA reduction", flush=True) X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) -print("Running Harmonic Alignment") +print("Running Harmonic Alignment", flush=True) ha_op = harmonicalignment.HarmonicAlignment( n_filters=8, n_pca_XY=n_pca_XY, n_eigenvectors=n_eigenvectors ) ha_op.align(X_pca, Y_pca) XY_aligned = ha_op.diffusion_map(n_eigenvectors=n_eigenvectors) -print("Storing output data structures") +print("Storing output data structures", flush=True) adata.obsm["aligned"] = XY_aligned[: X_pca.shape[0]] adata.obsm["mode2_aligned"] = XY_aligned[X_pca.shape[0] :] -print("Write output to file") +print("Write output to file", flush=True) adata.uns["method_id"] = "harmonic_alignment" adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py index bd4546076d..9fbdd0f68d 100644 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py +++ b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py @@ -4,7 +4,7 @@ import scanpy as sc -print(">> Running harmonic_alignment") +print(">> Running harmonic_alignment", flush=True) out = subprocess.run([ "./harmonic_alignment", "--input", "sample_dataset.h5ad", @@ -18,10 +18,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm @@ -34,4 +34,4 @@ assert "method_id" in adata.uns assert adata.uns["method_id"] == "harmonic_alignment" -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/mnn/test.py b/src/tasks/multimodal_data_integration/methods/mnn/test.py index cc8f323e4d..0549eceaed 100644 --- a/src/tasks/multimodal_data_integration/methods/mnn/test.py +++ b/src/tasks/multimodal_data_integration/methods/mnn/test.py @@ -4,7 +4,7 @@ import scanpy as sc -print(">> Running mnn") +print(">> Running mnn", flush=True) out = subprocess.run([ "./mnn", "--input", "sample_dataset.h5ad", @@ -18,10 +18,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm @@ -34,4 +34,4 @@ assert "method_id" in adata.uns assert adata.uns["method_id"] == "mnn" -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/script.py b/src/tasks/multimodal_data_integration/methods/sample_method/script.py index c9d8d6d35d..9e973ea262 100644 --- a/src/tasks/multimodal_data_integration/methods/sample_method/script.py +++ b/src/tasks/multimodal_data_integration/methods/sample_method/script.py @@ -1,15 +1,15 @@ -print("Loading dependencies") +print("Loading dependencies", flush=True) import scanpy as sc import numpy as np -print("Reading input h5ad file") +print("Reading input h5ad file", flush=True) adata = sc.read_h5ad(par["input"]) -print("Check parameters") +print("Check parameters", flush=True) new_shape = (adata.X.shape[0], 10) adata.obsm["aligned"] = np.random.normal(0, 0.1, new_shape) adata.obsm["mode2_aligned"] = np.random.normal(0, 0.1, new_shape) -print("Write output to file") +print("Write output to file", flush=True) adata.uns["method_id"] = "sample_method" adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/test.py b/src/tasks/multimodal_data_integration/methods/sample_method/test.py index 441788774c..496d910651 100644 --- a/src/tasks/multimodal_data_integration/methods/sample_method/test.py +++ b/src/tasks/multimodal_data_integration/methods/sample_method/test.py @@ -4,7 +4,7 @@ import scanpy as sc -print(">> Running sample_method") +print(">> Running sample_method", flush=True) out = subprocess.run([ "./sample_method", "--input", "sample_dataset.h5ad", @@ -18,10 +18,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that dataset fits expected API") +print(">> Check that dataset fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm @@ -34,4 +34,4 @@ assert "method_id" in adata.uns assert adata.uns["method_id"] == "sample_method" -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/scot/script.py b/src/tasks/multimodal_data_integration/methods/scot/script.py index 1427ea9f4f..3d815a07f7 100644 --- a/src/tasks/multimodal_data_integration/methods/scot/script.py +++ b/src/tasks/multimodal_data_integration/methods/scot/script.py @@ -8,7 +8,7 @@ resources_dir = "../../utils/" ## VIASH END -print("Loading dependencies") +print("Loading dependencies", flush=True) import scanpy as sc import sklearn.decomposition from SCOT import SCOT @@ -20,25 +20,25 @@ from preprocessing import sqrt_cpm -print("Reading input h5ad file") +print("Reading input h5ad file", flush=True) adata = sc.read_h5ad(par["input"]) -print("Normalising mode 1") +print("Normalising mode 1", flush=True) sqrt_cpm(adata) -print("Normalising mode 2") +print("Normalising mode 2", flush=True) log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") -print("Performing PCA reduction") +print("Performing PCA reduction", flush=True) n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) -print("Initialize SCOT") +print("Initialize SCOT", flush=True) scot = SCOT(X_pca, Y_pca) -print("Call the unbalanced alignment") +print("Call the unbalanced alignment", flush=True) # From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 X_new_unbal, y_new_unbal = scot.align( k=50, e=1e-3, rho=0.0005, normalize=True, balanced=par["balanced"] @@ -48,6 +48,6 @@ adata.obsm["aligned"] = X_new_unbal adata.obsm["mode2_aligned"] = y_new_unbal -print("Write output to file") +print("Write output to file", flush=True) adata.uns["method_id"] = "scot" adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/scot/test.py b/src/tasks/multimodal_data_integration/methods/scot/test.py index 9d13e54dfb..be4299104f 100644 --- a/src/tasks/multimodal_data_integration/methods/scot/test.py +++ b/src/tasks/multimodal_data_integration/methods/scot/test.py @@ -4,7 +4,7 @@ import scanpy as sc -print(">> Running scot") +print(">> Running scot", flush=True) out = subprocess.run([ "./scot", "--input", "sample_dataset.h5ad", @@ -18,10 +18,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") assert "aligned" in adata.obsm @@ -34,4 +34,4 @@ assert "method_id" in adata.uns assert adata.uns["method_id"] == "scot" -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py b/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py index 8625d9ae1b..cb7b05ad58 100644 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py +++ b/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py @@ -9,37 +9,37 @@ } ## VIASH END -print("Importing libraries") +print("Importing libraries", flush=True) import anndata import numpy as np import sklearn.decomposition import sklearn.neighbors -print("Reading adata file") +print("Reading adata file", flush=True) adata = anndata.read_h5ad(par["input"]) -print("Checking parameters") +print("Checking parameters", flush=True) n_svd = min([par["n_svd"], min(adata.X.shape) - 1]) n_neighbors = int(np.ceil(par["proportion_neighbors"] * adata.X.shape[0])) -print("Performing PCA") +print("Performing PCA", flush=True) X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) -print("Compute KNN on PCA") +print("Compute KNN on PCA", flush=True) _, indices_true = ( sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) .fit(X_pca) .kneighbors(X_pca) ) -print("Compute KNN on aligned matrix") +print("Compute KNN on aligned matrix", flush=True) _, indices_pred = ( sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) .fit(adata.obsm["aligned"]) .kneighbors(adata.obsm["mode2_aligned"]) ) -print("Check which neighbours match") +print("Check which neighbours match", flush=True) neighbors_match = np.zeros(n_neighbors, dtype=int) for i in range(adata.shape[0]): _, pred_matches, true_matches = np.intersect1d( @@ -51,15 +51,15 @@ axis=0, ) -print("Compute area under neighbours match curve") +print("Compute area under neighbours match curve", flush=True) neighbors_match_curve = neighbors_match / ( np.arange(1, n_neighbors + 1) * adata.shape[0] ) area_under_curve = np.mean(neighbors_match_curve) -print("Store metic value") +print("Store metic value", flush=True) adata.uns["metric_id"] = "knn_auc" adata.uns["metric_value"] = area_under_curve -print("Writing adata to file") +print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py b/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py index fe64c05c7c..f51fa6752a 100644 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py +++ b/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py @@ -5,7 +5,7 @@ import scanpy as sc import numpy as np -print(">> Running knn_auc") +print(">> Running knn_auc", flush=True) out = subprocess.run([ "./knn_auc", "--input", "sample_output.h5ad", @@ -19,10 +19,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that dataset fits expected API") +print(">> Check that dataset fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") # check id @@ -31,4 +31,4 @@ assert "metric_value" in adata.uns assert type(adata.uns["metric_value"]) is np.float64 -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/metrics/mse/script.py b/src/tasks/multimodal_data_integration/metrics/mse/script.py index c17058f6f0..e79320a8ed 100644 --- a/src/tasks/multimodal_data_integration/metrics/mse/script.py +++ b/src/tasks/multimodal_data_integration/metrics/mse/script.py @@ -7,16 +7,16 @@ } ## VIASH END -print("Importing libraries") +print("Importing libraries", flush=True) import anndata import scprep import numpy as np from scipy import sparse -print("Reading adata file") +print("Reading adata file", flush=True) adata = anndata.read_h5ad(par["input"]) -print("Computing MSE") +print("Computing MSE", flush=True) def _square(X): if sparse.issparse(X): X.data = X.data ** 2 @@ -32,9 +32,9 @@ def _square(X): error_abs = np.mean(np.sum(_square(X - Y))) metric_value = error_abs / error_random -print("Store metic value") +print("Store metic value", flush=True) adata.uns["metric_id"] = "mse" adata.uns["metric_value"] = metric_value -print("Writing adata to file") +print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/metrics/mse/test.py b/src/tasks/multimodal_data_integration/metrics/mse/test.py index 557e72537f..19ce0b1fea 100644 --- a/src/tasks/multimodal_data_integration/metrics/mse/test.py +++ b/src/tasks/multimodal_data_integration/metrics/mse/test.py @@ -5,7 +5,7 @@ import scanpy as sc import numpy as np -print(">> Running mse") +print(">> Running mse", flush=True) out = subprocess.run([ "./mse", "--input", "sample_output.h5ad", @@ -19,10 +19,10 @@ print(f"script: '{out.args}' exited with an error.") exit(out.returncode) -print(">> Checking whether file exists") +print(">> Checking whether file exists", flush=True) assert path.exists("output.h5ad") -print(">> Check that output fits expected API") +print(">> Check that output fits expected API", flush=True) adata = sc.read_h5ad("output.h5ad") # check id @@ -31,4 +31,4 @@ assert "metric_value" in adata.uns assert type(adata.uns["metric_value"]) is np.float64 -print(">> All tests passed successfully") +print(">> All tests passed successfully", flush=True) From 55e5ca389d52749c6128bf17230e166935f8fb90 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 25 Aug 2023 12:04:11 +0200 Subject: [PATCH 0981/1233] fix unit test Former-commit-id: 19ee4d855eda16a011abbbad8b61672516bf4eae --- src/datasets/processors/subsample/test_script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/datasets/processors/subsample/test_script.py b/src/datasets/processors/subsample/test_script.py index a2e27d29a1..44ff8cac69 100644 --- a/src/datasets/processors/subsample/test_script.py +++ b/src/datasets/processors/subsample/test_script.py @@ -38,7 +38,7 @@ def test_keep_functionality(run_component): # keep_features = list(input.var_names[:10]) # use genes with high enough expression - keep_features = ["ANP32E", "CBX5", "HMGB2", "MAPK13"] + keep_features = ["ANP32E", "CBX5", "HMGB2"] run_component([ "--input", input_path, From 1bdeb6170c4d0e4654ee315446954c3ce5c8d142 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 25 Aug 2023 12:39:38 +0200 Subject: [PATCH 0982/1233] Update/integrate last v1 changes (#214) * update migration scripts * update batch_int * update bat_int clus_overlap * update denoising * add cp10k norm * update schema * update label_projection * [WIP] spectral_features new control_method * add diffusion map method * update dim_red spectral_feature and diffu_map * update dim_red * generalise cp normalization * CPM -> CP10k * fix failing test * fix typo * update and rename rmse to distance correlation * set CP normalization from cpm to cp10k * fix typo cpm to cp * updated changelog --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 12f54cfbbfacafc618ac09dee819001308e8858c --- CHANGELOG.md | 8 +- src/common/comp_tests/check_method_config.py | 2 +- src/common/create_component/script.py | 2 +- src/common/schemas/defs_common.yaml | 2 +- .../normalization/log_cp/config.vsh.yaml | 22 ++++++ .../{log_cpm => log_cp}/script.py | 11 +-- .../normalization/log_cpm/config.vsh.yaml | 13 ---- .../{sqrt_cpm => sqrt_cp}/config.vsh.yaml | 11 ++- .../{sqrt_cpm => sqrt_cp}/script.py | 9 ++- src/datasets/processors/pca/script.py | 2 +- .../resource_test_scripts/multimodal.sh | 4 +- .../resource_test_scripts/pancreas.sh | 4 +- .../workflows/process_openproblems_v1/main.nf | 8 +- src/migration/check_migration.sh | 14 ++++ .../check_migration_status/script.py | 16 +++- .../no_integration_batch/config.vsh.yaml | 2 +- .../random_embed_cell/config.vsh.yaml | 2 +- .../random_embed_cell_jitter/config.vsh.yaml | 2 +- .../random_integration/config.vsh.yaml | 2 +- .../methods/bbknn/config.vsh.yaml | 6 +- .../methods/combat/config.vsh.yaml | 6 +- .../methods/fastmnn/config.vsh.yaml | 2 +- .../methods/mnn_correct/config.vsh.yaml | 2 +- .../methods/mnnpy/config.vsh.yaml | 4 +- .../methods/scanorama_embed/config.vsh.yaml | 6 +- .../methods/scanorama_feature/config.vsh.yaml | 6 +- .../methods/scanvi/config.vsh.yaml | 2 +- .../methods/scvi/config.vsh.yaml | 4 +- .../metrics/asw_batch/config.vsh.yaml | 2 +- .../metrics/asw_label/config.vsh.yaml | 2 +- .../cell_cycle_conservation/config.vsh.yaml | 2 +- .../clustering_overlap/config.vsh.yaml | 4 +- .../metrics/pcr/config.vsh.yaml | 2 +- .../batch_integration/workflows/run/main.nf | 2 +- .../no_denoising/config.vsh.yaml | 2 +- .../perfect_denoising/config.vsh.yaml | 2 +- .../denoising/methods/alra/config.vsh.yaml | 2 +- .../denoising/methods/dca/config.vsh.yaml | 2 +- .../methods/knn_smoothing/config.vsh.yaml | 2 +- .../denoising/methods/magic/config.vsh.yaml | 4 +- .../denoising/metrics/mse/config.vsh.yaml | 4 +- .../denoising/metrics/poisson/config.vsh.yaml | 5 +- src/tasks/denoising/workflows/run/main.nf | 2 +- src/tasks/denoising/workflows/run/run_test.sh | 2 +- .../workflows/run/run_test_on_tower.sh | 2 +- .../random_features/config.vsh.yaml | 2 +- .../spectral_features/config.vsh.yaml | 41 ++++++++++ .../true_features/config.vsh.yaml | 23 +----- .../control_methods/true_features/script.py | 12 +-- .../methods/densmap/config.vsh.yaml | 12 +-- .../methods/diffusion_map/config.vsh.yaml | 44 +++++++++++ .../methods/diffusion_map/script.py | 77 +++++++++++++++++++ .../methods/ivis/config.vsh.yaml | 4 +- .../methods/neuralee/config.vsh.yaml | 6 +- .../methods/pca/config.vsh.yaml | 8 +- .../methods/phate/config.vsh.yaml | 12 +-- .../methods/tsne/config.vsh.yaml | 8 +- .../methods/umap/config.vsh.yaml | 10 +-- .../metrics/coranking/config.vsh.yaml | 14 ++-- .../metrics/coranking/library.bib | 62 --------------- .../density_preservation/config.vsh.yaml | 11 ++- .../metrics/density_preservation/script.py | 25 +++--- .../distance_correlation/config.vsh.yaml | 49 ++++++++++++ .../{rmse => distance_correlation}/script.py | 23 +++--- .../metrics/rmse/config.vsh.yaml | 45 ----------- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../resources_test_scripts/pancreas.sh | 4 +- .../workflows/run/main.nf | 2 +- .../workflows/run/run_test.sh | 2 +- .../workflows/run/run_test_on_tower.sh | 2 +- .../majority_vote/config.vsh.yaml | 2 +- .../random_labels/config.vsh.yaml | 2 +- .../true_labels/config.vsh.yaml | 2 +- .../methods/knn/config.vsh.yaml | 6 +- .../logistic_regression/config.vsh.yaml | 6 +- .../methods/mlp/config.vsh.yaml | 6 +- .../methods/scanvi/config.vsh.yaml | 4 +- .../methods/scanvi_scarches/config.vsh.yaml | 4 + .../seurat_transferdata/config.vsh.yaml | 4 +- .../methods/xgboost/config.vsh.yaml | 6 +- .../metrics/accuracy/config.vsh.yaml | 2 +- .../metrics/f1/config.vsh.yaml | 6 +- .../resources_test_scripts/pancreas.sh | 4 +- .../label_projection/workflows/run/main.nf | 2 +- .../workflows/run/run_test.sh | 2 +- .../workflows/run/run_test_on_tower.sh | 2 +- 86 files changed, 455 insertions(+), 322 deletions(-) create mode 100644 src/datasets/normalization/log_cp/config.vsh.yaml rename src/datasets/normalization/{log_cpm => log_cp}/script.py (73%) delete mode 100644 src/datasets/normalization/log_cpm/config.vsh.yaml rename src/datasets/normalization/{sqrt_cpm => sqrt_cp}/config.vsh.yaml (52%) rename src/datasets/normalization/{sqrt_cpm => sqrt_cp}/script.py (80%) create mode 100644 src/migration/check_migration.sh create mode 100644 src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/methods/diffusion_map/script.py delete mode 100644 src/tasks/dimensionality_reduction/metrics/coranking/library.bib create mode 100644 src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml rename src/tasks/dimensionality_reduction/metrics/{rmse => distance_correlation}/script.py (70%) delete mode 100644 src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml diff --git a/CHANGELOG.md b/CHANGELOG.md index c63820536b..4c84ff9790 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ ## general +### NEW FUNCTIONALITY + +* Updated all current tasks in v2 to latest changes in OP v1 (PR #214) + ### MAJOR CHANGES * Relocate task directories to new `src/tasks/` location (PR #142). @@ -11,6 +15,8 @@ and `ghcr.io/openproblems-bio/base-r` (PR #168). * Update batch integration docker images to OpenProblems base images (PR #171). + +* Changed default normalization CPM to CP10k (PR #214) ### MINOR CHANGES @@ -274,7 +280,7 @@ * `methods/neuralee`: Migrated from v1. -* `metrics/rmse`: Migrated from v1, but will likely be removed. +* `metrics/distance_correlation`: Migrated from v1, but will likely be removed. * `metrics/trustworthiness`: Migrated from v1, but will likely be removed. diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index ecbb2dbaf2..61a2bf0f6f 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -98,7 +98,7 @@ def search_ref_bib(reference): assert arg_id in arg_names, f"Argument '{arg_id}' in `.functionality.info.variants['{paramset_id}']` is not an argument in `.functionality.arguments`." assert "preferred_normalization" in info, "preferred_normalization not an info field" -norm_methods = ["log_cpm", "counts", "log_scran_pooling", "sqrt_cpm", "l1_sqrt"] +norm_methods = ["log_cpm", "log_cp10k", "counts", "log_scran_pooling", "sqrt_cpm", "sqrt_cp10k", "l1_sqrt"] assert info["preferred_normalization"] in norm_methods, "info['preferred_normalization'] not one of '" + "', '".join(norm_methods) + "'." diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 1bc6d97cc5..1c7de0010c 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -80,7 +80,7 @@ def generate_info(par, component_type, pretty_name) -> str: | description: | | FILL IN: A (multi-line) description of how this method works. | # Which normalisation method this component prefers to use (required). - | preferred_normalization: log_cpm + | preferred_normalization: log_cp10k |''') if component_type == "method": str += strip_margin(f'''\ diff --git a/src/common/schemas/defs_common.yaml b/src/common/schemas/defs_common.yaml index 0032c0e1c6..a069d5cc35 100644 --- a/src/common/schemas/defs_common.yaml +++ b/src/common/schemas/defs_common.yaml @@ -59,7 +59,7 @@ definitions: required: [ type ] additionalProperties: false PreferredNormalization: - enum: [l1_sqrt, log_cpm, log_scran_pooling, sqrt_cpm, counts] + enum: [l1_sqrt, log_cpm, log_cp10k, log_scran_pooling, sqrt_cpm, sqrt_cp10k, counts] description: | Which normalization method a component prefers. diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml new file mode 100644 index 0000000000..4d1770f2c4 --- /dev/null +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -0,0 +1,22 @@ +__merge__: ../../api/comp_normalization.yaml +functionality: + name: "log_cp" + description: "Normalize data using Log CP" + resources: + - type: python_script + path: script.py + arguments: + - name: "--n_cp" + type: integer + default: 1e4 + description: "Number of counts per cell" + - name: "--norm_id" + type: string + default: log_cp10k + description: "normalization ID to use e.g. 1e6 -> log_cpm, 1e4 -> log_cp10k" +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_cpm/script.py b/src/datasets/normalization/log_cp/script.py similarity index 73% rename from src/datasets/normalization/log_cpm/script.py rename to src/datasets/normalization/log_cp/script.py index 6a28cbcc22..0fadc2ffe4 100644 --- a/src/datasets/normalization/log_cpm/script.py +++ b/src/datasets/normalization/log_cp/script.py @@ -4,11 +4,12 @@ par = { 'input': "resources_test/common/pancreas/dataset.h5ad", 'output': "output.h5ad", - 'layer_output': "log_cpm", - 'obs_size_factors': "log_cpm_size_factors" + 'layer_output': "log_cp10k", + 'obs_size_factors': "log_cp10k_size_factors", + 'n_cp': 1e6, } meta = { - "functionality_name": "normalize_log_cpm" + "functionality_name": "normalize_log_cp10k" } ## VIASH END @@ -18,7 +19,7 @@ print(">> Normalize data", flush=True) norm = sc.pp.normalize_total( adata, - target_sum=1e6, + target_sum=par["n_cp"], layer="counts", inplace=False ) @@ -27,7 +28,7 @@ print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = meta["functionality_name"] +adata.uns["normalization_id"] = par["norm_id"] print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_cpm/config.vsh.yaml b/src/datasets/normalization/log_cpm/config.vsh.yaml deleted file mode 100644 index 631bdbae10..0000000000 --- a/src/datasets/normalization/log_cpm/config.vsh.yaml +++ /dev/null @@ -1,13 +0,0 @@ -__merge__: ../../api/comp_normalization.yaml -functionality: - name: "log_cpm" - description: "Normalize data using Log CPM" - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 - - type: nextflow - directives: - label: [ lowmem, lowcpu ] diff --git a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml similarity index 52% rename from src/datasets/normalization/sqrt_cpm/config.vsh.yaml rename to src/datasets/normalization/sqrt_cp/config.vsh.yaml index dcf0b36b64..a347ec01d0 100644 --- a/src/datasets/normalization/sqrt_cpm/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -1,10 +1,19 @@ __merge__: ../../api/comp_normalization.yaml functionality: - name: "sqrt_cpm" + name: "sqrt_cp" description: "Normalize data using Log Sqrt" resources: - type: python_script path: script.py + arguments: + - name: "--n_cp" + type: integer + default: 1e4 + description: "Number of counts per cell" + - name: "--norm_id" + type: string + default: sqrt_cp10k + description: "normalization id to use e.g. 1e4 -> sqrt_cp10k, 1e6 -> sqrt_cpm" platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 diff --git a/src/datasets/normalization/sqrt_cpm/script.py b/src/datasets/normalization/sqrt_cp/script.py similarity index 80% rename from src/datasets/normalization/sqrt_cpm/script.py rename to src/datasets/normalization/sqrt_cp/script.py index f99227f3c9..af30b56083 100644 --- a/src/datasets/normalization/sqrt_cpm/script.py +++ b/src/datasets/normalization/sqrt_cp/script.py @@ -6,7 +6,8 @@ 'input': "resources_test/common/pancreas/dataset.h5ad", 'output': "output.h5ad", 'layer_output': "sqrt_cpm", - 'obs_size_factors': "size_factors_sqrt_cpm" + 'obs_size_factors': "size_factors_sqrt_cpm", + 'n_cp': 1e6, } meta = { "functionality_name": "normalize_sqrt_cpm" @@ -19,16 +20,16 @@ print(">> Normalize data", flush=True) norm = sc.pp.normalize_total( adata, - target_sum=1e6, + target_sum=par['n_cp'], layer="counts", inplace=False ) -lognorm = np.sqrt(norm["X"]) +lognorm = np.sqrt(norm['X']) print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = meta["functionality_name"] +adata.uns["normalization_id"] = par["norm_id"] print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/processors/pca/script.py b/src/datasets/processors/pca/script.py index ffc89c34c0..0990b97374 100644 --- a/src/datasets/processors/pca/script.py +++ b/src/datasets/processors/pca/script.py @@ -4,7 +4,7 @@ ### VIASH START par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'layer_input': 'log_cpm', + 'layer_input': 'log_cp10k', 'output': 'dataset.h5ad', 'obsm_embedding': 'X_pca', 'varm_loadings': 'pca_loadings', diff --git a/src/datasets/resource_test_scripts/multimodal.sh b/src/datasets/resource_test_scripts/multimodal.sh index fe0e9c472b..364efbf3ad 100644 --- a/src/datasets/resource_test_scripts/multimodal.sh +++ b/src/datasets/resource_test_scripts/multimodal.sh @@ -43,12 +43,12 @@ viash run src/datasets/processors/subsample/config.vsh.yaml -- \ # run sqrt cpm normalisation on mod 1 file -viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ +viash run src/datasets/normalization/sqrt_cp/config.vsh.yaml -- \ --input $DATASET_DIR/raw_mod1.h5ad \ --output $DATASET_DIR/normalized_mod1.h5ad # run log cpm normalisation on mod 2 file -viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ +viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ --input $DATASET_DIR/raw_mod2.h5ad \ --output $DATASET_DIR/normalized_mod2.h5ad diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index e78f738649..9a49f7c7de 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -42,8 +42,8 @@ viash run src/datasets/processors/subsample/config.vsh.yaml -- \ --output $DATASET_DIR/raw.h5ad \ --seed 123 -# run log cpm normalisation -viash run src/datasets/normalization/log_cpm/config.vsh.yaml -- \ +# run log cp10k normalisation +viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ --input $DATASET_DIR/raw.h5ad \ --output $DATASET_DIR/normalized.h5ad diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index aa6e0f4243..dfca3e8b49 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -7,9 +7,9 @@ targetDir = params.rootDir + "/target/nextflow" include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/main.nf" // normalization methods -include { log_cpm } from "$targetDir/datasets/normalization/log_cpm/main.nf" +include { log_cpm } from "$targetDir/datasets/normalization/log_cp/main.nf" include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" -include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cpm/main.nf" +include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" // dataset processors @@ -27,8 +27,8 @@ config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initialize_tracer() -// normalization_methods = [log_cpm, log_scran_pooling, sqrt_cpm, l1_sqrt -normalization_methods = [log_cpm, sqrt_cpm, l1_sqrt] +// normalization_methods = [log_cp, log_scran_pooling, sqrt_cp, l1_sqrt +normalization_methods = [log_cp, sqrt_cp, l1_sqrt] workflow { helpMessage(config) diff --git a/src/migration/check_migration.sh b/src/migration/check_migration.sh new file mode 100644 index 0000000000..1ce39634f2 --- /dev/null +++ b/src/migration/check_migration.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +# viash run src/common/get_git_sha/config.vsh.yaml -p native -- --input /home/kai/Documents/openroblems/openproblems --output output/op_git_sha.json + +TASK_IDS=`ls src/tasks` + +for task_id in $TASK_IDS; do + echo ">> Processing $task_id" + viash run src/common/get_method_info/config.vsh.yaml -- --input . --task_id $task_id --output output/${task_id}_method.json + viash run src/migration/check_migration_status/config.vsh.yaml -p native -- --git_sha resources_test/input_git_sha.json --comp_info output/${task_id}_method.json --output output/${task_id}_method_status.json + viash run src/common/get_metric_info/config.vsh.yaml -- --input . --task_id $task_id --output output/${task_id}_metric.json + viash run src/migration/check_migration_status/config.vsh.yaml -p native -- --git_sha resources_test/input_git_sha.json --comp_info output/${task_id}_metric.json --output output/${task_id}_metric_status.json + +done \ No newline at end of file diff --git a/src/migration/check_migration_status/script.py b/src/migration/check_migration_status/script.py index 86d0a2ba46..6e88b2d9ed 100644 --- a/src/migration/check_migration_status/script.py +++ b/src/migration/check_migration_status/script.py @@ -3,9 +3,9 @@ ## VIASH START par = { - 'git_sha': 'temp/openproblems-v1.json', - 'comp_info': 'temp/denoising_metrics.json', - 'output': 'temp/migration_status.json' + 'git_sha': 'resources_test/input_git_sha.json', + 'comp_info': 'output/denoising_metric.json', + 'output': 'output/denoising_metric_status.json' } ## VIASH END @@ -16,10 +16,18 @@ def check_status(comp_item: List[Dict[str, str]], git_objects: List[Dict[str, st git_object["sha"].""" v1_path = comp_item.get("v1", {}).get("path") + + if "metric_id" in comp_item: + v1_path = comp_item.get("v1.path") + if not v1_path: return "v1.path missing" v1_commit = comp_item.get("v1", {}).get("commit") + + if "metric_id" in comp_item: + v1_commit = comp_item.get("v1.commit") + if not v1_commit: return "v1.commit missing" @@ -28,7 +36,7 @@ def check_status(comp_item: List[Dict[str, str]], git_objects: List[Dict[str, st return "v1.path does not exist in git repo" git_sha = git_object[0]["sha"] - if git_sha == comp_item["v1_commit"]: + if git_sha == v1_commit: return "up to date" else: return f"out of date (sha: {git_sha})" diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index da3013e908..b57dbb1cf9 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index f6f6e89a56..a4ea2c49b8 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index 3e4a0fc924..faf4c6f702 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k arguments: - name: "--jitter" type: double diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index a9e0884ca5..9b43f82aea 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 129bac5cbf..742616c743 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -15,12 +15,12 @@ functionality: documentation_url: "https://github.com/Teichlab/bbknn#readme" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/bbknn.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: bbknn_full_unscaled: bbknn_full_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 4e01dfb1ec..0314e42438 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -18,12 +18,12 @@ functionality: documentation_url: "https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.combat.html" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/combat.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: combat_full_unscaled: combat_full_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml index a20640b119..b1ea4bec9e 100644 --- a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: reference: "haghverdi2018batch" repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: r_script path: script.R diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 12c3b5ef52..15f30ec456 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: reference: "haghverdi2018batch" repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: r_script path: script.R diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index 47123c7372..5fdf1f0a8b 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -17,11 +17,11 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/mnn.py commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: mnn_full_unscaled: mnn_full_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index ae4de238f1..654e8c6e25 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -13,12 +13,12 @@ functionality: documentation_url: "https://github.com/brianhie/scanorama#readme" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: scanorama_embed_full_unscaled: scanorama_embed_full_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 43b5e10062..b144b0e788 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -13,12 +13,12 @@ functionality: documentation_url: "https://github.com/brianhie/scanorama#readme" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanorama.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: scanorama_feature_full_unscaled: scanorama_feature_full_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 82f75714b8..41182a651c 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: scanvi_full_unscaled: resources: diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 75f1bcf6e5..d1bf368aa8 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -12,8 +12,8 @@ functionality: documentation_url: "https://github.com/YosefLab/scvi-tools#readme" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: scvi_full_unscaled: resources: diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index dbf6d97f4d..f265b058d8 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: maximize: true v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/sil_batch.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 50435d3ce6..6a5babce30 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: maximize: true v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/silhouette.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 95fb0804d4..69849dfc4b 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: maximize: true v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/cc_score.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 9e6558df6a..98ed7e3662 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: maximize: true v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/ari.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - name: nmi label: NMI summary: "NMI compares overlap by scaling using mean entropy terms and optimizing Louvain clustering to obtain the best match between clusters and labels." @@ -43,7 +43,7 @@ functionality: maximize: true v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/metrics/nmi.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 68704855a0..b043c2cd47 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: reference: luecken2022benchmarking v1: path: openproblems/tasks/_batch_integration/batch_integration_embed/metrics/pcr.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 min: 0 max: 1 maximize: true diff --git a/src/tasks/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run/main.nf index d79e51a705..942878fd94 100644 --- a/src/tasks/batch_integration/workflows/run/main.nf +++ b/src/tasks/batch_integration/workflows/run/main.nf @@ -117,7 +117,7 @@ workflow run_wf { def pref = config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cpm" && pref == "counts") || norm == pref + (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index f5267b9a22..f03199ab17 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "This method serves as a negative control, where the denoised data is a copy of the unaltered training data. This represents the scoring threshold if denoising was not performed on the data." v1: path: openproblems/tasks/denoising/methods/baseline.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: no_denoising: preferred_normalization: counts diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index b4d7f84cfe..27fcfa6953 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "This method serves as a positive control, where the test data is copied 1-to-1 to the denoised data. This makes it seem as if the data is perfectly denoised as it will be compared to the test data in the metrics." v1: path: openproblems/tasks/denoising/methods/baseline.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: perfect_denoising: preferred_normalization: counts diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 96bf990a7d..82398c806d 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: documentation_url: https://github.com/KlugerLab/ALRA/blob/master/README.md v1: path: openproblems/tasks/denoising/methods/alra.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: alra: preferred_normalization: counts diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index 125ee0e4a1..29c7b244ef 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -14,7 +14,7 @@ functionality: repository_url: "https://github.com/theislab/dca" v1: path: openproblems/tasks/denoising/methods/dca.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: dca: preferred_normalization: counts diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index 92f35e3240..b573412828 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: repository_url: "https://github.com/yanailab/knn-smoothing" v1: path: openproblems/tasks/denoising/methods/knn_smoothing.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: knn_smoothing: preferred_normalization: counts diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 48c6044fef..d3d7122c1a 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -3,7 +3,7 @@ functionality: name: "magic" info: label: MAGIC - summary: "MAGIC imputes and denoises scRNA-seq data using Euclidean distances and a Gaussian kernel to calculate the affinity matrix, followed by a Markov process and multiplication with the normalised data to obtain imputed values." + summary: "MAGIC imputes and denoises scRNA-seq data that is noisy or dropout-prone." description: "MAGIC (Markov Affinity-based Graph Imputation of Cells) is a method for imputation and denoising of noisy or dropout-prone single cell RNA-sequencing data. Given a normalised scRNA-seq expression matrix, it first calculates @@ -20,7 +20,7 @@ functionality: repository_url: "https://github.com/KrishnaswamyLab/MAGIC" v1: path: openproblems/tasks/denoising/methods/magic.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: magic: magic_approx: diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 89dc75d285..9013183fe4 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -10,10 +10,10 @@ functionality: reference: batson2019molecular v1: path: openproblems/tasks/denoising/metrics/mse.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 maximize: false min: 0 - max: +inf + max: "+.inf" resources: - type: python_script path: script.py diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index 1ef35f9d76..367570e8de 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -2,7 +2,6 @@ __merge__: ../../api/comp_metric.yaml functionality: name: "poisson" info: - reference: "batson2019molecular" metrics: - name: poisson label: Poisson Loss @@ -12,10 +11,10 @@ functionality: reference: batson2019molecular v1: path: openproblems/tasks/denoising/metrics/poisson.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 maximize: false min: 0 - max: +inf + max: "+.inf" resources: - type: python_script path: script.py diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf index 4b98ec7698..ed7585aa82 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run/main.nf @@ -72,7 +72,7 @@ workflow run_wf { def pref = config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cpm" && pref == "counts") || norm == pref + (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/denoising/workflows/run/run_test.sh b/src/tasks/denoising/workflows/run/run_test.sh index e671b93965..f6f0e8884c 100755 --- a/src/tasks/denoising/workflows/run/run_test.sh +++ b/src/tasks/denoising/workflows/run/run_test.sh @@ -22,7 +22,7 @@ nextflow \ -c src/wf_utils/labels_ci.config \ --id pancreas \ --dataset_id pancreas \ - --normalization_id log_cpm \ + --normalization_id log_cp10k \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output scores.tsv \ diff --git a/src/tasks/denoising/workflows/run/run_test_on_tower.sh b/src/tasks/denoising/workflows/run/run_test_on_tower.sh index 5634670594..912cd376dc 100644 --- a/src/tasks/denoising/workflows/run/run_test_on_tower.sh +++ b/src/tasks/denoising/workflows/run/run_test_on_tower.sh @@ -8,7 +8,7 @@ id: pancreas_subsample input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad dataset_id: pancreas -normalization_id: log_cpm +normalization_id: log_cp10k output: scores.tsv publish_dir: s3://openproblems-nextflow/output_test/v2/denoising HERE diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 9cbb060c57..6fe1089de7 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "This method serves as a negative control, where the data is randomly embedded into a two-dimensional space, with no attempt to preserve the original structure." v1: path: openproblems/tasks/dimensionality_reduction/methods/baseline.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: 80b37e7a6aa27df4436f400397564c01276817e0 preferred_normalization: counts variants: random_features: diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml new file mode 100644 index 0000000000..ae926ec5d0 --- /dev/null +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -0,0 +1,41 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: "spectral_features" + info: + label: Spectral Features + summary: "Positive control by Use 1000-dimensional diffusions maps as an embedding." + description: "This serves as a positive control since it uses 1000-dimensional diffusions maps as an embedding" + v1: + path: openproblems/tasks/dimensionality_reduction/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + variants: + spectral_features: + arguments: + - name: "--n_comps" + type: integer + default: 1000 + description: "Number of components to use for the embedding." + - name: t + type: integer + default: 1 + description: "Number to power the eigenvalues by." + - name: n_retries + type: integer + default: 1 + description: "Number of times to retry if the embedding fails, each time adding noise." + resources: + - type: python_script + path: /src/tasks/dimensionality_reduction/methods/diffusion_map/script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - umap-learn + - scipy + - numpy + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 37fb6bac0e..74d7f248e5 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -7,35 +7,16 @@ functionality: description: "This serves as a positive control since the original high-dimensional data is retained as is, without any loss of information" v1: path: openproblems/tasks/dimensionality_reduction/methods/baseline.py - commit: 4a0ee9b3731ff10d8cd2e584726a61b502aef613 - preferred_normalization: counts + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: true_features: - true_features_log_cpm: - preferred_normalization: log_cpm - use_normalized_layer: true - true_features_log_cpm_hvg: - preferred_normalization: log_cpm - use_normalized_layer: true - n_hvg: 1000 - arguments: - - name: "--use_normalized_layer" - type: boolean - default: false - description: Whether to work with the raw counts or the normalized counts. - - name: "--n_hvg" - type: integer - description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. - default: 1000 resources: - type: python_script path: script.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 - setup: - - type: python - packages: scanpy - type: nextflow directives: label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/script.py b/src/tasks/dimensionality_reduction/control_methods/true_features/script.py index aa8469051c..1a58cd4984 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/script.py +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/script.py @@ -4,8 +4,6 @@ par = { "input": "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output": "reduced.h5ad", - "n_hvg": 100, - "use_normalized_layer": False } meta = { "functionality_name": "true_features", @@ -16,15 +14,7 @@ input = ad.read_h5ad(par["input"]) print("Create high dimensionally embedding with all features", flush=True) -if par["use_normalized_layer"]: - X_emb = input.layers["counts"].toarray() -else: - X_emb = input.layers["normalized"].toarray() - -if par["n_hvg"]: - print(f"Select top {par['n_hvg']} high variable genes", flush=True) - idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] - X_emb = X_emb[:, idx] +X_emb = input.layers["normalized"].toarray() print("Create output AnnData", flush=True) output = ad.AnnData( diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index cfb1ccd926..626110cd9a 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -10,15 +10,15 @@ functionality: documentation_url: https://github.com/lmcinnes/umap#readme v1: path: openproblems/tasks/dimensionality_reduction/methods/umap.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: - densmap_logCPM: - densmap_pca_logCPM: + densmap_logCP10k: + densmap_pca_logCP10k: n_pca_dims: 50 - densmap_logCPM_1kHVG: + densmap_logCP10k_1kHVG: n_hvg: 1000 - densmap_pca_logCPM_1kHVG: + densmap_pca_logCP10k_1kHVG: n_pca_dims: 50 n_hvg: 1000 arguments: diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml new file mode 100644 index 0000000000..643a7b8bed --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -0,0 +1,44 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: "diffusion_maps" + info: + label: Diffusion maps + summary: "Positive control by Use 1000-dimensional diffusions maps as an embedding." + description: "This serves as a positive control since it uses 1000-dimensional diffusions maps as an embedding" + reference: coifman2006diffusion + documentation_url: https://github.com/openproblems-bio/openproblems + repository_url: https://github.com/openproblems-bio/openproblems + v1: + path: openproblems/tasks/dimensionality_reduction/methods/diffusion_map.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + variants: + diffusion_map: + arguments: + - name: "--n_comps" + type: integer + default: 2 + description: "Number of components to use for the embedding." + - name: t + type: integer + default: 1 + description: "Number to power the eigenvalues by." + - name: n_retries + type: integer + default: 1 + description: "Number of times to retry if the embedding fails, each time adding noise." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - umap-learn + - scipy + - numpy + - type: nextflow + directives: + label: [ highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/script.py b/src/tasks/dimensionality_reduction/methods/diffusion_map/script.py new file mode 100644 index 0000000000..cf8633120c --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/script.py @@ -0,0 +1,77 @@ +import anndata as ad +import umap + +## VIASH START +par = { + "input": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "output": "reduced.h5ad", + "n_comps": 2, +} +meta = { + "functionality_name": "foo", +} +## VIASH END + +def diffusion_map(graph, n_comps, t, n_retries): + import numpy as np + import scipy.sparse.linalg + + diag_data = np.asarray(graph.sum(axis=0)) + identity = scipy.sparse.identity(graph.shape[0], dtype=np.float64) + diag = scipy.sparse.spdiags( + 1.0 / np.sqrt(diag_data), 0, graph.shape[0], graph.shape[0] + ) + laplacian = identity - diag * graph * diag + num_lanczos_vectors = max(2 * n_comps + 1, int(np.sqrt(graph.shape[0]))) + try: + eigenvalues, eigenvectors = scipy.sparse.linalg.eigsh( + laplacian, + n_comps, + which="SM", + ncv=num_lanczos_vectors, + tol=1e-4, + v0=np.ones(laplacian.shape[0]), + maxiter=graph.shape[0] * 5, + ) + return (eigenvalues**t) * eigenvectors + except scipy.sparse.linalg.ArpackNoConvergence: + if n_retries > 0: + # add some noise and try again + graph_rand = graph.copy().tocoo() + graph_rand.row = np.random.choice( + graph_rand.shape[0], len(graph_rand.row), replace=True + ) + graph_rand.data *= 0.01 + return diffusion_map( + graph + graph_rand, n_comps, t, n_retries=n_retries - 1 + ) + else: + raise + +print("Load input data", flush=True) +input = ad.read_h5ad(par["input"]) + +print("Create high dimensionally embedding with all features", flush=True) + +n_comps = min(par["n_comps"], min(input.shape) - 2) + +graph = umap.UMAP(transform_mode="graph").fit_transform(input.layers["normalized"]) + +X_emb = diffusion_map(graph, n_comps, t=par["t"], n_retries=par["n_retries"]) + + +print("Create output AnnData", flush=True) +output = ad.AnnData( + obs=input.obs[[]], + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index 4d57c4df9d..c22d2d1fd6 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -17,8 +17,8 @@ functionality: documentation_url: "https://github.com/beringresearch/ivis#readme" v1: path: openproblems/tasks/dimensionality_reduction/methods/ivis.py - commit: 9ebb777b3b76337e731a3b99f4bf39462a15c4cc - preferred_normalization: log_cpm + commit: 93d2161a08da3edf249abedff5111fb5ce527552 + preferred_normalization: log_cp10k variants: ivis_logCPM_1kHVG: arguments: diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 6911b450a2..34e13c8c41 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -18,13 +18,13 @@ functionality: documentation_url: "https://github.com/HiBearME/NeuralEE#readme" v1: path: openproblems/tasks/dimensionality_reduction/methods/neuralee.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: neuralee_default: normalize: true n_hvg: 500 - neuralee_logCPM_1kHVG: + neuralee_logCP10k_1kHVG: normalize: false n_hvg: 1000 arguments: diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 7ae19d13e9..5ca15443c4 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -16,11 +16,11 @@ functionality: documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" v1: path: openproblems/tasks/dimensionality_reduction/methods/pca.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: log_cpm + commit: 154ccb9fd99113f3d28d9c3f139194539a0290f9 + preferred_normalization: log_cp10k variants: - pca_logCPM: - pca_logCPM_1kHVG: + pca_logCP10k: + pca_logCP10k_1kHVG: n_hvg: 1000 arguments: - name: "--n_hvg" diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index d69b8cc6f2..57b0e0eeac 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -18,17 +18,17 @@ functionality: documentation_url: "https://github.com/KrishnaswamyLab/PHATE#readme" v1: path: openproblems/tasks/dimensionality_reduction/methods/phate.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: sqrt_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: sqrt_cp10k variants: phate_default: phate_sqrt: gamma: 0 - phate_logCPM: - preferred_normalization: log_cpm - phate_logCPM_1kHVG: + phate_logCP10k: + preferred_normalization: log_cp10k + phate_logCP10k_1kHVG: n_hvg: 1000 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k arguments: - name: '--n_pca_dims' type: integer diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 0da62a6a83..1b3e9ca9f4 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -16,11 +16,11 @@ functionality: documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html#sklearn.manifold.TSNE" v1: path: openproblems/tasks/dimensionality_reduction/methods/tsne.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: log_cpm + commit: 154ccb9fd99113f3d28d9c3f139194539a0290f9 + preferred_normalization: log_cp10k variants: - tsne_logCPM: - tsne_logCPM_1kHVG: + tsne_logCP10k: + tsne_logCP10k_1kHVG: n_hvg: 1000 arguments: - name: "--n_hvg" diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 1aff2d0c2c..ddced67815 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -16,14 +16,14 @@ functionality: v1: path: openproblems/tasks/dimensionality_reduction/methods/umap.py commit: 14d70b330cae09527a6d4c4e552db240601e31cf - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: - umap_logCPM: - umap_pca_logCPM: + umap_logCP10k: + umap_pca_logCP10k: n_pca_dims: 50 - umap_logCPM_1kHVG: + umap_logCP10k_1kHVG: n_hvg: 1000 - umap_pca_logCPM_1kHVG: + umap_pca_logCP10k_1kHVG: n_pca_dims: 50 n_hvg: 1000 arguments: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 552b50fd04..a4cc208ba3 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -38,7 +38,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -59,7 +59,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -80,7 +80,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -101,7 +101,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -122,7 +122,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package @@ -143,7 +143,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/nn_ranking.py - commit: 14d70b330cae09527a6d4c4e552db240601e31cf + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 note: | The original v1 implementations consisted of a lot of helper functions which were derived from the pyDRMetrics package. This version uses the coRanking package diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/library.bib b/src/tasks/dimensionality_reduction/metrics/coranking/library.bib deleted file mode 100644 index 5ecdb67e51..0000000000 --- a/src/tasks/dimensionality_reduction/metrics/coranking/library.bib +++ /dev/null @@ -1,62 +0,0 @@ - -@misc{lueks2011evaluate, - doi = {10.48550/ARXIV.1110.3917}, - url = {https://arxiv.org/abs/1110.3917}, - author = {Lueks, Wouter and Mokbel, Bassam and Biehl, Michael and Hammer, Barbara}, - keywords = {Machine Learning (cs.LG), Information Retrieval (cs.IR), FOS: Computer and information sciences, FOS: Computer and information sciences}, - title = {How to Evaluate Dimensionality Reduction? - Improving the Co-ranking Matrix}, - publisher = {arXiv}, - year = {2011}, - copyright = {arXiv.org perpetual, non-exclusive license} -} -@article{kraemer2018dimred, - doi = {10.32614/rj-2018-039}, - url = {https://doi.org/10.32614/rj-2018-039}, - year = {2018}, - publisher = {The R Foundation}, - volume = {10}, - number = {1}, - pages = {342}, - author = {Guido Kraemer and Markus Reichstein and Miguel, D. Mahecha}, - title = {{dimRed} and {coRanking} - Unifying Dimensionality Reduction in R}, - journal = {The R Journal} -} -@article{chen2009local, - doi = {10.1198/jasa.2009.0111}, - url = {https://doi.org/10.1198/jasa.2009.0111}, - year = {2009}, - month = mar, - publisher = {Informa {UK} Limited}, - volume = {104}, - number = {485}, - pages = {209--219}, - author = {Lisha Chen and Andreas Buja}, - title = {Local Multidimensional Scaling for Nonlinear Dimension Reduction, Graph Drawing, and Proximity Analysis}, - journal = {Journal of the American Statistical Association} -} -@article{lee2009quality, - doi = {10.1016/j.neucom.2008.12.017}, - url = {https://doi.org/10.1016/j.neucom.2008.12.017}, - year = {2009}, - month = mar, - publisher = {Elsevier {BV}}, - volume = {72}, - number = {7-9}, - pages = {1431--1443}, - author = {John A. Lee and Michel Verleysen}, - title = {Quality assessment of dimensionality reduction: Rank-based criteria}, - journal = {Neurocomputing} -} -@article{venna2006local, - doi = {10.1016/j.neunet.2006.05.014}, - url = {https://doi.org/10.1016/j.neunet.2006.05.014}, - year = {2006}, - month = jul, - publisher = {Elsevier {BV}}, - volume = {19}, - number = {6-7}, - pages = {889--899}, - author = {Jarkko Venna and Samuel Kaski}, - title = {Local multidimensional scaling}, - journal = {Neural Networks} -} \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 91d10dcf43..ed671faedd 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -15,7 +15,16 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/density.py - commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + arguments: + - name: "--n_neighbors" + type: integer + default: 30 + description: "Number of neighbors to use for density estimation." + - name: "--seed" + type: integer + default: 42 + description: "Random seed." resources: - type: python_script path: script.py diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py b/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py index 9cae4d1f12..9bf44397c2 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/script.py @@ -11,6 +11,8 @@ "input_embedding": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", "input_solution": "resources_test/dimensionality_reduction/pancreas/test.h5ad", "output": "score.h5ad", + "n_neighbors": 30, + "seed": 42, } ## VIASH END @@ -84,27 +86,22 @@ def compute_density_preservation( return 0.0 print("Compute local radii in original data", flush=True) - _, ro, _ = UMAP( - n_neighbors=_K, - random_state=_SEED, - densmap=True, - output_dens=True - ).fit_transform(high_dim) + ro = _calculate_radii( + high_dim, + n_neighbors=n_neighbors, + random_state=random_state + ) print("Compute local radii of embedding", flush=True) re = _calculate_radii( X_emb, - n_neighbors=_K, - random_state=_SEED + n_neighbors=n_neighbors, + random_state=random_state ) print("Compute pearson correlation", flush=True) return pearsonr(ro, re)[0] -# number of neighbors -_K = 30 -# Fix seed -_SEED = 42 print("Load data", flush=True) input_solution = ad.read_h5ad(par["input_solution"]) @@ -116,8 +113,8 @@ def compute_density_preservation( density_preservation = compute_density_preservation( X_emb=X_emb, high_dim=high_dim, - n_neighbors=_K, - random_state=_SEED + n_neighbors=par["n_neighbors"], + random_state=par["seed"] ) print("Create output AnnData object", flush=True) diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml new file mode 100644 index 0000000000..7e30f9efbe --- /dev/null +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -0,0 +1,49 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: distance_correlation + info: + metrics: + - name: distance_correlation + label: Distance Correlation + summary: "Calculates the distance correlation by computing Spearman correlations between distances." + description: "Calculates the distance correlation by computing Spearman correlations between distances on the full (or processed) data matrix and the dimensionally-reduced matrix." + reference: kruskal1964mds + min: 0 + max: "+.inf" + maximize: false + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/distance_correlation.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + note: This metric was ported but will probably be removed soon. + - name: distance_correlation_spectral + label: Distance Correlation Spectral + summary: "Spearman correlation between all pairwise diffusion distances in the original and dimension-reduced data." + description: "Spearman correlation between all pairwise diffusion distances in the original and dimension-reduced data." + reference: coifman2006diffusion + min: 0 + max: "+.inf" + maximize: false + v1: + path: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + note: This metric was ported but will probably be removed soon. + arguments: + - name: "--spectral" + type: boolean_true + description: Calculate the spectral root mean squared error. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + packages: + - umap-learn + - scikit-learn + - numpy + - scipy + - type: nextflow + directives: + label: [ midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/script.py b/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py similarity index 70% rename from src/tasks/dimensionality_reduction/metrics/rmse/script.py rename to src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py index 4b33fe02ce..d461f271b4 100644 --- a/src/tasks/dimensionality_reduction/metrics/rmse/script.py +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py @@ -1,7 +1,7 @@ import anndata as ad import numpy as np import sklearn.decomposition -import scipy.optimize +import scipy.stats import scipy.spatial from sklearn.metrics import pairwise_distances import umap @@ -15,13 +15,13 @@ } ## VIASH END -def _rmse(X, X_emb): +def _distance_correlation(X, X_emb): high_dimensional_distance_vector = scipy.spatial.distance.pdist(X) low_dimensional_distance_vector = scipy.spatial.distance.pdist(X_emb) - _, rmse = scipy.optimize.nnls( - low_dimensional_distance_vector[:, None], high_dimensional_distance_vector + corr = scipy.stats.spearmanr( + low_dimensional_distance_vector, high_dimensional_distance_vector ) - return rmse + return corr print("Load data", flush=True) input_solution = ad.read_h5ad(par["input_solution"]) @@ -31,17 +31,18 @@ def _rmse(X, X_emb): X_emb = input_embedding.obsm["X_emb"] print("Compute NNLS residual after SVD", flush=True) -n_svd = 200 +n_svd = 500 svd_emb = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(high_dim) -rmse = _rmse(svd_emb, X_emb) +dist_corr = _distance_correlation(svd_emb, X_emb) +#! Explicitly not changing it to use diffusion map method as this will have a positive effect on the diffusion map method for this specific metric. print("Compute NLSS residual after spectral embedding", flush=True) -n_comps = min(200, min(input_solution.shape) - 2) +n_comps = min(1000, min(input_solution.shape) - 2) umap_graph = umap.UMAP(transform_mode="graph").fit_transform(high_dim) spectral_emb = umap.spectral.spectral_layout( high_dim, umap_graph, n_comps, random_state=np.random.default_rng() ) -rmse_spectral = _rmse(spectral_emb, X_emb) +dist_corr_spectral = _distance_correlation(spectral_emb, X_emb) print("Create output AnnData object", flush=True) output = ad.AnnData( @@ -49,8 +50,8 @@ def _rmse(X, X_emb): "dataset_id": input_solution.uns["dataset_id"], "normalization_id": input_solution.uns["normalization_id"], "method_id": input_embedding.uns["method_id"], - "metric_ids": [ "rmse", "rmse_spectral" ], - "metric_values": [ rmse, rmse_spectral ] + "metric_ids": [ "distance correlation", "distance_correlation_spectral" ], + "metric_values": [ dist_corr, dist_corr_spectral ] } ) diff --git a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml deleted file mode 100644 index 5874ffb3c1..0000000000 --- a/src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml +++ /dev/null @@ -1,45 +0,0 @@ -__merge__: ../../api/comp_metric.yaml -functionality: - name: "rmse" - info: - metrics: - - name: rmse - label: RMSE - summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." - description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of an SVD." - reference: kruskal1964mds - min: 0 - max: "+.inf" - maximize: false - - name: rmse_spectral - label: RMSE Spectral - summary: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." - description: "The residual after applying the Non-Negative Least Squares solver on the pairwise distances of a spectral embedding." - reference: coifman2006diffusion - min: 0 - max: "+.inf" - maximize: false - v1: - path: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py - commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b - note: This metric was ported but will probably be removed soon. - arguments: - - name: "--spectral" - type: boolean_true - description: Calculate the spectral root mean squared error. - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 - setup: - - type: python - packages: - - umap-learn - - scikit-learn - - numpy - - scipy - - type: nextflow - directives: - label: [ midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index ce65fc8b60..b56012ae74 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/trustworthiness.py - commit: c2470ce02e6f196267cec1c554ba7ae389c0956a + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 note: This metric is already included in the 'coranking' component and can be removed. resources: - type: python_script diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index c208311399..165181ca72 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -8,7 +8,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad +RAW_DATA=resources_test/common/pancreas/cp10k_dataset.h5ad DATASET_DIR=resources_test/dimensionality_reduction/pancreas if [ ! -f $RAW_DATA ]; then @@ -46,7 +46,7 @@ nextflow \ -profile docker \ --id pancreas \ --dataset_id pancreas \ - --normalization_id log_cpm \ + --normalization_id log_cp10k \ --input $DATASET_DIR/dataset.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index 9dd5b10231..6d0913191f 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -80,7 +80,7 @@ workflow run_wf { def pref = config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cpm" && pref == "counts") || norm == pref + (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run/run_test.sh index 3aeeb58baa..299f8accf8 100755 --- a/src/tasks/dimensionality_reduction/workflows/run/run_test.sh +++ b/src/tasks/dimensionality_reduction/workflows/run/run_test.sh @@ -21,7 +21,7 @@ nextflow \ -resume \ --id pancreas \ --dataset_id pancreas \ - --normalization_id log_cpm \ + --normalization_id log_cp10k \ --input $DATASET_DIR/dataset.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh b/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh index befcde4d49..f2ff994080 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh +++ b/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh @@ -8,7 +8,7 @@ id: pancreas_subsample input: s3://openproblems-data/$DATASET_DIR/dataset.h5ad input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad dataset_id: pancreas -normalization_id: log_cpm +normalization_id: log_cp10k output: scores.tsv publish_dir: s3://openproblems-nextflow/output_test/v2/dimensionality_reduction HERE diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 6cd01534c4..53142aaf9e 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "A control-type method that predicts all cells to belong to the most abundant cell type in the dataset" v1: path: openproblems/tasks/label_projection/methods/baseline.py - commit: b460ecb183328c857cbbf653488f522a4034a61c + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 variants: majority_vote: preferred_normalization: counts diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 014ee5249d..dc95a42468 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "A negative control, where the labels are randomly predicted without training the data." v1: path: openproblems/tasks/label_projection/methods/baseline.py - commit: b460ecb183328c857cbbf653488f522a4034a61c + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 preferred_normalization: counts variants: random_labels: diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index ef313a16ee..384c2cf92e 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: description: "A positive control, where the solution labels are copied 1 to 1 to the predicted data." v1: path: openproblems/tasks/label_projection/methods/baseline.py - commit: b460ecb183328c857cbbf653488f522a4034a61c + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 preferred_normalization: counts variants: true_labels: diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index 0841b7ebe4..12445bedd0 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -17,10 +17,10 @@ functionality: documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html" v1: path: openproblems/tasks/label_projection/methods/knn_classifier.py - commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: - knn_classifier_log_cpm: + knn_classifier_log_cp10k: knn_classifier_scran: preferred_normalization: log_scran_pooling resources: diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 8deac18a99..990b8cf368 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -14,10 +14,10 @@ functionality: documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html" v1: path: openproblems/tasks/label_projection/methods/logistic_regression.py - commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: - logistic_regression_log_cpm: + logistic_regression_log_cp10k: logistic_regression_scran: preferred_normalization: log_scran_pooling resources: diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 8ec1f9cbf0..8046a01e95 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -17,10 +17,10 @@ functionality: documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.neural_network.MLPClassifier.html" v1: path: openproblems/tasks/label_projection/methods/mlp.py - commit: c2470ce02e6f196267cec1c554ba7ae389c0956a - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: - mlp_log_cpm: + mlp_log_cp10k: mlp_scran: preferred_normalization: log_scran_pooling arguments: diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index f765b07c98..5cbc8fb3a4 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -17,8 +17,8 @@ functionality: documentation_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1: path: openproblems/tasks/label_projection/methods/scvi_tools.py - commit: 4bb8a7e04545a06c336d3d9364a1dd84fa2af1a4 - preferred_normalization: log_cpm + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 + preferred_normalization: log_cp10k variants: scanvi_all_genes: scanvi_hvg: diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 56662a542c..38df609144 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -17,8 +17,12 @@ functionality: documentation_url: https://docs.scvi-tools.org repository_url: https://github.com/scverse/scvi-tools preferred_normalization: counts + v1: + path: openproblems/tasks/label_projection/methods/scvi_tools.py + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 variants: scanvi_scarches: + #! TODO: add other scanvi_scarches variants # Component-specific parameters (optional) arguments: diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index b30629f6b5..045819ba47 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -18,8 +18,8 @@ functionality: documentation_url: "https://satijalab.org/seurat/articles/integration_mapping.html" v1: path: openproblems/tasks/label_projection/methods/seurat.py - commit: 3f19f0e87a8bc8b59c7521ba01917580aff81bc8 - preferred_normalization: log_cpm + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k variants: seurat: resources: diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index 2234967a79..c37e7611f9 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -14,10 +14,10 @@ functionality: documentation_url: "https://xgboost.readthedocs.io/en/stable/index.html" v1: path: openproblems/tasks/label_projection/methods/xgboost.py - commit: 123bb7b39c51c58e19ddf0fbbc1963c3dffde14c - preferred_normalization: log_cpm + commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 + preferred_normalization: log_cp10k variants: - xgboost_log_cpm: + xgboost_log_cp10k: xgboost_scran: preferred_normalization: log_scran_pooling resources: diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 9414a5eaad..11674fde5c 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: reference: grandini2020metrics v1: path: openproblems/tasks/label_projection/metrics/accuracy.py - commit: fcd5b876e7d0667da73a2858bc27c40224e19f65 + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index f78f4c8bba..ec6eece949 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: maximize: true v1: path: openproblems/tasks/label_projection/metrics/f1.py - commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - name: f1_macro label: F1 macro summary: "Unweighted mean of each label F1-score" @@ -24,7 +24,7 @@ functionality: maximize: true v1: path: openproblems/tasks/label_projection/metrics/f1.py - commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - name: f1_micro label: F1 micro summary: "Calculation of TP, FN and FP." @@ -35,7 +35,7 @@ functionality: maximize: true v1: path: openproblems/tasks/label_projection/metrics/f1.py - commit: bb16ca05ae1ce20ce59bfa7a879641b9300df6b0 + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script path: script.py diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index d9780a4425..bb3b687ba1 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad +RAW_DATA=resources_test/common/pancreas/cp10k_dataset.h5ad DATASET_DIR=resources_test/label_projection/pancreas if [ ! -f $RAW_DATA ]; then @@ -49,7 +49,7 @@ nextflow \ -resume \ --id pancreas \ --dataset_id pancreas \ - --normalization_id log_cpm \ + --normalization_id log_cp10k \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index bd54498e0c..d6f5146440 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -85,7 +85,7 @@ workflow run_wf { def pref = config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cpm" && pref == "counts") || norm == pref + (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/label_projection/workflows/run/run_test.sh b/src/tasks/label_projection/workflows/run/run_test.sh index b31c9ae4ac..a909381666 100755 --- a/src/tasks/label_projection/workflows/run/run_test.sh +++ b/src/tasks/label_projection/workflows/run/run_test.sh @@ -21,7 +21,7 @@ nextflow \ -resume \ --id pancreas \ --dataset_id pancreas \ - --normalization_id log_cpm \ + --normalization_id log_cp10k \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ diff --git a/src/tasks/label_projection/workflows/run/run_test_on_tower.sh b/src/tasks/label_projection/workflows/run/run_test_on_tower.sh index 27c7ee8e3d..cce0f3d89f 100644 --- a/src/tasks/label_projection/workflows/run/run_test_on_tower.sh +++ b/src/tasks/label_projection/workflows/run/run_test_on_tower.sh @@ -9,7 +9,7 @@ input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad dataset_id: pancreas -normalization_id: log_cpm +normalization_id: log_cp10k output: scores.tsv publish_dir: s3://openproblems-nextflow/output_test/v2/label_projection HERE From 3b966cde749ca4864e63e09774c0f0f779c93d0c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Aug 2023 14:22:01 +0200 Subject: [PATCH 0983/1233] Batch integration - Create separate solution file (#218) * Remove --hvg from methods * commit scanvi changes * remove hvg related code * wip commit * refactor the metrics * always flush * don't copy X when not needed * update readme Former-commit-id: 0ec105d78cceadb640528c4b4dd5fa166291f9ba --- src/tasks/batch_integration/README.md | 309 ++++++++++-------- .../api/comp_control_method_embedding.yaml | 2 +- .../api/comp_control_method_graph.yaml | 2 +- .../api/comp_method_embedding.yaml | 2 +- .../api/comp_method_feature.yaml | 2 +- .../api/comp_method_graph.yaml | 2 +- .../api/comp_metric_embedding.yaml | 4 + .../api/comp_metric_feature.yaml | 4 + .../api/comp_metric_graph.yaml | 4 + .../api/comp_process_dataset.yaml | 8 +- ...le_unintegrated.yaml => file_dataset.yaml} | 2 +- .../api/file_integrated_embedding.yaml | 2 +- .../api/file_integrated_feature.yaml | 2 +- .../api/file_integrated_graph.yaml | 10 +- .../batch_integration/api/file_solution.yaml | 61 ++++ .../metrics/asw_batch/script.py | 13 +- .../metrics/asw_label/script.py | 16 +- .../metrics/cell_cycle_conservation/script.py | 20 +- .../metrics/clustering_overlap/script.py | 21 +- .../metrics/graph_connectivity/script.py | 19 +- .../metrics/hvg_overlap/script.py | 25 +- .../metrics/isolated_label_asw/script.py | 18 +- .../metrics/isolated_label_f1/script.py | 20 +- .../batch_integration/metrics/kbet/script.py | 13 +- .../batch_integration/metrics/lisi/script.py | 29 +- .../batch_integration/metrics/pcr/script.py | 21 +- .../process_dataset/script.py | 6 +- .../resources_test_scripts/pancreas.sh | 9 +- 28 files changed, 398 insertions(+), 248 deletions(-) rename src/tasks/batch_integration/api/{file_unintegrated.yaml => file_dataset.yaml} (98%) create mode 100644 src/tasks/batch_integration/api/file_solution.yaml diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index e4c4a642dc..90ac1e848d 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -56,42 +56,47 @@ extensive benchmark of single-cell data integration methods flowchart LR file_common_dataset("Common dataset") comp_process_dataset[/"Data processor"/] - file_unintegrated("Unintegrated") + file_dataset("Dataset") + file_solution("Solution") comp_control_method_embedding[/"Control method (embedding)"/] comp_control_method_graaf[/"Control method (graph)"/] comp_method_embedding[/"Method (embedding)"/] comp_method_feature[/"Method (feature)"/] comp_method_graaf[/"Method (graph)"/] + comp_metric_embedding[/"Metric (embedding)"/] + comp_metric_feature[/"Metric (feature)"/] + comp_metric_graaf[/"Metric (graph)"/] file_integrated_embedding("Integrated embedding") file_integrated_graaf("Integrated Graph") file_integrated_feature("Integrated Feature") - comp_metric_embedding[/"Metric (embedding)"/] + file_score("Score") comp_transformer_embedding_to_graaf[/"Embedding to Graph"/] - comp_metric_graaf[/"Metric (graph)"/] - comp_metric_feature[/"Metric (feature)"/] comp_transformer_feature_to_embedding[/"Feature to Embedding"/] - file_score("Score") file_common_dataset---comp_process_dataset - comp_process_dataset-->file_unintegrated - file_unintegrated---comp_control_method_embedding - file_unintegrated---comp_control_method_graaf - file_unintegrated---comp_method_embedding - file_unintegrated---comp_method_feature - file_unintegrated---comp_method_graaf + comp_process_dataset-->file_dataset + comp_process_dataset-->file_solution + file_dataset---comp_control_method_embedding + file_dataset---comp_control_method_graaf + file_dataset---comp_method_embedding + file_dataset---comp_method_feature + file_dataset---comp_method_graaf + file_solution---comp_metric_embedding + file_solution---comp_metric_feature + file_solution---comp_metric_graaf comp_control_method_embedding-->file_integrated_embedding comp_control_method_graaf-->file_integrated_graaf comp_method_embedding-->file_integrated_embedding comp_method_feature-->file_integrated_feature comp_method_graaf-->file_integrated_graaf + comp_metric_embedding-->file_score + comp_metric_feature-->file_score + comp_metric_graaf-->file_score file_integrated_embedding---comp_metric_embedding file_integrated_embedding---comp_transformer_embedding_to_graaf file_integrated_graaf---comp_metric_graaf file_integrated_feature---comp_metric_feature file_integrated_feature---comp_transformer_feature_to_embedding - comp_metric_embedding-->file_score comp_transformer_embedding_to_graaf-->file_integrated_graaf - comp_metric_graaf-->file_score - comp_metric_feature-->file_score comp_transformer_feature_to_embedding-->file_integrated_embedding ``` @@ -162,14 +167,19 @@ Arguments:
-| Name | Type | Description | -|:-----------|:-------|:---------------------------------------------------------------| -| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | -| `--output` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | +| Name | Type | Description | +|:--------------------|:----------|:---------------------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output_dataset` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | +| `--output_solution` | `file` | (*Output*) Solution dataset. | +| `--obs_label` | `string` | (*Optional*) Which .obs slot to use as label. Default: `celltype`. | +| `--obs_batch` | `string` | (*Optional*) Which .obs slot to use as batch covariate. Default: `batch`. | +| `--hvgs` | `integer` | (*Optional*) Number of highly variable genes. Default: `2000`. | +| `--subset_hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. |
-## File format: Unintegrated +## File format: Dataset Unintegrated AnnData HDF5 file. @@ -215,6 +225,52 @@ Slot description: +## File format: Solution + +Solution dataset + +Example file: +`resources_test/batch_integration/pancreas/unintegrated.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'batch', 'label' + var: 'hvg' + obsm: 'X_pca' + obsp: 'knn_distances', 'knn_connectivities' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | + +
+ ## Component type: Control method (embedding) Path: @@ -226,11 +282,10 @@ Arguments:
-| Name | Type | Description | -|:-----------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | Unintegrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | -| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | +| Name | Type | Description | +|:-----------|:-------|:--------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. |
@@ -245,11 +300,10 @@ Arguments:
-| Name | Type | Description | -|:-----------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | Unintegrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | -| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | +| Name | Type | Description | +|:-----------|:-------|:-----------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. |
@@ -264,11 +318,10 @@ Arguments:
-| Name | Type | Description | -|:-----------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | Unintegrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | -| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | +| Name | Type | Description | +|:-----------|:-------|:--------------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. |
@@ -283,11 +336,10 @@ Arguments:
-| Name | Type | Description | -|:-----------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | Unintegrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | -| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | +| Name | Type | Description | +|:-----------|:-------|:-----------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. |
@@ -302,11 +354,67 @@ Arguments:
-| Name | Type | Description | -|:-----------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | Unintegrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | -| `--hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | +| Name | Type | Description | +|:-----------|:-------|:-----------------------------------------| +| `--input` | `file` | Unintegrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | + +
+ +## Component type: Metric (embedding) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration embedding metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:---------------------------------| +| `--input_integrated` | `file` | An integrated AnnData HDF5 file. | +| `--input_solution` | `file` | Solution dataset. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## Component type: Metric (feature) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration feature metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:------------------------------| +| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | +| `--input_solution` | `file` | Solution dataset. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## Component type: Metric (graph) + +Path: +[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) + +A batch integration graph metric. + +Arguments: + +
+ +| Name | Type | Description | +|:---------------------|:-------|:------------------------------| +| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | +| `--input_solution` | `file` | Solution dataset. | +| `--output` | `file` | (*Output*) Metric score file. |
@@ -331,7 +439,7 @@ Format: obsm: 'X_pca', 'X_emb' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id' @@ -355,7 +463,6 @@ Slot description: | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["output_type"]` | `string` | what kind of output has been generated. | @@ -378,9 +485,9 @@ Format: obs: 'batch', 'label' var: 'hvg' obsm: 'X_pca' - obsp: 'knn_distances', 'knn_connectivities', 'connectivities' + obsp: 'knn_distances', 'knn_connectivities', 'connectivities', 'distances' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'neighbors' @@ -397,6 +504,7 @@ Slot description: | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | | `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | +| `obsp["distances"]` | `double` | Neighbors connectivities matrix. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | @@ -404,7 +512,7 @@ Slot description: | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["output_type"]` | `string` | what kind of output has been generated. | +| `uns["neighbors"]` | `object` | Supplementary K nearest neighbors data. | @@ -429,7 +537,7 @@ Format: obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized', 'corrected_counts' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'output_type' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id' @@ -453,79 +561,57 @@ Slot description: | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | | `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["output_type"]` | `string` | what kind of output has been generated. | -## Component type: Metric (embedding) - -Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) - -A batch integration embedding metric. - -Arguments: - -
- -| Name | Type | Description | -|:---------------------|:-------|:---------------------------------| -| `--input_integrated` | `file` | An integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Metric score file. | +## File format: Score -
+Metric score file -## Component type: Embedding to Graph +Example file: `score.h5ad` -Path: -[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) +Description: -Transform an embedding to a graph output. +NA -Arguments: +Format:
-| Name | Type | Description | -|:-----------|:-------|:-----------------------------------------| -| `--input` | `file` | An integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. | + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values'
-## Component type: Metric (graph) - -Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) - -A batch integration graph metric. - -Arguments: +Slot description:
-| Name | Type | Description | -|:---------------------|:-------|:------------------------------| -| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Metric score file. | +| Slot | Type | Description | +|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |
-## Component type: Metric (feature) +## Component type: Embedding to Graph Path: -[`src/batch_integration/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/metrics) +[`src/batch_integration/transformers`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/batch_integration/transformers) -A batch integration feature metric. +Transform an embedding to a graph output. Arguments:
-| Name | Type | Description | -|:---------------------|:-------|:------------------------------| -| `--input_integrated` | `file` | Integrated AnnData HDF5 file. | -| `--output` | `file` | (*Output*) Metric score file. | +| Name | Type | Description | +|:-----------|:-------|:-----------------------------------------| +| `--input` | `file` | An integrated AnnData HDF5 file. | +| `--output` | `file` | (*Output*) Integrated AnnData HDF5 file. |
@@ -546,36 +632,3 @@ Arguments: | `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. | - -## File format: Score - -Metric score file - -Example file: `score.h5ad` - -Description: - -NA - -Format: - -
- - AnnData object - uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' - -
- -Slot description: - -
- -| Slot | Type | Description | -|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | -| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | - -
diff --git a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml index 09ecf0531b..9c4bc65ce5 100644 --- a/src/tasks/batch_integration/api/comp_control_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_embedding.yaml @@ -10,7 +10,7 @@ functionality: A batch integration control method which outputs a batch-corrected embedding. arguments: - name: --input - __merge__: file_unintegrated.yaml + __merge__: file_dataset.yaml direction: input required: true - name: --output diff --git a/src/tasks/batch_integration/api/comp_control_method_graph.yaml b/src/tasks/batch_integration/api/comp_control_method_graph.yaml index d855391c82..cba6f48f7a 100644 --- a/src/tasks/batch_integration/api/comp_control_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_control_method_graph.yaml @@ -9,7 +9,7 @@ functionality: description: | A batch integration control method which outputs a batch-corrected cell graphs. arguments: - - __merge__: file_unintegrated.yaml + - __merge__: file_dataset.yaml name: --input direction: input required: true diff --git a/src/tasks/batch_integration/api/comp_method_embedding.yaml b/src/tasks/batch_integration/api/comp_method_embedding.yaml index 9f9c661beb..86e7d7caf3 100644 --- a/src/tasks/batch_integration/api/comp_method_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_method_embedding.yaml @@ -10,7 +10,7 @@ functionality: A batch integration method which outputs a batch-corrected embedding. arguments: - name: --input - __merge__: file_unintegrated.yaml + __merge__: file_dataset.yaml direction: input required: true - name: --output diff --git a/src/tasks/batch_integration/api/comp_method_feature.yaml b/src/tasks/batch_integration/api/comp_method_feature.yaml index cab7baf02d..d609c2dd5b 100644 --- a/src/tasks/batch_integration/api/comp_method_feature.yaml +++ b/src/tasks/batch_integration/api/comp_method_feature.yaml @@ -10,7 +10,7 @@ functionality: A batch integration method which outputs a batch-corrected feature-space. arguments: - name: --input - __merge__: file_unintegrated.yaml + __merge__: file_dataset.yaml direction: input required: true - name: --output diff --git a/src/tasks/batch_integration/api/comp_method_graph.yaml b/src/tasks/batch_integration/api/comp_method_graph.yaml index e6adb287a3..2f37146e24 100644 --- a/src/tasks/batch_integration/api/comp_method_graph.yaml +++ b/src/tasks/batch_integration/api/comp_method_graph.yaml @@ -10,7 +10,7 @@ functionality: A batch integration method which outputs a batch-corrected cell graphs. arguments: - name: --input - __merge__: file_unintegrated.yaml + __merge__: file_dataset.yaml direction: input required: true - name: --output diff --git a/src/tasks/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml index d7bf03ce2a..6c23b2938d 100644 --- a/src/tasks/batch_integration/api/comp_metric_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_metric_embedding.yaml @@ -13,6 +13,10 @@ functionality: __merge__: file_integrated_embedding.yaml direction: input required: true + - name: --input_solution + __merge__: file_solution.yaml + direction: input + required: true - name: --output __merge__: file_score.yaml direction: output diff --git a/src/tasks/batch_integration/api/comp_metric_feature.yaml b/src/tasks/batch_integration/api/comp_metric_feature.yaml index 0680703a3b..2f741d0aa2 100644 --- a/src/tasks/batch_integration/api/comp_metric_feature.yaml +++ b/src/tasks/batch_integration/api/comp_metric_feature.yaml @@ -13,6 +13,10 @@ functionality: __merge__: file_integrated_feature.yaml direction: input required: true + - name: --input_solution + __merge__: file_solution.yaml + direction: input + required: true - name: --output __merge__: file_score.yaml direction: output diff --git a/src/tasks/batch_integration/api/comp_metric_graph.yaml b/src/tasks/batch_integration/api/comp_metric_graph.yaml index 82805717a5..66935b9663 100644 --- a/src/tasks/batch_integration/api/comp_metric_graph.yaml +++ b/src/tasks/batch_integration/api/comp_metric_graph.yaml @@ -13,6 +13,10 @@ functionality: __merge__: file_integrated_graph.yaml direction: input required: true + - name: --input_solution + __merge__: file_solution.yaml + direction: input + required: true - name: --output __merge__: file_score.yaml direction: output diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 775155cbea..d213eb3ca3 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -12,8 +12,12 @@ functionality: __merge__: /src/datasets/api/file_common_dataset.yaml direction: input required: true - - name: "--output" - __merge__: file_unintegrated.yaml + - name: "--output_dataset" + __merge__: file_dataset.yaml + direction: output + required: true + - name: "--output_solution" + __merge__: file_solution.yaml direction: output required: true - name: "--obs_label" diff --git a/src/tasks/batch_integration/api/file_unintegrated.yaml b/src/tasks/batch_integration/api/file_dataset.yaml similarity index 98% rename from src/tasks/batch_integration/api/file_unintegrated.yaml rename to src/tasks/batch_integration/api/file_dataset.yaml index 1ef3c09007..bd40fc7561 100644 --- a/src/tasks/batch_integration/api/file_unintegrated.yaml +++ b/src/tasks/batch_integration/api/file_dataset.yaml @@ -1,7 +1,7 @@ type: file example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" info: - label: "Unintegrated" + label: "Dataset" summary: Unintegrated AnnData HDF5 file. slots: layers: diff --git a/src/tasks/batch_integration/api/file_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml index c2c0c668ff..cd9d021031 100644 --- a/src/tasks/batch_integration/api/file_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -1,4 +1,4 @@ -__merge__: "file_unintegrated.yaml" +__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_embedding.h5ad" info: diff --git a/src/tasks/batch_integration/api/file_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml index bdb0a3bdb0..4e3979bedb 100644 --- a/src/tasks/batch_integration/api/file_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -1,4 +1,4 @@ -__merge__: "file_unintegrated.yaml" +__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_feature.h5ad" info: diff --git a/src/tasks/batch_integration/api/file_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml index 54b60d7720..6af14980eb 100644 --- a/src/tasks/batch_integration/api/file_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -1,4 +1,4 @@ -__merge__: "file_unintegrated.yaml" +__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_graph.h5ad" info: @@ -11,8 +11,16 @@ info: name: connectivities description: Neighbors connectivities matrix. required: true + - type: double + name: distances + description: Neighbors connectivities matrix. + required: true uns: - type: string name: method_id description: "A unique identifier for the method" required: true + - type: object + name: neighbors + description: Supplementary K nearest neighbors data. + required: true diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml new file mode 100644 index 0000000000..62ef36a9f4 --- /dev/null +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -0,0 +1,61 @@ +type: file +example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" +info: + label: "Solution" + summary: Solution dataset + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: string + name: label + description: label information + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: object + name: knn + description: Supplementary K nearest neighbors data. + required: true + diff --git a/src/tasks/batch_integration/metrics/asw_batch/script.py b/src/tasks/batch_integration/metrics/asw_batch/script.py index cb0fc92b54..fceda260d9 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/script.py +++ b/src/tasks/batch_integration/metrics/asw_batch/script.py @@ -1,6 +1,5 @@ import anndata as ad from scib.metrics import silhouette_batch -import yaml ## VIASH START par = { @@ -13,11 +12,13 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.obsm["X_emb"] = input_integrated.obsm["X_emb"] print('compute score', flush=True) score = silhouette_batch( - adata, + input_solution, batch_key='batch', label_key='label', embed='X_emb', @@ -26,9 +27,9 @@ print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/asw_label/script.py b/src/tasks/batch_integration/metrics/asw_label/script.py index be069fe0de..938efef5ac 100644 --- a/src/tasks/batch_integration/metrics/asw_label/script.py +++ b/src/tasks/batch_integration/metrics/asw_label/script.py @@ -13,21 +13,23 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.obsm["X_emb"] = input_integrated.obsm["X_emb"] -print('compute score') +print('compute score', flush=True) score = silhouette( - adata, + input_solution, label_key='label', embed='X_emb' ) -print("Create output AnnData object") +print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - "method_id": adata.uns['method_id'], + "dataset_id": input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + "method_id": input_integrated.uns['method_id'], "metric_ids": [meta['functionality_name']], "metric_values": [score] } diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index 296155df97..e6da9f1571 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -13,11 +13,9 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) - -adata.X = adata.layers['normalized'] - -adata_int = adata.copy() +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.X = input_solution.layers['normalized'] translator = { "homo_sapiens": "human", @@ -26,19 +24,19 @@ print('compute score', flush=True) score = cell_cycle( - adata, - adata_int, + input_solution, + input_integrated, batch_key='batch', embed='X_emb', - organism=translator[adata.uns['dataset_organism']] + organism=translator[input_solution.uns['dataset_organism']] ) print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/script.py b/src/tasks/batch_integration/metrics/clustering_overlap/script.py index 11420782ea..b92ecd66cb 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/script.py +++ b/src/tasks/batch_integration/metrics/clustering_overlap/script.py @@ -15,28 +15,35 @@ ## VIASH END print('Read input', flush=True) -input = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) + +input_solution.obsp["connectivities"] = input_integrated.obsp["connectivities"] +input_solution.obsp["distances"] = input_integrated.obsp["distances"] + +# TODO: if we don't copy neighbors over, the metric doesn't work +input_solution.uns["neighbors"] = input_integrated.uns["neighbors"] print('Run optimal Leiden clustering', flush=True) cluster_optimal_resolution( - adata=input, + adata=input_solution, label_key='label', cluster_key='cluster', cluster_function=sc.tl.leiden, ) print('Compute ARI score', flush=True) -ari_score = ari(input, group1='cluster', group2='label') +ari_score = ari(input_solution, group1='cluster', group2='label') print('Compute NMI score', flush=True) -nmi_score = nmi(input, group1='cluster', group2='label') +nmi_score = nmi(input_solution, group1='cluster', group2='label') print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": input.uns['dataset_id'], - 'normalization_id': input.uns['normalization_id'], - "method_id": input.uns['method_id'], + "dataset_id": input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + "method_id": input_integrated.uns['method_id'], "metric_ids": [ "ari", "nmi" ], "metric_values": [ ari_score, nmi_score ] } diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/script.py b/src/tasks/batch_integration/metrics/graph_connectivity/script.py index 581caab941..35a1b2367c 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/script.py +++ b/src/tasks/batch_integration/metrics/graph_connectivity/script.py @@ -12,20 +12,27 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) + +input_solution.obsp["connectivities"] = input_integrated.obsp["connectivities"] +input_solution.obsp["distances"] = input_integrated.obsp["distances"] + +# TODO: if we don't copy neighbors over, the metric doesn't work +input_solution.uns["neighbors"] = input_integrated.uns["neighbors"] print('compute score', flush=True) score = scib.metrics.graph_connectivity( - adata, - label_key='label', + input_solution, + label_key='label' ) print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/script.py b/src/tasks/batch_integration/metrics/hvg_overlap/script.py index dca69ab4bb..e3221765fd 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/script.py +++ b/src/tasks/batch_integration/metrics/hvg_overlap/script.py @@ -13,27 +13,24 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) - -print('prepare data') -adata_unint = adata.copy() -adata_unint.X = adata_unint.layers["normalized"] -adata.X = adata.layers["corrected_counts"] - -print('compute score') +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.X = input_solution.layers["normalized"] +input_integrated.X = input_integrated.layers["corrected_counts"] +print('compute score', flush=True) score = hvg_overlap( - adata_unint, - adata, + input_solution, + input_integrated, batch_key="batch" ) -print("Create output AnnData object") +print("Create output AnnData object", flush=True) output = ad.AnnData( uns={ - "dataset_id": adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - "method_id": adata.uns['method_id'], + "dataset_id": input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + "method_id": input_integrated.uns['method_id'], "metric_ids": [meta['functionality_name']], "metric_values": [score] } diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/script.py b/src/tasks/batch_integration/metrics/isolated_label_asw/script.py index 1613230a8f..176239665b 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/script.py +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/script.py @@ -13,16 +13,14 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.obsm["X_emb"] = input_integrated.obsm["X_emb"] -print('preprocess data', flush=True) -adata.X = adata.layers['normalized'] -adata_int = adata.copy() - -print('compute score') +print('compute score', flush=True) score = isolated_labels_asw( - adata, + input_solution, label_key='label', batch_key='batch', embed='X_emb', @@ -34,9 +32,9 @@ print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/script.py b/src/tasks/batch_integration/metrics/isolated_label_f1/script.py index f32167ed44..8c89b98f8f 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/script.py +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/script.py @@ -13,16 +13,18 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.obsp["connectivities"] = input_integrated.obsp["connectivities"] +input_solution.obsp["distances"] = input_integrated.obsp["distances"] -print('preprocess data', flush=True) -adata.X = adata.layers['normalized'] -adata_int = adata.copy() +# TODO: if we don't copy neighbors over, the metric doesn't work +input_solution.uns["neighbors"] = input_integrated.uns["neighbors"] -print('compute score') +print('compute score', flush=True) score = isolated_labels_f1( - adata, + input_solution, label_key='label', batch_key='batch', embed=None, @@ -34,9 +36,9 @@ print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/kbet/script.py b/src/tasks/batch_integration/metrics/kbet/script.py index cdbf4029f8..24cf8bdf69 100644 --- a/src/tasks/batch_integration/metrics/kbet/script.py +++ b/src/tasks/batch_integration/metrics/kbet/script.py @@ -13,12 +13,13 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.obsm["X_emb"] = input_integrated.obsm["X_emb"] print('compute score', flush=True) - score = kBET( - adata, + input_solution, batch_key="batch", label_key="label", type_="embed", @@ -31,9 +32,9 @@ print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/metrics/lisi/script.py b/src/tasks/batch_integration/metrics/lisi/script.py index 10e1aefce3..129389bff9 100644 --- a/src/tasks/batch_integration/metrics/lisi/script.py +++ b/src/tasks/batch_integration/metrics/lisi/script.py @@ -13,19 +13,18 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) -print('recompute kNN graph..', flush=True) -output_type = adata.uns['output_type'] -adata_tmp = recompute_knn( - adata, - type_=output_type, - use_rep= "X_emb" if output_type == 'embed' else "X_pca", -) +input_solution.obsp["connectivities"] = input_integrated.obsp["connectivities"] +input_solution.obsp["distances"] = input_integrated.obsp["distances"] + +# TODO: if we don't copy neighbors over, the metric doesn't work +input_solution.uns["neighbors"] = input_integrated.uns["neighbors"] print('compute iLISI score...', flush=True) ilisi_scores = lisi_graph_py( - adata=adata_tmp, + adata=input_solution, obs_key='batch', n_neighbors=90, perplexity=None, @@ -34,11 +33,11 @@ verbose=False, ) ilisi = np.nanmedian(ilisi_scores) -ilisi = (ilisi - 1) / (adata.obs['batch'].nunique() - 1) +ilisi = (ilisi - 1) / (input_solution.obs['batch'].nunique() - 1) print('compute cLISI scores...', flush=True) clisi_scores = lisi_graph_py( - adata=adata_tmp, + adata=input_solution, obs_key='label', n_neighbors=90, perplexity=None, @@ -47,15 +46,15 @@ verbose=False, ) clisi = np.nanmedian(clisi_scores) -nlabs = adata.obs['label'].nunique() +nlabs = input_solution.obs['label'].nunique() clisi = (nlabs - clisi) / (nlabs - 1) print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ 'ilisi_graph', 'clisi_graph' ], 'metric_values': [ ilisi, clisi ] } diff --git a/src/tasks/batch_integration/metrics/pcr/script.py b/src/tasks/batch_integration/metrics/pcr/script.py index 5e5d7edce6..392332963c 100644 --- a/src/tasks/batch_integration/metrics/pcr/script.py +++ b/src/tasks/batch_integration/metrics/pcr/script.py @@ -13,17 +13,14 @@ ## VIASH END print('Read input', flush=True) -adata = ad.read_h5ad(par['input_integrated']) +input_solution = ad.read_h5ad(par['input_solution']) +input_integrated = ad.read_h5ad(par['input_integrated']) +input_solution.X = input_solution.layers['normalized'] - -print('preprocess data', flush=True) -adata.X = adata.layers['normalized'] -adata_int = adata.copy() - -print('compute score') +print('compute score', flush=True) score = pcr_comparison( - adata, - adata_int, + input_solution, + input_integrated, embed='X_emb', covariate='batch', verbose=False @@ -32,9 +29,9 @@ print('Create output AnnData object', flush=True) output = ad.AnnData( uns={ - 'dataset_id': adata.uns['dataset_id'], - 'normalization_id': adata.uns['normalization_id'], - 'method_id': adata.uns['method_id'], + 'dataset_id': input_solution.uns['dataset_id'], + 'normalization_id': input_solution.uns['normalization_id'], + 'method_id': input_integrated.uns['method_id'], 'metric_ids': [ meta['functionality_name'] ], 'metric_values': [ score ] } diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index 8faf3f7bf6..f4ec46ec2c 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -55,7 +55,9 @@ def compute_batched_hvg(adata, n_hvgs): slot_info = read_config_slots_info(meta["config"], slot_mapping) print(">> Create output object", flush=True) -output = subset_anndata(adata_with_hvg, slot_info["output"]) +output_dataset = subset_anndata(adata_with_hvg, slot_info["output_dataset"]) +output_solution = subset_anndata(adata_with_hvg, slot_info["output_solution"]) print('Writing adatas to file', flush=True) -output.write(par['output'], compression='gzip') +output_dataset.write(par['output_dataset'], compression='gzip') +output_solution.write(par['output_solution'], compression='gzip') diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index 3a4dddda5e..cd88640498 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -20,22 +20,23 @@ mkdir -p $DATASET_DIR echo process data... viash run src/tasks/batch_integration/process_dataset/config.vsh.yaml -- \ --input $RAW_DATA \ - --output $DATASET_DIR/unintegrated.h5ad \ + --output_dataset $DATASET_DIR/dataset.h5ad \ + --output_solution $DATASET_DIR/solution.h5ad \ --hvgs 100 echo Running BBKNN viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/unintegrated.h5ad \ + --input $DATASET_DIR/dataset.h5ad \ --output $DATASET_DIR/integrated_graph.h5ad echo Running SCVI viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ - --input $DATASET_DIR/unintegrated.h5ad \ + --input $DATASET_DIR/dataset.h5ad \ --output $DATASET_DIR/integrated_embedding.h5ad echo Running combat viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/unintegrated.h5ad \ + --input $DATASET_DIR/dataset.h5ad \ --output $DATASET_DIR/integrated_feature.h5ad # run one metric From aa5274510351ee1d82c32d23a20c3f11ba60da87 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 30 Aug 2023 14:26:32 +0200 Subject: [PATCH 0984/1233] split fastmnn into fastmnn_feature and fastmnn_embed (#219) * split fastmnn into fastmnn_feature and fastmnn_embed * add workaround * replace outdated notation replace as(., "dgCMatrix") with as(., "sparseMatrix") * add v1 path Former-commit-id: e485faa7fbc056b86d500962183e1d5e1f00b3f7 --- .../config.vsh.yaml | 9 ++-- .../methods/fastmnn_feature/config.vsh.yaml | 41 +++++++++++++++++++ .../{fastmnn => fastmnn_feature}/script.R | 22 ++++------ 3 files changed, 56 insertions(+), 16 deletions(-) rename src/tasks/batch_integration/methods/{fastmnn => fastmnn_embedding}/config.vsh.yaml (83%) create mode 100644 src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml rename src/tasks/batch_integration/methods/{fastmnn => fastmnn_feature}/script.R (58%) diff --git a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml similarity index 83% rename from src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml rename to src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index b1ea4bec9e..344edf223a 100644 --- a/src/tasks/batch_integration/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -1,9 +1,9 @@ # use method api spec __merge__: ../../api/comp_method_embedding.yaml functionality: - name: fastmnn + name: fastmnn_embedding info: - label: fastMnn + label: fastMnn (embedding) summary: "A simpler version of the original mnnCorrect algorithm." description: | The fastMNN() approach is much simpler than the original mnnCorrect() algorithm, and proceeds in several steps. @@ -18,9 +18,12 @@ functionality: repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" preferred_normalization: log_cp10k + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/fastmnn.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: r_script - path: script.R + path: ../fastmnn_feature/script.R platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.1 diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml new file mode 100644 index 0000000000..6946cf2239 --- /dev/null +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -0,0 +1,41 @@ +# use method api spec +__merge__: ../../api/comp_method_feature.yaml +functionality: + name: fastmnn_feature + info: + label: fastMnn (feature) + summary: "A simpler version of the original mnnCorrect algorithm." + description: | + The fastMNN() approach is much simpler than the original mnnCorrect() algorithm, and proceeds in several steps. + + 1. Perform a multi-sample PCA on the (cosine-)normalized expression values to reduce dimensionality. + 2. Identify MNN pairs in the low-dimensional space between a reference batch and a target batch. + 3. Remove variation along the average batch vector in both reference and target batches. + 4. Correct the cells in the target batch towards the reference, using locally weighted correction vectors. + 5. Merge the corrected target batch with the reference, and repeat with the next target batch. + + reference: "haghverdi2018batch" + repository_url: "https://code.bioconductor.org/browse/batchelor/" + documentation_url: "https://bioconductor.org/packages/batchelor/" + preferred_normalization: log_cpm + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/fastmnn.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + # - type: r + # bioc: batchelor + # workaround for DelayedArray issue + - type: apt + packages: git + - type: r + script: + - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") + - type: nextflow + directives: + label: [ lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/fastmnn/script.R b/src/tasks/batch_integration/methods/fastmnn_feature/script.R similarity index 58% rename from src/tasks/batch_integration/methods/fastmnn/script.R rename to src/tasks/batch_integration/methods/fastmnn_feature/script.R index 6ae1ab84fe..7da33bc9cc 100644 --- a/src/tasks/batch_integration/methods/fastmnn/script.R +++ b/src/tasks/batch_integration/methods/fastmnn_feature/script.R @@ -27,20 +27,16 @@ out <- suppressWarnings(batchelor::fastMNN( )) cat("Reformat output\n") -obsm <- SingleCellExperiment::reducedDim(out, "corrected") -adata$obsm[["X_emb"]] <- obsm -# return_type == "feature" is currently not working in fastMNN +# reusing the same script for fastmnn_embed and fastmnn_feature +return_type <- gsub("fastmnn_", "", meta[["functionality_name"]]) -# # reusing the same script for mnn_correct and mnn_correct_feature -# return_type <- gsub("mnn_correct_", "", meta[["functionality_name"]]) - -# if (return_type == "feature") { -# layer <- SummarizedExperiment::assay(out, "corrected") -# adata$layers[["corrected_counts"]] <- as(t(layer), "sparseMatrix") -# } else if (return_type == "embedding") { -# obsm <- SingleCellExperiment::reducedDim(out, "corrected") -# adata$obsm[["X_emb"]] <- obsm -# } +if (return_type == "feature") { + layer <- as(SummarizedExperiment::assay(out, "reconstructed"), "sparseMatrix") + adata$layers[["corrected_counts"]] <- t(layer) +} else if (return_type == "embedding") { + obsm <- SingleCellExperiment::reducedDim(out, "corrected") + adata$obsm[["X_emb"]] <- obsm +} cat("Store outputs\n") adata$uns[["method_id"]] <- meta$functionality_name From 54fe7a9ecb9dedbea0ba411f26b6b90e449526ee Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 8 Sep 2023 16:29:49 +0200 Subject: [PATCH 0985/1233] Refactor workflows and datasets (#225) * don't simplify nxf module outputs * remove normalization_id en dataset_id from workflows * fix denoising file api * rename from_state to fromState and to_state to toState * fix configs * simplify test resource scripts Former-commit-id: 51487dbacb703d7abbc8c8f6402bb3fcfede70a8 --- _viash.yaml | 1 + .../resource_test_scripts/pancreas.sh | 8 +++- .../resource_test_scripts/pancreas_tasks.sh | 5 --- .../workflows/process_openproblems_v1/main.nf | 24 +++++------ .../workflows/run/config.vsh.yaml | 7 +++- .../batch_integration/workflows/run/main.nf | 24 +++++------ src/tasks/denoising/README.md | 4 +- src/tasks/denoising/api/file_dataset.yaml | 4 +- src/tasks/denoising/api/file_denoised.yaml | 8 +++- src/tasks/denoising/api/file_score.yaml | 2 +- src/tasks/denoising/api/file_test.yaml | 6 ++- src/tasks/denoising/api/file_train.yaml | 6 ++- .../resources_test_scripts/pancreas.sh | 35 ++++++++-------- .../denoising/workflows/run/config.vsh.yaml | 12 +----- src/tasks/denoising/workflows/run/main.nf | 42 ++++++++++--------- .../resources_test_scripts/pancreas.sh | 4 +- .../workflows/run/config.vsh.yaml | 8 +--- .../workflows/run/main.nf | 29 +++++++++---- .../resources_test_scripts/pancreas.sh | 5 +-- .../workflows/run/config.vsh.yaml | 8 ---- .../label_projection/workflows/run/main.nf | 39 ++++++++--------- .../methods/knnr_py/config.vsh.yaml | 1 + .../methods/knnr_r/config.vsh.yaml | 1 + .../methods/lm/config.vsh.yaml | 1 + .../methods/newwave_knnr/config.vsh.yaml | 1 + .../methods/random_forest/config.vsh.yaml | 1 + .../predict_modality/workflows/run/main.nf | 38 +++++++++-------- src/wf_utils/BenchmarkHelper.nf | 30 ++++++------- 28 files changed, 184 insertions(+), 170 deletions(-) delete mode 100755 src/datasets/resource_test_scripts/pancreas_tasks.sh diff --git a/_viash.yaml b/_viash.yaml index 12c157deb6..41872d9f1b 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -9,3 +9,4 @@ config_mods: | .platforms[.type == 'docker'].target_organization := 'openproblems-bio' .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems-v2' .platforms[.type == "nextflow"].directives.tag := "$id" + .platforms[.type == "nextflow"].auto.simplifyOutput := false diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 9a49f7c7de..50b28a50ee 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -62,4 +62,10 @@ viash run src/datasets/processors/knn/config.vsh.yaml -- \ --input $DATASET_DIR/hvg.h5ad \ --output $DATASET_DIR/dataset.h5ad -rm -r $DATASET_DIR/temp_* \ No newline at end of file +rm -r $DATASET_DIR/temp_* + +# rerun task process dataset components +src/tasks/batch_integration/resources_test_scripts/pancreas.sh +src/tasks/denoising/resources_test_scripts/pancreas.sh +src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +src/tasks/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/pancreas_tasks.sh b/src/datasets/resource_test_scripts/pancreas_tasks.sh deleted file mode 100755 index 803af8152c..0000000000 --- a/src/datasets/resource_test_scripts/pancreas_tasks.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -src/tasks/denoising/resources_test_scripts/pancreas.sh -src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh -src/tasks/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index dfca3e8b49..9edf15aa25 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -48,19 +48,19 @@ workflow run_wf { // fetch data from legacy openproblems | run_components( components: openproblems_v1, - from_state: [ + fromState: [ "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse", "dataset_name", "data_url", "data_reference", "dataset_summary", "dataset_description", "dataset_organism" ], - to_state: [ dataset: "output" ] + toState: [ dataset: "output" ] ) // run normalization methods | run_components( components: normalization_methods, id: { id, state, config -> id + "/" + config.functionality.name }, - from_state: [ input: "dataset" ], - to_state: [ + fromState: [ input: "dataset" ], + toState: [ normalization_id: config.functionality.name, output_normalization: "output" ] @@ -68,25 +68,25 @@ workflow run_wf { | run_components( components: pca, - from_state: [ input: "output_normalization" ], - to_state: [ pca: "output" ] + fromState: [ input: "output_normalization" ], + toState: [ pca: "output" ] ) | run_components( components: hvg, - from_state: [ input: "pca" ], - to_state: [ hvg: "output" ] + fromState: [ input: "pca" ], + toState: [ hvg: "output" ] ) | run_components( components: knn, - from_state: [ input: "hvg" ], - to_state: [ knn: "output" ] + fromState: [ input: "hvg" ], + toState: [ knn: "output" ] ) | run_components( components: check_dataset_schema, - from_state: {id, state, config -> + fromState: {id, state, config -> [ input: state.knn, meta: state.output_meta, @@ -94,7 +94,7 @@ workflow run_wf { checks: null ] }, - to_state: [], + toState: [], auto: [publish: true] ) diff --git a/src/tasks/batch_integration/workflows/run/config.vsh.yaml b/src/tasks/batch_integration/workflows/run/config.vsh.yaml index ad7028f7ba..7045a41fa8 100644 --- a/src/tasks/batch_integration/workflows/run/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run/config.vsh.yaml @@ -9,12 +9,17 @@ functionality: description: "The ID of the dataset" required: true - name: "--input" - type: "file" # todo: replace with includes + type: "file" + description: "A dataset" + required: true + example: dataset.h5ad - name: Outputs arguments: - name: "--output" direction: "output" type: file + description: A TSV file containing the scores of each of the methods + example: scores.tsv resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run/main.nf index 942878fd94..e0ef1268af 100644 --- a/src/tasks/batch_integration/workflows/run/main.nf +++ b/src/tasks/batch_integration/workflows/run/main.nf @@ -100,8 +100,8 @@ workflow run_wf { // extract the dataset metadata | run_components( components: check_dataset_schema, - from_state: ["input"], - to_state: { id, output, config -> + fromState: ["input"], + toState: { id, output, config -> new org.yaml.snakeyaml.Yaml().load(output.meta) } ) @@ -125,11 +125,11 @@ workflow run_wf { id + "." + config.functionality.name }, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: ["input"], + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: ["input"], - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ method_id: config.functionality.name, method_output: output.output, @@ -143,8 +143,8 @@ workflow run_wf { | run_components( components: feature_to_embed, filter: { id, state, config -> state.method_subtype == "feature"}, - from_state: [ input: "method_output" ], - to_state: { id, output, config -> + fromState: [ input: "method_output" ], + toState: { id, output, config -> [ method_output: output.output, method_subtype: config.functionality.info.subtype @@ -158,8 +158,8 @@ workflow run_wf { | run_components( components: embed_to_graph, filter: { id, state, config -> state.method_subtype == "embedding"}, - from_state: [ input: "method_output" ], - to_state: { id, output, config -> + fromState: [ input: "method_output" ], + toState: { id, output, config -> [ method_output: output.output, method_subtype: config.functionality.info.subtype @@ -175,8 +175,8 @@ workflow run_wf { filter: { id, state, config -> state.method_subtype == config.functionality.info.subtype }, - from_state: [input_integrated: "method_output"], - to_state: { id, output, config -> + fromState: [input_integrated: "method_output"], + toState: { id, output, config -> [ metric_id: config.functionality.name, metric_output: output.output diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index ab51f3e5a9..cda48318be 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -274,7 +274,7 @@ Arguments: NA -Example file: `resources_test/denoising/pancreas/magic.h5ad` +Example file: `resources_test/denoising/pancreas/denoised.h5ad` Description: @@ -307,7 +307,7 @@ Slot description: NA -Example file: `resources_test/denoising/pancreas/magic_poisson.h5ad` +Example file: `resources_test/denoising/pancreas/score.h5ad` Description: diff --git a/src/tasks/denoising/api/file_dataset.yaml b/src/tasks/denoising/api/file_dataset.yaml index b0b6fd10f8..327e0d5e59 100644 --- a/src/tasks/denoising/api/file_dataset.yaml +++ b/src/tasks/denoising/api/file_dataset.yaml @@ -1,14 +1,16 @@ type: file -description: "A preprocessed dataset" example: "resources_test/common/pancreas/dataset.h5ad" info: label: "Preprocessed dataset" + summary: A dataset containing raw counts and a dataset id. slots: layers: - type: integer name: counts description: Raw counts + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true diff --git a/src/tasks/denoising/api/file_denoised.yaml b/src/tasks/denoising/api/file_denoised.yaml index c60e1564a0..3f8ebc6e59 100644 --- a/src/tasks/denoising/api/file_denoised.yaml +++ b/src/tasks/denoising/api/file_denoised.yaml @@ -1,21 +1,25 @@ type: file -description: "The denoised data" -example: "resources_test/denoising/pancreas/magic.h5ad" +example: "resources_test/denoising/pancreas/denoised.h5ad" info: label: "Denoised data" + summary: A denoised dataset as output by a denoising method. slots: layers: - type: integer name: counts description: Raw counts + required: true - type: integer name: denoised description: denoised data + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true - type: string name: method_id description: "A unique identifier for the method" + required: true \ No newline at end of file diff --git a/src/tasks/denoising/api/file_score.yaml b/src/tasks/denoising/api/file_score.yaml index 04fb7a7330..4f34eeb7f7 100644 --- a/src/tasks/denoising/api/file_score.yaml +++ b/src/tasks/denoising/api/file_score.yaml @@ -1,6 +1,6 @@ type: file description: "Metric score file" -example: "resources_test/denoising/pancreas/magic_poisson.h5ad" +example: "resources_test/denoising/pancreas/score.h5ad" info: label: "Score" slots: diff --git a/src/tasks/denoising/api/file_test.yaml b/src/tasks/denoising/api/file_test.yaml index 98567d0dae..eddfa7b95f 100644 --- a/src/tasks/denoising/api/file_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -1,14 +1,16 @@ type: file -description: "The test data" example: "resources_test/denoising/pancreas/test.h5ad" info: label: "Test data" + summary: The subset of molecules used for the test dataset slots: layers: - type: integer name: counts description: Raw counts + required: true uns: - type: string name: dataset_id - description: "A unique identifier for the dataset" \ No newline at end of file + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/tasks/denoising/api/file_train.yaml b/src/tasks/denoising/api/file_train.yaml index f83051a6fe..302eae2d5c 100644 --- a/src/tasks/denoising/api/file_train.yaml +++ b/src/tasks/denoising/api/file_train.yaml @@ -1,14 +1,16 @@ type: file -description: "The training data" example: "resources_test/denoising/pancreas/train.h5ad" info: label: "Training data" + summary: The subset of molecules used for the training dataset slots: layers: - type: integer name: counts description: Raw counts + required: true uns: - type: string name: dataset_id - description: "A unique identifier for the dataset" \ No newline at end of file + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/tasks/denoising/resources_test_scripts/pancreas.sh b/src/tasks/denoising/resources_test_scripts/pancreas.sh index 0096c54db3..fb6bda4fab 100755 --- a/src/tasks/denoising/resources_test_scripts/pancreas.sh +++ b/src/tasks/denoising/resources_test_scripts/pancreas.sh @@ -19,23 +19,23 @@ fi mkdir -p $DATASET_DIR -# split dataset -viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output_train $DATASET_DIR/train.h5ad \ - --output_test $DATASET_DIR/test.h5ad \ - --seed 123 - -# run one method -viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ - --input_train $DATASET_DIR/train.h5ad \ - --output $DATASET_DIR/magic.h5ad - -# run one metric -viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ - --input_denoised $DATASET_DIR/magic.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --output $DATASET_DIR/magic_poisson.h5ad +# # split dataset +# viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ +# --input $RAW_DATA \ +# --output_train $DATASET_DIR/train.h5ad \ +# --output_test $DATASET_DIR/test.h5ad \ +# --seed 123 + +# # run one method +# viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ +# --input_train $DATASET_DIR/train.h5ad \ +# --output $DATASET_DIR/denoised.h5ad + +# # run one metric +# viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ +# --input_denoised $DATASET_DIR/denoised.h5ad \ +# --input_test $DATASET_DIR/test.h5ad \ +# --output $DATASET_DIR/score.h5ad # run benchmark export NXF_VER=22.04.5 @@ -46,7 +46,6 @@ nextflow \ -profile docker \ -resume \ --id pancreas \ - --dataset_id pancreas \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --output scores.tsv \ diff --git a/src/tasks/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run/config.vsh.yaml index 05ce8f8889..c14f308401 100644 --- a/src/tasks/denoising/workflows/run/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run/config.vsh.yaml @@ -8,18 +8,10 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - - name: "--normalization_id" - type: "string" - description: "The ID of the normalization used" - required: true - name: "--input_train" - type: "file" # todo: replace with includes + type: "file" - name: "--input_test" - type: "file" # todo: replace with includes + type: "file" - name: Outputs arguments: - name: "--output" diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf index ed7585aa82..88aa71215d 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run/main.nf @@ -1,8 +1,8 @@ -nextflow.enable.dsl=2 - sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + // import control methods include { no_denoising } from "$targetDir/denoising/control_methods/no_denoising/main.nf" include { perfect_denoising } from "$targetDir/denoising/control_methods/perfect_denoising/main.nf" @@ -62,26 +62,28 @@ workflow run_wf { output_ch = input_ch | preprocessInputs(config: config) - /// run all methods + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [ "input": "input_train" ], + toState: { id, output, state -> + // load output yaml file + def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + // add metadata from file to state + state + metadata + } + ) + + // run all methods | run_components( components: methods, - // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, config -> - def norm = state.normalization_id - def pref = config.functionality.info.preferred_normalization - // if the preferred normalisation is none at all, - // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref - }, - // define a new 'id' by appending the method name to the dataset id id: { id, state, config -> id + "." + config.functionality.name }, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: { id, state, config -> + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> def new_args = [ input_train: state.input_train, input_test: state.input_test @@ -90,8 +92,8 @@ workflow run_wf { }, - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ method_id: config.functionality.name, method_output: output.output @@ -102,13 +104,13 @@ workflow run_wf { // run all metrics | run_components( components: metrics, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: [ + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: [ input_test: "input_test", input_denoised: "method_output" ], - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ metric_id: config.functionality.name, metric_output: output.output diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index 165181ca72..b58b8007cb 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -8,7 +8,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/cp10k_dataset.h5ad +RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/dimensionality_reduction/pancreas if [ ! -f $RAW_DATA ]; then @@ -45,8 +45,6 @@ nextflow \ -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cp10k \ --input $DATASET_DIR/dataset.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ diff --git a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml index 3fc4113d1d..5c7427af0b 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml @@ -8,18 +8,12 @@ functionality: type: "string" description: "The ID of the normalized dataset" required: true - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - - name: "--input" + - name: "--input_dataset" type: "file" required: true - name: "--input_solution" type: "file" required: true - - name: "--normalization_id" - type: "string" - name: Outputs arguments: - name: "--output" diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index 6d0913191f..830ad2aa51 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -1,6 +1,8 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + // import control methods include { random_features } from "$targetDir/dimensionality_reduction/control_methods/random_features/main.nf" include { true_features } from "$targetDir/dimensionality_reduction/control_methods/true_features/main.nf" @@ -70,6 +72,15 @@ workflow run_wf { output_ch = input_ch | preprocessInputs(config: config) + // extract the dataset metadata + | run_components( + components: check_dataset_schema, + fromState: [input: "input_dataset"], + toState: { id, output, config -> + new org.yaml.snakeyaml.Yaml().load(output.meta) + } + ) + // run all methods | run_components( components: methods, @@ -88,10 +99,10 @@ workflow run_wf { id + "." + config.functionality.name }, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: { id, state, config -> + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> def new_args = [ - input: state.input + input: state.input_dataset ] if (config.functionality.info.type == "control_method") { new_args.input_solution = state.input_solution @@ -99,8 +110,8 @@ workflow run_wf { new_args }, - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ method_id: config.functionality.name, method_output: output.output @@ -111,15 +122,15 @@ workflow run_wf { // run all metrics | run_components( components: metrics, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: { id, state, config -> + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> [ input_solution: state.input_solution, input_embedding: state.method_output ] }, - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ metric_id: config.functionality.name, metric_output: output.output diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index bb3b687ba1..2beed71bb6 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/cp10k_dataset.h5ad +RAW_DATA=resources_test/common/pancreas/dataset.h5ad DATASET_DIR=resources_test/label_projection/pancreas if [ ! -f $RAW_DATA ]; then @@ -25,6 +25,7 @@ viash run src/tasks/label_projection/process_dataset/config.vsh.yaml -- \ --output_train $DATASET_DIR/train.h5ad \ --output_test $DATASET_DIR/test.h5ad \ --output_solution $DATASET_DIR/solution.h5ad \ + --method random \ --seed 123 # run one method @@ -48,8 +49,6 @@ nextflow \ -profile docker \ -resume \ --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cp10k \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ diff --git a/src/tasks/label_projection/workflows/run/config.vsh.yaml b/src/tasks/label_projection/workflows/run/config.vsh.yaml index 5ac96b82f2..b55bd8de96 100644 --- a/src/tasks/label_projection/workflows/run/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run/config.vsh.yaml @@ -8,14 +8,6 @@ functionality: type: "string" description: "The ID of the normalized dataset" required: true - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - - name: "--normalization_id" - type: "string" - description: "The ID of the normalization used" - required: true - name: "--input_train" # __merge__: ../../api/file_train.yaml type: file diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index d6f5146440..e74ef83bb3 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -1,6 +1,8 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + // import control methods include { true_labels } from "$targetDir/label_projection/control_methods/true_labels/main.nf" include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" @@ -71,9 +73,16 @@ workflow run_wf { // and fill in default values | preprocessInputs(config: config) - | view{ id, state -> - "input event: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, ...]" - } + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [ "input": "input_train" ], + toState: { id, output, state -> + // load output yaml file + def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + // add metadata from file to state + state + metadata + } + ) // run all methods | run_components( @@ -93,8 +102,8 @@ workflow run_wf { id + "." + config.functionality.name }, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: { id, state, config -> + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> def new_args = [ input_train: state.input_train, input_test: state.input_test @@ -105,8 +114,8 @@ workflow run_wf { new_args }, - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ method_id: config.functionality.name, method_output: output.output @@ -114,20 +123,16 @@ workflow run_wf { } ) - | view{ id, state -> - "after method: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, method_id: $state.method_id, ...]" - } - // run all metrics | run_components( components: metrics, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: [ + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: [ input_solution: "input_solution", input_prediction: "method_output" ], - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ metric_id: config.functionality.name, metric_output: output.output @@ -135,10 +140,6 @@ workflow run_wf { } ) - | view{ id, state -> - "after metric: [id: $id, dataset_id: $state.dataset_id, normalization_id: $state.normalization_id, method_id: $state.method_id, metric_id: $state.metric_id, ...]" - } - // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 1d188d18d2..96669a6d20 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: reference: fix1989discriminatory documentation_url: https://scikit-learn.org/stable/modules/neighbors.html repository_url: https://github.com/scikit-learn/scikit-learn + preferred_normalization: counts arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index cd70569e15..9425daea35 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: reference: fix1989discriminatory documentation_url: https://cran.r-project.org/package=FNN repository_url: https://github.com/cran/FNN + preferred_normalization: counts arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index f244e8f806..74670e8dbb 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: reference: wilkinson1973symbolic repository_url: https://github.com/RcppCore/RcppArmadillo documentation_url: https://cran.r-project.org/package=RcppArmadillo + preferred_normalization: counts arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index e3ba765967..e479a9432c 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: reference: agostinis2022newwave repository_url: https://github.com/fedeago/NewWave documentation_url: https://bioconductor.org/packages/release/bioc/html/NewWave.html + preferred_normalization: counts arguments: - name: "--newwave_maxiter" type: "integer" diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 3862c13ba8..4c971b545b 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -8,6 +8,7 @@ functionality: reference: breiman2001random documentation_url: https://www.stat.berkeley.edu/~breiman/RandomForests/reg_home.htm repository_url: https://github.com/cran/randomForest + preferred_normalization: counts arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run/main.nf index fc5bc3c346..652a232a20 100644 --- a/src/tasks/predict_modality/workflows/run/main.nf +++ b/src/tasks/predict_modality/workflows/run/main.nf @@ -1,6 +1,8 @@ sourceDir = params.rootDir + "/src" targetDir = params.rootDir + "/target/nextflow" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + // import control methods include { mean_per_gene } from "$targetDir/predict_modality/control_methods/mean_per_gene/main.nf" include { random_predict } from "$targetDir/predict_modality/control_methods/random_predict/main.nf" @@ -70,26 +72,28 @@ workflow run_wf { // and fill in default values | preprocessInputs(config: config) + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [ "input": "input_train_mod1" ], + toState: { id, output, state -> + // load output yaml file + def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + // add metadata from file to state + state + metadata + } + ) + // run all methods | run_components( components: methods, - // // use the 'filter' argument to only run a method on the normalisation the component is asking for - // filter: { id, state, config -> - // def norm = state.normalization_id - // def pref = config.functionality.info.preferred_normalization - // // if the preferred normalisation is none at all, - // // we can pass whichever dataset we want - // (norm == "log_cpm" && pref == "counts") || norm == pref - // }, - // define a new 'id' by appending the method name to the dataset id id: { id, state, config -> id + "." + config.functionality.name }, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: { id, state, config -> + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> def new_args = [ input_train_mod1: state.input_train_mod1, input_train_mod2: state.input_train_mod2, @@ -101,8 +105,8 @@ workflow run_wf { new_args }, - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ method_id: config.functionality.name, method_output: output.output @@ -113,13 +117,13 @@ workflow run_wf { // run all metrics | run_components( components: metrics, - // use 'from_state' to fetch the arguments the component requires from the overall state - from_state: [ + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: [ input_test_mod2: "input_test_mod2", input_prediction: "method_output" ], - // use 'to_state' to publish that component's outputs to the overall state - to_state: { id, output, config -> + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> [ metric_id: config.functionality.name, metric_output: output.output diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf index 42b1da4e61..d1ac0642ac 100644 --- a/src/wf_utils/BenchmarkHelper.nf +++ b/src/wf_utils/BenchmarkHelper.nf @@ -7,8 +7,8 @@ def run_components(Map args) { } assert components_.size() > 0: "pass at least one component to run_components" - def from_state_ = args.from_state - def to_state_ = args.to_state + def fromState_ = args.fromState + def toState_ = args.toState def filter_ = args.filter def id_ = args.id @@ -39,16 +39,16 @@ def run_components(Map args) { : filter_ch data_ch = id_ch | map{tup -> def new_data = tup[1] - if (from_state_ instanceof Map) { - new_data = from_state_.collectEntries{ key0, key1 -> + if (fromState_ instanceof Map) { + new_data = fromState_.collectEntries{ key0, key1 -> [key0, new_data[key1]] } - } else if (from_state_ instanceof List) { - new_data = from_state_.collectEntries{ key -> + } else if (fromState_ instanceof List) { + new_data = fromState_.collectEntries{ key -> [key, new_data[key]] } - } else if (from_state_ instanceof Closure) { - new_data = from_state_(tup[0], new_data, comp_config) + } else if (fromState_ instanceof Closure) { + new_data = fromState_(tup[0], new_data, comp_config) } tup.take(1) + [new_data] + tup.drop(1) } @@ -56,19 +56,19 @@ def run_components(Map args) { | comp_.run( auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] ) - post_ch = to_state_ + post_ch = toState_ ? out_ch | map{tup -> def new_outputs = tup[1] - if (to_state_ instanceof Map) { - new_outputs = to_state_.collectEntries{ key0, key1 -> + if (toState_ instanceof Map) { + new_outputs = toState_.collectEntries{ key0, key1 -> [key0, new_outputs[key1]] } - } else if (to_state_ instanceof List) { - new_outputs = to_state_.collectEntries{ key -> + } else if (toState_ instanceof List) { + new_outputs = toState_.collectEntries{ key -> [key, new_outputs[key]] } - } else if (to_state_ instanceof Closure) { - new_outputs = to_state_(tup[0], new_outputs, comp_config) + } else if (toState_ instanceof Closure) { + new_outputs = toState_(tup[0], new_outputs, comp_config) } [tup[0], tup[2] + new_outputs] + tup.drop(3) } From d109ab29559b3e4a90a88fa2ef921c24712b011d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Sep 2023 16:29:59 +0200 Subject: [PATCH 0986/1233] Bump tj-actions/changed-files from 38 to 39 (#228) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 38 to 39. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v38...v39) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 6181d459fb344a46e74f7aec4d9b0b209c7661e5 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 452c54e3f2..6f4a3c415b 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v38 + uses: tj-actions/changed-files@v39 with: separator: ";" diff_relative: true From 4778db11427891e9c780836f75591e991948217e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Sep 2023 16:30:06 +0200 Subject: [PATCH 0987/1233] Bump actions/checkout from 3 to 4 (#227) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: f3f27a989eb4b3805feb79ae1edd6d5e48cc76d9 --- .github/workflows/integration-test.yml | 6 +++--- .github/workflows/main-build.yml | 4 ++-- .github/workflows/release-build.yml | 8 ++++---- .github/workflows/viash-test.yml | 4 ++-- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 02abaa3513..409cb8a2b7 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -15,7 +15,7 @@ jobs: cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -85,7 +85,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -128,7 +128,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index d78bfe880c..4d97dc464e 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -14,7 +14,7 @@ jobs: cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -82,7 +82,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 9daa016c2d..dc07902732 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -20,7 +20,7 @@ jobs: cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -111,7 +111,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -155,7 +155,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 @@ -201,7 +201,7 @@ jobs: component: ${{ fromJson(needs.list.outputs.component_matrix) }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 6f4a3c415b..2fca5cd6fe 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -37,7 +37,7 @@ jobs: cache_key: ${{ steps.cache.outputs.cache_key }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: fetch-depth: 0 @@ -92,7 +92,7 @@ jobs: # Remove unnecessary files to free up space. Otherwise, we get 'no space left on device.' - uses: data-intuitive/reclaim-the-bytes@v2 - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: viash-io/viash-actions/setup@v4 From 60f52e382a30be24e4278e25f65e85da74cc58ce Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 8 Sep 2023 16:44:56 +0200 Subject: [PATCH 0988/1233] refactor multimodal data integration task (#201) * [WIP] harmonic alignment * refactor harmony method * add api files for methods * change git repo to original * refactor knn_auc metric * Delete unused files * add metric API files * WIP refactor mnn * WIP MNN method * fix testing * refactor scot mehod * refactor mse metric * add task_info * ci force * fix ci test * add directives * restore scot method * update scot github resource * restore scot import * add nextflow workflow * add nftower test script * fix mnn method * add procrustes method * Add v1 info * add control methods * fix mnn config * update NF workflow * update changelog * rename task to match_modality * add readme.qmd * rename task to match_modalities * update namesspace and paths * don't simplify nxf module outputs * remove normalization_id en dataset_id from workflows * fix denoising file api * rename from_state to fromState and to_state to toState * fix configs * simplify test resource scripts * rename mnn * update nf workflow * update scot method --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 06e942ab4095085026570b0265972b6535bb473c --- CHANGELOG.md | 47 +++++ src/common/library.bib | 12 ++ .../resource_test_scripts/multimodal.sh | 6 +- src/tasks/match_modalities/api/README.qmd | 8 + .../api/comp_control_method.yaml | 40 +++++ .../match_modalities/api/comp_method.yaml | 35 ++++ .../match_modalities/api/comp_metric.yaml | 31 ++++ .../api/comp_process_dataset.yaml | 32 ++++ .../api/file_integrated_mod1.yaml | 46 +++++ .../api/file_integrated_mod2.yaml | 46 +++++ src/tasks/match_modalities/api/file_mod1.yaml | 38 ++++ src/tasks/match_modalities/api/file_mod2.yaml | 38 ++++ .../match_modalities/api/file_score.yaml | 29 +++ src/tasks/match_modalities/api/task_info.yaml | 23 +++ .../random_features/config.vsh.yaml | 25 +++ .../control_methods/random_features/script.py | 31 ++++ .../true_features/config.vsh.yaml | 21 +++ .../control_methods/true_features/script.py | 30 ++++ .../methods/fastmnn/config.vsh.yaml | 34 ++++ .../match_modalities/methods/fastmnn/script.R | 37 ++++ .../harmonic_alignment/config.vsh.yaml | 38 ++++ .../methods/harmonic_alignment/script.py | 49 ++++++ .../methods/procrustes/config.vsh.yaml | 29 +++ .../methods/procrustes/script.py | 34 ++++ .../methods/scot/config.vsh.yaml | 30 ++++ .../match_modalities/methods/scot/script.py | 46 +++++ .../metrics/knn_auc/config.vsh.yaml | 36 ++++ .../metrics/knn_auc/script.py | 77 ++++++++ .../metrics/mse/config.vsh.yaml | 32 ++++ .../match_modalities/metrics/mse/script.py | 51 ++++++ .../workflows/run/config.vsh.yaml | 24 +++ .../match_modalities/workflows/run/main.nf | 165 ++++++++++++++++++ .../workflows/run/nextflow.config | 16 ++ .../workflows/run/run_test.sh | 30 ++++ .../workflows/run/run_test_on_tower.sh | 27 +++ .../multimodal_data_integration/README.md | 23 --- .../datasets/datasets_scprep_csv.tsv | 2 - .../datasets/sample_dataset/config.vsh.yaml | 41 ----- .../datasets/sample_dataset/script.py | 84 --------- .../datasets/sample_dataset/test.py | 63 ------- .../datasets/scprep_csv/config.vsh.yaml | 52 ------ .../datasets/scprep_csv/script.py | 52 ------ .../datasets/scprep_csv/test.py | 50 ------ .../harmonic_alignment/config.vsh.yaml | 55 ------ .../methods/harmonic_alignment/script.py | 59 ------- .../methods/harmonic_alignment/test.py | 37 ---- .../methods/mnn/config.vsh.yaml | 52 ------ .../methods/mnn/script.R | 51 ------ .../methods/mnn/test.py | 37 ---- .../methods/sample_method/config.vsh.yaml | 37 ---- .../methods/sample_method/script.py | 15 -- .../methods/sample_method/test.py | 37 ---- .../methods/scot/config.vsh.yaml | 54 ------ .../methods/scot/script.py | 53 ------ .../methods/scot/test.py | 37 ---- .../metrics/knn_auc/config.vsh.yaml | 48 ----- .../metrics/knn_auc/script.py | 65 ------- .../metrics/knn_auc/test.py | 34 ---- .../metrics/mse/config.vsh.yaml | 41 ----- .../metrics/mse/script.py | 40 ----- .../metrics/mse/test.py | 34 ---- .../utils/preprocessing.py | 52 ------ .../utils/utils.py | 97 ---------- .../workflows/run/main.nf | 75 -------- .../workflows/run/nextflow.config | 16 -- .../workflows/run/run_nextflow.sh | 21 --- 66 files changed, 1290 insertions(+), 1417 deletions(-) create mode 100644 src/tasks/match_modalities/api/README.qmd create mode 100644 src/tasks/match_modalities/api/comp_control_method.yaml create mode 100644 src/tasks/match_modalities/api/comp_method.yaml create mode 100644 src/tasks/match_modalities/api/comp_metric.yaml create mode 100644 src/tasks/match_modalities/api/comp_process_dataset.yaml create mode 100644 src/tasks/match_modalities/api/file_integrated_mod1.yaml create mode 100644 src/tasks/match_modalities/api/file_integrated_mod2.yaml create mode 100644 src/tasks/match_modalities/api/file_mod1.yaml create mode 100644 src/tasks/match_modalities/api/file_mod2.yaml create mode 100644 src/tasks/match_modalities/api/file_score.yaml create mode 100644 src/tasks/match_modalities/api/task_info.yaml create mode 100644 src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml create mode 100644 src/tasks/match_modalities/control_methods/random_features/script.py create mode 100644 src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml create mode 100644 src/tasks/match_modalities/control_methods/true_features/script.py create mode 100644 src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml create mode 100644 src/tasks/match_modalities/methods/fastmnn/script.R create mode 100644 src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml create mode 100644 src/tasks/match_modalities/methods/harmonic_alignment/script.py create mode 100644 src/tasks/match_modalities/methods/procrustes/config.vsh.yaml create mode 100644 src/tasks/match_modalities/methods/procrustes/script.py create mode 100644 src/tasks/match_modalities/methods/scot/config.vsh.yaml create mode 100644 src/tasks/match_modalities/methods/scot/script.py create mode 100644 src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml create mode 100644 src/tasks/match_modalities/metrics/knn_auc/script.py create mode 100644 src/tasks/match_modalities/metrics/mse/config.vsh.yaml create mode 100644 src/tasks/match_modalities/metrics/mse/script.py create mode 100644 src/tasks/match_modalities/workflows/run/config.vsh.yaml create mode 100644 src/tasks/match_modalities/workflows/run/main.nf create mode 100644 src/tasks/match_modalities/workflows/run/nextflow.config create mode 100755 src/tasks/match_modalities/workflows/run/run_test.sh create mode 100644 src/tasks/match_modalities/workflows/run/run_test_on_tower.sh delete mode 100644 src/tasks/multimodal_data_integration/README.md delete mode 100644 src/tasks/multimodal_data_integration/datasets/datasets_scprep_csv.tsv delete mode 100644 src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py delete mode 100644 src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py delete mode 100644 src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py delete mode 100644 src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py delete mode 100644 src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py delete mode 100644 src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py delete mode 100644 src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/methods/mnn/script.R delete mode 100644 src/tasks/multimodal_data_integration/methods/mnn/test.py delete mode 100644 src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/methods/sample_method/script.py delete mode 100644 src/tasks/multimodal_data_integration/methods/sample_method/test.py delete mode 100644 src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/methods/scot/script.py delete mode 100644 src/tasks/multimodal_data_integration/methods/scot/test.py delete mode 100644 src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/metrics/knn_auc/script.py delete mode 100644 src/tasks/multimodal_data_integration/metrics/knn_auc/test.py delete mode 100644 src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml delete mode 100644 src/tasks/multimodal_data_integration/metrics/mse/script.py delete mode 100644 src/tasks/multimodal_data_integration/metrics/mse/test.py delete mode 100644 src/tasks/multimodal_data_integration/utils/preprocessing.py delete mode 100644 src/tasks/multimodal_data_integration/utils/utils.py delete mode 100644 src/tasks/multimodal_data_integration/workflows/run/main.nf delete mode 100644 src/tasks/multimodal_data_integration/workflows/run/nextflow.config delete mode 100755 src/tasks/multimodal_data_integration/workflows/run/run_nextflow.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c84ff9790..c573ae74b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -304,3 +304,50 @@ * `metrics/rmse` should be removed because RMSE metrics don't really make sense here. * `metrics/trustworthiness` should be removed because it is already included in `metrics/coranking`. + + +## match_modalities (PR #201) + +### New functionality + +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the split, control method, method and metric components. + +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. + +* `control_methods`: Added a component for baseline methods specifically. + +* `resources_test/dimensionality_reduction/pancreas` with `src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh`. + +* Added `variant` key to config files to store variants (different input parameters) of every component. + +* `workflows/run`: Added nf-tower test script. + +### V1 migration + +* `control_methods/true_features`: Migrated from v1. Extracted from baseline method `True Features`. + +* `control_methods/random_features`: Migrated from v1. Extracted from baseline method `Random Features`. + +* `methods/harmonic_alignment`: Migrated from v1. + +* `methods/mnn`: Migrated from v1. + +* `methods/procrustes`: Migrated from v1. + +* `metrics/knn_auc`: Migrated from v1. + +* `metrics/mse`: Migrated from v1. + + +### Changes from V1 + +* `methods/scot`: Add new scot method. + +* Raw counts and normalized expression data is stored in `.layers["counts"]` and `.layers["normalized"]`, respectively, + instead of in `.X`. + +* The methods and metrics now take 2 modal datasets as input instead of 1. + + diff --git a/src/common/library.bib b/src/common/library.bib index abfcd7164c..1621b97334 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -343,6 +343,18 @@ @inproceedings{davis2006prauc @string{dec = {Dec.}} +@article{Demetci2020scot, + author = {Pinar Demetci and Rebecca Santorella and Bj{\"o}rn Sandstede and William Stafford Noble and Ritambhara Singh}, + title = {Gromov-Wasserstein optimal transport to align single-cell multi-omics data}, + elocation-id = {2020.04.28.066787}, + year = {2020}, + doi = {10.1101/2020.04.28.066787}, + publisher = {Cold Spring Harbor Laboratory}, + URL = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787}, + eprint = {https://www.biorxiv.org/content/early/2020/11/11/2020.04.28.066787.full.pdf}, + journal = {bioRxiv} +} + @article{dimitrov2022comparison, title = {Comparison of methods and resources for cell-cell communication inference from single-cell {RNA}-Seq data}, diff --git a/src/datasets/resource_test_scripts/multimodal.sh b/src/datasets/resource_test_scripts/multimodal.sh index 364efbf3ad..db6247c300 100644 --- a/src/datasets/resource_test_scripts/multimodal.sh +++ b/src/datasets/resource_test_scripts/multimodal.sh @@ -42,12 +42,12 @@ viash run src/datasets/processors/subsample/config.vsh.yaml -- \ --seed 123 -# run sqrt cpm normalisation on mod 1 file -viash run src/datasets/normalization/sqrt_cp/config.vsh.yaml -- \ +# run log cp10k normalisation on mod 1 file +viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ --input $DATASET_DIR/raw_mod1.h5ad \ --output $DATASET_DIR/normalized_mod1.h5ad -# run log cpm normalisation on mod 2 file +# run log cp10k normalisation on mod 2 file viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ --input $DATASET_DIR/raw_mod2.h5ad \ --output $DATASET_DIR/normalized_mod2.h5ad diff --git a/src/tasks/match_modalities/api/README.qmd b/src/tasks/match_modalities/api/README.qmd new file mode 100644 index 0000000000..d31a99367e --- /dev/null +++ b/src/tasks/match_modalities/api/README.qmd @@ -0,0 +1,8 @@ +--- +title: Component and file format specifications +format: gfm +--- + +This folder contains specifications for file formats and component interfaces. + +These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/match_modalities/api/comp_control_method.yaml b/src/tasks/match_modalities/api/comp_control_method.yaml new file mode 100644 index 0000000000..486d10be99 --- /dev/null +++ b/src/tasks/match_modalities/api/comp_control_method.yaml @@ -0,0 +1,40 @@ +functionality: + namespace: "match_modalities/control_methods" + info: + type: control_method + type_info: + label: Control method + summary: A multimodal data integration control method. + description: | + This folder contains control components for the task. + These components have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. + arguments: + - name: "--input_mod1" + __merge__: file_mod1.yaml + direction: input + required: true + - name: "--input_mod2" + __merge__: file_mod2.yaml + direction: input + required: true + - name: "--output_mod1" + __merge__: file_integrated_mod1.yaml + direction: output + required: true + - name: "--output_mod2" + __merge__: file_integrated_mod2.yaml + direction: output + required: true + test_resources: + - path: /resources_test/common/multimodal + dest: resources_test/common/multimodal + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib + - path: /src/common/api \ No newline at end of file diff --git a/src/tasks/match_modalities/api/comp_method.yaml b/src/tasks/match_modalities/api/comp_method.yaml new file mode 100644 index 0000000000..ce78af0147 --- /dev/null +++ b/src/tasks/match_modalities/api/comp_method.yaml @@ -0,0 +1,35 @@ +functionality: + namespace: "match_modalities/methods" + info: + type: method + type_info: + label: Method + summary: A multimodal data integration method. + description: | + A multimodal method to integrate data. + arguments: + - name: "--input_mod1" + __merge__: file_mod1.yaml + direction: input + required: true + - name: "--input_mod2" + __merge__: file_mod2.yaml + direction: input + required: true + - name: "--output_mod1" + __merge__: file_integrated_mod1.yaml + direction: output + required: true + - name: "--output_mod2" + __merge__: file_integrated_mod2.yaml + direction: output + required: true + test_resources: + - path: /resources_test/common/multimodal + dest: resources_test/common/multimodal + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib + - path: /src/common/api diff --git a/src/tasks/match_modalities/api/comp_metric.yaml b/src/tasks/match_modalities/api/comp_metric.yaml new file mode 100644 index 0000000000..2f1d7cafe8 --- /dev/null +++ b/src/tasks/match_modalities/api/comp_metric.yaml @@ -0,0 +1,31 @@ +functionality: + namespace: "match_modalities/metrics" + info: + type: metric + type_info: + label: Metric + summary: A multimodal data integration metric. + description: | + A metric for evaluating integrated data. + arguments: + - name: "--input_mod1" + __merge__: file_integrated_mod1.yaml + direction: input + required: true + - name: "--input_mod2" + __merge__: file_integrated_mod1.yaml + direction: input + required: true + - name: "--output" + __merge__: file_score.yaml + required: true + direction: output + test_resources: + - path: /resources_test/multimodal + dest: resources_test/multimodal + - type: python_script + path: /src/common/comp_tests/check_metric_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /src/common/library.bib + diff --git a/src/tasks/match_modalities/api/comp_process_dataset.yaml b/src/tasks/match_modalities/api/comp_process_dataset.yaml new file mode 100644 index 0000000000..13adb6ec84 --- /dev/null +++ b/src/tasks/match_modalities/api/comp_process_dataset.yaml @@ -0,0 +1,32 @@ +functionality: + namespace: "label_projection" + info: + type: process_dataset + type_info: + label: Data processor + summary: A label projection dataset processor. + description: | + A component for processing a Common Dataset into a task-specific dataset. + arguments: + - name: "--input" + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: input + required: true + - name: "--output_train" + __merge__: file_train.yaml + direction: output + required: true + - name: "--output_test" + __merge__: file_test.yaml + direction: output + required: true + - name: "--output_solution" + __merge__: file_solution.yaml + direction: output + required: true + test_resources: + - path: /resources_test/common/pancreas + dest: resources_test/common/pancreas + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + diff --git a/src/tasks/match_modalities/api/file_integrated_mod1.yaml b/src/tasks/match_modalities/api/file_integrated_mod1.yaml new file mode 100644 index 0000000000..87fbf669b4 --- /dev/null +++ b/src/tasks/match_modalities/api/file_integrated_mod1.yaml @@ -0,0 +1,46 @@ +type: file +example: "resources_test/multimodal/integrated_mod1.h5ad" +info: + label: "Integrated" + summary: "The integrated data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + - type: double + name: integrated + description: The resulting integrated embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: string + name: method_id + description: "Which method was used" + required: true diff --git a/src/tasks/match_modalities/api/file_integrated_mod2.yaml b/src/tasks/match_modalities/api/file_integrated_mod2.yaml new file mode 100644 index 0000000000..1fe32185c7 --- /dev/null +++ b/src/tasks/match_modalities/api/file_integrated_mod2.yaml @@ -0,0 +1,46 @@ +type: file +example: "resources_test/multimodal/integrated_mod2.h5ad" +info: + label: "Integrated" + summary: "The integrated data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + - type: double + name: integrated + description: The resulting integrated embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: string + name: method_id + description: "Which method was used" + required: true diff --git a/src/tasks/match_modalities/api/file_mod1.yaml b/src/tasks/match_modalities/api/file_mod1.yaml new file mode 100644 index 0000000000..4844c65acd --- /dev/null +++ b/src/tasks/match_modalities/api/file_mod1.yaml @@ -0,0 +1,38 @@ +type: file +example: "resources_test/common/multimodal/dataset_mod1.h5ad" +info: + label: "multimodal mod 1 data" + summary: "the first modal data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/file_mod2.yaml b/src/tasks/match_modalities/api/file_mod2.yaml new file mode 100644 index 0000000000..a4a4c4cc2e --- /dev/null +++ b/src/tasks/match_modalities/api/file_mod2.yaml @@ -0,0 +1,38 @@ +type: file +example: "resources_test/common/multimodal/dataset_mod2.h5ad" +info: + label: "multimodal mod 2 data" + summary: "the second modal data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/file_score.yaml b/src/tasks/match_modalities/api/file_score.yaml new file mode 100644 index 0000000000..a5158a2225 --- /dev/null +++ b/src/tasks/match_modalities/api/file_score.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/multimodal/score.h5ad" +info: + label: "Score" + summary: "Metric score file" + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + required: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true + required: true diff --git a/src/tasks/match_modalities/api/task_info.yaml b/src/tasks/match_modalities/api/task_info.yaml new file mode 100644 index 0000000000..4baeda74d0 --- /dev/null +++ b/src/tasks/match_modalities/api/task_info.yaml @@ -0,0 +1,23 @@ +name: match_modalities +label: Match Modalities +summary: | + Match modalities is the task of combining multiple datasets + that have been generated from the same set of samples. +motivation: "No motivation has been provided for this task." +description: | + Match modalities is the task of combining multiple datasets + that have been generated from the same set of samples. This task is + important for integrating datasets generated from different modalities + (e.g. RNA and ATAC) or from different technologies (e.g. 10x and + SmartSeq). The goal of this task is to evaluate methods for integrating + multimodal datasets. +authors: + - name: Robrecht Cannoodt + roles: [ author ] + info: + github: rcannood + orcid: "0000-0003-3641-729X" + - name: Kai Waldrant + roles: [ contributor ] + info: + github: KaiWaldrant \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml new file mode 100644 index 0000000000..5fb412ae9c --- /dev/null +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -0,0 +1,25 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: "random_features" + info: + label: Random Features + summary: "Randomly permutated features" + description: | + "Randomly permuted twice, once for use as the output for each modality, producing random features with no correlation between modalities." + preferred_normalization: log_cp10k + v1: + path: openproblems/tasks/matching_modalities/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + packages: + - numpy + - type: nextflow + directives: + label: [ lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/random_features/script.py b/src/tasks/match_modalities/control_methods/random_features/script.py new file mode 100644 index 0000000000..203e289762 --- /dev/null +++ b/src/tasks/match_modalities/control_methods/random_features/script.py @@ -0,0 +1,31 @@ +import anndata as ad +import numpy as np + +## VIASH START + +par = { + "input_mod1": "resources_test/common/multimodal/dataset_mod1.h5ad", + "input_mod2": "resources_test/common/multimodal/dataset_mod2.h5ad", + "output_mod1": "output.mod1.h5ad", + "output_mod2": "output.mod2.h5ad", +} + +meta = { + "functionality_name": "random_features" +} + +## VIASH END + +print("Reading input h5ad file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("Generating random features", flush=True) +adata_mod1.obsm["integrated"] = adata_mod1.obsm["X_svd"][np.random.permutation(np.arange(adata_mod1.shape[0]))] +adata_mod2.obsm["integrated"] = adata_mod1.obsm["X_svd"][np.random.permutation(np.arange(adata_mod1.shape[0]))] + +print("Write output to file", flush=True) +adata_mod1.uns["method_id"] = meta["functionality_name"] +adata_mod2.uns["method_id"] = meta["functionality_name"] +adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml new file mode 100644 index 0000000000..fd472d5e03 --- /dev/null +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -0,0 +1,21 @@ +__merge__: ../../api/comp_control_method.yaml +functionality: + name: "true_features" + info: + label: True Features + summary: "A 1 to 1 mapping of features between modalities" + description: | + "use the same features for both modalities" + preferred_normalization: log_cp10k + v1: + path: openproblems/tasks/matching_modalities/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/true_features/script.py b/src/tasks/match_modalities/control_methods/true_features/script.py new file mode 100644 index 0000000000..a3fb0fc9ea --- /dev/null +++ b/src/tasks/match_modalities/control_methods/true_features/script.py @@ -0,0 +1,30 @@ +import anndata as ad + +## VIASH START + +par = { + "input_mod1": "resources_test/common/multimodal/dataset_mod1.h5ad", + "input_mod2": "resources_test/common/multimodal/dataset_mod2.h5ad", + "output_mod1": "output.mod1.h5ad", + "output_mod2": "output.mod2.h5ad", +} + +meta = { + "functionality_name": "true_features" +} + +## VIASH END + +print("Reading input h5ad file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("Storing true features", flush=True) +adata_mod1.obsm["integrated"] = adata_mod1.obsm["X_svd"] +adata_mod2.obsm["integrated"] = adata_mod1.obsm["X_svd"] + +print("Write output to file", flush=True) +adata_mod1.uns["method_id"] = meta["functionality_name"] +adata_mod2.uns["method_id"] = meta["functionality_name"] +adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml new file mode 100644 index 0000000000..cee2751ca2 --- /dev/null +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -0,0 +1,34 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "fastmnn" + info: + label: "fastMNN" + summary: "A simpler version of the original mnnCorrect algorithm." + description: | + FastMNN is a simplified version of the mnnCorrect algorithm. Both use Mutual Nearest Neighbors to integrate multimodal single-cell data. + preferred_normalization: "log_cp10k" + variants: + mnn_log_cp10k: + mnn_log_scran_pooling: + # "The normalization only changes for the first modality dataset, the second still uses log_cp10k" + preferred_normalization: "log_scran_pooling" + reference: "haghverdi2018batch" + repository_url: "https://github.com/LTLA/batchelor" + documentation_url: "https://github.com/LTLA/batchelor#readme" + resources: + - type: r_script + path: ./script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: apt + packages: git + - type: r + cran: [Matrix, SingleCellExperiment] + script: + # Install batchelor from Bioconductor devel because the version on r2u is behind + - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/methods/fastmnn/script.R b/src/tasks/match_modalities/methods/fastmnn/script.R new file mode 100644 index 0000000000..65d93333bc --- /dev/null +++ b/src/tasks/match_modalities/methods/fastmnn/script.R @@ -0,0 +1,37 @@ +library(anndata, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) +requireNamespace("batchelor", quietly = TRUE) + +## VIASH START +par <- list( + input_mod1 = "resources_test/common/multimodal/dataset_mod1.h5ad", + input_mod2 = "resources_test/common/multimodal/dataset_mod2.h5ad", + output_mod1 = "output_mod1.h5ad", + output_mod2 = "output_mod2.h5ad" +) +## VIASH END + +cat("Reading input h5ad file\n") +adata_mod1 <- read_h5ad(par$input_mod1) +adata_mod2 <- read_h5ad(par$input_mod2) + +cat("Running MNN\n") +sce_mnn <- batchelor::fastMNN( + t(adata_mod1$obsm[["X_svd"]]), + t(adata_mod2$obsm[["X_svd"]]) +) + +cat("Storing output\n") +combined_recons <- t(SummarizedExperiment::assay(sce_mnn, "reconstructed")) +mode1_recons <- combined_recons[seq_len(nrow(adata_mod1$obsm[["X_svd"]])), , drop = FALSE] +mode2_recons <- combined_recons[-seq_len(nrow(adata_mod1$obsm[["X_svd"]])), , drop = FALSE] + +adata_mod1$obsm[["integrated"]] <- as.matrix(mode1_recons) +adata_mod2$obsm[["integrated"]] <- as.matrix(mode2_recons) + +cat("Writing to file\n") +adata_mod1$uns["method_id"] <- meta$functionality_name +adata_mod2$uns["method_id"] <- meta$functionality_name + +yyy <- adata_mod1$write_h5ad(par$output_mod1, compression = "gzip") +zzz <- adata_mod2$write_h5ad(par$output_mod2, compression = "gzip") diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml new file mode 100644 index 0000000000..06a5a0475c --- /dev/null +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -0,0 +1,38 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "harmonic_alignment" + info: + label: "Harmonic Alignment" + summary: "Harmonic Alignment" + description: | + Harmonic Alignment is a method for integrating multimodal single-cell data. It is based on the idea of aligning the eigenvectors of the Laplacian matrices of the two modalities. The alignment is achieved by solving a generalized eigenvalue problem. The method is described in the following paper: https://doi.org/10.1137/1.9781611976236.36 + preferred_normalization: "log_cp10k" + v1: + path: openproblems/tasks/matching_modalities/methods/harmonic_alignment.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + reference: "stanley2020harmonic" + documentation_url: "https://github.com/KrishnaswamyLab/harmonic-alignment#readme" + repository_url: "https://github.com/KrishnaswamyLab/harmonic-alignment" + arguments: + - name: "--n_pca_XY" + type: "integer" + default: 100 + description: "Default number of principal components on which to build graph." + - name: "--n_eigenvectors" + type: "integer" + default: 100 + description: "Number of eigenvectors of the normalized Laplacian on which to perform alignment." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + github: + - KrishnaswamyLab/harmonic-alignment#subdirectory=python + - type: nextflow + directives: + label: [ lowmem, lowcpu ] + diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/script.py b/src/tasks/match_modalities/methods/harmonic_alignment/script.py new file mode 100644 index 0000000000..9fdb5f7102 --- /dev/null +++ b/src/tasks/match_modalities/methods/harmonic_alignment/script.py @@ -0,0 +1,49 @@ +import anndata as ad +import harmonicalignment + +## VIASH START +par = { + "mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", + "mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "output" : "output.scot.h5ad", + "n_pca_XY" : 100, + "eigenvectors" : 100 +} + +meta = { + "functionality_name" : "harmonic_alignment" + } +## VIASH END + + +print("Reading input h5ad file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("Check parameters", flush=True) +n_eigenvectors = par["n_eigenvectors"] +n_pca_XY = par["n_pca_XY"] + +if adata_mod1.layers["normalized"].shape[0] <= n_eigenvectors: + n_eigenvectors = None +if adata_mod1.layers["normalized"].shape[0] <= n_pca_XY: + n_pca_XY = None + + +print("Running Harmonic Alignment", flush=True) +ha_op = harmonicalignment.HarmonicAlignment( + n_filters=8, n_pca_XY=n_pca_XY, n_eigenvectors=n_eigenvectors +) +ha_op.align(adata_mod1.obsm["X_svd"], adata_mod2.obsm["X_svd"]) +XY_aligned = ha_op.diffusion_map(n_eigenvectors=n_eigenvectors) + +print("Storing output data structures", flush=True) + +adata_mod1.obsm["integrated"] = XY_aligned[: adata_mod1.obsm["X_svd"].shape[0]] +adata_mod2.obsm["integrated"] = XY_aligned[-adata_mod2.obsm["X_svd"].shape[0] :] + +print("Write output to file", flush=True) +adata_mod1.uns["method_id"] = meta["functionality_name"] +adata_mod2.uns["method_id"] = meta["functionality_name"] +adata_mod1.write_h5ad(par["output_mod1"], compression = "gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression = "gzip") diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml new file mode 100644 index 0000000000..25f574fae7 --- /dev/null +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -0,0 +1,29 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "procrustes" + info: + label: Procrustes + summary: | + "Procrustes superimposition embeds cellular data from each modality into a common space." + description: | + "Procrustes superimposition embeds cellular data from each modality into a common space by aligning the 100-dimensional SVD embeddings to one another by using an isomorphic transformation that minimizes the root mean squared distance between points. The unmodified SVD embedding and the transformed second modality are used as output for the task." + v1: + path: openproblems/tasks/matching_modalities/methods/procrustes.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + reference: gower1975generalized + documentation_url: https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.procrustes.html + repository_url: https://github.com/scipy/scipy + preferred_normalization: "log_cp10k" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scipy + - type: nextflow + directives: + label: [ medcpu, medmem ] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/procrustes/script.py b/src/tasks/match_modalities/methods/procrustes/script.py new file mode 100644 index 0000000000..20afe28d91 --- /dev/null +++ b/src/tasks/match_modalities/methods/procrustes/script.py @@ -0,0 +1,34 @@ +import anndata as ad +import scipy.spatial + +## VIASH START + +par = { + "input_mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", + "input_mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "output_mod1" : "output.mod1.h5ad", + "output_mod2" : "output.mod2.h5ad", +} + +meta = { + "functionality_name" : "procrustes" +} + +## VIASH END + +print("Reading input h5ad file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("procrustes alignment", flush=True) +X_proc, Y_proc, _ = scipy.spatial.procrustes(adata_mod1.obsm["X_svd"], adata_mod2.obsm["X_svd"]) + +print("Storing output data", flush=True) +adata_mod1.obsm["integrated"] = X_proc +adata_mod2.obsm["integrated"] = Y_proc + +print("Write output to file", flush=True) +adata_mod1.uns["method_id"] = meta["functionality_name"] +adata_mod2.uns["method_id"] = meta["functionality_name"] +adata_mod1.write_h5ad(par["output_mod1"], compression = "gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression = "gzip") diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml new file mode 100644 index 0000000000..0c616338d6 --- /dev/null +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -0,0 +1,30 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "scot" + info: + label: "Single Cell Optimal Transport" + description: | + Single Cell Optimal Transport (SCOT) is a method for integrating multimodal single-cell data. It is based on the idea of aligning the distributions of the two modalities using optimal transport. + summary: "Run Single Cell Optimal Transport" + preferred_normalization: "log_cpm" + reference: Demetci2020scot + documentation_url: "https://github.com/rsinghlab/SCOT#readme" + repository_url: "https://github.com/rsinghlab/SCOT" + arguments: + - name: "--balanced" + type: "boolean_true" + description: "Determines whether balanced or unbalanced optimal transport. In the balanced case, the target and source distributions are assumed to have equal mass." + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: apt + packages: git + - type: docker + run: "cd /opt && git clone --depth 1 https://github.com/rsinghlab/SCOT.git && cd SCOT && pip install -r requirements.txt" + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/methods/scot/script.py b/src/tasks/match_modalities/methods/scot/script.py new file mode 100644 index 0000000000..e43b685131 --- /dev/null +++ b/src/tasks/match_modalities/methods/scot/script.py @@ -0,0 +1,46 @@ +import anndata as ad +import sys +sys.path.append("/opt/SCOT/src/") +import scotv1 +import pandas as pd + +# importing helper functions from common preprocessing.py file in resources dir +import sys + + +## VIASH START +par = { + "input_mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", + "input_mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "output_mod1" : "integrated_mod1.h5ad", + "output_mod2" : "integrated_mod2.h5ad", + "balanced":False, +} + +## VIASH END + + +print("Reading input h5ad file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + + +print("Initialize SCOT", flush=True) +scot = scotv1.SCOT(adata_mod1.obsm["X_svd"], adata_mod2.obsm["X_svd"]) + +print("Call the unbalanced alignment", flush=True) +# From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 +X_new_unbal, y_new_unbal = scot.align( + k=50, e=1e-3, normalize=True +) + + +print("store output", flush=True) +adata_mod1.obsm["integrated"] = X_new_unbal +adata_mod2.obsm["integrated"] = y_new_unbal + +print("Write output to file", flush=True) +adata_mod1.uns["method_id"] = meta["functionality_name"] +adata_mod2.uns["method_id"] = meta["functionality_name"] +adata_mod1.write_h5ad(par["output_mod1"], compression = "gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression = "gzip") diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml new file mode 100644 index 0000000000..68eba8c8cb --- /dev/null +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -0,0 +1,36 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: "knn_auc" + info: + metrics: + - label: KNN AUC + name: knn_auc + summary: "Compute the kNN Area Under the Curve" + description: | + "Compute the kNN Area Under the Curve" + reference: "" + min: 0 + max: 1 + maximize: true + v1: + path: openproblems/tasks/matching_modalities/metrics/knn_auc.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + arguments: + - name: "--proportion_neighbors" + type: "double" + default: 0.1 + description: The proportion of neighbours to use in computing the KNN. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + packages: + - numpy + - scikit-learn + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/metrics/knn_auc/script.py b/src/tasks/match_modalities/metrics/knn_auc/script.py new file mode 100644 index 0000000000..87083b6ae7 --- /dev/null +++ b/src/tasks/match_modalities/metrics/knn_auc/script.py @@ -0,0 +1,77 @@ +import anndata as ad +import numpy as np +import sklearn.decomposition +import sklearn.neighbors + +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input_mod1": "resources_test/multimodal/integrated_mod1.h5ad", + "input_mod2": "resources_test/multimodal/integrated_mod2.h5ad", + "output": "resources_test/multimodal/score.h5ad", + "proportion_neighbors": 0.1, +} + +meta = { + "functionality_name": "knn_auc" +} +## VIASH END + +print("Reading adata file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("Checking parameters", flush=True) +n_neighbors = int(np.ceil(par["proportion_neighbors"] * adata_mod1.layers["normalized"].shape[0])) + +print("Compute KNN on PCA", flush=True) +_, indices_true = ( + sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) + .fit(adata_mod1.obsm["X_svd"]) + .kneighbors(adata_mod1.obsm["X_svd"]) +) + +print("Compute KNN on integrated matrix", flush=True) +_, indices_pred = ( + sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) + .fit(adata_mod1.obsm["integrated"]) + .kneighbors(adata_mod2.obsm["integrated"]) +) + +print("Check which neighbours match", flush=True) +print("Check which neighbours match", flush=True) +neighbors_match = np.zeros(n_neighbors, dtype=int) +for i in range(adata_mod1.layers["normalized"].shape[0]): + _, pred_matches, true_matches = np.intersect1d( + indices_pred[i], indices_true[i], return_indices=True + ) + neighbors_match_idx = np.maximum(pred_matches, true_matches) + neighbors_match += np.sum( + np.arange(n_neighbors) >= neighbors_match_idx[:, None], + axis=0, + ) + +print("Compute area under neighbours match curve", flush=True) +print("Compute area under neighbours match curve", flush=True) +neighbors_match_curve = neighbors_match / ( + np.arange(1, n_neighbors + 1) * adata_mod1.layers["normalized"].shape[0] +) +area_under_curve = np.mean(neighbors_match_curve) + +print("Store metic value", flush=True) +output_metric = ad.AnnData( + layers={}, + obs=adata_mod1.obs[[]], + var=adata_mod1.var[[]], + uns={}, +) + +for key in adata_mod1.uns_keys(): + output_metric.uns[key] = adata_mod1.uns[key] + +output_metric.uns["metric_ids"] = meta["functionality_name"] +output_metric.uns["metric_values"] = area_under_curve + +print("Writing adata to file", flush=True) +output_metric.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml new file mode 100644 index 0000000000..8882856c75 --- /dev/null +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -0,0 +1,32 @@ +__merge__: ../../api/comp_metric.yaml +functionality: + name: "mse" + info: + metrics: + - label: "Mean Squared Error" + name: "mse" + summary: Compute the mean squared error. + description: | + The mean squared error (MSE) is a measure of the quality of an estimator. It is always non-negative, and values closer to zero are better. + reference: "" + maximize: true + min: 0 + max: "+.inf" + v1: + path: openproblems/tasks/matching_modalities/metrics/mse.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + resources: + - type: python_script + path: ./script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + packages: + - numpy + - scipy + - scprep + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/metrics/mse/script.py b/src/tasks/match_modalities/metrics/mse/script.py new file mode 100644 index 0000000000..6710b3dac2 --- /dev/null +++ b/src/tasks/match_modalities/metrics/mse/script.py @@ -0,0 +1,51 @@ +import anndata as ad +import scprep +import numpy as np +from scipy import sparse + +## VIASH START +# The code between the the comments above and below gets stripped away before +# execution. Here you can put anything that helps the prototyping of your script. +par = { + "input_mod1": "resources_test/multimodal/integrated_mod1.h5ad", + "input_mod2": "resources_test/multimodal/integrated_mod2.h5ad", + "output": "resources_test/multimodal/mse.h5ad" +} +## VIASH END + +print("Reading adata file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +print("Computing MSE", flush=True) +def _square(X): + if sparse.issparse(X): + X.data = X.data ** 2 + return X + else: + return scprep.utils.toarray(X) ** 2 + +X = scprep.utils.toarray(adata_mod1.obsm["integrated"]) +Y = scprep.utils.toarray(adata_mod2.obsm["integrated"]) + +X_shuffled = X[np.random.permutation(np.arange(X.shape[0])), :] +error_random = np.mean(np.sum(_square(X_shuffled - Y))) +error_abs = np.mean(np.sum(_square(X - Y))) +metric_value = error_abs / error_random + +output_metric = ad.AnnData( + layers={}, + obs=adata_mod1.obs[[]], + var=adata_mod1.var[[]], + uns={} +) + +for key in adata_mod1.uns_keys(): + output_metric.uns[key] = adata_mod1.uns[key] + +print("Store metic value", flush=True) +output_metric.uns["metric_ids"] = meta["functionality_name"] +output_metric.uns["metric_values"] = metric_value + +print("Writing adata to file", flush=True) +output_metric.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/match_modalities/workflows/run/config.vsh.yaml b/src/tasks/match_modalities/workflows/run/config.vsh.yaml new file mode 100644 index 0000000000..0ee57fa9a8 --- /dev/null +++ b/src/tasks/match_modalities/workflows/run/config.vsh.yaml @@ -0,0 +1,24 @@ +functionality: + name: "run_benchmark" + namespace: "match_modalities/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input_mod1" + type: "file" # todo: replace with includes + - name: "--input_mod2" + type: "file" + - name: Outputs + arguments: + - name: "--output" + direction: "output" + type: file + resources: + - type: nextflow_script + path: main.nf +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/main.nf b/src/tasks/match_modalities/workflows/run/main.nf new file mode 100644 index 0000000000..e6318d7dda --- /dev/null +++ b/src/tasks/match_modalities/workflows/run/main.nf @@ -0,0 +1,165 @@ +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + +// import control methods +include { random_features } from "$targetDir/match_modalities/control_methods/random_features/main.nf" params(params) +include { true_features } from "$targetDir/match_modalities/control_methods/true_features/main.nf" params(params) + +// import methods +include { fastmnn } from "$targetDir/match_modalities/methods/fastmnn/main.nf" params(params) +include { scot } from "$targetDir/match_modalities/methods/scot/main.nf" params(params) +include { harmonic_alignment } from "$targetDir/match_modalities/methods/harmonic_alignment/main.nf" params(params) +include { procrustes } from "$targetDir/match_modalities/methods/procrustes/main.nf" params(params) + +// import metrics +include { knn_auc } from "$targetDir/match_modalities/metrics/knn_auc/main.nf" params(params) +include { mse } from "$targetDir/match_modalities/metrics/mse/main.nf" params(params) + +// tsv generation component +include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) + +// import helper functions +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" + +// read in pipeline config +config = readConfig("$projectDir/config.vsh.yaml") + +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initialize_tracer() + +// collect method list +methods = [ + random_features, + true_features, + scot, + harmonic_alignment, + fastmnn, + procrustes +] + +// collect metric list +metrics = [ + knn_auc, + mse +] + +workflow { + helpMessage(config) + + // create channel from input parameters with + // arguments as defined in the config + channelFromParams(params, config) + | run_wf +} + + // run the workflow +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // based on the config file (config.vsh.yaml), run assertions on parameter sets + // and fill in default values + | preprocessInputs(config: config) + + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [ "input": "input_mod1" ], + toState: { id, output, state -> + // load output yaml file + def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + // add metadata from file to state + state + metadata + } + ) + + // run all methods + | run_components( + components: methods, + + // // use the 'filter' argument to only run a method on the normalisation the component is asking for + // filter: { id, state, config -> + // def norm = state.normalization_id + // def pref = config.functionality.info.preferred_normalization + // // if the preferred normalisation is none at all, + // // we can pass whichever dataset we want + // (norm == "log_cp10k" && pref == "counts") || norm == pref + // }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, config -> + id + "." + config.functionality.name + }, + + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, config -> + def new_args = [ + input_mod1: state.input_mod1, + input_mod2: state.input_mod2 + ] + new_args + }, + + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> + [ + method_id: config.functionality.name, + method_output_mod1: output.output_mod1, + method_output_mod2: output.output_mod2 + ] + } + ) + + // run all metrics + | run_components( + components: metrics, + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: [ + input_mod1: "method_output_mod1", + input_mod2: "method_output_mod2" + ], + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, config -> + [ + metric_id: config.functionality.name, + metric_output: output.output + ] + } + ) + + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | join_states{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + output: states[0].output + ] + [new_id, new_state] + } + + // convert to tsv and publish + | extract_scores.run( + auto: [publish: true] + ) + + emit: + output_ch + +} + +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = get_publish_dir() + + write_json(traces, file("$publish_dir/traces.json")) + // todo: add datasets logging + write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) + write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) +} diff --git a/src/tasks/match_modalities/workflows/run/nextflow.config b/src/tasks/match_modalities/workflows/run/nextflow.config new file mode 100644 index 0000000000..8511097c9b --- /dev/null +++ b/src/tasks/match_modalities/workflows/run/nextflow.config @@ -0,0 +1,16 @@ +manifest { + name = 'match_modalities/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=23.04.2' + description = 'multimodal data integration' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/run_test.sh b/src/tasks/match_modalities/workflows/run/run_test.sh new file mode 100755 index 0000000000..b4c410f85a --- /dev/null +++ b/src/tasks/match_modalities/workflows/run/run_test.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +# Run this prior to executing this script: +# viash ns build -q 'match_modalities|common' --setup cb --parallel + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/common/multimodal + +# choose a particular version of nextflow +export NXF_VER=23.04.2 + +nextflow \ + run . \ + -main-script src/tasks/match_modalities/workflows/run/main.nf \ + -resume \ + -c src/wf_utils/labels_ci.config \ + -profile docker \ + --id scicar \ + --input_mod1 $DATASET_DIR/dataset_mod1.h5ad \ + --input_mod2 $DATASET_DIR/dataset_mod2.h5ad \ + --output scores.tsv \ + --publish_dir output/match_modalities/ \ + + + diff --git a/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh b/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh new file mode 100644 index 0000000000..abe4f82f96 --- /dev/null +++ b/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +DATASET_DIR=resources_test/common/multimodal + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: scicar +input_mod1: s3://openproblems-data/$DATASET_DIR/dataset_mod1.h5ad +input_mod2: s3://openproblems-data/$DATASET_DIR/dataset_mod2.h5ad +output: scores.tsv +publish_dir: s3://openproblems-nextflow/output_test/v2/match_modalities +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision integration_build \ + --pull-latest \ + --main-script src/tasks/match_modalities/workflows/run/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/multimodal_data_integration/README.md b/src/tasks/multimodal_data_integration/README.md deleted file mode 100644 index 26bcd6b907..0000000000 --- a/src/tasks/multimodal_data_integration/README.md +++ /dev/null @@ -1,23 +0,0 @@ -# Multimodal data integration - -Structure of this task: - - src/multimodal_data_integration - ├── api Interface specifications for components and datasets in this task - ├── control_methods Control methods to compare methods against - ├── methods Methods to be benchmarked - ├── metrics Metrics used to quantify performance of methods - ├── README.md This file - ├── resources_scripts Scripts to process the datasets - ├── resources_test_scripts Scripts to process the test resources - ├── process_dataset Component to prepare common datasets - └── workflows Pipelines to run the full benchmark - -Relevant links: - -* [Description and results at openproblems.bio](https://openproblems.bio/benchmarks/multimodal_data_integration/) - -* [Experimental results](https://openproblems-experimental.netlify.app/results/multimodal_data_integration/) - - -* [Contribution guide](https://github.com/openproblems-bio/openproblems-v2/blob/main/CONTRIBUTING.md) diff --git a/src/tasks/multimodal_data_integration/datasets/datasets_scprep_csv.tsv b/src/tasks/multimodal_data_integration/datasets/datasets_scprep_csv.tsv deleted file mode 100644 index 5b837c1d26..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/datasets_scprep_csv.tsv +++ /dev/null @@ -1,2 +0,0 @@ -processor id input1 input2 compression accession_id doi organism cell_types technology -scprep_csv CBMC_8K_13AB_10x https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz gzip GSE100866 10.1038/nmeth.4380 human CL:2000001 dropseq diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml b/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml deleted file mode 100644 index e1ad3ca0c3..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/config.vsh.yaml +++ /dev/null @@ -1,41 +0,0 @@ -functionality: - status: disabled - name: "sample_dataset" - namespace: "multimodal_data_integration/datasets" - version: "dev" - description: "Sample dataset for testing purposes" - arguments: - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing both input matrices data" - required: true - - name: "--n_cells" - type: "integer" - default: 600 - description: "Number of cells" - - name: "--n_genes" - type: "integer" - default: 1500 - description: "Number of genes" - resources: - - type: python_script - path: script.py - - path: "../../utils/utils.py" - test_resources: - - type: python_script - path: test.py -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - anndata # needed by utils.py - - pandas # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py b/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py deleted file mode 100644 index ec85442fd9..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/script.py +++ /dev/null @@ -1,84 +0,0 @@ -print("Importing libraries", flush=True) -import scprep -import pandas as pd -import numpy as np -import scipy.sparse - -# adding resources dir to system path -# the resources dir contains all files listed in the '.functionality.resources' part of the -# viash config, amongst which is the 'utils.py' file we need. -import sys -sys.path.append(resources_dir) - -# importing helper functions from common utils.py file in resources dir -from utils import create_joint_adata -from utils import filter_joint_data_empty_cells -from utils import subset_joint_data - - -rna_cells_url = ( - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271044" - "&format=file&file=GSM3271044%5FRNA%5Fmouse%5Fkidney%5Fcell.txt.gz" -) -rna_genes_url = ( - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271044" - "&format=file&file=GSM3271044%5FRNA%5Fmouse%5Fkidney%5Fgene.txt.gz" -) -atac_cells_url = ( - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271045" - "&format=file&file=GSM3271045%5FATAC%5Fmouse%5Fkidney%5Fcell.txt.gz" -) -atac_genes_url = ( - "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM3271045" - "&format=file&file=GSM3271045%5FATAC%5Fmouse%5Fkidney%5Fpeak.txt.gz" -) - -print("Downloading input files", flush=True) -sys.stdout.flush() -rna_genes = pd.read_csv(rna_genes_url, low_memory=False, index_col=0) -atac_genes = pd.read_csv(atac_genes_url, low_memory=False, index_col=1) -rna_cells = pd.read_csv(rna_cells_url, low_memory=False, index_col=0) -atac_cells = pd.read_csv(atac_cells_url, low_memory=False, index_col=0) - -print("Creating joint adata object", flush=True) -keep_cells = np.intersect1d(rna_cells.index, atac_cells.index)[:200] -rna_cells = rna_cells.loc[keep_cells] -atac_cells = atac_cells.loc[keep_cells] - -rna_data = scipy.sparse.csr_matrix((len(keep_cells), len(rna_genes))) -atac_data = scipy.sparse.csr_matrix((len(keep_cells), len(atac_genes))) - -adata = create_joint_adata( - rna_data, - atac_data, - X_index=rna_cells.index, - X_columns=rna_genes.index, - Y_index=atac_cells.index, - Y_columns=atac_genes.index, -) - -print("Merging obs and var", flush=True) -adata.obs = rna_cells.loc[adata.obs.index] -adata.var = rna_genes -for key in atac_cells.columns: - adata.obs[key] = atac_cells[key] -adata.uns["mode2_varnames"] = [] -for key in atac_genes.columns: - varname = "mode2_var_{}".format(key) - adata.uns[varname] = atac_genes[key].values - adata.uns["mode2_varnames"].append(varname) - -adata.X = scipy.sparse.csr_matrix(np.random.poisson(0.1, adata.X.shape)).astype(np.float64) -adata.obsm["mode2"] = scipy.sparse.csr_matrix( - np.random.poisson(0.1, adata.obsm["mode2"].shape) -).astype(np.float64) - -adata = filter_joint_data_empty_cells(adata) - -print("Subsetting dataset", flush=True) -adata = subset_joint_data(adata, n_cells = par["n_cells"], n_genes = par["n_genes"]) - -adata.uns["dataset_id"] = "sample_dataset_test" - -print("Writing adata to file", flush=True) -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py b/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py deleted file mode 100644 index 43d47be23e..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/sample_dataset/test.py +++ /dev/null @@ -1,63 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import pandas -import numpy as np - -print(">> Running sample_dataset", flush=True) -out = subprocess.check_output([ - "./sample_dataset", - "--output", "output.h5ad" -]).decode("utf-8") - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") -assert "mode2" in adata.obsm -assert "mode2_obs" in adata.uns -assert "mode2_var" in adata.uns -assert np.all(adata.obs.index == adata.uns["mode2_obs"]) -assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] - -# check dataset id -assert "dataset_id" in adata.uns - -print(">> Running sample_dataset with different args", flush=True) -out = subprocess.run([ - "./sample_dataset", - "--output", "output.h5ad", - "--n_cells", "100", - "--n_genes", "200" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") -assert "mode2" in adata.obsm -assert "mode2_obs" in adata.uns -assert "mode2_var" in adata.uns -assert np.all(adata.obs.index == adata.uns["mode2_obs"]) -assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] - -# check shape based on args -assert adata.shape == (100, 200) - -# check dataset id -assert "dataset_id" in adata.uns - - - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml b/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml deleted file mode 100644 index 0461cecdc4..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/config.vsh.yaml +++ /dev/null @@ -1,52 +0,0 @@ -functionality: - status: disabled - name: "scprep_csv" - namespace: "multimodal_data_integration/datasets" - version: "dev" - description: "Create a modality alignment dataset from CSV using scprep." - arguments: - - name: "--id" - type: "string" - default: "citeseq_cbmc" - description: "The id of the output dataset id" - - name: "--input1" - type: "file" - default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz" - description: "Path or URL to the RNA counts as a gzipped csv file." - - name: "--input2" - type: "file" - default: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz" - description: "Path or URL to the ADT counts as a gzipped csv file." - - name: "--compression" - type: "string" - default: "gzip" - description: "For on-the-fly decompression of on-disk data. If 'infer' and filepath_or_buffer is path-like, then detect compression from the following extensions: '.gz', '.bz2', '.zip', or '.xz' (otherwise no decompression). If using 'zip', the ZIP file must contain only one data file to be read in. Set to None for no decompression." - - name: "--test" - type: "boolean_true" - description: "Subset the dataset" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing both input matrices data" - required: true - resources: - - type: python_script - path: script.py - - path: "../../utils/utils.py" - test_resources: - - type: python_script - path: test.py -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - scprep - - anndata # needed by utils.py - - pandas # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py b/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py deleted file mode 100644 index 1ad363d1b7..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/script.py +++ /dev/null @@ -1,52 +0,0 @@ -## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. -par = { - "id": "citeseq_cbmc", - "input1": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DRNA%5Fumi%2Ecsv%2Egz", - "input2": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100866&format=file&file=GSE100866%5FCBMC%5F8K%5F13AB%5F10X%2DADT%5Fumi%2Ecsv%2Egz", - "output": "output.h5ad", - "test": False, - "compression" = "gzip" -} -resources_dir = "../../utils/" -## VIASH END - -print("Importing libraries", flush=True) -import scprep - -# adding resources dir to system path -# the resources dir contains all files listed in the '.functionality.resources' part of the -# viash config, amongst which is the 'utils.py' file we need. -import sys -sys.path.append(resources_dir) - -# importing helper functions from common utils.py file in resources dir -from utils import create_joint_adata -from utils import filter_joint_data_empty_cells -from utils import subset_joint_data - -print("Downloading expression datasets from GEO (this might take a while)", flush=True) -sys.stdout.flush() - -# par["input1"] can be the path to a local file, or a url -adata1 = scprep.io.load_csv( - par["input1"], cell_axis="col", compression=par["compression"], sparse=True, chunksize=1000 -) -adata2 = scprep.io.load_csv( - par["input2"], cell_axis="col", compression=par["compression"], sparse=True, chunksize=1000 -) - -print("Transforming into adata", flush=True) -adata = create_joint_adata(adata1, adata2) -adata = filter_joint_data_empty_cells(adata) - -adata.uns["dataset_id"] = par["id"] - -if par["test"]: - print("Subsetting dataset", flush=True) - adata = subset_joint_data(adata) - adata.uns["dataset_id"] = par["id"] + "_test" - -print("Writing adata to file", flush=True) -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py b/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py deleted file mode 100644 index c9776ca640..0000000000 --- a/src/tasks/multimodal_data_integration/datasets/scprep_csv/test.py +++ /dev/null @@ -1,50 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import pandas -import numpy as np - -import urllib.request - -print(">> Downloading input file", flush=True) -# need to download file manually for now; viash docker platform tries to auto-mount them -urllib.request.urlretrieve("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE100nnn/GSE100866/suppl/GSE100866%5FCD8%5Fmerged%2DADT%5Fumi%2Ecsv%2Egz", "adt_umi.csv.gz") - -print(">> Running scprep_csv", flush=True) - -out = subprocess.run([ - "./scprep_csv", - "--id", "footest", - "--input1", "adt_umi.csv.gz", - "--input2", "adt_umi.csv.gz", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") -assert "mode2" in adata.obsm -assert "mode2_obs" in adata.uns -assert "mode2_var" in adata.uns -assert np.all(adata.obs.index == adata.uns["mode2_obs"]) -assert len(adata.uns["mode2_var"]) == adata.obsm["mode2"].shape[1] - -# since same file was used for both datasets -assert adata.shape == adata.obsm["mode2"].shape - -# check dataset id -assert "dataset_id" in adata.uns -assert adata.uns["dataset_id"] == "footest" - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml deleted file mode 100644 index 29684dad7e..0000000000 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/config.vsh.yaml +++ /dev/null @@ -1,55 +0,0 @@ -functionality: - status: disabled - name: "harmonic_alignment" - namespace: "multimodal_data_integration/methods" - version: "dev" - description: "Run Harmonic Alignment" - info: - method_name: "Harmonic Alignment" - paper_name: "Harmonic Alignment" - paper_doi: "10.1137/1.9781611976236.36" - paper_year: "2020" - code_url: "https://github.com/KrishnaswamyLab/harmonic-alignment" - arguments: - - name: "--input_mod1" - type: "file" - default: "dataset_mod1_censored.h5ad" - description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - - name: "--output" - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing both RNA and ADT data" - - name: "--n_svd" - type: "integer" - default: 100 - description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." - - name: "--n_pca_XY" - type: "integer" - default: 100 - description: "Default number of principal components on which to build graph." - - name: "--n_eigenvectors" - type: "integer" - default: 100 - description: "Number of eigenvectors of the normalized Laplacian on which to perform alignment." - resources: - - type: python_script - path: script.py - - path: "../../utils/preprocessing.py" - test_resources: - - type: python_script - path: test.py - - path: "../../resources/sample_dataset.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - anndata # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - scprep # needed by utils.py - - sklearn - - git+https://github.com/KrishnaswamyLab/harmonic-alignment#subdirectory=python - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py deleted file mode 100644 index 4a0de1d6c1..0000000000 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/script.py +++ /dev/null @@ -1,59 +0,0 @@ -print("Loading dependencies", flush=True) -import scanpy as sc -import harmonicalignment -import sklearn.decomposition - -## VIASH START -par = { - input = "output.h5ad", - output = "output.scot.h5ad", - n_svd = 100, - n_pca_XY = 100 - eigenvectors = 100 -} -resources_dir = "../../utils/" -## VIASH END - -# importing helper functions from common preprocessing.py file in resources dir -import sys -sys.path.append(resources_dir) -from preprocessing import log_cpm -from preprocessing import sqrt_cpm - -print("Reading input h5ad file", flush=True) -adata = sc.read_h5ad(par["input"]) - -print("Check parameters", flush=True) -n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) -n_eigenvectors = par["n_eigenvectors"] -n_pca_XY = par["n_pca_XY"] - -if adata.X.shape[0] <= n_eigenvectors: - n_eigenvectors = None -if adata.X.shape[0] <= n_pca_XY: - n_pca_XY = None - -print("Normalising mode 1", flush=True) -sqrt_cpm(adata) - -print("Normalising mode 2", flush=True) -log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") - -print("Performing PCA reduction", flush=True) -X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) -Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) - -print("Running Harmonic Alignment", flush=True) -ha_op = harmonicalignment.HarmonicAlignment( - n_filters=8, n_pca_XY=n_pca_XY, n_eigenvectors=n_eigenvectors -) -ha_op.align(X_pca, Y_pca) -XY_aligned = ha_op.diffusion_map(n_eigenvectors=n_eigenvectors) - -print("Storing output data structures", flush=True) -adata.obsm["aligned"] = XY_aligned[: X_pca.shape[0]] -adata.obsm["mode2_aligned"] = XY_aligned[X_pca.shape[0] :] - -print("Write output to file", flush=True) -adata.uns["method_id"] = "harmonic_alignment" -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py b/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py deleted file mode 100644 index 9fbdd0f68d..0000000000 --- a/src/tasks/multimodal_data_integration/methods/harmonic_alignment/test.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc - -print(">> Running harmonic_alignment", flush=True) -out = subprocess.run([ - "./harmonic_alignment", - "--input", "sample_dataset.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -assert "aligned" in adata.obsm -assert "mode2_aligned" in adata.obsm -assert adata.obsm["aligned"].shape[0] == adata.shape[0] -assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] -assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] - -# check dataset id -assert "method_id" in adata.uns -assert adata.uns["method_id"] == "harmonic_alignment" - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml deleted file mode 100644 index 6cbe90f7c3..0000000000 --- a/src/tasks/multimodal_data_integration/methods/mnn/config.vsh.yaml +++ /dev/null @@ -1,52 +0,0 @@ -functionality: - status: disabled - name: "mnn" - namespace: "multimodal_data_integration/methods" - version: "dev" - description: "Run Mutual Nearest Neighbours" - info: - method_label: "MNN" - method_name: "Mutual Nearest Neighbors" - paper_name: "Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors" - paper_doi: "10.1038/nbt.4091" - paper_year: "2018" - code_url: "https://github.com/LTLA/batchelor" - code_version: "1.7.14" - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - default: "input.h5ad" - description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing both RNA and ADT data" - - name: "--n_svd" - type: "integer" - default: 100 - description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." - resources: - - type: r_script - path: ./script.R - test_resources: - - type: python_script - path: test.py - - path: "../../resources/sample_dataset.h5ad" -platforms: - - type: docker - image: "dataintuitive/randpy:r4.0_py3.8_bioc3.12" # already includes some R, bioconductor & anndata packages - setup: - - type: r - cran: - - anndata - - Matrix - - sparsesvd - bioc: - - batchelor - - type: python - packages: - - scanpy # needed by tests - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/methods/mnn/script.R b/src/tasks/multimodal_data_integration/methods/mnn/script.R deleted file mode 100644 index c7f127d578..0000000000 --- a/src/tasks/multimodal_data_integration/methods/mnn/script.R +++ /dev/null @@ -1,51 +0,0 @@ -## VIASH START -par <- list( - input = "output.h5ad", - output = "output.mnn.h5ad", - n_svd = 100 -) -## VIASH END - -cat("Loading dependencies\n") -library(anndata, warn.conflicts = FALSE) -library(Matrix, warn.conflicts = FALSE) -requireNamespace("sparsesvd", quietly = TRUE) -requireNamespace("batchelor", quietly = TRUE) - -cat("Reading input h5ad file\n") -adata <- read_h5ad(par$input) - -# Convert data to friendly sparse format -mode1 <- as(adata$X, "CsparseMatrix") -mode2 <- as(adata$obsm[["mode2"]], "CsparseMatrix") - -# Check parameters -n_svd <- min( - par$n_svd, - ncol(mode1), - ncol(mode2) -) - -cat("Running SVD\n") -mode1_svd <- sparsesvd::sparsesvd(mode1, rank = n_svd) -mode1_svd_uv <- mode1_svd$u %*% diag(mode1_svd$d) -mode2_svd <- sparsesvd::sparsesvd(mode2, rank = n_svd) -mode2_svd_uv <- mode2_svd$u %*% diag(mode2_svd$d) - -cat("Running MNN\n") -sce_mnn <- batchelor::fastMNN( - t(mode1_svd_uv), - t(mode2_svd_uv) -) - -cat("Storing output\n") -combined_recons <- t(SummarizedExperiment::assay(sce_mnn, "reconstructed")) -mode1_recons <- combined_recons[seq_len(nrow(mode1_svd_uv)), , drop = FALSE] -mode2_recons <- combined_recons[-seq_len(nrow(mode1_svd_uv)), , drop = FALSE] - -adata$obsm[["aligned"]] <- as.matrix(mode1_recons) -adata$obsm[["mode2_aligned"]] <- as.matrix(mode2_recons) - -cat("Writing to file\n") -adata$uns["method_id"] = "mnn" -zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/mnn/test.py b/src/tasks/multimodal_data_integration/methods/mnn/test.py deleted file mode 100644 index 0549eceaed..0000000000 --- a/src/tasks/multimodal_data_integration/methods/mnn/test.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc - -print(">> Running mnn", flush=True) -out = subprocess.run([ - "./mnn", - "--input", "sample_dataset.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -assert "aligned" in adata.obsm -assert "mode2_aligned" in adata.obsm -assert adata.obsm["aligned"].shape[0] == adata.shape[0] -assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] -assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] - -# check dataset id -assert "method_id" in adata.uns -assert adata.uns["method_id"] == "mnn" - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml deleted file mode 100644 index a35c59ed83..0000000000 --- a/src/tasks/multimodal_data_integration/methods/sample_method/config.vsh.yaml +++ /dev/null @@ -1,37 +0,0 @@ -functionality: - status: disabled - name: "sample_method" - namespace: "multimodal_data_integration/methods" - version: "dev" - description: "Sample method" - info: - method_name: "Sample method" - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - default: "input.h5ad" - description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing both RNA and ADT data" - resources: - - type: python_script - path: ./script.py - test_resources: - - type: python_script - path: test.py - - path: "../../resources/sample_dataset.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - anndata # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/script.py b/src/tasks/multimodal_data_integration/methods/sample_method/script.py deleted file mode 100644 index 9e973ea262..0000000000 --- a/src/tasks/multimodal_data_integration/methods/sample_method/script.py +++ /dev/null @@ -1,15 +0,0 @@ -print("Loading dependencies", flush=True) -import scanpy as sc -import numpy as np - -print("Reading input h5ad file", flush=True) -adata = sc.read_h5ad(par["input"]) - -print("Check parameters", flush=True) -new_shape = (adata.X.shape[0], 10) -adata.obsm["aligned"] = np.random.normal(0, 0.1, new_shape) -adata.obsm["mode2_aligned"] = np.random.normal(0, 0.1, new_shape) - -print("Write output to file", flush=True) -adata.uns["method_id"] = "sample_method" -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/sample_method/test.py b/src/tasks/multimodal_data_integration/methods/sample_method/test.py deleted file mode 100644 index 496d910651..0000000000 --- a/src/tasks/multimodal_data_integration/methods/sample_method/test.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc - -print(">> Running sample_method", flush=True) -out = subprocess.run([ - "./sample_method", - "--input", "sample_dataset.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that dataset fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -assert "aligned" in adata.obsm -assert "mode2_aligned" in adata.obsm -assert adata.obsm["aligned"].shape[0] == adata.shape[0] -assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] -assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] - -# check dataset id -assert "method_id" in adata.uns -assert adata.uns["method_id"] == "sample_method" - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml b/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml deleted file mode 100644 index 2cda0a5af6..0000000000 --- a/src/tasks/multimodal_data_integration/methods/scot/config.vsh.yaml +++ /dev/null @@ -1,54 +0,0 @@ -functionality: - status: disabled - name: "scot" - namespace: "multimodal_data_integration/methods" - version: "dev" - description: "Run Single Cell Optimal Transport" - info: - method_label: "SCOT" - method_name: "Single Cell Optimal Transport" - paper_name: "Gromov-Wasserstein optimal transport to align single-cell multi-omics data" - paper_doi: "10.1101/2020.04.28.066787" - paper_year: "2020" - code_url: "https://github.com/rsinghlab/SCOT" - code_version: "0.2.0" - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - default: "input.h5ad" - description: "Input h5ad file containing at least `ad.X` and `ad.obsm['mode2']`." - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.scot.h5ad" - description: "Output h5ad file containing both RNA and ADT data" - - name: "--n_svd" - type: "integer" - default: 100 - description: "Number of SVDs to use. Bounded by the number of columns in `ad.X` and `ad.obsm['mode2']`." - - name: "--balanced" - type: "boolean_true" - description: "Determines whether balanced or unbalanced optimal transport. In the balanced case, the target and source distributions are assumed to have equal mass." - resources: - - type: python_script - path: script.py - - path: "../../utils/preprocessing.py" - test_resources: - - type: python_script - path: test.py - - path: "../../resources/sample_dataset.h5ad" -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - anndata # needed by utils.py - - scanpy # needed by utils.py - - numpy # needed by utils.py - - scprep # needed by utils.py - - sklearn - - git+https://github.com/atong01/SCOT - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/methods/scot/script.py b/src/tasks/multimodal_data_integration/methods/scot/script.py deleted file mode 100644 index 3d815a07f7..0000000000 --- a/src/tasks/multimodal_data_integration/methods/scot/script.py +++ /dev/null @@ -1,53 +0,0 @@ -## VIASH START -par = { - input = "output.h5ad", - output = "output.scot.h5ad", - n_svd = 100, - balanced=False, -} -resources_dir = "../../utils/" -## VIASH END - -print("Loading dependencies", flush=True) -import scanpy as sc -import sklearn.decomposition -from SCOT import SCOT - -# importing helper functions from common preprocessing.py file in resources dir -import sys -sys.path.append(resources_dir) -from preprocessing import log_cpm -from preprocessing import sqrt_cpm - - -print("Reading input h5ad file", flush=True) -adata = sc.read_h5ad(par["input"]) - -print("Normalising mode 1", flush=True) -sqrt_cpm(adata) - -print("Normalising mode 2", flush=True) -log_cpm(adata, obsm="mode2", obs="mode2_obs", var="mode2_var") - - -print("Performing PCA reduction", flush=True) -n_svd = min([par["n_svd"], min(adata.X.shape) - 1, min(adata.obsm["mode2"].shape) - 1]) -X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) -Y_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.obsm["mode2"]) - -print("Initialize SCOT", flush=True) -scot = SCOT(X_pca, Y_pca) - -print("Call the unbalanced alignment", flush=True) -# From https://github.com/rsinghlab/SCOT/blob/master/examples/unbalanced_GW_SNAREseq.ipynb # noqa: 501 -X_new_unbal, y_new_unbal = scot.align( - k=50, e=1e-3, rho=0.0005, normalize=True, balanced=par["balanced"] -) - -print() -adata.obsm["aligned"] = X_new_unbal -adata.obsm["mode2_aligned"] = y_new_unbal - -print("Write output to file", flush=True) -adata.uns["method_id"] = "scot" -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/methods/scot/test.py b/src/tasks/multimodal_data_integration/methods/scot/test.py deleted file mode 100644 index be4299104f..0000000000 --- a/src/tasks/multimodal_data_integration/methods/scot/test.py +++ /dev/null @@ -1,37 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc - -print(">> Running scot", flush=True) -out = subprocess.run([ - "./scot", - "--input", "sample_dataset.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -assert "aligned" in adata.obsm -assert "mode2_aligned" in adata.obsm -assert adata.obsm["aligned"].shape[0] == adata.shape[0] -assert adata.obsm["mode2_aligned"].shape[0] == adata.obsm["mode2"].shape[0] -assert adata.obsm["aligned"].shape[1] == adata.obsm["mode2_aligned"].shape[1] - -# check dataset id -assert "method_id" in adata.uns -assert adata.uns["method_id"] == "scot" - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml b/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml deleted file mode 100644 index 939aa83e92..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/config.vsh.yaml +++ /dev/null @@ -1,48 +0,0 @@ -functionality: - status: disabled - name: "knn_auc" - namespace: "multimodal_data_integration/metrics" - version: "dev" - description: "Compute the kNN Area Under the Curve" - info: - method_label: "KNN-AUC" - metric_name: "kNN Area Under the Curve" - maximize: "true" - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - default: "input.h5ad" - description: "File to input h5ad containing: `ad.X`, `ad.obsm['aligned']`, `ad.obsm['mode2_aligned']`" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing `ad.uns['metric_value']`" - - name: "--proportion_neighbors" - type: "double" - default: 0.1 - description: The propotion of neighbours to use in computing the KNN. - - name: "--n_svd" - type: integer - default: 100 - description: The maximum number of SVDs to use. - resources: - - type: python_script - path: script.py - test_resources: - - type: python_script - path: test.py - - path: ../../resources/sample_output.h5ad -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - anndata - - numpy - - sklearn - - scanpy - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py b/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py deleted file mode 100644 index cb7b05ad58..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/script.py +++ /dev/null @@ -1,65 +0,0 @@ -## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. -par = { - "input": "out_bash/multimodal_data_integration/methods/citeseq_cbmc_mnn.h5ad", - "output": "out_bash/multimodal_data_integration/metrics/citeseq_cbmc_mnn_knn_auc.h5ad", - "proportion_neighbors": 0.1, - "n_svd": 100 -} -## VIASH END - -print("Importing libraries", flush=True) -import anndata -import numpy as np -import sklearn.decomposition -import sklearn.neighbors - -print("Reading adata file", flush=True) -adata = anndata.read_h5ad(par["input"]) - -print("Checking parameters", flush=True) -n_svd = min([par["n_svd"], min(adata.X.shape) - 1]) -n_neighbors = int(np.ceil(par["proportion_neighbors"] * adata.X.shape[0])) - -print("Performing PCA", flush=True) -X_pca = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.X) - -print("Compute KNN on PCA", flush=True) -_, indices_true = ( - sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) - .fit(X_pca) - .kneighbors(X_pca) -) - -print("Compute KNN on aligned matrix", flush=True) -_, indices_pred = ( - sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) - .fit(adata.obsm["aligned"]) - .kneighbors(adata.obsm["mode2_aligned"]) -) - -print("Check which neighbours match", flush=True) -neighbors_match = np.zeros(n_neighbors, dtype=int) -for i in range(adata.shape[0]): - _, pred_matches, true_matches = np.intersect1d( - indices_pred[i], indices_true[i], return_indices=True - ) - neighbors_match_idx = np.maximum(pred_matches, true_matches) - neighbors_match += np.sum( - np.arange(n_neighbors) >= neighbors_match_idx[:, None], - axis=0, - ) - -print("Compute area under neighbours match curve", flush=True) -neighbors_match_curve = neighbors_match / ( - np.arange(1, n_neighbors + 1) * adata.shape[0] -) -area_under_curve = np.mean(neighbors_match_curve) - -print("Store metic value", flush=True) -adata.uns["metric_id"] = "knn_auc" -adata.uns["metric_value"] = area_under_curve - -print("Writing adata to file", flush=True) -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py b/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py deleted file mode 100644 index f51fa6752a..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/knn_auc/test.py +++ /dev/null @@ -1,34 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import numpy as np - -print(">> Running knn_auc", flush=True) -out = subprocess.run([ - "./knn_auc", - "--input", "sample_output.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that dataset fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -# check id -assert "metric_id" in adata.uns -assert adata.uns["metric_id"] == "knn_auc" -assert "metric_value" in adata.uns -assert type(adata.uns["metric_value"]) is np.float64 - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml b/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml deleted file mode 100644 index 025368fbef..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/mse/config.vsh.yaml +++ /dev/null @@ -1,41 +0,0 @@ -functionality: - status: disabled - name: "mse" - namespace: "multimodal_data_integration/metrics" - version: "dev" - description: "Compute the mean squared error" - info: - method_label: "MSE" - metric_name: "Mean Squared Error" - maximize: "true" - arguments: - - name: "--input" - alternatives: ["-i"] - type: "file" - default: "input.h5ad" - description: "File to input h5ad containing: `ad.X`, `ad.obsm['aligned']`, `ad.obsm['mode2_aligned']`" - - name: "--output" - alternatives: ["-o"] - type: "file" - direction: "output" - default: "output.h5ad" - description: "Output h5ad file containing `ad.uns['metric_value']`" - resources: - - type: python_script - path: ./script.py - test_resources: - - type: python_script - path: test.py - - path: ../../resources/sample_output.h5ad -platforms: - - type: docker - image: "python:3.8" - setup: - - type: python - packages: - - anndata - - numpy - - scipy - - scprep - - scanpy - - type: nextflow diff --git a/src/tasks/multimodal_data_integration/metrics/mse/script.py b/src/tasks/multimodal_data_integration/metrics/mse/script.py deleted file mode 100644 index e79320a8ed..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/mse/script.py +++ /dev/null @@ -1,40 +0,0 @@ -## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. -par = { - "input": "out_bash/multimodal_data_integration/methods/citeseq_cbmc_mnn.h5ad", - "output": "out_bash/multimodal_data_integration/metrics/citeseq_cbmc_mnn_knn_auc.h5ad" -} -## VIASH END - -print("Importing libraries", flush=True) -import anndata -import scprep -import numpy as np -from scipy import sparse - -print("Reading adata file", flush=True) -adata = anndata.read_h5ad(par["input"]) - -print("Computing MSE", flush=True) -def _square(X): - if sparse.issparse(X): - X.data = X.data ** 2 - return X - else: - return scprep.utils.toarray(X) ** 2 - -X = scprep.utils.toarray(adata.obsm["aligned"]) -Y = scprep.utils.toarray(adata.obsm["mode2_aligned"]) - -X_shuffled = X[np.random.permutation(np.arange(X.shape[0])), :] -error_random = np.mean(np.sum(_square(X_shuffled - Y))) -error_abs = np.mean(np.sum(_square(X - Y))) -metric_value = error_abs / error_random - -print("Store metic value", flush=True) -adata.uns["metric_id"] = "mse" -adata.uns["metric_value"] = metric_value - -print("Writing adata to file", flush=True) -adata.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/multimodal_data_integration/metrics/mse/test.py b/src/tasks/multimodal_data_integration/metrics/mse/test.py deleted file mode 100644 index 19ce0b1fea..0000000000 --- a/src/tasks/multimodal_data_integration/metrics/mse/test.py +++ /dev/null @@ -1,34 +0,0 @@ -import os -from os import path -import subprocess - -import scanpy as sc -import numpy as np - -print(">> Running mse", flush=True) -out = subprocess.run([ - "./mse", - "--input", "sample_output.h5ad", - "--output", "output.h5ad" -], stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{out.args}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether file exists", flush=True) -assert path.exists("output.h5ad") - -print(">> Check that output fits expected API", flush=True) -adata = sc.read_h5ad("output.h5ad") - -# check id -assert "metric_id" in adata.uns -assert adata.uns["metric_id"] == "mse" -assert "metric_value" in adata.uns -assert type(adata.uns["metric_value"]) is np.float64 - -print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/multimodal_data_integration/utils/preprocessing.py b/src/tasks/multimodal_data_integration/utils/preprocessing.py deleted file mode 100644 index 1d660ca146..0000000000 --- a/src/tasks/multimodal_data_integration/utils/preprocessing.py +++ /dev/null @@ -1,52 +0,0 @@ -import anndata -import functools -import scanpy as sc -import scprep - -def normalizer(func, *args, **kwargs): - """Decorate a normalization function.""" - - @functools.wraps(func) - def normalize(adata, *args, obsm=None, obs=None, var=None, **kwargs): - # log.debug("Running {} normalization".format(func.__name__)) - assert isinstance(adata, anndata.AnnData) - - if obsm is not None: - cache_name = "{}_{}".format(obsm, func.__name__) - if cache_name in adata.obsm: - adata.obsm[obsm] = adata.obsm[cache_name] - else: - obs = adata.uns[obs] if obs else adata.obs - var = adata.uns[var] if var else adata.var - adata_temp = anndata.AnnData(adata.obsm[obsm], obs=obs, var=var) - func(adata_temp, *args, **kwargs) - adata.obsm[obsm] = adata.obsm[cache_name] = adata_temp.X - else: - if func.__name__ in adata.layers: - adata.X = adata.layers[func.__name__] - else: - func(adata, *args, **kwargs) - adata.layers[func.__name__] = adata.X - - return normalize - -def _cpm(adata): - adata.layers["counts"] = adata.X.copy() - sc.pp.normalize_total(adata, target_sum=1e6, key_added="size_factors") - -@normalizer -def cpm(adata): - """Normalize data to counts per million.""" - _cpm(adata) - -@normalizer -def log_cpm(adata): - """Normalize data to log counts per million.""" - _cpm(adata) - sc.pp.log1p(adata) - -@normalizer -def sqrt_cpm(adata): - """Normalize data to sqrt counts per million.""" - _cpm(adata) - adata.X = scprep.transform.sqrt(adata.X) diff --git a/src/tasks/multimodal_data_integration/utils/utils.py b/src/tasks/multimodal_data_integration/utils/utils.py deleted file mode 100644 index 2dd5f2cc9d..0000000000 --- a/src/tasks/multimodal_data_integration/utils/utils.py +++ /dev/null @@ -1,97 +0,0 @@ -import anndata -import numpy as np -import pandas as pd -import scanpy as sc -import scprep - - -def subset_mode2_genes(adata, keep_genes): - """Randomly subset genes from adata.obsm["mode2"].""" - adata.obsm["mode2"] = adata.obsm["mode2"][:, keep_genes] - adata.uns["mode2_var"] = adata.uns["mode2_var"][keep_genes] - if "mode2_varnames" in adata.uns: - for varname in adata.uns["mode2_varnames"]: - adata.uns[varname] = adata.uns[varname][keep_genes] - return adata - - -def filter_joint_data_empty_cells(adata): - """Remove empty cells and genes from a multimodal dataset.""" - assert np.all(adata.uns["mode2_obs"] == adata.obs.index) - # filter cells - n_cells_mode1 = scprep.utils.toarray(adata.X.sum(axis=1)).flatten() - n_cells_mode2 = scprep.utils.toarray(adata.obsm["mode2"].sum(axis=1)).flatten() - keep_cells = np.minimum(n_cells_mode1, n_cells_mode2) > 1 - adata.uns["mode2_obs"] = adata.uns["mode2_obs"][keep_cells] - adata = adata[keep_cells, :].copy() - # filter genes - sc.pp.filter_genes(adata, min_counts=1) - n_genes_mode2 = scprep.utils.toarray(adata.obsm["mode2"].sum(axis=0)).flatten() - keep_genes_mode2 = n_genes_mode2 > 0 - adata = subset_mode2_genes(adata, keep_genes_mode2) - return adata - - -def create_joint_adata( - X, Y, X_index=None, X_columns=None, Y_index=None, Y_columns=None -): - """Create a multimodal dataset.""" - if X_index is None: - X_index = X.index - if X_columns is None: - X_columns = X.columns - if Y_index is None: - Y_index = Y.index - if Y_columns is None: - Y_columns = Y.columns - joint_index = np.sort(np.intersect1d(X_index, Y_index)) - try: - X = X.loc[joint_index] - Y = Y.loc[joint_index] - except AttributeError: - # keep only common observations - X_keep_idx = np.isin(X_index, joint_index) - Y_keep_idx = np.isin(Y_index, joint_index) - X = X[X_keep_idx] - Y = Y[Y_keep_idx] - - # reorder by alphabetical - X_index_sub = scprep.utils.toarray(X_index[X_keep_idx]) - Y_index_sub = scprep.utils.toarray(Y_index[Y_keep_idx]) - X = X[np.argsort(X_index_sub)] - Y = Y[np.argsort(Y_index_sub)] - - # check order is correct - assert (X_index_sub[np.argsort(X_index_sub)] == joint_index).all() - assert (Y_index_sub[np.argsort(Y_index_sub)] == joint_index).all() - adata = anndata.AnnData( - scprep.utils.to_array_or_spmatrix(X).tocsr(), - obs=pd.DataFrame(index=joint_index), - var=pd.DataFrame(index=X_columns), - ) - adata.obsm["mode2"] = scprep.utils.to_array_or_spmatrix(Y).tocsr() - adata.uns["mode2_obs"] = joint_index - adata.uns["mode2_var"] = scprep.utils.toarray(Y_columns) - return adata - - -def subset_joint_data(adata, n_cells=600, n_genes=1500): - """Randomly subset a multimodal dataset.""" - if adata.shape[0] > n_cells: - keep_cells = np.random.choice(adata.shape[0], n_cells, replace=False) - adata = adata[keep_cells].copy() - adata.uns["mode2_obs"] = adata.uns["mode2_obs"][keep_cells] - adata = filter_joint_data_empty_cells(adata) - - if adata.shape[1] > n_genes: - keep_mode1_genes = np.random.choice(adata.shape[1], n_genes, replace=False) - adata = adata[:, keep_mode1_genes].copy() - - if adata.obsm["mode2"].shape[1] > n_genes: - keep_genes_mode2 = np.random.choice( - adata.obsm["mode2"].shape[1], n_genes, replace=False - ) - adata = subset_mode2_genes(adata, keep_genes_mode2) - - adata = filter_joint_data_empty_cells(adata) - return adata \ No newline at end of file diff --git a/src/tasks/multimodal_data_integration/workflows/run/main.nf b/src/tasks/multimodal_data_integration/workflows/run/main.nf deleted file mode 100644 index ae06b48bd3..0000000000 --- a/src/tasks/multimodal_data_integration/workflows/run/main.nf +++ /dev/null @@ -1,75 +0,0 @@ -nextflow.enable.dsl=2 - -/* For now, you need to manually specify the - * root directory of this repository as follows. - * (it's a nextflow limitation I'm trying to figure out - * how to resolve.) */ - -targetDir = "${params.rootDir}/target/nextflow" - -// import dataset loaders -include { sample_dataset } from "$targetDir/multimodal_data_integration/datasets/sample_dataset/main.nf" params(params) -include { scprep_csv } from "$targetDir/multimodal_data_integration/datasets/scprep_csv/main.nf" params(params) - -// import methods -include { sample_method } from "$targetDir/multimodal_data_integration/methods/sample_method/main.nf" params(params) -include { mnn } from "$targetDir/multimodal_data_integration/methods/mnn/main.nf" params(params) -include { scot } from "$targetDir/multimodal_data_integration/methods/scot/main.nf" params(params) -include { harmonic_alignment } from "$targetDir/multimodal_data_integration/methods/harmonic_alignment/main.nf" params(params) - -// import metrics -include { knn_auc } from "$targetDir/multimodal_data_integration/metrics/knn_auc/main.nf" params(params) -include { mse } from "$targetDir/multimodal_data_integration/metrics/mse/main.nf" params(params) - -// import helper functions -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) - - -/******************************************************* -* Dataset processor workflows * -*******************************************************/ -// This workflow reads in a tsv containing some metadata about each dataset. -// For each entry in the metadata, a dataset is generated, usually by downloading -// and processing some files. The end result of each of these workflows -// should be simply a channel of [id, h5adfile, params] triplets. -// -// If the need arises, these workflows could be split off into a separate file. - -workflow get_scprep_csv_datasets { - main: - output_ = Channel.fromPath("$launchDir/src/multimodal_data_integration/datasets/datasets_scprep_csv.tsv") - | splitCsv(header: true, sep: "\t") - | map { row -> - [ row.id, [ "input1": file(row.input1), "input2": file(row.input2), "id": row.id ]] - } - | scprep_csv - emit: - output_ -} - -workflow get_sample_datasets { - main: - output_ = Channel.value( [ "sample_dataset", [:] ] ) - | sample_dataset - emit: - output_ -} - -/******************************************************* -* Main workflow * -*******************************************************/ - -workflow { - (get_sample_datasets & get_scprep_csv_datasets) - | mix - | (sample_method & mnn & scot & harmonic_alignment) - | mix - | (knn_auc & mse) - | mix - | toSortedList - | map{ it -> [ "combined", [ input: it.collect{ it[1] } ] ] } - | extract_scores.run( - auto: [ publish: true ] - ) - -} diff --git a/src/tasks/multimodal_data_integration/workflows/run/nextflow.config b/src/tasks/multimodal_data_integration/workflows/run/nextflow.config deleted file mode 100644 index e2de284c42..0000000000 --- a/src/tasks/multimodal_data_integration/workflows/run/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -// ADAPT rootDir ACCORDING TO RELATIVE PATH WITHIN PROJECT -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// set default container & default labels -process { - container = 'nextflow/bash:latest' - - withLabel: highmem { memory = 50.Gb } - withLabel: highcpu { cpus = 20 } -} diff --git a/src/tasks/multimodal_data_integration/workflows/run/run_nextflow.sh b/src/tasks/multimodal_data_integration/workflows/run/run_nextflow.sh deleted file mode 100755 index 84cc18c3b2..0000000000 --- a/src/tasks/multimodal_data_integration/workflows/run/run_nextflow.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# viash_build -q 'multimodal_data_integration|utils' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -# choose a particular version of nextflow -export NXF_VER=21.10.6 - -nextflow \ - run . \ - -main-script src/multimodal_data_integration/workflows/run/main.nf \ - --publish_dir output/multimodal_data_integration \ - -resume \ - -with-docker - From 50d582ac2d9148a0a1fc8889f4c0a21b53ba7513 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 15 Sep 2023 16:22:38 +0200 Subject: [PATCH 0989/1233] add images (#231) * add images * update changelog * remove images from batch_integration * remove images Former-commit-id: e8318199eeec56b249d05ba9c5a02cba2bd980d2 --- CHANGELOG.md | 2 ++ src/common/schemas/defs_common.yaml | 4 ++++ src/common/schemas/task_info.yaml | 2 ++ src/tasks/batch_integration/api/task_info.yaml | 1 + src/tasks/batch_integration/api/thumbnail.svg | 1 + src/tasks/denoising/api/task_info.yaml | 1 + src/tasks/denoising/api/thumbnail.svg | 1 + src/tasks/dimensionality_reduction/api/task_info.yaml | 1 + src/tasks/dimensionality_reduction/api/thumbnail.svg | 1 + src/tasks/label_projection/api/task_info.yaml | 1 + src/tasks/label_projection/api/thumbnail.svg | 1 + src/tasks/match_modalities/api/task_info.yaml | 1 + src/tasks/match_modalities/api/thumbnail.svg | 1 + 13 files changed, 18 insertions(+) create mode 100644 src/tasks/batch_integration/api/thumbnail.svg create mode 100644 src/tasks/denoising/api/thumbnail.svg create mode 100644 src/tasks/dimensionality_reduction/api/thumbnail.svg create mode 100644 src/tasks/label_projection/api/thumbnail.svg create mode 100644 src/tasks/match_modalities/api/thumbnail.svg diff --git a/CHANGELOG.md b/CHANGELOG.md index c573ae74b7..8773169a7b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,8 @@ * Update "baseline" to "control" (PR #146). +* Add task image thumbnails to api (PR #231). + ### BUG FIXES * `dimensionality_reduction/methods/tsne`: Use GitHub version of MulticoreTSNE. diff --git a/src/common/schemas/defs_common.yaml b/src/common/schemas/defs_common.yaml index a069d5cc35..8451cf5c52 100644 --- a/src/common/schemas/defs_common.yaml +++ b/src/common/schemas/defs_common.yaml @@ -88,6 +88,10 @@ definitions: description: | A unique, human-readable, short label. Used for creating summary tables and visualisations. maxLength: 50 + Image: + type: string + description: | + The name of the image file to use for the component on the website. Summary: type: string description: | diff --git a/src/common/schemas/task_info.yaml b/src/common/schemas/task_info.yaml index 3f3da8f822..143a5e3f93 100644 --- a/src/common/schemas/task_info.yaml +++ b/src/common/schemas/task_info.yaml @@ -10,6 +10,8 @@ properties: $ref: "defs_common.yaml#/definitions/Label" summary: $ref: "defs_common.yaml#/definitions/Summary" + image: + $ref: "defs_common.yaml#/definitions/Image" motivation: $ref: "defs_common.yaml#/definitions/Description" description: diff --git a/src/tasks/batch_integration/api/task_info.yaml b/src/tasks/batch_integration/api/task_info.yaml index a41b6db605..e76b641d5e 100644 --- a/src/tasks/batch_integration/api/task_info.yaml +++ b/src/tasks/batch_integration/api/task_info.yaml @@ -4,6 +4,7 @@ v1: path: openproblems/tasks/batch_integration/README.md commit: 637163fba7d74ab5393c2adbee5354dcf4d46f85 summary: Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. +image: thumbnail.svg motivation: | As single-cell technologies advance, single-cell datasets are growing both in size and complexity. Especially in consortia such as the Human Cell Atlas, individual studies combine data from multiple labs, each sequencing multiple individuals possibly with different technologies. diff --git a/src/tasks/batch_integration/api/thumbnail.svg b/src/tasks/batch_integration/api/thumbnail.svg new file mode 100644 index 0000000000..77626c5bfb --- /dev/null +++ b/src/tasks/batch_integration/api/thumbnail.svg @@ -0,0 +1 @@ +Batch 1Batch 2dim-2dim-1dim-2dim-1 \ No newline at end of file diff --git a/src/tasks/denoising/api/task_info.yaml b/src/tasks/denoising/api/task_info.yaml index d093409efc..f7de1118f2 100644 --- a/src/tasks/denoising/api/task_info.yaml +++ b/src/tasks/denoising/api/task_info.yaml @@ -4,6 +4,7 @@ v1: path: openproblems/tasks/denoising/README.md commit: 3fe9251ba906061b6769eed2ac9da0db5f8e26bb summary: "Removing noise in sparse single-cell RNA-sequencing count data" +image: "thumbnail.svg" motivation: | Single-cell RNA-Seq protocols only detect a fraction of the mRNA molecules present in each cell. As a result, the measurements (UMI counts) observed for each gene and each diff --git a/src/tasks/denoising/api/thumbnail.svg b/src/tasks/denoising/api/thumbnail.svg new file mode 100644 index 0000000000..65936f0e1e --- /dev/null +++ b/src/tasks/denoising/api/thumbnail.svg @@ -0,0 +1 @@ +dim-2dim-1dim-2dim-1 \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/task_info.yaml b/src/tasks/dimensionality_reduction/api/task_info.yaml index e22c15910e..e202497c99 100644 --- a/src/tasks/dimensionality_reduction/api/task_info.yaml +++ b/src/tasks/dimensionality_reduction/api/task_info.yaml @@ -4,6 +4,7 @@ v1: path: openproblems/tasks/dimensionality_reduction/README.md commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b summary: Reduction of high-dimensional datasets to 2D for visualization & interpretation +image: "thumbnail.svg" motivation: | Dimensionality reduction is one of the key challenges in single-cell data representation. Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly diff --git a/src/tasks/dimensionality_reduction/api/thumbnail.svg b/src/tasks/dimensionality_reduction/api/thumbnail.svg new file mode 100644 index 0000000000..62911379a1 --- /dev/null +++ b/src/tasks/dimensionality_reduction/api/thumbnail.svg @@ -0,0 +1 @@ +dim-2dim-1 \ No newline at end of file diff --git a/src/tasks/label_projection/api/task_info.yaml b/src/tasks/label_projection/api/task_info.yaml index 8ee865a131..07b6b0120d 100644 --- a/src/tasks/label_projection/api/task_info.yaml +++ b/src/tasks/label_projection/api/task_info.yaml @@ -4,6 +4,7 @@ v1: path: openproblems/tasks/label_projection/README.md commit: 817ea64a526c7251f74c9a7a6dba98e8602b94a8 summary: Automated cell type annotation from rich, labeled reference data +image: "thumbnail.svg" motivation: | A major challenge for integrating single cell datasets is creating matching cell type annotations for each cell. One of the most common strategies for diff --git a/src/tasks/label_projection/api/thumbnail.svg b/src/tasks/label_projection/api/thumbnail.svg new file mode 100644 index 0000000000..3a0c47b5c2 --- /dev/null +++ b/src/tasks/label_projection/api/thumbnail.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/src/tasks/match_modalities/api/task_info.yaml b/src/tasks/match_modalities/api/task_info.yaml index 4baeda74d0..2baa517cac 100644 --- a/src/tasks/match_modalities/api/task_info.yaml +++ b/src/tasks/match_modalities/api/task_info.yaml @@ -3,6 +3,7 @@ label: Match Modalities summary: | Match modalities is the task of combining multiple datasets that have been generated from the same set of samples. +image: "thumbnail.svg" motivation: "No motivation has been provided for this task." description: | Match modalities is the task of combining multiple datasets diff --git a/src/tasks/match_modalities/api/thumbnail.svg b/src/tasks/match_modalities/api/thumbnail.svg new file mode 100644 index 0000000000..07e326bc4a --- /dev/null +++ b/src/tasks/match_modalities/api/thumbnail.svg @@ -0,0 +1 @@ +RNAATACdim-2dim-1dim-2dim-1 \ No newline at end of file From 271ed6b8fa528d19f595b07f1c98bcae7fcb37d3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 15 Sep 2023 16:22:52 +0200 Subject: [PATCH 0990/1233] Bump docker/login-action from 2 to 3 (#229) Bumps [docker/login-action](https://github.com/docker/login-action) from 2 to 3. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/v2...v3) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 86d799adf18b770f2b141d2e275cac7ed169e973 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/main-build.yml | 2 +- .github/workflows/release-build.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 409cb8a2b7..671633f4d1 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -97,7 +97,7 @@ jobs: src: ${{ matrix.component.dir }} - name: Login to container registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ secrets.GTHB_USER }} diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 4d97dc464e..b1fa67c4c9 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -95,7 +95,7 @@ jobs: setup: build - name: Login to container registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ secrets.GTHB_USER }} diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index dc07902732..36a409fd5e 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -124,7 +124,7 @@ jobs: setup: build - name: Login to container registry - uses: docker/login-action@v2 + uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ secrets.GTHB_USER }} From 1de846afd85da98d6ae55ac92a746e50466e87a9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 20 Sep 2023 14:52:11 +0200 Subject: [PATCH 0991/1233] Refactoring nextflow helpers (#230) * refactoring nextflow helpers * fix script * fix script * fix workflow * fix wf * store slot names in check_dataset_schema, change toState processing,fix workflows * ci force * rework workflows * generate test resources with nextflow * refactor multimodal script into scicar_cell_lines * refactor test resources * ci force * refactor batch integration * update wf helper * also store id * fix api * update * fix workflows * fix check_dataset_schema test * clean up get_x_info components * fix copy component * fix tests * fix components * fix match modalities test * fix process_dataset * update readme * add test resource script for match_modalities --------- Co-authored-by: Kai Waldrant Former-commit-id: fbc9476f3a208567cfc0c08c3fed857e400f1012 --- src/common/api/get_info.yaml | 37 +- .../check_dataset_schema/config.vsh.yaml | 3 + src/common/check_dataset_schema/script.py | 23 +- src/common/check_dataset_schema/test.py | 109 +++--- src/common/comp_tests/check_get_info.py | 37 ++ src/common/copy/config.vsh.yaml | 27 ++ src/common/copy/script.sh | 15 + src/common/copy/test.sh | 21 ++ src/common/get_method_info/config.vsh.yaml | 3 +- src/common/get_method_info/script.R | 6 +- src/common/get_metric_info/config.vsh.yaml | 3 +- src/common/get_metric_info/script.R | 6 +- src/datasets/api/file_knn.yaml | 2 +- src/datasets/processors/subsample/script.py | 4 +- src/datasets/processors/svd/script.py | 4 +- .../resource_scripts/openproblems_v1.sh | 4 +- .../resource_test_scripts/bmmc_x_starter.sh | 20 + .../resource_test_scripts/multimodal.sh | 71 ---- .../resource_test_scripts/pancreas.sh | 76 ++-- .../scicar_cell_lines.sh | 44 +++ .../process_openproblems_v1/config.vsh.yaml | 82 +++- .../workflows/process_openproblems_v1/main.nf | 165 ++++++-- .../config.vsh.yaml | 131 +++++++ .../main.nf | 209 +++++++++++ .../nextflow.config | 16 + src/migration/check_migration_status/test.py | 4 +- src/migration/list_git_shas/config.vsh.yaml | 3 +- src/tasks/batch_integration/README.md | 58 ++- .../api/comp_process_dataset.yaml | 2 +- .../api/file_common_dataset.yaml | 61 +++ .../batch_integration/api/file_solution.yaml | 2 +- .../resources_scripts/process_datasets.sh | 51 +-- .../resources_scripts/run_benchmark.sh | 52 +-- .../resources_test_scripts/pancreas.sh | 40 +- .../process_datasets/config.vsh.yaml | 40 ++ .../workflows/process_datasets/main.nf | 77 ++++ .../{run => process_datasets}/nextflow.config | 0 .../process_datasets/run_nextflow.sh | 25 ++ .../{run => run_benchmark}/config.vsh.yaml | 7 +- .../workflows/{run => run_benchmark}/main.nf | 71 ++-- .../workflows/run_benchmark/nextflow.config | 16 + .../{run => run_benchmark}/run_nextflow.sh | 12 +- .../run_test_on_tower.sh | 2 +- src/tasks/denoising/README.md | 50 +-- .../resources_test_scripts/pancreas.sh | 34 +- src/tasks/denoising/workflows/run/main.nf | 28 +- .../resources_test_scripts/pancreas.sh | 4 +- .../workflows/run/main.nf | 37 +- .../label_projection/workflows/run/main.nf | 28 +- .../api/comp_control_method.yaml | 4 +- .../match_modalities/api/comp_method.yaml | 4 +- .../api/file_integrated_mod1.yaml | 2 +- .../api/file_integrated_mod2.yaml | 2 +- src/tasks/match_modalities/api/file_mod1.yaml | 2 +- src/tasks/match_modalities/api/file_mod2.yaml | 2 +- .../match_modalities/api/file_score.yaml | 2 +- .../control_methods/random_features/script.py | 4 +- .../control_methods/true_features/script.py | 4 +- .../match_modalities/methods/fastmnn/script.R | 4 +- .../methods/harmonic_alignment/script.py | 4 +- .../methods/procrustes/script.py | 4 +- .../match_modalities/methods/scot/script.py | 4 +- .../scicar_cell_lines.sh | 7 + .../match_modalities/workflows/run/main.nf | 28 +- .../workflows/run/run_test.sh | 2 +- .../workflows/run/run_test_on_tower.sh | 2 +- src/tasks/predict_modality/README.md | 6 +- .../api/file_dataset_other_mod.yaml | 2 +- .../api/file_dataset_rna.yaml | 2 +- .../predict_modality/process_dataset/script.R | 4 +- .../resources_test_scripts/bmmc_x_starter.sh | 18 +- .../predict_modality/workflows/run/main.nf | 28 +- src/wf_utils/BenchmarkHelper.nf | 355 +++++++++++++++++- src/wf_utils/WorkflowHelper.nf | 50 ++- 74 files changed, 1700 insertions(+), 668 deletions(-) create mode 100644 src/common/comp_tests/check_get_info.py create mode 100644 src/common/copy/config.vsh.yaml create mode 100644 src/common/copy/script.sh create mode 100644 src/common/copy/test.sh create mode 100755 src/datasets/resource_test_scripts/bmmc_x_starter.sh delete mode 100644 src/datasets/resource_test_scripts/multimodal.sh create mode 100755 src/datasets/resource_test_scripts/scicar_cell_lines.sh create mode 100644 src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml create mode 100644 src/datasets/workflows/process_openproblems_v1_multimodal/main.nf create mode 100644 src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config create mode 100644 src/tasks/batch_integration/api/file_common_dataset.yaml create mode 100644 src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/batch_integration/workflows/process_datasets/main.nf rename src/tasks/batch_integration/workflows/{run => process_datasets}/nextflow.config (100%) create mode 100755 src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh rename src/tasks/batch_integration/workflows/{run => run_benchmark}/config.vsh.yaml (78%) rename src/tasks/batch_integration/workflows/{run => run_benchmark}/main.nf (82%) create mode 100644 src/tasks/batch_integration/workflows/run_benchmark/nextflow.config rename src/tasks/batch_integration/workflows/{run => run_benchmark}/run_nextflow.sh (63%) rename src/tasks/batch_integration/workflows/{run => run_benchmark}/run_test_on_tower.sh (91%) create mode 100755 src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml index eac870dad4..c53d82c2c5 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/api/get_info.yaml @@ -20,39 +20,4 @@ functionality: - path: /_viash.yaml dest: openproblems-v2/_viash.yaml - type: python_script - path: generic_test.py - text: | - import subprocess - from os import path - import json - - input_path = meta["resources_dir"] + "/openproblems-v2" - task_id = "denoising" - output_path = "output.json" - - cmd = [ - meta['executable'], - "--input", input_path, - "--task_id", task_id, - "--output", output_path, - ] - - print(">> Running script as test", flush=True) - out = subprocess.run(cmd, stderr=subprocess.STDOUT) - - if out.stdout: - print(out.stdout) - - if out.returncode: - print(f"script: '{cmd}' exited with an error.") - exit(out.returncode) - - print(">> Checking whether output file exists", flush=True) - assert path.exists(output_path), "Output does not exist" - - print(">> Reading json file", flush=True) - with open(output_path, 'r') as f: - out = json.load(f) - print(out) - - print("All checks succeeded!", flush=True) \ No newline at end of file + path: /src/common/comp_tests/check_get_info.py \ No newline at end of file diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index dfd1baebe8..fb8769798a 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -49,5 +49,8 @@ functionality: platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 + test_setup: + - type: python + packages: viashpy - type: nextflow diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 727d3bf59f..7dc5969f9c 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -22,12 +22,13 @@ def check_structure(slot_info, adata_slot): return missing print('Load data', flush=True) -adata = ad.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input']).copy() # create data structure out = { "exit_code": 0, - "error": {} + "error": {}, + "data_schema": "ok" } def is_atomic(obj): @@ -46,11 +47,17 @@ def is_dict_of_atomics(obj): if par['meta'] is not None: print("Extract metadata from object", flush=True) - meta = { + uns = { key: val for key, val in adata.uns.items() if is_atomic(val) or is_list_of_atomics(val) or is_dict_of_atomics(val) } + structure = { + struct: list(getattr(adata, struct).keys()) + for struct + in ["obs", "var", "obsp", "varp", "obsm", "varm", "layers", "uns"] + } + meta = {"uns": uns, "structure": structure} with open(par["meta"], "w") as f: yaml.dump(meta, f, indent=2) @@ -61,20 +68,18 @@ def is_dict_of_atomics(obj): def_slots = data_struct['info']['slots'] - out["data_schema"] = "ok" - for slot in def_slots: - check = check_structure(def_slots[slot], getattr(adata, slot)) - if bool(check): + missing = check_structure(def_slots[slot], getattr(adata, slot)) + if missing: out['exit_code'] = 1 out['data_schema'] = 'not ok' - out['error'][slot] = check + out['error'][slot] = missing if par['checks'] is not None: with open(par["checks"], "w") as f: json.dump(out, f, indent=2) -if par['output'] is not None: +if par['output'] is not None and out["data_schema"] == "ok": shutil.copyfile(par["input"], par["output"]) if par['stop_on_error']: diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index aaba49c11e..40e633ae21 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -1,19 +1,18 @@ -import subprocess -from os import path +import sys +import re +import pytest import json +import subprocess -input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -input_correct_schema = "file_correct.yaml" -input_error_schema = "file_error.yaml" -output_checks = "checks.json" -output_path = "output.h5ad" -output_error_checks = "error_checks.json" -output_error_path = "error_output.h5ad" - +## VIASH START +## VIASH END +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" -with open(input_correct_schema, "w") as f: - f.write(''' +@pytest.fixture +def schema(tmp_path): + schema = tmp_path / "schema.yaml" + schema.write_text(""" type: file description: "A preprocessed dataset" example: "preprocessed.h5ad" @@ -28,11 +27,13 @@ - type: string name: dataset_id description: "A unique identifier for the dataset" - ''') - +""") + return schema -with open(input_error_schema, "w") as f: - f.write(''' +@pytest.fixture +def error_schema(tmp_path): + schema = tmp_path / "schema.yaml" + schema.write_text(""" type: file description: "A preprocessed dataset" example: "preprocessed.h5ad" @@ -50,60 +51,42 @@ - type: string name: error_test description: "A made up uns variable to test if error is picked up" - ''') + """) + return schema +def test_run(run_component, tmp_path, schema): + output_path = tmp_path / "output.h5ad" -cmd = [ - meta['executable'], + run_component([ "--input", input_path, - "--schema", input_correct_schema, - "--checks", output_checks, - "--output", output_path, -] - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT) + "--schema", str(schema), + "--output", str(output_path) + ]) -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{cmd}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether output file exists", flush=True) -assert path.exists(output_checks), "Output checks file does not exist" -assert path.exists(output_path), "Output path does not exist" - -print(">> Reading json file", flush=True) -with open(output_checks, 'r') as f: - out = json.load(f) - print(out) - - -# Check if an incomplete h5ad is captured -cmd_error = [ - meta['executable'], - "--input", input_path, - "--schema", input_error_schema, - "--stop_on_error", 'true', - "--checks", output_error_checks, - "--output", output_error_path, -] + assert output_path.exists(), "Output path does not exist" -print(">> Running script as test", flush=True) -out_error = subprocess.run(cmd_error) +def test_error(run_component, tmp_path, error_schema): + output_checks = tmp_path / "checks.json" + output_path = tmp_path / "output.h5ad" -print(">> Checking whether output file exists", flush=True) -assert path.exists(output_error_checks), "Output checks file does not exist" -assert path.exists(output_error_path), "Output path does not exist" + with pytest.raises(subprocess.CalledProcessError) as err: + run_component([ + "--input", input_path, + "--schema", str(error_schema), + "--stop_on_error", "true", + "--checks", str(output_checks), + "--output", str(output_path) + ]) + assert err.value.exitcode > 0 -assert out_error.returncode == 1, "Exit code should be 1" + assert output_checks.exists(), "Output checks file does not exist" + assert not output_path.exists(), "Output path does not exist" -print(">> Reading json file", flush=True) -with open(output_error_checks, 'r') as f: - out = json.load(f) - print(out) + with open(output_checks, "r") as f: + out = json.load(f) + assert out["exit_code"] > 0 + assert out["data_schema"] == "not ok" -print("All checks succeeded!", flush=True) +if __name__ == "__main__": + sys.exit(pytest.main([__file__])) diff --git a/src/common/comp_tests/check_get_info.py b/src/common/comp_tests/check_get_info.py new file mode 100644 index 0000000000..d62c06355a --- /dev/null +++ b/src/common/comp_tests/check_get_info.py @@ -0,0 +1,37 @@ +import subprocess +from os import path +import json + +## VIASH START +## VIASH END + +input_path = meta["resources_dir"] + "/openproblems-v2" +task_id = "denoising" +output_path = "output.json" + +cmd = [ + meta['executable'], + "--input", input_path, + "--task_id", task_id, + "--output", output_path, +] + +print(">> Running script as test", flush=True) +out = subprocess.run(cmd, stderr=subprocess.STDOUT) + +if out.stdout: + print(out.stdout) + +if out.returncode: + print(f"script: '{cmd}' exited with an error.") + exit(out.returncode) + +print(">> Checking whether output file exists", flush=True) +assert path.exists(output_path), "Output does not exist" + +print(">> Reading json file", flush=True) +with open(output_path, 'r') as f: + out = json.load(f) + print(out) + +print("All checks succeeded!", flush=True) \ No newline at end of file diff --git a/src/common/copy/config.vsh.yaml b/src/common/copy/config.vsh.yaml new file mode 100644 index 0000000000..150d36f181 --- /dev/null +++ b/src/common/copy/config.vsh.yaml @@ -0,0 +1,27 @@ +functionality: + name: copy + namespace: "common" + description: Publish an artifact and optionally rename with parameters + arguments: + - name: "--input" + alternatives: ["-i"] + type: file + direction: input + required: true + description: Input filename + - name: "--output" + alternatives: ["-o"] + type: file + direction: output + required: true + description: Output filename + resources: + - type: bash_script + path: script.sh + test_resources: + - type: bash_script + path: test.sh +platforms: + - type: docker + image: ubuntu:22.04 + - type: nextflow diff --git a/src/common/copy/script.sh b/src/common/copy/script.sh new file mode 100644 index 0000000000..1aeffceac0 --- /dev/null +++ b/src/common/copy/script.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +set -eo pipefail + +## VIASH START +par_input="input.txt" +par_output="output.txt" +## VIASH END + +parent=`dirname "$par_output"` +if [[ ! -d "$parent" ]]; then + mkdir -p "$parent" +fi + +cp -r "$par_input" "$par_output" \ No newline at end of file diff --git a/src/common/copy/test.sh b/src/common/copy/test.sh new file mode 100644 index 0000000000..cb1f509c0c --- /dev/null +++ b/src/common/copy/test.sh @@ -0,0 +1,21 @@ +#!/usr/bin/env bash +set -ex + +touch test_file.txt + +echo ">>> Testing if publish in local dir works" +"$meta_executable" \ + --input test_file.txt \ + --output another_file.txt + +[[ ! -f another_file.txt ]] && echo "It seems no output is generated" && exit 1 + +echo ">>> Testing if publish in local dir works" +"$meta_executable" \ + --input test_file.txt \ + --output adir/yadir/another_file.txt + +[[ ! -d adir ]] && echo "It seems no output is generated" && exit 1 +[[ ! -f adir/yadir/another_file.txt ]] && echo "It seems no output is generated" && exit 1 + +echo ">>> Test finished successfully" diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 8c322e5cd7..3c901f57cf 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -15,6 +15,5 @@ platforms: - type: apt packages: [ curl, default-jdk ] - type: docker - run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" + run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow - - type: native diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index da7936c621..2cfe58d390 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -1,6 +1,6 @@ -library(purrr) -library(dplyr) -library(rlang) +library(purrr, warn.conflicts = FALSE) +library(dplyr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 775a78232e..13ab319a02 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -15,6 +15,5 @@ platforms: - type: apt packages: [ curl, default-jdk ] - type: docker - run: "curl -fsSL get.viash.io | bash -s -- --bin /usr/local/bin/" + run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow - - type: native diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index d3544ce7bd..38c8232731 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -1,6 +1,6 @@ -library(purrr) -library(dplyr) -library(rlang) +library(purrr, warn.conflicts = FALSE) +library(dplyr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( diff --git a/src/datasets/api/file_knn.yaml b/src/datasets/api/file_knn.yaml index 80e6a69828..497430369e 100644 --- a/src/datasets/api/file_knn.yaml +++ b/src/datasets/api/file_knn.yaml @@ -1,6 +1,6 @@ __merge__: file_hvg.yaml type: file -example: "resources_test/common/pancreas/dataset.h5ad" +example: "resources_test/common/pancreas/knn.h5ad" info: label: "Dataset+PCA+HVG+kNN" summary: "A normalised data with a PCA embedding, HVG selection and a kNN graph" diff --git a/src/datasets/processors/subsample/script.py b/src/datasets/processors/subsample/script.py index 1b5d1b3992..c126c886ef 100644 --- a/src/datasets/processors/subsample/script.py +++ b/src/datasets/processors/subsample/script.py @@ -4,8 +4,8 @@ ### VIASH START par = { - "input": "resources_test/common/multimodal/temp_mod1_full.h5ad", - "input_mod2": "resources_test/common/multimodal/temp_mod2_full.h5ad", + "input": "resources_test/common/scicar_cell_lines/temp_mod1_full.h5ad", + "input_mod2": "resources_test/common/scicar_cell_lines/temp_mod2_full.h5ad", "n_obs": 600, "n_vars": 1500, "keep_celltype_categories": None, diff --git a/src/datasets/processors/svd/script.py b/src/datasets/processors/svd/script.py index c359615c60..d474d732ff 100644 --- a/src/datasets/processors/svd/script.py +++ b/src/datasets/processors/svd/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - "input": "resources_test/common/multimodal/normalized_mod1.h5ad", - "input_mod2": "resources_test/common/multimodal/normalized_mod2.h5ad", + "input": "resources_test/common/scicar_cell_lines/normalized_mod1.h5ad", + "input_mod2": "resources_test/common/scicar_cell_lines/normalized_mod2.h5ad", "output": "output.h5ad", "layer_input": "normalized", "obsm_embedding": "X_svd", diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 5fa3ab2d22..d7cd99be44 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -145,8 +145,8 @@ param_list: dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio -output_dataset: '$id/dataset.h5ad' -output_meta: '$id/dataset_meta.yaml' +output_dataset: dataset.h5ad +output_meta: dataset_metadata.yaml HERE fi diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh new file mode 100755 index 0000000000..298bd668a5 --- /dev/null +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" +DATASET_DIR="resources_test/common" + +SUBDIR="$DATASET_DIR/bmmc_cite_starter" +mkdir -p "$SUBDIR" +wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ + -O "$SUBDIR/dataset_rna.h5ad" +wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ + -O "$SUBDIR/dataset_adt.h5ad" + +SUBDIR="$DATASET_DIR/bmmc_multiome_starter" +mkdir -p "$SUBDIR" +wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ + -O "$SUBDIR/dataset_rna.h5ad" +wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ + -O "$SUBDIR/dataset_atac.h5ad" + +src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/multimodal.sh b/src/datasets/resource_test_scripts/multimodal.sh deleted file mode 100644 index db6247c300..0000000000 --- a/src/datasets/resource_test_scripts/multimodal.sh +++ /dev/null @@ -1,71 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#viash ns build -q 'datasets|common' --parallel --setup cb - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/common/multimodal - -set -e - -mkdir -p $DATASET_DIR - -# download dataset -viash run src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml -- \ - --obs_tissue "source" \ - --layer_counts "counts" \ - --obs_celltype "cell_name" \ - --dataset_id scicar_cell_lines \ - --dataset_name "sci-CAR cell lines" \ - --data_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ - --data_reference "cao2018joint" \ - --dataset_summary "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells" \ - --dataset_description "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells. Here, we use two sciCAR datasets that were obtained from the same study. The first dataset contains 4,825 cells from three cell lines (HEK293T cells, NIH/3T3 cells, and A549 cells) at multiple timepoints (0, 1 hour, 3 hours) after dexamethasone treatment. The second dataset contains 11,233 cells from wild-type adult mouse kidney." \ - --dataset_organism "[homo_sapiens, mus_musculus]" \ - --output_mod1 $DATASET_DIR/temp_mod1_full.h5ad \ - --output_mod2 $DATASET_DIR/temp_mod2_full.h5ad - - -# subsample -viash run src/datasets/processors/subsample/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_mod1_full.h5ad \ - --input_mod2 $DATASET_DIR/temp_mod2_full.h5ad \ - --n_obs 600 \ - --n_vars 1500 \ - --output $DATASET_DIR/raw_mod1.h5ad \ - --output_mod2 $DATASET_DIR/raw_mod2.h5ad \ - --seed 123 - - -# run log cp10k normalisation on mod 1 file -viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ - --input $DATASET_DIR/raw_mod1.h5ad \ - --output $DATASET_DIR/normalized_mod1.h5ad - -# run log cp10k normalisation on mod 2 file -viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ - --input $DATASET_DIR/raw_mod2.h5ad \ - --output $DATASET_DIR/normalized_mod2.h5ad - -# run svd -viash run src/datasets/processors/svd/config.vsh.yaml -- \ - --input $DATASET_DIR/normalized_mod1.h5ad \ - --input_mod2 $DATASET_DIR/normalized_mod2.h5ad \ - --output $DATASET_DIR/svd_mod1.h5ad \ - --output_mod2 $DATASET_DIR/svd_mod2.h5ad - -# run hvg -viash run src/datasets/processors/hvg/config.vsh.yaml -- \ - --input $DATASET_DIR/svd_mod1.h5ad \ - --output $DATASET_DIR/dataset_mod1.h5ad - -viash run src/datasets/processors/hvg/config.vsh.yaml -- \ - --input $DATASET_DIR/svd_mod2.h5ad \ - --output $DATASET_DIR/dataset_mod2.h5ad - -rm -r $DATASET_DIR/temp_* \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 50b28a50ee..2a6b804e27 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -9,62 +9,50 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -DATASET_DIR=resources_test/common/pancreas +DATASET_DIR=resources_test/common set -e mkdir -p $DATASET_DIR -# download dataset -viash run src/datasets/loaders/openproblems_v1/config.vsh.yaml -- \ - --obs_celltype "celltype" \ - --obs_batch "tech" \ - --layer_counts "counts" \ - --dataset_id pancreas \ - --dataset_name "Human pancreas" \ - --data_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ - --data_reference "luecken2022benchmarking" \ - --dataset_summary "Human pancreas cells dataset from the scIB benchmarks" \ - --dataset_description "Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq)." \ - --dataset_organism "homo_sapiens" \ - --output $DATASET_DIR/temp_dataset_full.h5ad - wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/g2m_genes_tirosh_hm.txt -O $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/s_genes_tirosh_hm.txt -O $DATASET_DIR/temp_s_genes_tirosh_hm.txt KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s_genes_tirosh_hm.txt | paste -sd ":" -` -# subsample -viash run src/datasets/processors/subsample/config.vsh.yaml -- \ - --input $DATASET_DIR/temp_dataset_full.h5ad \ - --keep_celltype_categories "acinar:beta" \ - --keep_batch_categories "celseq:inDrop4:smarter" \ - --keep_features "$KEEP_FEATURES" \ - --output $DATASET_DIR/raw.h5ad \ - --seed 123 - -# run log cp10k normalisation -viash run src/datasets/normalization/log_cp/config.vsh.yaml -- \ - --input $DATASET_DIR/raw.h5ad \ - --output $DATASET_DIR/normalized.h5ad - -# run pca -viash run src/datasets/processors/pca/config.vsh.yaml -- \ - --input $DATASET_DIR/normalized.h5ad \ - --output $DATASET_DIR/pca.h5ad - -# run hvg -viash run src/datasets/processors/hvg/config.vsh.yaml -- \ - --input $DATASET_DIR/pca.h5ad \ - --output $DATASET_DIR/hvg.h5ad - -# run knn -viash run src/datasets/processors/knn/config.vsh.yaml -- \ - --input $DATASET_DIR/hvg.h5ad \ - --output $DATASET_DIR/dataset.h5ad +# download dataset +nextflow run . \ + -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ + -profile docker \ + -resume \ + --id pancreas \ + --obs_celltype "celltype" \ + --obs_batch "tech" \ + --layer_counts "counts" \ + --dataset_id pancreas \ + --dataset_name "Human pancreas" \ + --data_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ + --data_reference "luecken2022benchmarking" \ + --dataset_summary "Human pancreas cells dataset from the scIB benchmarks" \ + --dataset_description "Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq)." \ + --dataset_organism "homo_sapiens" \ + --keep_celltype_categories "acinar:beta" \ + --keep_batch_categories "celseq:inDrop4:smarter" \ + --keep_features "$KEEP_FEATURES" \ + --seed 123 \ + --normalization_methods log_cp \ + --do_subsample true \ + --output_raw raw.h5ad \ + --output_normalized normalized.h5ad \ + --output_pca pca.h5ad \ + --output_hvg hvg.h5ad \ + --output_knn knn.h5ad \ + --output_dataset dataset.h5ad \ + --output_meta dataset_metadata.yaml \ + --publish_dir "$DATASET_DIR" rm -r $DATASET_DIR/temp_* -# rerun task process dataset components +# run task process dataset components src/tasks/batch_integration/resources_test_scripts/pancreas.sh src/tasks/denoising/resources_test_scripts/pancreas.sh src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh new file mode 100755 index 0000000000..414af8330f --- /dev/null +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -0,0 +1,44 @@ +#!/bin/bash +# +#make sure the following command has been executed +#viash ns build -q 'datasets|common' --parallel --setup cb + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +DATASET_DIR=resources_test/common + +set -e + +mkdir -p $DATASET_DIR + +# download dataset +nextflow run . \ + -main-script src/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + -profile docker \ + -resume \ + --id scicar_cell_lines \ + --obs_tissue "source" \ + --layer_counts "counts" \ + --obs_celltype "cell_name" \ + --dataset_id scicar_cell_lines \ + --dataset_name "sci-CAR cell lines" \ + --data_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ + --data_reference "cao2018joint" \ + --dataset_summary "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells" \ + --dataset_description "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells. Here, we use two sciCAR datasets that were obtained from the same study. The first dataset contains 4,825 cells from three cell lines (HEK293T cells, NIH/3T3 cells, and A549 cells) at multiple timepoints (0, 1 hour, 3 hours) after dexamethasone treatment. The second dataset contains 11,233 cells from wild-type adult mouse kidney." \ + --dataset_organism "[homo_sapiens, mus_musculus]" \ + --do_subsample true \ + --n_obs 600 \ + --n_vars 1500 \ + --seed 123 \ + --output_dataset_mod1 dataset_mod1.h5ad \ + --output_dataset_mod2 dataset_mod2.h5ad \ + --output_meta_mod1 dataset_metadata_mod1.yaml \ + --output_meta_mod2 dataset_metadata_mod2.yaml \ + --publish_dir "$DATASET_DIR" + +src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index b82f448ed8..b37ffbaa19 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -10,10 +10,6 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--obs_celltype" type: "string" description: "Location of where to find the observation cell types." @@ -33,6 +29,10 @@ functionality: description: Convert layers to a sparse CSR format. - name: Metadata arguments: + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true - name: "--dataset_name" type: string description: Nicely formatted name. @@ -57,6 +57,49 @@ functionality: type: string description: The organism of the dataset. required: false + - name: Sampling options + arguments: + - name: "--do_subsample" + type: boolean + default: false + description: "Whether or not to subsample the dataset" + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. + - name: "--keep_celltype_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + - name: Normalization + arguments: + - name: "--normalization_methods" + type: string + multiple: true + choices: ["log_cp", "sqrt_cp", "l1_sqrt"] + default: ["log_cp", "sqrt_cp", "l1_sqrt"] + description: "Which normalization methods to run." - name: Outputs arguments: - name: "--output_dataset" @@ -64,8 +107,8 @@ functionality: # todo: fix inherits in nxf # __merge__: ../../api/file_raw.yaml type: file - description: "A raw dataset" - example: "dataset.h5ad" + description: "A dataset" + default: "dataset.h5ad" info: label: "Raw dataset" slots: @@ -96,7 +139,32 @@ functionality: direction: "output" type: file description: "Dataset metadata" - example: "dataset_meta.yaml" + default: "dataset_metadata.yaml" + - name: "--output_raw" + direction: output + type: file + example: raw.h5ad + required: false + - name: "--output_normalized" + direction: output + type: file + example: normalized.h5ad + required: false + - name: "--output_pca" + direction: output + type: file + example: pca.h5ad + required: false + - name: "--output_hvg" + direction: output + type: file + example: hvg.h5ad + required: false + - name: "--output_knn" + direction: output + type: file + example: knn.h5ad + required: false resources: - type: nextflow_script path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 9edf15aa25..57511953b1 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -7,12 +7,13 @@ targetDir = params.rootDir + "/target/nextflow" include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/main.nf" // normalization methods -include { log_cpm } from "$targetDir/datasets/normalization/log_cp/main.nf" +include { log_cp } from "$targetDir/datasets/normalization/log_cp/main.nf" include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" -include { sqrt_cpm } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" +include { sqrt_cp } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" // dataset processors +include { subsample } from "$targetDir/datasets/processors/subsample/main.nf" include { pca } from "$targetDir/datasets/processors/pca/main.nf" include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" include { knn } from "$targetDir/datasets/processors/knn/main.nf" @@ -20,21 +21,21 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() -// normalization_methods = [log_cp, log_scran_pooling, sqrt_cp, l1_sqrt -normalization_methods = [log_cp, sqrt_cp, l1_sqrt] +normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] workflow { helpMessage(config) channelFromParams(params, config) | run_wf + | publishState([:]) } workflow run_wf { @@ -42,70 +43,154 @@ workflow run_wf { input_ch main: - output_ch = input_ch + dataset_ch = input_ch | preprocessInputs(config: config) // fetch data from legacy openproblems - | run_components( - components: openproblems_v1, - fromState: [ - "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", "sparse", - "dataset_name", "data_url", "data_reference", "dataset_summary", "dataset_description", "dataset_organism" - ], - toState: [ dataset: "output" ] + | openproblems_v1.run( + fromState: { id, state -> + def output_filename = + (!state.do_subsample && state.output_raw) ? + state.output_raw : + '$id.$key.output_raw.h5ad' + [ + dataset_id: state.dataset_id, + obs_celltype: state.obs_celltype, + obs_batch: state.obs_batch, + obs_tissue: state.obs_tussue, + layer_counts: state.layer_counts, + sparse: state.sparse, + dataset_name: state.dataset_name, + data_url: state.data_url, + data_reference: state.data_reference, + dataset_summary: state.dataset_summary, + dataset_description: state.dataset_description, + dataset_organism: state.dataset_organism, + output: output_filename + ] + }, + toState: [ + raw: "output" + ] ) - // run normalization methods - | run_components( - components: normalization_methods, - id: { id, state, config -> id + "/" + config.functionality.name }, - fromState: [ input: "dataset" ], + sampled_dataset_ch = dataset_ch + | filter{ id, state -> state.do_subsample } + | subsample.run( + fromState: { id, state -> + [ + input: state.raw, + n_obs: state.n_obs, + n_vars: state.n_vars, + keep_features: state.keep_features, + keep_celltype_categories: state.keep_celltype_categories, + keep_batch_categories: state.keep_batch_categories, + even: state.even, + seed: state.seed, + output: state.output_raw ?: '$id.$key.output_raw.h5ad', + output_mod2: null + ] + }, toState: [ - normalization_id: config.functionality.name, - output_normalization: "output" + raw: "output" ] ) + notsampled_dataset_ch = dataset_ch + | filter{ id, state -> !state.do_subsample } + + output_ch = sampled_dataset_ch + | concat(notsampled_dataset_ch) + + // run normalization methods + | runComponents( + components: normalization_methods, + id: { id, state, config -> + if (state.normalization_methods.size() > 1) { + id + "/" + config.functionality.name + } else { + id + } + }, + filter: { id, state, config -> + config.functionality.name in state.normalization_methods + }, + fromState: { id, state, config -> + [ + input: state.raw, + output: state.output_normalized ?: '$id.$key.output_normalized.h5ad' + ] + }, + toState: { id, output, state, config -> + state + [ + normalization_id: config.functionality.name, + normalized: output.output + ] + } + ) - | run_components( - components: pca, - fromState: [ input: "output_normalization" ], + | pca.run( + fromState: { id, state -> + [ + input: state.normalized, + output: state.output_pca ?: '$id.$key.output_pca.h5ad' + ] + }, toState: [ pca: "output" ] ) - | run_components( - components: hvg, - fromState: [ input: "pca" ], + | hvg.run( + fromState: { id, state -> + [ + input: state.pca, + output: state.output_hvg ?: '$id.$key.output_hvg.h5ad' + ] + }, toState: [ hvg: "output" ] ) - | run_components( - components: knn, - fromState: [ input: "hvg" ], + | knn.run( + fromState: { id, state -> + [ + input: state.hvg, + output: state.output_knn ?: '$id.$key.output_knn.h5ad' + ] + }, toState: [ knn: "output" ] ) - | run_components( - components: check_dataset_schema, - fromState: {id, state, config -> + | check_dataset_schema.run( + fromState: { id, state -> [ input: state.knn, - meta: state.output_meta, - output: state.output_dataset, + meta: state.output_meta ?: '$id.$key.output_meta.yaml', + output: state.output_dataset ?: '$id.$key.output_dataset.h5ad', checks: null ] }, - toState: [], - auto: [publish: true] + toState: [ dataset: "output", meta: "meta" ] ) + // only output the files for which an output file was specified + | setState{ id, state -> + [ + "output_dataset": state.output_dataset ? state.dataset : null, + "output_meta": state.output_meta ? state.meta : null, + "output_raw": state.output_raw ? state.raw : null, + "output_normalized": state.output_normalized ? state.normalized : null, + "output_pca": state.output_pca ? state.pca : null, + "output_hvg": state.output_hvg ? state.hvg : null, + "output_knn": state.output_knn ? state.knn : null + ] + } + emit: output_ch } // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) - write_json(normalization_methods.collect{it.config}, file("$publish_dir/normalization_methods.json")) + writeJson(traces, file("$publish_dir/traces.json")) + // writeJson(normalization_methods.collect{it.config}, file("$publish_dir/normalization_methods.json")) } \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml new file mode 100644 index 0000000000..54e86a7b1e --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -0,0 +1,131 @@ +functionality: + name: process_openproblems_v1_multimodal + namespace: datasets/workflows + description: | + Fetch and process legacy OpenProblems v1 multimodal datasets + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--obs_celltype" + type: "string" + description: "Location of where to find the observation cell types." + - name: "--obs_batch" + type: "string" + description: "Location of where to find the observation batch IDs." + - name: "--obs_tissue" + type: "string" + description: "Location of where to find the observation tissue information." + - name: "--layer_counts" + type: "string" + description: "In which layer to find the counts matrix. Leave undefined to use `.X`." + example: counts + - name: "--sparse" + type: boolean + default: true + description: Convert layers to a sparse CSR format. + - name: Metadata + arguments: + - name: "--dataset_id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--data_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--data_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Sampling options + arguments: + - name: "--do_subsample" + type: boolean + default: false + description: "Whether or not to subsample the dataset" + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. + - name: "--keep_celltype_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + - name: Normalization + arguments: + - name: "--normalization_methods" + type: string + multiple: true + choices: ["log_cp", "sqrt_cp", "l1_sqrt"] + default: ["log_cp"] + description: "Which normalization methods to run." + - name: Outputs + arguments: + - name: "--output_dataset_mod1" + direction: "output" + type: file + example: "dataset_mod1.h5ad" + - name: "--output_dataset_mod2" + direction: "output" + type: file + example: "dataset_mod2.h5ad" + - name: "--output_meta_mod1" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_mod1.yaml" + - name: "--output_meta_mod2" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_mod2.yaml" + resources: + - type: nextflow_script + path: main.nf + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf new file mode 100644 index 0000000000..4c50ae120a --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -0,0 +1,209 @@ +nextflow.enable.dsl=2 + +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +// dataset loaders +include { openproblems_v1_multimodal } from "$targetDir/datasets/loaders/openproblems_v1_multimodal/main.nf" + +// normalization methods +include { log_cp } from "$targetDir/datasets/normalization/log_cp/main.nf" +include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" +include { sqrt_cp } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" +include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" + +// dataset processors +include { subsample } from "$targetDir/datasets/processors/subsample/main.nf" +include { svd } from "$targetDir/datasets/processors/svd/main.nf" +include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" + +// helper functions +include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. +traces = initializeTracer() + +normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] + +workflow { + helpMessage(config) + + channelFromParams(params, config) + | run_wf + | publishState([:]) +} + +workflow run_wf { + take: + input_ch + + main: + dataset_ch = input_ch + | preprocessInputs(config: config) + + // fetch data from legacy openproblems + | openproblems_v1_multimodal.run( + fromState: { id, state -> + [ + dataset_id: state.dataset_id, + obs_celltype: state.obs_celltype, + obs_batch: state.obs_batch, + obs_tissue: state.obs_tussue, + layer_counts: state.layer_counts, + sparse: state.sparse, + dataset_name: state.dataset_name, + data_url: state.data_url, + data_reference: state.data_reference, + dataset_summary: state.dataset_summary, + dataset_description: state.dataset_description, + dataset_organism: state.dataset_organism + ] + }, + toState: [ + raw_mod1: "output_mod1", + raw_mod2: "output_mod2" + ] + ) + + sampled_dataset_ch = dataset_ch + | filter{ id, state -> state.do_subsample } + | subsample.run( + fromState: { id, state -> + [ + input: state.raw_mod1, + input_mod2: state.raw_mod2, + n_obs: state.n_obs, + n_vars: state.n_vars, + keep_features: state.keep_features, + keep_celltype_categories: state.keep_celltype_categories, + keep_batch_categories: state.keep_batch_categories, + even: state.even, + seed: state.seed, + output_mod2: '$id.$key.output_mod2.h5ad' // set value for optional output + ] + }, + toState: [ + raw_mod1: "output", + raw_mod2: "output_mod2" + ] + ) + notsampled_dataset_ch = dataset_ch + | filter{ id, state -> !state.do_subsample } + + output_ch = sampled_dataset_ch + | concat(notsampled_dataset_ch) + + // run normalization methods + | runComponents( + components: normalization_methods, + id: { id, state, config -> + if (state.normalization_methods.size() > 1) { + id + "/" + config.functionality.name + } else { + id + } + }, + filter: { id, state, config -> + config.functionality.name in state.normalization_methods + }, + fromState: { id, state, config -> + [ + input: state.raw_mod1, + output: '$id.$key.output_mod1.h5ad' + ] + }, + toState: { id, output, state, config -> + state + [ + normalization_id: config.functionality.name, + normalized_mod1: output.output + ] + } + ) + // run normalization methods on second modality + | runComponents( + components: normalization_methods, + filter: { id, state, config -> + config.functionality.name == state.normalization_id + }, + fromState: { id, state, config -> + [ + input: state.raw_mod2, + output: '$id.$key.output_mod2.h5ad' + ] + }, + toState: [normalized_mod2: "output"] + ) + + | svd.run( + fromState: { id, state -> + [ + input: state.normalized_mod1, + input_mod2: state.normalized_mod2, + output: '$id.$key.output_mod1.h5ad', + output_mod2: '$id.$key.output_mod2.h5ad' + ] + }, + toState: [ + svd_mod1: "output", + svd_mod2: "output_mod2" + ] + ) + + | hvg.run( + fromState: [ input: "svd_mod1" ], + toState: [ hvg_mod1: "output" ] + ) + + | hvg.run( + fromState: [ input: "svd_mod2" ], + toState: [ hvg_mod2: "output" ] + ) + + | check_dataset_schema.run( + fromState: { id, state -> + [ + input: state.hvg_mod1, + meta: state.output_meta_mod1 ?: '$id.$key.output_meta_mod1.yaml', + output: state.output_dataset_mod1 ?: '$id.$key.output_dataset_mod1.h5ad', + checks: null + ] + }, + toState: [ dataset_mod1: "output", meta_mod1: "meta" ] + ) + + | check_dataset_schema.run( + fromState: { id, state -> + [ + input: state.hvg_mod2, + meta: state.output_meta_mod2 ?: '$id.$key.output_meta_mod2.yaml', + output: state.output_dataset_mod2 ?: '$id.$key.output_dataset_mod2.h5ad', + checks: null + ] + }, + toState: [ dataset_mod2: "output", meta_mod2: "meta" ] + ) + + // only output the files for which an output file was specified + | setState{ id, state -> + [ + "output_dataset_mod1" : state.output_dataset_mod1 ? state.dataset_mod1: null, + "output_dataset_mod2" : state.output_dataset_mod2 ? state.dataset_mod2: null, + "output_meta_mod1" : state.output_meta_mod1 ? state.meta_mod1: null, + "output_meta_mod2" : state.output_meta_mod2 ? state.meta_mod2: null + ] + } + + emit: + output_ch +} + +// store the trace log in the publish dir +workflow.onComplete { + def publish_dir = getPublishDir() + + writeJson(traces, file("$publish_dir/traces.json")) +} \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config b/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config new file mode 100644 index 0000000000..c90cc0589c --- /dev/null +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config @@ -0,0 +1,16 @@ +manifest { + name = 'datasets/workflows/process_openproblems_v1_multimodal' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Fetch and process legacy OpenProblems v1 multimodal datasets' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/migration/check_migration_status/test.py b/src/migration/check_migration_status/test.py index a202a77b98..878a167215 100644 --- a/src/migration/check_migration_status/test.py +++ b/src/migration/check_migration_status/test.py @@ -2,8 +2,8 @@ from os import path import json -input_sha = meta["resources_dir"] + "resources_test/common/task_metadata/input_git_sha.json" -input_method_info = meta["resources_dir"] + "resources_test/common/task_metadata/method_info.json" +input_sha = meta["resources_dir"] + "/resources_test/common/task_metadata/input_git_sha.json" +input_method_info = meta["resources_dir"] + "/resources_test/common/task_metadata/method_info.json" output_path = "output.json" cmd = [ diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 6a0ba6a5ac..4c626ca6cc 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -36,5 +36,4 @@ platforms: test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" - - type: nextflow - - type: native \ No newline at end of file + - type: nextflow \ No newline at end of file diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 90ac1e848d..ec0018f93c 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -54,7 +54,7 @@ extensive benchmark of single-cell data integration methods ``` mermaid flowchart LR - file_common_dataset("Common dataset") + file_common_dataset("Common Dataset") comp_process_dataset[/"Data processor"/] file_dataset("Dataset") file_solution("Solution") @@ -100,29 +100,27 @@ flowchart LR comp_transformer_feature_to_embedding-->file_integrated_embedding ``` -## File format: Common dataset +## File format: Common Dataset -A dataset processed by the common dataset processing pipeline. +A subset of the common dataset. Example file: `resources_test/common/pancreas/dataset.h5ad` Description: -This dataset contains both raw counts and normalized data matrices, as -well as a PCA embedding, HVG selection and a kNN graph. +NA Format:
AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' + obs: 'celltype', 'batch' + var: 'hvg' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' - varm: 'pca_loadings' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn'
@@ -130,29 +128,20 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | -| `obs["batch"]` | `string` | (*Optional*) Batch information. | -| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalised expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_name"]` | `string` | Nicely formatted name. | -| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | -| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | -| `uns["dataset_summary"]` | `string` | Short description of the dataset. | -| `uns["dataset_description"]` | `string` | Long description of the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["pca_variance"]` | `double` | The PCA variance objects. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | Cell type information. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. |
@@ -169,7 +158,7 @@ Arguments: | Name | Type | Description | |:--------------------|:----------|:---------------------------------------------------------------------------| -| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--input` | `file` | A subset of the common dataset. | | `--output_dataset` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | | `--output_solution` | `file` | (*Output*) Solution dataset. | | `--obs_label` | `string` | (*Optional*) Which .obs slot to use as label. Default: `celltype`. | @@ -229,8 +218,7 @@ Slot description: Solution dataset -Example file: -`resources_test/batch_integration/pancreas/unintegrated.h5ad` +Example file: `resources_test/batch_integration/pancreas/solution.h5ad` Description: diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index d213eb3ca3..37706acdcf 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -9,7 +9,7 @@ functionality: A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/file_common_dataset.yaml + __merge__: file_common_dataset.yaml direction: input required: true - name: "--output_dataset" diff --git a/src/tasks/batch_integration/api/file_common_dataset.yaml b/src/tasks/batch_integration/api/file_common_dataset.yaml new file mode 100644 index 0000000000..03c8ce4fb2 --- /dev/null +++ b/src/tasks/batch_integration/api/file_common_dataset.yaml @@ -0,0 +1,61 @@ +type: file +example: "resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common Dataset" + summary: A subset of the common dataset. + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: celltype + description: Cell type information + required: true + - type: string + name: batch + description: Batch information + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + obsp: + - type: double + name: knn_distances + description: K nearest neighbors distance matrix. + required: true + - type: double + name: knn_connectivities + description: K nearest neighbors connectivities matrix. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: object + name: knn + description: Supplementary K nearest neighbors data. + required: true + diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml index 62ef36a9f4..10999fac2f 100644 --- a/src/tasks/batch_integration/api/file_solution.yaml +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" +example: "resources_test/batch_integration/pancreas/solution.h5ad" info: label: "Solution" summary: Solution dataset diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index bdf8413fab..1655086787 100755 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -6,6 +6,8 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + COMMON_DATASETS="resources/datasets/openproblems_v1" OUTPUT_DIR="resources/batch_integration/datasets/openproblems_v1" @@ -13,49 +15,14 @@ if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import anndata as ad -import glob -import yaml - -h5ad_files = glob.glob("$COMMON_DATASETS/**/*.h5ad", recursive=True) - -param_list = [] - -for h5ad_file in h5ad_files: - print(f"Checking {h5ad_file}") - adata = ad.read_h5ad(h5ad_file, backed=True) - - if "batch" in adata.obs and "celltype" in adata.obs: - dataset_id = adata.uns["dataset_id"].replace("/", ".") - normalization_id = adata.uns["normalization_id"] - id = dataset_id + "." + normalization_id - obj = { - 'id': id, - 'input': h5ad_file - } - param_list.append(obj) - -output = { - "param_list": param_list, - "obs_label": "celltype", - "obs_batch": "batch", - "output": "\$id.h5ad" -} - -with open("$params_file", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script target/nextflow/batch_integration/process_dataset/main.nf \ +nextflow run . \ + -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ -profile docker \ + -entry auto \ -resume \ - -params-file $params_file \ + --id resources \ + --input_dir resources/datasets/openproblems_v1 \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 1f92a7e227..7d24cbdc83 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -17,50 +17,14 @@ if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import anndata as ad -import glob -import yaml - -h5ad_files = glob.glob("$DATASETS_DIR/**/*.h5ad", recursive=True) - -# figure out where dataset files are stored -param_list = [] - -for h5ad_file in h5ad_files: - print(f"Checking {h5ad_file}") - adata = ad.read_h5ad(h5ad_file, backed=True) - - dataset_id = adata.uns["dataset_id"].replace("/", ".") - normalization_id = adata.uns["normalization_id"] - id = dataset_id + "." + normalization_id - - obj = { - 'id': id, - 'input': h5ad_file, - # 'dataset_id': dataset_id, - # 'normalization_id': normalization_id - } - param_list.append(obj) - -# write as output file -output = { - "param_list": param_list, -} - -with open("$params_file", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script src/tasks/batch_integration/workflows/run/main.nf \ +nextflow run . \ + -main-script src/tasks/batch_integration/workflows/run_benchmark/main.nf \ -profile docker \ -resume \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" + -entry auto \ + --id resources \ + --input_dir "$DATASETS_DIR" \ + --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index cd88640498..1a4dd94144 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -6,38 +6,34 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/batch_integration/pancreas - -if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 -fi +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/batch_integration mkdir -p $DATASET_DIR # process dataset -echo process data... -viash run src/tasks/batch_integration/process_dataset/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output_dataset $DATASET_DIR/dataset.h5ad \ - --output_solution $DATASET_DIR/solution.h5ad \ - --hvgs 100 +echo Running process_dataset +nextflow run . \ + -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + --id resources_test \ + --input_dir "$RAW_DATA" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ + --publish_dir "$DATASET_DIR" echo Running BBKNN viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/integrated_graph.h5ad + --input $DATASET_DIR/pancreas/dataset.h5ad \ + --output $DATASET_DIR/pancreas/integrated_graph.h5ad echo Running SCVI viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/integrated_embedding.h5ad + --input $DATASET_DIR/pancreas/dataset.h5ad \ + --output $DATASET_DIR/pancreas/integrated_embedding.h5ad echo Running combat viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/integrated_feature.h5ad - -# run one metric -echo run metrics... + --input $DATASET_DIR/pancreas/dataset.h5ad \ + --output $DATASET_DIR/pancreas/integrated_feature.h5ad \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..61a3fbe151 --- /dev/null +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,40 @@ +functionality: + name: "process_datasets" + namespace: "batch_integration/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input" + type: "file" + description: "A dataset" + required: true + example: dataset.h5ad + __merge__: "/src/tasks/batch_integration/api/file_common_dataset.yaml" + - name: Schemas + arguments: + - name: "--dataset_schema" + type: "file" + description: "The schema of the dataset to validate against" + required: true + default: "src/tasks/batch_integration/api/file_common_dataset.yaml" + - name: Outputs + arguments: + - name: "--output_dataset" + type: file + direction: output + required: true + example: dataset.h5ad + - name: "--output_solution" + type: file + direction: output + required: true + example: solution.h5ad + resources: + - type: nextflow_script + path: main.nf +platforms: + - type: nextflow diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..f00994f8b5 --- /dev/null +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -0,0 +1,77 @@ +nextflow.enable.dsl=2 + +sourceDir = params.rootDir + "/src" +targetDir = params.rootDir + "/target/nextflow" + +include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" +include { process_dataset } from "$targetDir/batch_integration/process_dataset/main.nf" + +// import helper functions +include { readConfig; processConfig; helpMessage; channelFromParams; preprocessInputs; readYaml; readJson } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; autoDetectStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" + +config = readConfig("$projectDir/config.vsh.yaml") + +workflow { + helpMessage(config) + + channelFromParams(params, config) + | run_wf + | publishState([:]) +} + +workflow auto { + autoDetectStates(params, config) + | run_wf + | publishState([:]) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + | preprocessInputs(config: config) + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + fromState: { id, state -> + [ + input: state.input, + schema: state.dataset_schema, + output: '$id.$key.output.h5ad', + stop_on_error: false, + checks: null + ] + }, + toState: { id, output, state -> + state + [ dataset: output.output ] + } + ) + + | filter { id, state -> + state.dataset != null + } + + | process_dataset.run( + fromState: [ + input: "dataset", + output_dataset: "output_dataset", + output_solution: "output_solution" + ], + toState: [dataset: "output_dataset", solution: "output_solution"] + ) + + // only output the files for which an output file was specified + | setState { id, state -> + [ + "output_dataset": state.output_dataset ? state.dataset : null, + "output_solution": state.output_solution ? state.solution : null + ] + } + + emit: + output_ch +} diff --git a/src/tasks/batch_integration/workflows/run/nextflow.config b/src/tasks/batch_integration/workflows/process_datasets/nextflow.config similarity index 100% rename from src/tasks/batch_integration/workflows/run/nextflow.config rename to src/tasks/batch_integration/workflows/process_datasets/nextflow.config diff --git a/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh new file mode 100755 index 0000000000..716bbbb552 --- /dev/null +++ b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id resources_test \ + --input_dir resources_test/common \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ + --publish_dir "output/test" \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml similarity index 78% rename from src/tasks/batch_integration/workflows/run/config.vsh.yaml rename to src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 7045a41fa8..a2030b92fd 100644 --- a/src/tasks/batch_integration/workflows/run/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -8,11 +8,16 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--input" + - name: "--input_dataset" type: "file" description: "A dataset" required: true example: dataset.h5ad + - name: "--input_solution" + type: "file" + description: "A solution" + required: true + example: solution.h5ad - name: Outputs arguments: - name: "--output" diff --git a/src/tasks/batch_integration/workflows/run/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf similarity index 82% rename from src/tasks/batch_integration/workflows/run/main.nf rename to src/tasks/batch_integration/workflows/run_benchmark/main.nf index e0ef1268af..fc1aa9c701 100644 --- a/src/tasks/batch_integration/workflows/run/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -5,9 +5,6 @@ targetDir = params.rootDir + "/target/nextflow" include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" -// import preprocessing -include { process_dataset } from "$targetDir/batch_integration/process_dataset/main.nf" - // import methods include { bbknn } from "$targetDir/batch_integration/methods/bbknn/main.nf" include { combat } from "$targetDir/batch_integration/methods/combat/main.nf" @@ -31,7 +28,6 @@ include { asw_label } from "$targetDir/batch_integration/metrics/asw_label/main. include { cell_cycle_conservation } from "$targetDir/batch_integration/metrics/cell_cycle_conservation/main.nf" include { clustering_overlap } from "$targetDir/batch_integration/metrics/clustering_overlap/main.nf" include { graph_connectivity } from "$targetDir/batch_integration/metrics/graph_connectivity/main.nf" -include { lisi } from "$targetDir/batch_integration/metrics/lisi/main.nf" include { hvg_overlap } from "$targetDir/batch_integration/metrics/hvg_overlap/main.nf" include { isolated_label_asw } from "$targetDir/batch_integration/metrics/isolated_label_asw/main.nf" include { isolated_label_f1 } from "$targetDir/batch_integration/metrics/isolated_label_f1/main.nf" @@ -44,12 +40,12 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; autoDetectStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // collect method list methods = [ @@ -76,7 +72,7 @@ metrics = [ isolated_label_f1, kbet, lisi, - pcr, + pcr ] @@ -85,6 +81,13 @@ workflow { channelFromParams(params, config) | run_wf + | publishState([:]) +} + +workflow auto { + autoDetectStates(params, config) + | run_wf + | publishState([:]) } workflow run_wf { @@ -98,17 +101,16 @@ workflow run_wf { | preprocessInputs(config: config) // extract the dataset metadata - | run_components( - components: check_dataset_schema, - fromState: ["input"], - toState: { id, output, config -> - new org.yaml.snakeyaml.Yaml().load(output.meta) + | check_dataset_schema.run( + fromState: [input: "input_dataset"], + toState: { id, output, state -> + state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns } ) // run all methods method_out_ch1 = dataset_ch - | run_components( + | runComponents( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for @@ -126,11 +128,11 @@ workflow run_wf { }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: ["input"], + fromState: [input: "input_dataset"], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output: output.output, method_subtype: config.functionality.info.subtype @@ -140,12 +142,12 @@ workflow run_wf { // append feature->embed transformations method_out_ch2 = method_out_ch1 - | run_components( + | runComponents( components: feature_to_embed, filter: { id, state, config -> state.method_subtype == "feature"}, fromState: [ input: "method_output" ], - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_output: output.output, method_subtype: config.functionality.info.subtype ] @@ -155,12 +157,12 @@ workflow run_wf { // append embed->graph transformations method_out_ch3 = method_out_ch2 - | run_components( + | runComponents( components: embed_to_graph, filter: { id, state, config -> state.method_subtype == "embedding"}, fromState: [ input: "method_output" ], - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_output: output.output, method_subtype: config.functionality.info.subtype ] @@ -170,14 +172,17 @@ workflow run_wf { // run metrics output_ch = method_out_ch3 - | run_components( + | runComponents( components: metrics, filter: { id, state, config -> state.method_subtype == config.functionality.info.subtype }, - fromState: [input_integrated: "method_output"], - toState: { id, output, config -> - [ + fromState: [ + input_integrated: "method_output", + input_solution: "input_solution" + ], + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -187,7 +192,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -197,9 +202,7 @@ workflow run_wf { } // convert to tsv and publish - | extract_scores.run( - auto: [publish: true] - ) + | extract_scores emit: output_ch @@ -207,10 +210,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJson(traces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + // writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) + // writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config b/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config new file mode 100644 index 0000000000..150119dfa2 --- /dev/null +++ b/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config @@ -0,0 +1,16 @@ +manifest { + name = 'batch_integration/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Batch integration' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/batch_integration/workflows/run/run_nextflow.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh similarity index 63% rename from src/tasks/batch_integration/workflows/run/run_nextflow.sh rename to src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh index dd7108da30..a0cf9f55dd 100755 --- a/src/tasks/batch_integration/workflows/run/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh @@ -11,19 +11,17 @@ cd "$REPO_ROOT" set -xe -DATASET_DIR=resources_test/batch_integration/pancreas +DATASET_DIR=resources_test/batch_integration # run benchmark export NXF_VER=22.04.5 # -profile docker \ nextflow run . \ - -main-script src/tasks/batch_integration/workflows/run/main.nf \ + -main-script src/tasks/batch_integration/workflows/run_benchmark/main.nf \ -profile docker \ -c src/wf_utils/labels_ci.config \ -resume \ - --id pancreas \ - --input $DATASET_DIR/unintegrated.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ - $@ \ No newline at end of file + --id foo \ + --input_dir $DATASET_DIR \ + --publish_dir "output" \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run/run_test_on_tower.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh similarity index 91% rename from src/tasks/batch_integration/workflows/run/run_test_on_tower.sh rename to src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh index e769eb77e1..b274c887e0 100644 --- a/src/tasks/batch_integration/workflows/run/run_test_on_tower.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh @@ -5,7 +5,7 @@ DATASET_DIR=resources_test/batch_integration/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE id: pancreas_subsample -input: s3://openproblems-data/$DATASET_DIR/unintegrated.h5ad +input: s3://openproblems-data/$DATASET_DIR/dataset.h5ad output: scores.tsv publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration HERE diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index cda48318be..fe16683e80 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -144,23 +144,23 @@ Arguments:
-| Name | Type | Description | -|:-----------------|:-------|:---------------------------------------------------------------| -| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | -| `--output_train` | `file` | (*Output*) The training data. | -| `--output_test` | `file` | (*Output*) The test data. | +| Name | Type | Description | +|:-----------------|:-------|:------------------------------------------------------------------| +| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | +| `--output_train` | `file` | (*Output*) The subset of molecules used for the training dataset. | +| `--output_test` | `file` | (*Output*) The subset of molecules used for the test dataset. |
## File format: Training data -NA +The subset of molecules used for the training dataset Example file: `resources_test/denoising/pancreas/train.h5ad` Description: -The training data +NA Format: @@ -185,13 +185,13 @@ Slot description: ## File format: Test data -NA +The subset of molecules used for the test dataset Example file: `resources_test/denoising/pancreas/test.h5ad` Description: -The test data +NA Format: @@ -225,11 +225,11 @@ Arguments:
-| Name | Type | Description | -|:----------------|:-------|:------------------------------| -| `--input_train` | `file` | The training data. | -| `--input_test` | `file` | The test data. | -| `--output` | `file` | (*Output*) The denoised data. | +| Name | Type | Description | +|:----------------|:-------|:---------------------------------------------------------------| +| `--input_train` | `file` | The subset of molecules used for the training dataset. | +| `--input_test` | `file` | The subset of molecules used for the test dataset. | +| `--output` | `file` | (*Output*) A denoised dataset as output by a denoising method. |
@@ -244,10 +244,10 @@ Arguments:
-| Name | Type | Description | -|:----------------|:-------|:------------------------------| -| `--input_train` | `file` | The training data. | -| `--output` | `file` | (*Output*) The denoised data. | +| Name | Type | Description | +|:----------------|:-------|:---------------------------------------------------------------| +| `--input_train` | `file` | The subset of molecules used for the training dataset. | +| `--output` | `file` | (*Output*) A denoised dataset as output by a denoising method. |
@@ -262,23 +262,23 @@ Arguments:
-| Name | Type | Description | -|:-------------------|:-------|:------------------------------| -| `--input_test` | `file` | The test data. | -| `--input_denoised` | `file` | The denoised data. | -| `--output` | `file` | (*Output*) Metric score file. | +| Name | Type | Description | +|:-------------------|:-------|:----------------------------------------------------| +| `--input_test` | `file` | The subset of molecules used for the test dataset. | +| `--input_denoised` | `file` | A denoised dataset as output by a denoising method. | +| `--output` | `file` | (*Output*) Metric score file. |
## File format: Denoised data -NA +A denoised dataset as output by a denoising method. Example file: `resources_test/denoising/pancreas/denoised.h5ad` Description: -The denoised data +NA Format: diff --git a/src/tasks/denoising/resources_test_scripts/pancreas.sh b/src/tasks/denoising/resources_test_scripts/pancreas.sh index fb6bda4fab..ddccd6bfa6 100755 --- a/src/tasks/denoising/resources_test_scripts/pancreas.sh +++ b/src/tasks/denoising/resources_test_scripts/pancreas.sh @@ -19,23 +19,23 @@ fi mkdir -p $DATASET_DIR -# # split dataset -# viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ -# --input $RAW_DATA \ -# --output_train $DATASET_DIR/train.h5ad \ -# --output_test $DATASET_DIR/test.h5ad \ -# --seed 123 - -# # run one method -# viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ -# --input_train $DATASET_DIR/train.h5ad \ -# --output $DATASET_DIR/denoised.h5ad - -# # run one metric -# viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ -# --input_denoised $DATASET_DIR/denoised.h5ad \ -# --input_test $DATASET_DIR/test.h5ad \ -# --output $DATASET_DIR/score.h5ad +# split dataset +viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ + --input $RAW_DATA \ + --output_train $DATASET_DIR/train.h5ad \ + --output_test $DATASET_DIR/test.h5ad \ + --seed 123 + +# run one method +viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ + --input_train $DATASET_DIR/train.h5ad \ + --output $DATASET_DIR/denoised.h5ad + +# run one metric +viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ + --input_denoised $DATASET_DIR/denoised.h5ad \ + --input_test $DATASET_DIR/test.h5ad \ + --output $DATASET_DIR/score.h5ad # run benchmark export NXF_VER=22.04.5 diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf index 88aa71215d..0bff9c3fc1 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run/main.nf @@ -22,12 +22,12 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // construct a map of methods (id -> method_module) methods = [ @@ -67,14 +67,14 @@ workflow run_wf { fromState: [ "input": "input_train" ], toState: { id, output, state -> // load output yaml file - def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state state + metadata } ) // run all methods - | run_components( + | runComponents( components: methods, // define a new 'id' by appending the method name to the dataset id @@ -93,8 +93,8 @@ workflow run_wf { // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output: output.output ] @@ -102,7 +102,7 @@ workflow run_wf { ) // run all metrics - | run_components( + | runComponents( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -110,8 +110,8 @@ workflow run_wf { input_denoised: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -121,7 +121,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -141,10 +141,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJson(traces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) + writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index b58b8007cb..d859352991 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -31,7 +31,7 @@ viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- --output $DATASET_DIR/embedding.h5ad # run one metric -viash run src/tasks/dimensionality_reduction/metrics/rmse/config.vsh.yaml -- \ +viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ --input_embedding $DATASET_DIR/embedding.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/score.h5ad @@ -45,7 +45,7 @@ nextflow \ -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ -profile docker \ --id pancreas \ - --input $DATASET_DIR/dataset.h5ad \ + --input_dataset $DATASET_DIR/dataset.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ --output scores.tsv \ --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index 830ad2aa51..c99a374f56 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -19,7 +19,7 @@ include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" // import metrics include { coranking } from "$targetDir/dimensionality_reduction/metrics/coranking/main.nf" include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" -include { rmse } from "$targetDir/dimensionality_reduction/metrics/rmse/main.nf" +include { distance_correlation } from "$targetDir/dimensionality_reduction/metrics/distance_correlation/main.nf" include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" // convert scores to tsv @@ -27,13 +27,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" // read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // collect method list methods = [ @@ -51,7 +51,7 @@ methods = [ metrics = [ coranking, density_preservation, - rmse, + distance_correlation, trustworthiness ] @@ -73,16 +73,15 @@ workflow run_wf { | preprocessInputs(config: config) // extract the dataset metadata - | run_components( - components: check_dataset_schema, + | check_dataset_schema.run( fromState: [input: "input_dataset"], - toState: { id, output, config -> - new org.yaml.snakeyaml.Yaml().load(output.meta) + toState: { id, output, state -> + state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns } ) // run all methods - | run_components( + | runComponents( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for @@ -111,8 +110,8 @@ workflow run_wf { }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output: output.output ] @@ -120,7 +119,7 @@ workflow run_wf { ) // run all metrics - | run_components( + | runComponents( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: { id, state, config -> @@ -130,8 +129,8 @@ workflow run_wf { ] }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -141,7 +140,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -161,10 +160,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJson(traces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) + writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index e74ef83bb3..d1b40d4968 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -26,13 +26,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" // read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // collect method list methods = [ @@ -78,14 +78,14 @@ workflow run_wf { fromState: [ "input": "input_train" ], toState: { id, output, state -> // load output yaml file - def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state state + metadata } ) // run all methods - | run_components( + | runComponents( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for @@ -115,8 +115,8 @@ workflow run_wf { }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output: output.output ] @@ -124,7 +124,7 @@ workflow run_wf { ) // run all metrics - | run_components( + | runComponents( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -132,8 +132,8 @@ workflow run_wf { input_prediction: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -143,7 +143,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -163,10 +163,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJson(traces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) + writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/match_modalities/api/comp_control_method.yaml b/src/tasks/match_modalities/api/comp_control_method.yaml index 486d10be99..420794ea26 100644 --- a/src/tasks/match_modalities/api/comp_control_method.yaml +++ b/src/tasks/match_modalities/api/comp_control_method.yaml @@ -30,8 +30,8 @@ functionality: direction: output required: true test_resources: - - path: /resources_test/common/multimodal - dest: resources_test/common/multimodal + - path: /resources_test/common/scicar_cell_lines + dest: resources_test/common/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script diff --git a/src/tasks/match_modalities/api/comp_method.yaml b/src/tasks/match_modalities/api/comp_method.yaml index ce78af0147..89e883bec0 100644 --- a/src/tasks/match_modalities/api/comp_method.yaml +++ b/src/tasks/match_modalities/api/comp_method.yaml @@ -25,8 +25,8 @@ functionality: direction: output required: true test_resources: - - path: /resources_test/common/multimodal - dest: resources_test/common/multimodal + - path: /resources_test/common/scicar_cell_lines + dest: resources_test/common/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script diff --git a/src/tasks/match_modalities/api/file_integrated_mod1.yaml b/src/tasks/match_modalities/api/file_integrated_mod1.yaml index 87fbf669b4..f46c429afc 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod1.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/multimodal/integrated_mod1.h5ad" +example: "resources_test/match_modalities/integrated_mod1.h5ad" info: label: "Integrated" summary: "The integrated data" diff --git a/src/tasks/match_modalities/api/file_integrated_mod2.yaml b/src/tasks/match_modalities/api/file_integrated_mod2.yaml index 1fe32185c7..3dae69c9ab 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod2.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/multimodal/integrated_mod2.h5ad" +example: "resources_test/match_modalities/integrated_mod2.h5ad" info: label: "Integrated" summary: "The integrated data" diff --git a/src/tasks/match_modalities/api/file_mod1.yaml b/src/tasks/match_modalities/api/file_mod1.yaml index 4844c65acd..60994c1d5c 100644 --- a/src/tasks/match_modalities/api/file_mod1.yaml +++ b/src/tasks/match_modalities/api/file_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/multimodal/dataset_mod1.h5ad" +example: "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad" info: label: "multimodal mod 1 data" summary: "the first modal data" diff --git a/src/tasks/match_modalities/api/file_mod2.yaml b/src/tasks/match_modalities/api/file_mod2.yaml index a4a4c4cc2e..ad32aeddeb 100644 --- a/src/tasks/match_modalities/api/file_mod2.yaml +++ b/src/tasks/match_modalities/api/file_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/multimodal/dataset_mod2.h5ad" +example: "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad" info: label: "multimodal mod 2 data" summary: "the second modal data" diff --git a/src/tasks/match_modalities/api/file_score.yaml b/src/tasks/match_modalities/api/file_score.yaml index a5158a2225..7c9818ecfb 100644 --- a/src/tasks/match_modalities/api/file_score.yaml +++ b/src/tasks/match_modalities/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/multimodal/score.h5ad" +example: "resources_test/match_modalities/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/match_modalities/control_methods/random_features/script.py b/src/tasks/match_modalities/control_methods/random_features/script.py index 203e289762..0c0b6ad5f1 100644 --- a/src/tasks/match_modalities/control_methods/random_features/script.py +++ b/src/tasks/match_modalities/control_methods/random_features/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - "input_mod1": "resources_test/common/multimodal/dataset_mod1.h5ad", - "input_mod2": "resources_test/common/multimodal/dataset_mod2.h5ad", + "input_mod1": "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2": "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", "output_mod1": "output.mod1.h5ad", "output_mod2": "output.mod2.h5ad", } diff --git a/src/tasks/match_modalities/control_methods/true_features/script.py b/src/tasks/match_modalities/control_methods/true_features/script.py index a3fb0fc9ea..e4b5a28292 100644 --- a/src/tasks/match_modalities/control_methods/true_features/script.py +++ b/src/tasks/match_modalities/control_methods/true_features/script.py @@ -3,8 +3,8 @@ ## VIASH START par = { - "input_mod1": "resources_test/common/multimodal/dataset_mod1.h5ad", - "input_mod2": "resources_test/common/multimodal/dataset_mod2.h5ad", + "input_mod1": "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2": "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", "output_mod1": "output.mod1.h5ad", "output_mod2": "output.mod2.h5ad", } diff --git a/src/tasks/match_modalities/methods/fastmnn/script.R b/src/tasks/match_modalities/methods/fastmnn/script.R index 65d93333bc..129f134e16 100644 --- a/src/tasks/match_modalities/methods/fastmnn/script.R +++ b/src/tasks/match_modalities/methods/fastmnn/script.R @@ -4,8 +4,8 @@ requireNamespace("batchelor", quietly = TRUE) ## VIASH START par <- list( - input_mod1 = "resources_test/common/multimodal/dataset_mod1.h5ad", - input_mod2 = "resources_test/common/multimodal/dataset_mod2.h5ad", + input_mod1 = "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + input_mod2 = "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", output_mod1 = "output_mod1.h5ad", output_mod2 = "output_mod2.h5ad" ) diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/script.py b/src/tasks/match_modalities/methods/harmonic_alignment/script.py index 9fdb5f7102..c2243badbd 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/script.py +++ b/src/tasks/match_modalities/methods/harmonic_alignment/script.py @@ -3,8 +3,8 @@ ## VIASH START par = { - "mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", - "mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "mod1" : "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "mod2" : "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", "output" : "output.scot.h5ad", "n_pca_XY" : 100, "eigenvectors" : 100 diff --git a/src/tasks/match_modalities/methods/procrustes/script.py b/src/tasks/match_modalities/methods/procrustes/script.py index 20afe28d91..fad63fa658 100644 --- a/src/tasks/match_modalities/methods/procrustes/script.py +++ b/src/tasks/match_modalities/methods/procrustes/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - "input_mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", - "input_mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "input_mod1" : "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2" : "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", "output_mod1" : "output.mod1.h5ad", "output_mod2" : "output.mod2.h5ad", } diff --git a/src/tasks/match_modalities/methods/scot/script.py b/src/tasks/match_modalities/methods/scot/script.py index e43b685131..925a727cae 100644 --- a/src/tasks/match_modalities/methods/scot/script.py +++ b/src/tasks/match_modalities/methods/scot/script.py @@ -10,8 +10,8 @@ ## VIASH START par = { - "input_mod1" : "resources_test/common/multimodal/dataset_mod1.h5ad", - "input_mod2" : "resources_test/common/multimodal/dataset_mod2.h5ad", + "input_mod1" : "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2" : "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", "output_mod1" : "integrated_mod1.h5ad", "output_mod2" : "integrated_mod2.h5ad", "balanced":False, diff --git a/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh new file mode 100755 index 0000000000..6dd04be88a --- /dev/null +++ b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +viash run src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml -- \ + --input_mod1 resources_test/common/scicar_cell_lines/dataset_mod1.h5ad \ + --input_mod2 resources_test/common/scicar_cell_lines/dataset_mod2.h5ad \ + --output_mod1 resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad \ + --output_mod2 resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/main.nf b/src/tasks/match_modalities/workflows/run/main.nf index e6318d7dda..e336b2e16f 100644 --- a/src/tasks/match_modalities/workflows/run/main.nf +++ b/src/tasks/match_modalities/workflows/run/main.nf @@ -22,13 +22,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { runComponents; joinStates; initializeTracer; writeJon; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" // read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // collect method list methods = [ @@ -72,14 +72,14 @@ workflow run_wf { fromState: [ "input": "input_mod1" ], toState: { id, output, state -> // load output yaml file - def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state state + metadata } ) // run all methods - | run_components( + | runComponents( components: methods, // // use the 'filter' argument to only run a method on the normalisation the component is asking for @@ -106,8 +106,8 @@ workflow run_wf { }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output_mod1: output.output_mod1, method_output_mod2: output.output_mod2 @@ -116,7 +116,7 @@ workflow run_wf { ) // run all metrics - | run_components( + | runComponents( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -124,8 +124,8 @@ workflow run_wf { input_mod2: "method_output_mod2" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -135,7 +135,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -156,10 +156,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJsontraces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + writeJsonmethods.collect{it.config}, file("$publish_dir/methods.json")) + writeJsonmetrics.collect{it.config}, file("$publish_dir/metrics.json")) } diff --git a/src/tasks/match_modalities/workflows/run/run_test.sh b/src/tasks/match_modalities/workflows/run/run_test.sh index b4c410f85a..a14859511d 100755 --- a/src/tasks/match_modalities/workflows/run/run_test.sh +++ b/src/tasks/match_modalities/workflows/run/run_test.sh @@ -9,7 +9,7 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -DATASET_DIR=resources_test/common/multimodal +DATASET_DIR=resources_test/common/scicar_cell_lines # choose a particular version of nextflow export NXF_VER=23.04.2 diff --git a/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh b/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh index abe4f82f96..4c2daa5691 100644 --- a/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh +++ b/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh @@ -1,6 +1,6 @@ #!/bin/bash -DATASET_DIR=resources_test/common/multimodal +DATASET_DIR=resources_test/common/scicar_cell_lines # try running on nf tower cat > /tmp/params.yaml << HERE diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index 37da76b8ec..9615286dc5 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -86,8 +86,7 @@ flowchart LR The RNA modality of the raw dataset. -Example file: -`resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad` +Example file: `resources_test/common/bmmc_cite_starter/dataset_rna.h5ad` Description: @@ -444,8 +443,7 @@ Slot description: The second modality of the raw dataset. Must be an ADT or an ATAC dataset -Example file: -`resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad` +Example file: `resources_test/common/bmmc_cite_starter/dataset_adt.h5ad` Description: diff --git a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml index d1b2c8714b..8035d80019 100644 --- a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml +++ b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad" +example: "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad" info: label: "Raw dataset mod2" summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" diff --git a/src/tasks/predict_modality/api/file_dataset_rna.yaml b/src/tasks/predict_modality/api/file_dataset_rna.yaml index c8c68478fd..92d4b5bc5b 100644 --- a/src/tasks/predict_modality/api/file_dataset_rna.yaml +++ b/src/tasks/predict_modality/api/file_dataset_rna.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" +example: "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad" info: label: "Raw dataset RNA" summary: "The RNA modality of the raw dataset." diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 171bc4a9c9..a9ece0b529 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -4,8 +4,8 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( - input_rna = "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad", - input_other_mod = "resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad", + input_rna = "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad", + input_other_mod = "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad.h5ad", output_train_mod1 = "resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad", output_train_mod2 = "resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad", output_test_mod1 = "resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad", diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh index 5753a22fa4..a9ecdd9ab0 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -10,8 +10,6 @@ REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" set -e -# TODO: Download the starter datasets from the source repository -# TODO TODO: Generate the datasets from the source GEO dataset generate_pm_test_resources () { DATASET_ID="$1" @@ -68,28 +66,28 @@ generate_pm_test_resources () { generate_pm_test_resources \ bmmc_cite_starter \ - resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad \ - resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad \ + resources_test/common/bmmc_cite_starter/dataset_rna.h5ad \ + resources_test/common/bmmc_cite_starter/dataset_adt.h5ad \ resources_test/predict_modality/bmmc_cite_starter \ "" generate_pm_test_resources \ bmmc_cite_starter_swapped \ - resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_adt.h5ad \ - resources_test/common/bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad \ + resources_test/common/bmmc_cite_starter/dataset_adt.h5ad \ + resources_test/common/bmmc_cite_starter/dataset_rna.h5ad \ resources_test/predict_modality/bmmc_cite_starter_swapped \ "--swap true" generate_pm_test_resources \ bmmc_multiome_starter \ - resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad \ - resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad \ + resources_test/common/bmmc_multiome_starter/dataset_rna.h5ad \ + resources_test/common/bmmc_multiome_starter/dataset_atac.h5ad \ resources_test/predict_modality/bmmc_multiome_starter \ "" generate_pm_test_resources \ bmmc_multiome_starter_swapped \ - resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad \ - resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad \ + resources_test/common/bmmc_multiome_starter/dataset_atac.h5ad \ + resources_test/common/bmmc_multiome_starter/dataset_rna.h5ad \ resources_test/predict_modality/bmmc_multiome_starter_swapped \ "--swap true" \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run/main.nf index 652a232a20..002e302f84 100644 --- a/src/tasks/predict_modality/workflows/run/main.nf +++ b/src/tasks/predict_modality/workflows/run/main.nf @@ -26,13 +26,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { run_components; join_states; initialize_tracer; write_json; get_publish_dir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" // read in pipeline config config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initialize_tracer() +traces = initializeTracer() // collect method list methods = [ @@ -77,14 +77,14 @@ workflow run_wf { fromState: [ "input": "input_train_mod1" ], toState: { id, output, state -> // load output yaml file - def metadata = new org.yaml.snakeyaml.Yaml().load(output.meta) + def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state state + metadata } ) // run all methods - | run_components( + | runComponents( components: methods, // define a new 'id' by appending the method name to the dataset id @@ -106,8 +106,8 @@ workflow run_wf { }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ method_id: config.functionality.name, method_output: output.output ] @@ -115,7 +115,7 @@ workflow run_wf { ) // run all metrics - | run_components( + | runComponents( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -123,8 +123,8 @@ workflow run_wf { input_prediction: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, config -> - [ + toState: { id, output, state, config -> + state + [ metric_id: config.functionality.name, metric_output: output.output ] @@ -134,7 +134,7 @@ workflow run_wf { // join all events into a new event where the new id is simply "output" and the new state consists of: // - "input": a list of score h5ads // - "output": the output argument of this workflow - | join_states{ ids, states -> + | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, @@ -154,10 +154,10 @@ workflow run_wf { // store the trace log in the publish dir workflow.onComplete { - def publish_dir = get_publish_dir() + def publish_dir = getPublishDir() - write_json(traces, file("$publish_dir/traces.json")) + writeJson(traces, file("$publish_dir/traces.json")) // todo: add datasets logging - write_json(methods.collect{it.config}, file("$publish_dir/methods.json")) - write_json(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) + writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf index d1ac0642ac..d110032abf 100644 --- a/src/wf_utils/BenchmarkHelper.nf +++ b/src/wf_utils/BenchmarkHelper.nf @@ -1,18 +1,18 @@ -def run_components(Map args) { - assert args.components: "run_components should be passed a list of components to run" +def runComponents(Map args) { + assert args.components: "runComponents should be passed a list of components to run" def components_ = args.components if (components_ !instanceof List) { components_ = [ components_ ] } - assert components_.size() > 0: "pass at least one component to run_components" + assert components_.size() > 0: "pass at least one component to runComponents" def fromState_ = args.fromState def toState_ = args.toState def filter_ = args.filter def id_ = args.id - workflow run_components_wf { + workflow runComponentsWf { take: input_ch main: @@ -58,19 +58,20 @@ def run_components(Map args) { ) post_ch = toState_ ? out_ch | map{tup -> - def new_outputs = tup[1] + def output = tup[1] + def old_state = tup[2] if (toState_ instanceof Map) { - new_outputs = toState_.collectEntries{ key0, key1 -> - [key0, new_outputs[key1]] + new_state = old_state + toState_.collectEntries{ key0, key1 -> + [key0, output[key1]] } } else if (toState_ instanceof List) { - new_outputs = toState_.collectEntries{ key -> - [key, new_outputs[key]] + new_state = old_state + toState_.collectEntries{ key -> + [key, output[key]] } } else if (toState_ instanceof Closure) { - new_outputs = toState_(tup[0], new_outputs, comp_config) + new_state = toState_(tup[0], output, old_state, comp_config) } - [tup[0], tup[2] + new_outputs] + tup.drop(3) + [tup[0], new_state] + tup.drop(3) } : out_ch @@ -86,11 +87,11 @@ def run_components(Map args) { emit: output_ch } - return run_components_wf + return runComponentsWf } -def join_states(Closure apply_) { - workflow join_states_wf { +def joinStates(Closure apply_) { + workflow joinStatesWf { take: input_ch main: output_ch = input_ch @@ -104,7 +105,7 @@ def join_states(Closure apply_) { emit: output_ch } - return join_states_wf + return joinStatesWf } @@ -130,7 +131,7 @@ class CustomTraceObserver implements nextflow.trace.TraceObserver { } } -def initialize_tracer() { +def initializeTracer() { def traces = Collections.synchronizedList([]) // add custom trace observer which stores traces in the traces object @@ -139,14 +140,328 @@ def initialize_tracer() { traces } -def write_json(data, file) { - assert data: "write_json: data should not be null" - assert file: "write_json: file should not be null" +def writeJson(data, file) { + assert data: "writeJson: data should not be null" + assert file: "writeJson: file should not be null" file.write(groovy.json.JsonOutput.toJson(data)) } -def get_publish_dir() { +import org.yaml.snakeyaml.DumperOptions +import org.yaml.snakeyaml.Yaml +import org.yaml.snakeyaml.nodes.Node +import org.yaml.snakeyaml.nodes.Tag +import org.yaml.snakeyaml.representer.Representer +import org.yaml.snakeyaml.representer.Represent + + + +// Custom representer to modify how certain objects are represented in YAML +class CustomRepresenter extends Representer { + class RepresentFile implements Represent { + public Node representData(Object data) { + File file = (File) data; + String value = file.name; + Tag tag = new Tag("!file"); + return representScalar(tag, value); + } + } + CustomRepresenter(DumperOptions options) { + super(options) + this.representers.put(File, new RepresentFile()) + } +} + +String toTaggedYamlBlob(Map data) { + def options = new DumperOptions() + options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK) + def representer = new CustomRepresenter(options) + def yaml = new Yaml(representer, options) + return yaml.dump(data) +} + + +import org.yaml.snakeyaml.TypeDescription +import org.yaml.snakeyaml.constructor.AbstractConstruct +import org.yaml.snakeyaml.constructor.Constructor + +// Custom constructor to modify how certain objects are parsed from YAML +class CustomConstructor extends Constructor { + File root + + class ConstructFile extends AbstractConstruct { + public Object construct(Node node) { + String filename = (String) constructScalar(node); + if (root != null) { + return new File(root, filename); + } + return new File(filename); + } + } + + CustomConstructor(File root = null) { + super() + this.root = root + // Handling !file tag and parse it back to a File type + this.yamlConstructors.put(new Tag("!file"), new ConstructFile()) + } +} + +def readTaggedYaml(File file) { + Constructor constructor = new CustomConstructor(file.absoluteFile.parentFile) + Yaml yaml = new Yaml(constructor) + return yaml.load(file.text) +} + +def getPublishDir() { return params.containsKey("publish_dir") ? params.publish_dir : params.containsKey("publishDir") ? params.publishDir : null +} + +process publishStateProc { + // todo: check publishpath? + publishDir path: "${getPublishDir()}/${id}/", mode: "copy" + tag "$id" + input: + tuple val(id), val(yamlBlob), path(inputFiles) + output: + tuple val(id), path{["state.yaml"] + inputFiles} + script: + """ + echo '${yamlBlob}' > state.yaml + """ +} + +def collectFiles(obj) { + if (obj instanceof java.io.File || obj instanceof Path) { + return [obj] + } else if (obj instanceof List && obj !instanceof String) { + return obj.collectMany{item -> + collectFiles(item) + } + } else if (obj instanceof Map) { + return obj.collectMany{key, item -> + collectFiles(item) + } + } else { + return [] + } +} + + +def iterateMap(obj, fun) { + if (obj instanceof List && obj !instanceof String) { + return obj.collect{item -> + iterateMap(item, fun) + } + } else if (obj instanceof Map) { + return obj.collectEntries{key, item -> + [key.toString(), iterateMap(item, fun)] + } + } else { + return fun(obj) + } +} + + +// def convertPathsToFile(obj) { +// if (obj instanceof File) { +// return obj +// } else if (obj instanceof Path) { +// return obj.toFile() +// } else if (obj instanceof List && obj !instanceof String) { +// return obj.collect{item -> +// convertPathsToFile(item) +// } +// } else if (obj instanceof Map) { +// return obj.collectEntries{key, item -> +// [key, convertPathsToFile(item)] +// } +// } else { +// return obj +// } +// } + +// def convertFilesToPath(obj) { +// if (obj instanceof File) { +// return obj.toPath() +// } else if (obj instanceof Path) { +// return obj +// } else if (obj instanceof List && obj !instanceof String) { +// return obj.collect{item -> +// convertFilesToPath(item) +// } +// } else if (obj instanceof Map) { +// return obj.collectEntries{key, item -> +// [key, convertFilesToPath(item)] +// } +// } else { +// return obj +// } +// } + +def convertPathsToFile(obj) { + iterateMap(obj, {x -> + if (x instanceof File) { + return x + } else if (x instanceof Path) { + return x.toFile() + } else { + return x + } + }) +} +def convertFilesToPath(obj) { + iterateMap(obj, {x -> + if (x instanceof Path) { + return x + } else if (x instanceof File) { + return x.toPath() + } else { + return x + } + }) +} + +def publishState(Map args) { + workflow publishStateWf { + take: input_ch + main: + input_ch + | map { tup -> + def id = tup[0] + def state = tup[1] + def files = collectFiles(state) + def convertedState = [id: id] + convertPathsToFile(state) + def yamlBlob = toTaggedYamlBlob(convertedState) + [id, yamlBlob, files] + } + | publishStateProc + emit: input_ch + } + return publishStateWf +} + + +include { processConfig; helpMessage; channelFromParams; readYamlBlob } from "./WorkflowHelper.nf" + + +def autoDetectStates(Map params, Map config) { + // TODO: do a deep clone of config + def auto_config = config.clone() + auto_config.functionality = auto_config.functionality.clone() + // override arguments + auto_config.functionality.argument_groups = [] + auto_config.functionality.arguments = [ + [ + type: "file", + name: "--input_dir", + example: "/path/to/input/directory", + description: "Path to input directory containing the datasets to be integrated.", + required: true + ], + [ + type: "string", + name: "--filter", + example: "foo/.*/state.yaml", + description: "Regex to filter state files by path.", + required: false + ], + // to do: make this a yaml blob? + [ + type: "string", + name: "--rename_keys", + example: ["newKey1:oldKey1", "newKey2:oldKey2"], + description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", + required: false, + multiple: true, + multiple_sep: "," + ], + [ + type: "string", + name: "--settings", + example: '{"output_dataset": "dataset.h5ad", "k": 10}', + description: "Global arguments as a JSON glob to be passed to all components.", + required: false + ] + ] + + // run auto config through processConfig once more + auto_config = processConfig(auto_config) + + workflow autoDetectStatesWf { + helpMessage(auto_config) + + output_ch = + channelFromParams(params, auto_config) + | flatMap { autoId, args -> + + def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] + + // look for state files in input dir + def stateFiles = file("${args.input_dir}/**/state.yaml") + + // filter state files by regex + if (args.filter) { + stateFiles = stateFiles.findAll{ stateFile -> + def stateFileStr = stateFile.toString() + def matcher = stateFileStr =~ args.filter + matcher.matches()} + } + + // read in states + def states = stateFiles.collect { stateFile -> + def state_ = convertFilesToPath(readTaggedYaml(stateFile.toFile())) + [state_.id, state_] + } + + // construct renameMap + if (args.rename_keys) { + def renameMap = args.rename_keys.collectEntries{renameString -> + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename' should be of the form 'newKey:oldKey,newKey:oldKey'" + split + } + + // rename keys in state, only let states through which have all keys + // also add global settings + states = states.collectMany{id, state -> + def newState = [:] + + for (key in renameMap.keySet()) { + def origKey = renameMap[key] + if (!(state.containsKey(origKey))) { + return [] + } + newState[key] = state[origKey] + } + + [[id, globalSettings + newState]] + } + } + + states + } + emit: + output_ch + } + + return autoDetectStatesWf +} + +def setState(fun) { + workflow setStateWf { + take: input_ch + main: + output_ch = input_ch + | map { tup -> + def id = tup[0] + def state = tup[1] + def unfilteredState = fun(id, state) + def newState = unfilteredState.findAll{key, val -> val != null} + [id, newState] + tup.drop(2) + } + emit: output_ch + } + return setStateWf } \ No newline at end of file diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index 69b9941abd..ad711d2665 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -6,10 +6,33 @@ import java.util.regex.Pattern import java.io.BufferedReader import java.io.FileReader import java.nio.file.Paths +import java.nio.file.Files import groovy.json.JsonSlurper import groovy.text.SimpleTemplateEngine import org.yaml.snakeyaml.Yaml +// Recurse upwards until we find a '.build.yaml' file +def findBuildYamlFile(path) { + def child = path.resolve(".build.yaml") + if (Files.isDirectory(path) && Files.exists(child)) { + return child + } else { + def parent = path.getParent() + if (parent == null) { + return null + } else { + return findBuildYamlFile(parent) + } + } +} + +// get the root of the target folder +def getRootDir() { + def dir = findBuildYamlFile(projectDir.toAbsolutePath()) + assert dir != null: "Could not find .build.yaml in the folder structure" + dir.getParent() +} + // param helpers // def paramExists(name) { return params.containsKey(name) && params[name] != "" @@ -31,16 +54,16 @@ def getChild(parent, child) { } } -def readCsv(file) { +def readCsv(file_path) { def output = [] - def inputFile = file !instanceof File ? new File(file) : file + def inputFile = file_path !instanceof Path ? file(file_path) : file_path // todo: allow escaped quotes in string // todo: allow single quotes? def splitRegex = Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') def removeQuote = Pattern.compile('''"(.*)"''') - def br = new BufferedReader(new FileReader(inputFile)) + def br = Files.newBufferedReader(inputFile) def row = -1 def header = null @@ -59,6 +82,11 @@ def readCsv(file) { while (br.ready()) { def line = br.readLine() row++ + if (line == null) { + br.close() + break + } + if (!line.startsWith("#")) { def predata = splitRegex.split(line, -1) def data = predata.collect{field -> @@ -87,8 +115,8 @@ def readJsonBlob(str) { jsonSlurper.parseText(str) } -def readJson(file) { - def inputFile = file !instanceof File ? new File(file) : file +def readJson(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path) : file_path def jsonSlurper = new JsonSlurper() jsonSlurper.parse(inputFile) } @@ -98,8 +126,8 @@ def readYamlBlob(str) { yamlSlurper.load(str) } -def readYaml(file) { - def inputFile = file !instanceof File ? new File(file) : file +def readYaml(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path) : file_path def yamlSlurper = new Yaml() yamlSlurper.load(inputFile) } @@ -119,7 +147,8 @@ def processArgument(arg) { arg.create_parent = arg.create_parent != null ? arg.create_parent : true } - if (arg.type == "file" && arg.direction == "output") { + // add default values to required output files which haven't already got a default + if (arg.type == "file" && arg.direction == "output" && arg.default == null && arg.required) { def mult = arg.multiple ? "_*" : "" def extSearch = "" if (arg.default != null) { @@ -748,7 +777,10 @@ private List> _parseParamListArguments(Map params, Map confi def paramListFile = paramListOut[0] def paramSets = paramListOut[1] // these are the actual parameters from reading the blob/file - // data checks + return checkParamListArguments(paramListFile, paramSets, config) +} + +def checkParamListArguments(paramListFile, paramSets, config) { assert paramSets instanceof List: "--param_list should contain a list of maps" for (value in paramSets) { assert value instanceof Map: "--param_list should contain a list of maps" From 83cfb66704061d4e60c0a29d2d0481d689c8fa0d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 21 Sep 2023 15:23:52 +0200 Subject: [PATCH 0992/1233] rename autoDetectStates to findStates Former-commit-id: b7c6e5a60e9ea4f19fd8121e09be01c46ad9359a --- .../workflows/process_datasets/main.nf | 4 +- .../workflows/run_benchmark/main.nf | 4 +- src/wf_utils/BenchmarkHelper.nf | 43 ++----------------- 3 files changed, 7 insertions(+), 44 deletions(-) diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index f00994f8b5..0f948aad82 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -8,7 +8,7 @@ include { process_dataset } from "$targetDir/batch_integration/process_dataset/m // import helper functions include { readConfig; processConfig; helpMessage; channelFromParams; preprocessInputs; readYaml; readJson } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; autoDetectStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -21,7 +21,7 @@ workflow { } workflow auto { - autoDetectStates(params, config) + findStates(params, config) | run_wf | publishState([:]) } diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index fc1aa9c701..f92174c17c 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -40,7 +40,7 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; autoDetectStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -85,7 +85,7 @@ workflow { } workflow auto { - autoDetectStates(params, config) + findStates(params, config) | run_wf | publishState([:]) } diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf index d110032abf..6934f27988 100644 --- a/src/wf_utils/BenchmarkHelper.nf +++ b/src/wf_utils/BenchmarkHelper.nf @@ -263,43 +263,6 @@ def iterateMap(obj, fun) { } } - -// def convertPathsToFile(obj) { -// if (obj instanceof File) { -// return obj -// } else if (obj instanceof Path) { -// return obj.toFile() -// } else if (obj instanceof List && obj !instanceof String) { -// return obj.collect{item -> -// convertPathsToFile(item) -// } -// } else if (obj instanceof Map) { -// return obj.collectEntries{key, item -> -// [key, convertPathsToFile(item)] -// } -// } else { -// return obj -// } -// } - -// def convertFilesToPath(obj) { -// if (obj instanceof File) { -// return obj.toPath() -// } else if (obj instanceof Path) { -// return obj -// } else if (obj instanceof List && obj !instanceof String) { -// return obj.collect{item -> -// convertFilesToPath(item) -// } -// } else if (obj instanceof Map) { -// return obj.collectEntries{key, item -> -// [key, convertFilesToPath(item)] -// } -// } else { -// return obj -// } -// } - def convertPathsToFile(obj) { iterateMap(obj, {x -> if (x instanceof File) { @@ -346,7 +309,7 @@ def publishState(Map args) { include { processConfig; helpMessage; channelFromParams; readYamlBlob } from "./WorkflowHelper.nf" -def autoDetectStates(Map params, Map config) { +def findStates(Map params, Map config) { // TODO: do a deep clone of config def auto_config = config.clone() auto_config.functionality = auto_config.functionality.clone() @@ -389,7 +352,7 @@ def autoDetectStates(Map params, Map config) { // run auto config through processConfig once more auto_config = processConfig(auto_config) - workflow autoDetectStatesWf { + workflow findStatesWf { helpMessage(auto_config) output_ch = @@ -446,7 +409,7 @@ def autoDetectStates(Map params, Map config) { output_ch } - return autoDetectStatesWf + return findStatesWf } def setState(fun) { From 34f0b7342e62b8caf54c9e69cb5b7a5fbe4262ae Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 21 Sep 2023 15:24:25 +0200 Subject: [PATCH 0993/1233] rename publishState to publishStates Former-commit-id: f165dba4553a20ec000b52da491dad6256f8e8a4 --- src/datasets/workflows/process_openproblems_v1/main.nf | 4 ++-- .../process_openproblems_v1_multimodal/main.nf | 4 ++-- .../workflows/process_datasets/main.nf | 6 +++--- .../batch_integration/workflows/run_benchmark/main.nf | 6 +++--- src/wf_utils/BenchmarkHelper.nf | 10 +++++----- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 57511953b1..8df22566a6 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -21,7 +21,7 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -35,7 +35,7 @@ workflow { channelFromParams(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow run_wf { diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 4c50ae120a..d08bc0398b 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -20,7 +20,7 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -34,7 +34,7 @@ workflow { channelFromParams(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow run_wf { diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index 0f948aad82..23d7ad12cc 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -8,7 +8,7 @@ include { process_dataset } from "$targetDir/batch_integration/process_dataset/m // import helper functions include { readConfig; processConfig; helpMessage; channelFromParams; preprocessInputs; readYaml; readJson } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -17,13 +17,13 @@ workflow { channelFromParams(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow auto { findStates(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow run_wf { diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index f92174c17c..be05a552de 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -40,7 +40,7 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishState; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") @@ -81,13 +81,13 @@ workflow { channelFromParams(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow auto { findStates(params, config) | run_wf - | publishState([:]) + | publishStates([:]) } workflow run_wf { diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf index 6934f27988..e9816b197f 100644 --- a/src/wf_utils/BenchmarkHelper.nf +++ b/src/wf_utils/BenchmarkHelper.nf @@ -218,7 +218,7 @@ def getPublishDir() { null } -process publishStateProc { +process publishStatesProc { // todo: check publishpath? publishDir path: "${getPublishDir()}/${id}/", mode: "copy" tag "$id" @@ -286,8 +286,8 @@ def convertFilesToPath(obj) { }) } -def publishState(Map args) { - workflow publishStateWf { +def publishStates(Map args) { + workflow publishStatesWf { take: input_ch main: input_ch @@ -299,10 +299,10 @@ def publishState(Map args) { def yamlBlob = toTaggedYamlBlob(convertedState) [id, yamlBlob, files] } - | publishStateProc + | publishStatesProc emit: input_ch } - return publishStateWf + return publishStatesWf } From 329afc3e18ba96a58f084774a02c00e91df7a07d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 21 Sep 2023 15:25:13 +0200 Subject: [PATCH 0994/1233] remove unused helper Former-commit-id: 49dfa257fba73b5c25a4c5178258e9d5da5a2819 --- src/wf_utils/DataflowHelper.nf | 197 --------------------------------- 1 file changed, 197 deletions(-) delete mode 100644 src/wf_utils/DataflowHelper.nf diff --git a/src/wf_utils/DataflowHelper.nf b/src/wf_utils/DataflowHelper.nf deleted file mode 100644 index 213af64c7c..0000000000 --- a/src/wf_utils/DataflowHelper.nf +++ /dev/null @@ -1,197 +0,0 @@ -/* usage: -| setWorkflowArguments( - pca: [ "input": "input", "obsm_output": "obsm_pca" ] - harmonypy: [ "obs_covariates": "obs_covariates", "obsm_input": "obsm_pca" ], - find_neighbors: [ "obsm_input": "obsm_pca" ], - umap: [ "output": "output" ] -) -*/ - -def setWorkflowArguments(Map args) { - wfKey = args.key != null ? args.key : "setWorkflowArguments" - args.keySet().removeAll(["key"]) - - - /* - data = [a:1, b:2, c:3] - // args = [foo: ["a", "b"], bar: ["b"]] - args = [foo: [a: 'a', out: "b"], bar: [in: "b"]] - */ - - workflow setWorkflowArgumentsInstance { - take: - input_ - - main: - output_ = input_ - | map{ tup -> - assert tup.size() : "Event should have length 2 or greater. Expected format: [id, data]." - def id = tup[0] - def data = tup[1] - def passthrough = tup.drop(2) - - // determine new data - def toRemove = args.collectMany{ _, dataKeys -> - // dataKeys is a map but could also be a list - dataKeys instanceof List ? dataKeys : dataKeys.values() - }.unique() - def newData = data.findAll{!toRemove.contains(it.key)} - - // determine splitargs - def splitArgs = args. - collectEntries{procKey, dataKeys -> - // dataKeys is a map but could also be a list - newSplitData = dataKeys - .collectEntries{ val -> - newKey = val instanceof String ? val : val.key - origKey = val instanceof String ? val : val.value - [ newKey, data[origKey] ] - } - .findAll{it.value} - [procKey, newSplitData] - } - - // return output - [ id, newData, splitArgs] + passthrough - } - - emit: - output_ - } - - return setWorkflowArgumentsInstance.cloneWithName(wfKey) -} - -/* usage: -| getWorkflowArguments("harmonypy") -*/ - - -def getWorkflowArguments(Map args) { - def inputKey = args.inputKey != null ? args.inputKey : "input" - def wfKey = "getWorkflowArguments_" + args.key - - workflow getWorkflowArgumentsInstance { - take: - input_ - - main: - output_ = input_ - | map{ tup -> - assert tup.size() : "Event should have length 3 or greater. Expected format: [id, data, splitArgs]." - - def id = tup[0] - def data = tup[1] - def splitArgs = tup[2].clone() - - def passthrough = tup.drop(3) - - // try to infer arg name - if (data !instanceof Map) { - data = [[ inputKey, data ]].collectEntries() - } - assert splitArgs instanceof Map: "Third element of event (id: $id) should be a map" - assert splitArgs.containsKey(args.key): "Third element of event (id: $id) should have a key ${args.key}" - - def newData = data + splitArgs.remove(args.key) - - [ id, newData, splitArgs] + passthrough - } - - emit: - output_ - } - - return getWorkflowArgumentsInstance.cloneWithName(wfKey) - -} - - -def strictMap(Closure clos) { - def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount - - workflow strictMapWf { - take: - input_ - - main: - output_ = input_ - | map{ tup -> - if (tup.size() != numArgs) { - throw new RuntimeException("Closure does not have the same number of arguments as channel tuple.\nNumber of closure arguments: $numArgs\nChannel tuple: $tup") - } - clos(tup) - } - - emit: - output_ - } - - return strictMapWf -} - -def passthroughMap(Closure clos) { - def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount - - workflow passthroughMapWf { - take: - input_ - - main: - output_ = input_ - | map{ tup -> - def out = clos(tup.take(numArgs)) - out + tup.drop(numArgs) - } - - emit: - output_ - } - - return passthroughMapWf -} - -def passthroughFlatMap(Closure clos) { - def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount - - workflow passthroughFlatMapWf { - take: - input_ - - main: - output_ = input_ - | flatMap{ tup -> - def out = clos(tup.take(numArgs)) - def pt = tup.drop(numArgs) - for (o in out) { - o.addAll(pt) - } - out - } - - emit: - output_ - } - - return passthroughFlatMapWf -} - -def passthroughFilter(Closure clos) { - def numArgs = clos.class.methods.find{it.name == "call"}.parameterCount - - workflow passthroughFilterWf { - take: - input_ - - main: - output_ = input_ - | filter{ tup -> - clos(tup.take(numArgs)) - } - - emit: - output_ - } - - return passthroughFilterWf -} \ No newline at end of file From e98818ab1290c4df50adc9b4115839f43f695408 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 23 Sep 2023 06:26:21 +0200 Subject: [PATCH 0995/1233] fix test resources Former-commit-id: 0c96e0cb3ff3aa9648a029e7c91add93ecfc80ad --- src/tasks/batch_integration/api/file_dataset.yaml | 2 +- src/tasks/match_modalities/api/comp_metric.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/tasks/batch_integration/api/file_dataset.yaml b/src/tasks/batch_integration/api/file_dataset.yaml index bd40fc7561..2ea6d0a94a 100644 --- a/src/tasks/batch_integration/api/file_dataset.yaml +++ b/src/tasks/batch_integration/api/file_dataset.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/batch_integration/pancreas/unintegrated.h5ad" +example: "resources_test/batch_integration/pancreas/dataset.h5ad" info: label: "Dataset" summary: Unintegrated AnnData HDF5 file. diff --git a/src/tasks/match_modalities/api/comp_metric.yaml b/src/tasks/match_modalities/api/comp_metric.yaml index 2f1d7cafe8..857f62bb07 100644 --- a/src/tasks/match_modalities/api/comp_metric.yaml +++ b/src/tasks/match_modalities/api/comp_metric.yaml @@ -21,8 +21,8 @@ functionality: required: true direction: output test_resources: - - path: /resources_test/multimodal - dest: resources_test/multimodal + - path: /resources_test/common/scicar_cell_lines + dest: resources_test/common/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script From 9538a609e70bbeaf2735324657c2f7de3713ae04 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 27 Sep 2023 14:21:18 +0200 Subject: [PATCH 0996/1233] use path instead of file Former-commit-id: ac645395f81bd9217bc5b6f3bbff9180ae15ee57 --- src/wf_utils/BenchmarkHelper.nf | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf index e9816b197f..57aefdbdd2 100644 --- a/src/wf_utils/BenchmarkHelper.nf +++ b/src/wf_utils/BenchmarkHelper.nf @@ -159,8 +159,8 @@ import org.yaml.snakeyaml.representer.Represent class CustomRepresenter extends Representer { class RepresentFile implements Represent { public Node representData(Object data) { - File file = (File) data; - String value = file.name; + Path file = (Path) data; + String value = file.getFileName(); Tag tag = new Tag("!file"); return representScalar(tag, value); } @@ -186,19 +186,19 @@ import org.yaml.snakeyaml.constructor.Constructor // Custom constructor to modify how certain objects are parsed from YAML class CustomConstructor extends Constructor { - File root + Path root class ConstructFile extends AbstractConstruct { public Object construct(Node node) { String filename = (String) constructScalar(node); if (root != null) { - return new File(root, filename); + return root.resolve(filename); } - return new File(filename); + return java.nio.file.Paths.get(filename); } } - CustomConstructor(File root = null) { + CustomConstructor(Path root = null) { super() this.root = root // Handling !file tag and parse it back to a File type @@ -206,10 +206,10 @@ class CustomConstructor extends Constructor { } } -def readTaggedYaml(File file) { - Constructor constructor = new CustomConstructor(file.absoluteFile.parentFile) +def readTaggedYaml(Path path) { + Constructor constructor = new CustomConstructor(path.getParent()) Yaml yaml = new Yaml(constructor) - return yaml.load(file.text) + return yaml.load(path.text) } def getPublishDir() { @@ -295,14 +295,13 @@ def publishStates(Map args) { def id = tup[0] def state = tup[1] def files = collectFiles(state) - def convertedState = [id: id] + convertPathsToFile(state) - def yamlBlob = toTaggedYamlBlob(convertedState) + def yamlBlob = toTaggedYamlBlob([id: id] + state) [id, yamlBlob, files] } | publishStatesProc emit: input_ch } - return publishStatesWf + return publishStateWf } @@ -317,7 +316,7 @@ def findStates(Map params, Map config) { auto_config.functionality.argument_groups = [] auto_config.functionality.arguments = [ [ - type: "file", + type: "string", name: "--input_dir", example: "/path/to/input/directory", description: "Path to input directory containing the datasets to be integrated.", @@ -374,7 +373,7 @@ def findStates(Map params, Map config) { // read in states def states = stateFiles.collect { stateFile -> - def state_ = convertFilesToPath(readTaggedYaml(stateFile.toFile())) + def state_ = readTaggedYaml(stateFile) [state_.id, state_] } From 6af27cd2235b8e4ddaef94620eb669b5e2a2847e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 27 Sep 2023 15:58:53 +0200 Subject: [PATCH 0997/1233] update wfhelper (#233) Former-commit-id: d69435f854518c08dd34cd590f614fbaa254e5b7 --- .../workflows/process_openproblems_v1/main.nf | 4 +- .../main.nf | 2 +- .../resources_scripts/process_datasets.sh | 2 +- .../resources_scripts/run_benchmark.sh | 2 +- .../resources_test_scripts/pancreas.sh | 2 +- .../workflows/process_datasets/main.nf | 2 +- .../process_datasets/run_nextflow.sh | 2 +- .../workflows/run_benchmark/main.nf | 5 +- .../workflows/run_benchmark/run_nextflow.sh | 2 +- src/wf_utils/WorkflowHelper.nf | 3796 +++++++++++++---- 10 files changed, 2897 insertions(+), 922 deletions(-) diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 8df22566a6..1310dae61f 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -21,12 +21,12 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() +traces = collectTraces() normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index d08bc0398b..b1e0ddf0ab 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -20,7 +20,7 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index 1655086787..da935f8cca 100755 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -22,7 +22,7 @@ nextflow run . \ -entry auto \ -resume \ --id resources \ - --input_dir resources/datasets/openproblems_v1 \ + --input_states "resources/datasets/openproblems_v1/**/state.yaml" \ --rename_keys 'input:output_dataset' \ --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 7d24cbdc83..61f9a8d65b 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -24,7 +24,7 @@ nextflow run . \ -resume \ -entry auto \ --id resources \ - --input_dir "$DATASETS_DIR" \ + --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ --settings '{"output": "scores.tsv"}' \ --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index 1a4dd94144..5c9cdd93c8 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -18,7 +18,7 @@ nextflow run . \ -profile docker \ -entry auto \ --id resources_test \ - --input_dir "$RAW_DATA" \ + --input_states "$RAW_DATA/**/state.yaml" \ --rename_keys 'input:output_dataset' \ --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ --publish_dir "$DATASET_DIR" diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index 23d7ad12cc..276f3c1f76 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -8,7 +8,7 @@ include { process_dataset } from "$targetDir/batch_integration/process_dataset/m // import helper functions include { readConfig; processConfig; helpMessage; channelFromParams; preprocessInputs; readYaml; readJson } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState; findStates } from sourceDir + "/wf_utils/WorkflowHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") diff --git a/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh index 716bbbb552..211d631c34 100755 --- a/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh @@ -19,7 +19,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --id resources_test \ - --input_dir resources_test/common \ + --input_states "resources_test/common/**/state.yaml" \ --rename_keys 'input:output_dataset' \ --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ --publish_dir "output/test" \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index be05a552de..98e7b11c46 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -40,12 +40,13 @@ include { extract_scores } from "$targetDir/common/extract_scores/main.nf" // import helper functions include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; joinStates; initializeTracer; writeJson; getPublishDir; findStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" +include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" +include { joinStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" config = readConfig("$projectDir/config.vsh.yaml") // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() +traces = collectTraces() // collect method list methods = [ diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh index a0cf9f55dd..8428b15d90 100755 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh @@ -23,5 +23,5 @@ nextflow run . \ -c src/wf_utils/labels_ci.config \ -resume \ --id foo \ - --input_dir $DATASET_DIR \ + --input_states "$DATASET_DIR/**/state.yaml" \ --publish_dir "output" \ No newline at end of file diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index ad711d2665..3d4d3d39e1 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -1,141 +1,36 @@ -///////////////////////////////////// -// Viash Workflow helper functions // -///////////////////////////////////// - -import java.util.regex.Pattern -import java.io.BufferedReader -import java.io.FileReader -import java.nio.file.Paths -import java.nio.file.Files -import groovy.json.JsonSlurper -import groovy.text.SimpleTemplateEngine -import org.yaml.snakeyaml.Yaml +//////////////////////////// +// VDSL3 helper functions // +//////////////////////////// -// Recurse upwards until we find a '.build.yaml' file -def findBuildYamlFile(path) { - def child = path.resolve(".build.yaml") - if (Files.isDirectory(path) && Files.exists(child)) { - return child - } else { - def parent = path.getParent() - if (parent == null) { - return null - } else { - return findBuildYamlFile(parent) - } - } -} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgumentGroup.nf' +def _processArgumentGroup(argumentGroups, name, arguments) { + def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() -// get the root of the target folder -def getRootDir() { - def dir = findBuildYamlFile(projectDir.toAbsolutePath()) - assert dir != null: "Could not find .build.yaml in the folder structure" - dir.getParent() -} + // Check if 'arguments' is in 'argumentGroups'. + def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} -// param helpers // -def paramExists(name) { - return params.containsKey(name) && params[name] != "" -} + // Check whether an argument group of 'name' exists. + def existing = argumentGroups.find{gr -> name == gr.name} -def assertParamExists(name, description) { - if (!paramExists(name)) { - exit 1, "ERROR: Please provide a --${name} parameter ${description}" - } -} + // if there are no arguments missing from the argument group, just return the existing group (if any) + if (argumentsNotInGroup.isEmpty()) { + return existing == null ? [] : [existing] + + // if there are missing arguments and there is an existing group, add the missing arguments to it + } else if (existing != null) { + def newEx = existing.clone() + newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) + return [newEx] -// helper functions for reading params from file // -def getChild(parent, child) { - if (child.contains("://") || Paths.get(child).isAbsolute()) { - child + // else create a new group } else { - def parentAbsolute = Paths.get(parent).toAbsolutePath().toString() - parentAbsolute.replaceAll('/[^/]*$', "/") + child - } -} - -def readCsv(file_path) { - def output = [] - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - - // todo: allow escaped quotes in string - // todo: allow single quotes? - def splitRegex = Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') - def removeQuote = Pattern.compile('''"(.*)"''') - - def br = Files.newBufferedReader(inputFile) - - def row = -1 - def header = null - while (br.ready() && header == null) { - def line = br.readLine() - row++ - if (!line.startsWith("#")) { - header = splitRegex.split(line, -1).collect{field -> - m = removeQuote.matcher(field) - m.find() ? m.replaceFirst('$1') : field - } - } - } - assert header != null: "CSV file should contain a header" - - while (br.ready()) { - def line = br.readLine() - row++ - if (line == null) { - br.close() - break - } - - if (!line.startsWith("#")) { - def predata = splitRegex.split(line, -1) - def data = predata.collect{field -> - if (field == "") { - return null - } - m = removeQuote.matcher(field) - if (m.find()) { - return m.replaceFirst('$1') - } else { - return field - } - } - assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" - - def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} - output.add(dataMap) - } + def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] + return [newEx] } - - output -} - -def readJsonBlob(str) { - def jsonSlurper = new JsonSlurper() - jsonSlurper.parseText(str) } -def readJson(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - def jsonSlurper = new JsonSlurper() - jsonSlurper.parse(inputFile) -} - -def readYamlBlob(str) { - def yamlSlurper = new Yaml() - yamlSlurper.load(str) -} - -def readYaml(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - def yamlSlurper = new Yaml() - yamlSlurper.load(inputFile) -} - -// helper functions for reading a viash config in groovy // - -// based on how Functionality.scala is implemented -def processArgument(arg) { +// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgument.nf' +def _processArgument(arg) { arg.multiple = arg.multiple != null ? arg.multiple : false arg.required = arg.required != null ? arg.required : false arg.direction = arg.direction != null ? arg.direction : "input" @@ -147,8 +42,8 @@ def processArgument(arg) { arg.create_parent = arg.create_parent != null ? arg.create_parent : true } - // add default values to required output files which haven't already got a default - if (arg.type == "file" && arg.direction == "output" && arg.default == null && arg.required) { + // add default values to output files which haven't already got a default + if (arg.type == "file" && arg.direction == "output" && arg.default == null) { def mult = arg.multiple ? "_*" : "" def extSearch = "" if (arg.default != null) { @@ -162,6 +57,9 @@ def processArgument(arg) { def extSearchResult = extSearch.find("\\.[^\\.]+\$") def ext = extSearchResult != null ? extSearchResult : "" arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" + if (arg.multiple) { + arg.default = [arg.default] + } } if (!arg.multiple) { @@ -183,912 +81,2988 @@ def processArgument(arg) { arg } -// based on how Functionality.scala is implemented -def processArgumentGroup(argumentGroups, name, arguments) { - def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() - - // Check if 'arguments' is in 'argumentGroups'. - def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} - - // Check whether an argument group of 'name' exists. - def existing = argumentGroups.find{gr -> name == gr.name} - - // if there are no arguments missing from the argument group, just return the existing group (if any) - if (argumentsNotInGroup.isEmpty()) { - return existing == null ? [] : [existing] +// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/processInputsOutputs.nf' +def typeCheck(String stage, Map par, Object value, String id, String key) { + // expectedClass will only be != null if value is not of the expected type + def expectedClass = null - // if there are missing arguments and there is an existing group, add the missing arguments to it - } else if (existing != null) { - def newEx = existing.clone() - newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) - return [newEx] - - // else create a new group - } else { - def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] - return [newEx] - } -} - -// based on how Functionality.scala is implemented -def processConfig(config) { - // TODO: assert .functionality etc. - if (config.functionality.inputs) { - System.err.println("Warning: .functionality.inputs is deprecated. Please use .functionality.arguments instead.") - } - if (config.functionality.outputs) { - System.err.println("Warning: .functionality.outputs is deprecated. Please use .functionality.arguments instead.") - } - - // set defaults for inputs - config.functionality.inputs = - (config.functionality.inputs != null ? config.functionality.inputs : []).collect{arg -> - arg.type = arg.type != null ? arg.type : "file" - arg.direction = "input" - processArgument(arg) + if (!par.required && value == null) { + expectedClass = null + } else if (par.multiple) { + if (value instanceof List) { + try { + value = value.collect { listVal -> + typeCheck(stage, par + [multiple: false], listVal, id, key) + } + } catch (Exception e) { + expectedClass = "List[${par.type}]" + } + } else { + expectedClass = "List[${par.type}]" } - // set defaults for outputs - config.functionality.outputs = - (config.functionality.outputs != null ? config.functionality.outputs : []).collect{arg -> - arg.type = arg.type != null ? arg.type : "file" - arg.direction = "output" - processArgument(arg) + } else if (par.type == "string") { + if (value instanceof GString) { + value = value.toString() } - // set defaults for arguments - config.functionality.arguments = - (config.functionality.arguments != null ? config.functionality.arguments : []).collect{arg -> - processArgument(arg) + expectedClass = value instanceof String ? null : "String" + } else if (par.type == "integer") { + expectedClass = value instanceof Integer ? null : "Integer" + } else if (par.type == "long") { + if (value instanceof Integer) { + value = value.toLong() } - // set defaults for argument_group arguments - config.functionality.argument_groups = - (config.functionality.argument_groups != null ? config.functionality.argument_groups : []).collect{grp -> - grp.arguments = (grp.arguments != null ? grp.arguments : []).collect{arg -> - arg instanceof String ? arg.replaceAll("^-*", "") : processArgument(arg) + expectedClass = value instanceof Long ? null : "Long" + } else if (par.type == "boolean") { + expectedClass = value instanceof Boolean ? null : "Boolean" + } else if (par.type == "file") { + if (stage == "output" || par.direction == "input") { + if (value instanceof File) { + value = value.toPath() } - grp + expectedClass = value instanceof Path ? null : "Path" + } else { // stage == "input" && par.direction == "output" + if (value instanceof GString) { + value = value.toString() + } + expectedClass = value instanceof String ? null : "String" } + } else { + expectedClass = par.type + } - // create combined arguments list - config.functionality.allArguments = - config.functionality.inputs + - config.functionality.outputs + - config.functionality.arguments + - config.functionality.argument_groups.collectMany{ group -> - group.arguments.findAll{ it !instanceof String } - } + if (expectedClass != null) { + error "Error in module '${key}' id '${id}': ${stage} argument '${par.plainName}' has the wrong type. " + + "Expected type: ${expectedClass}. Found type: ${value.getClass()}" + } - // add missing argument groups (based on Functionality::allArgumentGroups()) - def argGroups = config.functionality.argument_groups - def inputGroup = processArgumentGroup(argGroups, "Inputs", config.functionality.inputs) - def outputGroup = processArgumentGroup(argGroups, "Outputs", config.functionality.outputs) - def defaultGroup = processArgumentGroup(argGroups, "Arguments", config.functionality.arguments) - def groupsFiltered = argGroups.findAll(gr -> !(["Inputs", "Outputs", "Arguments"].contains(gr.name))) - config.functionality.allArgumentGroups = inputGroup + outputGroup + defaultGroup + groupsFiltered - - config + return value } -def readConfig(file) { - def config = readYaml(file != null ? file : "$projectDir/config.vsh.yaml") - processConfig(config) -} - -// recursively merge two maps -def mergeMap(Map lhs, Map rhs) { - return rhs.inject(lhs.clone()) { map, entry -> - if (map[entry.key] instanceof Map && entry.value instanceof Map) { - map[entry.key] = mergeMap(map[entry.key], entry.value) - } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { - map[entry.key] += entry.value - } else { - map[entry.key] = entry.value +Map processInputs(Map inputs, Map config, String id, String key) { + if (!workflow.stubRun) { + config.functionality.allArguments.each { arg -> + if (arg.required) { + assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : + "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing" + } } - return map - } -} - -def addGlobalParams(config) { - def localConfig = [ - "functionality" : [ - "argument_groups": [ - [ - "name": "Nextflow input-output arguments", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "arguments" : [ - [ - 'name': '--publish_dir', - 'required': true, - 'type': 'string', - 'description': 'Path to an output directory.', - 'example': 'output/', - 'multiple': false - ], - [ - 'name': '--param_list', - 'required': false, - 'type': 'string', - 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. - | - |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. - |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. - |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. - |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. - | - |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), - 'example': 'my_params.yaml', - 'multiple': false, - 'hidden': true - ], - ] - ] - ] - ] - ] - return processConfig(mergeMap(config, localConfig)) -} + inputs = inputs.collectEntries { name, value -> + def par = config.functionality.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } + assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument" -// helper functions for generating help // + value = typeCheck("input", par, value, id, key) -// based on io.viash.helpers.Format.wordWrap -def formatWordWrap(str, maxLength) { - def words = str.split("\\s").toList() + [ name, value ] + } + } + return inputs +} - def word = null - def line = "" - def lines = [] - while(!words.isEmpty()) { - word = words.pop() - if (line.length() + word.length() + 1 <= maxLength) { - line = line + " " + word - } else { - lines.add(line) - line = word +Map processOutputs(Map outputs, Map config, String id, String key) { + if (!workflow.stubRun) { + config.functionality.allArguments.each { arg -> + if (arg.direction == "output" && arg.required) { + assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : + "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing" + } } - if (words.isEmpty()) { - lines.add(line) + + outputs = outputs.collectEntries { name, value -> + def par = config.functionality.allArguments.find { it.plainName == name && it.direction == "output" } + assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument" + + value = typeCheck("output", par, value, id, key) + + [ name, value ] } } - return lines + return outputs } -// based on Format.paragraphWrap -def paragraphWrap(str, maxLength) { - def outLines = [] - str.split("\n").each{par -> - def words = par.split("\\s").toList() +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/applyConfig.nf' - def word = null - def line = words.pop() - while(!words.isEmpty()) { - word = words.pop() - if (line.length() + word.length() + 1 <= maxLength) { - line = line + " " + word - } else { +/** + * Apply the argument settings specified in a Viash config to a list of parameter sets. + * - Split the parameter values according to their seperator if + * the parameter accepts multiple values + * - Cast the parameters to their corect types. + * - Assertions: + * ~ Check if any unknown parameters are found + * ~ Check if the ID of the parameter set is unique across all sets. + * + * @return The input parameters that have been processed. + */ + +List applyConfig(List parameterSets, Map config){ + def processedparameterSets = parameterSets.collect({ parameterSet -> + def id = parameterSet[0] + def paramValues = parameterSet[1] + def passthrough = parameterSet.drop(2) + def processedSet = applyConfigToOneParameterSet(paramValues, config) + [id, processedSet] + passthrough + }) + + _checkUniqueIds(processedparameterSets) + return processedparameterSets +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/applyConfigToOneParameterSet.nf' +/** + * Cast parameters to the correct type as defined in the Viash config + * + * @param parValues A Map of input arguments. + * + * @return The input arguments that have been cast to the type from the viash config. + */ +private Map _castParamTypes(Map parValues, Map config) { + // Cast the input to the correct type according to viash config + def castParValues = parValues.collectEntries({ parName, parValue -> + def paramSettings = config.functionality.allArguments.find({it.plainName == parName}) + // dont parse parameters like publish_dir ( in which case paramSettings = null) + def parType = paramSettings ? paramSettings.get("type", null) : null + + // turn parValue into a list, if it isn't one already + if (parValue !instanceof Collection) { + parValue = [parValue] + } + + if (parType == "file" && paramSettings.get("direction", "input") == "input") { + parValue = parValue.collectMany{ parValueItem -> + if (parValueItem instanceof String) { + parValueItem = file(parValueItem) + } + if (parValueItem !instanceof Collection) { + parValueItem = [parValueItem] + } + parValueItem + } + // cast Paths to File? Or vice versa? + // parValue = parValue.collect{ + // if (path instanceof Path) { + // [path.toFile()] + // } else { + // [path] + // } + // } + } else if (parType == "integer") { + parValue = parValue.collect{it as Integer} + } else if (parType == "double") { + parValue = parValue.collect{it as Double} + } else if (parType == "boolean" || + parType == "boolean_true" || + parType == "boolean_false") { + parValue = parValue.collect{it as Boolean} + } + + // simplify list to value if need be + if (paramSettings && !paramSettings.multiple) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + + [parName, parValue] + }) + return castParValues +} + +/** + * Apply the argument settings specified in a Viash config to a single parameter set. + * - Split the parameter values according to their seperator if + * the parameter accepts multiple values + * - Cast the parameters to their corect types. + * - Assertions: + * ~ Check if any unknown parameters are found + * + * @param paramValues A Map of parameter to be processed. All parameters must + * also be specified in the Viash config. + * @param config: A Map of the Viash configuration. This Map can be generated from + * the config file using the readConfig() function. + * @return The input parameters that have been processed. + */ +Map applyConfigToOneParameterSet(Map paramValues, Map config){ + def splitParamValues = _splitParams(paramValues, config) + def castParamValues = _castParamTypes(splitParamValues, config) + + // Check if any unexpected arguments were passed + def knownParams = config.functionality.allArguments.collect({it.plainName}) + ["publishDir", "publish_dir"] + castParamValues.each({parName, parValue -> + assert parName in knownParams: "Unknown parameter. Parameter $parName should be in $knownParams" + }) + return castParamValues +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf' +/** + * Resolve the file paths in the parameters relative to given path + * + * @param paramList A Map containing parameters to process. + * This function assumes that files are still of type String. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * @param relativeTo path of a file to resolve the parameters values to. + * + * @return A map of parameters where the location of the input file parameters have been resolved + * resolved relatively to the provided path. + */ +private Map _resolvePathsRelativeTo(Map paramList, Map config, String relativeTo) { + paramList.collectEntries { parName, parValue -> + argSettings = config.functionality.allArguments.find{it.plainName == parName} + if (argSettings && argSettings.type == "file" && argSettings.direction == "input") { + if (parValue instanceof Collection) { + parValue = parValue.collect({path -> + path !instanceof String ? path : file(_getChild(relativeTo, path)) + }) + } else { + parValue = parValue !instanceof String ? path : file(_getChild(relativeTo, parValue)) + } + } + [parName, parValue] + } +} + +/** + * Parse nextflow parameters based on settings defined in a viash config + * and return a nextflow channel. + * + * @param params Input parameters from nextflow. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A list of parameter sets that were parsed from the 'param_list' argument value. + */ +private List> _parseParamListArguments(Map params, Map config){ + // first try to guess the format (if not set in params) + def paramListFormat = _guessParamListFormat(params) + + // get the correct parser function for the detected params_list format + def paramListParsers = [ + "csv": {[it, readCsv(it)]}, + "json": {[it, readJson(it)]}, + "yaml": {[it, readYaml(it)]}, + "yaml_blob": {[null, readYamlBlob(it)]}, + "asis": {[null, it]}, + "none": {[null, [[:]]]} + ] + assert paramListParsers.containsKey(paramListFormat): + "Format of provided --param_list not recognised.\n" + + "You can use '--param_list_format' to manually specify the format.\n" + + "Found: '$paramListFormat'. Expected: one of 'csv', 'json', "+ + "'yaml', 'yaml_blob', 'asis' or 'none'" + def paramListParser = paramListParsers.get(paramListFormat) + + // fetch multi param inputs + def paramListOut = paramListParser(params.containsKey("param_list") ? params.param_list : "") + // multiFile is null if the value passed to param_list was not a file (e.g a blob) + // If the value was indeed a file, multiFile contains the location that file (used later). + def paramListFile = paramListOut[0] + def paramSets = paramListOut[1] // these are the actual parameters from reading the blob/file + + // data checks + assert paramSets instanceof List: "--param_list should contain a list of maps" + for (value in paramSets) { + assert value instanceof Map: "--param_list should contain a list of maps" + } + + // id is argument + def idIsArgument = config.functionality.allArguments.find({it.plainName == "id"}) != null + + // Reformat from List to List> by adding the ID as first element of a Tuple2 + paramSets = paramSets.collect({ paramValues -> + def paramId = paramValues.id + if (!idIsArgument) { + paramValues = paramValues.findAll{k, v -> k != "id"} + } + [paramId, paramValues] + }) + + // Split parameters with 'multiple: true' + paramSets = paramSets.collect({ id, paramValues -> + def splitParamValues = _splitParams(paramValues, config) + [id, splitParamValues] + }) + + // The paths of input files inside a param_list file may have been specified relatively to the + // location of the param_list file. These paths must be made absolute. + if (paramListFile){ + paramSets = paramSets.collect({ id, paramValues -> + def relativeParamValues = _resolvePathsRelativeTo(paramValues, config, paramListFile) + [id, relativeParamValues] + }) + } + + return paramSets +} + +/** + * Parse nextflow parameters based on settings defined in a viash config. + * Return a list of parameter sets, each parameter set corresponding to + * an event in a nextflow channel. The output from this function can be used + * with Channel.fromList to create a nextflow channel with Vdsl3 formatted + * events. + * + * This function performs: + * - A filtering of the params which can be found in the config file. + * - Process the params_list argument which allows a user to to initialise + * a Vsdl3 channel with multiple parameter sets. Possible formats are + * csv, json, yaml, or simply a yaml_blob. A csv should have column names + * which correspond to the different arguments of this pipeline. A json or a yaml + * file should be a list of maps, each of which has keys corresponding to the + * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. + * When passing a csv, json or yaml, relative path names are relativized to the + * location of the parameter file. + * - Combine the parameter sets into a vdsl3 Channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A list of parameters with the first element of the event being + * the event ID and the second element containing a map of the parsed parameters. + */ + +private List>> _paramsToParamSets(Map params, Map config){ + /* parse regular parameters (not in param_list) */ + /*************************************************/ + def globalParams = config.functionality.allArguments + .findAll { params.containsKey(it.plainName) } + .collectEntries { [ it.plainName, params[it.plainName] ] } + def globalID = params.get("id", null) + def globalParamsValues = applyConfigToOneParameterSet(globalParams, config) + + /* process params_list arguments */ + /*********************************/ + def paramSets = _parseParamListArguments(params, config) + def parameterSetsWithConfigApplied = applyConfig(paramSets, config) + + /* combine arguments into channel */ + /**********************************/ + def processedParams = parameterSetsWithConfigApplied.indexed().collect{ index, paramSet -> + def id = paramSet[0] + def parValues = paramSet[1] + id = [id, globalID].find({it != null}) // first non-null element + + if (workflow.stubRun) { + // if stub run, explicitly add an id if missing + id = id ? id : "stub" + index + } + assert id != null: "Each parameter set should have at least an 'id'" + // Add regular parameters together with parameters passed with 'param_list' + def combinedArgsValues = globalParamsValues + parValues + + // Remove parameters which are null, if the default is also null + combinedArgsValues = combinedArgsValues.collectEntries{paramName, paramValue -> + parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) + if ( paramValue != null || parameterSettings.get("default", null) != null ) { + [paramName, paramValue] + } + } + [id, combinedArgsValues] + } + + // Check if ids (first element of each list) is unique + _checkUniqueIds(processedParams) + return processedParams +} + +/** + * Parse nextflow parameters based on settings defined in a viash config + * and return a nextflow channel. + * + * @param params Input parameters. Can optionaly contain a 'param_list' key that + * provides a list of arguments that can be split up into multiple events + * in the output channel possible formats of param_lists are: a csv file, + * json file, a yaml file or a yaml blob. Each parameters set (event) must + * have a unique ID. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A nextflow Channel with events. Events are formatted as a tuple that contains + * first contains the ID of the event and as second element holds a parameter map. + * + * + */ +def channelFromParams(Map params, Map config) { + processedParams = _paramsToParamSets(params, config) + return Channel.fromList(processedParams) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_checkUniqueIds.nf' + +/** + * Check if the ids are unique across parameter sets + * + * @param parameterSets a list of parameter sets. + */ +private void _checkUniqueIds(List>> parameterSets) { + def ppIds = parameterSets.collect{it[0]} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/checkUniqueIds.nf' +def checkUniqueIds(Map args) { + def stopOnError = args.stopOnError == null ? args.stopOnError : true + + def idChecker = new IDChecker() + + return filter { tup -> + if (!idChecker.observe(tup[0])) { + if (stopOnError) { + error "Duplicate id: ${tup[0]}" + } else { + log.warn "Duplicate id: ${tup[0]}, removing duplicate entry" + return false + } + } + return true + } +} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_getChild.nf' + +// helper functions for reading params from file // +def _getChild(parent, child) { + if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { + child + } else { + def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() + parentAbsolute.replaceAll('/[^/]*$', "/") + child + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_guessParamListFormat.nf' + +def _guessParamListFormat(params) { + if (!params.containsKey("param_list") || params.param_list == null) { + "none" + } else { + def param_list = params.param_list + + if (param_list !instanceof String) { + "asis" + } else if (param_list.endsWith(".csv")) { + "csv" + } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { + "json" + } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { + "yaml" + } else { + "yaml_blob" + } + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/IDChecker.nf' +class IDChecker { + final def items = [] as Set + + @groovy.transform.WithWriteLock + boolean observe(String item) { + if (items.contains(item)) { + return false + } else { + items << item + return true + } + } + + @groovy.transform.WithReadLock + boolean contains(String item) { + return items.contains(item) + } + + @groovy.transform.WithReadLock + Set getItems() { + return items.clone() + } +} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/paramsToChannel.nf' +def paramsToChannel(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: paramsToChannel has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } + Channel.fromList(paramsToList(params, config)) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/paramsToList.nf' +viashChannelDeprecationWarningPrinted = false + +def paramsToList(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: paramsToList has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } + // fetch default params from functionality + def defaultArgs = config.functionality.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // fetch overrides in params + def paramArgs = config.functionality.allArguments + .findAll { params.containsKey(it.plainName) } + .collectEntries { [ it.plainName, params[it.plainName] ] } + + // check multi input params + // objects should be closures and not functions, thanks to FunctionDef + def multiParamFormat = _guessParamListFormat(params) + + def multiOptionFunctions = [ + "csv": {[it, readCsv(it)]}, + "json": {[it, readJson(it)]}, + "yaml": {[it, readYaml(it)]}, + "yaml_blob": {[null, readYamlBlob(it)]}, + "asis": {[null, it]}, + "none": {[null, [[:]]]} + ] + assert multiOptionFunctions.containsKey(multiParamFormat): + "Format of provided --param_list not recognised.\n" + + "You can use '--param_list_format' to manually specify the format.\n" + + "Found: '$multiParamFormat'. Expected: one of 'csv', 'json', 'yaml', 'yaml_blob', 'asis' or 'none'" + + // fetch multi param inputs + def multiOptionFun = multiOptionFunctions.get(multiParamFormat) + // todo: add try catch + def multiOptionOut = multiOptionFun(params.containsKey("param_list") ? params.param_list : "") + def paramList = multiOptionOut[1] + def multiFile = multiOptionOut[0] + + // data checks + assert paramList instanceof List: "--param_list should contain a list of maps" + for (value in paramList) { + assert value instanceof Map: "--param_list should contain a list of maps" + } + + // combine parameters + def processedParams = paramList.collect{ multiParam -> + // combine params + def combinedArgs = defaultArgs + paramArgs + multiParam + + if (workflow.stubRun) { + // if stub run, explicitly add an id if missing + combinedArgs = [id: "stub"] + combinedArgs + } else { + // else check whether required arguments exist + config.functionality.allArguments + .findAll { it.required } + .forEach { par -> + assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" + } + } + + // process arguments + def inputs = config.functionality.allArguments + .findAll{ par -> combinedArgs.containsKey(par.plainName) } + .collectEntries { par -> + // split on 'multiple_sep' + if (par.multiple) { + parData = combinedArgs[par.plainName] + if (parData instanceof List) { + parData = parData.collect{it instanceof String ? it.split(par.multiple_sep) : it } + } else if (parData instanceof String) { + parData = parData.split(par.multiple_sep) + } else if (parData == null) { + parData = [] + } else { + parData = [ parData ] + } + } else { + parData = [ combinedArgs[par.plainName] ] + } + + // flatten + parData = parData.flatten() + + // cast types + if (par.type == "file" && ((par.direction != null ? par.direction : "input") == "input")) { + parData = parData.collect{path -> + if (path !instanceof String) { + path + } else if (multiFile) { + file(_getChild(multiFile, path)) + } else { + file(path) + } + }.flatten() + } else if (par.type == "integer") { + parData = parData.collect{it as Integer} + } else if (par.type == "double") { + parData = parData.collect{it as Double} + } else if (par.type == "boolean" || par.type == "boolean_true" || par.type == "boolean_false") { + parData = parData.collect{it as Boolean} + } + // simplify list to value if need be + if (!par.multiple) { + assert parData.size() == 1 : + "Error: argument ${par.plainName} has too many values.\n" + + " Expected amount: 1. Found: ${parData.size()}" + parData = parData[0] + } + + // return pair + [ par.plainName, parData ] + } + // remove parameters which were explicitly set to null + .findAll{ par -> par != null } + } + + + // check processed params + processedParams.forEach { args -> + assert args.containsKey("id"): "Each argument set should have an 'id'. Argument set: $args" + } + def ppIds = processedParams.collect{it.id} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" + + processedParams +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/preprocessInputs.nf' +// This helper file will be deprecated soon +preprocessInputsDeprecationWarningPrinted = false + +def preprocessInputsDeprecationWarning() { + if (!preprocessInputsDeprecationWarningPrinted) { + preprocessInputsDeprecationWarningPrinted = true + System.err.println("Warning: preprocessInputs() will be deprecated Viash 0.9.0.") + } +} + +/** + * Process a list of Vdsl3 formatted parameters and apply a Viash config to them: + * - Gather default parameters from the Viash config and make + * sure that they are correctly formatted (see applyConfig method). + * - Format the input parameters (also using the applyConfig method). + * - Apply the default parameter to the input parameters. + * - Do some assertions: + * ~ Check if the event IDs in the channel are unique. + * + * @param params A list of parameter sets as Tuples. The first element of the tuples + * must be a unique id of the parameter set, and the second element + * must contain the parameters themselves. Optional extra elements + * of the tuples will be passed to the output as is. + * @param config A Map of the Viash configuration. This Map can be generated from + * the config file using the readConfig() function. + * + * @return A list of processed parameters sets as tuples. + */ + +private List _preprocessInputsList(List params, Map config) { + // Get different parameter types (used throughout this function) + def defaultArgs = config.functionality.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // Apply config to default parameters + def parsedDefaultValues = applyConfigToOneParameterSet(defaultArgs, config) + + // Apply config to input parameters + def parsedInputParamSets = applyConfig(params, config) + + // Merge two parameter sets together + def parsedArgs = parsedInputParamSets.collect({ parsedInputParamSet -> + def id = parsedInputParamSet[0] + def parValues = parsedInputParamSet[1] + def passthrough = parsedInputParamSet.drop(2) + def parValuesWithDefault = parsedDefaultValues + parValues + [id, parValuesWithDefault] + passthrough + }) + _checkUniqueIds(parsedArgs) + + return parsedArgs +} + +/** + * Generate a nextflow Workflow that allows processing a channel of + * Vdsl3 formatted events and apply a Viash config to them: + * - Gather default parameters from the Viash config and make + * sure that they are correctly formatted (see applyConfig method). + * - Format the input parameters (also using the applyConfig method). + * - Apply the default parameter to the input parameters. + * - Do some assertions: + * ~ Check if the event IDs in the channel are unique. + * + * The events in the channel are formatted as tuples, with the + * first element of the tuples being a unique id of the parameter set, + * and the second element containg the the parameters themselves. + * Optional extra elements of the tuples will be passed to the output as is. + * + * @param args A map that must contain a 'config' key that points + * to a parsed config (see readConfig()). Optionally, a + * 'key' key can be provided which can be used to create a unique + * name for the workflow process. + * + * @return A workflow that allows processing a channel of Vdsl3 formatted events + * and apply a Viash config to them. + */ +def preprocessInputs(Map args) { + preprocessInputsDeprecationWarning() + + wfKey = args.key != null ? args.key : "preprocessInputs" + config = args.config + workflow preprocessInputsInstance { + take: + input_ch + + main: + assert config instanceof Map : + "Error in preprocessInputs: config must be a map. " + + "Expected class: Map. Found: config.getClass() is ${config.getClass()}" + + output_ch = input_ch + | toSortedList + | map { paramList -> _preprocessInputsList(paramList, config) } + | flatMap + emit: + output_ch + } + + return preprocessInputsInstance.cloneWithName(wfKey) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf' +/** + * Run a list of components on a stream of data. + * + * @param components: list of Viash VDSL3 modules to run + * @param fromState: a closure, a map or a list of keys to extract from the input data. + * If a closure, it will be called with the id, the data and the component config. + * @param toState: a closure, a map or a list of keys to extract from the output data + * If a closure, it will be called with the id, the output data, the old state and the component config. + * @param filter: filter function to apply to the input. + * It will be called with the id, the data and the component config. + * @param id: id to use for the output data + * If a closure, it will be called with the id, the data and the component config. + * @param auto: auto options to pass to the components + * + * @return: a workflow that runs the components + **/ +def runComponents(Map args) { + assert args.components: "runComponents should be passed a list of components to run" + + def components_ = args.components + if (components_ !instanceof List) { + components_ = [ components_ ] + } + assert components_.size() > 0: "pass at least one component to runComponents" + + def fromState_ = args.fromState + def toState_ = args.toState + def filter_ = args.filter + def id_ = args.id + + workflow runComponentsWf { + take: input_ch + main: + + // generate one channel per method + out_chs = components_.collect{ comp_ -> + def comp_config = comp_.config + + filter_ch = filter_ + ? input_ch | filter{tup -> + filter_(tup[0], tup[1], comp_config) + } + : input_ch + id_ch = id_ + ? filter_ch | map{tup -> + // def new_id = id_(tup[0], tup[1], comp_config) + def new_id = tup[0] + if (id_ instanceof String) { + new_id = id_ + } else if (id_ instanceof Closure) { + new_id = id_(new_id, tup[1], comp_config) + } + [new_id] + tup.drop(1) + } + : filter_ch + data_ch = id_ch | map{tup -> + def new_data = tup[1] + if (fromState_ instanceof Map) { + new_data = fromState_.collectEntries{ key0, key1 -> + [key0, new_data[key1]] + } + } else if (fromState_ instanceof List) { + new_data = fromState_.collectEntries{ key -> + [key, new_data[key]] + } + } else if (fromState_ instanceof Closure) { + new_data = fromState_(tup[0], new_data, comp_config) + } + tup.take(1) + [new_data] + tup.drop(1) + } + out_ch = data_ch + | comp_.run( + auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] + ) + post_ch = toState_ + ? out_ch | map{tup -> + def output = tup[1] + def old_state = tup[2] + if (toState_ instanceofRunCompoMap) { + new_state = old_state + toState_.collectEntries{ key0, key1 -> + [key0, output[key1]] + } + } else if (toState_ instanceof List) { + new_state = old_state + toState_.collectEntries{ key -> + [key, output[key]] + } + } else if (toState_ instanceof Closure) { + new_state = toState_(tup[0], output, old_state, comp_config) + } + [tup[0], new_state] + tup.drop(3) + } + : out_ch + + post_ch + } + + // mix all results + output_ch = + (out_chs.size == 1) + ? out_chs[0] + : out_chs[0].mix(*out_chs.drop(1)) + + emit: output_ch + } + + return runComponentsWf +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/safeJoin.nf' +def safeJoin(targetChannel, sourceChannel, key) { + def sourceIDs = new IDChecker() + + def sourceCheck = sourceChannel + | map { tup -> + sourceIDs.observe(tup[0]) + tup + } + def targetCheck = targetChannel + | map { tup -> + def id = tup[0] + // def id = tup[1].containsKey("_meta").containsKey("join_id") ? tup[1]._meta.join_id : tup[0] + + if (!sourceIDs.contains(id)) { + error ( + "Error in module '${key}' when merging output with original state.\n" + + " Reason: output with id '${id}' could not be joined with source channel.\n" + + " If the IDs in the output channel differ from the input channel,\n" + + " please set `tup[1]._meta.join_id to the original ID.\n" + + " Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + + " Unexpected ID in the output channel: '${id}.\n" + + " Example input event: [\"id\", [input: file(...)]],\n" + + " Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]" + ) + } + + tup + } + targetCheck.join(sourceCheck) +} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf' +/** + * Split parameters for arguments that accept multiple values using their separator + * + * @param paramList A Map containing parameters to split. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A Map of parameters where the parameter values have been split into a list using + * their seperator. + */ +Map _splitParams(Map parValues, Map config){ + def parsedParamValues = parValues.collectEntries { parName, parValue -> + def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) + + if (!parameterSettings) { + // if argument is not found, do not alter + return [parName, parValue] + } + if (parameterSettings.multiple) { // Check if parameter can accept multiple values + if (parValue instanceof Collection) { + parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } + } else if (parValue instanceof String) { + parValue = parValue.split(parameterSettings.multiple_sep) + } else if (parValue == null) { + parValue = [] + } else { + parValue = [ parValue ] + } + parValue = parValue.flatten() + } + // For all parameters check if multiple values are only passed for + // arguments that allow it. Quietly simplify lists of length 1. + if (!parameterSettings.multiple && parValue instanceof Collection) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + [parName, parValue] + } + return parsedParamValues +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/viashChannel.nf' + +def viashChannel(params, config) { + if (!viashChannelDeprecationWarningPrinted) { + viashChannelDeprecationWarningPrinted = true + System.err.println("Warning: viashChannel has deprecated in Viash 0.7.0. " + + "Please use a combination of channelFromParams and preprocessInputs.") + } + paramsToChannel(params, config) + | map{tup -> [tup.id, tup]} +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/addGlobalParams.nf' +def addGlobalArguments(config) { + def localConfig = [ + "functionality" : [ + "argument_groups": [ + [ + "name": "Nextflow input-output arguments", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "arguments" : [ + [ + 'name': '--publish_dir', + 'required': true, + 'type': 'string', + 'description': 'Path to an output directory.', + 'example': 'output/', + 'multiple': false + ], + [ + 'name': '--param_list', + 'required': false, + 'type': 'string', + 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. + | + |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. + |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. + |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. + |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. + | + |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), + 'example': 'my_params.yaml', + 'multiple': false, + 'hidden': true + ], + ] + ] + ] + ] + ] + + return processConfig(_mergeMap(config, localConfig)) +} + +def _mergeMap(Map lhs, Map rhs) { + return rhs.inject(lhs.clone()) { map, entry -> + if (map[entry.key] instanceof Map && entry.value instanceof Map) { + map[entry.key] = _mergeMap(map[entry.key], entry.value) + } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { + map[entry.key] += entry.value + } else { + map[entry.key] = entry.value + } + return map + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/generateHelp.nf' +def _generateArgumentHelp(param) { + // alternatives are not supported + // def names = param.alternatives ::: List(param.name) + + def unnamedProps = [ + ["required parameter", param.required], + ["multiple values allowed", param.multiple], + ["output", param.direction.toLowerCase() == "output"], + ["file must exist", param.type == "file" && param.must_exist] + ].findAll{it[1]}.collect{it[0]} + + def dflt = null + if (param.default != null) { + if (param.default instanceof List) { + dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") + } else { + dflt = param.default.toString() + } + } + def example = null + if (param.example != null) { + if (param.example instanceof List) { + example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") + } else { + example = param.example.toString() + } + } + def min = param.min?.toString() + def max = param.max?.toString() + + def escapeChoice = { choice -> + def s1 = choice.replaceAll("\\n", "\\\\n") + def s2 = s1.replaceAll("\"", """\\\"""") + s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 + } + def choices = param.choices == null ? + null : + "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" + + def namedPropsStr = [ + ["type", ([param.type] + unnamedProps).join(", ")], + ["default", dflt], + ["example", example], + ["choices", choices], + ["min", min], + ["max", max] + ] + .findAll{it[1]} + .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} + .join("") + + def descStr = param.description == null ? + "" : + _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") + + "\n --" + param.plainName + + namedPropsStr + + descStr +} + +// Based on Helper.generateHelp() in Helper.scala +def _generateHelp(config) { + def fun = config.functionality + + // PART 1: NAME AND VERSION + def nameStr = fun.name + + (fun.version == null ? "" : " " + fun.version) + + // PART 2: DESCRIPTION + def descrStr = fun.description == null ? + "" : + "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n") + + // PART 3: Usage + def usageStr = fun.usage == null ? + "" : + "\n\nUsage:\n" + fun.usage.trim() + + // PART 4: Options + def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> + def name = argGroup.name + def descriptionStr = argGroup.description == null ? + "" : + "\n " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" + def arguments = argGroup.arguments.collect{arg -> + arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg + }.findAll{it != null} + def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)} + + "\n\n$name:" + + descriptionStr + + argumentStrs.join("\n") + } + + // FINAL: combine + def out = nameStr + + descrStr + + usageStr + + argGroupStrs.join("") + + return out +} + +// based on Format._paragraphWrap +def _paragraphWrap(str, maxLength) { + def outLines = [] + str.split("\n").each{par -> + def words = par.split("\\s").toList() + + def word = null + def line = words.pop() + while(!words.isEmpty()) { + word = words.pop() + if (line.length() + word.length() + 1 <= maxLength) { + line = line + " " + word + } else { outLines.add(line) line = word } } - if (words.isEmpty()) { - outLines.add(line) + if (words.isEmpty()) { + outLines.add(line) + } + } + return outLines +} + +def helpMessage(config) { + if (params.containsKey("help") && params.help) { + def mergedConfig = addGlobalArguments(config) + def helpStr = _generateHelp(mergedConfig) + println(helpStr) + exit 0 + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/processConfig.nf' +def processConfig(config) { + // TODO: assert .functionality etc. + if (config.functionality.inputs) { + System.err.println("Warning: .functionality.inputs is deprecated. Please use .functionality.arguments instead.") + } + if (config.functionality.outputs) { + System.err.println("Warning: .functionality.outputs is deprecated. Please use .functionality.arguments instead.") + } + + // set defaults for inputs + config.functionality.inputs = + (config.functionality.inputs != null ? config.functionality.inputs : []).collect{arg -> + arg.type = arg.type != null ? arg.type : "file" + arg.direction = "input" + _processArgument(arg) + } + // set defaults for outputs + config.functionality.outputs = + (config.functionality.outputs != null ? config.functionality.outputs : []).collect{arg -> + arg.type = arg.type != null ? arg.type : "file" + arg.direction = "output" + _processArgument(arg) + } + // set defaults for arguments + config.functionality.arguments = + (config.functionality.arguments != null ? config.functionality.arguments : []).collect{arg -> + _processArgument(arg) + } + // set defaults for argument_group arguments + config.functionality.argument_groups = + (config.functionality.argument_groups != null ? config.functionality.argument_groups : []).collect{grp -> + grp.arguments = (grp.arguments != null ? grp.arguments : []).collect{arg -> + arg instanceof String ? arg.replaceAll("^-*", "") : _processArgument(arg) + } + grp + } + + // create combined arguments list + config.functionality.allArguments = + config.functionality.inputs + + config.functionality.outputs + + config.functionality.arguments + + config.functionality.argument_groups.collectMany{ group -> + group.arguments.findAll{ it !instanceof String } + } + + // add missing argument groups (based on Functionality::allArgumentGroups()) + def argGroups = config.functionality.argument_groups + def inputGroup = _processArgumentGroup(argGroups, "Inputs", config.functionality.inputs) + def outputGroup = _processArgumentGroup(argGroups, "Outputs", config.functionality.outputs) + def defaultGroup = _processArgumentGroup(argGroups, "Arguments", config.functionality.arguments) + def groupsFiltered = argGroups.findAll(gr -> !(["Inputs", "Outputs", "Arguments"].contains(gr.name))) + config.functionality.allArgumentGroups = inputGroup + outputGroup + defaultGroup + groupsFiltered + + config +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/readConfig.nf' + +def readConfig(file) { + def config = readYaml(file != null ? file : "$projectDir/config.vsh.yaml") + processConfig(config) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/collectTraces.nf' +class CustomTraceObserver implements nextflow.trace.TraceObserver { + List traces + + CustomTraceObserver(List traces) { + this.traces = traces + } + + @Override + void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } + + @Override + void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { + def trace2 = trace.store.clone() + trace2.script = null + traces.add(trace2) + } +} + +def collectTraces() { + def traces = Collections.synchronizedList([]) + + // add custom trace observer which stores traces in the traces object + session.observers.add(new CustomTraceObserver(traces)) + + traces +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/getPublishDir.nf' +def getPublishDir() { + return params.containsKey("publish_dir") ? params.publish_dir : + params.containsKey("publishDir") ? params.publishDir : + null +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/getRootDir.nf' + +// Recurse upwards until we find a '.build.yaml' file +def _findBuildYamlFile(path) { + def child = path.resolve(".build.yaml") + if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) { + return child + } else { + def parent = path.getParent() + if (parent == null) { + return null + } else { + return _findBuildYamlFile(parent) + } + } +} + +// get the root of the target folder +def getRootDir() { + def dir = _findBuildYamlFile(projectDir.toAbsolutePath()) + assert dir != null: "Could not find .build.yaml in the folder structure" + dir.getParent() +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/iterateMap.nf' +/** + * Recursively apply a function over the leaves of an object. + * @param obj The object to iterate over. + * @param fun The function to apply to each value. + * @return The object with the function applied to each value. + */ +def iterateMap(obj, fun) { + if (obj instanceof List && obj !instanceof String) { + return obj.collect{item -> + iterateMap(item, fun) + } + } else if (obj instanceof Map) { + return obj.collectEntries{key, item -> + [key.toString(), iterateMap(item, fun)] + } + } else { + return fun(obj) + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/niceView.nf' +/** + * A view for printing the event of each channel as a YAML blob. + * This is useful for debugging. + */ +def niceView() { + workflow niceViewWf { + take: input + main: + output = input + | view{toYamlBlob(it)} + emit: output + } + return niceViewWf +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf' + +def readCsv(file_path) { + def output = [] + def inputFile = file_path !instanceof Path ? file(file_path) : file_path + + // todo: allow escaped quotes in string + // todo: allow single quotes? + def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') + def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''') + + def br = java.nio.file.Files.newBufferedReader(inputFile) + + def row = -1 + def header = null + while (br.ready() && header == null) { + def line = br.readLine() + row++ + if (!line.startsWith("#")) { + header = splitRegex.split(line, -1).collect{field -> + m = removeQuote.matcher(field) + m.find() ? m.replaceFirst('$1') : field + } + } + } + assert header != null: "CSV file should contain a header" + + while (br.ready()) { + def line = br.readLine() + row++ + if (line == null) { + br.close() + break + } + + if (!line.startsWith("#")) { + def predata = splitRegex.split(line, -1) + def data = predata.collect{field -> + if (field == "") { + return null + } + m = removeQuote.matcher(field) + if (m.find()) { + return m.replaceFirst('$1') + } else { + return field + } + } + assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" + + def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} + output.add(dataMap) + } + } + + output +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJsonBlob.nf' +def readJsonBlob(str) { + def jsonSlurper = new groovy.json.JsonSlurper() + jsonSlurper.parseText(str) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJson.nf' +def readJson(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path) : file_path + def jsonSlurper = new groovy.json.JsonSlurper() + jsonSlurper.parse(inputFile) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readTaggedYaml.nf' +// Custom constructor to modify how certain objects are parsed from YAML +class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { + Path root + + class ConstructFile extends org.yaml.snakeyaml.constructor.AbstractConstruct { + public Object construct(org.yaml.snakeyaml.nodes.Node node) { + String filename = (String) constructScalar(node); + if (root != null) { + return root.resolve(filename); + } + return java.nio.file.Paths.get(filename); + } + } + + CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) { + super(options) + this.root = root + // Handling !file tag and parse it back to a File type + this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructFile()) + } +} + +def readTaggedYaml(Path path) { + def options = new org.yaml.snakeyaml.LoaderOptions() + def constructor = new CustomConstructor(options, path.getParent()) + def yaml = new org.yaml.snakeyaml.Yaml(constructor) + return yaml.load(path.text) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYamlBlob.nf' +def readYamlBlob(str) { + def yamlSlurper = new org.yaml.snakeyaml.Yaml() + yamlSlurper.load(str) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYaml.nf' +def readYaml(file_path) { + def inputFile = file_path !instanceof Path ? file(file_path) : file_path + def yamlSlurper = new org.yaml.snakeyaml.Yaml() + yamlSlurper.load(inputFile) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toJsonBlob.nf' +String toJsonBlob(Map data) { + return groovy.json.JsonOutput.toJson(data) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toTaggedYamlBlob.nf' +// Custom representer to modify how certain objects are represented in YAML +class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { + class RepresentFile implements org.yaml.snakeyaml.representer.Represent { + public org.yaml.snakeyaml.nodes.Node representData(Object data) { + Path file = (Path) data; + String value = file.getFileName(); + def tag = new org.yaml.snakeyaml.nodes.Tag("!file"); + return representScalar(tag, value); + } + } + CustomRepresenter(org.yaml.snakeyaml.DumperOptions options) { + super(options) + this.representers.put(File, new RepresentFile()) + } +} + +String toTaggedYamlBlob(Map data) { + def options = new org.yaml.snakeyaml.DumperOptions() + options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) + def representer = new CustomRepresenter(options) + def yaml = new org.yaml.snakeyaml.Yaml(representer, options) + return yaml.dump(data) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toYamlBlob.nf' +String toYamlBlob(Map data) { + def options = new org.yaml.snakeyaml.DumperOptions() + options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) + options.setPrettyFlow(true) + def yaml = new org.yaml.snakeyaml.Yaml(options) + def cleanData = iterateMap(data, {it.toString()}) + return yaml.dump(data) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/writeJson.nf' +void writeJson(data, file) { + assert data: "writeJson: data should not be null" + assert file: "writeJson: file should not be null" + file.write(toJsonBlob(data)) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/writeYaml.nf' +void writeYaml(data, file) { + assert data: "writeYaml: data should not be null" + assert file: "writeYaml: file should not be null" + file.write(toYamlBlob(data)) +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/findStates.nf' +def findStates(Map params, Map config) { + // TODO: do a deep clone of config + def auto_config = config.clone() + auto_config.functionality = auto_config.functionality.clone() + // override arguments + auto_config.functionality.argument_groups = [] + auto_config.functionality.arguments = [ + [ + type: "file", + name: "--input_states", + example: "/path/to/input/directory/**/state.yaml", + description: "Path to input directory containing the datasets to be integrated.", + required: true, + multiple: true, + multiple_sep: ";" + ], + [ + type: "string", + name: "--filter", + example: "foo/.*/state.yaml", + description: "Regex to filter state files by path.", + required: false + ], + // to do: make this a yaml blob? + [ + type: "string", + name: "--rename_keys", + example: ["newKey1:oldKey1", "newKey2:oldKey2"], + description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", + required: false, + multiple: true, + multiple_sep: "," + ], + [ + type: "string", + name: "--settings", + example: '{"output_dataset": "dataset.h5ad", "k": 10}', + description: "Global arguments as a JSON glob to be passed to all components.", + required: false + ] + ] + + // run auto config through processConfig once more + auto_config = processConfig(auto_config) + + workflow findStatesWf { + helpMessage(auto_config) + + output_ch = + channelFromParams(params, auto_config) + | flatMap { autoId, args -> + + def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] + + // look for state files in input dir + def stateFiles = args.input_states + + // filter state files by regex + if (args.filter) { + stateFiles = stateFiles.findAll{ stateFile -> + def stateFileStr = stateFile.toString() + def matcher = stateFileStr =~ args.filter + matcher.matches()} + } + + // read in states + def states = stateFiles.collect { stateFile -> + def state_ = readTaggedYaml(stateFile) + [state_.id, state_] + } + + // construct renameMap + if (args.rename_keys) { + def renameMap = args.rename_keys.collectEntries{renameString -> + def split = renameString.split(":") + assert split.size() == 2: "Argument 'rename' should be of the form 'newKey:oldKey,newKey:oldKey'" + split + } + + // rename keys in state, only let states through which have all keys + // also add global settings + states = states.collectMany{id, state -> + def newState = [:] + + for (key in renameMap.keySet()) { + def origKey = renameMap[key] + if (!(state.containsKey(origKey))) { + return [] + } + newState[key] = state[origKey] + } + + [[id, globalSettings + newState]] + } + } + + states + } + emit: + output_ch + } + + return findStatesWf +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf' +def collectFiles(obj) { + if (obj instanceof java.io.File || obj instanceof Path) { + return [obj] + } else if (obj instanceof List && obj !instanceof String) { + return obj.collectMany{item -> + collectFiles(item) + } + } else if (obj instanceof Map) { + return obj.collectMany{key, item -> + collectFiles(item) + } + } else { + return [] + } +} + +/** + * Recurse through a state and collect all input files and their target output filenames. + * @param obj The state to recurse through. + * @param prefix The prefix to prepend to the output filenames. + */ +def collectInputOutputPaths(obj, prefix) { + if (obj instanceof File || obj instanceof Path) { + def path = obj instanceof Path ? obj : obj.toPath() + def ext = path.getFileName().find("\\.[^\\.]+\$") ?: "" + def newFilename = prefix + ext + return [[obj, newFilename]] + } else if (obj instanceof List && obj !instanceof String) { + return obj.withIndex().collectMany{item, ix -> + collectInputOutputPaths(item, prefix + "_" + ix) + } + } else if (obj instanceof Map) { + return obj.collectMany{key, item -> + collectInputOutputPaths(item, prefix + "." + key) } + } else { + return [] } - return outLines } -def generateArgumentHelp(param) { - // alternatives are not supported - // def names = param.alternatives ::: List(param.name) - - def unnamedProps = [ - ["required parameter", param.required], - ["multiple values allowed", param.multiple], - ["output", param.direction.toLowerCase() == "output"], - ["file must exist", param.type == "file" && param.must_exist] - ].findAll{it[1]}.collect{it[0]} +def publishStates(Map args) { + def key_ = args.get("key") - def dflt = null - if (param.default != null) { - if (param.default instanceof List) { - dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - dflt = param.default.toString() - } + workflow publishStatesWf { + take: input_ch + main: + input_ch + | map { tup -> + def id_ = tup[0] + def state_ = tup[1] + + // the input files and the target output filenames + def inputOutputFiles_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose() + def inputFiles_ = inputOutputFiles_[0] + def outputFiles_ = inputOutputFiles_[1] + + // convert state to yaml blob + def yamlBlob_ = toTaggedYamlBlob([id: id_] + state_) + + // adds a leading dot to the id (after any folder names) + // example: foo -> .foo, foo/bar -> foo/.bar + def idWithDot_ = id_.replaceAll("^(.+/)?([^/]+)", "\$1.\$2") + def yamlFile = '$id.$key.state.yaml' + .replaceAll('\\$id', idWithDot_) + .replaceAll('\\$key', key_) + + [id_, yamlBlob_, yamlFile, inputFiles_, outputFiles_] + } + | publishStatesProc + emit: input_ch } - def example = null - if (param.example != null) { - if (param.example instanceof List) { - example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - example = param.example.toString() + return publishStatesWf +} +process publishStatesProc { + // todo: check publishpath? + publishDir path: "${getPublishDir()}/", mode: "copy" + tag "$id" + input: + tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) + output: + tuple val(id), path{[yamlFile] + outputFiles} + script: + def copyCommands = [ + inputFiles instanceof List ? inputFiles : [inputFiles], + outputFiles instanceof List ? outputFiles : [outputFiles] + ] + .transpose() + .collectMany{infile, outfile -> + if (infile.toString() != outfile.toString()) { + ["cp -r '${infile.toString()}' '${outfile.toString()}'"] + } else { + // no need to copy if infile is the same as outfile + [] + } } + """ + mkdir -p "\$(dirname '${yamlFile}')" + echo "Storing state as yaml" + echo '${yamlBlob}' > '${yamlFile}' + echo "Copying output files to destination folder" + ${copyCommands.join("\n ")} + """ +} + + +// this assumes that the state contains no other values other than those specified in the config +def publishStatesByConfig(Map args) { + def key_ = args.get("key") + def config = args.get("config") + + workflow publishStatesSimpleWf { + take: input_ch + main: + input_ch + | map { tup -> + def id_ = tup[0] + def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] + def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] + + // the processed state is a list of [key, value, srcPath, destPath] tuples, where + // - key, value is part of the state to be saved to disk + // - srcPath and destPath are lists of files to be copied from src to dest + def processedState = + config.functionality.allArguments + .findAll { it.direction == "output" } + .collectMany { par -> + def plainName_ = par.plainName + // if the state does not contain the key, it's an + // optional argument for which the component did + // not generate any output + if (!state_.containsKey(plainName_)) { + return [] + } + def value = state_[plainName_] + // if the parameter is not a file, it should be stored + // in the state as-is, but is not something that needs + // to be copied from the source path to the dest path + if (par.type != "file") { + return [[key: plainName_, value: value, srcPath: [], destPath: []]] + } + // if the orig state does not contain this filename, + // it's an optional argument for which the user specified + // that it should not be returned as a state + if (!origState_.containsKey(plainName_)) { + return [] + } + def filenameTemplate = origState_[plainName_] + // if the pararameter is multiple: true, fetch the template + if (par.multiple && filenameTemplate instanceof List) { + filenameTemplate = filenameTemplate[0] + } + // instantiate the template + filename = filenameTemplate + .replaceAll('\\$id', id_) + .replaceAll('\\$key', key_) + if (par.multiple) { + // if the parameter is multiple: true, the filename + // should contain a wildcard '*' that is replaced with + // the index of the file + assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" + def outputPerFile = value.withIndex().collect{ val, ix -> + def destPath = filename.replace("*", ix.toString()) + def destFile = java.nio.file.Paths.get(destPath) + def srcPath = val instanceof File ? val.toPath() : val + [value: destFile, srcPath: srcPath, destPath: destPath] + } + def transposedOutputs = ["value", "srcPath", "destPath"].collectEntries{ key -> + [key, outputPerFile.collect{dic -> dic[key]}] + } + return [[key: plainName_] + transposedOutputs] + } else { + def destFile = java.nio.file.Paths.get(filename) + def srcPath = value instanceof File ? value.toPath() : value + return [[key: plainName_, value: destFile, srcPath: [srcPath], destPath: [filename]]] + } + } + + def updatedState_ = processedState.collectEntries{[it.key, it.value]} + def inputFiles_ = processedState.collectMany{it.srcPath} + def outputFiles_ = processedState.collectMany{it.destPath} + + // convert state to yaml blob + def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_) + + // adds a leading dot to the id (after any folder names) + // example: foo -> .foo, foo/bar -> foo/.bar + // TODO: allow defining the state.yaml template + def idWithDot_ = id_.replaceAll("^(.+/)?([^/]+)", "\$1.\$2") + def yamlFile = '$id.$key.state.yaml' + .replaceAll('\\$id', idWithDot_) + .replaceAll('\\$key', key_) + + [id_, yamlBlob_, yamlFile, inputFiles_, outputFiles_] + } + | publishStatesProc + emit: input_ch + } + return publishStatesSimpleWf +} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/setState.nf' +def setState(fun) { + assert fun instanceof Closure || fun instanceof Map || fun instanceof List : + "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}" + + // if fun is a List, convert to map + if (fun instanceof List) { + // check whether fun is a list[string] + assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings" + fun = fun.collectEntries{[it, it]} } - def min = param.min?.toString() - def max = param.max?.toString() - def escapeChoice = { choice -> - def s1 = choice.replaceAll("\\n", "\\\\n") - def s2 = s1.replaceAll("\"", """\\\"""") - s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 + // if fun is a map, convert to closure + if (fun instanceof Map) { + // check whether fun is a map[string, string] + assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings" + assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings" + def funMap = fun.clone() + // turn the map into a closure to be used later on + fun = { id_, state_ -> + assert state_ instanceof Map : "Error in setState: the state is not a Map" + funMap.collectMany{newkey, origkey -> + if (state_.containsKey(origkey)) { + [[newkey, state_[origkey]]] + } else { + [] + } + }.collectEntries() + } } - def choices = param.choices == null ? - null : - "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" - def namedPropsStr = [ - ["type", ([param.type] + unnamedProps).join(", ")], - ["default", dflt], - ["example", example], - ["choices", choices], - ["min", min], - ["max", max] - ] - .findAll{it[1]} - .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} - .join("") - - def descStr = param.description == null ? - "" : - paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") - - "\n --" + param.plainName + - namedPropsStr + - descStr + map { tup -> + def id = tup[0] + def state = tup[1] + def unfilteredState = fun(id, state) + def newState = unfilteredState.findAll{key, val -> val != null} + [id, newState] + tup.drop(2) + } } -// Based on Helper.generateHelp() in Helper.scala -def generateHelp(config) { - def fun = config.functionality +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processAuto.nf' +// TODO: unit test processAuto +def processAuto(Map auto) { + // remove null values + auto = auto.findAll{k, v -> v != null} - // PART 1: NAME AND VERSION - def nameStr = fun.name + - (fun.version == null ? "" : " " + fun.version) + // check for unexpected keys + def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"] + def unexpectedKeys = auto.keySet() - expectedKeys + assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'" - // PART 2: DESCRIPTION - def descrStr = fun.description == null ? - "" : - "\n\n" + paragraphWrap(fun.description.trim(), 80).join("\n") + // check auto.simplifyInput + assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean" - // PART 3: Usage - def usageStr = fun.usage == null ? - "" : - "\n\nUsage:\n" + fun.usage.trim() + // check auto.simplifyOutput + assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean" - // PART 4: Options - def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> - def name = argGroup.name - def descriptionStr = argGroup.description == null ? - "" : - "\n " + paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" - def arguments = argGroup.arguments.collect{arg -> - arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg - }.findAll{it != null} - def argumentStrs = arguments.collect{param -> generateArgumentHelp(param)} - - "\n\n$name:" + - descriptionStr + - argumentStrs.join("\n") - } + // check auto.transcript + assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean" - // FINAL: combine - def out = nameStr + - descrStr + - usageStr + - argGroupStrs.join("") + // check auto.publish + assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'" - return out + return auto.subMap(expectedKeys) } -def helpMessage(config) { - if (paramExists("help")) { - def mergedConfig = addGlobalParams(config) - def helpStr = generateHelp(mergedConfig) - println(helpStr) - exit 0 +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processDirectives.nf' +def assertMapKeys(map, expectedKeys, requiredKeys, mapName) { + assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}" + map.forEach { key, val -> + assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map" + } + requiredKeys.forEach { requiredKey -> + assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map" } } -def _guessParamListFormat(params) { - if (!params.containsKey("param_list") || params.param_list == null) { - "none" - } else { - def param_list = params.param_list +// TODO: unit test processDirectives +def processDirectives(Map drctv) { + // remove null values + drctv = drctv.findAll{k, v -> v != null} - if (param_list !instanceof String) { - "asis" - } else if (param_list.endsWith(".csv")) { - "csv" - } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { - "json" - } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { - "yaml" - } else { - "yaml_blob" + // check for unexpected keys + def expectedKeys = [ + "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time" + ] + def unexpectedKeys = drctv.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'" + + /* DIRECTIVE accelerator + accepted examples: + - [ limit: 4, type: "nvidia-tesla-k80" ] + */ + if (drctv.containsKey("accelerator")) { + assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator") + } + + /* DIRECTIVE afterScript + accepted examples: + - "source /cluster/bin/cleanup" + */ + if (drctv.containsKey("afterScript")) { + assert drctv["afterScript"] instanceof CharSequence + } + + /* DIRECTIVE beforeScript + accepted examples: + - "source /cluster/bin/setup" + */ + if (drctv.containsKey("beforeScript")) { + assert drctv["beforeScript"] instanceof CharSequence + } + + /* DIRECTIVE cache + accepted examples: + - true + - false + - "deep" + - "lenient" + */ + if (drctv.containsKey("cache")) { + assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean + if (drctv["cache"] instanceof CharSequence) { + assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache" } } -} -viashChannelDeprecationWarningPrinted = false + /* DIRECTIVE conda + accepted examples: + - "bwa=0.7.15" + - "bwa=0.7.15 fastqc=0.11.5" + - ["bwa=0.7.15", "fastqc=0.11.5"] + */ + if (drctv.containsKey("conda")) { + if (drctv["conda"] instanceof List) { + drctv["conda"] = drctv["conda"].join(" ") + } + assert drctv["conda"] instanceof CharSequence + } -def paramsToList(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: paramsToList has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") + /* DIRECTIVE container + accepted examples: + - "foo/bar:tag" + - [ registry: "reg", image: "im", tag: "ta" ] + is transformed to "reg/im:ta" + - [ image: "im" ] + is transformed to "im:latest" + */ + if (drctv.containsKey("container")) { + assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence + if (drctv["container"] instanceof Map) { + def m = drctv["container"] + assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container") + def part1 = + System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : + params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove? + m.registry ? m.registry + "/" : + "" + def part2 = m.image + def part3 = m.tag ? ":" + m.tag : ":latest" + drctv["container"] = part1 + part2 + part3 + } } - // fetch default params from functionality - def defaultArgs = config.functionality.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - // fetch overrides in params - def paramArgs = config.functionality.allArguments - .findAll { params.containsKey(it.plainName) } - .collectEntries { [ it.plainName, params[it.plainName] ] } - - // check multi input params - // objects should be closures and not functions, thanks to FunctionDef - def multiParamFormat = _guessParamListFormat(params) + /* DIRECTIVE containerOptions + accepted examples: + - "--foo bar" + - ["--foo bar", "-f b"] + */ + if (drctv.containsKey("containerOptions")) { + if (drctv["containerOptions"] instanceof List) { + drctv["containerOptions"] = drctv["containerOptions"].join(" ") + } + assert drctv["containerOptions"] instanceof CharSequence + } - def multiOptionFunctions = [ - "csv": {[it, readCsv(it)]}, - "json": {[it, readJson(it)]}, - "yaml": {[it, readYaml(it)]}, - "yaml_blob": {[null, readYamlBlob(it)]}, - "asis": {[null, it]}, - "none": {[null, [[:]]]} - ] - assert multiOptionFunctions.containsKey(multiParamFormat): - "Format of provided --param_list not recognised.\n" + - "You can use '--param_list_format' to manually specify the format.\n" + - "Found: '$multiParamFormat'. Expected: one of 'csv', 'json', 'yaml', 'yaml_blob', 'asis' or 'none'" + /* DIRECTIVE cpus + accepted examples: + - 1 + - 10 + */ + if (drctv.containsKey("cpus")) { + assert drctv["cpus"] instanceof Integer + } - // fetch multi param inputs - def multiOptionFun = multiOptionFunctions.get(multiParamFormat) - // todo: add try catch - def multiOptionOut = multiOptionFun(params.containsKey("param_list") ? params.param_list : "") - def paramList = multiOptionOut[1] - def multiFile = multiOptionOut[0] + /* DIRECTIVE disk + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("disk")) { + assert drctv["disk"] instanceof CharSequence + // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures + } - // data checks - assert paramList instanceof List: "--param_list should contain a list of maps" - for (value in paramList) { - assert value instanceof Map: "--param_list should contain a list of maps" + /* DIRECTIVE echo + accepted examples: + - true + - false + */ + if (drctv.containsKey("echo")) { + assert drctv["echo"] instanceof Boolean } - - // combine parameters - def processedParams = paramList.collect{ multiParam -> - // combine params - def combinedArgs = defaultArgs + paramArgs + multiParam - if (workflow.stubRun) { - // if stub run, explicitly add an id if missing - combinedArgs = [id: "stub"] + combinedArgs - } else { - // else check whether required arguments exist - config.functionality.allArguments - .findAll { it.required } - .forEach { par -> - assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" - } - } - - // process arguments - def inputs = config.functionality.allArguments - .findAll{ par -> combinedArgs.containsKey(par.plainName) } - .collectEntries { par -> - // split on 'multiple_sep' - if (par.multiple) { - parData = combinedArgs[par.plainName] - if (parData instanceof List) { - parData = parData.collect{it instanceof String ? it.split(par.multiple_sep) : it } - } else if (parData instanceof String) { - parData = parData.split(par.multiple_sep) - } else if (parData == null) { - parData = [] - } else { - parData = [ parData ] - } - } else { - parData = [ combinedArgs[par.plainName] ] - } + /* DIRECTIVE errorStrategy + accepted examples: + - "terminate" + - "finish" + */ + if (drctv.containsKey("errorStrategy")) { + assert drctv["errorStrategy"] instanceof CharSequence + assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy" + } - // flatten - parData = parData.flatten() + /* DIRECTIVE executor + accepted examples: + - "local" + - "sge" + */ + if (drctv.containsKey("executor")) { + assert drctv["executor"] instanceof CharSequence + assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor" + } - // cast types - if (par.type == "file" && ((par.direction != null ? par.direction : "input") == "input")) { - parData = parData.collect{path -> - if (path !instanceof String) { - path - } else if (multiFile) { - file(getChild(multiFile, path)) - } else { - file(path) - } - }.flatten() - } else if (par.type == "integer") { - parData = parData.collect{it as Integer} - } else if (par.type == "double") { - parData = parData.collect{it as Double} - } else if (par.type == "boolean" || par.type == "boolean_true" || par.type == "boolean_false") { - parData = parData.collect{it as Boolean} - } - // simplify list to value if need be - if (!par.multiple) { - assert parData.size() == 1 : - "Error: argument ${par.plainName} has too many values.\n" + - " Expected amount: 1. Found: ${parData.size()}" - parData = parData[0] - } + /* DIRECTIVE machineType + accepted examples: + - "n1-highmem-8" + */ + if (drctv.containsKey("machineType")) { + assert drctv["machineType"] instanceof CharSequence + } - // return pair - [ par.plainName, parData ] - } - // remove parameters which were explicitly set to null - .findAll{ par -> par != null } - } - - - // check processed params - processedParams.forEach { args -> - assert args.containsKey("id"): "Each argument set should have an 'id'. Argument set: $args" + /* DIRECTIVE maxErrors + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxErrors")) { + assert drctv["maxErrors"] instanceof Integer + } + + /* DIRECTIVE maxForks + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxForks")) { + assert drctv["maxForks"] instanceof Integer } - def ppIds = processedParams.collect{it.id} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" - processedParams -} + /* DIRECTIVE maxRetries + accepted examples: + - 1 + - 3 + */ + if (drctv.containsKey("maxRetries")) { + assert drctv["maxRetries"] instanceof Integer + } -def paramsToChannel(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: paramsToChannel has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") + /* DIRECTIVE memory + accepted examples: + - "1 GB" + - "2TB" + - "3.2KB" + - "10.B" + */ + if (drctv.containsKey("memory")) { + assert drctv["memory"] instanceof CharSequence + // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") + // ^ does not allow closures } - Channel.fromList(paramsToList(params, config)) -} -def viashChannel(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: viashChannel has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") + /* DIRECTIVE module + accepted examples: + - "ncbi-blast/2.2.27" + - "ncbi-blast/2.2.27:t_coffee/10.0" + - ["ncbi-blast/2.2.27", "t_coffee/10.0"] + */ + if (drctv.containsKey("module")) { + if (drctv["module"] instanceof List) { + drctv["module"] = drctv["module"].join(":") + } + assert drctv["module"] instanceof CharSequence } - paramsToChannel(params, config) - | map{tup -> [tup.id, tup]} -} -/** - * Split parameters for arguments that accept multiple values using their separator - * - * @param paramList A Map containing parameters to split. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A Map of parameters where the parameter values have been split into a list using - * their seperator. - */ -Map _splitParams(Map parValues, Map config){ - def parsedParamValues = parValues.collectEntries { parName, parValue -> - def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) + /* DIRECTIVE penv + accepted examples: + - "smp" + */ + if (drctv.containsKey("penv")) { + assert drctv["penv"] instanceof CharSequence + } - if (!parameterSettings) { - // if argument is not found, do not alter - return [parName, parValue] + /* DIRECTIVE pod + accepted examples: + - [ label: "key", value: "val" ] + - [ annotation: "key", value: "val" ] + - [ env: "key", value: "val" ] + - [ [label: "l", value: "v"], [env: "e", value: "v"]] + */ + if (drctv.containsKey("pod")) { + if (drctv["pod"] instanceof Map) { + drctv["pod"] = [ drctv["pod"] ] } - if (parameterSettings.multiple) { // Check if parameter can accept multiple values - if (parValue instanceof Collection) { - parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } - } else if (parValue instanceof String) { - parValue = parValue.split(parameterSettings.multiple_sep) - } else if (parValue == null) { - parValue = [] - } else { - parValue = [ parValue ] - } - parValue = parValue.flatten() + assert drctv["pod"] instanceof List + drctv["pod"].forEach { pod -> + assert pod instanceof Map + // TODO: should more checks be added? + // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod + // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...? } - // For all parameters check if multiple values are only passed for - // arguments that allow it. Quietly simplify lists of length 1. - if (!parameterSettings.multiple && parValue instanceof Collection) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] + } + + /* DIRECTIVE publishDir + accepted examples: + - [] + - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ] + - "/path/to/dir" + is transformed to [[ path: "/path/to/dir" ]] + - [ path: "/path/to/dir", mode: "cache" ] + is transformed to [[ path: "/path/to/dir", mode: "cache" ]] + */ + // TODO: should we also look at params["publishDir"]? + if (drctv.containsKey("publishDir")) { + def pblsh = drctv["publishDir"] + + // check different options + assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence + + // turn into list if not already so + // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work. + pblsh = pblsh instanceof List ? pblsh : [ pblsh ] + + // check elements of publishDir + pblsh = pblsh.collect{ elem -> + // turn into map if not already so + elem = elem instanceof CharSequence ? [ path: elem ] : elem + + // check types and keys + assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}" + assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir") + + // check elements in map + assert elem.containsKey("path") + assert elem["path"] instanceof CharSequence + if (elem.containsKey("mode")) { + assert elem["mode"] instanceof CharSequence + assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ] + } + if (elem.containsKey("overwrite")) { + assert elem["overwrite"] instanceof Boolean + } + if (elem.containsKey("pattern")) { + assert elem["pattern"] instanceof CharSequence + } + if (elem.containsKey("saveAs")) { + assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'" + } + if (elem.containsKey("enabled")) { + assert elem["enabled"] instanceof Boolean + } + + // return final result + elem } - [parName, parValue] + // store final directive + drctv["publishDir"] = pblsh } - return parsedParamValues -} -/** - * Check if the ids are unique across parameter sets - * - * @param parameterSets a list of parameter sets. - */ -private void _checkUniqueIds(List>> parameterSets) { - def ppIds = parameterSets.collect{it[0]} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" -} + /* DIRECTIVE queue + accepted examples: + - "long" + - "short,long" + - ["short", "long"] + */ + if (drctv.containsKey("queue")) { + if (drctv["queue"] instanceof List) { + drctv["queue"] = drctv["queue"].join(",") + } + assert drctv["queue"] instanceof CharSequence + } -/** - * Resolve the file paths in the parameters relative to given path - * - * @param paramList A Map containing parameters to process. - * This function assumes that files are still of type String. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * @param relativeTo path of a file to resolve the parameters values to. - * - * @return A map of parameters where the location of the input file parameters have been resolved - * resolved relatively to the provided path. - */ -private Map _resolvePathsRelativeTo(Map paramList, Map config, String relativeTo) { - paramList.collectEntries { parName, parValue -> - argSettings = config.functionality.allArguments.find{it.plainName == parName} - if (argSettings && argSettings.type == "file" && argSettings.direction == "input") { - if (parValue instanceof Collection) { - parValue = parValue.collect({path -> - path !instanceof String ? path : file(getChild(relativeTo, path)) - }) - } else { - parValue = parValue !instanceof String ? path : file(getChild(relativeTo, parValue)) - } + /* DIRECTIVE label + accepted examples: + - "big_mem" + - "big_cpu" + - ["big_mem", "big_cpu"] + */ + if (drctv.containsKey("label")) { + if (drctv["label"] instanceof CharSequence) { + drctv["label"] = [ drctv["label"] ] + } + assert drctv["label"] instanceof List + drctv["label"].forEach { label -> + assert label instanceof CharSequence + // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?") + // ^ does not allow closures } - [parName, parValue] } -} -/** - * Parse nextflow parameters based on settings defined in a viash config - * and return a nextflow channel. - * - * @param params Input parameters from nextflow. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A list of parameter sets that were parsed from the 'param_list' argument value. - */ -private List> _parseParamListArguments(Map params, Map config){ - // first try to guess the format (if not set in params) - def paramListFormat = _guessParamListFormat(params) + /* DIRECTIVE scratch + accepted examples: + - true + - "/path/to/scratch" + - '$MY_PATH_TO_SCRATCH' + - "ram-disk" + */ + if (drctv.containsKey("scratch")) { + assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence + } - // get the correct parser function for the detected params_list format - def paramListParsers = [ - "csv": {[it, readCsv(it)]}, - "json": {[it, readJson(it)]}, - "yaml": {[it, readYaml(it)]}, - "yaml_blob": {[null, readYamlBlob(it)]}, - "asis": {[null, it]}, - "none": {[null, [[:]]]} - ] - assert paramListParsers.containsKey(paramListFormat): - "Format of provided --param_list not recognised.\n" + - "You can use '--param_list_format' to manually specify the format.\n" + - "Found: '$paramListFormat'. Expected: one of 'csv', 'json', "+ - "'yaml', 'yaml_blob', 'asis' or 'none'" - def paramListParser = paramListParsers.get(paramListFormat) + /* DIRECTIVE storeDir + accepted examples: + - "/path/to/storeDir" + */ + if (drctv.containsKey("storeDir")) { + assert drctv["storeDir"] instanceof CharSequence + } - // fetch multi param inputs - def paramListOut = paramListParser(params.containsKey("param_list") ? params.param_list : "") - // multiFile is null if the value passed to param_list was not a file (e.g a blob) - // If the value was indeed a file, multiFile contains the location that file (used later). - def paramListFile = paramListOut[0] - def paramSets = paramListOut[1] // these are the actual parameters from reading the blob/file + /* DIRECTIVE stageInMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageInMode")) { + assert drctv["stageInMode"] instanceof CharSequence + assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"] + } - return checkParamListArguments(paramListFile, paramSets, config) -} + /* DIRECTIVE stageOutMode + accepted examples: + - "copy" + - "link" + */ + if (drctv.containsKey("stageOutMode")) { + assert drctv["stageOutMode"] instanceof CharSequence + assert drctv["stageOutMode"] in ["copy", "move", "rsync"] + } -def checkParamListArguments(paramListFile, paramSets, config) { - assert paramSets instanceof List: "--param_list should contain a list of maps" - for (value in paramSets) { - assert value instanceof Map: "--param_list should contain a list of maps" + /* DIRECTIVE tag + accepted examples: + - "foo" + - '$id' + */ + if (drctv.containsKey("tag")) { + assert drctv["tag"] instanceof CharSequence } - // Reformat from List to List> by adding the ID as first element of a Tuple2 - paramSets = paramSets.collect({ paramValues -> - [paramValues.get("id", null), paramValues.findAll{it.key != 'id'}] - }) - // Split parameters with 'multiple: true' - paramSets = paramSets.collect({ id, paramValues -> - def splitParamValues = _splitParams(paramValues, config) - [id, splitParamValues] - }) - - // The paths of input files inside a param_list file may have been specified relatively to the - // location of the param_list file. These paths must be made absolute. - if (paramListFile){ - paramSets = paramSets.collect({ id, paramValues -> - def relativeParamValues = _resolvePathsRelativeTo(paramValues, config, paramListFile) - [id, relativeParamValues] - }) + /* DIRECTIVE time + accepted examples: + - "1h" + - "2days" + - "1day 6hours 3minutes 30seconds" + */ + if (drctv.containsKey("time")) { + assert drctv["time"] instanceof CharSequence + // todo: validation regex? } - return paramSets + return drctv } -/** - * Cast parameters to the correct type as defined in the Viash config - * - * @param parValues A Map of input arguments. - * - * @return The input arguments that have been cast to the type from the viash config. - */ +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processWorkflowArgs.nf' +// depends on: thisConfig, thisDefaultWorkflowArgs +def processWorkflowArgs(Map args) { + // override defaults with args + def workflowArgs = thisDefaultWorkflowArgs + args -private Map _castParamTypes(Map parValues, Map config) { - // Cast the input to the correct type according to viash config - def castParValues = parValues.collectEntries({ parName, parValue -> - paramSettings = config.functionality.allArguments.find({it.plainName == parName}) - // dont parse parameters like publish_dir ( in which case paramSettings = null) - parType = paramSettings ? paramSettings.get("type", null) : null - if (parValue !instanceof Collection) { - parValue = [parValue] + // check whether 'key' exists + assert workflowArgs.containsKey("key") : "Error in module '${thisConfig.functionality.name}': key is a required argument" + + // if 'key' is a closure, apply it to the original key + if (workflowArgs["key"] instanceof Closure) { + workflowArgs["key"] = workflowArgs["key"](thisConfig.functionality.name) + } + def key = workflowArgs["key"] + assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}" + assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}" + + // check for any unexpected keys + def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "fromState", "toState", "args", "renameKeys", "debug"] + def unexpectedKeys = workflowArgs.keySet() - expectedKeys + assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'" + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument" + assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}" + workflowArgs["directives"] = processDirectives(thisDefaultWorkflowArgs.directives + workflowArgs["directives"]) + + // check whether directives exists and apply defaults + assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument" + assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}" + workflowArgs["auto"] = processAuto(thisDefaultWorkflowArgs.auto + workflowArgs["auto"]) + + // auto define publish, if so desired + if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" + + // " Example: params.publish_dir = \"./output/\"" + def publishDir = getPublishDir() + + if (publishDir != null) { + workflowArgs.directives.publishDir = [[ + path: publishDir, + saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default + mode: "copy" + ]] } - if (parType == "file" && ((paramSettings.direction != null ? paramSettings.direction : "input") == "input")) { - parValue = parValue.collect{ path -> - if (path !instanceof String) { - path - } else { - file(path) - } - } - } else if (parType == "integer") { - parValue = parValue.collect{it as Integer} - } else if (parType == "double") { - parValue = parValue.collect{it as Double} - } else if (parType == "boolean" || - parType == "boolean_true" || - parType == "boolean_false") { - parValue = parValue.collect{it as Boolean} + } + + // auto define transcript, if so desired + if (workflowArgs.auto.transcript == true) { + // can't assert at this level thanks to the no_publish profile + // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : + // "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" + + // " Example: params.transcripts_dir = \"./transcripts/\"" + def transcriptsDir = + params.containsKey("transcripts_dir") ? params.transcripts_dir : + params.containsKey("transcriptsDir") ? params.transcriptsDir : + params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" : + params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : + null + if (transcriptsDir != null) { + def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss') + def transcriptsPublishDir = [ + path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/", + saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", + mode: "copy" + ] + def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : [] + workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir } + } - // simplify list to value if need be - if (paramSettings && !paramSettings.multiple) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] + // if this is a stubrun, remove certain directives? + if (workflow.stubRun) { + workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"]) + } + + for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam]) { + assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}" } - [parName, parValue] - }) - return castParValues + } + + // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well? + for (nam in ["renameKeys"]) { + if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) { + log.warn "module '$key': workflow argument '$nam' will be deprecated in Viash 0.9.0. Please use 'fromState' and 'toState' instead." + } + } + + // check fromState + workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, thisConfig) + + // check toState + workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, thisConfig) + + // return output + return workflowArgs } -/** - * Apply the argument settings specified in a Viash config to a single parameter set. - * - Split the parameter values according to their seperator if - * the parameter accepts multiple values - * - Cast the parameters to their corect types. - * - Assertions: - * ~ Check if any unknown parameters are found - * - * @param paramValues A Map of parameter to be processed. All parameters must - * also be specified in the Viash config. - * @param config: A Map of the Viash configuration. This Map can be generated from - * the config file using the readConfig() function. - * @return The input parameters that have been processed. - */ -Map applyConfigToOneParameterSet(Map paramValues, Map config){ - def splitParamValues = _splitParams(paramValues, config) - def castParamValues = _castParamTypes(splitParamValues, config) +def _processFromState(fromState, key_, config_) { + assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List : + "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}" + if (fromState == null) { + return null + } + + // if fromState is a List, convert to map + if (fromState instanceof List) { + // check whether fromstate is a list[string] + assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings" + fromState = fromState.collectEntries{[it, it]} + } - // Check if any unexpected arguments were passed - def knownParams = config.functionality.allArguments.collect({it.plainName}) + ["publishDir", "publish_dir"] - castParamValues.each({parName, parValue -> - assert parName in knownParams: "Unknown parameter. Parameter $parName should be in $knownParams" - }) - return castParamValues + // if fromState is a map, convert to closure + if (fromState instanceof Map) { + // check whether fromstate is a map[string, string] + assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings" + assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings" + def fromStateMap = fromState.clone() + def requiredInputNames = thisConfig.functionality.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName} + // turn the map into a closure to be used later on + fromState = { it -> + def state = it[1] + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def data = fromStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (state.containsKey(origkey)) { + [[newkey, state[origkey]]] + } else if (!requiredInputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state") + } + }.collectEntries() + data + } + } + + return fromState } -/** - * Apply the argument settings specified in a Viash config to a list of parameter sets. - * - Split the parameter values according to their seperator if - * the parameter accepts multiple values - * - Cast the parameters to their corect types. - * - Assertions: - * ~ Check if any unknown parameters are found - * ~ Check if the ID of the parameter set is unique across all sets. - * - * @return The input parameters that have been processed. - */ +def _processToState(toState, key_, config_) { + if (toState == null) { + toState = { tup -> tup[1] } + } -List applyConfig(List parameterSets, Map config){ - def processedparameterSets = parameterSets.collect({ parameterSet -> - def id = parameterSet[0] - def paramValues = parameterSet[1] - def passthrough = parameterSet.drop(2) - def processedSet = applyConfigToOneParameterSet(paramValues, config) - [id, processedSet] + passthrough - }) + // toState should be a closure, map[string, string], or list[string] + assert toState instanceof Closure || toState instanceof Map || toState instanceof List : + "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}" - _checkUniqueIds(processedparameterSets) - return processedparameterSets + // if toState is a List, convert to map + if (toState instanceof List) { + // check whether toState is a list[string] + assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings" + toState = toState.collectEntries{[it, it]} + } + + // if toState is a map, convert to closure + if (toState instanceof Map) { + // check whether toState is a map[string, string] + assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings" + assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings" + def toStateMap = toState.clone() + def requiredOutputNames = config_.functionality.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName} + // turn the map into a closure to be used later on + toState = { it -> + def output = it[1] + def state = it[2] + assert output instanceof Map : "Error in module '$key_': the output is not a Map" + assert state instanceof Map : "Error in module '$key_': the state is not a Map" + def extraEntries = toStateMap.collectMany{newkey, origkey -> + // check whether newkey corresponds to a required argument + if (output.containsKey(origkey)) { + [[newkey, output[origkey]]] + } else if (!requiredOutputNames.contains(origkey)) { + [] + } else { + throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output") + } + }.collectEntries() + state + extraEntries + } + } + + return toState } -/** - * Parse nextflow parameters based on settings defined in a viash config. - * Return a list of parameter sets, each parameter set corresponding to - * an event in a nextflow channel. The output from this function can be used - * with Channel.fromList to create a nextflow channel with Vdsl3 formatted - * events. - * - * This function performs: - * - A filtering of the params which can be found in the config file. - * - Process the params_list argument which allows a user to to initialise - * a Vsdl3 channel with multiple parameter sets. Possible formats are - * csv, json, yaml, or simply a yaml_blob. A csv should have column names - * which correspond to the different arguments of this pipeline. A json or a yaml - * file should be a list of maps, each of which has keys corresponding to the - * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. - * When passing a csv, json or yaml, relative path names are relativized to the - * location of the parameter file. - * - Combine the parameter sets into a vdsl3 Channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A list of parameters with the first element of the event being - * the event ID and the second element containing a map of the parsed parameters. - */ - -private List>> _paramsToParamSets(Map params, Map config){ - /* parse regular parameters (not in param_list) */ - /*************************************************/ - def globalParams = config.functionality.allArguments - .findAll { params.containsKey(it.plainName) } - .collectEntries { [ it.plainName, params[it.plainName] ] } - def globalID = params.get("id", null) - def globalParamsValues = applyConfigToOneParameterSet(globalParams.findAll{it.key != 'id'}, config) +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/vdsl3ProcessFactory.nf' +// depends on: thisConfig, thisScript, session? +def vdsl3ProcessFactory(Map workflowArgs) { + // autodetect process key + def wfKey = workflowArgs["key"] + def procKeyPrefix = "${wfKey}_process" + def meta = nextflow.script.ScriptMeta.current() + def existing = meta.getProcessNames().findAll{it.startsWith(procKeyPrefix)} + def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()} + def newNumber = (numbers + [-1]).max() + 1 + + def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber" + + if (newNumber > 0) { + log.warn "Key for module '${wfKey}' is duplicated.\n", + "If you run a component multiple times in the same workflow,\n" + + "it's recommended you set a unique key for every call,\n" + + "for example: ${wfKey}.run(key: \"foo\")." + } - /* process params_list arguments */ - /*********************************/ - def paramSets = _parseParamListArguments(params, config) - def parameterSetsWithConfigApplied = applyConfig(paramSets, config) + // subset directives and convert to list of tuples + def drctv = workflowArgs.directives - /* combine arguments into channel */ - /**********************************/ - def processedParams = parameterSetsWithConfigApplied.indexed().collect{ index, paramSet -> - def id = paramSet[0] - def parValues = paramSet[1] - id = [id, globalID].find({it != null}) // first non-null element - - if (workflow.stubRun) { - // if stub run, explicitly add an id if missing - id = id ? id : "stub" + index + // TODO: unit test the two commands below + // convert publish array into tags + def valueToStr = { val -> + // ignore closures + if (val instanceof CharSequence) { + if (!val.matches('^[{].*[}]$')) { + '"' + val + '"' + } else { + val + } + } else if (val instanceof List) { + "[" + val.collect{valueToStr(it)}.join(", ") + "]" + } else if (val instanceof Map) { + "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]" + } else { + val.inspect() } - assert id != null: "Each parameter set should have at least an ID." - // Add regular parameters together with parameters passed with 'param_list' - def combinedArgsValues = globalParamsValues + parValues + } - // Remove parameters which are null, if the default is also null - combinedArgsValues = combinedArgsValues.collectEntries{paramName, paramValue -> - parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) - if ( paramValue != null || parameterSettings.get("default", null) != null ) { - [paramName, paramValue] + // multiple entries allowed: label, publishdir + def drctvStrs = drctv.collect { key, value -> + if (key in ["label", "publishDir"]) { + value.collect{ val -> + if (val instanceof Map) { + "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else if (val == null) { + "" + } else { + "\n$key " + valueToStr(val) + } + }.join() + } else if (value instanceof Map) { + "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") + } else { + "\n$key " + valueToStr(value) + } + }.join() + + def inputPaths = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' } + .join() + + def outputPaths = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + // insert dummy into every output (see nextflow-io/nextflow#2678) + if (!par.multiple) { + ', path{[".exitcode", args.' + par.plainName + ']}' + } else { + ', path{[".exitcode"] + args.' + par.plainName + '}' } } - [id, combinedArgsValues] + .join() + + // TODO: move this functionality somewhere else? + if (workflowArgs.auto.transcript) { + outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}' + } else { + outputPaths = outputPaths + ', path{[".exitcode"]}' } - // Check if ids (first element of each list) is unique - _checkUniqueIds(processedParams) - return processedParams -} + // create dirs for output files (based on BashWrapper.createParentFiles) + def createParentStr = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "output" && it.create_parent } + .collect { par -> + "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + } + .join("\n") + + // construct inputFileExports + def inputFileExports = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } + .collect { par -> + viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" + "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" + } -/** - * Parse nextflow parameters based on settings defined in a viash config - * and return a nextflow channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A nextflow Channel with events. Events are formatted as a tuple that contains - * first contains the ID of the event and as second element holds a parameter map. - * - * - */ -def channelFromParams(Map params, Map config) { - processedParams = _paramsToParamSets(params, config) - return Channel.fromList(processedParams) + // NOTE: if using docker, use /tmp instead of tmpDir! + def tmpDir = java.nio.file.Paths.get( + System.getenv('NXF_TEMP') ?: + System.getenv('VIASH_TEMP') ?: + System.getenv('VIASH_TMPDIR') ?: + System.getenv('VIASH_TEMPDIR') ?: + System.getenv('VIASH_TMP') ?: + System.getenv('TEMP') ?: + System.getenv('TMPDIR') ?: + System.getenv('TEMPDIR') ?: + System.getenv('TMP') ?: + '/tmp' + ).toAbsolutePath() + + // construct stub + def stub = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .collect { par -> + "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" + } + .join("\n") + + // escape script + def escapedScript = thisScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"') + + // publishdir assert + def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? + """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n Example: --publish_dir './output/'" """ : + "" + + // generate process string + def procStr = + """nextflow.enable.dsl=2 + | + |process $procKey {$drctvStrs + |input: + | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") + |output: + | tuple val("\$id")$outputPaths, optional: true + |stub: + |\"\"\" + |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; } + |$stub + |\"\"\" + |script:$assertStr + |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } + |def parInject = args + | .findAll{key, value -> value != null} + | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} + | .join("\\n") + |\"\"\" + |# meta exports + |# export VIASH_META_RESOURCES_DIR="\${resourcesDir.toRealPath().toAbsolutePath()}" + |export VIASH_META_RESOURCES_DIR="\${resourcesDir}" + |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}" + |export VIASH_META_FUNCTIONALITY_NAME="${thisConfig.functionality.name}" + |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_FUNCTIONALITY_NAME" + |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" + |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" } + |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" } + |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then + | export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 )) + | export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+1023) / 1024 )) + | export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+1023) / 1024 )) + | export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+1023) / 1024 )) + | export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+1023) / 1024 )) + |fi + | + |# meta synonyms + |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR" + |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR" + | + |# create output dirs if need be + |function mkdir_parent { + | for file in "\\\$@"; do + | mkdir -p "\\\$(dirname "\\\$file")" + | done + |} + |$createParentStr + | + |# argument exports${inputFileExports.join()} + |\$parInject + | + |# process script + |${escapedScript} + |\"\"\" + |} + |""".stripMargin() + + // TODO: print on debug + // if (workflowArgs.debug == true) { + // println("######################\n$procStr\n######################") + // } + + // create runtime process + def ownerParams = new nextflow.script.ScriptBinding.ParamsMap() + def binding = new nextflow.script.ScriptBinding().setParams(ownerParams) + def module = new nextflow.script.IncludeDef.Module(name: procKey) + def scriptParser = new nextflow.script.ScriptParser(session) + .setModule(true) + .setBinding(binding) + scriptParser.scriptPath = meta.getScriptPath() + def moduleScript = scriptParser.runScript(procStr) + .getScript() + + // register module in meta + meta.addModule(moduleScript, module.name, module.alias) + + // retrieve and return process from meta + return meta.getProcess(procKey) } -/** - * Process a list of Vdsl3 formatted parameters and apply a Viash config to them: - * - Gather default parameters from the Viash config and make - * sure that they are correctly formatted (see applyConfig method). - * - Format the input parameters (also using the applyConfig method). - * - Apply the default parameter to the input parameters. - * - Do some assertions: - * ~ Check if the event IDs in the channel are unique. - * - * @param params A list of parameter sets as Tuples. The first element of the tuples - * must be a unique id of the parameter set, and the second element - * must contain the parameters themselves. Optional extra elements - * of the tuples will be passed to the output as is. - * @param config A Map of the Viash configuration. This Map can be generated from - * the config file using the readConfig() function. - * - * @return A list of processed parameters sets as tuples. - */ +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/vdsl3WorkflowFactory.nf' +// depends on: thisConfig, resourcesDir +def vdsl3WorkflowFactory(Map args) { + def key = args["key"] + def processObj = null -private List _preprocessInputsList(List params, Map config) { - // Get different parameter types (used throughout this function) - def defaultArgs = config.functionality.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } + workflow processWf { + take: input_ + main: - // Apply config to default parameters - def parsedDefaultValues = applyConfigToOneParameterSet(defaultArgs, config) + if (processObj == null) { + processObj = vdsl3ProcessFactory(args) + } + + output_ = input_ + | map { tuple -> + def id = tuple[0] + def data_ = tuple[1] + + if (workflow.stubRun) { + // add id if missing + data_ = [id: 'stub'] + data_ + } - // Apply config to input parameters - def parsedInputParamSets = applyConfig(params, config) + // process input files separately + def inputPaths = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "input" } + .collect { par -> + def val = data_.containsKey(par.plainName) ? data_[par.plainName] : [] + def inputFiles = [] + if (val == null) { + inputFiles = [] + } else if (val instanceof List) { + inputFiles = val + } else if (val instanceof Path) { + inputFiles = [ val ] + } else { + inputFiles = [] + } + if (!workflow.stubRun) { + // throw error when an input file doesn't exist + inputFiles.each{ file -> + assert file.exists() : + "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" + + " Required input file does not exist.\n" + + " Path: '$file'.\n" + + " Expected input file to exist" + } + } + inputFiles + } + + // remove input files + def argsExclInputFiles = thisConfig.functionality.allArguments + .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) } + .collectEntries { par -> + def parName = par.plainName + def val = data_[parName] + if (par.multiple && val instanceof Collection) { + val = val.join(par.multiple_sep) + } + if (par.direction == "output" && par.type == "file") { + val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) + } + [parName, val] + } - // Merge two parameter sets together - def parsedArgs = parsedInputParamSets.collect({ parsedInputParamSet -> - def id = parsedInputParamSet[0] - def parValues = parsedInputParamSet[1] - def passthrough = parsedInputParamSet.drop(2) - def parValuesWithDefault = parsedDefaultValues + parValues - [id, parValuesWithDefault] + passthrough - }) - _checkUniqueIds(parsedArgs) + [ id ] + inputPaths + [ argsExclInputFiles, resourcesDir ] + } + | processObj + | map { output -> + def outputFiles = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "output" } + .indexed() + .collectEntries{ index, par -> + out = output[index + 1] + // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678) + if (!out instanceof List || out.size() <= 1) { + if (par.multiple) { + out = [] + } else { + assert !par.required : + "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" + + " Required output file is missing" + out = null + } + } else if (out.size() == 2 && !par.multiple) { + out = out[1] + } else { + out = out.drop(1) + } + [ par.plainName, out ] + } + + // drop null outputs + outputFiles.removeAll{it.value == null} - return parsedArgs + [ output[0], outputFiles ] + } + emit: output_ + } + + return processWf } -/** - * Generate a nextflow Workflow that allows processing a channel of - * Vdsl3 formatted events and apply a Viash config to them: - * - Gather default parameters from the Viash config and make - * sure that they are correctly formatted (see applyConfig method). - * - Format the input parameters (also using the applyConfig method). - * - Apply the default parameter to the input parameters. - * - Do some assertions: - * ~ Check if the event IDs in the channel are unique. - * - * The events in the channel are formatted as tuples, with the - * first element of the tuples being a unique id of the parameter set, - * and the second element containg the the parameters themselves. - * Optional extra elements of the tuples will be passed to the output as is. - * - * @param args A map that must contain a 'config' key that points - * to a parsed config (see readConfig()). Optionally, a - * 'key' key can be provided which can be used to create a unique - * name for the workflow process. - * - * @return A workflow that allows processing a channel of Vdsl3 formatted events - * and apply a Viash config to them. - */ -def preprocessInputs(Map args) { - wfKey = args.key != null ? args.key : "preprocessInputs" - config = args.config - workflow preprocessInputsInstance { - take: - input_ch +// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf' +def _debug(workflowArgs, debugKey) { + if (workflowArgs.debug) { + view { "process '${workflowArgs.key}' $debugKey tuple: $it" } + } else { + map { it } + } +} + +// depends on: thisConfig, innerWorkflowFactory +def workflowFactory(Map args) { + def workflowArgs = processWorkflowArgs(args) + def key_ = workflowArgs["key"] + + workflow workflowInstance { + take: input_ main: - assert config instanceof Map : - "Error in preprocessInputs: config must be a map. " + - "Expected class: Map. Found: config.getClass() is ${config.getClass()}" + mid1_ = input_ + | checkUniqueIds([:]) + | _debug(workflowArgs, "input") + | map { tuple -> + tuple = tuple.clone() + + if (workflowArgs.map) { + tuple = workflowArgs.map(tuple) + } + if (workflowArgs.mapId) { + tuple[0] = workflowArgs.mapId(tuple[0]) + } + if (workflowArgs.mapData) { + tuple[1] = workflowArgs.mapData(tuple[1]) + } + if (workflowArgs.mapPassthrough) { + tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2)) + } - output_ch = input_ch - | toSortedList - | map { paramList -> _preprocessInputsList(paramList, config) } - | flatMap - emit: - output_ch + // check tuple + assert tuple instanceof List : + "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}" + assert tuple.size() >= 2 : + "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: tuple.size() == ${tuple.size()}" + + // check id field + assert tuple[0] instanceof CharSequence : + "Error in module '${key_}': first element of tuple in channel should be a String\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Found: ${tuple[0]}" + + // match file to input file + if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) { + def inputFiles = thisConfig.functionality.allArguments + .findAll { it.type == "file" && it.direction == "input" } + + assert inputFiles.size() == 1 : + "Error in module '${key_}' id '${tuple[0]}'.\n" + + " Anonymous file inputs are only allowed when the process has exactly one file input.\n" + + " Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}" + + tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries() + } + + // check data field + assert tuple[1] instanceof Map : + "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" + + " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // rename keys of data field in tuple + if (workflowArgs.renameKeys) { + assert workflowArgs.renameKeys instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}" + assert tuple[1] instanceof Map : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" + + // TODO: allow renameKeys to be a function? + workflowArgs.renameKeys.each { newKey, oldKey -> + assert newKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}" + assert oldKey instanceof CharSequence : + "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + + " Example: renameKeys: ['new_key': 'old_key'].\n" + + " Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}" + assert tuple[1].containsKey(oldKey) : + "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" + + " Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'" + tuple[1].put(newKey, tuple[1][oldKey]) + } + tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey }) + } + tuple + } + + if (workflowArgs.filter) { + mid2_ = mid1_ + | filter{workflowArgs.filter(it)} + } else { + mid2_ = mid1_ + } + + if (workflowArgs.fromState) { + mid3_ = mid2_ + | map{ + def new_data = workflowArgs.fromState(it.take(2)) + [it[0], new_data] + } + } else { + mid3_ = mid2_ + } + + // fill in defaults + mid4_ = mid3_ + | map { tuple -> + def id_ = tuple[0] + def data_ = tuple[1] + + // TODO: could move fromState to here + + // fetch default params from functionality + def defaultArgs = thisConfig.functionality.allArguments + .findAll { it.containsKey("default") } + .collectEntries { [ it.plainName, it.default ] } + + // fetch overrides in params + def paramArgs = thisConfig.functionality.allArguments + .findAll { par -> + def argKey = key_ + "__" + par.plainName + params.containsKey(argKey) + } + .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] } + + // fetch overrides in data + def dataArgs = thisConfig.functionality.allArguments + .findAll { data_.containsKey(it.plainName) } + .collectEntries { [ it.plainName, data_[it.plainName] ] } + + // combine params + def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs + + // remove arguments with explicit null values + combinedArgs + .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"} + + combinedArgs = processInputs(combinedArgs, thisConfig, id_, key_) + + [id_, combinedArgs] + tuple.drop(2) + } + + // TODO: move some of the _meta.join_id wrangling to the safeJoin() function. + + out0_ = mid4_ + | _debug(workflowArgs, "processed") + // run workflow + | innerWorkflowFactory(workflowArgs) + // check output tuple + | map { id_, output_ -> + + // see if output map contains metadata + def meta_ = + output_ instanceof Map && output_.containsKey("_meta") ? + output_["_meta"] : + [:] + if (!meta_.containsKey("join_id")) { + meta_ = meta_ + ["join_id": id_] + } + + // remove metadata + output_ = output_.findAll{k, v -> k != "_meta"} + + output_ = processOutputs(output_, thisConfig, id_, key_) + + if (workflowArgs.auto.simplifyOutput && output_.size() == 1) { + output_ = output_.values()[0] + } + + [meta_.join_id, meta_, id_, output_] + } + // | view{"out0_: ${it.take(3)}"} + + // TODO: this join will fail if the keys changed during the innerWorkflowFactory + // join the output [join_id, meta, id, output] with the previous state [id, state, ...] + out1_ = safeJoin(out0_, mid2_, key_) + // input tuple format: [join_id, meta, id, output, prev_state, ...] + // output tuple format: [join_id, meta, id, new_state, ...] + | map{ tup -> + def new_state = workflowArgs.toState(tup.drop(2).take(3)) + tup.take(3) + [new_state] + tup.drop(5) + } + + if (workflowArgs.auto.publish == "state") { + out1pub_ = out1_ + // input tuple format: [join_id, meta, id, new_state, ...] + // output tuple format: [join_id, meta, id, new_state] + | map{ tup -> + tup.take(4) + } + + safeJoin(out1pub_, mid4_, key_) + // input tuple format: [join_id, meta, id, new_state, orig_state, ...] + // output tuple format: [id, new_state, orig_state] + | map { tup -> + tup.drop(2).take(3) + } + | publishStatesByConfig(key: key_, config: thisConfig) + } + + // remove join_id and meta + out2_ = out1_ + | map { tup -> + // input tuple format: [join_id, meta, id, new_state, ...] + // output tuple format: [id, new_state, ...] + tup.drop(2) + } + | _debug(workflowArgs, "output") + + out2_ + + emit: out2_ } - return preprocessInputsInstance.cloneWithName(wfKey) + def wf = workflowInstance.cloneWithName(key_) + + // add factory function + wf.metaClass.run = { runArgs -> + workflowFactory(runArgs) + } + // add config to module for later introspection + wf.metaClass.config = thisConfig + + return wf } From 7e0db4d77444d5b39fd523cd3ff0e9b39d13ace2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 27 Sep 2023 16:39:43 +0200 Subject: [PATCH 0998/1233] add nf directive labels (#234) Former-commit-id: 5e8d67198c3f63c00cf19a93f5359fac78180536 --- src/common/check_dataset_schema/config.vsh.yaml | 3 ++- src/common/extract_scores/config.vsh.yaml | 2 ++ .../control_methods/no_integration_batch/config.vsh.yaml | 2 ++ .../control_methods/random_embed_cell/config.vsh.yaml | 2 ++ .../control_methods/random_embed_cell_jitter/config.vsh.yaml | 2 ++ .../control_methods/random_integration/config.vsh.yaml | 2 ++ 6 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index fb8769798a..7702deee58 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -53,4 +53,5 @@ platforms: - type: python packages: viashpy - type: nextflow - + directives: + label: [ "highmem", "highcpu"] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index a7c65412e1..74d3c53069 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -31,3 +31,5 @@ platforms: - type: r cran: [ tidyverse ] - type: nextflow + directives: + label: [ "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index b57dbb1cf9..1a32559f4b 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -22,3 +22,5 @@ platforms: - scanpy - numpy - type: nextflow + directives: + label: [ "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index a4ea2c49b8..35a99d1fd9 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -21,3 +21,5 @@ platforms: pypi: - scikit-learn - type: nextflow + directives: + label: [ "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index faf4c6f702..57550a8962 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: - numpy - scipy - type: nextflow + directives: + label: [ "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index 9b43f82aea..4f344d14aa 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -21,3 +21,5 @@ platforms: pypi: - numpy - type: nextflow + directives: + label: [ "lowmem", "lowcpu"] \ No newline at end of file From d86aaf5d8c3255a86952c120932bc3ffc4e6d6ec Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 27 Sep 2023 17:25:53 +0200 Subject: [PATCH 0999/1233] fix wfhelper Former-commit-id: d6be258e0f1e2bc4942f071f5be9151dce20ae1d --- src/wf_utils/WorkflowHelper.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index 3d4d3d39e1..6e1af47971 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -906,7 +906,7 @@ def runComponents(Map args) { ? out_ch | map{tup -> def output = tup[1] def old_state = tup[2] - if (toState_ instanceofRunCompoMap) { + if (toState_ instanceof Map) { new_state = old_state + toState_.collectEntries{ key0, key1 -> [key0, output[key1]] } From 653b3c98102292b317d2ecf0b66e57177d5204e1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 27 Sep 2023 19:58:39 +0200 Subject: [PATCH 1000/1233] fix toTaggedYamlBlob Former-commit-id: fcfa91ae338880285902c549ea7e4a8f76c9a278 --- src/wf_utils/WorkflowHelper.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index 6e1af47971..b9f8fef49b 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -1456,7 +1456,7 @@ def readJson(file_path) { class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { Path root - class ConstructFile extends org.yaml.snakeyaml.constructor.AbstractConstruct { + class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct { public Object construct(org.yaml.snakeyaml.nodes.Node node) { String filename = (String) constructScalar(node); if (root != null) { @@ -1470,7 +1470,7 @@ class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { super(options) this.root = root // Handling !file tag and parse it back to a File type - this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructFile()) + this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath()) } } @@ -1502,7 +1502,7 @@ String toJsonBlob(Map data) { // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toTaggedYamlBlob.nf' // Custom representer to modify how certain objects are represented in YAML class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { - class RepresentFile implements org.yaml.snakeyaml.representer.Represent { + class RepresentPath implements org.yaml.snakeyaml.representer.Represent { public org.yaml.snakeyaml.nodes.Node representData(Object data) { Path file = (Path) data; String value = file.getFileName(); @@ -1512,7 +1512,7 @@ class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { } CustomRepresenter(org.yaml.snakeyaml.DumperOptions options) { super(options) - this.representers.put(File, new RepresentFile()) + this.representers.put(Path, new RepresentPath()) } } From 7f3bf8cf8d7f907d71c2cdfe50ce305b3a4f5dfb Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 28 Sep 2023 11:06:56 +0200 Subject: [PATCH 1001/1233] add time labels Former-commit-id: 36111080873f3960251feb6167a07632da218de5 --- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 2 +- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 2 +- src/datasets/normalization/log_cp/config.vsh.yaml | 2 +- src/datasets/normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cp/config.vsh.yaml | 2 +- .../control_methods/no_integration_batch/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell_jitter/config.vsh.yaml | 2 +- .../control_methods/random_integration/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- .../methods/fastmnn_embedding/config.vsh.yaml | 2 +- .../batch_integration/methods/fastmnn_feature/config.vsh.yaml | 2 +- .../batch_integration/methods/mnn_correct/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../methods/scanorama_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scanvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 2 +- .../metrics/clustering_overlap/config.vsh.yaml | 2 +- .../metrics/graph_connectivity/config.vsh.yaml | 2 +- .../batch_integration/metrics/hvg_overlap/config.vsh.yaml | 2 +- .../metrics/isolated_label_asw/config.vsh.yaml | 2 +- .../metrics/isolated_label_f1/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/kbet/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/lisi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/pcr/config.vsh.yaml | 2 +- .../denoising/control_methods/no_denoising/config.vsh.yaml | 2 +- .../control_methods/perfect_denoising/config.vsh.yaml | 2 +- src/tasks/denoising/methods/alra/config.vsh.yaml | 2 +- src/tasks/denoising/methods/dca/config.vsh.yaml | 2 +- src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml | 2 +- src/tasks/denoising/methods/magic/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/mse/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/spectral_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/densmap/config.vsh.yaml | 2 +- .../methods/diffusion_map/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/ivis/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/neuralee/config.vsh.yaml | 2 +- src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../dimensionality_reduction/metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 2 +- .../metrics/distance_correlation/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../dimensionality_reduction/process_dataset/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/mlp/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/scanvi/config.vsh.yaml | 2 +- .../label_projection/methods/scanvi_scarches/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/xgboost/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml | 2 +- .../methods/harmonic_alignment/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/procrustes/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/mse/config.vsh.yaml | 2 +- .../control_methods/meanpergene/config.vsh.yaml | 2 +- .../control_methods/random_predict/config.vsh.yaml | 2 +- .../predict_modality/control_methods/solution/config.vsh.yaml | 2 +- .../predict_modality/control_methods/zeros/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/lm/config.vsh.yaml | 2 +- .../predict_modality/methods/newwave_knnr/config.vsh.yaml | 2 +- .../predict_modality/methods/random_forest/config.vsh.yaml | 2 +- src/tasks/predict_modality/metrics/correlation/config.vsh.yaml | 2 +- src/tasks/predict_modality/metrics/mse/config.vsh.yaml | 2 +- src/tasks/predict_modality/process_dataset/config.vsh.yaml | 2 +- src/wf_utils/labels.config | 3 +++ 88 files changed, 90 insertions(+), 87 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 7702deee58..b86c36efa9 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -54,4 +54,4 @@ platforms: packages: viashpy - type: nextflow directives: - label: [ "highmem", "highcpu"] + label: [ "midtime", "highmem", "highcpu"] diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 1c7de0010c..76d95679f9 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -62,7 +62,7 @@ def create_config(par, component_type, pretty_name, script_path) -> str: | # Allows turning the component into a Nextflow module / pipeline. | - type: nextflow | directives: - | label: [midmem, midcpu] + | label: [ "midtime",midmem, midcpu] |''' ) diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index dc4b5dbc21..d7ca9914da 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -50,5 +50,5 @@ platforms: - type: native - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 74d3c53069..057c152583 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -32,4 +32,4 @@ platforms: cran: [ tidyverse ] - type: nextflow directives: - label: [ "lowmem", "lowcpu"] + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 2f4e422c4a..1be6c0a5d0 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -24,4 +24,4 @@ platforms: - numpy - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index 4d1770f2c4..8c44e58275 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 9fbf3bf670..cd23327af4 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -15,4 +15,4 @@ platforms: pip: scanpy - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index a347ec01d0..fd2f7b0a98 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index 1a32559f4b..b29d9ea2b1 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -23,4 +23,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "lowmem", "lowcpu"] + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index 35a99d1fd9..37e69892a3 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -22,4 +22,4 @@ platforms: - scikit-learn - type: nextflow directives: - label: [ "lowmem", "lowcpu"] \ No newline at end of file + label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index 57550a8962..7f6060e9ff 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -28,4 +28,4 @@ platforms: - scipy - type: nextflow directives: - label: [ "lowmem", "lowcpu"] \ No newline at end of file + label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index 4f344d14aa..9bd2cd7450 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -22,4 +22,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "lowmem", "lowcpu"] \ No newline at end of file + label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 742616c743..7c5a443999 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -34,4 +34,4 @@ platforms: - bbknn - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 0314e42438..6c288aa93e 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -36,4 +36,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index 344edf223a..73804df050 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: - batchelor - type: nextflow directives: - label: [ lowcpu, highmem ] + label: [ "midtime", lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index 6946cf2239..5a4fe19f9e 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") - type: nextflow directives: - label: [ lowcpu, highmem ] + label: [ "midtime", lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 15f30ec456..4d13027ce3 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -24,4 +24,4 @@ platforms: - batchelor - type: nextflow directives: - label: [ lowcpu, highmem ] + label: [ "midtime", lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index 5fdf1f0a8b..173c6fb11d 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -44,4 +44,4 @@ platforms: - chriscainx/mnnpy - type: nextflow directives: - label: [ lowcpu, lowmem ] + label: [ "midtime", lowcpu, lowmem ] diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 654e8c6e25..c3e53ec343 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -32,4 +32,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] \ No newline at end of file + label: [ "midtime", midmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index b144b0e788..c4eb65026b 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -32,4 +32,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 41182a651c..1e14e1bc3b 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -41,4 +41,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index d1bf368aa8..c233d44ff9 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -29,4 +29,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index f265b058d8..a28cf98f70 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -45,4 +45,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 6a5babce30..341a9e58db 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 69849dfc4b..2f3545481a 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -42,4 +42,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 98ed7e3662..182a6312b1 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -56,4 +56,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index 4e6b0642bf..62582c327b 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -42,4 +42,4 @@ platforms: - scib==1.1.4 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index 32d09ce523..33304872b4 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -41,4 +41,4 @@ platforms: - scib==1.1.4 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index 45de30b5db..2ccd2fd4c7 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -35,4 +35,4 @@ platforms: - scib==1.1.4 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index 08db06865d..89d831ca30 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -47,4 +47,4 @@ platforms: - scib==1.1.4 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index 161ba1802f..d08b79dfed 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -51,4 +51,4 @@ platforms: - anndata2ri - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index 73edbfd341..7ab0048384 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -50,4 +50,4 @@ platforms: - git+https://github.com/theislab/scib.git@v1.1.4 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index b043c2cd47..10715a43e0 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -39,4 +39,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index f03199ab17..0690a6b792 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index 27fcfa6953..25f6febd9d 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 82398c806d..7317aeb306 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -39,4 +39,4 @@ platforms: github: KlugerLab/ALRA - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index 29c7b244ef..0eb27673d0 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -35,4 +35,4 @@ platforms: - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index b573412828..a5b87fef59 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index d3d7122c1a..122fa9dc79 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -60,4 +60,4 @@ platforms: pip: [scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 9013183fe4..babbe7a6b6 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -27,4 +27,4 @@ platforms: - scprep - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index 367570e8de..fc325d7895 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -26,4 +26,4 @@ platforms: pip: scprep - type: nextflow directives: - label: [ midmem, midcpu ] \ No newline at end of file + label: [ "midtime", midmem, midcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 6fe1089de7..8f7a7aed35 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ highmem, highcpu ] \ No newline at end of file + label: [ "midtime", highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index ae926ec5d0..6aaad03d4d 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: - numpy - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 74d7f248e5..82244872c0 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 626110cd9a..8890a89795 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -41,4 +41,4 @@ platforms: - type: native - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index 643a7b8bed..c1a22ef996 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -41,4 +41,4 @@ platforms: - numpy - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index c22d2d1fd6..c4681c86d5 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -42,4 +42,4 @@ platforms: - ivis[cpu] - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 34e13c8c41..02f7e88b56 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -52,4 +52,4 @@ platforms: - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 5ca15443c4..3b4dd6d400 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -37,4 +37,4 @@ platforms: packages: scanpy - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 57b0e0eeac..6d4b7943ac 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -55,4 +55,4 @@ platforms: - "scikit-learn<1.2" - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 1b3e9ca9f4..75159f80ec 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - DmitryUlyanov/Multicore-TSNE - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index ddced67815..143af87aaa 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - umap-learn - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index a4cc208ba3..0f81b422c5 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -163,4 +163,4 @@ platforms: cran: [ coRanking, bit64 ] - type: nextflow directives: - label: [ highmem, midcpu ] + label: [ "midtime", highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index ed671faedd..f3e1b6aacc 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -39,4 +39,4 @@ platforms: - umap-learn - type: nextflow directives: - label: [ lowmem, midcpu ] + label: [ "midtime", lowmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index 7e30f9efbe..a69c14283c 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - scipy - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index b56012ae74..88b707e9a8 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -28,4 +28,4 @@ platforms: - numpy - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 17f7eaa2b1..55fb1e71e3 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -10,4 +10,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 53142aaf9e..48a2ba8f3c 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index dc95a42468..027781c078 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -22,4 +22,4 @@ platforms: packages: scanpy - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index 384c2cf92e..13df85ac08 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index 12445bedd0..aa8e25533a 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -34,4 +34,4 @@ platforms: packages: [scikit-learn, jsonschema] - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 990b8cf368..3b908ae7b2 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -31,4 +31,4 @@ platforms: packages: scikit-learn - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 8046a01e95..2c490e80c0 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -44,4 +44,4 @@ platforms: packages: scikit-learn - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 5cbc8fb3a4..3d29e25549 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -41,4 +41,4 @@ platforms: - scarches - type: nextflow directives: - label: [ midmem, highcpu, gpu ] + label: [ "midtime", midmem, highcpu, gpu ] diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 38df609144..0dbfce04ad 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -61,4 +61,4 @@ platforms: pypi: scvi-tools - type: nextflow directives: - label: [midmem, midcpu] + label: [ "midtime",midmem, midcpu] diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 045819ba47..928c85a5e4 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: cran: [ Matrix>=1.5.3, Seurat, rlang, bit64 ] - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index c37e7611f9..11d99ed5d3 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -31,4 +31,4 @@ platforms: packages: xgboost - type: nextflow directives: - label: [ midmem, midcpu ] + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml index 5fb412ae9c..921d746133 100644 --- a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -22,4 +22,4 @@ platforms: - numpy - type: nextflow directives: - label: [ lowmem, lowcpu ] \ No newline at end of file + label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml index fd472d5e03..8a0d1872b7 100644 --- a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -18,4 +18,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] \ No newline at end of file + label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml index cee2751ca2..01d04d881f 100644 --- a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -31,4 +31,4 @@ platforms: - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml index 06a5a0475c..ef34705c68 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -34,5 +34,5 @@ platforms: - KrishnaswamyLab/harmonic-alignment#subdirectory=python - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index 25f574fae7..a25ca276af 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -26,4 +26,4 @@ platforms: - scipy - type: nextflow directives: - label: [ medcpu, medmem ] \ No newline at end of file + label: [ "midtime", medcpu, medmem ] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index 0c616338d6..20f1bc1aaa 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -27,4 +27,4 @@ platforms: run: "cd /opt && git clone --depth 1 https://github.com/rsinghlab/SCOT.git && cd SCOT && pip install -r requirements.txt" - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index 68eba8c8cb..61b0013a01 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: - scikit-learn - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index 8882856c75..9507718990 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -29,4 +29,4 @@ platforms: - scprep - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 950b09c86b..61895787c5 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -13,5 +13,5 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml index 973f13ec46..c2e11990ac 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -16,4 +16,4 @@ platforms: cran: [ bit64] - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index 9e9419b385..c60e967a60 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -16,4 +16,4 @@ platforms: cran: [ bit64] - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml index 9819b74835..fc1a2fb078 100644 --- a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -13,4 +13,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 96669a6d20..5ccc6118af 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -30,4 +30,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index 9425daea35..0e8b034f7c 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: cran: [ lmds, FNN, proxyC, bit64 ] - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 74670e8dbb..444a8f5d00 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -29,4 +29,4 @@ platforms: cran: [ lmds, RcppArmadillo, pbapply, bit64] - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index e479a9432c..40e9e058d8 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -40,4 +40,4 @@ platforms: github: [Jiefei-Wang/SharedObject, fedeago/NewWave] - type: nextflow directives: - label: [ highmem, highcpu ] + label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 4c971b545b..5e6f978a53 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: cran: [ lmds, ranger, pbapply, bit64 ] - type: nextflow directives: - label: [ highmem, highcpu ] \ No newline at end of file + label: [ "midtime", highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index 8130364eba..6f5fcaf8e6 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -63,4 +63,4 @@ platforms: github: dynverse/dynutils - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml index 052268beaf..6cd843f953 100644 --- a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -27,4 +27,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index fef6c2b40b..8ec27a6c46 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -17,4 +17,4 @@ platforms: cran: [ bit64 ] - type: nextflow directives: - label: [ midmem, lowcpu ] + label: [ "midtime", midmem, lowcpu ] diff --git a/src/wf_utils/labels.config b/src/wf_utils/labels.config index a7a3cf47ab..8fc9040f8f 100644 --- a/src/wf_utils/labels.config +++ b/src/wf_utils/labels.config @@ -5,4 +5,7 @@ process { withLabel: midcpu { cpus = 15 } withLabel: highmem { memory = 100.Gb } withLabel: highcpu { cpus = 30 } + withLabel: lowtime { time = 1h } + withLabel: midtime { time = 4h } + withLabel: hightime { time = 8h } } From 37ad122a7872b6ee570f7cf4172b6bf1b1ef1651 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 28 Sep 2023 15:16:09 +0200 Subject: [PATCH 1002/1233] Fix nf tower batch integration (#236) * fix time labels * fix nf-ower errors * add directives Former-commit-id: b88e0981d4eaa9469d2220907b5b217e08f49383 --- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/script.py | 4 +++- .../transformers/embed_to_graph/config.vsh.yaml | 2 ++ .../transformers/feature_to_embed/config.vsh.yaml | 2 ++ src/wf_utils/labels.config | 6 +++--- src/wf_utils/labels_ci.config | 3 +++ 6 files changed, 14 insertions(+), 5 deletions(-) diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 6c288aa93e..c3b39a7c28 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -36,4 +36,4 @@ platforms: - scib==1.1.3 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [ "midtime", highmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index e6da9f1571..f0a24193a5 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -19,7 +19,9 @@ translator = { "homo_sapiens": "human", - "mus_musculus": "mouse" + "mus_musculus": "mouse", + "danio_rerio": "zebrafish", + "caenorhabditis_elegans": "C. elegans" } print('compute score', flush=True) diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index cbcea84eeb..77a2d076f6 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -16,3 +16,5 @@ platforms: - type: python pypi: scanpy - type: nextflow + directives: + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 3f1f5986cf..85e5be5dff 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -17,3 +17,5 @@ platforms: - type: python pypi: scanpy - type: nextflow + directives: + label: [ "midtime", midmem, lowcpu ] diff --git a/src/wf_utils/labels.config b/src/wf_utils/labels.config index 8fc9040f8f..9a29d57c48 100644 --- a/src/wf_utils/labels.config +++ b/src/wf_utils/labels.config @@ -5,7 +5,7 @@ process { withLabel: midcpu { cpus = 15 } withLabel: highmem { memory = 100.Gb } withLabel: highcpu { cpus = 30 } - withLabel: lowtime { time = 1h } - withLabel: midtime { time = 4h } - withLabel: hightime { time = 8h } + withLabel: lowtime { time = 1.h } + withLabel: midtime { time = 4.h } + withLabel: hightime { time = 8.h } } diff --git a/src/wf_utils/labels_ci.config b/src/wf_utils/labels_ci.config index ca02bb15c8..5161976609 100644 --- a/src/wf_utils/labels_ci.config +++ b/src/wf_utils/labels_ci.config @@ -5,4 +5,7 @@ process { withLabel: midcpu { cpus = 2 } withLabel: highmem { memory = 5.Gb } withLabel: highcpu { cpus = 2 } + withLabel: lowtime { time = 1.h } + withLabel: midtime { time = 4.h } + withLabel: hightime { time = 8.h } } From 163dc439ee10946f0b4eaa0ae21e5de5721f134d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 28 Sep 2023 20:55:30 +0200 Subject: [PATCH 1003/1233] fix metrics (#239) Former-commit-id: ce1c92b93e39eac2f5574b5dc714e91d8ab714de --- src/tasks/match_modalities/api/comp_metric.yaml | 4 ++-- src/tasks/match_modalities/api/file_integrated_mod1.yaml | 2 +- src/tasks/match_modalities/api/file_integrated_mod2.yaml | 2 +- src/tasks/match_modalities/api/file_mod1.yaml | 4 ++-- src/tasks/match_modalities/api/file_mod2.yaml | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/tasks/match_modalities/api/comp_metric.yaml b/src/tasks/match_modalities/api/comp_metric.yaml index 857f62bb07..6548c2a6cf 100644 --- a/src/tasks/match_modalities/api/comp_metric.yaml +++ b/src/tasks/match_modalities/api/comp_metric.yaml @@ -21,8 +21,8 @@ functionality: required: true direction: output test_resources: - - path: /resources_test/common/scicar_cell_lines - dest: resources_test/common/scicar_cell_lines + - path: /resources_test/match_modalities/scicar_cell_lines + dest: resources_test/match_modalities/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_metric_config.py - type: python_script diff --git a/src/tasks/match_modalities/api/file_integrated_mod1.yaml b/src/tasks/match_modalities/api/file_integrated_mod1.yaml index f46c429afc..97580facfc 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod1.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/match_modalities/integrated_mod1.h5ad" +example: "resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad" info: label: "Integrated" summary: "The integrated data" diff --git a/src/tasks/match_modalities/api/file_integrated_mod2.yaml b/src/tasks/match_modalities/api/file_integrated_mod2.yaml index 3dae69c9ab..f3324ffc9a 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod2.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/match_modalities/integrated_mod2.h5ad" +example: "resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad" info: label: "Integrated" summary: "The integrated data" diff --git a/src/tasks/match_modalities/api/file_mod1.yaml b/src/tasks/match_modalities/api/file_mod1.yaml index 60994c1d5c..d3e8570847 100644 --- a/src/tasks/match_modalities/api/file_mod1.yaml +++ b/src/tasks/match_modalities/api/file_mod1.yaml @@ -1,8 +1,8 @@ type: file example: "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad" info: - label: "multimodal mod 1 data" - summary: "the first modal data" + label: "Modality 1" + summary: "The first modality of a multimodal dataset." slots: layers: - type: integer diff --git a/src/tasks/match_modalities/api/file_mod2.yaml b/src/tasks/match_modalities/api/file_mod2.yaml index ad32aeddeb..665d833376 100644 --- a/src/tasks/match_modalities/api/file_mod2.yaml +++ b/src/tasks/match_modalities/api/file_mod2.yaml @@ -1,8 +1,8 @@ type: file example: "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad" info: - label: "multimodal mod 2 data" - summary: "the second modal data" + label: "Modality 2" + summary: "The second modality of a multimodal dataset." slots: layers: - type: integer From e54c64fe80d6217d503d299ec84a8ee527a08262 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michaela=20M=C3=BCller?= <51025211+mumichae@users.noreply.github.com> Date: Thu, 28 Sep 2023 21:17:21 +0200 Subject: [PATCH 1004/1233] Add more methods (#223) * add scalex feature and embed * change to base_python image --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 96598b8e4fe591f01071ebe5c18dd50553c5edf3 --- .../methods/scalex_embed/config.vsh.yaml | 45 ++++++++++++++++++ .../methods/scalex_embed/script.py | 41 +++++++++++++++++ .../methods/scalex_feature/config.vsh.yaml | 46 +++++++++++++++++++ .../methods/scalex_feature/script.py | 41 +++++++++++++++++ .../methods/scanvi/config.vsh.yaml | 2 +- 5 files changed, 174 insertions(+), 1 deletion(-) create mode 100644 src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/scalex_embed/script.py create mode 100644 src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/scalex_feature/script.py diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml new file mode 100644 index 0000000000..ebc34650c5 --- /dev/null +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -0,0 +1,45 @@ +# The API specifies which type of component this is. +# It contains specifications for: +# - The input/output files +# - Common parameters +# - A unit test +__merge__: ../../api/comp_method_embedding.yaml + +functionality: + # A unique identifier for your component (required). + # Can contain only lowercase letters or underscores. + name: scalex_embed + # Metadata for your component + info: + # A relatively short label, used when rendering visualisarions (required) + label: SCALEX + # A one sentence summary of how this method works (required). Used when + # rendering summary tables. + summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space + description : | + SCALEX is a method for integrating heterogeneous single-cell data online using a VAE framework. Its generalised encoder disentangles batch-related components from batch-invariant biological components, which are then projected into a common cell-embedding space. + reference: xiong2021online + repository_url: https://github.com/jsxlei/SCALEX + documentation_url: https://scalex.readthedocs.io + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + variants: + scalex_feature_unscaled: + scanorama_feature_scaled: + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scalex + - numpy<1.24 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scalex_embed/script.py b/src/tasks/batch_integration/methods/scalex_embed/script.py new file mode 100644 index 0000000000..52f4d09428 --- /dev/null +++ b/src/tasks/batch_integration/methods/scalex_embed/script.py @@ -0,0 +1,41 @@ +import anndata as ad +import scanpy as sc +import scalex + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'hvg': True, +} +meta = { + 'functionality_name' : 'foo', + 'config': 'bar' +} +## VIASH END + + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Run SCALEX', flush=True) +adata.X = adata.layers['normalized'] +adata = scalex.SCALEX( + adata, + batch_key="batch", + ignore_umap=True, + impute=adata.obs["batch"].cat.categories[0], + processed=True, + max_iteration=40, + min_features=None, + min_cells=None, + n_top_features=0, + outdir=None, + gpu=0, +) +adata.obsm["X_emb"] = adata.obsm["latent"] + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml new file mode 100644 index 0000000000..75933e04d1 --- /dev/null +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -0,0 +1,46 @@ +# The API specifies which type of component this is. +# It contains specifications for: +# - The input/output files +# - Common parameters +# - A unit test +__merge__: ../../api/comp_method_feature.yaml + +functionality: + # A unique identifier for your component (required). + # Can contain only lowercase letters or underscores. + name: scalex_feature + + # Metadata for your component + info: + # A relatively short label, used when rendering visualisarions (required) + label: SCALEX + # A one sentence summary of how this method works (required). Used when + # rendering summary tables. + summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space + description : | + SCALEX is a method for integrating heterogeneous single-cell data online using a VAE framework. Its generalised encoder disentangles batch-related components from batch-invariant biological components, which are then projected into a common cell-embedding space. + reference: xiong2021online + repository_url: https://github.com/jsxlei/SCALEX + documentation_url: https://scalex.readthedocs.io + v1: + path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cpm + variants: + scalex_feature_unscaled: + scanorama_feature_scaled: + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - scalex + - numpy<1.24 + - type: nextflow + directives: + label: [ lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scalex_feature/script.py b/src/tasks/batch_integration/methods/scalex_feature/script.py new file mode 100644 index 0000000000..b67c85c932 --- /dev/null +++ b/src/tasks/batch_integration/methods/scalex_feature/script.py @@ -0,0 +1,41 @@ +import anndata as ad +import scanpy as sc +import scalex + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'hvg': True, +} +meta = { + 'functionality_name' : 'foo', + 'config': 'bar' +} +## VIASH END + + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Run SCALEX', flush=True) +adata.X = adata.layers['normalized'] +adata = scalex.SCALEX( + adata, + batch_key="batch", + ignore_umap=True, + impute=adata.obs["batch"].cat.categories[0], + processed=True, + max_iteration=40, + min_features=None, + min_cells=None, + n_top_features=0, + outdir=None, + gpu=0, +) +adata.layers['corrected_counts'] = adata.layers["impute"] + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 1e14e1bc3b..8e33c9b30e 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.1 setup: - type: python pypi: From 90eaeac1d7940252212d87055df432b3e6641ec2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 29 Sep 2023 14:35:23 +0200 Subject: [PATCH 1005/1233] add a slash repllacement to the id (#240) Former-commit-id: 5095f8d4f25c4c7a284a2b30c4d7f159df75eb77 --- src/tasks/batch_integration/workflows/run_benchmark/main.nf | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 98e7b11c46..676ce242d8 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -101,6 +101,12 @@ workflow run_wf { dataset_ch = input_ch | preprocessInputs(config: config) + | map { id, state -> + def newId = id.replaceAll(/\//, "_") + + [newId, state] + } + // extract the dataset metadata | check_dataset_schema.run( fromState: [input: "input_dataset"], From abc565097cdfcd9dfed0abfdda4d7362e21f9764 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 2 Oct 2023 09:59:15 +0200 Subject: [PATCH 1006/1233] fix workflowhelper Former-commit-id: 5f2a6838e6a4cfaa1d7bd1651b1c8c83f5033da4 --- src/wf_utils/WorkflowHelper.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index b9f8fef49b..a9dd0ad24d 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -1679,7 +1679,7 @@ def collectFiles(obj) { def collectInputOutputPaths(obj, prefix) { if (obj instanceof File || obj instanceof Path) { def path = obj instanceof Path ? obj : obj.toPath() - def ext = path.getFileName().find("\\.[^\\.]+\$") ?: "" + def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: "" def newFilename = prefix + ext return [[obj, newFilename]] } else if (obj instanceof List && obj !instanceof String) { From 41d2e3a2ff9306f44a2b4702bca9a25e9d8543d2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 4 Oct 2023 14:58:52 +0200 Subject: [PATCH 1007/1233] fix issue with missing key in publishstates Former-commit-id: e230935f327ca7e54a71b93dace3b55806b1ead5 --- .../workflows/run_benchmark/main.nf | 4 +- src/wf_utils/WorkflowHelper.nf | 663 +++++------------- 2 files changed, 184 insertions(+), 483 deletions(-) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 676ce242d8..76053a23aa 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -82,13 +82,13 @@ workflow { channelFromParams(params, config) | run_wf - | publishStates([:]) + | publishStates(key: config.functionality.name) } workflow auto { findStates(params, config) | run_wf - | publishStates([:]) + | publishStates(key: config.functionality.name) } workflow run_wf { diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf index a9dd0ad24d..6d79970d2d 100644 --- a/src/wf_utils/WorkflowHelper.nf +++ b/src/wf_utils/WorkflowHelper.nf @@ -2,33 +2,6 @@ // VDSL3 helper functions // //////////////////////////// -// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgumentGroup.nf' -def _processArgumentGroup(argumentGroups, name, arguments) { - def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() - - // Check if 'arguments' is in 'argumentGroups'. - def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} - - // Check whether an argument group of 'name' exists. - def existing = argumentGroups.find{gr -> name == gr.name} - - // if there are no arguments missing from the argument group, just return the existing group (if any) - if (argumentsNotInGroup.isEmpty()) { - return existing == null ? [] : [existing] - - // if there are missing arguments and there is an existing group, add the missing arguments to it - } else if (existing != null) { - def newEx = existing.clone() - newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) - return [newEx] - - // else create a new group - } else { - def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] - return [newEx] - } -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgument.nf' def _processArgument(arg) { arg.multiple = arg.multiple != null ? arg.multiple : false @@ -81,6 +54,33 @@ def _processArgument(arg) { arg } +// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgumentGroup.nf' +def _processArgumentGroup(argumentGroups, name, arguments) { + def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() + + // Check if 'arguments' is in 'argumentGroups'. + def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} + + // Check whether an argument group of 'name' exists. + def existing = argumentGroups.find{gr -> name == gr.name} + + // if there are no arguments missing from the argument group, just return the existing group (if any) + if (argumentsNotInGroup.isEmpty()) { + return existing == null ? [] : [existing] + + // if there are missing arguments and there is an existing group, add the missing arguments to it + } else if (existing != null) { + def newEx = existing.clone() + newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) + return [newEx] + + // else create a new group + } else { + def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] + return [newEx] + } +} + // helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/processInputsOutputs.nf' def typeCheck(String stage, Map par, Object value, String id, String key) { // expectedClass will only be != null if value is not of the expected type @@ -112,7 +112,7 @@ def typeCheck(String stage, Map par, Object value, String id, String key) { value = value.toLong() } expectedClass = value instanceof Long ? null : "Long" - } else if (par.type == "boolean") { + } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { expectedClass = value instanceof Boolean ? null : "Boolean" } else if (par.type == "file") { if (stage == "output" || par.direction == "input") { @@ -180,6 +180,120 @@ Map processOutputs(Map outputs, Map config, String id, String key) { return outputs } +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/IDChecker.nf' +class IDChecker { + final def items = [] as Set + + @groovy.transform.WithWriteLock + boolean observe(String item) { + if (items.contains(item)) { + return false + } else { + items << item + return true + } + } + + @groovy.transform.WithReadLock + boolean contains(String item) { + return items.contains(item) + } + + @groovy.transform.WithReadLock + Set getItems() { + return items.clone() + } +} +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_checkUniqueIds.nf' + +/** + * Check if the ids are unique across parameter sets + * + * @param parameterSets a list of parameter sets. + */ +private void _checkUniqueIds(List>> parameterSets) { + def ppIds = parameterSets.collect{it[0]} + assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_getChild.nf' + +// helper functions for reading params from file // +def _getChild(parent, child) { + if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { + child + } else { + def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() + parentAbsolute.replaceAll('/[^/]*$', "/") + child + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_guessParamListFormat.nf' + +def _guessParamListFormat(params) { + if (!params.containsKey("param_list") || params.param_list == null) { + "none" + } else { + def param_list = params.param_list + + if (param_list !instanceof String) { + "asis" + } else if (param_list.endsWith(".csv")) { + "csv" + } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { + "json" + } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { + "yaml" + } else { + "yaml_blob" + } + } +} + +// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf' +/** + * Split parameters for arguments that accept multiple values using their separator + * + * @param paramList A Map containing parameters to split. + * @param config A Map of the Viash configuration. This Map can be generated from the config file + * using the readConfig() function. + * + * @return A Map of parameters where the parameter values have been split into a list using + * their seperator. + */ +Map _splitParams(Map parValues, Map config){ + def parsedParamValues = parValues.collectEntries { parName, parValue -> + def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) + + if (!parameterSettings) { + // if argument is not found, do not alter + return [parName, parValue] + } + if (parameterSettings.multiple) { // Check if parameter can accept multiple values + if (parValue instanceof Collection) { + parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } + } else if (parValue instanceof String) { + parValue = parValue.split(parameterSettings.multiple_sep) + } else if (parValue == null) { + parValue = [] + } else { + parValue = [ parValue ] + } + parValue = parValue.flatten() + } + // For all parameters check if multiple values are only passed for + // arguments that allow it. Quietly simplify lists of length 1. + if (!parameterSettings.multiple && parValue instanceof Collection) { + assert parValue.size() == 1 : + "Error: argument ${parName} has too many values.\n" + + " Expected amount: 1. Found: ${parValue.size()}" + parValue = parValue[0] + } + [parName, parValue] + } + return parsedParamValues +} + // helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/applyConfig.nf' /** @@ -493,18 +607,6 @@ def channelFromParams(Map params, Map config) { return Channel.fromList(processedParams) } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_checkUniqueIds.nf' - -/** - * Check if the ids are unique across parameter sets - * - * @param parameterSets a list of parameter sets. - */ -private void _checkUniqueIds(List>> parameterSets) { - def ppIds = parameterSets.collect{it[0]} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/checkUniqueIds.nf' def checkUniqueIds(Map args) { def stopOnError = args.stopOnError == null ? args.stopOnError : true @@ -523,64 +625,6 @@ def checkUniqueIds(Map args) { return true } } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_getChild.nf' - -// helper functions for reading params from file // -def _getChild(parent, child) { - if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { - child - } else { - def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() - parentAbsolute.replaceAll('/[^/]*$', "/") + child - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_guessParamListFormat.nf' - -def _guessParamListFormat(params) { - if (!params.containsKey("param_list") || params.param_list == null) { - "none" - } else { - def param_list = params.param_list - - if (param_list !instanceof String) { - "asis" - } else if (param_list.endsWith(".csv")) { - "csv" - } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { - "json" - } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { - "yaml" - } else { - "yaml_blob" - } - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/IDChecker.nf' -class IDChecker { - final def items = [] as Set - - @groovy.transform.WithWriteLock - boolean observe(String item) { - if (items.contains(item)) { - return false - } else { - items << item - return true - } - } - - @groovy.transform.WithReadLock - boolean contains(String item) { - return items.contains(item) - } - - @groovy.transform.WithReadLock - Set getItems() { - return items.clone() - } -} // helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/paramsToChannel.nf' def paramsToChannel(params, config) { if (!viashChannelDeprecationWarningPrinted) { @@ -957,60 +1001,17 @@ def safeJoin(targetChannel, sourceChannel, key) { " If the IDs in the output channel differ from the input channel,\n" + " please set `tup[1]._meta.join_id to the original ID.\n" + " Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + - " Unexpected ID in the output channel: '${id}.\n" + + " Unexpected ID in the output channel: '${id}'.\n" + " Example input event: [\"id\", [input: file(...)]],\n" + " Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]" ) } + // TODO: add link to our documentation on how to fix this tup } targetCheck.join(sourceCheck) } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf' -/** - * Split parameters for arguments that accept multiple values using their separator - * - * @param paramList A Map containing parameters to split. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A Map of parameters where the parameter values have been split into a list using - * their seperator. - */ -Map _splitParams(Map parValues, Map config){ - def parsedParamValues = parValues.collectEntries { parName, parValue -> - def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) - - if (!parameterSettings) { - // if argument is not found, do not alter - return [parName, parValue] - } - if (parameterSettings.multiple) { // Check if parameter can accept multiple values - if (parValue instanceof Collection) { - parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } - } else if (parValue instanceof String) { - parValue = parValue.split(parameterSettings.multiple_sep) - } else if (parValue == null) { - parValue = [] - } else { - parValue = [ parValue ] - } - parValue = parValue.flatten() - } - // For all parameters check if multiple values are only passed for - // arguments that allow it. Quietly simplify lists of length 1. - if (!parameterSettings.multiple && parValue instanceof Collection) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] - } - [parName, parValue] - } - return parsedParamValues -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/viashChannel.nf' def viashChannel(params, config) { @@ -1338,7 +1339,7 @@ def _findBuildYamlFile(path) { // get the root of the target folder def getRootDir() { - def dir = _findBuildYamlFile(projectDir.toAbsolutePath()) + def dir = _findBuildYamlFile(moduleDir.normalize()) assert dir != null: "Could not find .build.yaml in the folder structure" dir.getParent() } @@ -1438,12 +1439,6 @@ def readCsv(file_path) { output } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJsonBlob.nf' -def readJsonBlob(str) { - def jsonSlurper = new groovy.json.JsonSlurper() - jsonSlurper.parseText(str) -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJson.nf' def readJson(file_path) { def inputFile = file_path !instanceof Path ? file(file_path) : file_path @@ -1451,6 +1446,12 @@ def readJson(file_path) { jsonSlurper.parse(inputFile) } +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJsonBlob.nf' +def readJsonBlob(str) { + def jsonSlurper = new groovy.json.JsonSlurper() + jsonSlurper.parseText(str) +} + // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readTaggedYaml.nf' // Custom constructor to modify how certain objects are parsed from YAML class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { @@ -1481,12 +1482,6 @@ def readTaggedYaml(Path path) { return yaml.load(path.text) } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYamlBlob.nf' -def readYamlBlob(str) { - def yamlSlurper = new org.yaml.snakeyaml.Yaml() - yamlSlurper.load(str) -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYaml.nf' def readYaml(file_path) { def inputFile = file_path !instanceof Path ? file(file_path) : file_path @@ -1494,8 +1489,14 @@ def readYaml(file_path) { yamlSlurper.load(inputFile) } +// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYamlBlob.nf' +def readYamlBlob(str) { + def yamlSlurper = new org.yaml.snakeyaml.Yaml() + yamlSlurper.load(str) +} + // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toJsonBlob.nf' -String toJsonBlob(Map data) { +String toJsonBlob(data) { return groovy.json.JsonOutput.toJson(data) } @@ -1503,20 +1504,33 @@ String toJsonBlob(Map data) { // Custom representer to modify how certain objects are represented in YAML class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { class RepresentPath implements org.yaml.snakeyaml.representer.Represent { + public String getFileName(Object obj) { + if (obj instanceof Path) { + def file = (Path) obj; + return file.getFileName().toString(); + } else if (obj instanceof File) { + def file = (File) obj; + return file.getName(); + } else { + throw new IllegalArgumentException("Object: " + obj + " is not a Path or File"); + } + } + public org.yaml.snakeyaml.nodes.Node representData(Object data) { - Path file = (Path) data; - String value = file.getFileName(); + String filename = getFileName(data); def tag = new org.yaml.snakeyaml.nodes.Tag("!file"); - return representScalar(tag, value); + return representScalar(tag, filename); } } CustomRepresenter(org.yaml.snakeyaml.DumperOptions options) { super(options) + this.representers.put(sun.nio.fs.UnixPath, new RepresentPath()) this.representers.put(Path, new RepresentPath()) + this.representers.put(File, new RepresentPath()) } } -String toTaggedYamlBlob(Map data) { +String toTaggedYamlBlob(data) { def options = new org.yaml.snakeyaml.DumperOptions() options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) def representer = new CustomRepresenter(options) @@ -1525,7 +1539,7 @@ String toTaggedYamlBlob(Map data) { } // helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toYamlBlob.nf' -String toYamlBlob(Map data) { +String toYamlBlob(data) { def options = new org.yaml.snakeyaml.DumperOptions() options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) options.setPrettyFlow(true) @@ -1697,6 +1711,8 @@ def collectInputOutputPaths(obj, prefix) { def publishStates(Map args) { def key_ = args.get("key") + + assert key_ != null : "publishStates: key must be specified" workflow publishStatesWf { take: input_ch @@ -1762,8 +1778,11 @@ process publishStatesProc { // this assumes that the state contains no other values other than those specified in the config def publishStatesByConfig(Map args) { - def key_ = args.get("key") def config = args.get("config") + assert config != null : "publishStatesByConfig: config must be specified" + + def key_ = args.get("key", config.functionality.name) + assert key_ != null : "publishStatesByConfig: key must be specified" workflow publishStatesSimpleWf { take: input_ch @@ -2508,324 +2527,6 @@ def _processToState(toState, key_, config_) { return toState } -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/vdsl3ProcessFactory.nf' -// depends on: thisConfig, thisScript, session? -def vdsl3ProcessFactory(Map workflowArgs) { - // autodetect process key - def wfKey = workflowArgs["key"] - def procKeyPrefix = "${wfKey}_process" - def meta = nextflow.script.ScriptMeta.current() - def existing = meta.getProcessNames().findAll{it.startsWith(procKeyPrefix)} - def numbers = existing.collect{it.replace(procKeyPrefix, "0").toInteger()} - def newNumber = (numbers + [-1]).max() + 1 - - def procKey = newNumber == 0 ? procKeyPrefix : "$procKeyPrefix$newNumber" - - if (newNumber > 0) { - log.warn "Key for module '${wfKey}' is duplicated.\n", - "If you run a component multiple times in the same workflow,\n" + - "it's recommended you set a unique key for every call,\n" + - "for example: ${wfKey}.run(key: \"foo\")." - } - - // subset directives and convert to list of tuples - def drctv = workflowArgs.directives - - // TODO: unit test the two commands below - // convert publish array into tags - def valueToStr = { val -> - // ignore closures - if (val instanceof CharSequence) { - if (!val.matches('^[{].*[}]$')) { - '"' + val + '"' - } else { - val - } - } else if (val instanceof List) { - "[" + val.collect{valueToStr(it)}.join(", ") + "]" - } else if (val instanceof Map) { - "[" + val.collect{k, v -> k + ": " + valueToStr(v)}.join(", ") + "]" - } else { - val.inspect() - } - } - - // multiple entries allowed: label, publishdir - def drctvStrs = drctv.collect { key, value -> - if (key in ["label", "publishDir"]) { - value.collect{ val -> - if (val instanceof Map) { - "\n$key " + val.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") - } else if (val == null) { - "" - } else { - "\n$key " + valueToStr(val) - } - }.join() - } else if (value instanceof Map) { - "\n$key " + value.collect{ k, v -> k + ": " + valueToStr(v) }.join(", ") - } else { - "\n$key " + valueToStr(value) - } - }.join() - - def inputPaths = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "input" } - .collect { ', path(viash_par_' + it.plainName + ', stageAs: "_viash_par/' + it.plainName + '_?/*")' } - .join() - - def outputPaths = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "output" } - .collect { par -> - // insert dummy into every output (see nextflow-io/nextflow#2678) - if (!par.multiple) { - ', path{[".exitcode", args.' + par.plainName + ']}' - } else { - ', path{[".exitcode"] + args.' + par.plainName + '}' - } - } - .join() - - // TODO: move this functionality somewhere else? - if (workflowArgs.auto.transcript) { - outputPaths = outputPaths + ', path{[".exitcode", ".command*"]}' - } else { - outputPaths = outputPaths + ', path{[".exitcode"]}' - } - - // create dirs for output files (based on BashWrapper.createParentFiles) - def createParentStr = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "output" && it.create_parent } - .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"mkdir_parent \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"] : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" - } - .join("\n") - - // construct inputFileExports - def inputFileExports = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction.toLowerCase() == "input" } - .collect { par -> - viash_par_contents = "(viash_par_${par.plainName} instanceof List ? viash_par_${par.plainName}.join(\"${par.multiple_sep}\") : viash_par_${par.plainName})" - "\n\${viash_par_${par.plainName}.empty ? \"\" : \"export VIASH_PAR_${par.plainName.toUpperCase()}=\\\"\" + ${viash_par_contents} + \"\\\"\"}" - } - - // NOTE: if using docker, use /tmp instead of tmpDir! - def tmpDir = java.nio.file.Paths.get( - System.getenv('NXF_TEMP') ?: - System.getenv('VIASH_TEMP') ?: - System.getenv('VIASH_TMPDIR') ?: - System.getenv('VIASH_TEMPDIR') ?: - System.getenv('VIASH_TMP') ?: - System.getenv('TEMP') ?: - System.getenv('TMPDIR') ?: - System.getenv('TEMPDIR') ?: - System.getenv('TMP') ?: - '/tmp' - ).toAbsolutePath() - - // construct stub - def stub = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "output" } - .collect { par -> - "\${ args.containsKey(\"${par.plainName}\") ? \"touch2 \\\"\" + (args[\"${par.plainName}\"] instanceof String ? args[\"${par.plainName}\"].replace(\"_*\", \"_0\") : args[\"${par.plainName}\"].join('\" \"')) + \"\\\"\" : \"\" }" - } - .join("\n") - - // escape script - def escapedScript = thisScript.replace('\\', '\\\\').replace('$', '\\$').replace('"""', '\\"\\"\\"') - - // publishdir assert - def assertStr = (workflowArgs.auto.publish == true) || workflowArgs.auto.transcript ? - """\nassert task.publishDir.size() > 0: "if auto.publish is true, params.publish_dir needs to be defined.\\n Example: --publish_dir './output/'" """ : - "" - - // generate process string - def procStr = - """nextflow.enable.dsl=2 - | - |process $procKey {$drctvStrs - |input: - | tuple val(id)$inputPaths, val(args), path(resourcesDir, stageAs: ".viash_meta_resources") - |output: - | tuple val("\$id")$outputPaths, optional: true - |stub: - |\"\"\" - |touch2() { mkdir -p "\\\$(dirname "\\\$1")" && touch "\\\$1" ; } - |$stub - |\"\"\" - |script:$assertStr - |def escapeText = { s -> s.toString().replaceAll('([`"])', '\\\\\\\\\$1') } - |def parInject = args - | .findAll{key, value -> value != null} - | .collect{key, value -> "export VIASH_PAR_\${key.toUpperCase()}=\\\"\${escapeText(value)}\\\""} - | .join("\\n") - |\"\"\" - |# meta exports - |# export VIASH_META_RESOURCES_DIR="\${resourcesDir.toRealPath().toAbsolutePath()}" - |export VIASH_META_RESOURCES_DIR="\${resourcesDir}" - |export VIASH_META_TEMP_DIR="${['docker', 'podman', 'charliecloud'].any{ it == workflow.containerEngine } ? '/tmp' : tmpDir}" - |export VIASH_META_FUNCTIONALITY_NAME="${thisConfig.functionality.name}" - |# export VIASH_META_EXECUTABLE="\\\$VIASH_META_RESOURCES_DIR/\\\$VIASH_META_FUNCTIONALITY_NAME" - |export VIASH_META_CONFIG="\\\$VIASH_META_RESOURCES_DIR/.config.vsh.yaml" - |\${task.cpus ? "export VIASH_META_CPUS=\$task.cpus" : "" } - |\${task.memory?.bytes != null ? "export VIASH_META_MEMORY_B=\$task.memory.bytes" : "" } - |if [ ! -z \\\${VIASH_META_MEMORY_B+x} ]; then - | export VIASH_META_MEMORY_KB=\\\$(( (\\\$VIASH_META_MEMORY_B+1023) / 1024 )) - | export VIASH_META_MEMORY_MB=\\\$(( (\\\$VIASH_META_MEMORY_KB+1023) / 1024 )) - | export VIASH_META_MEMORY_GB=\\\$(( (\\\$VIASH_META_MEMORY_MB+1023) / 1024 )) - | export VIASH_META_MEMORY_TB=\\\$(( (\\\$VIASH_META_MEMORY_GB+1023) / 1024 )) - | export VIASH_META_MEMORY_PB=\\\$(( (\\\$VIASH_META_MEMORY_TB+1023) / 1024 )) - |fi - | - |# meta synonyms - |export VIASH_TEMP="\\\$VIASH_META_TEMP_DIR" - |export TEMP_DIR="\\\$VIASH_META_TEMP_DIR" - | - |# create output dirs if need be - |function mkdir_parent { - | for file in "\\\$@"; do - | mkdir -p "\\\$(dirname "\\\$file")" - | done - |} - |$createParentStr - | - |# argument exports${inputFileExports.join()} - |\$parInject - | - |# process script - |${escapedScript} - |\"\"\" - |} - |""".stripMargin() - - // TODO: print on debug - // if (workflowArgs.debug == true) { - // println("######################\n$procStr\n######################") - // } - - // create runtime process - def ownerParams = new nextflow.script.ScriptBinding.ParamsMap() - def binding = new nextflow.script.ScriptBinding().setParams(ownerParams) - def module = new nextflow.script.IncludeDef.Module(name: procKey) - def scriptParser = new nextflow.script.ScriptParser(session) - .setModule(true) - .setBinding(binding) - scriptParser.scriptPath = meta.getScriptPath() - def moduleScript = scriptParser.runScript(procStr) - .getScript() - - // register module in meta - meta.addModule(moduleScript, module.name, module.alias) - - // retrieve and return process from meta - return meta.getProcess(procKey) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/vdsl3WorkflowFactory.nf' -// depends on: thisConfig, resourcesDir -def vdsl3WorkflowFactory(Map args) { - def key = args["key"] - def processObj = null - - workflow processWf { - take: input_ - main: - - if (processObj == null) { - processObj = vdsl3ProcessFactory(args) - } - - output_ = input_ - | map { tuple -> - def id = tuple[0] - def data_ = tuple[1] - - if (workflow.stubRun) { - // add id if missing - data_ = [id: 'stub'] + data_ - } - - // process input files separately - def inputPaths = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "input" } - .collect { par -> - def val = data_.containsKey(par.plainName) ? data_[par.plainName] : [] - def inputFiles = [] - if (val == null) { - inputFiles = [] - } else if (val instanceof List) { - inputFiles = val - } else if (val instanceof Path) { - inputFiles = [ val ] - } else { - inputFiles = [] - } - if (!workflow.stubRun) { - // throw error when an input file doesn't exist - inputFiles.each{ file -> - assert file.exists() : - "Error in module '${key}' id '${id}' argument '${par.plainName}'.\n" + - " Required input file does not exist.\n" + - " Path: '$file'.\n" + - " Expected input file to exist" - } - } - inputFiles - } - - // remove input files - def argsExclInputFiles = thisConfig.functionality.allArguments - .findAll { (it.type != "file" || it.direction != "input") && data_.containsKey(it.plainName) } - .collectEntries { par -> - def parName = par.plainName - def val = data_[parName] - if (par.multiple && val instanceof Collection) { - val = val.join(par.multiple_sep) - } - if (par.direction == "output" && par.type == "file") { - val = val.replaceAll('\\$id', id).replaceAll('\\$key', key) - } - [parName, val] - } - - [ id ] + inputPaths + [ argsExclInputFiles, resourcesDir ] - } - | processObj - | map { output -> - def outputFiles = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "output" } - .indexed() - .collectEntries{ index, par -> - out = output[index + 1] - // strip dummy '.exitcode' file from output (see nextflow-io/nextflow#2678) - if (!out instanceof List || out.size() <= 1) { - if (par.multiple) { - out = [] - } else { - assert !par.required : - "Error in module '${key}' id '${output[0]}' argument '${par.plainName}'.\n" + - " Required output file is missing" - out = null - } - } else if (out.size() == 2 && !par.multiple) { - out = out[1] - } else { - out = out.drop(1) - } - [ par.plainName, out ] - } - - // drop null outputs - outputFiles.removeAll{it.value == null} - - [ output[0], outputFiles ] - } - emit: output_ - } - - return processWf -} - // helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf' def _debug(workflowArgs, debugKey) { if (workflowArgs.debug) { From b3ee8c236dbeb6116280484837d1d931ac8797a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michaela=20M=C3=BCller?= <51025211+mumichae@users.noreply.github.com> Date: Wed, 4 Oct 2023 15:25:58 +0200 Subject: [PATCH 1008/1233] add rliger and pyliger code (#232) * add rliger and pyliger code * simplify rliger method * fix pyliger method * overwrite gene selection for liger with all genes --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 3e8ca3ffdb50238962a5372a79ebeaa678999fa0 --- .../methods/liger/config.vsh.yaml | 28 +++++++ .../batch_integration/methods/liger/script.R | 82 +++++++++++++++++++ .../methods/pyliger/config.vsh.yaml | 34 ++++++++ .../methods/pyliger/script.py | 72 ++++++++++++++++ 4 files changed, 216 insertions(+) create mode 100644 src/tasks/batch_integration/methods/liger/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/liger/script.R create mode 100644 src/tasks/batch_integration/methods/pyliger/config.vsh.yaml create mode 100644 src/tasks/batch_integration/methods/pyliger/script.py diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml new file mode 100644 index 0000000000..dc52786129 --- /dev/null +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -0,0 +1,28 @@ +# use method api spec +__merge__: ../../api/comp_method_embedding.yaml +functionality: + name: liger + info: + label: LIGER + summary: Linked Inference of Genomic Experimental Relationships + description: | + LIGER or linked inference of genomic experimental relationships uses iNMF + deriving and implementing a novel coordinate descent algorithm to efficiently + do the factorization. Joint clustering is performed and factor loadings are + normalised. + reference: welch2019 + repository_url: https://github.com/welch-lab/liger + documentation_url: https://github.com/welch-lab/liger + preferred_normalization: log_cpm + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.1 + setup: + - type: r + cran: rliger + - type: nextflow + directives: + label: [ lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/liger/script.R b/src/tasks/batch_integration/methods/liger/script.R new file mode 100644 index 0000000000..be9f6351e5 --- /dev/null +++ b/src/tasks/batch_integration/methods/liger/script.R @@ -0,0 +1,82 @@ +cat(">> Load dependencies\n") +requireNamespace("anndata", quietly = TRUE) +requireNamespace("rliger", quietly = TRUE) + +## VIASH START +par <- list( + input = "resources_test/batch_integration/pancreas/dataset.h5ad", + output = "output.h5ad" +) +meta <- list( + functionality_name = "liger" +) +## VIASH END + +cat("Read input\n") +adata <- anndata::read_h5ad(par$input) + +anndataToLiger <- function(adata) { + # fetch batch names + batch <- adata$obs$batch + batch_names <- as.character(unique(batch)) + + # restructure data + raw_data <- lapply(batch_names, function(batch_name) { + Matrix::t(adata$layers[["counts"]][batch == batch_name, , drop = FALSE]) + }) + names(raw_data) <- batch_names + + rliger::createLiger(raw.data = raw_data, remove.missing = FALSE) +} + +addNormalizedDataToLiger <- function(adata, lobj) { + norm_data <- lapply(names(lobj@raw.data), function(name) { + norm <- adata$layers[["normalized"]] + # subset + norm <- norm[ + colnames(lobj@raw.data[[name]]), + rownames(lobj@raw.data[[name]]), + drop = FALSE + ] + # transpose + norm <- Matrix::t(norm) + + # turn into dgcMatrix + as(as(norm, "denseMatrix"), "CsparseMatrix") + }) + names(norm_data) <- names(lobj@raw.data) + + lobj@norm.data <- norm_data + + lobj +} + +cat(">> Create Liger Data object\n") +lobj <- anndataToLiger(adata) + +cat(">> Normalize data\n") +lobj <- addNormalizedDataToLiger(adata, lobj) + +# could also use the rliger normalization instead +# lobj <- rliger::normalize(lobj) + +cat(">> Select genes\n") +# lobj <- rliger::selectGenes(lobj) +# overwrite gene selection to include all genes +lobj@var.genes <- adata$var_names + +cat(">> Perform scaling\n") +lobj <- rliger::scaleNotCenter(lobj, remove.missing = FALSE) + +cat(">> Joint Matrix Factorization\n") +lobj <- rliger::optimizeALS(lobj, k = 20) + +cat(">> Quantile normalization\n") +lobj <- rliger::quantile_norm(lobj) + +cat(">> Store dimred in adata\n") +adata$obsm[["X_emb"]] <- lobj@H.norm[rownames(adata), , drop = FALSE] +adata$uns[["method_id"]] <- meta$functionality_name + +cat(">> Write AnnData to disk\n") +zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml new file mode 100644 index 0000000000..acf3e2f83d --- /dev/null +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -0,0 +1,34 @@ +# use method api spec +__merge__: ../../api/comp_method_embedding.yaml +functionality: + name: pyliger + info: + label: pyliger + summary: Python implementation of LIGER (Linked Inference of Genomic Experimental Relationships + description: | + LIGER (installed as rliger) is a package for integrating and analyzing multiple + single-cell datasets, developed by the Macosko lab and maintained/extended by the + Welch lab. It relies on integrative non-negative matrix factorization to identify + shared and dataset-specific factors. + reference: welch2019 + repository_url: https://github.com/welch-lab/pyliger + documentation_url: https://github.com/welch-lab/pyliger + preferred_normalization: log_cpm + variants: + liger_unscaled: + liger_scaled: + preferred_normalization: log_cpm_scaled + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.1 + setup: + - type: python + pypi: + - umap-learn[plot] + - pyliger + - type: nextflow + directives: + label: [ lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/pyliger/script.py b/src/tasks/batch_integration/methods/pyliger/script.py new file mode 100644 index 0000000000..59cb2b895c --- /dev/null +++ b/src/tasks/batch_integration/methods/pyliger/script.py @@ -0,0 +1,72 @@ +import anndata as ad +import numpy as np +import pyliger + +## VIASH START +par = { + 'input': 'resources_test/batch_integration/pancreas/dataset.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'pyliger' +} +## VIASH END + +print('>> Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('>> Prepare data', flush=True) +adata_per_batch = [] +for batch in adata.obs['batch'].unique(): + adb = adata[adata.obs['batch'] == batch].copy() + + # move counts + adb.X = adb.layers['counts'] + del adb.layers['counts'] + + # move normalized data + adb.layers["norm_data"] = adb.layers["normalized"] + del adb.layers["normalized"] + + # save row sum and sum of squares for further use + norm_sum = np.ravel(np.sum(adb.layers["norm_data"], axis=0)) + norm_sum_sq = np.ravel(np.sum(adb.layers["norm_data"].power(2), axis=0)) + adb.var["norm_sum"] = norm_sum + adb.var["norm_sum_sq"] = norm_sum_sq + adb.var["norm_mean"] = norm_sum / adb.shape[0] + + # set more metadata + adb.obs.index.name = 'cell_barcode' + adb.var.index.name = 'gene_id' + adb.uns['sample_name'] = batch + + # append to list + adata_per_batch.append(adb) + +print('Create liger object', flush=True) +lobj = pyliger.create_liger( + adata_per_batch, + remove_missing=False +) + +# do not select genes +lobj.var_genes = adata.var_names + +print('>> Scaling', flush=True) +pyliger.scale_not_center(lobj, remove_missing=False) + +print('>> Optimize ALS', flush=True) +pyliger.optimize_ALS(lobj, k=20) + +print('>> Quantile normalization', flush=True) +pyliger.quantile_norm(lobj) + +print('>> Concatenate outputs', flush=True) +ad_out = ad.concat(lobj.adata_list) + +print('>> Store output', flush=True) +adata.obsm['X_emb'] = ad_out[adata.obs_names, :].obsm['H_norm'] +adata.uns['method_id'] = meta['functionality_name'] + +print("Write output to disk", flush=True) +adata.write_h5ad(par['output'], compression='gzip') From 0d4ae99b00ee4a9dcf1085a788657af56e68a4d9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 4 Oct 2023 15:50:30 +0200 Subject: [PATCH 1009/1233] add more methods Former-commit-id: 9f7f899bdeefa44318d9a79c02b704baa8b1e605 --- .../workflows/run_benchmark/main.nf | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 76053a23aa..ed032b0acf 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -8,8 +8,17 @@ include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/ma // import methods include { bbknn } from "$targetDir/batch_integration/methods/bbknn/main.nf" include { combat } from "$targetDir/batch_integration/methods/combat/main.nf" +include { fastmnn_embedding } from "$targetDir/batch_integration/methods/fastmnn_embedding/main.nf" +include { fastmnn_feature } from "$targetDir/batch_integration/methods/fastmnn_feature/main.nf" +include { liger } from "$targetDir/batch_integration/methods/liger/main.nf" +include { mnn_correct } from "$targetDir/batch_integration/methods/mnn_correct/main.nf" +include { mnnpy } from "$targetDir/batch_integration/methods/mnnpy/main.nf" +include { pyliger } from "$targetDir/batch_integration/methods/pyliger/main.nf" +include { scalex_embed } from "$targetDir/batch_integration/methods/scalex_embed/main.nf" +include { scalex_feature } from "$targetDir/batch_integration/methods/scalex_feature/main.nf" include { scanorama_embed } from "$targetDir/batch_integration/methods/scanorama_embed/main.nf" include { scanorama_feature } from "$targetDir/batch_integration/methods/scanorama_feature/main.nf" +include { scanvi } from "$targetDir/batch_integration/methods/scanvi/main.nf" include { scvi } from "$targetDir/batch_integration/methods/scvi/main.nf" // import control methods @@ -52,8 +61,17 @@ traces = collectTraces() methods = [ bbknn, combat, + fastmnn_embedding, + fastmnn_feature, + liger, + mnn_correct, + mnnpy, + pyliger, + scalex_embed, + scalex_feature, scanorama_embed, scanorama_feature, + scanvi, scvi, no_integration_batch, random_embed_cell, From 22112bb78d4efaeccb8e77a478197aab55933f48 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 4 Oct 2023 16:58:41 +0200 Subject: [PATCH 1010/1233] fix configs Former-commit-id: adb47c7601ec22c56e2e1b1c6919a523d5ba2023 --- .../batch_integration/methods/fastmnn_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/liger/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/pyliger/config.vsh.yaml | 4 ++-- .../batch_integration/methods/scalex_embed/config.vsh.yaml | 4 ++-- .../batch_integration/methods/scalex_feature/config.vsh.yaml | 4 ++-- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 2 +- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index 5a4fe19f9e..c82466c677 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: reference: "haghverdi2018batch" repository_url: "https://code.bioconductor.org/browse/batchelor/" documentation_url: "https://bioconductor.org/packages/batchelor/" - preferred_normalization: log_cpm + preferred_normalization: log_cp10k v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/fastmnn.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index dc52786129..5ce057ee53 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: reference: welch2019 repository_url: https://github.com/welch-lab/liger documentation_url: https://github.com/welch-lab/liger - preferred_normalization: log_cpm + preferred_normalization: log_cp10k resources: - type: r_script path: script.R diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index acf3e2f83d..b3a09a5e2a 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -13,11 +13,11 @@ functionality: reference: welch2019 repository_url: https://github.com/welch-lab/pyliger documentation_url: https://github.com/welch-lab/pyliger - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: liger_unscaled: liger_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index ebc34650c5..6b82d97489 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -24,11 +24,11 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: scalex_feature_unscaled: scanorama_feature_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 75933e04d1..3711f3975e 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -25,11 +25,11 @@ functionality: v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scalex.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cpm + preferred_normalization: log_cp10k variants: scalex_feature_unscaled: scanorama_feature_scaled: - preferred_normalization: log_cpm_scaled + preferred_normalization: log_cp10k_scaled resources: - type: python_script path: script.py diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index 20f1bc1aaa..82ec6690fb 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -6,7 +6,7 @@ functionality: description: | Single Cell Optimal Transport (SCOT) is a method for integrating multimodal single-cell data. It is based on the idea of aligning the distributions of the two modalities using optimal transport. summary: "Run Single Cell Optimal Transport" - preferred_normalization: "log_cpm" + preferred_normalization: "log_cp10k" reference: Demetci2020scot documentation_url: "https://github.com/rsinghlab/SCOT#readme" repository_url: "https://github.com/rsinghlab/SCOT" From 224170462b05cc996a499227d501b5cf03b1070c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 5 Oct 2023 14:29:55 +0200 Subject: [PATCH 1011/1233] Viash 0.8.x (#242) * changes for upcoming viash 0.8.0 release * switch to rc1 * update batch_integration * update denoising * update dimensionality_reduction * update dim_red config file * update label_projection * update predict_modality * update match_modalities * remove general workflow * split workflows batch_integration * update multmodal dataset workflow * readd auto wf in batch integration * undo findStates changes * use run_wf instead of run_benchmark * add joinStates * update viash_version * add time directive * update base image * set torch to <2.1 --------- Co-authored-by: Kai Waldrant Former-commit-id: 957d08c57d40382f21515e2fecb1ea6654506561 --- _viash.yaml | 2 +- nextflow.config | 5 + .../resource_scripts/openproblems_v1.sh | 5 +- .../process_openproblems_v1/config.vsh.yaml | 12 ++ .../workflows/process_openproblems_v1/main.nf | 40 +---- .../config.vsh.yaml | 11 ++ .../main.nf | 41 +---- .../methods/fastmnn_embedding/config.vsh.yaml | 2 +- .../methods/fastmnn_feature/config.vsh.yaml | 2 +- .../methods/liger/config.vsh.yaml | 2 +- .../methods/mnn_correct/config.vsh.yaml | 2 +- .../methods/pyliger/config.vsh.yaml | 2 +- .../methods/scalex_embed/config.vsh.yaml | 5 +- .../methods/scalex_feature/config.vsh.yaml | 5 +- .../process_datasets/config.vsh.yaml | 4 + .../workflows/process_datasets/main.nf | 23 --- .../workflows/run_benchmark/config.vsh.yaml | 35 ++++ .../workflows/run_benchmark/main.nf | 170 +++++++----------- .../workflows/run_benchmark/run_nextflow.sh | 27 --- .../workflows/run_benchmark/run_test.sh | 30 ++++ .../denoising/workflows/run/config.vsh.yaml | 12 ++ src/tasks/denoising/workflows/run/main.nf | 70 ++------ .../workflows/run/config.vsh.yaml | 16 ++ .../workflows/run/main.nf | 76 +++----- .../workflows/run/config.vsh.yaml | 15 ++ .../label_projection/workflows/run/main.nf | 86 +++------ .../workflows/run/config.vsh.yaml | 12 ++ .../match_modalities/workflows/run/main.nf | 77 ++------ .../workflows/run/config.vsh.yaml | 15 ++ .../predict_modality/workflows/run/main.nf | 84 +++------ 30 files changed, 344 insertions(+), 544 deletions(-) delete mode 100755 src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh create mode 100755 src/tasks/batch_integration/workflows/run_benchmark/run_test.sh diff --git a/_viash.yaml b/_viash.yaml index 41872d9f1b..05830699c4 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.7.5 +viash_version: 0.8.0-RC2 source: src target: target diff --git a/nextflow.config b/nextflow.config index ac14c601b7..0fb77d8756 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,3 +1,8 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } + +includeConfig("./src/wf_utils/ProfilesHelper.config") +includeConfig("./src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index d7cd99be44..af9ed202ab 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -151,9 +151,8 @@ HERE fi export NXF_VER=23.04.2 -nextflow \ - run . \ - -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ -profile docker \ -resume \ -params-file "$params_file" \ diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index b37ffbaa19..6cc183b9f0 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -168,6 +168,18 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: datasets/loaders/openproblems_v1 + - name: datasets/normalization/log_cp + - name: datasets/normalization/log_scran_pooling + - name: datasets/normalization/sqrt_cp + - name: datasets/normalization/l1_sqrt + - name: datasets/processors/subsample + - name: datasets/processors/pca + - name: datasets/processors/hvg + - name: datasets/processors/knn + - name: common/check_dataset_schema # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 1310dae61f..cad55c7f5f 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -1,50 +1,14 @@ -nextflow.enable.dsl=2 - -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -// dataset loaders -include { openproblems_v1 } from "$targetDir/datasets/loaders/openproblems_v1/main.nf" - -// normalization methods -include { log_cp } from "$targetDir/datasets/normalization/log_cp/main.nf" -include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" -include { sqrt_cp } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" -include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" - -// dataset processors -include { subsample } from "$targetDir/datasets/processors/subsample/main.nf" -include { pca } from "$targetDir/datasets/processors/pca/main.nf" -include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" -include { knn } from "$targetDir/datasets/processors/knn/main.nf" -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" - -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = collectTraces() -normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] - -workflow { - helpMessage(config) - - channelFromParams(params, config) - | run_wf - | publishStates([:]) -} - workflow run_wf { take: input_ch main: + normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] + dataset_ch = input_ch - | preprocessInputs(config: config) // fetch data from legacy openproblems | openproblems_v1.run( diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 54e86a7b1e..04bb8e06e1 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -123,6 +123,17 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: datasets/loaders/openproblems_v1_multimodal + - name: datasets/normalization/log_cp + - name: datasets/normalization/log_scran_pooling + - name: datasets/normalization/sqrt_cp + - name: datasets/normalization/l1_sqrt + - name: datasets/processors/subsample + - name: datasets/processors/svd + - name: datasets/processors/hvg + - name: common/check_dataset_schema # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index b1e0ddf0ab..3920e45aa8 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -1,49 +1,16 @@ -nextflow.enable.dsl=2 - -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -// dataset loaders -include { openproblems_v1_multimodal } from "$targetDir/datasets/loaders/openproblems_v1_multimodal/main.nf" - -// normalization methods -include { log_cp } from "$targetDir/datasets/normalization/log_cp/main.nf" -include { log_scran_pooling } from "$targetDir/datasets/normalization/log_scran_pooling/main.nf" -include { sqrt_cp } from "$targetDir/datasets/normalization/sqrt_cp/main.nf" -include { l1_sqrt } from "$targetDir/datasets/normalization/l1_sqrt/main.nf" - -// dataset processors -include { subsample } from "$targetDir/datasets/processors/subsample/main.nf" -include { svd } from "$targetDir/datasets/processors/svd/main.nf" -include { hvg } from "$targetDir/datasets/processors/hvg/main.nf" -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" - -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] - -workflow { - helpMessage(config) - - channelFromParams(params, config) - | run_wf - | publishStates([:]) -} - workflow run_wf { take: input_ch main: + + normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] + + dataset_ch = input_ch - | preprocessInputs(config: config) // fetch data from legacy openproblems | openproblems_v1_multimodal.run( diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index 73804df050..3a06155602 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: ../fastmnn_feature/script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index c82466c677..d45d828008 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: # - type: r # bioc: batchelor diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index 5ce057ee53..60494ca364 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -25,4 +25,4 @@ platforms: cran: rliger - type: nextflow directives: - label: [ lowcpu, highmem ] + label: [ lowcpu, highmem, midtime ] diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 4d13027ce3..7cbf7e82f6 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r bioc: diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index b3a09a5e2a..e1346e1117 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -31,4 +31,4 @@ platforms: - pyliger - type: nextflow directives: - label: [ lowcpu, highmem ] + label: [ lowcpu, highmem, midtime ] diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index 6b82d97489..6ef5a38685 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -34,12 +34,13 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: - scalex - numpy<1.24 + - torch<2.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ lowmem, lowcpu, midtime ] diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 3711f3975e..2592d24390 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -35,12 +35,13 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: - scalex - numpy<1.24 + - torch<2.1 - type: nextflow directives: - label: [ lowmem, lowcpu ] + label: [ lowmem, lowcpu, midtime ] diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index 61a3fbe151..1ee4f4b23d 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -36,5 +36,9 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: batch_integration/process_dataset platforms: - type: nextflow diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index 276f3c1f76..e14bb0f4f5 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -1,25 +1,3 @@ -nextflow.enable.dsl=2 - -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" -include { process_dataset } from "$targetDir/batch_integration/process_dataset/main.nf" - -// import helper functions -include { readConfig; processConfig; helpMessage; channelFromParams; preprocessInputs; readYaml; readJson } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; setState; findStates } from sourceDir + "/wf_utils/WorkflowHelper.nf" - -config = readConfig("$projectDir/config.vsh.yaml") - -workflow { - helpMessage(config) - - channelFromParams(params, config) - | run_wf - | publishStates([:]) -} - workflow auto { findStates(params, config) | run_wf @@ -32,7 +10,6 @@ workflow run_wf { main: output_ch = input_ch - | preprocessInputs(config: config) // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index a2030b92fd..982e77a013 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -28,5 +28,40 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: batch_integration/methods/bbknn + - name: batch_integration/methods/combat + - name: batch_integration/methods/fastmnn_embedding + - name: batch_integration/methods/fastmnn_feature + - name: batch_integration/methods/liger + - name: batch_integration/methods/mnn_correct + - name: batch_integration/methods/mnnpy + - name: batch_integration/methods/pyliger + - name: batch_integration/methods/scalex_embed + - name: batch_integration/methods/scalex_feature + - name: batch_integration/methods/scanorama_embed + - name: batch_integration/methods/scanorama_feature + - name: batch_integration/methods/scanvi + - name: batch_integration/methods/scvi + - name: batch_integration/control_methods/no_integration_batch + - name: batch_integration/control_methods/random_embed_cell + - name: batch_integration/control_methods/random_embed_cell_jitter + - name: batch_integration/control_methods/random_integration + - name: batch_integration/transformers/feature_to_embed + - name: batch_integration/transformers/embed_to_graph + - name: batch_integration/metrics/asw_batch + - name: batch_integration/metrics/asw_label + - name: batch_integration/metrics/cell_cycle_conservation + - name: batch_integration/metrics/clustering_overlap + - name: batch_integration/metrics/graph_connectivity + - name: batch_integration/metrics/hvg_overlap + - name: batch_integration/metrics/isolated_label_asw + - name: batch_integration/metrics/isolated_label_f1 + - name: batch_integration/metrics/kbet + - name: batch_integration/metrics/lisi + - name: batch_integration/metrics/pcr platforms: - type: nextflow diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index ed032b0acf..61a5ede18f 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -1,123 +1,51 @@ -nextflow.enable.dsl=2 - -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import methods -include { bbknn } from "$targetDir/batch_integration/methods/bbknn/main.nf" -include { combat } from "$targetDir/batch_integration/methods/combat/main.nf" -include { fastmnn_embedding } from "$targetDir/batch_integration/methods/fastmnn_embedding/main.nf" -include { fastmnn_feature } from "$targetDir/batch_integration/methods/fastmnn_feature/main.nf" -include { liger } from "$targetDir/batch_integration/methods/liger/main.nf" -include { mnn_correct } from "$targetDir/batch_integration/methods/mnn_correct/main.nf" -include { mnnpy } from "$targetDir/batch_integration/methods/mnnpy/main.nf" -include { pyliger } from "$targetDir/batch_integration/methods/pyliger/main.nf" -include { scalex_embed } from "$targetDir/batch_integration/methods/scalex_embed/main.nf" -include { scalex_feature } from "$targetDir/batch_integration/methods/scalex_feature/main.nf" -include { scanorama_embed } from "$targetDir/batch_integration/methods/scanorama_embed/main.nf" -include { scanorama_feature } from "$targetDir/batch_integration/methods/scanorama_feature/main.nf" -include { scanvi } from "$targetDir/batch_integration/methods/scanvi/main.nf" -include { scvi } from "$targetDir/batch_integration/methods/scvi/main.nf" - -// import control methods -include { no_integration_batch } from "$targetDir/batch_integration/control_methods/no_integration_batch/main.nf" -include { random_embed_cell } from "$targetDir/batch_integration/control_methods/random_embed_cell/main.nf" -include { random_embed_cell_jitter } from "$targetDir/batch_integration/control_methods/random_embed_cell_jitter/main.nf" -include { random_integration } from "$targetDir/batch_integration/control_methods/random_integration/main.nf" - -// import transformers -include { feature_to_embed } from "$targetDir/batch_integration/transformers/feature_to_embed/main.nf" -include { embed_to_graph } from "$targetDir/batch_integration/transformers/embed_to_graph/main.nf" - -// import metrics -include { asw_batch } from "$targetDir/batch_integration/metrics/asw_batch/main.nf" -include { asw_label } from "$targetDir/batch_integration/metrics/asw_label/main.nf" -include { cell_cycle_conservation } from "$targetDir/batch_integration/metrics/cell_cycle_conservation/main.nf" -include { clustering_overlap } from "$targetDir/batch_integration/metrics/clustering_overlap/main.nf" -include { graph_connectivity } from "$targetDir/batch_integration/metrics/graph_connectivity/main.nf" -include { hvg_overlap } from "$targetDir/batch_integration/metrics/hvg_overlap/main.nf" -include { isolated_label_asw } from "$targetDir/batch_integration/metrics/isolated_label_asw/main.nf" -include { isolated_label_f1 } from "$targetDir/batch_integration/metrics/isolated_label_f1/main.nf" -include { kbet } from "$targetDir/batch_integration/metrics/kbet/main.nf" -include { lisi } from "$targetDir/batch_integration/metrics/lisi/main.nf" -include { pcr } from "$targetDir/batch_integration/metrics/pcr/main.nf" - -// tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs; readYaml } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { publishStates; runComponents; collectTraces; writeJson; getPublishDir; findStates; setState } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { joinStates } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = collectTraces() -// collect method list -methods = [ - bbknn, - combat, - fastmnn_embedding, - fastmnn_feature, - liger, - mnn_correct, - mnnpy, - pyliger, - scalex_embed, - scalex_feature, - scanorama_embed, - scanorama_feature, - scanvi, - scvi, - no_integration_batch, - random_embed_cell, - random_embed_cell_jitter, - random_integration -] - -// collect metric list -metrics = [ - asw_batch, - asw_label, - cell_cycle_conservation, - clustering_overlap, - graph_connectivity, - hvg_overlap, - isolated_label_asw, - isolated_label_f1, - kbet, - lisi, - pcr -] - - -workflow { - helpMessage(config) - - channelFromParams(params, config) - | run_wf - | publishStates(key: config.functionality.name) -} - -workflow auto { - findStates(params, config) - | run_wf - | publishStates(key: config.functionality.name) -} - workflow run_wf { take: input_ch main: + // collect method list + methods = [ + bbknn, + combat, + fastmnn_embedding, + fastmnn_feature, + liger, + mnn_correct, + mnnpy, + pyliger, + scalex_embed, + scalex_feature, + scanorama_embed, + scanorama_feature, + scanvi, + scvi, + no_integration_batch, + random_embed_cell, + random_embed_cell_jitter, + random_integration + ] + + // collect metric list + metrics = [ + asw_batch, + asw_label, + cell_cycle_conservation, + clustering_overlap, + graph_connectivity, + hvg_overlap, + isolated_label_asw, + isolated_label_f1, + kbet, + lisi, + pcr + ] + // process input parameter channel dataset_ch = input_ch - | preprocessInputs(config: config) | map { id, state -> def newId = id.replaceAll(/\//, "_") @@ -233,6 +161,12 @@ workflow run_wf { output_ch } +workflow auto { + findStates(params, thisConfig) + | run_wf + | publishStates([key: thisConfig.functionality.name]) +} + // store the trace log in the publish dir workflow.onComplete { def publish_dir = getPublishDir() @@ -241,4 +175,22 @@ workflow.onComplete { // todo: add datasets logging // writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) // writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) +} + +def joinStates(Closure apply_) { + workflow joinStatesWf { + take: input_ch + main: + output_ch = input_ch + | toSortedList + | filter{ it.size() > 0 } + | map{ tups -> + def ids = tups.collect{it[0]} + def states = tups.collect{it[1]} + apply_(ids, states) + } + + emit: output_ch + } + return joinStatesWf } \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh deleted file mode 100755 index 8428b15d90..0000000000 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_nextflow.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# bin/viash_build -q 'batch_integration' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -set -xe - -DATASET_DIR=resources_test/batch_integration - -# run benchmark -export NXF_VER=22.04.5 - - # -profile docker \ -nextflow run . \ - -main-script src/tasks/batch_integration/workflows/run_benchmark/main.nf \ - -profile docker \ - -c src/wf_utils/labels_ci.config \ - -resume \ - --id foo \ - --input_states "$DATASET_DIR/**/state.yaml" \ - --publish_dir "output" \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh new file mode 100755 index 0000000000..b8c6c9ac77 --- /dev/null +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/batch_integration" +OUTPUT_DIR="resources_test/batch_integration/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + --id resources \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run/config.vsh.yaml index c14f308401..cb095012e3 100644 --- a/src/tasks/denoising/workflows/run/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run/config.vsh.yaml @@ -20,5 +20,17 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: denoising/control_methods/no_denoising + - name: denoising/control_methods/perfect_denoising + - name: denoising/methods/alra + - name: denoising/methods/dca + - name: denoising/methods/knn_smoothing + - name: denoising/methods/magic + - name: denoising/metrics/mse + - name: denoising/metrics/poisson platforms: - type: nextflow diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run/main.nf index 0bff9c3fc1..3f37c4dbf8 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run/main.nf @@ -1,66 +1,28 @@ -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import control methods -include { no_denoising } from "$targetDir/denoising/control_methods/no_denoising/main.nf" -include { perfect_denoising } from "$targetDir/denoising/control_methods/perfect_denoising/main.nf" - -// import methods -include { alra } from "$targetDir/denoising/methods/alra/main.nf" -include { dca } from "$targetDir/denoising/methods/dca/main.nf" -include { knn_smoothing } from "$targetDir/denoising/methods/knn_smoothing/main.nf" -include { magic } from "$targetDir/denoising/methods/magic/main.nf" - -// import metrics -include { mse } from "$targetDir/denoising/metrics/mse/main.nf" -include { poisson } from "$targetDir/denoising/metrics/poisson/main.nf" - -// tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -// construct a map of methods (id -> method_module) -methods = [ - no_denoising, - perfect_denoising, - alra, - dca, - knn_smoothing, - magic -] - -metrics = [ - mse, - poisson -] - - -workflow { - helpMessage(config) - - // create channel from input parameters with - // arguments as defined in the config - channelFromParams(params, config) - | run_wf -} - workflow run_wf { take: input_ch main: + // construct a map of methods (id -> method_module) + methods = [ + no_denoising, + perfect_denoising, + alra, + dca, + knn_smoothing, + magic + ] + + metrics = [ + mse, + poisson + ] + + output_ch = input_ch - | preprocessInputs(config: config) // extract the dataset metadata | check_dataset_schema.run( diff --git a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml index 5c7427af0b..88345c3be8 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml @@ -24,6 +24,22 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: dimensionality_reduction/control_methods/random_features + - name: dimensionality_reduction/control_methods/true_features + - name: dimensionality_reduction/methods/densmap + - name: dimensionality_reduction/methods/neuralee + - name: dimensionality_reduction/methods/pca + - name: dimensionality_reduction/methods/phate + - name: dimensionality_reduction/methods/tsne + - name: dimensionality_reduction/methods/umap + - name: dimensionality_reduction/metrics/coranking + - name: dimensionality_reduction/metrics/density_preservation + - name: dimensionality_reduction/metrics/distance_correlation + - name: dimensionality_reduction/metrics/trustworthiness # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run/main.nf index c99a374f56..f6ba9535c6 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run/main.nf @@ -1,60 +1,6 @@ -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import control methods -include { random_features } from "$targetDir/dimensionality_reduction/control_methods/random_features/main.nf" -include { true_features } from "$targetDir/dimensionality_reduction/control_methods/true_features/main.nf" - -// import methods -include { densmap } from "$targetDir/dimensionality_reduction/methods/densmap/main.nf" -// include { ivis } from "$targetDir/dimensionality_reduction/methods/ivis/main.nf" -include { neuralee } from "$targetDir/dimensionality_reduction/methods/neuralee/main.nf" -include { pca } from "$targetDir/dimensionality_reduction/methods/pca/main.nf" -include { phate } from "$targetDir/dimensionality_reduction/methods/phate/main.nf" -include { tsne } from "$targetDir/dimensionality_reduction/methods/tsne/main.nf" -include { umap } from "$targetDir/dimensionality_reduction/methods/umap/main.nf" - -// import metrics -include { coranking } from "$targetDir/dimensionality_reduction/metrics/coranking/main.nf" -include { density_preservation } from "$targetDir/dimensionality_reduction/metrics/density_preservation/main.nf" -include { distance_correlation } from "$targetDir/dimensionality_reduction/metrics/distance_correlation/main.nf" -include { trustworthiness } from "$targetDir/dimensionality_reduction/metrics/trustworthiness/main.nf" - -// convert scores to tsv -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -// read in pipeline config -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -// collect method list -methods = [ - random_features, - true_features, - densmap, - neuralee, - pca, - phate, - tsne, - umap -] - -// collect metric list -metrics = [ - coranking, - density_preservation, - distance_correlation, - trustworthiness -] - workflow { helpMessage(config) @@ -69,8 +15,28 @@ workflow run_wf { input_ch main: + + // collect method list + methods = [ + random_features, + true_features, + densmap, + neuralee, + pca, + phate, + tsne, + umap + ] + + // collect metric list + metrics = [ + coranking, + density_preservation, + distance_correlation, + trustworthiness + ] + output_ch = input_ch - | preprocessInputs(config: config) // extract the dataset metadata | check_dataset_schema.run( diff --git a/src/tasks/label_projection/workflows/run/config.vsh.yaml b/src/tasks/label_projection/workflows/run/config.vsh.yaml index b55bd8de96..df85f2cfea 100644 --- a/src/tasks/label_projection/workflows/run/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run/config.vsh.yaml @@ -32,6 +32,21 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: label_projection/control_methods/true_labels + - name: label_projection/control_methods/majority_vote + - name: label_projection/control_methods/random_labels + - name: label_projection/methods/knn + - name: label_projection/methods/logistic_regression + - name: label_projection/methods/mlp + - name: label_projection/methods/scanvi + - name: label_projection/methods/scanvi_scarches + - name: label_projection/methods/xgboost + - name: label_projection/metrics/accuracy + - name: label_projection/metrics/f1 # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run/main.nf index d1b40d4968..6c212a74c1 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run/main.nf @@ -1,77 +1,33 @@ -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import control methods -include { true_labels } from "$targetDir/label_projection/control_methods/true_labels/main.nf" -include { majority_vote } from "$targetDir/label_projection/control_methods/majority_vote/main.nf" -include { random_labels } from "$targetDir/label_projection/control_methods/random_labels/main.nf" - -// import methods -include { knn } from "$targetDir/label_projection/methods/knn/main.nf" -include { logistic_regression } from "$targetDir/label_projection/methods/logistic_regression/main.nf" -include { mlp } from "$targetDir/label_projection/methods/mlp/main.nf" -include { scanvi } from "$targetDir/label_projection/methods/scanvi/main.nf" -include { scanvi_scarches } from "$targetDir/label_projection/methods/scanvi_scarches/main.nf" -// include { seurat_transferdata } from "$targetDir/label_projection/methods/seurat_transferdata/main.nf" -include { xgboost } from "$targetDir/label_projection/methods/xgboost/main.nf" - -// import metrics -include { accuracy } from "$targetDir/label_projection/metrics/accuracy/main.nf" -include { f1 } from "$targetDir/label_projection/metrics/f1/main.nf" - -// convert scores to tsv -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -// read in pipeline config -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -// collect method list -methods = [ - true_labels, - majority_vote, - random_labels, - knn, - logistic_regression, - mlp, - scanvi, - scanvi_scarches, - // seurat_transferdata, - xgboost -] - -// collect metric list -metrics = [ - accuracy, - f1 -] - -workflow { - helpMessage(config) - - // create channel from input parameters with - // arguments as defined in the config - channelFromParams(params, config) - | run_wf -} - workflow run_wf { take: input_ch main: + + // collect method list + methods = [ + true_labels, + majority_vote, + random_labels, + knn, + logistic_regression, + mlp, + scanvi, + scanvi_scarches, + // seurat_transferdata, + xgboost + ] + + // collect metric list + metrics = [ + accuracy, + f1 + ] + output_ch = input_ch - // based on the config file (config.vsh.yaml), run assertions on parameter sets - // and fill in default values - | preprocessInputs(config: config) // extract the dataset metadata | check_dataset_schema.run( diff --git a/src/tasks/match_modalities/workflows/run/config.vsh.yaml b/src/tasks/match_modalities/workflows/run/config.vsh.yaml index 0ee57fa9a8..690d3407b0 100644 --- a/src/tasks/match_modalities/workflows/run/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run/config.vsh.yaml @@ -20,5 +20,17 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: match_modalities/control_methods/random_features + - name: match_modalities/control_methods/true_features + - name: match_modalities/methods/fastmnn + - name: match_modalities/methods/scot + - name: match_modalities/methods/harmonic_alignment + - name: match_modalities/methods/procrustes + - name: match_modalities/metrics/knn_auc + - name: match_modalities/metrics/mse platforms: - type: nextflow \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/main.nf b/src/tasks/match_modalities/workflows/run/main.nf index e336b2e16f..62d65fa112 100644 --- a/src/tasks/match_modalities/workflows/run/main.nf +++ b/src/tasks/match_modalities/workflows/run/main.nf @@ -1,71 +1,30 @@ -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import control methods -include { random_features } from "$targetDir/match_modalities/control_methods/random_features/main.nf" params(params) -include { true_features } from "$targetDir/match_modalities/control_methods/true_features/main.nf" params(params) - -// import methods -include { fastmnn } from "$targetDir/match_modalities/methods/fastmnn/main.nf" params(params) -include { scot } from "$targetDir/match_modalities/methods/scot/main.nf" params(params) -include { harmonic_alignment } from "$targetDir/match_modalities/methods/harmonic_alignment/main.nf" params(params) -include { procrustes } from "$targetDir/match_modalities/methods/procrustes/main.nf" params(params) - -// import metrics -include { knn_auc } from "$targetDir/match_modalities/metrics/knn_auc/main.nf" params(params) -include { mse } from "$targetDir/match_modalities/metrics/mse/main.nf" params(params) - -// tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" params(params) - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { runComponents; joinStates; initializeTracer; writeJon; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -// read in pipeline config -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -// collect method list -methods = [ - random_features, - true_features, - scot, - harmonic_alignment, - fastmnn, - procrustes -] - -// collect metric list -metrics = [ - knn_auc, - mse -] - -workflow { - helpMessage(config) - - // create channel from input parameters with - // arguments as defined in the config - channelFromParams(params, config) - | run_wf -} - - // run the workflow +// run the workflow workflow run_wf { take: input_ch main: - output_ch = input_ch - // based on the config file (config.vsh.yaml), run assertions on parameter sets - // and fill in default values - | preprocessInputs(config: config) + // collect method list + methods = [ + random_features, + true_features, + scot, + harmonic_alignment, + fastmnn, + procrustes + ] + + // collect metric list + metrics = [ + knn_auc, + mse + ] + + output_ch = input_ch // extract the dataset metadata | check_dataset_schema.run( diff --git a/src/tasks/predict_modality/workflows/run/config.vsh.yaml b/src/tasks/predict_modality/workflows/run/config.vsh.yaml index 70c4356a0e..3e08a91355 100644 --- a/src/tasks/predict_modality/workflows/run/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run/config.vsh.yaml @@ -24,5 +24,20 @@ functionality: resources: - type: nextflow_script path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: common/extract_scores + - name: predict_modality/control_methods/mean_per_gene + - name: predict_modality/control_methods/random_predict + - name: predict_modality/control_methods/zeros + - name: predict_modality/control_methods/solution + - name: predict_modality/methods/knnr_py + - name: predict_modality/methods/knnr_r + - name: predict_modality/methods/lm + - name: predict_modality/methods/newwave_knnr + - name: predict_modality/methods/random_forest + - name: predict_modality/metrics/correlation + - name: predict_modality/metrics/mse platforms: - type: nextflow \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run/main.nf index 002e302f84..bbd773c96c 100644 --- a/src/tasks/predict_modality/workflows/run/main.nf +++ b/src/tasks/predict_modality/workflows/run/main.nf @@ -1,76 +1,32 @@ -sourceDir = params.rootDir + "/src" -targetDir = params.rootDir + "/target/nextflow" - -include { check_dataset_schema } from "$targetDir/common/check_dataset_schema/main.nf" - -// import control methods -include { mean_per_gene } from "$targetDir/predict_modality/control_methods/mean_per_gene/main.nf" -include { random_predict } from "$targetDir/predict_modality/control_methods/random_predict/main.nf" -include { zeros } from "$targetDir/predict_modality/control_methods/zeros/main.nf" -include { solution } from "$targetDir/predict_modality/control_methods/solution/main.nf" - -// import methods -include { knnr_py } from "$targetDir/predict_modality/methods/knnr_py/main.nf" -include { knnr_r } from "$targetDir/predict_modality/methods/knnr_r/main.nf" -include { lm } from "$targetDir/predict_modality/methods/lm/main.nf" -include { newwave_knnr } from "$targetDir/predict_modality/methods/newwave_knnr/main.nf" -include { random_forest } from "$targetDir/predict_modality/methods/random_forest/main.nf" - - -// import metrics -include { correlation } from "$targetDir/predict_modality/metrics/correlation/main.nf" -include { mse } from "$targetDir/predict_modality/metrics/mse/main.nf" - -// tsv generation component -include { extract_scores } from "$targetDir/common/extract_scores/main.nf" - -// import helper functions -include { readConfig; helpMessage; channelFromParams; preprocessInputs } from sourceDir + "/wf_utils/WorkflowHelper.nf" -include { runComponents; joinStates; initializeTracer; writeJson; getPublishDir } from sourceDir + "/wf_utils/BenchmarkHelper.nf" - -// read in pipeline config -config = readConfig("$projectDir/config.vsh.yaml") - // add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. traces = initializeTracer() -// collect method list -methods = [ - mean_per_gene, - random_predict, - zeros, - solution, - knnr_py, - knnr_r, - lm, - newwave_knnr, - random_forest -] - -// collect metric list -metrics = [ - correlation, - mse -] - -workflow { - helpMessage(config) - - // create channel from input parameters with - // arguments as defined in the config - channelFromParams(params, config) - | run_wf -} - workflow run_wf { take: input_ch main: + + // collect method list + methods = [ + mean_per_gene, + random_predict, + zeros, + solution, + knnr_py, + knnr_r, + lm, + newwave_knnr, + random_forest + ] + + // collect metric list + metrics = [ + correlation, + mse + ] + output_ch = input_ch - // based on the config file (config.vsh.yaml), run assertions on parameter sets - // and fill in default values - | preprocessInputs(config: config) // extract the dataset metadata | check_dataset_schema.run( From ec41c6287feedd77f461ca1b6229e044441ee030 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 5 Oct 2023 17:06:38 +0200 Subject: [PATCH 1012/1233] temp disable schemas and files (#244) Former-commit-id: 7ae14da15eafab154ade65b6dd31d535a6336b0d --- .github/workflows/main-build.yml | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index b1fa67c4c9..b45aaafe29 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -28,21 +28,21 @@ jobs: config_mod: .functionality.version := 'main_build' parallel: true - - name: Build nextflow schemas - uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 - with: - workflows: src - components: src - viash_pro_token: ${{ secrets.GTHB_PAT }} - tools_version: 'main_build' + # - name: Build nextflow schemas + # uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 + # with: + # workflows: src + # components: src + # viash_pro_token: ${{ secrets.GTHB_PAT }} + # tools_version: 'main_build' - - name: Build parameter files - uses: viash-io/viash-actions/pro/build-nextflow-params@v4 - with: - workflows: src - components: src - viash_pro_token: ${{ secrets.GTHB_PAT }} - tools_version: 'main_build' + # - name: Build parameter files + # uses: viash-io/viash-actions/pro/build-nextflow-params@v4 + # with: + # workflows: src + # components: src + # viash_pro_token: ${{ secrets.GTHB_PAT }} + # tools_version: 'main_build' - name: Deploy to target branch uses: peaceiris/actions-gh-pages@v3 From 3db696fde859e86cb51258944f94e3173375ec4f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 5 Oct 2023 17:18:32 +0200 Subject: [PATCH 1013/1233] fix labels Former-commit-id: 53580cb64e350ec4a1ae10614c5016af31bd281b --- .../batch_integration/methods/scalex_embed/config.vsh.yaml | 2 +- .../batch_integration/methods/scalex_feature/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_feature/config.vsh.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index 6ef5a38685..0ee13aa2d1 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: # Metadata for your component info: # A relatively short label, used when rendering visualisarions (required) - label: SCALEX + label: SCALEX (embedding) # A one sentence summary of how this method works (required). Used when # rendering summary tables. summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 2592d24390..340b72b704 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -13,7 +13,7 @@ functionality: # Metadata for your component info: # A relatively short label, used when rendering visualisarions (required) - label: SCALEX + label: SCALEX (feature) # A one sentence summary of how this method works (required). Used when # rendering summary tables. summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index c3e53ec343..5b1d53862d 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -3,7 +3,7 @@ __merge__: ../../api/comp_method_embedding.yaml functionality: name: scanorama_embed info: - label: Scanorama + label: Scanorama (embedding) summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" description: | diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index c4eb65026b..8d14bcf41a 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -3,7 +3,7 @@ __merge__: ../../api/comp_method_feature.yaml functionality: name: scanorama_feature info: - label: Scanorama + label: Scanorama (feature) summary: "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" description: | From f07e2a7ea838727c4af194e857ea4d1ad118c408 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 5 Oct 2023 17:23:10 +0200 Subject: [PATCH 1014/1233] use api files for wf input files Former-commit-id: adb94dc60b83de38e544fce8b3ea10afa1ea77c2 --- .../workflows/run_benchmark/config.vsh.yaml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 982e77a013..afe4e27c6a 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -9,15 +9,11 @@ functionality: description: "The ID of the dataset" required: true - name: "--input_dataset" - type: "file" - description: "A dataset" + __merge__: ../../api/file_dataset.yaml required: true - example: dataset.h5ad - name: "--input_solution" - type: "file" - description: "A solution" + __merge__: ../../api/file_dataset.yaml required: true - example: solution.h5ad - name: Outputs arguments: - name: "--output" @@ -25,6 +21,7 @@ functionality: type: file description: A TSV file containing the scores of each of the methods example: scores.tsv + required: true resources: - type: nextflow_script path: main.nf From 269ecdca3b10197603fac74ae071bdeaafc6d38d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 7 Oct 2023 18:37:08 +0200 Subject: [PATCH 1015/1233] use __merge__ of API files in batch int workflows (#246) Former-commit-id: dbf4c0b37ea7012290e28de88b76ebe501bbb363 --- .../workflows/process_datasets/config.vsh.yaml | 12 ++++-------- .../workflows/run_benchmark/config.vsh.yaml | 6 ++++-- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index 1ee4f4b23d..e25ac6548f 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -9,8 +9,6 @@ functionality: description: "The ID of the dataset" required: true - name: "--input" - type: "file" - description: "A dataset" required: true example: dataset.h5ad __merge__: "/src/tasks/batch_integration/api/file_common_dataset.yaml" @@ -24,15 +22,13 @@ functionality: - name: Outputs arguments: - name: "--output_dataset" - type: file - direction: output + __merge__: /src/tasks/batch_integration/api/file_dataset.yaml required: true - example: dataset.h5ad - - name: "--output_solution" - type: file direction: output + - name: "--output_solution" + __merge__: /src/tasks/batch_integration/api/file_solution.yaml required: true - example: solution.h5ad + direction: output resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index afe4e27c6a..152caa772c 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -9,11 +9,13 @@ functionality: description: "The ID of the dataset" required: true - name: "--input_dataset" - __merge__: ../../api/file_dataset.yaml + __merge__: /src/tasks/batch_integration/api/file_dataset.yaml required: true + direction: input - name: "--input_solution" - __merge__: ../../api/file_dataset.yaml + __merge__: /src/tasks/batch_integration/api/file_solution.yaml required: true + direction: input - name: Outputs arguments: - name: "--output" From 09d934e202c97fd18e1f092eb4b8f46e27c5f164 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 9 Oct 2023 11:43:03 +0200 Subject: [PATCH 1016/1233] Fix datasets workflows (#251) * add normalization_id argument to all normalization methods * update process_openproblems_v1 workflow * update opv1 wf * wip multimodal data * switch to viash 0.8.0 rc3 * fill in metadata fields * fix sh * remove norm_id from configs Former-commit-id: 6bad8d6d4dd2e92a4b6f0f5e77534274cf021d3c --- _viash.yaml | 2 +- src/datasets/api/comp_normalization.yaml | 4 + src/datasets/normalization/l1_sqrt/script.py | 2 +- .../normalization/log_cp/config.vsh.yaml | 4 - src/datasets/normalization/log_cp/script.py | 2 +- .../normalization/log_scran_pooling/script.R | 6 +- .../normalization/sqrt_cp/config.vsh.yaml | 4 - src/datasets/normalization/sqrt_cp/script.py | 2 +- .../resource_scripts/openproblems_v1.sh | 11 +- .../openproblems_v1_multimodal.sh | 33 ++- .../resource_test_scripts/bmmc_x_starter.sh | 2 +- .../resource_test_scripts/pancreas.sh | 29 +-- .../scicar_cell_lines.sh | 14 +- .../process_openproblems_v1/config.vsh.yaml | 62 ++---- .../workflows/process_openproblems_v1/main.nf | 170 ++++++--------- .../config.vsh.yaml | 4 +- .../main.nf | 204 +++++++++--------- 17 files changed, 255 insertions(+), 300 deletions(-) diff --git a/_viash.yaml b/_viash.yaml index 05830699c4..8489b0252d 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.8.0-RC2 +viash_version: 0.8.0-RC3 source: src target: target diff --git a/src/datasets/api/comp_normalization.yaml b/src/datasets/api/comp_normalization.yaml index e79534950b..6f2c1ffa64 100644 --- a/src/datasets/api/comp_normalization.yaml +++ b/src/datasets/api/comp_normalization.yaml @@ -17,6 +17,10 @@ functionality: __merge__: file_normalized.yaml direction: output required: true + - name: "--normalization_id" + type: string + description: "The normalization id to store in the dataset metadata. If not specified, the functionality name will be used." + required: false - name: "--layer_output" type: string default: "normalized" diff --git a/src/datasets/normalization/l1_sqrt/script.py b/src/datasets/normalization/l1_sqrt/script.py index e3e5d04a81..84480bf14c 100644 --- a/src/datasets/normalization/l1_sqrt/script.py +++ b/src/datasets/normalization/l1_sqrt/script.py @@ -23,7 +23,7 @@ print("Store output in adata", flush=True) adata.layers[par["layer_output"]] = l1_sqrt -adata.uns["normalization_id"] = meta['functionality_name'] +adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) print("Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index 8c44e58275..ea476d9a2b 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -10,10 +10,6 @@ functionality: type: integer default: 1e4 description: "Number of counts per cell" - - name: "--norm_id" - type: string - default: log_cp10k - description: "normalization ID to use e.g. 1e6 -> log_cpm, 1e4 -> log_cp10k" platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 diff --git a/src/datasets/normalization/log_cp/script.py b/src/datasets/normalization/log_cp/script.py index 0fadc2ffe4..71fc3e3a66 100644 --- a/src/datasets/normalization/log_cp/script.py +++ b/src/datasets/normalization/log_cp/script.py @@ -28,7 +28,7 @@ print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = par["norm_id"] +adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_scran_pooling/script.R b/src/datasets/normalization/log_scran_pooling/script.R index d4b36cb754..be51e21f38 100644 --- a/src/datasets/normalization/log_scran_pooling/script.R +++ b/src/datasets/normalization/log_scran_pooling/script.R @@ -28,7 +28,11 @@ lognorm <- log1p(sweep(adata$layers[["counts"]], 1, size_factors, "*")) cat(">> Storing in anndata\n") adata$obs[[par$obs_size_factors]] <- size_factors adata$layers[[par$layer_output]] <- lognorm -adata$uns[["normalization_id"]] <- meta[["functionality_name"]] +norm_id <- par[["normalization_id"]] +if (is.null(norm_id)) { + norm_id <- meta[["functionality_name"]] +} +adata$uns[["normalization_id"]] <- norm_id cat(">> Writing to file\n") zzz <- adata$write_h5ad(par$output, compression = "gzip") diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index fd2f7b0a98..b350031697 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -10,10 +10,6 @@ functionality: type: integer default: 1e4 description: "Number of counts per cell" - - name: "--norm_id" - type: string - default: sqrt_cp10k - description: "normalization id to use e.g. 1e4 -> sqrt_cp10k, 1e6 -> sqrt_cpm" platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 diff --git a/src/datasets/normalization/sqrt_cp/script.py b/src/datasets/normalization/sqrt_cp/script.py index af30b56083..76c645d6e9 100644 --- a/src/datasets/normalization/sqrt_cp/script.py +++ b/src/datasets/normalization/sqrt_cp/script.py @@ -29,7 +29,7 @@ print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = par["norm_id"] +adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index af9ed202ab..c8f4c92571 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -145,8 +145,15 @@ param_list: dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio -output_dataset: dataset.h5ad -output_meta: dataset_metadata.yaml +normalization_id: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null HERE fi diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 1598c3091d..7b8a6a50a7 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -20,27 +20,52 @@ if [ ! -f $params_file ]; then cat > "$params_file" << 'HERE' param_list: - id: citeseq_cbmc + dataset_id: citeseq_cbmc + dataset_name: "CITE-Seq CBMC" + dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" + dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." + data_reference: stoeckius2017simultaneous + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 + dataset_organism: homo_sapiens layer_counts: counts - id: scicar_cell_lines + dataset_id: scicar_cell_lines + dataset_name: "sci-CAR Cell Lines" + dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" + dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." + data_reference: cao2018joint + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_organism: [homo_sapiens, mus_musculus] obs_celltype: cell_name layer_counts: counts - id: scicar_mouse_kidney + dataset_id: scicar_mouse_kidney + dataset_name: "sci-CAR Mouse Kidney" + dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" + dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." + data_reference: cao2018joint + data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_organism: mus_musculus obs_celltype: cell_name obs_batch: replicate layer_counts: counts -output: '$id.h5ad' +normalization_id: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset_mod1: '$id/dataset_mod1.h5ad' +output_dataset_mod1: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod2.h5ad' +output_state: '$id/state.yaml' HERE fi export NXF_VER=22.04.5 nextflow \ run . \ - -main-script src/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ -profile docker \ -resume \ -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ - -with-tower + --publish_dir "$OUTPUT_DIR" diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh index 298bd668a5..81fabe3970 100755 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -17,4 +17,4 @@ wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_mult wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ -O "$SUBDIR/dataset_atac.h5ad" -src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file +# src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 2a6b804e27..c9b9dac984 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -21,7 +21,7 @@ KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s # download dataset nextflow run . \ - -main-script src/datasets/workflows/process_openproblems_v1/main.nf \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ -profile docker \ -resume \ --id pancreas \ @@ -39,21 +39,22 @@ nextflow run . \ --keep_batch_categories "celseq:inDrop4:smarter" \ --keep_features "$KEEP_FEATURES" \ --seed 123 \ - --normalization_methods log_cp \ + --normalization_methods log_cp10k \ --do_subsample true \ - --output_raw raw.h5ad \ - --output_normalized normalized.h5ad \ - --output_pca pca.h5ad \ - --output_hvg hvg.h5ad \ - --output_knn knn.h5ad \ - --output_dataset dataset.h5ad \ - --output_meta dataset_metadata.yaml \ + --output_raw '$id/raw.h5ad' \ + --output_normalized '$id/normalized.h5ad' \ + --output_pca '$id/pca.h5ad' \ + --output_hvg '$id/hvg.h5ad' \ + --output_knn '$id/knn.h5ad' \ + --output_dataset '$id/dataset.h5ad' \ + --output_meta '$id/dataset_meta.yaml' \ + --output_state '$id/state.yaml' \ --publish_dir "$DATASET_DIR" rm -r $DATASET_DIR/temp_* -# run task process dataset components -src/tasks/batch_integration/resources_test_scripts/pancreas.sh -src/tasks/denoising/resources_test_scripts/pancreas.sh -src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh -src/tasks/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file +# # run task process dataset components +# src/tasks/batch_integration/resources_test_scripts/pancreas.sh +# src/tasks/denoising/resources_test_scripts/pancreas.sh +# src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +# src/tasks/label_projection/resources_test_scripts/pancreas.sh diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 414af8330f..0b754c7632 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -17,7 +17,7 @@ mkdir -p $DATASET_DIR # download dataset nextflow run . \ - -main-script src/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ -profile docker \ -resume \ --id scicar_cell_lines \ @@ -35,10 +35,12 @@ nextflow run . \ --n_obs 600 \ --n_vars 1500 \ --seed 123 \ - --output_dataset_mod1 dataset_mod1.h5ad \ - --output_dataset_mod2 dataset_mod2.h5ad \ - --output_meta_mod1 dataset_metadata_mod1.yaml \ - --output_meta_mod2 dataset_metadata_mod2.yaml \ + --normalization_methods log_cp10k \ + --output_dataset_mod1 '$id/dataset_mod1.h5ad' \ + --output_dataset_mod2 '$id/dataset_mod2.h5ad' \ + --output_meta_mod1 '$id/dataset_metadata_mod1.yaml' \ + --output_meta_mod2 '$id/dataset_metadata_mod2.yaml' \ + --output_state '$id/state.yaml' \ --publish_dir "$DATASET_DIR" -src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh \ No newline at end of file +# src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 6cc183b9f0..8e7846636d 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -97,73 +97,39 @@ functionality: - name: "--normalization_methods" type: string multiple: true - choices: ["log_cp", "sqrt_cp", "l1_sqrt"] - default: ["log_cp", "sqrt_cp", "l1_sqrt"] + choices: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt", "log_scran_pooling"] + default: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt"] description: "Which normalization methods to run." - name: Outputs arguments: - name: "--output_dataset" + __merge__: /src/datasets/api/file_common_dataset.yaml direction: "output" - # todo: fix inherits in nxf - # __merge__: ../../api/file_raw.yaml - type: file - description: "A dataset" - default: "dataset.h5ad" - info: - label: "Raw dataset" - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - obs: - - type: string - name: celltype - description: Cell type information - required: false - - type: string - name: batch - description: Batch information - required: false - - type: string - name: tissue - description: Tissue information - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true + required: true - name: "--output_meta" direction: "output" type: file description: "Dataset metadata" default: "dataset_metadata.yaml" - name: "--output_raw" - direction: output - type: file - example: raw.h5ad + __merge__: /src/datasets/api/file_raw.yaml + direction: "output" required: false - name: "--output_normalized" - direction: output - type: file - example: normalized.h5ad + __merge__: /src/datasets/api/file_normalized.yaml + direction: "output" required: false - name: "--output_pca" - direction: output - type: file - example: pca.h5ad + __merge__: /src/datasets/api/file_pca.yaml + direction: "output" required: false - name: "--output_hvg" - direction: output - type: file - example: hvg.h5ad + __merge__: /src/datasets/api/file_hvg.yaml + direction: "output" required: false - name: "--output_knn" - direction: output - type: file - example: knn.h5ad + __merge__: /src/datasets/api/file_knn.yaml + direction: "output" required: false resources: - type: nextflow_script diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index cad55c7f5f..91968fd34d 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -1,137 +1,104 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = collectTraces() - workflow run_wf { take: input_ch main: - normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] - dataset_ch = input_ch + // create different normalization methods by overriding the defaults + normalization_methods = [ + log_cp.run( + key: "log_cp10k", + args: [normalization_id: "log_cp10k", n_cp: 10000], + ), + log_cp.run( + key: "log_cpm", + args: [normalization_id: "log_cpm", n_cp: 1000000], + ), + sqrt_cp.run( + key: "sqrt_cp10k", + args: [normalization_id: "sqrt_cp10k", n_cp: 10000], + ), + sqrt_cp.run( + key: "sqrt_cpm", + args: [normalization_id: "sqrt_cpm", n_cp: 1000000], + ), + l1_sqrt, + log_scran_pooling + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } // fetch data from legacy openproblems | openproblems_v1.run( - fromState: { id, state -> - def output_filename = - (!state.do_subsample && state.output_raw) ? - state.output_raw : - '$id.$key.output_raw.h5ad' - [ - dataset_id: state.dataset_id, - obs_celltype: state.obs_celltype, - obs_batch: state.obs_batch, - obs_tissue: state.obs_tussue, - layer_counts: state.layer_counts, - sparse: state.sparse, - dataset_name: state.dataset_name, - data_url: state.data_url, - data_reference: state.data_reference, - dataset_summary: state.dataset_summary, - dataset_description: state.dataset_description, - dataset_organism: state.dataset_organism, - output: output_filename - ] - }, - toState: [ - raw: "output" - ] + fromState: [ + "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", + "sparse", "dataset_name", "data_url", "data_reference", "dataset_summary", + "dataset_description", "dataset_organism" + ], + toState: ["raw": "output"] ) - - sampled_dataset_ch = dataset_ch - | filter{ id, state -> state.do_subsample } + + // subsample if so desired | subsample.run( - fromState: { id, state -> - [ - input: state.raw, - n_obs: state.n_obs, - n_vars: state.n_vars, - keep_features: state.keep_features, - keep_celltype_categories: state.keep_celltype_categories, - keep_batch_categories: state.keep_batch_categories, - even: state.even, - seed: state.seed, - output: state.output_raw ?: '$id.$key.output_raw.h5ad', - output_mod2: null - ] - }, - toState: [ - raw: "output" - ] + runIf: { id, state -> state.do_subsample }, + fromState: [ + "input": "raw", + "n_obs": "n_obs", + "n_vars": "n_vars", + "keep_features": "keep_features", + "keep_celltype_categories": "keep_celltype_categories", + "keep_batch_categories": "keep_batch_categories", + "even": "even", + "seed": "seed" + ], + args: [output_mod2: null], + toState: [raw: "output"] ) - notsampled_dataset_ch = dataset_ch - | filter{ id, state -> !state.do_subsample } - - output_ch = sampled_dataset_ch - | concat(notsampled_dataset_ch) - // run normalization methods - | runComponents( + | runEach( components: normalization_methods, - id: { id, state, config -> + id: { id, state, comp -> if (state.normalization_methods.size() > 1) { - id + "/" + config.functionality.name + id + "/" + comp.name } else { id } }, - filter: { id, state, config -> - config.functionality.name in state.normalization_methods + filter: { id, state, comp -> + comp.name in state.normalization_methods }, - fromState: { id, state, config -> - [ - input: state.raw, - output: state.output_normalized ?: '$id.$key.output_normalized.h5ad' - ] - }, - toState: { id, output, state, config -> - state + [ - normalization_id: config.functionality.name, - normalized: output.output - ] - } + fromState: ["input": "raw"], + toState: ["normalized": "output"] ) | pca.run( - fromState: { id, state -> - [ - input: state.normalized, - output: state.output_pca ?: '$id.$key.output_pca.h5ad' - ] - }, - toState: [ pca: "output" ] + fromState: ["input": "normalized"], + toState: ["pca": "output" ] ) | hvg.run( - fromState: { id, state -> - [ - input: state.pca, - output: state.output_hvg ?: '$id.$key.output_hvg.h5ad' - ] - }, - toState: [ hvg: "output" ] + fromState: ["input": "pca"], + toState: ["hvg": "output"] ) | knn.run( - fromState: { id, state -> - [ - input: state.hvg, - output: state.output_knn ?: '$id.$key.output_knn.h5ad' - ] - }, - toState: [ knn: "output" ] + fromState: ["input": "hvg"], + toState: ["knn": "output"] ) | check_dataset_schema.run( fromState: { id, state -> [ input: state.knn, - meta: state.output_meta ?: '$id.$key.output_meta.yaml', - output: state.output_dataset ?: '$id.$key.output_dataset.h5ad', checks: null ] }, - toState: [ dataset: "output", meta: "meta" ] + toState: ["dataset": "output", "meta": "meta"] ) // only output the files for which an output file was specified @@ -143,18 +110,11 @@ workflow run_wf { "output_normalized": state.output_normalized ? state.normalized : null, "output_pca": state.output_pca ? state.pca : null, "output_hvg": state.output_hvg ? state.hvg : null, - "output_knn": state.output_knn ? state.knn : null + "output_knn": state.output_knn ? state.knn : null, + "_meta": state._meta ] } emit: output_ch -} - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) - // writeJson(normalization_methods.collect{it.config}, file("$publish_dir/normalization_methods.json")) } \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 04bb8e06e1..0494c3d3ba 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -97,8 +97,8 @@ functionality: - name: "--normalization_methods" type: string multiple: true - choices: ["log_cp", "sqrt_cp", "l1_sqrt"] - default: ["log_cp"] + choices: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt", "log_scran_pooling"] + default: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt"] description: "Which normalization methods to run." - name: Outputs arguments: diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 3920e45aa8..b60b97f67a 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -1,157 +1,157 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() - workflow run_wf { take: input_ch main: - normalization_methods = [log_cp, sqrt_cp, l1_sqrt, log_scran_pooling] - - - dataset_ch = input_ch + // create different normalization methods by overriding the defaults + normalization_methods = [ + log_cp.run( + key: "log_cp10k", + args: [normalization_id: "log_cp10k", n_cp: 10000] + ), + log_cp.run( + key: "log_cpm", + args: [normalization_id: "log_cpm", n_cp: 1000000] + ), + sqrt_cp.run( + key: "sqrt_cp10k", + args: [normalization_id: "sqrt_cp10k", n_cp: 10000] + ), + sqrt_cp.run( + key: "sqrt_cpm", + args: [normalization_id: "sqrt_cpm", n_cp: 1000000] + ), + l1_sqrt, + log_scran_pooling + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } // fetch data from legacy openproblems | openproblems_v1_multimodal.run( - fromState: { id, state -> - [ - dataset_id: state.dataset_id, - obs_celltype: state.obs_celltype, - obs_batch: state.obs_batch, - obs_tissue: state.obs_tussue, - layer_counts: state.layer_counts, - sparse: state.sparse, - dataset_name: state.dataset_name, - data_url: state.data_url, - data_reference: state.data_reference, - dataset_summary: state.dataset_summary, - dataset_description: state.dataset_description, - dataset_organism: state.dataset_organism - ] - }, - toState: [ - raw_mod1: "output_mod1", - raw_mod2: "output_mod2" + fromState: [ + "dataset_id": "dataset_id", + "obs_celltype": "obs_celltype", + "obs_batch": "obs_batch", + "obs_tissue": "obs_tissue", + "layer_counts": "layer_counts", + "sparse": "sparse", + "dataset_name": "dataset_name", + "data_url": "data_url", + "data_reference": "data_reference", + "dataset_summary": "dataset_summary", + "dataset_description": "dataset_description", + "dataset_organism": "dataset_organism" + ], + toState: [ + "raw_mod1": "output_mod1", + "raw_mod2": "output_mod2" ] ) - sampled_dataset_ch = dataset_ch - | filter{ id, state -> state.do_subsample } + // subsample if need be | subsample.run( - fromState: { id, state -> - [ - input: state.raw_mod1, - input_mod2: state.raw_mod2, - n_obs: state.n_obs, - n_vars: state.n_vars, - keep_features: state.keep_features, - keep_celltype_categories: state.keep_celltype_categories, - keep_batch_categories: state.keep_batch_categories, - even: state.even, - seed: state.seed, - output_mod2: '$id.$key.output_mod2.h5ad' // set value for optional output - ] - }, + runIf: { id, state -> state.do_subsample }, + fromState: [ + "input": "raw_mod1", + "input_mod2": "raw_mod2", + "n_obs": "n_obs", + "n_vars": "n_vars", + "keep_features": "keep_features", + "keep_celltype_categories": "keep_celltype_categories", + "keep_batch_categories": "keep_batch_categories", + "even": "even", + "seed": "seed" + ], toState: [ - raw_mod1: "output", - raw_mod2: "output_mod2" + "raw_mod1": "output", + "raw_mod2": "output_mod2" ] ) - notsampled_dataset_ch = dataset_ch - | filter{ id, state -> !state.do_subsample } - - output_ch = sampled_dataset_ch - | concat(notsampled_dataset_ch) // run normalization methods - | runComponents( + | runEach( components: normalization_methods, - id: { id, state, config -> + id: { id, state, comp -> if (state.normalization_methods.size() > 1) { - id + "/" + config.functionality.name + id + "/" + comp.name } else { id } }, - filter: { id, state, config -> - config.functionality.name in state.normalization_methods - }, - fromState: { id, state, config -> - [ - input: state.raw_mod1, - output: '$id.$key.output_mod1.h5ad' - ] + filter: { id, state, comp -> + comp.name in state.normalization_methods }, - toState: { id, output, state, config -> + fromState: ["input": "raw_mod1"], + toState: { id, output, state, comp -> state + [ - normalization_id: config.functionality.name, - normalized_mod1: output.output + "normalization_id": comp.name, + "normalized_mod1": output.output ] } ) + // run normalization methods on second modality - | runComponents( + | runEach( components: normalization_methods, - filter: { id, state, config -> - config.functionality.name == state.normalization_id - }, - fromState: { id, state, config -> - [ - input: state.raw_mod2, - output: '$id.$key.output_mod2.h5ad' - ] + filter: { id, state, comp -> + comp.name == state.normalization_id }, - toState: [normalized_mod2: "output"] + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] ) | svd.run( - fromState: { id, state -> - [ - input: state.normalized_mod1, - input_mod2: state.normalized_mod2, - output: '$id.$key.output_mod1.h5ad', - output_mod2: '$id.$key.output_mod2.h5ad' - ] - }, + fromState: [ + "input": "normalized_mod1", + "input_mod2": "normalized_mod2" + ], toState: [ - svd_mod1: "output", - svd_mod2: "output_mod2" + "svd_mod1": "output", + "svd_mod2": "output_mod2" ] ) | hvg.run( - fromState: [ input: "svd_mod1" ], - toState: [ hvg_mod1: "output" ] + fromState: [ "input": "svd_mod1" ], + toState: [ "hvg_mod1": "output" ] ) | hvg.run( - fromState: [ input: "svd_mod2" ], - toState: [ hvg_mod2: "output" ] + fromState: [ "input": "svd_mod2" ], + toState: [ "hvg_mod2": "output" ] ) | check_dataset_schema.run( fromState: { id, state -> [ - input: state.hvg_mod1, - meta: state.output_meta_mod1 ?: '$id.$key.output_meta_mod1.yaml', - output: state.output_dataset_mod1 ?: '$id.$key.output_dataset_mod1.h5ad', - checks: null + "input": state.hvg_mod1, + "checks": null ] }, - toState: [ dataset_mod1: "output", meta_mod1: "meta" ] + toState: [ + "dataset_mod1": "output", + "meta_mod1": "meta" + ] ) | check_dataset_schema.run( fromState: { id, state -> [ - input: state.hvg_mod2, - meta: state.output_meta_mod2 ?: '$id.$key.output_meta_mod2.yaml', - output: state.output_dataset_mod2 ?: '$id.$key.output_dataset_mod2.h5ad', - checks: null + "input": state.hvg_mod2, + "checks": null ] }, - toState: [ dataset_mod2: "output", meta_mod2: "meta" ] + toState: [ + "dataset_mod2": "output", + "meta_mod2": "meta" + ] ) // only output the files for which an output file was specified @@ -160,17 +160,11 @@ workflow run_wf { "output_dataset_mod1" : state.output_dataset_mod1 ? state.dataset_mod1: null, "output_dataset_mod2" : state.output_dataset_mod2 ? state.dataset_mod2: null, "output_meta_mod1" : state.output_meta_mod1 ? state.meta_mod1: null, - "output_meta_mod2" : state.output_meta_mod2 ? state.meta_mod2: null + "output_meta_mod2" : state.output_meta_mod2 ? state.meta_mod2: null, + "_meta": state._meta ] } emit: output_ch } - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) -} \ No newline at end of file From 7e0ae54229f3c490c746a367912c916bbb939b56 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 10 Oct 2023 15:59:30 +0200 Subject: [PATCH 1017/1233] Update batch integration workflows (#253) * Add key in process_datasets * add nf-tower scripts * add normalization_id argument to all normalization methods * update process_openproblems_v1 workflow * add config_mods * update to main-script path * update opv1 wf * wip multimodal data * switch to viash 0.8.0 rc3 * fill in metadata fields * fix sh * fix batchint * fix script * simplify nf * update wf * remove dataset_id from the dataset workflow arguments * remove id from batch integration benchmark workflow * update to viash 0.8.0-rc4 * move set -e --------- Co-authored-by: Kai Waldrant Former-commit-id: e60945955df548e0f3991f0b48078e8f8fa7be4a --- _viash.yaml | 4 +- .../process_openproblems_v1/config.vsh.yaml | 4 - .../workflows/process_openproblems_v1/main.nf | 15 ++- .../config.vsh.yaml | 4 - .../main.nf | 2 +- .../nf_tower_scripts/run_benchmark.sh | 27 +++++ .../run_test.sh} | 9 +- .../resources_test_scripts/pancreas.sh | 11 +- .../process_datasets/config.vsh.yaml | 4 - .../workflows/process_datasets/main.nf | 34 +++--- .../process_datasets/run_nextflow.sh | 2 +- .../workflows/run_benchmark/config.vsh.yaml | 4 - .../workflows/run_benchmark/main.nf | 103 +++++++----------- .../workflows/run_benchmark/run_test.sh | 3 +- 14 files changed, 114 insertions(+), 112 deletions(-) create mode 100644 src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh rename src/tasks/batch_integration/{workflows/run_benchmark/run_test_on_tower.sh => nf_tower_scripts/run_test.sh} (71%) diff --git a/_viash.yaml b/_viash.yaml index 8489b0252d..ece42d62a8 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.8.0-RC3 +viash_version: 0.8.0-RC4 source: src target: target @@ -10,3 +10,5 @@ config_mods: | .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems-v2' .platforms[.type == "nextflow"].directives.tag := "$id" .platforms[.type == "nextflow"].auto.simplifyOutput := false + .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", lowcpu : "cpus = 5", midmem : "memory = 50.Gb", midcpu : "cpus = 15", highmem : "memory = 100.Gb", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h" } + .platforms[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'" \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 8e7846636d..9575d690a1 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -29,10 +29,6 @@ functionality: description: Convert layers to a sparse CSR format. - name: Metadata arguments: - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--dataset_name" type: string description: Nicely formatted name. diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 91968fd34d..66b434a883 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -36,9 +36,18 @@ workflow run_wf { // fetch data from legacy openproblems | openproblems_v1.run( fromState: [ - "dataset_id", "obs_celltype", "obs_batch", "obs_tissue", "layer_counts", - "sparse", "dataset_name", "data_url", "data_reference", "dataset_summary", - "dataset_description", "dataset_organism" + "dataset_id": "id", + "obs_celltype": "obs_celltype", + "obs_batch": "obs_batch", + "obs_tissue": "obs_tissue", + "layer_counts": "layer_counts", + "sparse": "sparse", + "dataset_name": "dataset_name", + "data_url": "data_url", + "data_reference": "data_reference", + "dataset_summary": "dataset_summary", + "dataset_description": "dataset_description", + "dataset_organism": "dataset_organism", ], toState: ["raw": "output"] ) diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 0494c3d3ba..3f604e8b30 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -29,10 +29,6 @@ functionality: description: Convert layers to a sparse CSR format. - name: Metadata arguments: - - name: "--dataset_id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--dataset_name" type: string description: Nicely formatted name. diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index b60b97f67a..f50e769f23 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -36,7 +36,7 @@ workflow run_wf { // fetch data from legacy openproblems | openproblems_v1_multimodal.run( fromState: [ - "dataset_id": "dataset_id", + "dataset_id": "id", "obs_celltype": "obs_celltype", "obs_batch": "obs_batch", "obs_tissue": "obs_tissue", diff --git a/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh b/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh new file mode 100644 index 0000000000..ef527d8a82 --- /dev/null +++ b/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,27 @@ +#!/bin/bash + + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: batch_integration +input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/batch_integration +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh b/src/tasks/batch_integration/nf_tower_scripts/run_test.sh similarity index 71% rename from src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh rename to src/tasks/batch_integration/nf_tower_scripts/run_test.sh index b274c887e0..f9ee29fa4c 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_test_on_tower.sh +++ b/src/tasks/batch_integration/nf_tower_scripts/run_test.sh @@ -4,10 +4,11 @@ DATASET_DIR=resources_test/batch_integration/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE -id: pancreas_subsample -input: s3://openproblems-data/$DATASET_DIR/dataset.h5ad -output: scores.tsv -publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration +id: batch_integration_test +input_states: s3://openproblems-data/resources_test/batch_integration/**/state.yaml +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration/ HERE cat > /tmp/nextflow.config << HERE diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh index 5c9cdd93c8..5fa80a3bf1 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/pancreas.sh @@ -6,6 +6,8 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + RAW_DATA=resources_test/common DATASET_DIR=resources_test/batch_integration @@ -14,14 +16,15 @@ mkdir -p $DATASET_DIR # process dataset echo Running process_dataset nextflow run . \ - -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ + -main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ -profile docker \ -entry auto \ - --id resources_test \ --input_states "$RAW_DATA/**/state.yaml" \ --rename_keys 'input:output_dataset' \ - --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ - --publish_dir "$DATASET_DIR" + --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved echo Running BBKNN viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index e25ac6548f..40fe2d4b2a 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--input" required: true example: dataset.h5ad diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index e14bb0f4f5..557799041d 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -1,7 +1,8 @@ workflow auto { - findStates(params, config) - | run_wf - | publishStates([:]) + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) } workflow run_wf { @@ -14,20 +15,18 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( - fromState: { id, state -> - [ - input: state.input, - schema: state.dataset_schema, - output: '$id.$key.output.h5ad', - stop_on_error: false, - checks: null - ] - }, - toState: { id, output, state -> - state + [ dataset: output.output ] - } + fromState: [ + "input": "input", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false, + "checks": null + ], + toState: ["dataset": "output"] ) + // remove datasets which didn't pass the schema check | filter { id, state -> state.dataset != null } @@ -38,7 +37,10 @@ workflow run_wf { output_dataset: "output_dataset", output_solution: "output_solution" ], - toState: [dataset: "output_dataset", solution: "output_solution"] + toState: [ + dataset: "output_dataset", + solution: "output_solution" + ] ) // only output the files for which an output file was specified diff --git a/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh index 211d631c34..28e9382879 100755 --- a/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh +++ b/src/tasks/batch_integration/workflows/process_datasets/run_nextflow.sh @@ -14,7 +14,7 @@ set -e export NXF_VER=22.04.5 nextflow run . \ - -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ + -main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ -profile docker \ -entry auto \ -c src/wf_utils/labels_ci.config \ diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 152caa772c..8bce72d67d 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--input_dataset" __merge__: /src/tasks/batch_integration/api/file_dataset.yaml required: true diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 61a5ede18f..4e9b10ed7e 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -1,5 +1,9 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = collectTraces() +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} workflow run_wf { take: @@ -47,10 +51,9 @@ workflow run_wf { // process input parameter channel dataset_ch = input_ch - | map { id, state -> - def newId = id.replaceAll(/\//, "_") - - [newId, state] + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] } // extract the dataset metadata @@ -61,48 +64,49 @@ workflow run_wf { } ) - // run all methods + // run all methods method_out_ch1 = dataset_ch - | runComponents( + | runEach( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, config -> + filter: { id, state, comp -> def norm = state.normalization_id - def pref = config.functionality.info.preferred_normalization + def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name + id: { id, state, comp -> + id + "." + comp.config.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [input: "input_dataset"], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - method_id: config.functionality.name, + method_id: comp.config.functionality.name, method_output: output.output, - method_subtype: config.functionality.info.subtype + method_subtype: comp.config.functionality.info.subtype ] } ) + // append feature->embed transformations method_out_ch2 = method_out_ch1 - | runComponents( + | runEach( components: feature_to_embed, - filter: { id, state, config -> state.method_subtype == "feature"}, + filter: { id, state, comp -> state.method_subtype == "feature"}, fromState: [ input: "method_output" ], - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ method_output: output.output, - method_subtype: config.functionality.info.subtype + method_subtype: comp.config.functionality.info.subtype ] } ) @@ -110,14 +114,14 @@ workflow run_wf { // append embed->graph transformations method_out_ch3 = method_out_ch2 - | runComponents( + | runEach( components: embed_to_graph, - filter: { id, state, config -> state.method_subtype == "embedding"}, + filter: { id, state, comp -> state.method_subtype == "embedding"}, fromState: [ input: "method_output" ], - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ method_output: output.output, - method_subtype: config.functionality.info.subtype + method_subtype: comp.config.functionality.info.subtype ] } ) @@ -125,18 +129,18 @@ workflow run_wf { // run metrics output_ch = method_out_ch3 - | runComponents( + | runEach( components: metrics, - filter: { id, state, config -> - state.method_subtype == config.functionality.info.subtype + filter: { id, state, comp -> + state.method_subtype == comp.config.functionality.info.subtype }, fromState: [ input_integrated: "method_output", input_solution: "input_solution" ], - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - metric_id: config.functionality.name, + metric_id: comp.config.functionality.name, metric_output: output.output ] } @@ -149,48 +153,19 @@ workflow run_wf { def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0].output + _meta: states[0]._meta ] [new_id, new_state] } // convert to tsv and publish - | extract_scores + | extract_scores.run( + fromState: ["input"], + toState: ["output"] + ) + + | setState(["output", "_meta"]) emit: output_ch } - -workflow auto { - findStates(params, thisConfig) - | run_wf - | publishStates([key: thisConfig.functionality.name]) -} - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) - // todo: add datasets logging - // writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) - // writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) -} - -def joinStates(Closure apply_) { - workflow joinStatesWf { - take: input_ch - main: - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ tups -> - def ids = tups.collect{it[0]} - def states = tups.collect{it[1]} - apply_(ids, states) - } - - emit: output_ch - } - return joinStatesWf -} \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh index b8c6c9ac77..43690c2475 100755 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh @@ -11,7 +11,7 @@ set -e # export TOWER_WORKSPACE_ID=53907369739130 DATASETS_DIR="resources_test/batch_integration" -OUTPUT_DIR="resources_test/batch_integration/benchmarks/openproblems_v1" +OUTPUT_DIR="output/temp" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" @@ -23,7 +23,6 @@ nextflow run . \ -profile docker \ -resume \ -entry auto \ - --id resources \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ --settings '{"output": "scores.tsv"}' \ From 7170765c80dbcbd12eb5a464b426e1a1e14ea917 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 13:54:26 +0200 Subject: [PATCH 1018/1233] Fix_dimred (#254) * Add key in process_datasets * add nf-tower scripts * add normalization_id argument to all normalization methods * update process_openproblems_v1 workflow * add config_mods * update to main-script path * update process_datasets workflow * update run_benchmark workflow * add nf_rower_scripts * fix param typo in nf_tower_scripts * update opv1 wf * wip multimodal data * switch to viash 0.8.0 rc3 * fill in metadata fields * fix sh * fix batchint * fix script * simplify nf * update wf * remove dataset_id from the dataset workflow arguments * remove id from batch integration benchmark workflow * wip refactor wfs * fix scripts * wip dimred and also make changes to batch int and datasets * fix dataset workflows * fix batch int * fix dimred * update wfs * update readme * bump viash version * fix workflows * add back normalization id * undo workarounds * Update src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml Co-authored-by: Kai Waldrant --------- Co-authored-by: Kai Waldrant Former-commit-id: 3da9d9e85806a8f399cc727235bc1e3196126743 --- _viash.yaml | 2 +- .../resource_scripts/openproblems_v1.sh | 34 +++------ .../openproblems_v1_multimodal.sh | 13 ++-- .../resource_test_scripts/pancreas.sh | 1 - .../workflows/process_openproblems_v1/main.nf | 74 ++++++++++-------- .../main.nf | 10 ++- src/tasks/batch_integration/README.md | 3 +- .../resources_scripts/process_datasets.sh | 16 ++-- .../resources_scripts/run_benchmark.sh | 7 +- .../process_datasets/config.vsh.yaml | 7 +- .../workflows/process_datasets/main.nf | 15 +++- .../workflows/run_benchmark/config.vsh.yaml | 4 +- .../denoising/workflows/run/config.vsh.yaml | 4 - .../api/file_common_dataset.yaml | 29 +++++++ .../nf_tower_scripts/run_benchmark.sh | 27 +++++++ .../run_test.sh} | 16 ++-- .../resources_scripts/process_datasets.sh | 64 +++------------- .../resources_scripts/run_benchmark.sh | 65 +++------------- .../resources_test_scripts/pancreas.sh | 76 ++++++++++--------- .../process_datasets/config.vsh.yaml | 35 +++++++++ .../workflows/process_datasets/main.nf | 56 ++++++++++++++ .../workflows/process_datasets/run_test.sh | 25 ++++++ .../workflows/run/run_test.sh | 28 ------- .../{run => run_benchmark}/config.vsh.yaml | 12 ++- .../workflows/{run => run_benchmark}/main.nf | 69 ++++++++--------- .../{run => run_benchmark}/nextflow.config | 0 .../workflows/run_benchmark/run_test.sh | 31 ++++++++ .../workflows/run/config.vsh.yaml | 4 - .../workflows/run/config.vsh.yaml | 4 - .../workflows/run/config.vsh.yaml | 4 - 30 files changed, 406 insertions(+), 329 deletions(-) create mode 100644 src/tasks/dimensionality_reduction/api/file_common_dataset.yaml create mode 100644 src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh rename src/tasks/dimensionality_reduction/{workflows/run/run_test_on_tower.sh => nf_tower_scripts/run_test.sh} (54%) create mode 100644 src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf create mode 100644 src/tasks/dimensionality_reduction/workflows/process_datasets/run_test.sh delete mode 100755 src/tasks/dimensionality_reduction/workflows/run/run_test.sh rename src/tasks/dimensionality_reduction/workflows/{run => run_benchmark}/config.vsh.yaml (85%) rename src/tasks/dimensionality_reduction/workflows/{run => run_benchmark}/main.nf (64%) rename src/tasks/dimensionality_reduction/workflows/{run => run_benchmark}/nextflow.config (100%) create mode 100755 src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh diff --git a/_viash.yaml b/_viash.yaml index ece42d62a8..dd1e0534ac 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.8.0-RC4 +viash_version: 0.8.0-RC5 source: src target: target diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index c8f4c92571..9815ea652c 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -22,7 +22,6 @@ param_list: - id: allen_brain_atlas obs_celltype: label layer_counts: counts - dataset_id: allen_brain_atlas dataset_name: Mouse Brain Atlas data_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 data_reference: tasic2016adult @@ -35,7 +34,6 @@ param_list: obs_batch: experiment_code obs_tissue: tissue layer_counts: counts - dataset_id: cengen dataset_name: CeNGEN data_url: https://www.cengen.org data_reference: hammarlund2018cengen @@ -48,7 +46,6 @@ param_list: obs_batch: batch obs_tissue: tissue layer_counts: counts - dataset_id: immune_cells dataset_name: Human immune data_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html data_reference: luecken2022benchmarking @@ -59,7 +56,6 @@ param_list: - id: mouse_blood_olsson_labelled obs_celltype: celltype layer_counts: counts - dataset_id: mouse_blood_olsson_labelled dataset_name: Mouse myeloid data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 data_reference: olsson2016single @@ -70,7 +66,6 @@ param_list: - id: mouse_hspc_nestorowa2016 obs_celltype: cell_type_label layer_counts: counts - dataset_id: mouse_hspc_nestorowa2016 dataset_name: Mouse HSPC data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 data_reference: nestorowa2016single @@ -82,7 +77,6 @@ param_list: obs_celltype: celltype obs_batch: tech layer_counts: counts - dataset_id: pancreas dataset_name: Human pancreas data_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html data_reference: luecken2022benchmarking @@ -90,21 +84,20 @@ param_list: dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). dataset_organism: homo_sapiens - - id: tabula_muris_senis_droplet_lung - obs_celltype: cell_type - obs_batch: donor_id - layer_counts: counts - dataset_id: tabula_muris_senis_droplet_lung - dataset_name: Tabula Muris Senis Lung - data_url: https://tabula-muris-senis.ds.czbiohub.org - data_reference: tabula2020single - dataset_summary: Aging mouse lung cells from Tabula Muris Senis - dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. - dataset_organism: mus_musculus + # disabled as this is not working in openproblemsv1 + # - id: tabula_muris_senis_droplet_lung + # obs_celltype: cell_type + # obs_batch: donor_id + # layer_counts: counts + # dataset_name: Tabula Muris Senis Lung + # data_url: https://tabula-muris-senis.ds.czbiohub.org + # data_reference: tabula2020single + # dataset_summary: Aging mouse lung cells from Tabula Muris Senis + # dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. + # dataset_organism: mus_musculus - id: tenx_1k_pbmc layer_counts: counts - dataset_id: tenx_1k_pbmc dataset_name: 1k PBMCs data_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 data_reference: 10x2018pbmc @@ -114,7 +107,6 @@ param_list: - id: tenx_5k_pbmc layer_counts: counts - dataset_id: tenx_5k_pbmc dataset_name: 5k PBMCs data_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 data_reference: 10x2019pbmc @@ -125,7 +117,6 @@ param_list: - id: tnbc_wu2021 obs_celltype: celltype_minor layer_counts: counts - dataset_id: tnbc_wu2021 dataset_name: Triple-Negative Breast Cancer data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 data_reference: wu2021single @@ -137,7 +128,6 @@ param_list: obs_celltype: cell_type obs_batch: lab layer_counts: counts - dataset_id: zebrafish dataset_name: Zebrafish embryonic cells data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 data_reference: wagner2018single @@ -145,7 +135,7 @@ param_list: dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio -normalization_id: [log_cp10k, sqrt_cp10k, l1_sqrt] +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset: '$id/dataset.h5ad' output_meta: '$id/dataset_metadata.yaml' output_state: '$id/state.yaml' diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 7b8a6a50a7..3adfd1e4f1 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -20,7 +20,6 @@ if [ ! -f $params_file ]; then cat > "$params_file" << 'HERE' param_list: - id: citeseq_cbmc - dataset_id: citeseq_cbmc dataset_name: "CITE-Seq CBMC" dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." @@ -30,18 +29,16 @@ param_list: layer_counts: counts - id: scicar_cell_lines - dataset_id: scicar_cell_lines dataset_name: "sci-CAR Cell Lines" dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." data_reference: cao2018joint data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 - dataset_organism: [homo_sapiens, mus_musculus] + dataset_organism: "[homo_sapiens, mus_musculus]" obs_celltype: cell_name layer_counts: counts - id: scicar_mouse_kidney - dataset_id: scicar_mouse_kidney dataset_name: "sci-CAR Mouse Kidney" dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." @@ -52,11 +49,11 @@ param_list: obs_batch: replicate layer_counts: counts -normalization_id: [log_cp10k, sqrt_cp10k, l1_sqrt] +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset_mod1: '$id/dataset_mod1.h5ad' -output_dataset_mod1: '$id/dataset_mod2.h5ad' -output_meta_mod1: '$id/dataset_metadata_mod1.h5ad' -output_meta_mod1: '$id/dataset_metadata_mod2.h5ad' +output_dataset_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' HERE fi diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index c9b9dac984..1890be57de 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -28,7 +28,6 @@ nextflow run . \ --obs_celltype "celltype" \ --obs_batch "tech" \ --layer_counts "counts" \ - --dataset_id pancreas \ --dataset_name "Human pancreas" \ --data_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ --data_reference "luecken2022benchmarking" \ diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 66b434a883..6ae0782394 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -22,8 +22,14 @@ workflow run_wf { key: "sqrt_cpm", args: [normalization_id: "sqrt_cpm", n_cp: 1000000], ), - l1_sqrt, - log_scran_pooling + l1_sqrt.run( + key: "l1_sqrt", + args: [normalization_id: "l1_sqrt"], + ), + log_scran_pooling.run( + key: "log_scran_pooling", + args: [normalization_id: "log_scran_pooling"], + ) ] output_ch = input_ch @@ -49,14 +55,14 @@ workflow run_wf { "dataset_description": "dataset_description", "dataset_organism": "dataset_organism", ], - toState: ["raw": "output"] + toState: ["output_raw": "output"] ) // subsample if so desired | subsample.run( runIf: { id, state -> state.do_subsample }, fromState: [ - "input": "raw", + "input": "output_raw", "n_obs": "n_obs", "n_vars": "n_vars", "keep_features": "keep_features", @@ -66,7 +72,7 @@ workflow run_wf { "seed": "seed" ], args: [output_mod2: null], - toState: [raw: "output"] + toState: ["output_raw": "output"] ) | runEach( @@ -81,49 +87,53 @@ workflow run_wf { filter: { id, state, comp -> comp.name in state.normalization_methods }, - fromState: ["input": "raw"], - toState: ["normalized": "output"] + fromState: ["input": "output_raw"], + toState: ["output_normalized": "output"] ) | pca.run( - fromState: ["input": "normalized"], - toState: ["pca": "output" ] + fromState: ["input": "output_normalized"], + toState: ["output_pca": "output" ] ) | hvg.run( - fromState: ["input": "pca"], - toState: ["hvg": "output"] + fromState: ["input": "output_pca"], + toState: ["output_hvg": "output"] ) | knn.run( - fromState: ["input": "hvg"], - toState: ["knn": "output"] + fromState: ["input": "output_hvg"], + toState: ["output_knn": "output"] ) | check_dataset_schema.run( - fromState: { id, state -> - [ - input: state.knn, - checks: null - ] - }, - toState: ["dataset": "output", "meta": "meta"] + fromState: ["input": "output_knn"], + toState: ["output_dataset": "output", "output_meta": "meta"] ) - // only output the files for which an output file was specified - | setState{ id, state -> - [ - "output_dataset": state.output_dataset ? state.dataset : null, - "output_meta": state.output_meta ? state.meta : null, - "output_raw": state.output_raw ? state.raw : null, - "output_normalized": state.output_normalized ? state.normalized : null, - "output_pca": state.output_pca ? state.pca : null, - "output_hvg": state.output_hvg ? state.hvg : null, - "output_knn": state.output_knn ? state.knn : null, - "_meta": state._meta - ] + | filter{ id, state -> + def uns = (new org.yaml.snakeyaml.Yaml().load(state.output_meta)).uns + def expected_id = "${uns.dataset_id}/${uns.normalization_id}" + + def is_ok = id == expected_id + + if (!is_ok) { + println("DETECTED ID MISMATCH: $id != $expected_id.\nState: $state\n") + } } + // only output the files for which an output file was specified + | setState([ + "output_dataset", + "output_meta", + "output_raw", + "output_normalized", + "output_pca", + "output_hvg", + "output_knn", + "_meta" + ]) + emit: output_ch } \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index f50e769f23..ad39d4ba90 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -22,8 +22,14 @@ workflow run_wf { key: "sqrt_cpm", args: [normalization_id: "sqrt_cpm", n_cp: 1000000] ), - l1_sqrt, - log_scran_pooling + l1_sqrt.run( + key: "l1_sqrt", + args: [normalization_id: "l1_sqrt"] + ), + log_scran_pooling.run( + key: "log_scran_pooling", + args: [normalization_id: "log_scran_pooling"] + ) ] output_ch = input_ch diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index ec0018f93c..2d5ed3bbf3 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -172,8 +172,7 @@ Arguments: Unintegrated AnnData HDF5 file. -Example file: -`resources_test/batch_integration/pancreas/unintegrated.h5ad` +Example file: `resources_test/batch_integration/pancreas/dataset.h5ad` Description: diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index da935f8cca..1ffe878348 100755 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -11,18 +11,16 @@ set -e COMMON_DATASETS="resources/datasets/openproblems_v1" OUTPUT_DIR="resources/batch_integration/datasets/openproblems_v1" -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - export NXF_VER=22.04.5 + nextflow run . \ - -main-script src/tasks/batch_integration/workflows/process_datasets/main.nf \ + -main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ -profile docker \ -entry auto \ -resume \ - --id resources \ - --input_states "resources/datasets/openproblems_v1/**/state.yaml" \ + --input_states "$COMMON_DATASETS/**/state.yaml" \ --rename_keys 'input:output_dataset' \ - --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 61f9a8d65b..979a16b87e 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -19,12 +19,13 @@ fi export NXF_VER=22.04.5 nextflow run . \ - -main-script src/tasks/batch_integration/workflows/run_benchmark/main.nf \ + -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ -profile docker \ -resume \ -entry auto \ - --id resources \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index 40fe2d4b2a..c9bf906135 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -5,16 +5,15 @@ functionality: - name: Inputs arguments: - name: "--input" - required: true - example: dataset.h5ad __merge__: "/src/tasks/batch_integration/api/file_common_dataset.yaml" - - name: Schemas - arguments: + required: true + direction: input - name: "--dataset_schema" type: "file" description: "The schema of the dataset to validate against" required: true default: "src/tasks/batch_integration/api/file_common_dataset.yaml" + direction: input - name: Outputs arguments: - name: "--output_dataset" diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index 557799041d..f46fdaadc8 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -20,13 +20,22 @@ workflow run_wf { "schema": "dataset_schema" ], args: [ - "stop_on_error": false, - "checks": null + "stop_on_error": false ], - toState: ["dataset": "output"] + toState: [ + "dataset": "output", + "dataset_checks": "checks" + ] ) // remove datasets which didn't pass the schema check + | view { id, state -> + if (state.dataset == null) { + "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" + } else { + null + } + } | filter { id, state -> state.dataset != null } diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 8bce72d67d..2b4089cb99 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -15,11 +15,11 @@ functionality: - name: Outputs arguments: - name: "--output" - direction: "output" type: file + required: true + direction: output description: A TSV file containing the scores of each of the methods example: scores.tsv - required: true resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run/config.vsh.yaml index cb095012e3..478aef9b58 100644 --- a/src/tasks/denoising/workflows/run/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--input_train" type: "file" - name: "--input_test" diff --git a/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml new file mode 100644 index 0000000000..8061f8f0c5 --- /dev/null +++ b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/dimensionality_reduction/pancreas/dataset.h5ad" +info: + label: "Dataset" + summary: "The dataset to pass to a method." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + var: + - type: double + name: hvg_score + description: High variability gene score (normalized dispersion). The greater, the more variable. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh new file mode 100644 index 0000000000..b6ae2b094f --- /dev/null +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,27 @@ +#!/bin/bash + + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: dimensionality_reduction +input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/dimensionality_reduction +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh similarity index 54% rename from src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh rename to src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh index f2ff994080..9f3cdbfe9b 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/run_test_on_tower.sh +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh @@ -1,15 +1,12 @@ #!/bin/bash -DATASET_DIR=resources_test/dimensionality_reduction/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE -id: pancreas_subsample -input: s3://openproblems-data/$DATASET_DIR/dataset.h5ad -input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad -dataset_id: pancreas -normalization_id: log_cp10k -output: scores.tsv +id: dimensionality_reduction +input_states: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output_test/v2/dimensionality_reduction HERE @@ -20,10 +17,11 @@ process { HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision integration_build \ + --revision main_build \ --pull-latest \ - --main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ + --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ --compute-env 7IkB9ckC81O0dgNemcPJTD \ --params-file /tmp/params.yaml \ + --entry-name auto \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index dd0de0ddbc..e625796d42 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -6,61 +6,19 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + COMMON_DATASETS="resources/datasets/openproblems_v1" OUTPUT_DIR="resources/dimensionality_reduction/datasets/openproblems_v1" -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import anndata as ad -import glob -import yaml - -h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") - -param_list = [] - -for h5ad_file in h5ad_files: - print(f"Checking {h5ad_file}") - adata = ad.read_h5ad(h5ad_file, backed=True) - - # TODO: fix this criterion to whatever it is you need - # if "batch" in adata.obs and "celltype" in adata.obs: - dataset_id = adata.uns["dataset_id"].replace("/", ".") - normalization_id = adata.uns["normalization_id"] - id = dataset_id + "." + normalization_id - obj = { - 'id': id, - 'input': h5ad_file, - 'dataset_id': dataset_id, - 'normalization_id': normalization_id - } - param_list.append(obj) - -output = { - "param_list": param_list, - "obs_label": "celltype", - "obs_batch": "batch", - "seed": 123, - "output_train": "\$id.train.h5ad", - "output_test": "\$id.test.h5ad" -} - -with open("$params_file", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script target/nextflow/dimensionality_reduction/process_dataset/main.nf \ + +nextflow run . \ + -main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ -profile docker \ - -resume \ - -params-file $params_file \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + -entry auto \ + --input_states "$COMMON_DATASETS/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index 3eecb22b2e..bda19a77e0 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -8,65 +8,24 @@ cd "$REPO_ROOT" set -e -export TOWER_WORKSPACE_ID=53907369739130 +# export TOWER_WORKSPACE_ID=53907369739130 -DATASETS_DIR="resources/dimensionality_reduction/datasets/openproblems_v1" -OUTPUT_DIR="resources/dimensionality_reduction/benchmarks/openproblems_v1" +DATASETS_DIR="resources/dimensionality_reduction" +OUTPUT_DIR="output/test" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import yaml - -dataset_dir = "$DATASETS_DIR" -output_dir = "$OUTPUT_DIR" - -# read split datasets yaml -with open(dataset_dir + "/params.yaml", "r") as file: - split_list = yaml.safe_load(file) -datasets = split_list['param_list'] - -# figure out where dataset/solution files were stored -param_list = [] - -for dataset in datasets: - id = dataset["id"] - input_train = dataset_dir + "/" + id + ".train.h5ad" - input_solution = dataset_dir + "/" + id + ".test.h5ad" - - obj = { - 'id': id, - 'dataset_id': dataset["dataset_id"], - 'normalization_id': dataset["normalization_id"], - 'input': input_train, - 'input_solution': input_solution - } - param_list.append(obj) - -# write as output file -output = { - "param_list": param_list, -} - -with open(output_dir + "/params.yaml", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ +nextflow run . \ + -main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ -profile docker \ -resume \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ - -with-tower - -bin/tools/docker/nextflow/process_log/process_log \ - --output "$OUTPUT_DIR/nextflow_log.tsv" + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR"\ + --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index d859352991..ab194bf5d7 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -8,44 +8,48 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/dimensionality_reduction/pancreas +set -e -if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 -fi +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/dimensionality_reduction mkdir -p $DATASET_DIR -# split dataset -viash run src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output_dataset $DATASET_DIR/dataset.h5ad \ - --output_solution $DATASET_DIR/solution.h5ad - - -# run one method -viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/embedding.h5ad - -# run one metric -viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ - --input_embedding $DATASET_DIR/embedding.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output $DATASET_DIR/score.h5ad - -# run benchmark -export NXF_VER=22.04.5 - -# after having added a split dataset component -nextflow \ - run . \ - -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ +# process dataset +echo Running process_dataset +nextflow run . \ + -main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ -profile docker \ - --id pancreas \ - --input_dataset $DATASET_DIR/dataset.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ No newline at end of file + -entry auto \ + --input_states "$RAW_DATA/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved + + +# # run one method +# viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ +# --input $DATASET_DIR/dataset.h5ad \ +# --output $DATASET_DIR/embedding.h5ad + +# # run one metric +# viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ +# --input_embedding $DATASET_DIR/embedding.h5ad \ +# --input_solution $DATASET_DIR/solution.h5ad \ +# --output $DATASET_DIR/score.h5ad + +# # run benchmark +# export NXF_VER=22.04.5 + +# # after having added a split dataset component +# nextflow \ +# run . \ +# -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ +# -profile docker \ +# --id pancreas \ +# --input_dataset $DATASET_DIR/dataset.h5ad \ +# --input_solution $DATASET_DIR/solution.h5ad \ +# --output scores.tsv \ +# --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..bd80704db5 --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,35 @@ +functionality: + name: "process_datasets" + namespace: "dimensionality_reduction/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __merge__: "/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" + required: true + direction: input + - name: "--dataset_schema" + type: "file" + required: true + direction: input + description: "The schema of the dataset to validate against" + default: "src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" + - name: Outputs + arguments: + - name: "--output_dataset" + __merge__: /src/tasks/dimensionality_reduction/api/file_dataset.yaml + required: true + direction: output + - name: "--output_solution" + __merge__: /src/tasks/dimensionality_reduction/api/file_solution.yaml + required: true + direction: output + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: dimensionality_reduction/process_dataset +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..653a21c763 --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf @@ -0,0 +1,56 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + fromState: [ + "input": "input", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false, + "checks": null + ], + toState: ["dataset": "output"] + ) + + // remove datasets which didn't pass the schema check + | filter { id, state -> + state.dataset != null + } + + | process_dataset.run( + fromState: [ + input: "dataset", + output_dataset: "output_dataset", + output_solution: "output_solution" + ], + toState: [ + dataset: "output_dataset", + solution: "output_solution" + ] + ) + + // only output the files for which an output file was specified + | setState { id, state -> + [ + "output_dataset": state.output_dataset ? state.dataset : null, + "output_solution": state.output_solution ? state.solution : null + ] + } + + emit: + output_ch +} \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/run_test.sh b/src/tasks/dimensionality_reduction/workflows/process_datasets/run_test.sh new file mode 100644 index 0000000000..d16cd7736f --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/run_test.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id run_test \ + --input_states "resources_test/common/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' \ + --publish_dir "resources_test/dimensionality_reduction" \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run/run_test.sh deleted file mode 100755 index 299f8accf8..0000000000 --- a/src/tasks/dimensionality_reduction/workflows/run/run_test.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/dimensionality_reduction/pancreas - -# run benchmark -export NXF_VER=23.04.2 - -nextflow \ - run . \ - -main-script src/tasks/dimensionality_reduction/workflows/run/main.nf \ - -profile docker \ - -resume \ - --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cp10k \ - --input $DATASET_DIR/dataset.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output scores.tsv \ - --publish_dir output/dimensionality_reduction/ \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml similarity index 85% rename from src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml rename to src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 88345c3be8..18efc35f98 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -4,23 +4,21 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the normalized dataset" - required: true - name: "--input_dataset" - type: "file" + __merge__: "/src/tasks/dimensionality_reduction/api/file_dataset.yaml" required: true + direction: input - name: "--input_solution" - type: "file" + __merge__: "/src/tasks/dimensionality_reduction/api/file_solution.yaml" required: true + direction: input - name: Outputs arguments: - name: "--output" - direction: "output" type: file example: output.tsv required: true + direction: output resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/dimensionality_reduction/workflows/run/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf similarity index 64% rename from src/tasks/dimensionality_reduction/workflows/run/main.nf rename to src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index f6ba9535c6..979143b66c 100644 --- a/src/tasks/dimensionality_reduction/workflows/run/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -1,13 +1,8 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() - -workflow { - helpMessage(config) - - // create channel from input parameters with - // arguments as defined in the config - channelFromParams(params, config) - | run_wf +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) } workflow run_wf { @@ -38,6 +33,11 @@ workflow run_wf { output_ch = input_ch + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + // extract the dataset metadata | check_dataset_schema.run( fromState: [input: "input_dataset"], @@ -47,57 +47,57 @@ workflow run_wf { ) // run all methods - | runComponents( + | runEach( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, config -> + filter: { id, state, comp -> def norm = state.normalization_id - def pref = config.functionality.info.preferred_normalization + def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name + id: { id, state, comp -> + id + "." + comp.config.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> + fromState: { id, state, comp -> def new_args = [ input: state.input_dataset ] - if (config.functionality.info.type == "control_method") { + if (comp.config.functionality.info.type == "control_method") { new_args.input_solution = state.input_solution } new_args }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - method_id: config.functionality.name, + method_id: comp.config.functionality.name, method_output: output.output ] } ) // run all metrics - | runComponents( + | runEach( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> + fromState: { id, state, comp -> [ input_solution: state.input_solution, input_embedding: state.method_output ] }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - metric_id: config.functionality.name, + metric_id: comp.config.functionality.name, metric_output: output.output ] } @@ -110,26 +110,19 @@ workflow run_wf { def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0].output + _meta: states[0]._meta ] [new_id, new_state] } - // convert to tsv and publish - | extract_scores.run( - auto: [publish: true] - ) + // convert to tsv and publish + | extract_scores.run( + fromState: ["input"], + toState: ["output"] + ) + + | setState(["output", "_meta"]) emit: output_ch } - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) - // todo: add datasets logging - writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) - writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) -} \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run/nextflow.config b/src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config similarity index 100% rename from src/tasks/dimensionality_reduction/workflows/run/nextflow.config rename to src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh new file mode 100755 index 0000000000..05f7294e22 --- /dev/null +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/dimensionality_reduction" +OUTPUT_DIR="resources_test/dimensionality_reduction/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id resources_test \ + --input_states "$DATASETS_DIR/**/*state.yaml" \ + --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/config.vsh.yaml b/src/tasks/label_projection/workflows/run/config.vsh.yaml index df85f2cfea..ad14b0f7f3 100644 --- a/src/tasks/label_projection/workflows/run/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the normalized dataset" - required: true - name: "--input_train" # __merge__: ../../api/file_train.yaml type: file diff --git a/src/tasks/match_modalities/workflows/run/config.vsh.yaml b/src/tasks/match_modalities/workflows/run/config.vsh.yaml index 690d3407b0..8d2586e81c 100644 --- a/src/tasks/match_modalities/workflows/run/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--input_mod1" type: "file" # todo: replace with includes - name: "--input_mod2" diff --git a/src/tasks/predict_modality/workflows/run/config.vsh.yaml b/src/tasks/predict_modality/workflows/run/config.vsh.yaml index 3e08a91355..1ba8a7677e 100644 --- a/src/tasks/predict_modality/workflows/run/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run/config.vsh.yaml @@ -4,10 +4,6 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--id" - type: "string" - description: "The ID of the dataset" - required: true - name: "--input_train_mod1" type: "file" # todo: replace with includes - name: "--input_train_mod2" From 661bbb96f9e7f75e2db8b0aa7460444a07baeb7a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 14:08:25 +0200 Subject: [PATCH 1019/1233] improve error message Former-commit-id: 5f71a6678c484f424d461c776861a277c59b4eca --- .../workflows/process_openproblems_v1/main.nf | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 6ae0782394..4e784ee1d5 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -88,7 +88,12 @@ workflow run_wf { comp.name in state.normalization_methods }, fromState: ["input": "output_raw"], - toState: ["output_normalized": "output"] + toState: { id, state, output, comp -> + state + [ + output_normalization: output.output, + normalization_id: comp.name + ] + } ) | pca.run( @@ -118,8 +123,10 @@ workflow run_wf { def is_ok = id == expected_id if (!is_ok) { - println("DETECTED ID MISMATCH: $id != $expected_id.\nState: $state\n") + println("DETECTED ID MISMATCH: $id != $expected_id.\nTuple:\n${toYamlBlob([id, state])}\n") } + + is_ok } // only output the files for which an output file was specified From 7d23b26a445634be0d7dd66c0744c56900de5f33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michaela=20M=C3=BCller?= <51025211+mumichae@users.noreply.github.com> Date: Wed, 11 Oct 2023 14:54:44 +0200 Subject: [PATCH 1020/1233] cell cycle only for human or mouse for now, else return np.nan (#255) Former-commit-id: 9e6ca5c57cf36e7ebe0f3171dddfc856a3e0fea7 --- .../metrics/cell_cycle_conservation/script.py | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index f0a24193a5..e295ca6786 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -25,13 +25,17 @@ } print('compute score', flush=True) -score = cell_cycle( - input_solution, - input_integrated, - batch_key='batch', - embed='X_emb', - organism=translator[input_solution.uns['dataset_organism']] -) +organism = translator[input_solution.uns['dataset_organism']] +if organism not in ["human", "mouse"]: + score = np.nan +else: + score = cell_cycle( + input_solution, + input_integrated, + batch_key='batch', + embed='X_emb', + organism=organism, + ) print('Create output AnnData object', flush=True) output = ad.AnnData( From d899de4fca29c6e1ff5b24cfcb43473f36dc4657 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 15:24:09 +0200 Subject: [PATCH 1021/1233] Various fixes (#256) * use tmp file in resource scripts * fix dataset workflow * simply workflow * fix DR Former-commit-id: a5acc125ae62f20df60f3eddc2db53c8f76de8ad --- .../resource_scripts/openproblems_v1.sh | 6 ++--- .../openproblems_v1_multimodal.sh | 6 ++--- .../workflows/process_openproblems_v1/main.nf | 10 +++++--- .../main.nf | 24 +++++++++---------- .../workflows/process_datasets/main.nf | 15 +++--------- 5 files changed, 25 insertions(+), 36 deletions(-) diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 9815ea652c..1c146b98df 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -14,10 +14,9 @@ if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" +params_file="/tmp/datasets_openproblems_v1_params.yaml" -if [ ! -f $params_file ]; then - cat > "$params_file" << 'HERE' +cat > "$params_file" << 'HERE' param_list: - id: allen_brain_atlas obs_celltype: label @@ -145,7 +144,6 @@ output_pca: force_null output_hvg: force_null output_knn: force_null HERE -fi export NXF_VER=23.04.2 nextflow run . \ diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 3adfd1e4f1..f6e67dd12a 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -14,10 +14,9 @@ if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" +params_file="/tmp/datasets_openproblems_v1_multimodal_params.yaml" -if [ ! -f $params_file ]; then - cat > "$params_file" << 'HERE' +cat > "$params_file" << 'HERE' param_list: - id: citeseq_cbmc dataset_name: "CITE-Seq CBMC" @@ -56,7 +55,6 @@ output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' HERE -fi export NXF_VER=22.04.5 nextflow \ diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 4e784ee1d5..00411529e1 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -88,9 +88,9 @@ workflow run_wf { comp.name in state.normalization_methods }, fromState: ["input": "output_raw"], - toState: { id, state, output, comp -> + toState: { id, output, state, comp -> state + [ - output_normalization: output.output, + output_normalized: output.output, normalization_id: comp.name ] } @@ -116,9 +116,13 @@ workflow run_wf { toState: ["output_dataset": "output", "output_meta": "meta"] ) + // TODO: remove this filter if we're sure the mismatch issue no longer occurs | filter{ id, state -> def uns = (new org.yaml.snakeyaml.Yaml().load(state.output_meta)).uns - def expected_id = "${uns.dataset_id}/${uns.normalization_id}" + def expected_id = state.normalization_methods.size() > 1 ? + "${uns.dataset_id}/${uns.normalization_id}" : + uns.dataset_id + expected_id = expected_id.replaceAll("_subsample", "") def is_ok = id == expected_id diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index ad39d4ba90..00eb39d073 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -142,8 +142,8 @@ workflow run_wf { ] }, toState: [ - "dataset_mod1": "output", - "meta_mod1": "meta" + "output_dataset_mod1": "output", + "output_meta_mod1": "meta" ] ) @@ -155,21 +155,19 @@ workflow run_wf { ] }, toState: [ - "dataset_mod2": "output", - "meta_mod2": "meta" + "output_dataset_mod2": "output", + "output_meta_mod2": "meta" ] ) // only output the files for which an output file was specified - | setState{ id, state -> - [ - "output_dataset_mod1" : state.output_dataset_mod1 ? state.dataset_mod1: null, - "output_dataset_mod2" : state.output_dataset_mod2 ? state.dataset_mod2: null, - "output_meta_mod1" : state.output_meta_mod1 ? state.meta_mod1: null, - "output_meta_mod2" : state.output_meta_mod2 ? state.meta_mod2: null, - "_meta": state._meta - ] - } + | setState([ + "output_dataset_mod1", + "output_dataset_mod2", + "output_meta_mod1", + "output_meta_mod2", + "_meta" + ]) emit: output_ch diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf index 653a21c763..38c35f072e 100644 --- a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf @@ -32,24 +32,15 @@ workflow run_wf { } | process_dataset.run( - fromState: [ - input: "dataset", + fromState: [input: "dataset"], + toState: [ output_dataset: "output_dataset", output_solution: "output_solution" - ], - toState: [ - dataset: "output_dataset", - solution: "output_solution" ] ) // only output the files for which an output file was specified - | setState { id, state -> - [ - "output_dataset": state.output_dataset ? state.dataset : null, - "output_solution": state.output_solution ? state.solution : null - ] - } + | setState(["output_dataset", "output_solution"]) emit: output_ch From 86a390be8b11361d3314ef80dcfd02259d7503dd Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 16:14:12 +0200 Subject: [PATCH 1022/1233] Denoising/update nextflow workflows (#249) * add nf-tower scripts batch_integration * fix typo * WIP * fix process_datasets * WIP * Update nf workflows * update run scripts * fix typo in workflow * undo batch_integration changes * use merge in workflow configs * update base image version * Update process_datasets workflow * fix scripts & workflows * update run_benchmark workflow * add review updates --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: d8ad72fdd75bee3b1a92c2861f232bcbd10e63d2 --- _viash.yaml | 2 +- .../workflows/process_datasets/main.nf | 22 +---- .../denoising/api/file_common_dataset.yaml | 16 ++++ .../no_denoising/config.vsh.yaml | 2 +- .../perfect_denoising/config.vsh.yaml | 2 +- .../denoising/methods/alra/config.vsh.yaml | 2 +- .../denoising/methods/dca/config.vsh.yaml | 2 +- .../methods/knn_smoothing/config.vsh.yaml | 2 +- .../denoising/methods/magic/config.vsh.yaml | 2 +- .../denoising/metrics/mse/config.vsh.yaml | 2 +- .../denoising/metrics/poisson/config.vsh.yaml | 2 +- .../nf_tower_scripts/run_benchmark.sh | 28 +++++++ .../run_test.sh} | 15 ++-- .../resources_scripts/process_datasets.sh | 62 +++----------- .../resources_scripts/run_benchmark.sh | 82 ++----------------- .../resources_test_scripts/pancreas.sh | 67 ++++++++------- .../process_datasets/config.vsh.yaml | 36 ++++++++ .../workflows/process_datasets/main.nf | 49 +++++++++++ .../process_datasets/nextflow.config | 16 ++++ .../workflows/process_datasets/run_test.sh | 25 ++++++ src/tasks/denoising/workflows/run/run_test.sh | 29 ------- .../{run => run_benchmark}/config.vsh.yaml | 13 ++- .../workflows/{run => run_benchmark}/main.nf | 61 +++++++------- .../{run => run_benchmark}/nextflow.config | 0 .../workflows/run_benchmark/run_test.sh | 31 +++++++ 25 files changed, 314 insertions(+), 256 deletions(-) create mode 100644 src/tasks/denoising/api/file_common_dataset.yaml create mode 100644 src/tasks/denoising/nf_tower_scripts/run_benchmark.sh rename src/tasks/denoising/{workflows/run/run_test_on_tower.sh => nf_tower_scripts/run_test.sh} (63%) create mode 100644 src/tasks/denoising/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/denoising/workflows/process_datasets/main.nf create mode 100644 src/tasks/denoising/workflows/process_datasets/nextflow.config create mode 100755 src/tasks/denoising/workflows/process_datasets/run_test.sh delete mode 100755 src/tasks/denoising/workflows/run/run_test.sh rename src/tasks/denoising/workflows/{run => run_benchmark}/config.vsh.yaml (67%) rename src/tasks/denoising/workflows/{run => run_benchmark}/main.nf (65%) rename src/tasks/denoising/workflows/{run => run_benchmark}/nextflow.config (100%) create mode 100755 src/tasks/denoising/workflows/run_benchmark/run_test.sh diff --git a/_viash.yaml b/_viash.yaml index dd1e0534ac..abb716012b 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.8.0-RC5 +viash_version: 0.8.0-RC6 source: src target: target diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index f46fdaadc8..517db44bb7 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -29,36 +29,20 @@ workflow run_wf { ) // remove datasets which didn't pass the schema check - | view { id, state -> - if (state.dataset == null) { - "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" - } else { - null - } - } | filter { id, state -> state.dataset != null } | process_dataset.run( - fromState: [ - input: "dataset", + fromState: [ input: "dataset" ], + toState: [ output_dataset: "output_dataset", output_solution: "output_solution" - ], - toState: [ - dataset: "output_dataset", - solution: "output_solution" ] ) // only output the files for which an output file was specified - | setState { id, state -> - [ - "output_dataset": state.output_dataset ? state.dataset : null, - "output_solution": state.output_solution ? state.solution : null - ] - } + | setState(["output_dataset", "output_solution"]) emit: output_ch diff --git a/src/tasks/denoising/api/file_common_dataset.yaml b/src/tasks/denoising/api/file_common_dataset.yaml new file mode 100644 index 0000000000..0f5551a4ca --- /dev/null +++ b/src/tasks/denoising/api/file_common_dataset.yaml @@ -0,0 +1,16 @@ +type: file +example: "resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common Dataset" + summary: A subset of the common dataset. + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index 0690a6b792..ce6238fe0e 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index 25f6febd9d..ab4d71164e 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 7317aeb306..e9526009c0 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ Matrix, bit64, rsvd ] diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index 0eb27673d0..046eceb8a4 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index a5b87fef59..d872b8fdab 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 122fa9dc79..02b570f418 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index babbe7a6b6..70e0cc5dae 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index fc325d7895..dd96338862 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pip: scprep diff --git a/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh b/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh new file mode 100644 index 0000000000..099b248244 --- /dev/null +++ b/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +DATASET_DIR=resources_test/denoising/pancreas + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: denoising +input_states: s3://openproblems-data/resources/denoising/datasets/**/*state.yaml +rename_keys: 'input_train:output_train,input_test:output_test' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/denoising +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/run_test_on_tower.sh b/src/tasks/denoising/nf_tower_scripts/run_test.sh similarity index 63% rename from src/tasks/denoising/workflows/run/run_test_on_tower.sh rename to src/tasks/denoising/nf_tower_scripts/run_test.sh index 912cd376dc..a9b35a8d3e 100644 --- a/src/tasks/denoising/workflows/run/run_test_on_tower.sh +++ b/src/tasks/denoising/nf_tower_scripts/run_test.sh @@ -4,13 +4,11 @@ DATASET_DIR=resources_test/denoising/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE -id: pancreas_subsample -input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad -input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad -dataset_id: pancreas -normalization_id: log_cp10k -output: scores.tsv -publish_dir: s3://openproblems-nextflow/output_test/v2/denoising +id: denoising_test +input_states: s3://openproblems-data/resources_test/denoising/pancreas/ +rename_keys: 'input_train:output_train,input_test:output_test' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output_test/v2/denoising/ HERE cat > /tmp/nextflow.config << HERE @@ -22,8 +20,9 @@ HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ - --main-script src/tasks/denoising/workflows/run/main.nf \ + --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ --compute-env 7IkB9ckC81O0dgNemcPJTD \ --params-file /tmp/params.yaml \ + --entry-name auto \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 0cb7073463..213f6b0d4c 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -6,59 +6,21 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + COMMON_DATASETS="resources/datasets/openproblems_v1" OUTPUT_DIR="resources/denoising/datasets/openproblems_v1" -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import anndata as ad -import glob -import yaml - -h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") - -# this task doesn't use normalizations -# -param_list = {} - -for h5ad_file in h5ad_files: - print(f"Checking {h5ad_file}") - adata = ad.read_h5ad(h5ad_file, backed=True) - if "counts" in adata.layers: - dataset_id = adata.uns["dataset_id"].replace("/", ".") - obj = { - 'id': dataset_id, - 'input': h5ad_file, - 'dataset_id': dataset_id, - } - param_list[dataset_id] = obj - -output = { - "param_list": list(param_list.values()), - "seed": 123, - "output_train": "\$id.train.h5ad", - "output_test": "\$id.test.h5ad" -} - -with open("$params_file", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script target/nextflow/denoising/process_dataset/main.nf \ + +nextflow run . \ + -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ -profile docker \ + -entry auto \ -resume \ - -params-file $params_file \ - --publish_dir "$OUTPUT_DIR" - -bin/tools/docker/nextflow/process_log/process_log \ - --output "$OUTPUT_DIR/nextflow_log.tsv" \ No newline at end of file + --input_states "$COMMON_DATASETS/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index ee0557166f..635b9332f1 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -8,78 +8,14 @@ cd "$REPO_ROOT" set -e -export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/denoising/datasets/openproblems_v1" -OUTPUT_DIR="resources/denoising/benchmarks/openproblems_v1" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import yaml -import os - -dataset_dir = "$DATASETS_DIR" -output_dir = "$OUTPUT_DIR" - -# read split datasets yaml -with open(dataset_dir + "/params.yaml", "r") as file: - split_list = yaml.safe_load(file) -datasets = split_list['param_list'] - -# figure out where train/test files were stored -param_list = [] - -for dataset in datasets: - id = dataset["id"] - input_train = dataset_dir + "/" + id + ".train.h5ad" - input_test = dataset_dir + "/" + id + ".test.h5ad" - - if os.path.exists(input_test): - obj = { - 'id': id, - 'id': id, - 'id': id, - 'dataset_id': dataset["dataset_id"], - 'input_train': input_train, - 'input_test': input_test - } - param_list.append(obj) - -# write as output file -output = { - "param_list": param_list, -} - -with open(output_dir + "/params.yaml", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script src/tasks/denoising/workflows/run/main.nf \ - -profile docker \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ - -with-tower -bin/tools/docker/nextflow/process_log/process_log \ - --output "$OUTPUT_DIR/nextflow_log.tsv" - -# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' -# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' - -# nextflow run . \ -# -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ -# -profile docker \ -# --input_train resources_test/label_projection/pancreas/train.h5ad \ -# --input_test resources_test/label_projection/pancreas/test.h5ad \ -# --input_solution resources_test/label_projection/pancreas/solution.h5ad \ -# --publish_dir foo \ No newline at end of file +nextflow run . \ + -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "resources/batch_integration/datasets/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ + --publish_dir "resources/batch_integration/benchmarks/openproblems_v1" \ No newline at end of file diff --git a/src/tasks/denoising/resources_test_scripts/pancreas.sh b/src/tasks/denoising/resources_test_scripts/pancreas.sh index ddccd6bfa6..c737b39c2e 100755 --- a/src/tasks/denoising/resources_test_scripts/pancreas.sh +++ b/src/tasks/denoising/resources_test_scripts/pancreas.sh @@ -1,7 +1,4 @@ #!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'denoising|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -9,44 +6,46 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/denoising/pancreas +set -e -if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 -fi +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/denoising mkdir -p $DATASET_DIR -# split dataset -viash run src/tasks/denoising/process_dataset/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output_train $DATASET_DIR/train.h5ad \ - --output_test $DATASET_DIR/test.h5ad \ - --seed 123 +# process dataset +echo Running process_dataset +nextflow run . \ + -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + --input_states "$RAW_DATA/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' # run one method viash run src/tasks/denoising/methods/magic/config.vsh.yaml -- \ - --input_train $DATASET_DIR/train.h5ad \ - --output $DATASET_DIR/denoised.h5ad + --input_train $DATASET_DIR/pancreas/train.h5ad \ + --output $DATASET_DIR/pancreas/denoised.h5ad # run one metric viash run src/tasks/denoising/metrics/poisson/config.vsh.yaml -- \ - --input_denoised $DATASET_DIR/denoised.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --output $DATASET_DIR/score.h5ad - -# run benchmark -export NXF_VER=22.04.5 - -nextflow \ - run . \ - -main-script src/tasks/denoising/workflows/run/main.nf \ - -profile docker \ - -resume \ - --id pancreas \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ No newline at end of file + --input_denoised $DATASET_DIR/pancreas/denoised.h5ad \ + --input_test $DATASET_DIR/pancreas/test.h5ad \ + --output $DATASET_DIR/pancreas/score.h5ad + +# # run benchmark +# export NXF_VER=22.04.5 + +# nextflow \ +# run . \ +# -main-script src/tasks/denoising/workflows/run/main.nf \ +# -profile docker \ +# -resume \ +# --id pancreas \ +# --input_train $DATASET_DIR/train.h5ad \ +# --input_test $DATASET_DIR/test.h5ad \ +# --output scores.tsv \ +# --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..1ce58796c5 --- /dev/null +++ b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,36 @@ +functionality: + name: "process_datasets" + namespace: "denoising/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + required: true + example: dataset.h5ad + __merge__: "/src/tasks/denoising/api/file_common_dataset.yaml" + - name: Schemas + arguments: + - name: "--dataset_schema" + type: "file" + description: "The schema of the dataset to validate against" + required: true + default: "src/tasks/denoising/api/file_common_dataset.yaml" + - name: Outputs + arguments: + - name: "--output_train" + __merge__: "/src/tasks/denoising/api/file_train.yaml" + direction: output + required: true + - name: "--output_test" + __merge__: "/src/tasks/denoising/api/file_test.yaml" + direction: output + required: true + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: denoising/process_dataset +platforms: + - type: nextflow diff --git a/src/tasks/denoising/workflows/process_datasets/main.nf b/src/tasks/denoising/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..8d52e1d81a --- /dev/null +++ b/src/tasks/denoising/workflows/process_datasets/main.nf @@ -0,0 +1,49 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + fromState: [ + "input": "input", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset": "output", + "dataset_checks": "checks" + ] + ) + + // remove datasets which didn't pass the schema check + | filter { id, state -> + state.dataset != null + } + + | process_dataset.run( + fromState: [ input: "dataset" ], + toState: [ + output_train: "output_train", + output_test: "output_test" + ] + ) + + // only output the files for which an output file was specified + | setState(["output_train", "output_test"]) + + emit: + output_ch +} diff --git a/src/tasks/denoising/workflows/process_datasets/nextflow.config b/src/tasks/denoising/workflows/process_datasets/nextflow.config new file mode 100644 index 0000000000..150119dfa2 --- /dev/null +++ b/src/tasks/denoising/workflows/process_datasets/nextflow.config @@ -0,0 +1,16 @@ +manifest { + name = 'batch_integration/workflows/run' + mainScript = 'main.nf' + nextflowVersion = '!>=22.04.5' + description = 'Batch integration' +} + +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() +} + +// include common settings +includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") +includeConfig("${params.rootDir}/src/wf_utils/labels.config") + +process.errorStrategy = 'ignore' diff --git a/src/tasks/denoising/workflows/process_datasets/run_test.sh b/src/tasks/denoising/workflows/process_datasets/run_test.sh new file mode 100755 index 0000000000..ed8484693b --- /dev/null +++ b/src/tasks/denoising/workflows/process_datasets/run_test.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id run_test \ + --input_states "resources_test/common/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "train.h5ad", "output_test": "test.h5ad"}' \ + --publish_dir "resources_test/denoising" \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/run_test.sh b/src/tasks/denoising/workflows/run/run_test.sh deleted file mode 100755 index f6f0e8884c..0000000000 --- a/src/tasks/denoising/workflows/run/run_test.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#viash ns build -q 'denoising|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/denoising/pancreas - -# run benchmark -export NXF_VER=23.04.2 - -nextflow \ - run . \ - -main-script src/tasks/denoising/workflows/run/main.nf \ - -profile docker \ - -resume \ - -c src/wf_utils/labels_ci.config \ - --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cp10k \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --output scores.tsv \ - --publish_dir output/denoising/ \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml similarity index 67% rename from src/tasks/denoising/workflows/run/config.vsh.yaml rename to src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index 478aef9b58..e7d70583c1 100644 --- a/src/tasks/denoising/workflows/run/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -5,14 +5,21 @@ functionality: - name: Inputs arguments: - name: "--input_train" - type: "file" + __merge__: "/src/tasks/denoising/api/file_train.yaml" + required: true + direction: input - name: "--input_test" - type: "file" + __merge__: "/src/tasks/denoising/api/file_test.yaml" + required: true + direction: input - name: Outputs arguments: - name: "--output" - direction: "output" type: file + required: true + direction: output + description: A TSV file containing the scores of each of the methods + example: scores.tsv resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/denoising/workflows/run/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf similarity index 65% rename from src/tasks/denoising/workflows/run/main.nf rename to src/tasks/denoising/workflows/run_benchmark/main.nf index 3f37c4dbf8..c9eb53c511 100644 --- a/src/tasks/denoising/workflows/run/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -1,5 +1,9 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} workflow run_wf { take: @@ -20,9 +24,14 @@ workflow run_wf { mse, poisson ] - + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } // extract the dataset metadata | check_dataset_schema.run( @@ -36,35 +45,32 @@ workflow run_wf { ) // run all methods - | runComponents( + | runEach( components: methods, // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name + id: { id, state, comp -> + id + "." + comp.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> - def new_args = [ - input_train: state.input_train, - input_test: state.input_test - ] - new_args - }, + fromState: [ + input_train: "input_train", + input_test: "input_test" + ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - method_id: config.functionality.name, + method_id: comp.functionality.name, method_output: output.output ] } ) // run all metrics - | runComponents( + | runEach( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -72,9 +78,9 @@ workflow run_wf { input_denoised: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - metric_id: config.functionality.name, + metric_id: comp.functionality.name, metric_output: output.output ] } @@ -93,20 +99,13 @@ workflow run_wf { } // convert to tsv and publish - | extract_scores.run( - auto: [publish: true] - ) + | extract_scores.run( + fromState: ["input"], + toState: ["output"] + ) + + | setState(["output", "_meta"]) emit: output_ch -} - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) - // todo: add datasets logging - writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) - writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/denoising/workflows/run/nextflow.config b/src/tasks/denoising/workflows/run_benchmark/nextflow.config similarity index 100% rename from src/tasks/denoising/workflows/run/nextflow.config rename to src/tasks/denoising/workflows/run_benchmark/nextflow.config diff --git a/src/tasks/denoising/workflows/run_benchmark/run_test.sh b/src/tasks/denoising/workflows/run_benchmark/run_test.sh new file mode 100755 index 0000000000..46f46f8eb2 --- /dev/null +++ b/src/tasks/denoising/workflows/run_benchmark/run_test.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/denoising" +OUTPUT_DIR="resources_test/denoising/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id resources \ + --input_states "$DATASETS_DIR/**/.*state.yaml" \ + --rename_keys 'input_train:output_train,input_test:output_test' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file From 9445f572f081b8d937f03c9b17c59ed7d0cfca56 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 16:17:15 +0200 Subject: [PATCH 1023/1233] update base image versions Former-commit-id: a52040479aa2aaf02758922c0d4827b4a22aee6d --- .../control_methods/meanpergene/config.vsh.yaml | 2 +- .../control_methods/random_predict/config.vsh.yaml | 5 +---- .../control_methods/solution/config.vsh.yaml | 5 +---- .../predict_modality/control_methods/zeros/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml | 4 ++-- src/tasks/predict_modality/methods/lm/config.vsh.yaml | 4 ++-- .../predict_modality/methods/newwave_knnr/config.vsh.yaml | 4 ++-- .../predict_modality/methods/random_forest/config.vsh.yaml | 4 ++-- .../predict_modality/metrics/correlation/config.vsh.yaml | 4 ++-- src/tasks/predict_modality/metrics/mse/config.vsh.yaml | 2 +- 11 files changed, 16 insertions(+), 22 deletions(-) diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 61895787c5..87cde8ab9c 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml index c2e11990ac..ba77d5c1a5 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -10,10 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 - setup: - - type: r - cran: [ bit64] + image: ghcr.io/openproblems-bio/base_r:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index c60e967a60..63d64bfe29 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -10,10 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 - setup: - - type: r - cran: [ bit64] + image: ghcr.io/openproblems-bio/base_r:1.0.2] - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml index fc1a2fb078..5e15d92fe1 100644 --- a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 5ccc6118af..99e0a5f4be 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index 0e8b034f7c..6a5570fa5c 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -27,10 +27,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ lmds, FNN, proxyC, bit64 ] + cran: [ lmds, FNN, proxyC] - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 444a8f5d00..244137fc4f 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -23,10 +23,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ lmds, RcppArmadillo, pbapply, bit64] + cran: [ lmds, RcppArmadillo, pbapply] - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 40e9e058d8..f3a37d053e 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -31,10 +31,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ lmds, FNN, proxy, proxyC, bit64 ] + cran: [ lmds, FNN, proxy, proxyC] bioc: [ SingleCellExperiment, NewWave ] - type: r github: [Jiefei-Wang/SharedObject, fedeago/NewWave] diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 5e6f978a53..d8d5435c99 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -27,10 +27,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ lmds, ranger, pbapply, bit64 ] + cran: [ lmds, ranger, pbapply] - type: nextflow directives: label: [ "midtime", highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index 6f5fcaf8e6..71dbea0b90 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -56,10 +56,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ proxyC, testthat, bit64 ] + cran: [ proxyC, testthat] github: dynverse/dynutils - type: nextflow directives: diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml index 6cd843f953..3383eddc2a 100644 --- a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] From 69d28a06e257968167671f00534f14aebfcb147d Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 16:17:53 +0200 Subject: [PATCH 1024/1233] remove nextflow config Former-commit-id: 63964fbf7af4e9520f5ea99d38f3f4e5cadf9863 --- .../workflows/run/nextflow.config | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 src/tasks/predict_modality/workflows/run/nextflow.config diff --git a/src/tasks/predict_modality/workflows/run/nextflow.config b/src/tasks/predict_modality/workflows/run/nextflow.config deleted file mode 100644 index d0feacc62f..0000000000 --- a/src/tasks/predict_modality/workflows/run/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'predict_modality/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Predict modality' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' \ No newline at end of file From 22d7d514c47dffcb1b034a51740218c6a25104f4 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 16:54:02 +0200 Subject: [PATCH 1025/1233] add process_datasets workflow Former-commit-id: 38a559d106069d1b05510f4296c891649ed7e4c3 --- .../process_datasets/config.vsh.yaml | 47 ++++++++++ .../workflows/process_datasets/main.nf | 89 +++++++++++++++++++ 2 files changed, 136 insertions(+) create mode 100644 src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/predict_modality/workflows/process_datasets/main.nf diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..211454f33c --- /dev/null +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,47 @@ +functionality: + name: "process_datasets" + namespace: "predict_modality/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input_rna" + __merge__: "/src/tasks/predict_modality/api/file_dataset_rna.yaml" + required: true + direction: input + - name: "--input_other_mod" + __merge__: "/src/tasks/predict_modality/api/file_dataset_other_mod.yaml" + direction: input + required: true + - name: "--dataset_schema" + type: "file" + description: "The schema of the dataset to validate against" + required: true + default: "src/tasks/predict_modality/api/file_common_dataset.yaml" + direction: input + - name: Outputs + arguments: + - name: "--output_train_mod1" + __merge__: /src/tasks/predict_modality/api/file_train_mod1.yaml + direction: output + required: true + - name: "--output_train_mod2" + __merge__: /src/tasks/predict_modality/api/file_train_mod2.yaml + direction: output + required: true + - name: "--output_test_mod1" + __merge__: /src/tasks/predict_modality/api/file_test_mod1.yaml + direction: "output" + required: true + - name: "--output_test_mod2" + __merge__: /src/tasks/predict_modality/api/file_test_mod2.yaml + direction: output + required: true + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: predict_modality/process_dataset +platforms: + - type: nextflow diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..d1c590bdfa --- /dev/null +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -0,0 +1,89 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + fromState: [ + "input": "input_rna", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset_rna": "output", + "dataset_checks": "checks" + ] + ) + + | check_dataset_schema.run( + fromState: [ + "input": "input_other_mod", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset_other_mod": "output", + "dataset_checks": "checks" + ] + ) + + // remove datasets which didn't pass the schema check + | view { id, state -> + if (state.dataset_rna == null) { + "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" + } else if (state.dataset_other_mod == null) { + "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" + } else { + null + } + } + | filter { id, state -> + state.dataset_rna != null, + state.dataset_other_mod != null + } + + | process_dataset.run( + fromState: [ + input_rna: "dataset_rna", + input_other_mod: "dataset_other_mod", + output_train_mod1: "output_train_mod1", + output_train_mod2: "output_train_mod2", + output_test_mod1: "output_test_mod1", + output_test_mod2: "output_test_mod2" + ], + toState: [ + train_mod1: "output_train_mod1", + train_mod2: "output_train_mod2", + test_mod1: "output_test_mod1", + test_mod2: "output_test_mod2" + ] + ) + + // only output the files for which an output file was specified + | setState { id, state -> + [ + "output_train_mod1": state.output_train_mod1 ? state.train_mod1 : null, + "output_train_mod2": state.output_train_mod2 ? state.train_mod2 : null, + "output_test_mod1": state.output_test_mod1 ? state.test_mod1 : null, + "output_test_mod2": state.output_test_mod2 ? state.test_mod2 : null, + ] + } + + emit: + output_ch +} From 916ea36152e6606241316e02bd1c47734741becd Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 20:32:20 +0200 Subject: [PATCH 1026/1233] Update label projection (#258) * add nf-tower scripts batch_integration * fix typo * WIP * fix process_datasets * WIP * Update nf workflows * update run scripts * fix typo in workflow * undo batch_integration changes * use merge in workflow configs * update base image version * Update process_datasets workflow * fix scripts & workflows * update label proj * remove newline --------- Co-authored-by: Kai Waldrant Former-commit-id: 0c7d3f78deff2ffa8ae1957aa473a5fcc6ba866f --- .../api/comp_process_dataset.yaml | 2 +- .../api/file_common_dataset.yaml | 48 +++++++++++ .../resources_scripts/process_datasets.sh | 63 +++------------ .../resources_scripts/run_benchmark.sh | 79 +++---------------- .../resources_test_scripts/pancreas.sh | 60 +++++++------- .../process_datasets/config.vsh.yaml | 39 +++++++++ .../workflows/process_datasets/main.nf | 50 ++++++++++++ .../workflows/run/nextflow.config | 16 ---- .../workflows/run/run_test.sh | 29 ------- .../workflows/run/run_test_on_tower.sh | 30 ------- .../{run => run_benchmark}/config.vsh.yaml | 14 ++-- .../workflows/{run => run_benchmark}/main.nf | 59 +++++++------- 12 files changed, 228 insertions(+), 261 deletions(-) create mode 100644 src/tasks/label_projection/api/file_common_dataset.yaml create mode 100644 src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/label_projection/workflows/process_datasets/main.nf delete mode 100644 src/tasks/label_projection/workflows/run/nextflow.config delete mode 100755 src/tasks/label_projection/workflows/run/run_test.sh delete mode 100644 src/tasks/label_projection/workflows/run/run_test_on_tower.sh rename src/tasks/label_projection/workflows/{run => run_benchmark}/config.vsh.yaml (79%) rename src/tasks/label_projection/workflows/{run => run_benchmark}/main.nf (65%) diff --git a/src/tasks/label_projection/api/comp_process_dataset.yaml b/src/tasks/label_projection/api/comp_process_dataset.yaml index 13adb6ec84..03c2ea3726 100644 --- a/src/tasks/label_projection/api/comp_process_dataset.yaml +++ b/src/tasks/label_projection/api/comp_process_dataset.yaml @@ -9,7 +9,7 @@ functionality: A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input" - __merge__: /src/datasets/api/file_common_dataset.yaml + __merge__: file_common_dataset.yaml direction: input required: true - name: "--output_train" diff --git a/src/tasks/label_projection/api/file_common_dataset.yaml b/src/tasks/label_projection/api/file_common_dataset.yaml new file mode 100644 index 0000000000..2cbd64b47f --- /dev/null +++ b/src/tasks/label_projection/api/file_common_dataset.yaml @@ -0,0 +1,48 @@ +type: file +example: "resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common Dataset" + summary: A subset of the common dataset. + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized expression values + required: true + obs: + - type: string + name: celltype + description: Cell type information + required: true + - type: string + name: batch + description: Batch information + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index 9e16f606d0..4cca9cb8de 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -6,60 +6,21 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + COMMON_DATASETS="resources/datasets/openproblems_v1" OUTPUT_DIR="resources/label_projection/datasets/openproblems_v1" -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import anndata as ad -import glob -import yaml - -h5ad_files = glob.glob("$COMMON_DATASETS/**.h5ad") - -param_list = [] - -for h5ad_file in h5ad_files: - print(f"Checking {h5ad_file}") - adata = ad.read_h5ad(h5ad_file, backed=True) - if "batch" in adata.obs and "celltype" in adata.obs: - dataset_id = adata.uns["dataset_id"].replace("/", ".") - normalization_id = adata.uns["normalization_id"] - id = dataset_id + "." + normalization_id - obj = { - 'id': id, - 'input': h5ad_file, - 'dataset_id': dataset_id, - 'normalization_id': normalization_id - } - param_list.append(obj) - -output = { - "param_list": param_list, - "obs_label": "celltype", - "obs_batch": "batch", - "seed": 123, - "output_train": "\$id.train.h5ad", - "output_test": "\$id.test.h5ad", - "output_solution": "\$id.solution.h5ad" -} - -with open("$params_file", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script target/nextflow/label_projection/process_dataset/main.nf \ + +nextflow run . \ + -main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ -profile docker \ + -entry auto \ -resume \ - -params-file $params_file \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --input_states "$COMMON_DATASETS/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 42cf975be8..19b3e61598 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -8,77 +8,24 @@ cd "$REPO_ROOT" set -e -export TOWER_WORKSPACE_ID=53907369739130 +# export TOWER_WORKSPACE_ID=53907369739130 -DATASETS_DIR="resources/label_projection/datasets/openproblems_v1" -OUTPUT_DIR="resources/label_projection/benchmarks/openproblems_v1" +DATASETS_DIR="resources/label_projection" +OUTPUT_DIR="output/test" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi -params_file="$OUTPUT_DIR/params.yaml" - -if [ ! -f $params_file ]; then - python << HERE -import yaml - -dataset_dir = "$DATASETS_DIR" -output_dir = "$OUTPUT_DIR" - -# read split datasets yaml -with open(dataset_dir + "/params.yaml", "r") as file: - split_list = yaml.safe_load(file) -datasets = split_list['param_list'] - -# figure out where train/test/solution files were stored -param_list = [] - -for dataset in datasets: - id = dataset["id"] - input_train = dataset_dir + "/" + id + ".train.h5ad" - input_test = dataset_dir + "/" + id + ".test.h5ad" - input_solution = dataset_dir + "/" + id + ".solution.h5ad" - - obj = { - 'id': id, - 'dataset_id': dataset["dataset_id"], - 'normalization_id': dataset["normalization_id"], - 'input_train': input_train, - 'input_test': input_test, - 'input_solution': input_solution - } - param_list.append(obj) - -# write as output file -output = { - "param_list": param_list, -} - -with open(output_dir + "/params.yaml", "w") as file: - yaml.dump(output, file) -HERE -fi - export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script src/tasks/label_projection/workflows/run/main.nf \ +nextflow run . \ + -main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ -profile docker \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" \ - -with-tower - -bin/tools/docker/nextflow/process_log/process_log \ - --output "$OUTPUT_DIR/nextflow_log.tsv" - -# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "id: $id, args: $args"' -# viash ns build -q label_projection -c '.platforms[.type == "nextflow"].directives.tag := "$id"' - -# nextflow run . \ -# -main-script target/nextflow/label_projection/control_methods/majority_vote/main.nf \ -# -profile docker \ -# --input_train resources_test/label_projection/pancreas/train.h5ad \ -# --input_test resources_test/label_projection/pancreas/test.h5ad \ -# --input_solution resources_test/label_projection/pancreas/solution.h5ad \ -# --publish_dir foo \ No newline at end of file + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_train:output_train,input_test:output_test,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR"\ + --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index 2beed71bb6..11767605a9 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -1,7 +1,4 @@ #!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -9,24 +6,25 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -RAW_DATA=resources_test/common/pancreas/dataset.h5ad -DATASET_DIR=resources_test/label_projection/pancreas +set -e -if [ ! -f $RAW_DATA ]; then - echo "Error! Could not find raw data" - exit 1 -fi +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/label_projection mkdir -p $DATASET_DIR -# split dataset -viash run src/tasks/label_projection/process_dataset/config.vsh.yaml -- \ - --input $RAW_DATA \ - --output_train $DATASET_DIR/train.h5ad \ - --output_test $DATASET_DIR/test.h5ad \ - --output_solution $DATASET_DIR/solution.h5ad \ - --method random \ - --seed 123 +# process dataset +echo Running process_dataset +nextflow run . \ + -main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + --input_states "$RAW_DATA/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved # run one method viash run src/tasks/label_projection/methods/knn/config.vsh.yaml -- \ @@ -40,17 +38,17 @@ viash run src/tasks/label_projection/metrics/accuracy/config.vsh.yaml -- \ --input_solution $DATASET_DIR/solution.h5ad \ --output $DATASET_DIR/knn_accuracy.h5ad -# run benchmark -export NXF_VER=22.04.5 - -nextflow \ - run . \ - -main-script src/tasks/label_projection/workflows/run/main.nf \ - -profile docker \ - -resume \ - --id pancreas \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ No newline at end of file +# # run benchmark +# export NXF_VER=22.04.5 + +# nextflow \ +# run . \ +# -main-script src/tasks/label_projection/workflows/run/main.nf \ +# -profile docker \ +# -resume \ +# --id pancreas \ +# --input_train $DATASET_DIR/train.h5ad \ +# --input_test $DATASET_DIR/test.h5ad \ +# --input_solution $DATASET_DIR/solution.h5ad \ +# --output scores.tsv \ +# --publish_dir $DATASET_DIR/ \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..77fb6fdbbe --- /dev/null +++ b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,39 @@ +functionality: + name: "process_datasets" + namespace: "label_projection/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __merge__: "/src/tasks/label_projection/api/file_common_dataset.yaml" + required: true + direction: input + - name: "--dataset_schema" + type: "file" + description: "The schema of the dataset to validate against" + required: true + default: "src/tasks/label_projection/api/file_common_dataset.yaml" + direction: input + - name: Outputs + arguments: + - name: "--output_train" + __merge__: /src/tasks/label_projection/api/file_train.yaml + required: true + direction: output + - name: "--output_test" + __merge__: /src/tasks/label_projection/api/file_test.yaml + required: true + direction: output + - name: "--output_solution" + __merge__: /src/tasks/label_projection/api/file_solution.yaml + required: true + direction: output + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: label_projection/process_dataset +platforms: + - type: nextflow diff --git a/src/tasks/label_projection/workflows/process_datasets/main.nf b/src/tasks/label_projection/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..54675d9f9b --- /dev/null +++ b/src/tasks/label_projection/workflows/process_datasets/main.nf @@ -0,0 +1,50 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + fromState: [ + "input": "input", + "schema": "dataset_schema" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset": "output", + "dataset_checks": "checks" + ] + ) + + // remove datasets which didn't pass the schema check + | filter { id, state -> + state.dataset != null + } + + | process_dataset.run( + fromState: [ input: "dataset" ], + toState: [ + output_train: "output_train", + output_test: "output_test", + output_solution: "output_solution" + ] + ) + + // only output the files for which an output file was specified + | setState(["output_train", "output_test", "output_solution"]) + + emit: + output_ch +} diff --git a/src/tasks/label_projection/workflows/run/nextflow.config b/src/tasks/label_projection/workflows/run/nextflow.config deleted file mode 100644 index 826337a8b1..0000000000 --- a/src/tasks/label_projection/workflows/run/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'label_projection/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Label projection' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/tasks/label_projection/workflows/run/run_test.sh b/src/tasks/label_projection/workflows/run/run_test.sh deleted file mode 100755 index a909381666..0000000000 --- a/src/tasks/label_projection/workflows/run/run_test.sh +++ /dev/null @@ -1,29 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/label_projection/pancreas - -# run benchmark -export NXF_VER=23.04.2 - -nextflow \ - run . \ - -main-script src/tasks/label_projection/workflows/run/main.nf \ - -profile docker \ - -resume \ - --id pancreas \ - --dataset_id pancreas \ - --normalization_id log_cp10k \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output scores.tsv \ - --publish_dir output/label_projection/ \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/run_test_on_tower.sh b/src/tasks/label_projection/workflows/run/run_test_on_tower.sh deleted file mode 100644 index cce0f3d89f..0000000000 --- a/src/tasks/label_projection/workflows/run/run_test_on_tower.sh +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/bash - -DATASET_DIR=resources_test/label_projection/pancreas - -# try running on nf tower -cat > /tmp/params.yaml << HERE -id: pancreas_subsample -input_train: s3://openproblems-data/$DATASET_DIR/train.h5ad -input_test: s3://openproblems-data/$DATASET_DIR/test.h5ad -input_solution: s3://openproblems-data/$DATASET_DIR/solution.h5ad -dataset_id: pancreas -normalization_id: log_cp10k -output: scores.tsv -publish_dir: s3://openproblems-nextflow/output_test/v2/label_projection -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script src/tasks/label_projection/workflows/run/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml similarity index 79% rename from src/tasks/label_projection/workflows/run/config.vsh.yaml rename to src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index ad14b0f7f3..28feee8e9f 100644 --- a/src/tasks/label_projection/workflows/run/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -5,26 +5,28 @@ functionality: - name: Inputs arguments: - name: "--input_train" - # __merge__: ../../api/file_train.yaml + __merge__: /src/tasks/label_projection/api/file_train.yaml type: file direction: input required: true - name: "--input_test" - # __merge__: ../../api/file_test.yaml + __merge__: /src/tasks/label_projection/api/file_test.yaml type: file direction: input required: true - name: "--input_solution" - # __merge__: ../../api/file_solution.yaml + __merge__: /src/tasks/label_projection/api/file_solution.yaml type: file direction: input required: true - name: Outputs arguments: - name: "--output" - direction: "output" + direction: output type: file example: output.tsv + description: A TSV file containing the scores of each of the methods + required: true resources: - type: nextflow_script path: main.nf @@ -43,9 +45,5 @@ functionality: - name: label_projection/methods/xgboost - name: label_projection/metrics/accuracy - name: label_projection/metrics/f1 - # test_resources: - # - type: nextflow_script - # path: main.nf - # entrypoint: test_wf platforms: - type: nextflow \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/run/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf similarity index 65% rename from src/tasks/label_projection/workflows/run/main.nf rename to src/tasks/label_projection/workflows/run_benchmark/main.nf index 6c212a74c1..aa458b08f9 100644 --- a/src/tasks/label_projection/workflows/run/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -1,5 +1,9 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} workflow run_wf { take: @@ -29,6 +33,11 @@ workflow run_wf { output_ch = input_ch + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + // extract the dataset metadata | check_dataset_schema.run( fromState: [ "input": "input_train" ], @@ -41,46 +50,46 @@ workflow run_wf { ) // run all methods - | runComponents( + | runEach( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, config -> + filter: { id, state, comp -> def norm = state.normalization_id - def pref = config.functionality.info.preferred_normalization + def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want (norm == "log_cp10k" && pref == "counts") || norm == pref }, // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name + id: { id, state, comp -> + id + "." + comp.config.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> + fromState: { id, state, comp -> def new_args = [ input_train: state.input_train, input_test: state.input_test ] - if (config.functionality.info.type == "control_method") { + if (comp.config.functionality.info.type == "control_method") { new_args.input_solution = state.input_solution } new_args }, // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - method_id: config.functionality.name, + method_id: comp.config.functionality.name, method_output: output.output ] } ) // run all metrics - | runComponents( + | runEach( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -88,41 +97,33 @@ workflow run_wf { input_prediction: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - metric_id: config.functionality.name, + metric_id: comp.config.functionality.name, metric_output: output.output ] } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow + // join all events into a new event | joinStates{ ids, states -> def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0].output + _meta: states[0]._meta ] [new_id, new_state] } // convert to tsv and publish | extract_scores.run( - auto: [publish: true] + fromState: ["input"], + toState: ["output"] ) - emit: - output_ch -} + | setState(["output", "_meta"]) -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - writeJson(traces, file("$publish_dir/traces.json")) - // todo: add datasets logging - writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) - writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) + emit: + output_ch } \ No newline at end of file From 672ef83fbb61083afe1d1db21d147ade472568bd Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 21:06:13 +0200 Subject: [PATCH 1027/1233] fix process_datasets Former-commit-id: 12ab79bf02eab6e18deb90714a4b902bc387e82b --- .../process_datasets/config.vsh.yaml | 34 +++++++++---------- .../workflows/process_datasets/main.nf | 2 +- .../workflows/process_datasets/run_test.sh | 28 +++++++++++++++ 3 files changed, 46 insertions(+), 18 deletions(-) create mode 100644 src/tasks/predict_modality/workflows/process_datasets/run_test.sh diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index 211454f33c..272a53c4c1 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -5,11 +5,11 @@ functionality: - name: Inputs arguments: - name: "--input_rna" - __merge__: "/src/tasks/predict_modality/api/file_dataset_rna.yaml" + __merge__: "/src/tasks/predict_modality/api/file_common_dataset_rna.yaml" required: true direction: input - name: "--input_other_mod" - __merge__: "/src/tasks/predict_modality/api/file_dataset_other_mod.yaml" + __merge__: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" direction: input required: true - name: "--dataset_schema" @@ -21,21 +21,21 @@ functionality: - name: Outputs arguments: - name: "--output_train_mod1" - __merge__: /src/tasks/predict_modality/api/file_train_mod1.yaml - direction: output - required: true - - name: "--output_train_mod2" - __merge__: /src/tasks/predict_modality/api/file_train_mod2.yaml - direction: output - required: true - - name: "--output_test_mod1" - __merge__: /src/tasks/predict_modality/api/file_test_mod1.yaml - direction: "output" - required: true - - name: "--output_test_mod2" - __merge__: /src/tasks/predict_modality/api/file_test_mod2.yaml - direction: output - required: true + __merge__: /src/tasks/predict_modality/api/file_train_mod1.yaml + direction: output + required: true + - name: "--output_train_mod2" + __merge__: /src/tasks/predict_modality/api/file_train_mod2.yaml + direction: output + required: true + - name: "--output_test_mod1" + __merge__: /src/tasks/predict_modality/api/file_test_mod1.yaml + direction: "output" + required: true + - name: "--output_test_mod2" + __merge__: /src/tasks/predict_modality/api/file_test_mod2.yaml + direction: output + required: true resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index d1c590bdfa..e509ce1f52 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -80,7 +80,7 @@ workflow run_wf { "output_train_mod1": state.output_train_mod1 ? state.train_mod1 : null, "output_train_mod2": state.output_train_mod2 ? state.train_mod2 : null, "output_test_mod1": state.output_test_mod1 ? state.test_mod1 : null, - "output_test_mod2": state.output_test_mod2 ? state.test_mod2 : null, + "output_test_mod2": state.output_test_mod2 ? state.test_mod2 : null ] } diff --git a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh new file mode 100644 index 0000000000..825b60ca90 --- /dev/null +++ b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +DATASETS_DIR="resources_test/common" +OUTPUT_DIR="resources_test/predict_modality" + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id run_test \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ + --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file From 945ef3165fbd9febe8e3449e90d0fe853b09a9c1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 21:06:38 +0200 Subject: [PATCH 1028/1233] add common datasets Former-commit-id: bb0b68859f78db5969e7cef3821be5e9156ba98d --- .../api/file_common_dataset_other_mod.yaml | 43 +++++++++++++++++++ .../api/file_common_dataset_rna.yaml | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml create mode 100644 src/tasks/predict_modality/api/file_common_dataset_rna.yaml diff --git a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml new file mode 100644 index 0000000000..8035d80019 --- /dev/null +++ b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml @@ -0,0 +1,43 @@ +type: file +example: "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad" +info: + label: "Raw dataset mod2" + summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" + slots: + X: + type: double + description: Normalized expression values + required: true + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml new file mode 100644 index 0000000000..92d4b5bc5b --- /dev/null +++ b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml @@ -0,0 +1,43 @@ +type: file +example: "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad" +info: + label: "Raw dataset RNA" + summary: "The RNA modality of the raw dataset." + slots: + X: + type: double + description: Normalized expression values + required: true + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: batch + description: Batch information + required: true + - type: double + name: size_factors + description: The size factors of the cells prior to normalization. + required: false + var: + - type: string + name: gene_ids + description: The gene identifiers (if available) + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: gene_activity_var_names + description: "Names of the gene activity matrix" + required: false + obsm: + - type: double + name: gene_activity + description: ATAC gene activity + required: false \ No newline at end of file From cd5c1a0082544e6b32947a5057d5474ad0072d44 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 21:07:00 +0200 Subject: [PATCH 1029/1233] wip run_benchmark Former-commit-id: a580777132da57d33153dcf459beb91b7e6137ef --- nxf-tmp.0nZVhn | 0 nxf-tmp.5mFiyd | 0 .../control_methods/solution/config.vsh.yaml | 2 +- .../workflows/run/run_test.sh | 37 -------- .../{run => run_benchmark}/config.vsh.yaml | 21 +++-- .../workflows/{run => run_benchmark}/main.nf | 84 +++++++++++-------- .../workflows/run_benchmark/run_test.sh | 28 +++++++ 7 files changed, 92 insertions(+), 80 deletions(-) create mode 100644 nxf-tmp.0nZVhn create mode 100644 nxf-tmp.5mFiyd delete mode 100755 src/tasks/predict_modality/workflows/run/run_test.sh rename src/tasks/predict_modality/workflows/{run => run_benchmark}/config.vsh.yaml (62%) rename src/tasks/predict_modality/workflows/{run => run_benchmark}/main.nf (53%) create mode 100755 src/tasks/predict_modality/workflows/run_benchmark/run_test.sh diff --git a/nxf-tmp.0nZVhn b/nxf-tmp.0nZVhn new file mode 100644 index 0000000000..e69de29bb2 diff --git a/nxf-tmp.5mFiyd b/nxf-tmp.5mFiyd new file mode 100644 index 0000000000..e69de29bb2 diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index 63d64bfe29..3019e1d764 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2] + image: ghcr.io/openproblems-bio/base_r:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/predict_modality/workflows/run/run_test.sh b/src/tasks/predict_modality/workflows/run/run_test.sh deleted file mode 100755 index 2aa603e738..0000000000 --- a/src/tasks/predict_modality/workflows/run/run_test.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'label_projection|common' - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -# run benchmark -export NXF_VER=23.04.2 - -cat > /tmp/params.yaml << HERE -param_list: -HERE - -# for id in bmmc_cite_starter bmmc_cite_starter_swapped bmmc_multiome_starter bmmc_multiome_starter_swapped; do -for id in `ls resources_test/predict_modality/`; do -cat >> /tmp/params.yaml << HERE - - id: $id - input_train_mod1: resources_test/predict_modality/$id/train_mod1.h5ad - input_train_mod2: resources_test/predict_modality/$id/train_mod2.h5ad - input_test_mod1: resources_test/predict_modality/$id/test_mod1.h5ad - input_test_mod2: resources_test/predict_modality/$id/test_mod2.h5ad -HERE -done - -nextflow \ - run . \ - -main-script src/tasks/predict_modality/workflows/run/main.nf \ - -profile docker \ - -resume \ - -params-file /tmp/params.yaml \ - --output scores.tsv \ - --publish_dir output/predict_modality/ \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml similarity index 62% rename from src/tasks/predict_modality/workflows/run/config.vsh.yaml rename to src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index 1ba8a7677e..7726f1708f 100644 --- a/src/tasks/predict_modality/workflows/run/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -5,18 +5,29 @@ functionality: - name: Inputs arguments: - name: "--input_train_mod1" - type: "file" # todo: replace with includes + __merge__: /src/tasks/predict_modality/api/file_train_mod1.yaml + required: true + direction: input - name: "--input_train_mod2" - type: "file" + __merge__: /src/tasks/predict_modality/api/file_train_mod2.yaml + required: true + direction: input - name: "--input_test_mod1" - type: "file" # todo: replace with includes + __merge__: /src/tasks/predict_modality/api/file_test_mod1.yaml + required: true + direction: input - name: "--input_test_mod2" - type: "file" # todo: replace with includes + __merge__: /src/tasks/predict_modality/api/file_test_mod2.yaml + required: true + direction: input - name: Outputs arguments: - name: "--output" - direction: "output" type: file + required: true + direction: output + description: A TSV file containing the scores of each of the methods + example: scores.tsv resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/predict_modality/workflows/run/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf similarity index 53% rename from src/tasks/predict_modality/workflows/run/main.nf rename to src/tasks/predict_modality/workflows/run_benchmark/main.nf index bbd773c96c..efada6be5c 100644 --- a/src/tasks/predict_modality/workflows/run/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -1,5 +1,9 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} workflow run_wf { take: @@ -28,50 +32,63 @@ workflow run_wf { output_ch = input_ch + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + // extract the dataset metadata | check_dataset_schema.run( fromState: [ "input": "input_train_mod1" ], toState: { id, output, state -> - // load output yaml file - def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - // add metadata from file to state - state + metadata + state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + } + ) + + | check_dataset_schema.run( + fromState: [ "input": "input_train_mod2" ], + toState: { id, output, state -> + state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns } ) // run all methods - | runComponents( + | runEach( components: methods, + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, comp -> + def norm = state.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cp10k" && pref == "counts") || norm == pref + }, + // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name + id: { id, state, comp -> + id + "." + comp.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> - def new_args = [ - input_train_mod1: state.input_train_mod1, - input_train_mod2: state.input_train_mod2, - input_test_mod1: state.input_test_mod1 - ] - if (config.functionality.info.type == "control_method") { - new_args.input_test_mod2 = state.input_test_mod2 - } - new_args - }, + fromState: [ + input_train_mod1: "input_train_mod1", + input_train_mod2: "input_train_mod2", + input_test_mod1: "input_test_mod1", + input_test_mod2: "input_test_mod2" + ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - method_id: config.functionality.name, + method_id: comp.functionality.name, method_output: output.output ] } ) // run all metrics - | runComponents( + | runEach( components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ @@ -79,9 +96,9 @@ workflow run_wf { input_prediction: "method_output" ], // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> + toState: { id, output, state, comp -> state + [ - metric_id: config.functionality.name, + metric_id: comp.functionality.name, metric_output: output.output ] } @@ -94,26 +111,19 @@ workflow run_wf { def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0].output + _meta: states[0]._meta ] [new_id, new_state] } // convert to tsv and publish | extract_scores.run( - auto: [publish: true] + fromState: ["input"], + toState: ["output"] ) + | setState(["output", "_meta"]) + emit: output_ch -} - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJson(traces, file("$publish_dir/traces.json")) - // todo: add datasets logging - writeJson(methods.collect{it.config}, file("$publish_dir/methods.json")) - writeJson(metrics.collect{it.config}, file("$publish_dir/metrics.json")) } \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh new file mode 100755 index 0000000000..4745ad180d --- /dev/null +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +DATASETS_DIR="resources_test/predict_modality" +OUTPUT_DIR="output/predict_modality" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi +# run benchmark +export NXF_VER=23.04.2 + +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file From c0f36d048486579d3a5f6c45485b389b0a7f342a Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 11 Oct 2023 21:30:52 +0200 Subject: [PATCH 1030/1233] update process datasets Former-commit-id: 8b54c49d62138fd565d09e3542127db20c11c279 --- .../workflows/process_datasets/config.vsh.yaml | 10 ++++++++-- .../workflows/process_datasets/main.nf | 8 +++++--- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index 272a53c4c1..b327ce5463 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -12,11 +12,17 @@ functionality: __merge__: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" direction: input required: true - - name: "--dataset_schema" + - name: "--dataset_schema_rna" type: "file" description: "The schema of the dataset to validate against" required: true - default: "src/tasks/predict_modality/api/file_common_dataset.yaml" + default: "src/tasks/predict_modality/api/file_common_dataset_rna.yaml" + direction: input + - name: "--dataset_schema_other_mod" + type: "file" + description: "The schema of the dataset to validate against" + required: true + default: "src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" direction: input - name: Outputs arguments: diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index e509ce1f52..99e6c3feb0 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -15,9 +15,10 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( + key: "check_dataset_schema_rna", fromState: [ "input": "input_rna", - "schema": "dataset_schema" + "schema": "dataset_schema_rna" ], args: [ "stop_on_error": false @@ -29,9 +30,10 @@ workflow run_wf { ) | check_dataset_schema.run( + key: "check_dataset_schema_other_mod", fromState: [ "input": "input_other_mod", - "schema": "dataset_schema" + "schema": "dataset_schema_other_mod" ], args: [ "stop_on_error": false @@ -53,7 +55,7 @@ workflow run_wf { } } | filter { id, state -> - state.dataset_rna != null, + state.dataset_rna != null && state.dataset_other_mod != null } From 875ab32fd1f0ecf621548492ca7577b407b97484 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 21:42:43 +0200 Subject: [PATCH 1031/1233] minor updates to script Former-commit-id: 055a7afca3e15b7247fda7f85deb1411acf9130b --- .../resources_test_scripts/bmmc_x_starter.sh | 28 +++++++++---------- .../workflows/process_datasets/run_test.sh | 0 2 files changed, 14 insertions(+), 14 deletions(-) mode change 100644 => 100755 src/tasks/predict_modality/workflows/process_datasets/run_test.sh diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh index a9ecdd9ab0..d42b38ec56 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -48,20 +48,20 @@ generate_pm_test_resources () { --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ --output $DATASET_DIR/score.h5ad - # run benchmark on test data - export NXF_VER=22.04.5 - - nextflow run . \ - -main-script src/tasks/predict_modality/workflows/run/main.nf \ - -profile docker \ - -c src/wf_utils/labels_ci.config \ - --id "$DATASET_ID" \ - --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ - --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ - --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ - --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ + # # run benchmark on test data + # export NXF_VER=22.04.5 + + # nextflow run . \ + # -main-script src/tasks/predict_modality/workflows/run/main.nf \ + # -profile docker \ + # -c src/wf_utils/labels_ci.config \ + # --id "$DATASET_ID" \ + # --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ + # --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ + # --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ + # --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ + # --output scores.tsv \ + # --publish_dir $DATASET_DIR/ } generate_pm_test_resources \ diff --git a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh old mode 100644 new mode 100755 From 86828c828682b3afc5f561e76c1bd18d9be5d6fb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 11 Oct 2023 21:47:21 +0200 Subject: [PATCH 1032/1233] minor changes to scripts and paths Former-commit-id: 98ba43408b34bc25c24a70ea3a1c58a1f34e7cac --- .../resource_test_scripts/bmmc_x_starter.sh | 3 +- .../resource_test_scripts/pancreas.sh | 10 +++--- .../scicar_cell_lines.sh | 3 +- .../resources_test_scripts/pancreas.sh | 20 +++++------ src/tasks/label_projection/README.md | 4 +-- .../label_projection/api/file_prediction.yaml | 2 +- .../label_projection/api/file_score.yaml | 2 +- .../resources_test_scripts/pancreas.sh | 36 +++++++++---------- 8 files changed, 41 insertions(+), 39 deletions(-) diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh index 81fabe3970..5a4018e7af 100755 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -17,4 +17,5 @@ wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_mult wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ -O "$SUBDIR/dataset_atac.h5ad" -# src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file +# run task process dataset components +src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 1890be57de..15d52aeb7d 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -52,8 +52,8 @@ nextflow run . \ rm -r $DATASET_DIR/temp_* -# # run task process dataset components -# src/tasks/batch_integration/resources_test_scripts/pancreas.sh -# src/tasks/denoising/resources_test_scripts/pancreas.sh -# src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh -# src/tasks/label_projection/resources_test_scripts/pancreas.sh +# run task process dataset components +src/tasks/batch_integration/resources_test_scripts/pancreas.sh +src/tasks/denoising/resources_test_scripts/pancreas.sh +src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +src/tasks/label_projection/resources_test_scripts/pancreas.sh diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 0b754c7632..c0a07031fb 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -43,4 +43,5 @@ nextflow run . \ --output_state '$id/state.yaml' \ --publish_dir "$DATASET_DIR" -# src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh \ No newline at end of file +# run task process dataset components +src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index ab194bf5d7..dc5bbd5b79 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -29,16 +29,16 @@ nextflow run . \ # output_state should be moved to settings once workaround is solved -# # run one method -# viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ -# --input $DATASET_DIR/dataset.h5ad \ -# --output $DATASET_DIR/embedding.h5ad - -# # run one metric -# viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ -# --input_embedding $DATASET_DIR/embedding.h5ad \ -# --input_solution $DATASET_DIR/solution.h5ad \ -# --output $DATASET_DIR/score.h5ad +# run one method +viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ + --input $DATASET_DIR/dataset.h5ad \ + --output $DATASET_DIR/embedding.h5ad + +# run one metric +viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ + --input_embedding $DATASET_DIR/embedding.h5ad \ + --input_solution $DATASET_DIR/solution.h5ad \ + --output $DATASET_DIR/score.h5ad # # run benchmark # export NXF_VER=22.04.5 diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index ffc7ec4f67..f0b6d1d68c 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -332,7 +332,7 @@ Arguments: The prediction file -Example file: `resources_test/label_projection/pancreas/knn.h5ad` +Example file: `resources_test/label_projection/pancreas/prediction.h5ad` Description: @@ -366,7 +366,7 @@ Slot description: Metric score file Example file: -`resources_test/label_projection/pancreas/knn_accuracy.h5ad` +`resources_test/label_projection/pancreas/score.h5ad` Description: diff --git a/src/tasks/label_projection/api/file_prediction.yaml b/src/tasks/label_projection/api/file_prediction.yaml index adbb0327fe..36efa87af0 100644 --- a/src/tasks/label_projection/api/file_prediction.yaml +++ b/src/tasks/label_projection/api/file_prediction.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/label_projection/pancreas/knn.h5ad" +example: "resources_test/label_projection/pancreas/prediction.h5ad" info: label: "Prediction" summary: "The prediction file" diff --git a/src/tasks/label_projection/api/file_score.yaml b/src/tasks/label_projection/api/file_score.yaml index 997bdda587..7ee5eaa8ee 100644 --- a/src/tasks/label_projection/api/file_score.yaml +++ b/src/tasks/label_projection/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/label_projection/pancreas/knn_accuracy.h5ad" +example: "resources_test/label_projection/pancreas/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index 2beed71bb6..aa924608c2 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -32,25 +32,25 @@ viash run src/tasks/label_projection/process_dataset/config.vsh.yaml -- \ viash run src/tasks/label_projection/methods/knn/config.vsh.yaml -- \ --input_train $DATASET_DIR/train.h5ad \ --input_test $DATASET_DIR/test.h5ad \ - --output $DATASET_DIR/knn.h5ad + --output $DATASET_DIR/prediction.h5ad # run one metric viash run src/tasks/label_projection/metrics/accuracy/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/knn.h5ad \ + --input_prediction $DATASET_DIR/prediction.h5ad \ --input_solution $DATASET_DIR/solution.h5ad \ - --output $DATASET_DIR/knn_accuracy.h5ad - -# run benchmark -export NXF_VER=22.04.5 - -nextflow \ - run . \ - -main-script src/tasks/label_projection/workflows/run/main.nf \ - -profile docker \ - -resume \ - --id pancreas \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output scores.tsv \ - --publish_dir $DATASET_DIR/ \ No newline at end of file + --output $DATASET_DIR/score.h5ad + +# # run benchmark +# export NXF_VER=22.04.5 + +# nextflow \ +# run . \ +# -main-script src/tasks/label_projection/workflows/run/main.nf \ +# -profile docker \ +# -resume \ +# --id pancreas \ +# --input_train $DATASET_DIR/train.h5ad \ +# --input_test $DATASET_DIR/test.h5ad \ +# --input_solution $DATASET_DIR/solution.h5ad \ +# --output scores.tsv \ +# --publish_dir $DATASET_DIR/ \ No newline at end of file From af4b5ca0ba4fb9890f1dc57c6c524edd43d6caaa Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 10:25:54 +0200 Subject: [PATCH 1033/1233] Update check_dataset_schema Former-commit-id: 3d9bc789ca159e58af2260859a4bc0ccf7397d34 --- src/common/check_dataset_schema/script.py | 7 +++++++ src/common/check_dataset_schema/test.py | 4 ++++ 2 files changed, 11 insertions(+) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 7dc5969f9c..ef3412a6b5 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -69,7 +69,14 @@ def is_dict_of_atomics(obj): def_slots = data_struct['info']['slots'] for slot in def_slots: + missing_x = False + if slot == "X": + if adata.X is None: + missing_x = True + continue missing = check_structure(def_slots[slot], getattr(adata, slot)) + if missing_x: + missing.append("X") if missing: out['exit_code'] = 1 out['data_schema'] = 'not ok' diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 40e633ae21..2e4b083341 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -40,6 +40,10 @@ def error_schema(tmp_path): info: label: "Preprocessed dataset" slots: + X: + type: double + description: Normalized expression values + required: true layers: - type: integer name: counts From a763961a8160ddbc93d2ea32c519f172a65179a0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 12 Oct 2023 13:40:49 +0200 Subject: [PATCH 1034/1233] Update match modalities (#259) * add nf-tower scripts batch_integration * fix typo * WIP * fix process_datasets * WIP * Update nf workflows * update run scripts * fix typo in workflow * undo batch_integration changes * use merge in workflow configs * update base image version * Update process_datasets workflow * fix scripts & workflows * update label proj * remove newline * wip * fix scripts & components * remove api readmes, update task readmes * fix examples * fix test resources * use integrated objects * turn np float into native float --------- Co-authored-by: Kai Waldrant Former-commit-id: 3ee9310b7ad6621174be81431888fcbeb9e9af33 --- _viash.yaml | 2 +- src/tasks/batch_integration/api/README.md | 8 - src/tasks/batch_integration/api/README.qmd | 8 - src/tasks/denoising/api/README.md | 8 - src/tasks/denoising/api/README.qmd | 8 - .../dimensionality_reduction/api/README.md | 8 - .../dimensionality_reduction/api/README.qmd | 8 - src/tasks/label_projection/README.md | 61 +-- src/tasks/label_projection/api/README.md | 8 - src/tasks/label_projection/api/README.qmd | 8 - src/tasks/match_modalities/README.md | 500 ++++++++++++++++++ src/tasks/match_modalities/api/README.qmd | 8 - .../api/comp_control_method.yaml | 16 +- .../match_modalities/api/comp_method.yaml | 8 +- .../match_modalities/api/comp_metric.yaml | 14 +- .../api/comp_process_dataset.yaml | 32 +- ...od1.yaml => file_common_dataset_mod1.yaml} | 16 +- ...od2.yaml => file_common_dataset_mod2.yaml} | 16 +- .../api/file_dataset_mod1.yaml | 29 + .../api/file_dataset_mod2.yaml | 29 + .../api/file_integrated_mod1.yaml | 28 +- .../api/file_integrated_mod2.yaml | 28 +- .../match_modalities/api/file_score.yaml | 2 +- .../api/file_solution_mod1.yaml | 34 ++ .../api/file_solution_mod2.yaml | 34 ++ src/tasks/match_modalities/api/task_info.yaml | 41 +- .../control_methods/random_features/script.py | 1 + .../control_methods/true_features/script.py | 45 +- .../methods/harmonic_alignment/script.py | 5 +- .../methods/procrustes/config.vsh.yaml | 2 +- .../match_modalities/methods/scot/script.py | 1 - .../metrics/knn_auc/script.py | 58 +- .../metrics/mse/config.vsh.yaml | 3 +- .../match_modalities/metrics/mse/script.py | 53 +- .../process_dataset/config.vsh.yaml | 16 + .../process_dataset/script.py | 64 +++ .../resources_scripts/process_datasets.sh | 26 + .../resources_scripts/run_benchmark.sh | 31 ++ .../scicar_cell_lines.sh | 37 +- .../process_datasets/config.vsh.yaml | 53 ++ .../workflows/process_datasets/main.nf | 69 +++ .../match_modalities/workflows/run/main.nf | 124 ----- .../workflows/run/nextflow.config | 16 - .../workflows/run/run_test.sh | 30 -- .../workflows/run/run_test_on_tower.sh | 27 - .../{run => run_benchmark}/config.vsh.yaml | 21 +- .../workflows/run_benchmark/main.nf | 131 +++++ 47 files changed, 1280 insertions(+), 495 deletions(-) delete mode 100644 src/tasks/batch_integration/api/README.md delete mode 100644 src/tasks/batch_integration/api/README.qmd delete mode 100644 src/tasks/denoising/api/README.md delete mode 100644 src/tasks/denoising/api/README.qmd delete mode 100644 src/tasks/dimensionality_reduction/api/README.md delete mode 100644 src/tasks/dimensionality_reduction/api/README.qmd delete mode 100644 src/tasks/label_projection/api/README.md delete mode 100644 src/tasks/label_projection/api/README.qmd create mode 100644 src/tasks/match_modalities/README.md delete mode 100644 src/tasks/match_modalities/api/README.qmd rename src/tasks/match_modalities/api/{file_mod1.yaml => file_common_dataset_mod1.yaml} (65%) rename src/tasks/match_modalities/api/{file_mod2.yaml => file_common_dataset_mod2.yaml} (65%) create mode 100644 src/tasks/match_modalities/api/file_dataset_mod1.yaml create mode 100644 src/tasks/match_modalities/api/file_dataset_mod2.yaml create mode 100644 src/tasks/match_modalities/api/file_solution_mod1.yaml create mode 100644 src/tasks/match_modalities/api/file_solution_mod2.yaml create mode 100644 src/tasks/match_modalities/process_dataset/config.vsh.yaml create mode 100644 src/tasks/match_modalities/process_dataset/script.py create mode 100755 src/tasks/match_modalities/resources_scripts/process_datasets.sh create mode 100755 src/tasks/match_modalities/resources_scripts/run_benchmark.sh create mode 100644 src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/match_modalities/workflows/process_datasets/main.nf delete mode 100644 src/tasks/match_modalities/workflows/run/main.nf delete mode 100644 src/tasks/match_modalities/workflows/run/nextflow.config delete mode 100755 src/tasks/match_modalities/workflows/run/run_test.sh delete mode 100644 src/tasks/match_modalities/workflows/run/run_test_on_tower.sh rename src/tasks/match_modalities/workflows/{run => run_benchmark}/config.vsh.yaml (53%) create mode 100644 src/tasks/match_modalities/workflows/run_benchmark/main.nf diff --git a/_viash.yaml b/_viash.yaml index abb716012b..925378d60e 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -10,5 +10,5 @@ config_mods: | .platforms[.type == 'docker'].target_image_source := 'https://github.com/openproblems-bio/openproblems-v2' .platforms[.type == "nextflow"].directives.tag := "$id" .platforms[.type == "nextflow"].auto.simplifyOutput := false - .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", lowcpu : "cpus = 5", midmem : "memory = 50.Gb", midcpu : "cpus = 15", highmem : "memory = 100.Gb", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h" } + .platforms[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h" } .platforms[.type == "nextflow"].config.script := "process.errorStrategy = 'ignore'" \ No newline at end of file diff --git a/src/tasks/batch_integration/api/README.md b/src/tasks/batch_integration/api/README.md deleted file mode 100644 index 7c3b9c8d87..0000000000 --- a/src/tasks/batch_integration/api/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Component and file format specifications - -This folder contains specifications for file formats and component -interfaces. - -These are not only used for documentation (i.e. to document the file -format of inputs and outputs of a component), but also for unit testing -and validation of output files. diff --git a/src/tasks/batch_integration/api/README.qmd b/src/tasks/batch_integration/api/README.qmd deleted file mode 100644 index d31a99367e..0000000000 --- a/src/tasks/batch_integration/api/README.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Component and file format specifications -format: gfm ---- - -This folder contains specifications for file formats and component interfaces. - -These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/denoising/api/README.md b/src/tasks/denoising/api/README.md deleted file mode 100644 index 7c3b9c8d87..0000000000 --- a/src/tasks/denoising/api/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Component and file format specifications - -This folder contains specifications for file formats and component -interfaces. - -These are not only used for documentation (i.e. to document the file -format of inputs and outputs of a component), but also for unit testing -and validation of output files. diff --git a/src/tasks/denoising/api/README.qmd b/src/tasks/denoising/api/README.qmd deleted file mode 100644 index d31a99367e..0000000000 --- a/src/tasks/denoising/api/README.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Component and file format specifications -format: gfm ---- - -This folder contains specifications for file formats and component interfaces. - -These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/README.md b/src/tasks/dimensionality_reduction/api/README.md deleted file mode 100644 index 7c3b9c8d87..0000000000 --- a/src/tasks/dimensionality_reduction/api/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Component and file format specifications - -This folder contains specifications for file formats and component -interfaces. - -These are not only used for documentation (i.e. to document the file -format of inputs and outputs of a component), but also for unit testing -and validation of output files. diff --git a/src/tasks/dimensionality_reduction/api/README.qmd b/src/tasks/dimensionality_reduction/api/README.qmd deleted file mode 100644 index d31a99367e..0000000000 --- a/src/tasks/dimensionality_reduction/api/README.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Component and file format specifications -format: gfm ---- - -This folder contains specifications for file formats and component interfaces. - -These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index ffc7ec4f67..1003be3312 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -46,7 +46,7 @@ labels onto the test set. ``` mermaid flowchart LR - file_common_dataset("Common dataset") + file_common_dataset("Common Dataset") comp_process_dataset[/"Data processor"/] file_train("Training data") file_test("Test data") @@ -72,29 +72,26 @@ flowchart LR file_prediction---comp_metric ``` -## File format: Common dataset +## File format: Common Dataset -A dataset processed by the common dataset processing pipeline. +A subset of the common dataset. Example file: `resources_test/common/pancreas/dataset.h5ad` Description: -This dataset contains both raw counts and normalized data matrices, as -well as a PCA embedding, HVG selection and a kNN graph. +NA Format:
AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' + obs: 'celltype', 'batch' var: 'hvg', 'hvg_score' obsm: 'X_pca' - obsp: 'knn_distances', 'knn_connectivities' - varm: 'pca_loadings' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + uns: 'dataset_id', 'normalization_id'
@@ -102,29 +99,17 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | -| `obs["batch"]` | `string` | (*Optional*) Batch information. | -| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalised expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_name"]` | `string` | Nicely formatted name. | -| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | -| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | -| `uns["dataset_summary"]` | `string` | Short description of the dataset. | -| `uns["dataset_description"]` | `string` | Long description of the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["pca_variance"]` | `double` | The PCA variance objects. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------------------------------------------| +| `obs["celltype"]` | `string` | Cell type information. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -139,12 +124,12 @@ Arguments:
-| Name | Type | Description | -|:--------------------|:-------|:---------------------------------------------------------------| -| `--input` | `file` | A dataset processed by the common dataset processing pipeline. | -| `--output_train` | `file` | (*Output*) The training data. | -| `--output_test` | `file` | (*Output*) The test data (without labels). | -| `--output_solution` | `file` | (*Output*) The solution for the test data. | +| Name | Type | Description | +|:--------------------|:-------|:-------------------------------------------| +| `--input` | `file` | A subset of the common dataset. | +| `--output_train` | `file` | (*Output*) The training data. | +| `--output_test` | `file` | (*Output*) The test data (without labels). | +| `--output_solution` | `file` | (*Output*) The solution for the test data. |
diff --git a/src/tasks/label_projection/api/README.md b/src/tasks/label_projection/api/README.md deleted file mode 100644 index 7c3b9c8d87..0000000000 --- a/src/tasks/label_projection/api/README.md +++ /dev/null @@ -1,8 +0,0 @@ -# Component and file format specifications - -This folder contains specifications for file formats and component -interfaces. - -These are not only used for documentation (i.e. to document the file -format of inputs and outputs of a component), but also for unit testing -and validation of output files. diff --git a/src/tasks/label_projection/api/README.qmd b/src/tasks/label_projection/api/README.qmd deleted file mode 100644 index d31a99367e..0000000000 --- a/src/tasks/label_projection/api/README.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Component and file format specifications -format: gfm ---- - -This folder contains specifications for file formats and component interfaces. - -These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/match_modalities/README.md b/src/tasks/match_modalities/README.md new file mode 100644 index 0000000000..e9692e2b5b --- /dev/null +++ b/src/tasks/match_modalities/README.md @@ -0,0 +1,500 @@ +# Match Modalities + +Match cells across datasets of the same set of samples on different +technologies / modalities. + +Path: +[`src/tasks/match_modalities`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/match_modalities) + +## Motivation + +Cellular function is regulated by the complex interplay of different +types of biological molecules (DNA, RNA, proteins, etc.), which +determine the state of a cell. Several recently described technologies +allow for simultaneous measurement of different aspects of cellular +state. For example, sci-CAR \[@cao2018joint\] jointly profiles RNA +expression and chromatin accessibility on the same cell and CITE-seq +\[@stoeckius2017simultaneous\] measures surface protein abundance and +RNA expression from each cell. These technologies enable us to better +understand cellular function, however datasets are still rare and there +are tradeoffs that these measurements make for to profile multiple +modalities. + +Joint methods can be more expensive or lower throughput or more noisy +than measuring a single modality at a time. Therefore it is useful to +develop methods that are capable of integrating measurements of the same +biological system but obtained using different technologies on different +cells. + +## Description + +In this task, the goal is to learn a latent space where cells profiled +by different technologies in different modalities are matched if they +have the same state. We use jointly profiled data as ground truth so +that we can evaluate when the observations from the same cell acquired +using different modalities are similar. A perfect result has each of the +paired observations sharing the same coordinates in the latent space. A +method that can achieve this would be able to match datasets across +modalities to enable multimodal cellular analysis from separately +measured profiles. + +## Authors & contributors + +| name | roles | +|:------------------|:-------------------| +| Scott Gigante | author, maintainer | +| Alex Tong | author | +| Robrecht Cannoodt | author | +| Kai Waldrant | contributor | + +## API + +``` mermaid +flowchart LR + file_common_dataset_mod1("Common dataset mod1") + comp_process_dataset[/"Data processor"/] + file_dataset_mod1("Modality 1") + file_dataset_mod2("Modality 2") + file_solution_mod1("Solution mod1") + file_solution_mod2("Solution mod1") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + file_integrated_mod1("Integrated mod1") + file_integrated_mod2("Integrated mod2") + file_score("Score") + file_common_dataset_mod2("Common dataset mod2") + file_common_dataset_mod1---comp_process_dataset + comp_process_dataset-->file_dataset_mod1 + comp_process_dataset-->file_dataset_mod2 + comp_process_dataset-->file_solution_mod1 + comp_process_dataset-->file_solution_mod2 + file_dataset_mod1---comp_control_method + file_dataset_mod1---comp_method + file_dataset_mod2---comp_control_method + file_dataset_mod2---comp_method + file_solution_mod1---comp_control_method + file_solution_mod1---comp_metric + file_solution_mod2---comp_control_method + file_solution_mod2---comp_metric + comp_control_method-->file_integrated_mod1 + comp_control_method-->file_integrated_mod2 + comp_method-->file_integrated_mod1 + comp_method-->file_integrated_mod2 + comp_metric-->file_score + file_integrated_mod1---comp_metric + file_integrated_mod2---comp_metric + file_common_dataset_mod2---comp_process_dataset +``` + +## File format: Common dataset mod1 + +The first modality (RNA) of a dataset processed by the common multimodal +dataset processing pipeline. + +Example file: +`resources_test/common/scicar_cell_lines/dataset_mod1.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## Component type: Data processor + +Path: +[`src/match_modalities`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities) + +A match modalities dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------------|:-------|:---------------------------------------------------------------------------------------------------------------| +| `--input_mod1` | `file` | The first modality (RNA) of a dataset processed by the common multimodal dataset processing pipeline. | +| `--input_mod2` | `file` | The second modality (ADT or ATAC) of a dataset processed by the common multimodal dataset processing pipeline. | +| `--output_mod1` | `file` | (*Output*) The first modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--output_mod2` | `file` | (*Output*) The second modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--output_solution_mod1` | `file` | (*Output*) The ground truth information for the first modality. | +| `--output_solution_mod2` | `file` | (*Output*) The ground truth information for the second modality. | + +
+ +## File format: Modality 1 + +The first modality of a multimodal dataset. The cells of this dataset +are randomly permuted. + +Example file: +`resources_test/common/scicar_cell_lines/dataset_mod1.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Modality 2 + +The second modality of a multimodal dataset. The cells of this dataset +are randomly permuted. + +Example file: +`resources_test/common/scicar_cell_lines/dataset_mod2.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Solution mod1 + +The ground truth information for the first modality + +Example file: +`resources_test/common/scicar_cell_lines/solution_mod1.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'permutation_indices' + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-----------------------------------------------------------| +| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## File format: Solution mod1 + +The ground truth information for the second modality + +Example file: +`resources_test/common/scicar_cell_lines/solution_mod2.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obs: 'permutation_indices' + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:-----------------------------------------------------------| +| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
+ +## Component type: Control method + +Path: +[`src/match_modalities/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/control_methods) + +A multimodal data integration control method. + +Arguments: + +
+ +| Name | Type | Description | +|:------------------------|:-------|:----------------------------------------------------------------------------------------------| +| `--input_mod1` | `file` | The first modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--input_mod2` | `file` | The second modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--input_solution_mod1` | `file` | The ground truth information for the first modality. | +| `--input_solution_mod2` | `file` | The ground truth information for the second modality. | +| `--output_mod1` | `file` | (*Output*) The integrated embedding for the first modality. | +| `--output_mod2` | `file` | (*Output*) The integrated embedding for the second modality. | + +
+ +## Component type: Method + +Path: +[`src/match_modalities/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/methods) + +A multimodal data integration method. + +Arguments: + +
+ +| Name | Type | Description | +|:----------------|:-------|:----------------------------------------------------------------------------------------------| +| `--input_mod1` | `file` | The first modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--input_mod2` | `file` | The second modality of a multimodal dataset. The cells of this dataset are randomly permuted. | +| `--output_mod1` | `file` | (*Output*) The integrated embedding for the first modality. | +| `--output_mod2` | `file` | (*Output*) The integrated embedding for the second modality. | + +
+ +## Component type: Metric + +Path: +[`src/match_modalities/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/match_modalities/metrics) + +A multimodal data integration metric. + +Arguments: + +
+ +| Name | Type | Description | +|:--------------------------|:-------|:------------------------------------------------------| +| `--input_integrated_mod1` | `file` | The integrated embedding for the first modality. | +| `--input_integrated_mod2` | `file` | The integrated embedding for the second modality. | +| `--input_solution_mod1` | `file` | The ground truth information for the first modality. | +| `--input_solution_mod2` | `file` | The ground truth information for the second modality. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Integrated mod1 + +The integrated embedding for the first modality + +Example file: +`resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obsm: 'integrated' + uns: 'dataset_id', 'normalization_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:-------------------------------------| +| `obsm["integrated"]` | `double` | An integrated embedding. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | Which method was used. | + +
+ +## File format: Integrated mod2 + +The integrated embedding for the second modality + +Example file: +`resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + obsm: 'integrated' + uns: 'dataset_id', 'normalization_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:-------------------------------------| +| `obsm["integrated"]` | `double` | An integrated embedding. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | Which method was used. | + +
+ +## File format: Score + +Metric score file + +Example file: `resources_test/match_modalities/score.h5ad` + +Description: + +NA + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'normalization_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
+ +## File format: Common dataset mod2 + +The second modality (ADT or ATAC) of a dataset processed by the common +multimodal dataset processing pipeline. + +Example file: +`resources_test/common/scicar_cell_lines/dataset_mod2.h5ad` + +Description: + +This dataset contains both raw counts and normalized data matrices, as +well as a PCA embedding, HVG selection and a kNN graph. + +Format: + +
+ + AnnData object + obsm: 'X_svd' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'normalization_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:--------------------------|:----------|:-------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | + +
diff --git a/src/tasks/match_modalities/api/README.qmd b/src/tasks/match_modalities/api/README.qmd deleted file mode 100644 index d31a99367e..0000000000 --- a/src/tasks/match_modalities/api/README.qmd +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Component and file format specifications -format: gfm ---- - -This folder contains specifications for file formats and component interfaces. - -These are not only used for documentation (i.e. to document the file format of inputs and outputs of a component), but also for unit testing and validation of output files. \ No newline at end of file diff --git a/src/tasks/match_modalities/api/comp_control_method.yaml b/src/tasks/match_modalities/api/comp_control_method.yaml index 420794ea26..3610edbd3f 100644 --- a/src/tasks/match_modalities/api/comp_control_method.yaml +++ b/src/tasks/match_modalities/api/comp_control_method.yaml @@ -14,11 +14,19 @@ functionality: in the task. arguments: - name: "--input_mod1" - __merge__: file_mod1.yaml + __merge__: file_dataset_mod1.yaml direction: input required: true - name: "--input_mod2" - __merge__: file_mod2.yaml + __merge__: file_dataset_mod2.yaml + direction: input + required: true + - name: "--input_solution_mod1" + __merge__: file_solution_mod1.yaml + direction: input + required: true + - name: "--input_solution_mod2" + __merge__: file_solution_mod2.yaml direction: input required: true - name: "--output_mod1" @@ -30,8 +38,8 @@ functionality: direction: output required: true test_resources: - - path: /resources_test/common/scicar_cell_lines - dest: resources_test/common/scicar_cell_lines + - path: /resources_test/match_modalities/scicar_cell_lines + dest: resources_test/match_modalities/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script diff --git a/src/tasks/match_modalities/api/comp_method.yaml b/src/tasks/match_modalities/api/comp_method.yaml index 89e883bec0..57ff6a3318 100644 --- a/src/tasks/match_modalities/api/comp_method.yaml +++ b/src/tasks/match_modalities/api/comp_method.yaml @@ -9,11 +9,11 @@ functionality: A multimodal method to integrate data. arguments: - name: "--input_mod1" - __merge__: file_mod1.yaml + __merge__: file_dataset_mod1.yaml direction: input required: true - name: "--input_mod2" - __merge__: file_mod2.yaml + __merge__: file_dataset_mod2.yaml direction: input required: true - name: "--output_mod1" @@ -25,8 +25,8 @@ functionality: direction: output required: true test_resources: - - path: /resources_test/common/scicar_cell_lines - dest: resources_test/common/scicar_cell_lines + - path: /resources_test/match_modalities/scicar_cell_lines + dest: resources_test/match_modalities/scicar_cell_lines - type: python_script path: /src/common/comp_tests/check_method_config.py - type: python_script diff --git a/src/tasks/match_modalities/api/comp_metric.yaml b/src/tasks/match_modalities/api/comp_metric.yaml index 6548c2a6cf..220598bbbf 100644 --- a/src/tasks/match_modalities/api/comp_metric.yaml +++ b/src/tasks/match_modalities/api/comp_metric.yaml @@ -8,12 +8,20 @@ functionality: description: | A metric for evaluating integrated data. arguments: - - name: "--input_mod1" + - name: "--input_integrated_mod1" __merge__: file_integrated_mod1.yaml direction: input required: true - - name: "--input_mod2" - __merge__: file_integrated_mod1.yaml + - name: "--input_integrated_mod2" + __merge__: file_integrated_mod2.yaml + direction: input + required: true + - name: "--input_solution_mod1" + __merge__: file_solution_mod1.yaml + direction: input + required: true + - name: "--input_solution_mod2" + __merge__: file_solution_mod2.yaml direction: input required: true - name: "--output" diff --git a/src/tasks/match_modalities/api/comp_process_dataset.yaml b/src/tasks/match_modalities/api/comp_process_dataset.yaml index 13adb6ec84..a48a0957b1 100644 --- a/src/tasks/match_modalities/api/comp_process_dataset.yaml +++ b/src/tasks/match_modalities/api/comp_process_dataset.yaml @@ -1,32 +1,40 @@ functionality: - namespace: "label_projection" + namespace: "match_modalities" info: type: process_dataset type_info: label: Data processor - summary: A label projection dataset processor. + summary: A match modalities dataset processor. description: | A component for processing a Common Dataset into a task-specific dataset. arguments: - - name: "--input" - __merge__: /src/datasets/api/file_common_dataset.yaml + - name: "--input_mod1" + __merge__: file_common_dataset_mod1.yaml direction: input required: true - - name: "--output_train" - __merge__: file_train.yaml + - name: "--input_mod2" + __merge__: file_common_dataset_mod2.yaml + direction: input + required: true + - name: "--output_mod1" + __merge__: file_dataset_mod1.yaml + direction: output + required: true + - name: "--output_mod2" + __merge__: file_dataset_mod2.yaml direction: output required: true - - name: "--output_test" - __merge__: file_test.yaml + - name: "--output_solution_mod1" + __merge__: file_solution_mod1.yaml direction: output required: true - - name: "--output_solution" - __merge__: file_solution.yaml + - name: "--output_solution_mod2" + __merge__: file_solution_mod2.yaml direction: output required: true test_resources: - - path: /resources_test/common/pancreas - dest: resources_test/common/pancreas + - path: /resources_test/common/scicar_cell_lines + dest: resources_test/common/scicar_cell_lines - type: python_script path: /src/common/comp_tests/run_and_check_adata.py diff --git a/src/tasks/match_modalities/api/file_mod1.yaml b/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml similarity index 65% rename from src/tasks/match_modalities/api/file_mod1.yaml rename to src/tasks/match_modalities/api/file_common_dataset_mod1.yaml index d3e8570847..fec9d27fa9 100644 --- a/src/tasks/match_modalities/api/file_mod1.yaml +++ b/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml @@ -1,8 +1,11 @@ type: file example: "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad" info: - label: "Modality 1" - summary: "The first modality of a multimodal dataset." + label: "Common dataset mod1" + summary: The first modality (RNA) of a dataset processed by the common multimodal dataset processing pipeline. + description: | + This dataset contains both raw counts and normalized data matrices, + as well as a PCA embedding, HVG selection and a kNN graph. slots: layers: - type: integer @@ -13,15 +16,6 @@ info: name: normalized description: Normalized counts required: true - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true obsm: - type: double name: X_svd diff --git a/src/tasks/match_modalities/api/file_mod2.yaml b/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml similarity index 65% rename from src/tasks/match_modalities/api/file_mod2.yaml rename to src/tasks/match_modalities/api/file_common_dataset_mod2.yaml index 665d833376..9c63692c61 100644 --- a/src/tasks/match_modalities/api/file_mod2.yaml +++ b/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml @@ -1,8 +1,11 @@ type: file example: "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad" info: - label: "Modality 2" - summary: "The second modality of a multimodal dataset." + label: "Common dataset mod2" + summary: The second modality (ADT or ATAC) of a dataset processed by the common multimodal dataset processing pipeline. + description: | + This dataset contains both raw counts and normalized data matrices, + as well as a PCA embedding, HVG selection and a kNN graph. slots: layers: - type: integer @@ -13,15 +16,6 @@ info: name: normalized description: Normalized counts required: true - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true obsm: - type: double name: X_svd diff --git a/src/tasks/match_modalities/api/file_dataset_mod1.yaml b/src/tasks/match_modalities/api/file_dataset_mod1.yaml new file mode 100644 index 0000000000..aece4dc975 --- /dev/null +++ b/src/tasks/match_modalities/api/file_dataset_mod1.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/match_modalities/scicar_cell_lines/dataset_mod1.h5ad" +info: + label: "Modality 1" + summary: "The first modality of a multimodal dataset. The cells of this dataset are randomly permuted." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/file_dataset_mod2.yaml b/src/tasks/match_modalities/api/file_dataset_mod2.yaml new file mode 100644 index 0000000000..9c140e3de8 --- /dev/null +++ b/src/tasks/match_modalities/api/file_dataset_mod2.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad" +info: + label: "Modality 2" + summary: "The second modality of a multimodal dataset. The cells of this dataset are randomly permuted." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/file_integrated_mod1.yaml b/src/tasks/match_modalities/api/file_integrated_mod1.yaml index 97580facfc..72f363de1f 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod1.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod1.yaml @@ -1,35 +1,13 @@ type: file example: "resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad" info: - label: "Integrated" - summary: "The integrated data" + label: "Integrated mod1" + summary: "The integrated embedding for the first modality" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalized counts - required: true - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true obsm: - - type: double - name: X_svd - description: The resulting SVD PCA embedding. - required: true - type: double name: integrated - description: The resulting integrated embedding. + description: An integrated embedding. required: true uns: - type: string diff --git a/src/tasks/match_modalities/api/file_integrated_mod2.yaml b/src/tasks/match_modalities/api/file_integrated_mod2.yaml index f3324ffc9a..644bf052d4 100644 --- a/src/tasks/match_modalities/api/file_integrated_mod2.yaml +++ b/src/tasks/match_modalities/api/file_integrated_mod2.yaml @@ -1,35 +1,13 @@ type: file example: "resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad" info: - label: "Integrated" - summary: "The integrated data" + label: "Integrated mod2" + summary: "The integrated embedding for the second modality" slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - - type: double - name: normalized - description: Normalized counts - required: true - var: - - type: boolean - name: hvg - description: Whether or not the feature is considered to be a 'highly variable gene' - required: true - - type: integer - name: hvg_score - description: A ranking of the features by hvg. - required: true obsm: - - type: double - name: X_svd - description: The resulting SVD PCA embedding. - required: true - type: double name: integrated - description: The resulting integrated embedding. + description: An integrated embedding. required: true uns: - type: string diff --git a/src/tasks/match_modalities/api/file_score.yaml b/src/tasks/match_modalities/api/file_score.yaml index 7c9818ecfb..7d66bde3c3 100644 --- a/src/tasks/match_modalities/api/file_score.yaml +++ b/src/tasks/match_modalities/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/match_modalities/score.h5ad" +example: "resources_test/match_modalities/scicar_cell_lines/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/match_modalities/api/file_solution_mod1.yaml b/src/tasks/match_modalities/api/file_solution_mod1.yaml new file mode 100644 index 0000000000..2a9d52dc82 --- /dev/null +++ b/src/tasks/match_modalities/api/file_solution_mod1.yaml @@ -0,0 +1,34 @@ +type: file +example: "resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad" +info: + label: "Solution mod1" + summary: "The ground truth information for the first modality" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + obs: + - type: integer + name: permutation_indices + description: "Indices with which to revert the permutation of the cells" + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/file_solution_mod2.yaml b/src/tasks/match_modalities/api/file_solution_mod2.yaml new file mode 100644 index 0000000000..03009a7e1b --- /dev/null +++ b/src/tasks/match_modalities/api/file_solution_mod2.yaml @@ -0,0 +1,34 @@ +type: file +example: "resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad" +info: + label: "Solution mod1" + summary: "The ground truth information for the second modality" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + - type: double + name: normalized + description: Normalized counts + required: true + obs: + - type: integer + name: permutation_indices + description: "Indices with which to revert the permutation of the cells" + required: true + obsm: + - type: double + name: X_svd + description: The resulting SVD PCA embedding. + required: true + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/match_modalities/api/task_info.yaml b/src/tasks/match_modalities/api/task_info.yaml index 2baa517cac..bc5550df16 100644 --- a/src/tasks/match_modalities/api/task_info.yaml +++ b/src/tasks/match_modalities/api/task_info.yaml @@ -1,18 +1,41 @@ name: match_modalities label: Match Modalities summary: | - Match modalities is the task of combining multiple datasets - that have been generated from the same set of samples. + Match cells across datasets of the same set of samples on different technologies / modalities. image: "thumbnail.svg" -motivation: "No motivation has been provided for this task." +motivation: | + Cellular function is regulated by the complex interplay of different types of biological + molecules (DNA, RNA, proteins, etc.), which determine the state of a cell. Several + recently described technologies allow for simultaneous measurement of different aspects + of cellular state. For example, sci-CAR [@cao2018joint] + jointly profiles RNA expression and chromatin accessibility on the same cell and + CITE-seq [@stoeckius2017simultaneous] measures + surface protein abundance and RNA expression from each cell. These technologies enable + us to better understand cellular function, however datasets are still rare and there are + tradeoffs that these measurements make for to profile multiple modalities. + + Joint methods can be more expensive or lower throughput or more noisy than measuring a + single modality at a time. Therefore it is useful to develop methods that are capable + of integrating measurements of the same biological system but obtained using different + technologies on different cells. description: | - Match modalities is the task of combining multiple datasets - that have been generated from the same set of samples. This task is - important for integrating datasets generated from different modalities - (e.g. RNA and ATAC) or from different technologies (e.g. 10x and - SmartSeq). The goal of this task is to evaluate methods for integrating - multimodal datasets. + In this task, the goal is to learn a latent space where cells profiled by different + technologies in different modalities are matched if they have the same state. We use + jointly profiled data as ground truth so that we can evaluate when the observations + from the same cell acquired using different modalities are similar. A perfect result + has each of the paired observations sharing the same coordinates in the latent space. + A method that can achieve this would be able to match datasets across modalities to + enable multimodal cellular analysis from separately measured profiles. authors: + - name: "Scott Gigante" + roles: [ author, maintainer ] + info: + github: scottgigante + orcid: "0000-0002-4544-2764" + - name: Alex Tong + roles: [ author ] + info: + github: atong01 - name: Robrecht Cannoodt roles: [ author ] info: diff --git a/src/tasks/match_modalities/control_methods/random_features/script.py b/src/tasks/match_modalities/control_methods/random_features/script.py index 0c0b6ad5f1..d10bb72b27 100644 --- a/src/tasks/match_modalities/control_methods/random_features/script.py +++ b/src/tasks/match_modalities/control_methods/random_features/script.py @@ -21,6 +21,7 @@ adata_mod2 = ad.read_h5ad(par["input_mod2"]) print("Generating random features", flush=True) +# todo: do we actually need to permute this once more adata_mod1.obsm["integrated"] = adata_mod1.obsm["X_svd"][np.random.permutation(np.arange(adata_mod1.shape[0]))] adata_mod2.obsm["integrated"] = adata_mod1.obsm["X_svd"][np.random.permutation(np.arange(adata_mod1.shape[0]))] diff --git a/src/tasks/match_modalities/control_methods/true_features/script.py b/src/tasks/match_modalities/control_methods/true_features/script.py index e4b5a28292..2fd06b5a10 100644 --- a/src/tasks/match_modalities/control_methods/true_features/script.py +++ b/src/tasks/match_modalities/control_methods/true_features/script.py @@ -1,18 +1,17 @@ import anndata as ad ## VIASH START - par = { - "input_mod1": "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", - "input_mod2": "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", - "output_mod1": "output.mod1.h5ad", - "output_mod2": "output.mod2.h5ad", + "input_mod1": "resources_test/match_modalities/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2": "resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad", + "input_solution_mod1": "resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad", + "input_solution_mod2": "resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad", + "output_mod1": "output.mod1.h5ad", + "output_mod2": "output.mod2.h5ad", } - meta = { "functionality_name": "true_features" } - ## VIASH END print("Reading input h5ad file", flush=True) @@ -20,11 +19,31 @@ adata_mod2 = ad.read_h5ad(par["input_mod2"]) print("Storing true features", flush=True) -adata_mod1.obsm["integrated"] = adata_mod1.obsm["X_svd"] -adata_mod2.obsm["integrated"] = adata_mod1.obsm["X_svd"] +output_mod1 = ad.AnnData( + obs=adata_mod1.obs[[]], + var=adata_mod1.var[[]], + obsm={ + "integrated": adata_mod1.obsm["X_svd"] + }, + uns={ + "dataset_id": adata_mod1.uns["dataset_id"], + "normalization_id": adata_mod1.uns["normalization_id"], + "method_id": meta["functionality_name"] + } +) +output_mod2 = ad.AnnData( + obs=adata_mod2.obs[[]], + var=adata_mod2.var[[]], + obsm={ + "integrated": adata_mod2.obsm["X_svd"] + }, + uns={ + "dataset_id": adata_mod2.uns["dataset_id"], + "normalization_id": adata_mod2.uns["normalization_id"], + "method_id": meta["functionality_name"] + } +) print("Write output to file", flush=True) -adata_mod1.uns["method_id"] = meta["functionality_name"] -adata_mod2.uns["method_id"] = meta["functionality_name"] -adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") -adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") +output_mod1.write_h5ad(par["output_mod1"], compression="gzip") +output_mod2.write_h5ad(par["output_mod2"], compression="gzip") diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/script.py b/src/tasks/match_modalities/methods/harmonic_alignment/script.py index c2243badbd..abe2eece7c 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/script.py +++ b/src/tasks/match_modalities/methods/harmonic_alignment/script.py @@ -9,10 +9,9 @@ "n_pca_XY" : 100, "eigenvectors" : 100 } - meta = { - "functionality_name" : "harmonic_alignment" - } + "functionality_name" : "harmonic_alignment" +} ## VIASH END diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index a25ca276af..e21b3febe5 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -26,4 +26,4 @@ platforms: - scipy - type: nextflow directives: - label: [ "midtime", medcpu, medmem ] \ No newline at end of file + label: [ "midtime", midmem, midcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/scot/script.py b/src/tasks/match_modalities/methods/scot/script.py index 925a727cae..d6e629c565 100644 --- a/src/tasks/match_modalities/methods/scot/script.py +++ b/src/tasks/match_modalities/methods/scot/script.py @@ -16,7 +16,6 @@ "output_mod2" : "integrated_mod2.h5ad", "balanced":False, } - ## VIASH END diff --git a/src/tasks/match_modalities/metrics/knn_auc/script.py b/src/tasks/match_modalities/metrics/knn_auc/script.py index 87083b6ae7..0af2c08566 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/script.py +++ b/src/tasks/match_modalities/metrics/knn_auc/script.py @@ -4,45 +4,45 @@ import sklearn.neighbors ## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. par = { - "input_mod1": "resources_test/multimodal/integrated_mod1.h5ad", - "input_mod2": "resources_test/multimodal/integrated_mod2.h5ad", - "output": "resources_test/multimodal/score.h5ad", - "proportion_neighbors": 0.1, + "input_integrated_mod1": "resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad", + "input_integrated_mod2": "resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad", + "input_solution_mod1": "resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad", + "input_solution_mod2": "resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad", + "output": "resources_test/multimodal/score.h5ad", + "proportion_neighbors": 0.1, } - meta = { "functionality_name": "knn_auc" } ## VIASH END print("Reading adata file", flush=True) -adata_mod1 = ad.read_h5ad(par["input_mod1"]) -adata_mod2 = ad.read_h5ad(par["input_mod2"]) +input_solution_mod1 = ad.read_h5ad(par["input_solution_mod1"]) +input_solution_mod2 = ad.read_h5ad(par["input_solution_mod2"]) + +input_integrated_mod1 = ad.read_h5ad(par["input_integrated_mod1"])[input_solution_mod1.obs["permutation_indices"]] +input_integrated_mod2 = ad.read_h5ad(par["input_integrated_mod2"])[input_solution_mod2.obs["permutation_indices"]] print("Checking parameters", flush=True) -n_neighbors = int(np.ceil(par["proportion_neighbors"] * adata_mod1.layers["normalized"].shape[0])) +n_neighbors = int(np.ceil(par["proportion_neighbors"] * input_solution_mod1.n_obs)) print("Compute KNN on PCA", flush=True) _, indices_true = ( sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) - .fit(adata_mod1.obsm["X_svd"]) - .kneighbors(adata_mod1.obsm["X_svd"]) + .fit(input_solution_mod1.obsm["X_svd"]) + .kneighbors(input_solution_mod2.obsm["X_svd"]) ) -print("Compute KNN on integrated matrix", flush=True) _, indices_pred = ( sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) - .fit(adata_mod1.obsm["integrated"]) - .kneighbors(adata_mod2.obsm["integrated"]) + .fit(input_integrated_mod1.obsm["integrated"]) + .kneighbors(input_integrated_mod2.obsm["integrated"]) ) -print("Check which neighbours match", flush=True) print("Check which neighbours match", flush=True) neighbors_match = np.zeros(n_neighbors, dtype=int) -for i in range(adata_mod1.layers["normalized"].shape[0]): +for i in range(input_solution_mod1.n_obs): _, pred_matches, true_matches = np.intersect1d( indices_pred[i], indices_true[i], return_indices=True ) @@ -52,26 +52,24 @@ axis=0, ) -print("Compute area under neighbours match curve", flush=True) print("Compute area under neighbours match curve", flush=True) neighbors_match_curve = neighbors_match / ( - np.arange(1, n_neighbors + 1) * adata_mod1.layers["normalized"].shape[0] + np.arange(1, n_neighbors + 1) * input_solution_mod1.n_obs ) area_under_curve = np.mean(neighbors_match_curve) -print("Store metic value", flush=True) +print("Store metric value", flush=True) +uns = { + "dataset_id": input_solution_mod1.uns["dataset_id"], + "normalization_id": input_solution_mod1.uns["normalization_id"], + "method_id": input_integrated_mod1.uns["method_id"], + "metric_ids": "knn_auc", + "metric_values": area_under_curve +} output_metric = ad.AnnData( - layers={}, - obs=adata_mod1.obs[[]], - var=adata_mod1.var[[]], - uns={}, + shape=(0,0), + uns=uns ) -for key in adata_mod1.uns_keys(): - output_metric.uns[key] = adata_mod1.uns[key] - -output_metric.uns["metric_ids"] = meta["functionality_name"] -output_metric.uns["metric_values"] = area_under_curve - print("Writing adata to file", flush=True) output_metric.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index 9507718990..cd3f22bf0d 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -17,7 +17,7 @@ functionality: commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 resources: - type: python_script - path: ./script.py + path: script.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.1 @@ -26,7 +26,6 @@ platforms: packages: - numpy - scipy - - scprep - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/match_modalities/metrics/mse/script.py b/src/tasks/match_modalities/metrics/mse/script.py index 6710b3dac2..b03487c6eb 100644 --- a/src/tasks/match_modalities/metrics/mse/script.py +++ b/src/tasks/match_modalities/metrics/mse/script.py @@ -1,21 +1,26 @@ import anndata as ad -import scprep import numpy as np from scipy import sparse ## VIASH START -# The code between the the comments above and below gets stripped away before -# execution. Here you can put anything that helps the prototyping of your script. par = { - "input_mod1": "resources_test/multimodal/integrated_mod1.h5ad", - "input_mod2": "resources_test/multimodal/integrated_mod2.h5ad", - "output": "resources_test/multimodal/mse.h5ad" + "input_integrated_mod1": "resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad", + "input_integrated_mod2": "resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad", + "input_solution_mod1": "resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad", + "input_solution_mod2": "resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad", + "output": "resources_test/multimodal/score.h5ad", +} +meta = { + "functionality_name": "knn_auc" } ## VIASH END print("Reading adata file", flush=True) -adata_mod1 = ad.read_h5ad(par["input_mod1"]) -adata_mod2 = ad.read_h5ad(par["input_mod2"]) +input_solution_mod1 = ad.read_h5ad(par["input_solution_mod1"]) +input_solution_mod2 = ad.read_h5ad(par["input_solution_mod2"]) + +input_integrated_mod1 = ad.read_h5ad(par["input_integrated_mod1"])[input_solution_mod1.obs["permutation_indices"]] +input_integrated_mod2 = ad.read_h5ad(par["input_integrated_mod2"])[input_solution_mod2.obs["permutation_indices"]] print("Computing MSE", flush=True) def _square(X): @@ -23,29 +28,29 @@ def _square(X): X.data = X.data ** 2 return X else: - return scprep.utils.toarray(X) ** 2 + return X ** 2 -X = scprep.utils.toarray(adata_mod1.obsm["integrated"]) -Y = scprep.utils.toarray(adata_mod2.obsm["integrated"]) + +X = input_integrated_mod1.obsm["integrated"].toarray() +Y = input_integrated_mod2.obsm["integrated"].toarray() X_shuffled = X[np.random.permutation(np.arange(X.shape[0])), :] error_random = np.mean(np.sum(_square(X_shuffled - Y))) error_abs = np.mean(np.sum(_square(X - Y))) -metric_value = error_abs / error_random - +metric_value = (error_abs / error_random).item() + +print("Store metric value", flush=True) +uns = { + "dataset_id": input_solution_mod1.uns["dataset_id"], + "normalization_id": input_solution_mod1.uns["normalization_id"], + "method_id": input_integrated_mod1.uns["method_id"], + "metric_ids": "mse", + "metric_values": metric_value +} output_metric = ad.AnnData( - layers={}, - obs=adata_mod1.obs[[]], - var=adata_mod1.var[[]], - uns={} + shape=(0,0), + uns=uns ) -for key in adata_mod1.uns_keys(): - output_metric.uns[key] = adata_mod1.uns[key] - -print("Store metic value", flush=True) -output_metric.uns["metric_ids"] = meta["functionality_name"] -output_metric.uns["metric_values"] = metric_value - print("Writing adata to file", flush=True) output_metric.write_h5ad(par["output"], compression = "gzip") diff --git a/src/tasks/match_modalities/process_dataset/config.vsh.yaml b/src/tasks/match_modalities/process_dataset/config.vsh.yaml new file mode 100644 index 0000000000..79b03ce982 --- /dev/null +++ b/src/tasks/match_modalities/process_dataset/config.vsh.yaml @@ -0,0 +1,16 @@ +__merge__: ../api/comp_process_dataset.yaml +functionality: + name: "process_dataset" + arguments: + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + resources: + - type: python_script + path: script.py + - path: /src/common/helper_functions/subset_anndata.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + - type: nextflow diff --git a/src/tasks/match_modalities/process_dataset/script.py b/src/tasks/match_modalities/process_dataset/script.py new file mode 100644 index 0000000000..d90d5e3965 --- /dev/null +++ b/src/tasks/match_modalities/process_dataset/script.py @@ -0,0 +1,64 @@ +import sys +import random +import numpy as np +import anndata as ad + +## VIASH START +par = { + "input_mod1": "resources_test/common/scicar_cell_lines/dataset_mod1.h5ad", + "input_mod2": "resources_test/common/scicar_cell_lines/dataset_mod2.h5ad", + "output_mod1": "output_mod1.h5ad", + "output_mod2": "output_mod2.h5ad", + "output_solution_mod1": "output_solution_mod1.h5ad", + "output_solution_mod2": "output_solution_mod2.h5ad", + "seed": 123 +} +meta = { + "resources_dir": "src/common/helper_functions/", + "config": "src/tasks/match_modalities/process_dataset/.config.vsh.yaml" +} +## VIASH END + +# import helper functions +sys.path.append(meta["resources_dir"]) +from subset_anndata import read_config_slots_info, subset_anndata + +# set seed if need be +if par["seed"]: + print(f">> Setting seed to {par['seed']}") + random.seed(par["seed"]) + +print(">> Load data", flush=True) +input_mod1 = ad.read_h5ad(par["input_mod1"]) +input_mod2 = ad.read_h5ad(par["input_mod2"]) + +print(f">> Permute input data") +mod1_perm = np.random.permutation(np.arange(input_mod1.n_obs)) +mod2_perm = np.random.permutation(np.arange(input_mod2.n_obs)) + +output_mod1 = input_mod1[mod1_perm] +output_mod1.obs_names = [f"cell_mod1_{i}" for i in range(output_mod1.n_obs)] +output_mod2 = input_mod2[mod2_perm] +output_mod2.obs_names = [f"cell_mod2_{i}" for i in range(output_mod2.n_obs)] + +print(f">> Create solution objects") +output_solution_mod1 = input_mod1.copy() +output_solution_mod1.obs["permutation_indices"] = np.argsort(mod1_perm) +output_solution_mod2 = input_mod2.copy() +output_solution_mod2.obs["permutation_indices"] = np.argsort(mod2_perm) + +# subset the different adatas +print(">> Read slot info from config file", flush=True) +slot_info = read_config_slots_info(meta["config"]) + +print(">> Subset anndatas", flush=True) +output_mod1 = subset_anndata(output_mod1, slot_info["output_mod1"]) +output_mod2 = subset_anndata(output_mod2, slot_info["output_mod2"]) +output_solution_mod1 = subset_anndata(output_solution_mod1, slot_info["output_solution_mod1"]) +output_solution_mod2 = subset_anndata(output_solution_mod2, slot_info["output_solution_mod2"]) + +print(">> Writing data", flush=True) +output_mod1.write_h5ad(par["output_mod1"]) +output_mod2.write_h5ad(par["output_mod2"]) +output_solution_mod1.write_h5ad(par["output_solution_mod1"]) +output_solution_mod2.write_h5ad(par["output_solution_mod2"]) diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh new file mode 100755 index 0000000000..f3a7acc797 --- /dev/null +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +COMMON_DATASETS="resources/datasets/openproblems_v1_multimodal" +OUTPUT_DIR="resources/match_modalities/datasets/openproblems_v1_multimodal" + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -resume \ + --input_states "$COMMON_DATASETS/**/state.yaml" \ + --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ + --settings '{"output_mod1": "$id/output_mod1.h5ad", "output_mod2": "$id/output_mod2.h5ad", "output_solution_mod1": "$id/output_solution_mod1.h5ad", "output_solution_mod2": "$id/output_solution_mod2.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..19b3e61598 --- /dev/null +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources/label_projection" +OUTPUT_DIR="output/test" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_train:output_train,input_test:output_test,input_solution:output_solution' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR"\ + --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh index 6dd04be88a..91e90d52dd 100755 --- a/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh +++ b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh @@ -1,7 +1,34 @@ #!/bin/bash -viash run src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml -- \ - --input_mod1 resources_test/common/scicar_cell_lines/dataset_mod1.h5ad \ - --input_mod2 resources_test/common/scicar_cell_lines/dataset_mod2.h5ad \ - --output_mod1 resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad \ - --output_mod2 resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad \ No newline at end of file +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/match_modalities + +mkdir -p $DATASET_DIR + +# process dataset +echo Running process_dataset +nextflow run . \ + -main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + --input_states "$RAW_DATA/**/state.yaml" \ + --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ + --settings '{"output_mod1": "$id/dataset_mod1.h5ad", "output_mod2": "$id/dataset_mod2.h5ad", "output_solution_mod1": "$id/solution_mod1.h5ad", "output_solution_mod2": "$id/solution_mod2.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved + +# run one method +viash run src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml -- \ + --input_mod1 $DATASET_DIR/scicar_cell_lines/dataset_mod1.h5ad \ + --input_mod2 $DATASET_DIR/scicar_cell_lines/dataset_mod2.h5ad \ + --output_mod1 $DATASET_DIR/scicar_cell_lines/integrated_mod1.h5ad \ + --output_mod2 $DATASET_DIR/scicar_cell_lines/integrated_mod2.h5ad diff --git a/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..0145373661 --- /dev/null +++ b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,53 @@ +functionality: + name: "process_datasets" + namespace: "match_modalities/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input_mod1" + __merge__: "/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml" + required: true + direction: input + - name: "--input_mod2" + __merge__: "/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" + required: true + direction: input + - name: "--dataset_schema_mod1" + type: "file" + description: "The schema of the dataset mod1 to validate against" + required: true + default: "src/tasks/match_modalities/api/file_common_dataset_mod1.yaml" + direction: input + - name: "--dataset_schema_mod2" + type: "file" + description: "The schema of the dataset mod2 to validate against" + required: true + default: "src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" + direction: input + - name: Outputs + arguments: + - name: "--output_mod1" + __merge__: /src/tasks/match_modalities/api/file_dataset_mod1.yaml + required: true + direction: output + - name: "--output_mod2" + __merge__: /src/tasks/match_modalities/api/file_dataset_mod2.yaml + required: true + direction: output + - name: "--output_solution_mod1" + __merge__: /src/tasks/match_modalities/api/file_solution_mod1.yaml + required: true + direction: output + - name: "--output_solution_mod2" + __merge__: /src/tasks/match_modalities/api/file_solution_mod2.yaml + required: true + direction: output + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema + - name: match_modalities/process_dataset +platforms: + - type: nextflow diff --git a/src/tasks/match_modalities/workflows/process_datasets/main.nf b/src/tasks/match_modalities/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..9e6c9fea6c --- /dev/null +++ b/src/tasks/match_modalities/workflows/process_datasets/main.nf @@ -0,0 +1,69 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // TODO: check schema based on the values in `config` + // instead of having to provide a separate schema file + | check_dataset_schema.run( + key: "check_dataset_schema_mod1", + fromState: [ + "input": "input_mod1", + "schema": "dataset_schema_mod1" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset_mod1": "output" + ] + ) + | check_dataset_schema.run( + key: "check_dataset_schema_mod2", + fromState: [ + "input": "input_mod2", + "schema": "dataset_schema_mod2" + ], + args: [ + "stop_on_error": false + ], + toState: [ + "dataset_mod2": "output" + ] + ) + + // remove datasets which didn't pass the schema check + | filter { id, state -> + state.dataset_mod1 != null && state.dataset_mod2 != null + } + + | process_dataset.run( + fromState: [ input_mod1: "dataset_mod1", input_mod2: "dataset_mod2" ], + toState: [ + "output_mod1", + "output_mod2", + "output_solution_mod1", + "output_solution_mod2" + ] + ) + + // only output the files for which an output file was specified + | setState([ + "output_mod1", + "output_mod2", + "output_solution_mod1", + "output_solution_mod2" + ]) + + emit: + output_ch +} diff --git a/src/tasks/match_modalities/workflows/run/main.nf b/src/tasks/match_modalities/workflows/run/main.nf deleted file mode 100644 index 62d65fa112..0000000000 --- a/src/tasks/match_modalities/workflows/run/main.nf +++ /dev/null @@ -1,124 +0,0 @@ -// add custom tracer to nextflow to capture exit codes, memory usage, cpu usage, etc. -traces = initializeTracer() - -// run the workflow -workflow run_wf { - take: - input_ch - - main: - - // collect method list - methods = [ - random_features, - true_features, - scot, - harmonic_alignment, - fastmnn, - procrustes - ] - - // collect metric list - metrics = [ - knn_auc, - mse - ] - - output_ch = input_ch - - // extract the dataset metadata - | check_dataset_schema.run( - fromState: [ "input": "input_mod1" ], - toState: { id, output, state -> - // load output yaml file - def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - // add metadata from file to state - state + metadata - } - ) - - // run all methods - | runComponents( - components: methods, - - // // use the 'filter' argument to only run a method on the normalisation the component is asking for - // filter: { id, state, config -> - // def norm = state.normalization_id - // def pref = config.functionality.info.preferred_normalization - // // if the preferred normalisation is none at all, - // // we can pass whichever dataset we want - // (norm == "log_cp10k" && pref == "counts") || norm == pref - // }, - - // define a new 'id' by appending the method name to the dataset id - id: { id, state, config -> - id + "." + config.functionality.name - }, - - // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: { id, state, config -> - def new_args = [ - input_mod1: state.input_mod1, - input_mod2: state.input_mod2 - ] - new_args - }, - - // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> - state + [ - method_id: config.functionality.name, - method_output_mod1: output.output_mod1, - method_output_mod2: output.output_mod2 - ] - } - ) - - // run all metrics - | runComponents( - components: metrics, - // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: [ - input_mod1: "method_output_mod1", - input_mod2: "method_output_mod2" - ], - // use 'toState' to publish that component's outputs to the overall state - toState: { id, output, state, config -> - state + [ - metric_id: config.functionality.name, - metric_output: output.output - ] - } - ) - - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - output: states[0].output - ] - [new_id, new_state] - } - - // convert to tsv and publish - | extract_scores.run( - auto: [publish: true] - ) - - emit: - output_ch - -} - -// store the trace log in the publish dir -workflow.onComplete { - def publish_dir = getPublishDir() - - writeJsontraces, file("$publish_dir/traces.json")) - // todo: add datasets logging - writeJsonmethods.collect{it.config}, file("$publish_dir/methods.json")) - writeJsonmetrics.collect{it.config}, file("$publish_dir/metrics.json")) -} diff --git a/src/tasks/match_modalities/workflows/run/nextflow.config b/src/tasks/match_modalities/workflows/run/nextflow.config deleted file mode 100644 index 8511097c9b..0000000000 --- a/src/tasks/match_modalities/workflows/run/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'match_modalities/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=23.04.2' - description = 'multimodal data integration' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/run_test.sh b/src/tasks/match_modalities/workflows/run/run_test.sh deleted file mode 100755 index a14859511d..0000000000 --- a/src/tasks/match_modalities/workflows/run/run_test.sh +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/bash - -# Run this prior to executing this script: -# viash ns build -q 'match_modalities|common' --setup cb --parallel - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -DATASET_DIR=resources_test/common/scicar_cell_lines - -# choose a particular version of nextflow -export NXF_VER=23.04.2 - -nextflow \ - run . \ - -main-script src/tasks/match_modalities/workflows/run/main.nf \ - -resume \ - -c src/wf_utils/labels_ci.config \ - -profile docker \ - --id scicar \ - --input_mod1 $DATASET_DIR/dataset_mod1.h5ad \ - --input_mod2 $DATASET_DIR/dataset_mod2.h5ad \ - --output scores.tsv \ - --publish_dir output/match_modalities/ \ - - - diff --git a/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh b/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh deleted file mode 100644 index 4c2daa5691..0000000000 --- a/src/tasks/match_modalities/workflows/run/run_test_on_tower.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -DATASET_DIR=resources_test/common/scicar_cell_lines - -# try running on nf tower -cat > /tmp/params.yaml << HERE -id: scicar -input_mod1: s3://openproblems-data/$DATASET_DIR/dataset_mod1.h5ad -input_mod2: s3://openproblems-data/$DATASET_DIR/dataset_mod2.h5ad -output: scores.tsv -publish_dir: s3://openproblems-nextflow/output_test/v2/match_modalities -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision integration_build \ - --pull-latest \ - --main-script src/tasks/match_modalities/workflows/run/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/run/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml similarity index 53% rename from src/tasks/match_modalities/workflows/run/config.vsh.yaml rename to src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index 8d2586e81c..a3c4f2d8d5 100644 --- a/src/tasks/match_modalities/workflows/run/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -5,14 +5,29 @@ functionality: - name: Inputs arguments: - name: "--input_mod1" - type: "file" # todo: replace with includes + __merge__: /src/tasks/match_modalities/api/file_dataset_mod1.yaml + direction: input + required: true - name: "--input_mod2" - type: "file" + __merge__: /src/tasks/match_modalities/api/file_dataset_mod2.yaml + direction: input + required: true + - name: "--input_solution_mod1" + __merge__: /src/tasks/match_modalities/api/file_solution_mod1.yaml + direction: input + required: true + - name: "--input_solution_mod2" + __merge__: /src/tasks/match_modalities/api/file_solution_mod2.yaml + direction: input + required: true - name: Outputs arguments: - name: "--output" - direction: "output" + direction: output type: file + example: output.tsv + description: A TSV file containing the scores of each of the methods + required: true resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf new file mode 100644 index 0000000000..db135b3a01 --- /dev/null +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -0,0 +1,131 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + + // collect method list + methods = [ + random_features, + true_features, + scot, + harmonic_alignment, + fastmnn, + procrustes + ] + + // collect metric list + metrics = [ + knn_auc, + mse + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [ "input": "input_mod1" ], + toState: { id, output, state -> + // load output yaml file + def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + // add metadata from file to state + state + metadata + } + ) + + // run all methods + | runEach( + components: methods, + + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, comp -> + def norm = state.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cp10k" && pref == "counts") || norm == pref + }, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, + + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, comp -> + def new_args = [ + input_mod1: state.input_mod1, + input_mod2: state.input_mod2 + ] + if (comp.config.functionality.info.type == "control_method") { + new_args.input_solution_mod1 = state.input_solution_mod1 + new_args.input_solution_mod2 = state.input_solution_mod2 + } + new_args + }, + + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, state, comp -> + state + [ + method_id: comp.config.functionality.name, + method_output_mod1: output.output_mod1, + method_output_mod2: output.output_mod2 + ] + } + ) + + // run all metrics + | runEach( + components: metrics, + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: [ + input_mod1: "method_output_mod1", + input_mod2: "method_output_mod2", + input_solution_mod1: "input_solution_mod1", + input_solution_mod2: "input_solution_mod2" + ], + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, state, comp -> + state + [ + metric_id: comp.config.functionality.name, + metric_output: output.output + ] + } + ) + + // join all events into a new event where the new id is simply "output" and the new state consists of: + // - "input": a list of score h5ads + // - "output": the output argument of this workflow + | joinStates{ ids, states -> + def new_id = "output" + def new_state = [ + input: states.collect{it.metric_output}, + _meta: states[0]._meta + ] + [new_id, new_state] + } + + // convert to tsv and publish + | extract_scores.run( + fromState: ["input"], + toState: ["output"] + ) + + | setState(["output", "_meta"]) + + emit: + output_ch + +} From 63bc2719dbe7d4ea5020451d14b00d4fb2d9337c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:28:08 +0200 Subject: [PATCH 1035/1233] finalise process_datasets Former-commit-id: 4bc9079feb473a2c311429a578825d1ee2502c9d --- src/common/check_dataset_schema/script.py | 4 +- .../resource_test_scripts/bmmc_x_starter.sh | 44 +++++---- .../resources_test_scripts/bmmc_x_starter.sh | 90 ++++--------------- .../workflows/process_datasets/main.nf | 31 +++---- .../workflows/process_datasets/run_test.sh | 6 +- 5 files changed, 60 insertions(+), 115 deletions(-) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index ef3412a6b5..67b1c3400b 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -68,13 +68,15 @@ def is_dict_of_atomics(obj): def_slots = data_struct['info']['slots'] + missing= [] for slot in def_slots: missing_x = False if slot == "X": if adata.X is None: missing_x = True continue - missing = check_structure(def_slots[slot], getattr(adata, slot)) + if "required" in def_slots[slot] and def_slots[slot]["required"]: + missing = check_structure(def_slots[slot], getattr(adata, slot)) if missing_x: missing.append("X") if missing: diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh index 5a4018e7af..4ed8b40aae 100755 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -1,21 +1,33 @@ #!/bin/bash -NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" -DATASET_DIR="resources_test/common" +# NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" +# DATASET_DIR="resources_test/common" -SUBDIR="$DATASET_DIR/bmmc_cite_starter" -mkdir -p "$SUBDIR" -wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ - -O "$SUBDIR/dataset_rna.h5ad" -wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ - -O "$SUBDIR/dataset_adt.h5ad" +# SUBDIR="$DATASET_DIR/bmmc_cite_starter" +# mkdir -p "$SUBDIR" +# wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ +# -O "$SUBDIR/dataset_rna.h5ad" +# wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ +# -O "$SUBDIR/dataset_adt.h5ad" -SUBDIR="$DATASET_DIR/bmmc_multiome_starter" -mkdir -p "$SUBDIR" -wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ - -O "$SUBDIR/dataset_rna.h5ad" -wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ - -O "$SUBDIR/dataset_atac.h5ad" +cat > "$SUBDIR/state.yaml" << HERE +id: bmmc_cite_starter +output_dataset_rna: !file dataset_rna.h5ad +output_dataset_other_mod: !file dataset_adt.h5ad +HERE -# run task process dataset components -src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file +# SUBDIR="$DATASET_DIR/bmmc_multiome_starter" +# mkdir -p "$SUBDIR" +# wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ +# -O "$SUBDIR/dataset_rna.h5ad" +# wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ +# -O "$SUBDIR/dataset_atac.h5ad" + +cat > "$SUBDIR/state.yaml" << HERE +id: bmmc_multiome_starter +output_dataset_rna: !file dataset_rna.h5ad +output_dataset_other_mod: !file dataset_atac.h5ad +HERE + +# # run task process dataset components +# src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh index d42b38ec56..6278cc0988 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -1,7 +1,7 @@ #!/bin/bash -# -#make sure the following command has been executed -#viash ns build -q 'predict_modality|common' --parallel --setup cb + +# Run this prior to executing this script: +# bin/viash_build -q 'batch_integration' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -11,29 +11,21 @@ cd "$REPO_ROOT" set -e -generate_pm_test_resources () { - DATASET_ID="$1" - MOD_1_DATA="$2" - MOD_2_DATA="$3" - DATASET_DIR="$4" - FLAGS="$5" - - if [ ! -f $MOD_1_DATA ]; then - echo "Error! Could not find raw data" - exit 1 - fi - - mkdir -p $DATASET_DIR +DATASETS_DIR="resources_test/common" +OUTPUT_DIR="resources_test/predict_modality" +export NXF_VER=22.04.5 - # process_dataset - viash run src/tasks/predict_modality/process_dataset/config.vsh.yaml -- \ - --input_rna $MOD_1_DATA \ - --input_other_mod $MOD_2_DATA \ - --output_train_mod1 $DATASET_DIR/train_mod1.h5ad \ - --output_train_mod2 $DATASET_DIR/train_mod2.h5ad \ - --output_test_mod1 $DATASET_DIR/test_mod1.h5ad \ - --output_test_mod2 $DATASET_DIR/test_mod2.h5ad $FLAGS +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ + --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' # run one method viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ @@ -41,53 +33,3 @@ generate_pm_test_resources () { --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ --output $DATASET_DIR/prediction.h5ad - - # run one metric - viash run src/tasks/predict_modality/metrics/mse/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/prediction.h5ad \ - --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ - --output $DATASET_DIR/score.h5ad - - # # run benchmark on test data - # export NXF_VER=22.04.5 - - # nextflow run . \ - # -main-script src/tasks/predict_modality/workflows/run/main.nf \ - # -profile docker \ - # -c src/wf_utils/labels_ci.config \ - # --id "$DATASET_ID" \ - # --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ - # --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ - # --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ - # --input_test_mod2 $DATASET_DIR/test_mod2.h5ad \ - # --output scores.tsv \ - # --publish_dir $DATASET_DIR/ -} - -generate_pm_test_resources \ - bmmc_cite_starter \ - resources_test/common/bmmc_cite_starter/dataset_rna.h5ad \ - resources_test/common/bmmc_cite_starter/dataset_adt.h5ad \ - resources_test/predict_modality/bmmc_cite_starter \ - "" - -generate_pm_test_resources \ - bmmc_cite_starter_swapped \ - resources_test/common/bmmc_cite_starter/dataset_adt.h5ad \ - resources_test/common/bmmc_cite_starter/dataset_rna.h5ad \ - resources_test/predict_modality/bmmc_cite_starter_swapped \ - "--swap true" - -generate_pm_test_resources \ - bmmc_multiome_starter \ - resources_test/common/bmmc_multiome_starter/dataset_rna.h5ad \ - resources_test/common/bmmc_multiome_starter/dataset_atac.h5ad \ - resources_test/predict_modality/bmmc_multiome_starter \ - "" - -generate_pm_test_resources \ - bmmc_multiome_starter_swapped \ - resources_test/common/bmmc_multiome_starter/dataset_atac.h5ad \ - resources_test/common/bmmc_multiome_starter/dataset_rna.h5ad \ - resources_test/predict_modality/bmmc_multiome_starter_swapped \ - "--swap true" \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 99e6c3feb0..ae2c637070 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -45,15 +45,6 @@ workflow run_wf { ) // remove datasets which didn't pass the schema check - | view { id, state -> - if (state.dataset_rna == null) { - "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" - } else if (state.dataset_other_mod == null) { - "Dataset ${state.input} did not pass the schema check. Checks: ${state.dataset_checks}" - } else { - null - } - } | filter { id, state -> state.dataset_rna != null && state.dataset_other_mod != null @@ -69,22 +60,20 @@ workflow run_wf { output_test_mod2: "output_test_mod2" ], toState: [ - train_mod1: "output_train_mod1", - train_mod2: "output_train_mod2", - test_mod1: "output_test_mod1", - test_mod2: "output_test_mod2" + "output_train_mod1", + "output_train_mod2", + "output_test_mod1", + "output_test_mod2" ] ) // only output the files for which an output file was specified - | setState { id, state -> - [ - "output_train_mod1": state.output_train_mod1 ? state.train_mod1 : null, - "output_train_mod2": state.output_train_mod2 ? state.train_mod2 : null, - "output_test_mod1": state.output_test_mod1 ? state.test_mod1 : null, - "output_test_mod2": state.output_test_mod2 ? state.test_mod2 : null - ] - } + | setState ([ + "output_train_mod1", + "output_train_mod2", + "output_test_mod1", + "output_test_mod2" + ]) emit: output_ch diff --git a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh index 825b60ca90..d7d4529e0c 100755 --- a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh +++ b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh @@ -12,7 +12,7 @@ cd "$REPO_ROOT" set -e DATASETS_DIR="resources_test/common" -OUTPUT_DIR="resources_test/predict_modality" +OUTPUT_DIR="output/test" export NXF_VER=22.04.5 @@ -21,8 +21,8 @@ nextflow run . \ -profile docker \ -entry auto \ -c src/wf_utils/labels_ci.config \ - --id run_test \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' \ No newline at end of file From 655414d764c17023a21db6cd1618a4ae53a0e992 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:34:50 +0200 Subject: [PATCH 1036/1233] add resources_scripts Former-commit-id: 6b3869fba248ad08bfb34c4a06c70d5a1f456aca --- .../resources_scripts/process_datasets.sh | 26 ++++++++++++++++ .../resources_scripts/run_benchmark.sh | 31 +++++++++++++++++++ .../workflows/run_benchmark/run_test.sh | 3 +- 3 files changed, 59 insertions(+), 1 deletion(-) create mode 100755 src/tasks/predict_modality/resources_scripts/process_datasets.sh create mode 100755 src/tasks/predict_modality/resources_scripts/run_benchmark.sh diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh new file mode 100755 index 0000000000..4272b8b62f --- /dev/null +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +COMMON_DATASETS="resources/datasets/openproblems_v1_multimodal" +OUTPUT_DIR="resources/predict_modality/datasets/openproblems_v1_multimodal" + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -resume \ + --input_states "$COMMON_DATASETS/**/state.yaml" \ + --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ + --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' +# output_state should be moved to settings once workaround is solved \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..d4049b86d4 --- /dev/null +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/predict_modality" +OUTPUT_DIR="output/predict_modality" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ + --settings '{"output": "scores.tsv"}' \ + --publish_dir "$OUTPUT_DIR"\ + --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index 4745ad180d..ab742e170a 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -25,4 +25,5 @@ nextflow run . \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' \ No newline at end of file From 3ce42d05fd59d13b93efc40a26a66d20cfbb117b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 12 Oct 2023 14:36:06 +0200 Subject: [PATCH 1037/1233] remove temp files Former-commit-id: 5a0d44ddd2ff162229ec3e6403f2b4c045d06677 --- nxf-tmp.0nZVhn | 0 nxf-tmp.5mFiyd | 0 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 nxf-tmp.0nZVhn delete mode 100644 nxf-tmp.5mFiyd diff --git a/nxf-tmp.0nZVhn b/nxf-tmp.0nZVhn deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/nxf-tmp.5mFiyd b/nxf-tmp.5mFiyd deleted file mode 100644 index e69de29bb2..0000000000 From 25b4e939c5cb7aa286c7c0d9a0cf72bc5bbf58b8 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:37:52 +0200 Subject: [PATCH 1038/1233] fix denoising run_benchmark Former-commit-id: 69155f5a279b570a82da299c1af5d75be26ad1d3 --- src/tasks/denoising/workflows/run_benchmark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index c9eb53c511..9cccd3ea6a 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -93,7 +93,7 @@ workflow run_wf { def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0].output + output: states[0]._meta ] [new_id, new_state] } From 6d3c15f90cb73593c8a32818e11b63d1675ceed5 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:42:30 +0200 Subject: [PATCH 1039/1233] uncomment Former-commit-id: 02df606f650e4798ccb41fc2cd6b2d0a963bd2f6 --- .../resource_test_scripts/bmmc_x_starter.sh | 32 +++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh index 4ed8b40aae..38d97831bb 100755 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -1,14 +1,14 @@ #!/bin/bash -# NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" -# DATASET_DIR="resources_test/common" +NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" +DATASET_DIR="resources_test/common" -# SUBDIR="$DATASET_DIR/bmmc_cite_starter" -# mkdir -p "$SUBDIR" -# wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ -# -O "$SUBDIR/dataset_rna.h5ad" -# wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ -# -O "$SUBDIR/dataset_adt.h5ad" +SUBDIR="$DATASET_DIR/bmmc_cite_starter" +mkdir -p "$SUBDIR" +wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ + -O "$SUBDIR/dataset_rna.h5ad" +wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ + -O "$SUBDIR/dataset_adt.h5ad" cat > "$SUBDIR/state.yaml" << HERE id: bmmc_cite_starter @@ -16,12 +16,12 @@ output_dataset_rna: !file dataset_rna.h5ad output_dataset_other_mod: !file dataset_adt.h5ad HERE -# SUBDIR="$DATASET_DIR/bmmc_multiome_starter" -# mkdir -p "$SUBDIR" -# wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ -# -O "$SUBDIR/dataset_rna.h5ad" -# wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ -# -O "$SUBDIR/dataset_atac.h5ad" +SUBDIR="$DATASET_DIR/bmmc_multiome_starter" +mkdir -p "$SUBDIR" +wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ + -O "$SUBDIR/dataset_rna.h5ad" +wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ + -O "$SUBDIR/dataset_atac.h5ad" cat > "$SUBDIR/state.yaml" << HERE id: bmmc_multiome_starter @@ -29,5 +29,5 @@ output_dataset_rna: !file dataset_rna.h5ad output_dataset_other_mod: !file dataset_atac.h5ad HERE -# # run task process dataset components -# src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file +# run task process dataset components +src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file From feb91d2bcf8bc794095a501b026fd51e903373d8 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:42:55 +0200 Subject: [PATCH 1040/1233] Update src/tasks/denoising/workflows/run_benchmark/main.nf Co-authored-by: Robrecht Cannoodt Former-commit-id: f959a75fec34119f4b0142313b3cef95f23b4bc9 --- src/tasks/denoising/workflows/run_benchmark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 9cccd3ea6a..97a74f76e5 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -93,7 +93,7 @@ workflow run_wf { def new_id = "output" def new_state = [ input: states.collect{it.metric_output}, - output: states[0]._meta + _meta: states[0]._meta ] [new_id, new_state] } From ba5bfb727783b0f1c5d3ce5e01eb3a1184e831b1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 14:43:14 +0200 Subject: [PATCH 1041/1233] Update src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh Co-authored-by: Robrecht Cannoodt Former-commit-id: 70b8ea317f25296c7bc527d7d5fbfd53812698a4 --- .../predict_modality/resources_test_scripts/bmmc_x_starter.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh index 6278cc0988..595045115e 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -1,8 +1,5 @@ #!/bin/bash -# Run this prior to executing this script: -# bin/viash_build -q 'batch_integration' - # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) From 5e394894d7fd2baa5fb6d457dffae228874fcabc Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 15:03:23 +0200 Subject: [PATCH 1042/1233] update test Former-commit-id: a63f3d750f85ebb474b92f19546ba13eebaaae60 --- src/common/check_dataset_schema/test.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 2e4b083341..9efb91e41b 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -23,10 +23,12 @@ def schema(tmp_path): - type: integer name: counts description: Raw counts + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true """) return schema @@ -48,13 +50,16 @@ def error_schema(tmp_path): - type: integer name: counts description: Raw counts + required: true uns: - type: string name: dataset_id description: "A unique identifier for the dataset" + required: true - type: string name: error_test description: "A made up uns variable to test if error is picked up" + required: true """) return schema From 84809af702dd8cc244f71f3e12275940167295de Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 15:16:27 +0200 Subject: [PATCH 1043/1233] add `.config` Former-commit-id: c735af5544b7c98564e01ddf75464994180629d1 --- .../workflows/run_benchmark/main.nf | 23 +++++++++++-------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index efada6be5c..d53b2881e0 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -67,21 +67,26 @@ workflow run_wf { // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> - id + "." + comp.functionality.name + id + "." + comp.config.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState: [ - input_train_mod1: "input_train_mod1", - input_train_mod2: "input_train_mod2", - input_test_mod1: "input_test_mod1", - input_test_mod2: "input_test_mod2" - ], + fromState:fromState: { id, state, comp -> + def new_args = [ + input_train_mod1: state.input_train_mod1, + input_train_mod2: state.input_train_mod2, + input_test_mod1: state.input_test_mod1 + ] + if (comp.config.functionality.info.type == "control_method") { + new_args.input_test_mod2 = state.input_test_mod2 + } + new_args + }, // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp -> state + [ - method_id: comp.functionality.name, + method_id: comp.config.functionality.name, method_output: output.output ] } @@ -98,7 +103,7 @@ workflow run_wf { // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp -> state + [ - metric_id: comp.functionality.name, + metric_id: comp.config.functionality.name, metric_output: output.output ] } From dab5185fe50ca96b42ce6778345dce2c616aafb2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 15:38:03 +0200 Subject: [PATCH 1044/1233] fix check_dataset_schema Former-commit-id: 60a7f7da514028dcb07b2c10fe45d9b6979e3c11 --- src/common/check_dataset_schema/script.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 67b1c3400b..3925504652 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -17,7 +17,7 @@ def check_structure(slot_info, adata_slot): missing = [] for obj in slot_info: - if obj['name'] not in adata_slot: + if 'required' in obj and obj['required'] and obj['name'] not in adata_slot: missing.append(obj['name']) return missing @@ -75,8 +75,7 @@ def is_dict_of_atomics(obj): if adata.X is None: missing_x = True continue - if "required" in def_slots[slot] and def_slots[slot]["required"]: - missing = check_structure(def_slots[slot], getattr(adata, slot)) + missing = check_structure(def_slots[slot], getattr(adata, slot)) if missing_x: missing.append("X") if missing: From ae32396a8ce025a5a937b8a4a2ceda44bbfd23e0 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 15:59:05 +0200 Subject: [PATCH 1045/1233] fix nextflow test errors (#261) * fix denoising * fix match modality metrics input Former-commit-id: 4d7d9f6e8adfbc47655b10b09a8bce4257c2e633 --- src/tasks/denoising/workflows/run_benchmark/main.nf | 6 +++--- src/tasks/match_modalities/workflows/run_benchmark/main.nf | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 97a74f76e5..fd03e0c8df 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -50,7 +50,7 @@ workflow run_wf { // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> - id + "." + comp.functionality.name + id + "." + comp.config.functionality.name }, // use 'fromState' to fetch the arguments the component requires from the overall state @@ -63,7 +63,7 @@ workflow run_wf { // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp -> state + [ - method_id: comp.functionality.name, + method_id: comp.config.functionality.name, method_output: output.output ] } @@ -80,7 +80,7 @@ workflow run_wf { // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp -> state + [ - metric_id: comp.functionality.name, + metric_id: comp.config.functionality.name, metric_output: output.output ] } diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index db135b3a01..65dfcb8cdb 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -91,8 +91,8 @@ workflow run_wf { components: metrics, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ - input_mod1: "method_output_mod1", - input_mod2: "method_output_mod2", + input_integrated_mod1: "method_output_mod1", + input_integrated_mod2: "method_output_mod2", input_solution_mod1: "input_solution_mod1", input_solution_mod2: "input_solution_mod2" ], From 2c655195a01231ed7eea23e8c854fac8e7c578d7 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 16:39:53 +0200 Subject: [PATCH 1046/1233] fix predict_modal Former-commit-id: 21e74d20a4141527bb0b4702b63bf43bc3cd484a --- src/tasks/predict_modality/workflows/run_benchmark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index d53b2881e0..d77d2a26fe 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -71,7 +71,7 @@ workflow run_wf { }, // use 'fromState' to fetch the arguments the component requires from the overall state - fromState:fromState: { id, state, comp -> + fromState: { id, state, comp -> def new_args = [ input_train_mod1: state.input_train_mod1, input_train_mod2: state.input_train_mod2, From e800f6492c4895383a3262d4602443133c904c14 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 12 Oct 2023 17:01:34 +0200 Subject: [PATCH 1047/1233] fix final bugs Former-commit-id: 6c36ac29de72f8309cd0482c7c786b2b857a247e --- src/common/check_dataset_schema/script.py | 2 +- .../workflows/run_benchmark/main.nf | 23 +++++++------------ .../workflows/run_benchmark/run_test.sh | 1 + 3 files changed, 10 insertions(+), 16 deletions(-) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 3925504652..8ecdeeb7b4 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -17,7 +17,7 @@ def check_structure(slot_info, adata_slot): missing = [] for obj in slot_info: - if 'required' in obj and obj['required'] and obj['name'] not in adata_slot: + if obj.get('required') and obj['name'] not in adata_slot: missing.append(obj['name']) return missing diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index d77d2a26fe..3b391d016b 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -45,25 +45,18 @@ workflow run_wf { } ) - | check_dataset_schema.run( - fromState: [ "input": "input_train_mod2" ], - toState: { id, output, state -> - state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - } - ) - // run all methods | runEach( components: methods, - // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, comp -> - def norm = state.normalization_id - def pref = comp.config.functionality.info.preferred_normalization - // if the preferred normalisation is none at all, - // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref - }, + // // use the 'filter' argument to only run a method on the normalisation the component is asking for + // filter: { id, state, comp -> + // def norm = state.normalization_id + // def pref = comp.config.functionality.info.preferred_normalization + // // if the preferred normalisation is none at all, + // // we can pass whichever dataset we want + // (norm == "log_cp10k" && pref == "counts") || norm == pref + // }, // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index ab742e170a..7f96e00d0a 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -22,6 +22,7 @@ nextflow run . \ -profile docker \ -resume \ -entry auto \ + -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ --settings '{"output": "scores.tsv"}' \ From 81fc11022e72d7d03284db0575fdff8f2868f3eb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 12 Oct 2023 17:59:40 +0200 Subject: [PATCH 1048/1233] fix dr test resource script (#264) Former-commit-id: f74841e104979cc7431d70f267b09f9c1539636e --- .../resources_test_scripts/pancreas.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh index dc5bbd5b79..03ec1659b6 100755 --- a/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh +++ b/src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh @@ -31,14 +31,14 @@ nextflow run . \ # run one method viash run src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml -- \ - --input $DATASET_DIR/dataset.h5ad \ - --output $DATASET_DIR/embedding.h5ad + --input $DATASET_DIR/pancreas/dataset.h5ad \ + --output $DATASET_DIR/pancreas/embedding.h5ad # run one metric viash run src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml -- \ - --input_embedding $DATASET_DIR/embedding.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output $DATASET_DIR/score.h5ad + --input_embedding $DATASET_DIR/pancreas/embedding.h5ad \ + --input_solution $DATASET_DIR/pancreas/solution.h5ad \ + --output $DATASET_DIR/pancreas/score.h5ad # # run benchmark # export NXF_VER=22.04.5 From 33191d9b30c4e2563ed2758e70d9fc8fcfeb0d02 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 12 Oct 2023 20:25:30 +0200 Subject: [PATCH 1049/1233] bump base images to base_*:1.0.2 (#263) Former-commit-id: 2077e79e1793e34d2975d1bbbd90de2ee83834c1 --- src/common/check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 4 ++-- src/common/create_task_readme/config.vsh.yaml | 2 +- src/common/extract_scores/config.vsh.yaml | 2 +- src/common/get_api_info/config.vsh.yaml | 2 +- src/common/get_method_info/config.vsh.yaml | 2 +- src/common/get_metric_info/config.vsh.yaml | 2 +- src/common/get_results/config.vsh.yaml | 2 +- src/common/get_task_info/config.vsh.yaml | 2 +- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 2 +- .../loaders/openproblems_v1_multimodal/config.vsh.yaml | 2 +- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 2 +- src/datasets/normalization/log_cp/config.vsh.yaml | 2 +- src/datasets/normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/datasets/normalization/sqrt_cp/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- src/datasets/processors/subsample/config.vsh.yaml | 2 +- src/datasets/processors/svd/config.vsh.yaml | 2 +- src/migration/check_migration_status/config.vsh.yaml | 2 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../control_methods/no_integration_batch/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell/config.vsh.yaml | 2 +- .../control_methods/random_embed_cell_jitter/config.vsh.yaml | 2 +- .../control_methods/random_integration/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/liger/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/pyliger/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../methods/scanorama_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scanvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 2 +- .../metrics/clustering_overlap/config.vsh.yaml | 2 +- .../metrics/graph_connectivity/config.vsh.yaml | 2 +- .../batch_integration/metrics/hvg_overlap/config.vsh.yaml | 2 +- .../metrics/isolated_label_asw/config.vsh.yaml | 2 +- .../metrics/isolated_label_f1/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/kbet/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/lisi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/pcr/config.vsh.yaml | 2 +- src/tasks/batch_integration/process_dataset/config.vsh.yaml | 2 +- .../transformers/embed_to_graph/config.vsh.yaml | 2 +- .../transformers/feature_to_embed/config.vsh.yaml | 2 +- src/tasks/denoising/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/spectral_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/densmap/config.vsh.yaml | 2 +- .../methods/diffusion_map/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/ivis/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/neuralee/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/pca/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/phate/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/tsne/config.vsh.yaml | 2 +- .../dimensionality_reduction/methods/umap/config.vsh.yaml | 2 +- .../metrics/coranking/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 2 +- .../metrics/distance_correlation/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- .../dimensionality_reduction/process_dataset/config.vsh.yaml | 2 +- .../control_methods/majority_vote/config.vsh.yaml | 2 +- .../control_methods/random_labels/config.vsh.yaml | 2 +- .../control_methods/true_labels/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/knn/config.vsh.yaml | 2 +- .../methods/logistic_regression/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/mlp/config.vsh.yaml | 2 +- .../label_projection/methods/scanvi_scarches/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 2 +- src/tasks/label_projection/methods/xgboost/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/f1/config.vsh.yaml | 2 +- src/tasks/label_projection/process_dataset/config.vsh.yaml | 2 +- .../control_methods/random_features/config.vsh.yaml | 2 +- .../control_methods/true_features/config.vsh.yaml | 2 +- .../methods/harmonic_alignment/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/procrustes/config.vsh.yaml | 2 +- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml | 2 +- src/tasks/match_modalities/metrics/mse/config.vsh.yaml | 2 +- src/tasks/predict_modality/process_dataset/config.vsh.yaml | 2 +- 87 files changed, 88 insertions(+), 88 deletions(-) diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index b86c36efa9..d72ca46949 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 test_setup: - type: python packages: viashpy diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml index 7c78fd9d94..44922bdf50 100644 --- a/src/common/check_yaml_schema/config.vsh.yaml +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 76d95679f9..aa2b9ef201 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -141,11 +141,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base_python:1.0.1" + image_str = "ghcr.io/openproblems-bio/base_python:1.0.2" setup_type = "python" package_example = "scib==1.1.3" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base_r:1.0.1" + image_str = "ghcr.io/openproblems-bio/base_r:1.0.2" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index d7ca9914da..b869dbf5eb 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 057c152583..40cabb5d39 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 03a8958d7b..7314795ab8 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index 3c901f57cf..fb858e3e85 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index 13ab319a02..ffe1f03ea9 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 3bc4f93974..1a6bd543ed 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ tidyverse ] diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/get_task_info/config.vsh.yaml index 924fceadfc..2822fa9443 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/get_task_info/config.vsh.yaml @@ -8,6 +8,6 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow - type: native diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 6e4fa0e20d..0e8e75c428 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: apt packages: git diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index dc2db19f50..65cf2808a2 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: apt packages: git diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 1be6c0a5d0..81e8ac9bdb 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index ea476d9a2b..858677d284 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index cd23327af4..6ac7bcc811 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ Matrix, rlang, bit64, scran, BiocParallel ] diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index b350031697..be80374d67 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 376009359c..f0f5e87efe 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,5 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 8626769323..ecc3bd6a82 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,5 +7,5 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 1d6cd05a51..5af00240cf 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,5 +11,5 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 9a80d32143..c0a7673eeb 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 test_setup: - type: python packages: diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index 550d540e1d..5e97eab73f 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: [scikit-learn] diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index f41f58a353..56e2c4b1b0 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 4c626ca6cc..1dbbb90ae4 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 8214a5925c..013704966a 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index b29d9ea2b1..1f18bb0bee 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index 37e69892a3..bf525fad0f 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index 7f6060e9ff..d0ab554ec3 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index 9bd2cd7450..a190913dba 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.0 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 7c5a443999..52217665c3 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index c3b39a7c28..bd857f4e4a 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index 60494ca364..f262c931d5 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: rliger diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index e1346e1117..8255a85a97 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 5b1d53862d..7bd2d56107 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 8d14bcf41a..2cec87c577 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 8e33c9b30e..7eaf674b26 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index c233d44ff9..89af44209e 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -21,7 +21,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index a28cf98f70..14b47fc7b4 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 341a9e58db..f4d037f296 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 2f3545481a..78bae7b655 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 182a6312b1..a9643660e6 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -49,7 +49,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index 62582c327b..cacda59b01 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index 33304872b4..a458636f27 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index 2ccd2fd4c7..5e81c2e303 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index 89d831ca30..ad452e452f 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index d08b79dfed..4a46752754 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r github: theislab/kBET diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index 7ab0048384..66531afcbd 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -43,7 +43,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 10715a43e0..53c7307756 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index c463d416a6..5b8b7447a5 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 77a2d076f6..694cd6e2b0 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: scanpy diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 85e5be5dff..0cf8b5f002 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: scanpy diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 747733efe3..057663cb29 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 8f7a7aed35..bf2f1d61c4 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index 6aaad03d4d..295b30c8f6 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: /src/tasks/dimensionality_reduction/methods/diffusion_map/script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 82244872c0..5b534b356a 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 8890a89795..d168caaada 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index c1a22ef996..35ad00d903 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index c4681c86d5..d369c90298 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index 02f7e88b56..c665d23a12 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -44,7 +44,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 3b4dd6d400..ea6565a461 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -31,7 +31,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scanpy diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 6d4b7943ac..8b060e796c 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 75159f80ec..3502f49d01 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: apt packages: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 143af87aaa..6b26daae75 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,7 +39,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 0f81b422c5..eb23ba8ece 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -157,7 +157,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ coRanking, bit64 ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index f3e1b6aacc..168531b210 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index a69c14283c..7867071dd1 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 88b707e9a8..79c3f5dde8 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 55fb1e71e3..d320b8eb8f 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 48a2ba8f3c..5cc589db65 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 027781c078..8e75645036 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scanpy diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index 13df85ac08..c43152d7c1 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index aa8e25533a..782757f2e8 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: [scikit-learn, jsonschema] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 3b908ae7b2..449a0757c9 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 2c490e80c0..580d663cf8 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -38,7 +38,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 0dbfce04ad..039f256e47 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 # Add custom dependencies here setup: - type: python diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 928c85a5e4..8c81554e21 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ Matrix>=1.5.3, Seurat, rlang, bit64 ] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index 11d99ed5d3..4d3271b571 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: xgboost diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 11674fde5c..896175c452 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index ec6eece949..9c8c91c86a 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index eb5a564cdb..5f9b8f363b 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,5 +25,5 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml index 921d746133..440184da0a 100644 --- a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml index 8a0d1872b7..3c5f47eee8 100644 --- a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml index ef34705c68..f45eacd319 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python github: diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index e21b3febe5..69f3fcda29 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python pypi: diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index 82ec6690fb..e6dddc9ccb 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: apt packages: git diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index 61b0013a01..16a66a4853 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index cd3f22bf0d..06fff957c8 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.1 + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python packages: diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index 8ec27a6c46..ece7137647 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.1 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r cran: [ bit64 ] From 191a6650399ec6fc8289216014a4e96f6443014c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 13 Oct 2023 16:27:02 +0200 Subject: [PATCH 1050/1233] add labels Former-commit-id: a0025fd35ad14910a40a7d06e864dd176a8de24e --- .github/ISSUE_TEMPLATE/bug_report.md | 2 +- .github/ISSUE_TEMPLATE/feature_request.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 74514987e3..9a8a64b4d2 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -2,7 +2,7 @@ name: Bug report about: Create a report to help us improve title: '' -labels: '' +labels: [bug] assignees: '' --- diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index bbcbbe7d61..c17d3c0dfb 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -2,7 +2,7 @@ name: Feature request about: Suggest an idea for this project title: '' -labels: '' +labels: [enhancement] assignees: '' --- From e159fc4f804190a1b588c6bbbd826e9f8aba0e3f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 13 Oct 2023 21:44:16 +0200 Subject: [PATCH 1051/1233] fix bugs from nf_tower full benchmark run (#265) * add filter to run_benchmark * add labels to lab_proj metrics * add labels check in test * add temp fix for #266 * Update src/tasks/denoising/workflows/run_benchmark/main.nf Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 929b141b52bebee33e0834915c624e910d08073d --- src/common/comp_tests/check_method_config.py | 17 ++++++++++++++++ src/common/comp_tests/check_metric_config.py | 20 ++++++++++++++++++- .../denoising/workflows/run_benchmark/main.nf | 9 +++++++++ .../methods/densmap/config.vsh.yaml | 1 + .../methods/umap/config.vsh.yaml | 1 + .../metrics/accuracy/config.vsh.yaml | 2 ++ .../metrics/f1/config.vsh.yaml | 2 ++ 7 files changed, 51 insertions(+), 1 deletion(-) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 61a2bf0f6f..a2c2dde274 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -15,6 +15,10 @@ _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] +TIME_LABELS = ["lowtime", "midtime", "longtime"] +MEM_LABELS = ["lowmem", "midmem", "highmem"] +CPU_LABELS = ["lowcpu", "midcpu", "highcpu"] + def _load_bib(): with open(f"{meta['resources_dir']}/library.bib", "r") as file: return file.read() @@ -101,6 +105,19 @@ def search_ref_bib(reference): norm_methods = ["log_cpm", "log_cp10k", "counts", "log_scran_pooling", "sqrt_cpm", "sqrt_cp10k", "l1_sqrt"] assert info["preferred_normalization"] in norm_methods, "info['preferred_normalization'] not one of '" + "', '".join(norm_methods) + "'." +print("Check platform fields", flush=True) +platforms = config['platforms'] +for platform in platforms: + if not platform["type"] == "nextflow": + continue + nextflow= platform + +assert nextflow, "nextflow not a platform" +assert nextflow["directives"], "directives not a field in nextflow platform" +assert nextflow["directives"]["label"], "label not a field in nextflow platform directives" +assert [i for i in nextflow["directives"]["label"] if i in TIME_LABELS], "time label not filled in" +assert [i for i in nextflow["directives"]["label"] if i in MEM_LABELS], "mem label not filled in" +assert [i for i in nextflow["directives"]["label"] if i in CPU_LABELS], "cpu label not filled in" print("All checks succeeded!", flush=True) diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index e8ff523dda..487d89e8fd 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -17,6 +17,10 @@ _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] +TIME_LABELS = ["lowtime", "midtime", "longtime"] +MEM_LABELS = ["lowmem", "midmem", "highmem"] +CPU_LABELS = ["lowcpu", "midcpu", "highcpu"] + def _load_bib(): bib_path = meta["resources_dir"]+"/library.bib" @@ -102,11 +106,25 @@ def check_metric(metric: Dict[str, str]) -> str: print("Check info fields", flush=True) info = config['functionality']['info'] -print(info) assert "type" in info, "type not an info field" assert info["type"] == "metric" , f"got {info['type']} expected 'metric'" assert "metrics" in info, "metrics not an info field" for metric in info["metrics"]: check_metric(metric) +print("Check platform fields", flush=True) +platforms = config['platforms'] +for platform in platforms: + if not platform["type"] == "nextflow": + continue + nextflow= platform + +assert nextflow, "nextflow not a platform" +assert nextflow["directives"], "directives not a field in nextflow platform" +assert nextflow["directives"]["label"], "label not a field in nextflow platform directives" + +assert [i for i in nextflow["directives"]["label"] if i in TIME_LABELS], "time label not filled in" +assert [i for i in nextflow["directives"]["label"] if i in MEM_LABELS], "mem label not filled in" +assert [i for i in nextflow["directives"]["label"] if i in CPU_LABELS], "cpu label not filled in" + print("All checks succeeded!", flush=True) diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index fd03e0c8df..37c46de440 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -48,6 +48,15 @@ workflow run_wf { | runEach( components: methods, + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, comp -> + def norm = state.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cp10k" && pref == "counts") || norm == pref + }, + // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> id + "." + comp.config.functionality.name diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index d168caaada..ef539de6fb 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -38,6 +38,7 @@ platforms: - type: python packages: - umap-learn + - pynndescent==0.5.8 - type: native - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 6b26daae75..4de3253c9b 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -44,6 +44,7 @@ platforms: - type: python packages: - umap-learn + - pynndescent==0.5.8 - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index 896175c452..b1b4883b8f 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -24,3 +24,5 @@ platforms: - type: python packages: scikit-learn - type: nextflow + directives: + label: [midtime, midmem, midcpu] diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index 9c8c91c86a..980557c8ef 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -46,3 +46,5 @@ platforms: - type: python packages: scikit-learn - type: nextflow + directives: + label: [midtime, midmem, midcpu] From 8aa961c5b8fe06a9c64173e934db4a378ea487e3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 20 Oct 2023 13:41:10 +0200 Subject: [PATCH 1052/1233] Fix/nf tower issues (#275) * fix #271 * fix #272 * fix #273 Former-commit-id: 6c73b94b2d4f4e85e3b4fcf78e761f67814e575f --- .../metrics/cell_cycle_conservation/script.py | 7 +++---- src/tasks/denoising/metrics/mse/config.vsh.yaml | 2 +- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 2 +- .../metrics/distance_correlation/config.vsh.yaml | 2 +- .../metrics/trustworthiness/config.vsh.yaml | 2 +- 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index e295ca6786..3edc77ba88 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -1,5 +1,6 @@ import anndata as ad from scib.metrics import cell_cycle +import numpy as np ## VIASH START par = { @@ -20,15 +21,13 @@ translator = { "homo_sapiens": "human", "mus_musculus": "mouse", - "danio_rerio": "zebrafish", - "caenorhabditis_elegans": "C. elegans" } print('compute score', flush=True) -organism = translator[input_solution.uns['dataset_organism']] -if organism not in ["human", "mouse"]: +if input_solution.uns['dataset_organism'] not in translator: score = np.nan else: + organism = translator[input_solution.uns['dataset_organism']] score = cell_cycle( input_solution, input_integrated, diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index 70e0cc5dae..ff3da70675 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -27,4 +27,4 @@ platforms: - scprep - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index dd96338862..3160cf94ed 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -26,4 +26,4 @@ platforms: pip: scprep - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] \ No newline at end of file + label: [ midtime, highmem, midcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index 7867071dd1..b7ff90bf28 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - scipy - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index 79c3f5dde8..b2c7311706 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -28,4 +28,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [ midtime, highmem, lowcpu ] From b0aa8df5ccc9d6187992095d70b65ef421945065 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 23 Oct 2023 21:23:30 +0200 Subject: [PATCH 1053/1233] switch to viash 0.8.0 Former-commit-id: db4e821066d235e1b39a2071f84de5315ddc7fe1 --- _viash.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_viash.yaml b/_viash.yaml index 925378d60e..b4621a2b92 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,4 +1,4 @@ -viash_version: 0.8.0-RC6 +viash_version: 0.8.0 source: src target: target From 7f478fe7b2a11cb2ff7c0e3fd13d1270c54816c6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 24 Oct 2023 07:39:36 +0200 Subject: [PATCH 1054/1233] Fix create_component (#276) * switch to base_python image * switch to specific tag * add debug statements * pin to specific sha * revert to ruamel.yaml<0.18 for now Former-commit-id: 7a7c58fe73821e2ac90ec6804252bfe2dfa5aa7b --- src/common/create_component/config.vsh.yaml | 2 +- src/common/create_component/script.py | 10 ++++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index 5c829462ad..cc5afe388c 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -64,7 +64,7 @@ platforms: image: python:3.10-slim setup: - type: python - pypi: ruamel.yaml + pypi: ruamel.yaml<0.18 - type: native - type: nextflow diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index aa2b9ef201..175d027382 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -398,11 +398,14 @@ def create_r_script(par, api_spec, type): def main(par): ####### CHECK INPUTS ####### + print("Check inputs", flush=True) assert re.match("[a-z][a-z0-9_]*", par["name"]), "Name should match the regular expression '[a-z][a-z0-9_]*'. Example: 'my_component'." assert len(par['name']) <= 50, "Method name should be at most 50 characters." pretty_name = re.sub("_", " ", par['name']).title() + ####### CHECK LANGUAGE ####### + print("Check language", flush=True) # check language and determine script path if par["language"] == "python": script_path = "script.py" @@ -412,6 +415,7 @@ def main(par): sys.exit(f"Unrecognized language parameter '{par['language']}'.") ## CHECK API FILE + print("Check API file", flush=True) api_file = Path(par["api_file"]) viash_yaml = Path(par["viash_yaml"]) project_dir = viash_yaml.parent @@ -424,6 +428,7 @@ def main(par): | Possible values for --type: {', '.join(comp_types)}.""")) ## READ API FILE + print("Read API file", flush=True) api = read_and_merge_yaml(api_file) comp_type = api.get("functionality", {}).get("info", {}).get("type", {}) if not comp_type: @@ -433,10 +438,12 @@ def main(par): | Please fix the formatting of the API file.""")) ####### CREATE OUTPUT DIR ####### + print("Create output dir", flush=True) out_dir = Path(par["output"]) out_dir.mkdir(exist_ok=True) ####### CREATE CONFIG ####### + print("Create config", flush=True) config_file = out_dir / "config.vsh.yaml" # get config template @@ -446,6 +453,7 @@ def main(par): f.write(config_str) ####### CREATE SCRIPT ####### + print("Create script", flush=True) script_file = out_dir / script_path # set reasonable values @@ -461,6 +469,8 @@ def main(par): with open(script_file, "w") as f: f.write(script_out) + print("Done!", flush=True) + if __name__ == "__main__": main(par) From fae4ad36b404c0c7dd33a7bd39c6a081ffbebfe8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 15 Nov 2023 13:47:18 +0100 Subject: [PATCH 1055/1233] undo batchelor workaround (#226) Former-commit-id: 35c3a656a1fa41fb52474cd0fca43c5fea254962 --- .../methods/fastmnn_feature/config.vsh.yaml | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index d45d828008..186e190647 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -28,14 +28,8 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - # - type: r - # bioc: batchelor - # workaround for DelayedArray issue - - type: apt - packages: git - type: r - script: - - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") + bioc: batchelor - type: nextflow directives: label: [ "midtime", lowcpu, highmem ] From 99659d9dfeb5718fc9ae834dd10844254b741284 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:47:40 +0100 Subject: [PATCH 1056/1233] Bump nf-core/setup-nextflow from 1.3.0 to 1.4.0 (#280) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.3.0 to 1.4.0. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.3.0...v1.4.0) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: d42fd20d578ce556e27bd1d99612e78e241bdab6 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 671633f4d1..59f8fb2d75 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -132,7 +132,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.3.0 + - uses: nf-core/setup-nextflow@v1.4.0 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 36a409fd5e..b9c771838a 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -159,7 +159,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.3.0 + - uses: nf-core/setup-nextflow@v1.4.0 # build target dir # use containers from release branch, hopefully these are available From 72d96b8986333a526063d2a66a6e0dbc36c03dc1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:47:54 +0100 Subject: [PATCH 1057/1233] Bump tj-actions/changed-files from 39 to 40 (#281) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 39 to 40. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v39...v40) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: b7be1d787738731cf68e524c9df23d30ca217131 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 2fca5cd6fe..a2b22dd142 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v39 + uses: tj-actions/changed-files@v40 with: separator: ";" diff_relative: true From 3c40e48b28ba3cbea0e2376210f215518c5165ed Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 15 Nov 2023 13:48:33 +0100 Subject: [PATCH 1058/1233] update ruamel.yaml safe_load (#279) Former-commit-id: 005bd558d9cf905a9b9b40a40cc96b4ad3b6f327 --- src/common/create_component/config.vsh.yaml | 2 +- src/common/create_component/test.py | 5 +++-- src/common/helper_functions/read_and_merge_yaml.py | 7 +++++-- 3 files changed, 9 insertions(+), 5 deletions(-) diff --git a/src/common/create_component/config.vsh.yaml b/src/common/create_component/config.vsh.yaml index cc5afe388c..5c829462ad 100644 --- a/src/common/create_component/config.vsh.yaml +++ b/src/common/create_component/config.vsh.yaml @@ -64,7 +64,7 @@ platforms: image: python:3.10-slim setup: - type: python - pypi: ruamel.yaml<0.18 + pypi: ruamel.yaml - type: native - type: nextflow diff --git a/src/common/create_component/test.py b/src/common/create_component/test.py index 28b493bd46..16da1bd854 100644 --- a/src/common/create_component/test.py +++ b/src/common/create_component/test.py @@ -1,7 +1,7 @@ import os import subprocess from os import path -import ruamel.yaml as yaml +from ruamel.yaml import YAML ## VIASH START meta = { @@ -40,8 +40,9 @@ assert os.path.exists(script_f), "Script file does not exist" print('>> Checking file contents', flush=True) +yaml = YAML(typ='safe', pure=True) with open(conf_f) as f: - conf_data = yaml.safe_load(f) + conf_data = yaml.load(f) assert conf_data['functionality']['name'] == 'test_method', "Name should be equal to 'test_method'" # assert conf_data['platforms'][0]['image'] == 'python:3.10', "Python image should be equal to python:3.10" diff --git a/src/common/helper_functions/read_and_merge_yaml.py b/src/common/helper_functions/read_and_merge_yaml.py index 7c62507fb5..b74995aed1 100644 --- a/src/common/helper_functions/read_and_merge_yaml.py +++ b/src/common/helper_functions/read_and_merge_yaml.py @@ -7,9 +7,12 @@ def read_and_merge_yaml(path): Arguments: path -- Path to the Viash YAML""" - import ruamel.yaml as yaml + from ruamel.yaml import YAML + + yaml = YAML(typ='safe', pure=True) + with open(path, 'r') as stream: - data = yaml.safe_load(stream) + data = yaml.load(stream) return _ram_process_merge(data, path) def _ram_deep_merge(dict1, dict2): From 1794f89de5886a4639164095fbb20b4baba64c1e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 22 Nov 2023 15:44:08 +0100 Subject: [PATCH 1059/1233] Align result format to what is expected from website (#269) * wip attempt at storing metadata as part of the pipeline * extract scores as yaml * fix metadata storage * undo extract scores changes * make sure check_dataset_schema also works with np.ndarray and pd.core.series.Series * fix is_atomic * simplify types * require less resources * remove unnecessary changes * collect data in separate steps * revert andata import * add trace collectin for seqera platform * refactor get_results * update get_method info * update metric * refactor task_info * WIP workflow transform inf yamls * fix common workflow * remove local trace * update transform workflow cmd * remove view * WIP fix test * update res test scripts * fix test resource script * fix common tests * fix typo * disable api_info comp * add labelsto common configs * add nf_tower test * convert nan to none * wip add normalize results * add normalize function * update workflow * fix adding resources * fix errors in get_results output * add method info * reformat nextflow wf * ignore different normalization methods in the dataset meta * add missing uns fields * clean up script * use solution to check dataset uns * fix comment in script * flatten method info results --------- Co-authored-by: Kai Waldrant Former-commit-id: deb7899383ba38bc5f236dd148a454b9a71187ce --- src/common/api/get_info.yaml | 11 +- .../check_dataset_schema/config.vsh.yaml | 2 +- src/common/check_dataset_schema/script.py | 41 ++- src/common/comp_tests/check_get_info.py | 2 +- src/common/get_api_info/config.vsh.yaml | 3 + src/common/get_method_info/config.vsh.yaml | 6 + src/common/get_method_info/script.R | 30 ++- src/common/get_metric_info/config.vsh.yaml | 6 + src/common/get_metric_info/script.R | 9 +- src/common/get_results/config.vsh.yaml | 31 ++- src/common/get_results/script.R | 46 ---- src/common/get_results/script.py | 246 ++++++++++++++++++ src/common/get_task_info/script.py | 22 -- .../resources_test_scripts/task_metadata.sh | 26 +- .../workflows/transform_meta/config.vsh.yaml | 84 ++++++ src/common/workflows/transform_meta/main.nf | 90 +++++++ .../transform_meta/run_nf_tower_test.sh | 38 +++ .../workflows/transform_meta/run_test.sh | 50 ++++ .../config.vsh.yaml | 8 +- src/common/yaml_to_json/script.py | 21 ++ src/datasets/api/file_normalized.yaml | 7 +- .../api/file_common_dataset.yaml | 27 +- .../batch_integration/api/file_solution.yaml | 24 +- .../process_dataset/script.py | 13 +- .../workflows/run_benchmark/config.vsh.yaml | 21 +- .../workflows/run_benchmark/main.nf | 123 ++++++--- .../workflows/run_benchmark/run_test.sh | 6 +- 27 files changed, 832 insertions(+), 161 deletions(-) delete mode 100644 src/common/get_results/script.R create mode 100644 src/common/get_results/script.py delete mode 100644 src/common/get_task_info/script.py create mode 100644 src/common/workflows/transform_meta/config.vsh.yaml create mode 100644 src/common/workflows/transform_meta/main.nf create mode 100644 src/common/workflows/transform_meta/run_nf_tower_test.sh create mode 100644 src/common/workflows/transform_meta/run_test.sh rename src/common/{get_task_info => yaml_to_json}/config.vsh.yaml (55%) create mode 100644 src/common/yaml_to_json/script.py diff --git a/src/common/api/get_info.yaml b/src/common/api/get_info.yaml index c53d82c2c5..faf2351f44 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/api/get_info.yaml @@ -2,9 +2,8 @@ functionality: arguments: - name: "--input" type: "file" - multiple: false - example: ../openproblems-v2 - description: "the root repo" + example: + description: "A yaml file" - name: "--task_id" type: "string" description: "A task dir" @@ -15,9 +14,9 @@ functionality: default: "output.json" description: "Output json" test_resources: + - type: python_script + path: /src/common/comp_tests/check_get_info.py - path: /src dest: openproblems-v2/src - path: /_viash.yaml - dest: openproblems-v2/_viash.yaml - - type: python_script - path: /src/common/comp_tests/check_get_info.py \ No newline at end of file + dest: openproblems-v2/_viash.yaml \ No newline at end of file diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index d72ca46949..2fe62151c4 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -54,4 +54,4 @@ platforms: packages: viashpy - type: nextflow directives: - label: [ "midtime", "highmem", "highcpu"] + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index 8ecdeeb7b4..ef02af85c1 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -2,6 +2,8 @@ import yaml import shutil import json +import numpy as np +import pandas as pd ## VIASH START par = { @@ -32,26 +34,49 @@ def check_structure(slot_info, adata_slot): } def is_atomic(obj): - return isinstance(obj, str) or isinstance(obj, int) or isinstance(obj, bool) + return isinstance(obj, str) or isinstance(obj, int) or isinstance(obj, bool) or isinstance(obj, float) + +def to_atomic(obj): + if isinstance(obj, np.float64): + return float(obj) + elif isinstance(obj, np.int64): + return int(obj) + elif isinstance(obj, np.bool_): + return bool(obj) + elif isinstance(obj, np.str_): + return str(obj) + return obj def is_list_of_atomics(obj): - if not isinstance(obj, list): + if not isinstance(obj, (list,pd.core.series.Series,np.ndarray)): return False return all(is_atomic(elem) for elem in obj) +def to_list_of_atomics(obj): + if isinstance(obj, pd.core.series.Series): + obj = obj.to_numpy() + if isinstance(obj, np.ndarray): + obj = obj.tolist() + return [to_atomic(elem) for elem in obj] + def is_dict_of_atomics(obj): if not isinstance(obj, dict): return False - return all(is_atomic(elem) for key, elem in obj.items()) + return all(is_atomic(elem) for _, elem in obj.items()) +def to_dict_of_atomics(obj): + return {k: to_atomic(v) for k, v in obj.items()} if par['meta'] is not None: print("Extract metadata from object", flush=True) - uns = { - key: val - for key, val in adata.uns.items() - if is_atomic(val) or is_list_of_atomics(val) or is_dict_of_atomics(val) - } + uns = {} + for key, val in adata.uns.items(): + if is_atomic(val): + uns[key] = to_atomic(val) + elif is_list_of_atomics(val): + uns[key] = to_list_of_atomics(val) + elif is_dict_of_atomics(val): + uns[key] = to_dict_of_atomics(val) structure = { struct: list(getattr(adata, struct).keys()) for struct diff --git a/src/common/comp_tests/check_get_info.py b/src/common/comp_tests/check_get_info.py index d62c06355a..a00f1d702d 100644 --- a/src/common/comp_tests/check_get_info.py +++ b/src/common/comp_tests/check_get_info.py @@ -5,7 +5,7 @@ ## VIASH START ## VIASH END -input_path = meta["resources_dir"] + "/openproblems-v2" +input_path = meta["resources_dir"] + "/test_file.yaml" task_id = "denoising" output_path = "output.json" diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/get_api_info/config.vsh.yaml index 7314795ab8..19a062e00b 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/get_api_info/config.vsh.yaml @@ -1,5 +1,6 @@ __merge__: ../api/get_info.yaml functionality: + status: disabled name: "get_api_info" namespace: "common" description: "Extract api info" @@ -13,4 +14,6 @@ platforms: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] - type: native diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/get_method_info/config.vsh.yaml index fb858e3e85..d1fe3e99f6 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/get_method_info/config.vsh.yaml @@ -6,6 +6,10 @@ functionality: resources: - type: r_script path: script.R + test_resources: + - type: file + path: /resources_test/common/task_metadata/method_configs.yaml + dest: test_file.yaml platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 @@ -17,3 +21,5 @@ platforms: - type: docker run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] diff --git a/src/common/get_method_info/script.R b/src/common/get_method_info/script.R index 2cfe58d390..a322050132 100644 --- a/src/common/get_method_info/script.R +++ b/src/common/get_method_info/script.R @@ -4,18 +4,13 @@ library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( - input = ".", + input = "output/temp/method_configs.yaml", task_id = "label_projection", - output = "output/method_info.json" + output = "output/test/method_info.json" ) ## VIASH END -ns_list <- processx::run( - "viash", - c("ns", "list", "-q", "methods", "--src", paste("src/tasks", par$task_id, sep = "/")), - wd = par$input -) -configs <- yaml::yaml.load(ns_list$stdout) +configs <- yaml::yaml.load_file(par$input) out <- map(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) @@ -27,6 +22,8 @@ out <- map(configs, function(config) { info$method_id <- config$functionality$name info$namespace <- config$functionality$namespace info$is_baseline <- grepl("control", info$type) + info$commit_sha <- config$info$git_commit %||% "missing-sha" + info$code_version <- "missing-version" # rename fields to v1 format info$method_name <- info$label @@ -39,6 +36,23 @@ out <- map(configs, function(config) { info$reference <- NULL info$code_url <- info$repository_url info$repository_url <- NULL + info$v1.path <- info$v1$path + info$v1$path <- NULL + info$v1.commit <- info$v1$commit + info$v1$commit <- NULL + info$v1 <- NULL + info$type_info.label <- info$type_info$label + info$type_info$label <- NULL + info$type_info.summary <- info$type_info$summary + info$type_info$summary <- NULL + info$type_info.description <- info$type_info$description + info$type_info$description <- NULL + info$type_info <- NULL + if (length(info$variants) > 0) { + info$variants <- NULL + } + + # todo: show warning when certain data is missing and return null? diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/get_metric_info/config.vsh.yaml index ffe1f03ea9..443c22723a 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/get_metric_info/config.vsh.yaml @@ -6,6 +6,10 @@ functionality: resources: - type: r_script path: script.R + test_resources: + - type: file + path: /resources_test/common/task_metadata/metric_configs.yaml + dest: test_file.yaml platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 @@ -17,3 +21,5 @@ platforms: - type: docker run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 38c8232731..970604fc88 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -4,18 +4,13 @@ library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( - input = ".", + input = "output/temp/metric_configs.yaml", task_id = "batch_integration", output = "output/metric_info.json" ) ## VIASH END -ns_list <- processx::run( - "viash", - c("ns", "list", "-q", "metrics", "--src", paste("src/tasks", par$task_id, sep = "/")), - wd = par$input -) -configs <- yaml::yaml.load(ns_list$stdout) +configs <- yaml::yaml.load_file(par$input) df <- map_df(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index 1a6bd543ed..d9546c766c 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -1,31 +1,40 @@ functionality: - name: "get_execution_info" + name: "get_results" namespace: "common" description: "Extract execution info" arguments: - name: "--input_scores" type: "file" - multiple: true - example: resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.tsv + example: resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.yaml description: "Scores file" - name: "--input_execution" type: "file" - multiple: true - example: resources/label_projection/benchmarks/openproblems_v1/nextflow_log.tsv + example: resources/label_projection/benchmarks/openproblems_v1/trace.txt description: "Nextflow log file" + - name: "--methods_meta" + type: "file" + example: meta_methods.json + description: "File containing methods metadata" + - name: "--metrics_meta" + type: "file" + example: meta_metrics.json + description: "File containing metrics metadata" + - name: "--task_id" + type: "string" + example: "label_projection" + description: "Task id" - name: "--output" type: "file" direction: "output" default: "output.json" description: "Output json" resources: - - type: r_script - path: script.R + - type: python_script + path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 - setup: - - type: r - cran: [ tidyverse ] + image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] - type: native diff --git a/src/common/get_results/script.R b/src/common/get_results/script.R deleted file mode 100644 index 5e8c253834..0000000000 --- a/src/common/get_results/script.R +++ /dev/null @@ -1,46 +0,0 @@ -library(tidyverse) -library(rlang) - -## VIASH START -par <- list( - input_scores = "resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.tsv", - input_execution = "resources/label_projection/benchmarks/openproblems_v1/nextflow_log.tsv", - output = "resources/label_projection/output/results.yaml" -) -## VIASH END - -# read scores -raw_scores <- read_tsv(par$input_scores) %>% - spread(metric_ids, metric_values) - -# read nxf log -id_regex <- "^(.*)\\.([^\\.]*)" -nxf_log <- read_tsv(par$input_execution) %>% - mutate( - id = tag, - dataset_id = gsub("^([^\\.]*)\\.([^\\.]*).*", "\\1/\\2", id), - method_id = gsub(".*\\.", "", id) - ) - -# process execution info -execution_info <- nxf_log %>% - transmute( - method_id, - dataset_id, - status, - realtime = lubridate::duration(toupper(realtime)), - pcpu = as.numeric(gsub("%", "", pcpu)), - vmem_gb = as.numeric(gsub(" GB", "", vmem)), - peak_vmem_gb = as.numeric(gsub(" GB", "", peak_vmem)), - read_bytes_mb = as.numeric(gsub(" MB", "", read_bytes)), - write_bytes_mb = as.numeric(gsub(" MB", "", write_bytes)) - ) - -df <- full_join(raw_scores, execution_info, by = c("method_id", "dataset_id")) - -jsonlite::write_json( - purrr::transpose(df), - par$output, - auto_unbox = TRUE, - pretty = TRUE -) \ No newline at end of file diff --git a/src/common/get_results/script.py b/src/common/get_results/script.py new file mode 100644 index 0000000000..6216ad4f09 --- /dev/null +++ b/src/common/get_results/script.py @@ -0,0 +1,246 @@ +import yaml +import json +from pandas import read_csv +from datetime import timedelta +import re +import numpy as np + +## VIASH START + +par = { + 'input_scores': 'output/v2/batch_integration/output.run_benchmark.output_scores.yaml', + 'input_execution': 'output/v2/batch_integration/trace.txt', + 'methods_meta': 'output/get_info/method_info.json', + 'metrics_meta': 'output/get_info/metric_info.json', + 'task_id': 'batch_integration', + 'output': 'output/temp/results.json' +} + +meta = { +} + +## VIASH END + +def load_meta (meta_file): + ''' + Load the meta information + ''' + with open(meta_file, 'r') as f: + meta = json.load(f) + return meta + +def get_info (id, type,meta_info): + ''' + Get the information of the method or metric + ''' + key = type + "_id" + for info in meta_info: + if info.get(key) == id: + return info + +def fix_values_scaled(metric_result): + for i, value in enumerate(metric_result): + if np.isnan(value): + metric_result[i] = 0.0 + return metric_result + +def fix_nan_scaled(metrics): + for metric in metrics: + if np.isnan(metrics[metric]) or np.isinf(metrics[metric]): + metrics[metric] = 0 + + return metrics + +def fix_nan (metrics): + for metric in metrics: + if np.isnan(metrics[metric]): + metrics[metric] = "NaN" + elif np.isneginf(metrics[metric]): + metrics[metric] = "-Inf" + elif np.isinf(metrics[metric]): + metrics[metric] = "Inf" + + return metrics + +def organise_score (scores): + ''' + combine all the metric values into one dictionary per method, dataset and normalization + ''' + score_temp = {} + for score in scores: + score_id = score["dataset_id"] + "_" + score["method_id"] + "_" + score["normalization_id"] + + if score.get("metric_values") is None: + score["metric_values"] = [None] * len(score["metric_ids"]) + # for i, value in enumerate(score["metric_values"]): + # if np.isnan(value): + # score["metric_values"][i] = None + comb_metric = zip(score["metric_ids"], score["metric_values"]) + score["metric_values"] = dict(comb_metric) + score["task_id"] = par["task_id"] + del score["metric_ids"] + if score_temp.get(score_id) is None: + score_temp[score_id] = score + else: + score_temp[score_id]["metric_values"].update(score["metric_values"]) + + return score_temp + +def normalize_scores (scores, method_info, metric_info): + """ + Normalize the scores + """ + + metric_names=list(set([metric["metric_id"] for metric in metric_info])) + + baseline_methods = [method["method_id"] for method in method_info if method["is_baseline"] ] + metric_not_maximize = [metric["metric_id"] for metric in metric_info if not metric["maximize"]] + per_dataset = {} + for id, score in scores.items(): + if per_dataset.get(score["dataset_id"]) is None: + per_dataset[score["dataset_id"]] = [] + + per_dataset[score["dataset_id"]].append(score) + + for id, dataset_results in per_dataset.items(): + for result in dataset_results: + result["scaled_scores"] = result["metric_values"].copy() + + for metric_name in metric_names: + metric_values = [] + baseline_values = [] + for result in dataset_results: + if metric_name in result["metric_values"]: + metric_values.append(result["metric_values"][metric_name]) + else: + result["metric_values"][metric_name]= float("nan") + metric_values.append(0.0) + if result["method_id"] in baseline_methods: + if metric_name in result["metric_values"]: + baseline_values.append(result["metric_values"][metric_name]) + + baseline_values = fix_values_scaled(baseline_values) + baseline_values = np.array(baseline_values) + baseline_min = np.nanmin(baseline_values) + baseline_range = np.nanmax(baseline_values) - baseline_min + metric_values = np.array(metric_values) + metric_values -= baseline_min + metric_values /= np.where(baseline_range != 0, baseline_range, 1) + + if metric_name in metric_not_maximize: + metric_values = 1 - metric_values + for result, score in zip(dataset_results,metric_values): + result["scaled_scores"][metric_name] = score + + return per_dataset + +def convert_size (df, col): + ''' + Convert the size to MB and to float type + ''' + mask_kb = df[col].str.contains("KB") + mask_mb = df[col].str.contains("MB") + mask_gb = df[col].str.contains("GB") + if mask_kb.any(): + df.loc[mask_kb, col] = df.loc[mask_kb, col].str.replace(" KB", "").astype(float)/1024 + + if mask_mb.any(): + df.loc[mask_mb, col] = df.loc[mask_mb, col].str.replace(" MB", "").astype(float) + + + if mask_gb.any(): + df.loc[mask_gb, col] = df.loc[mask_gb, col].str.replace(" GB", "").astype(float)*1024 + return df + +def convert_duration(duration_str): + ''' + Convert the duration to seconds + ''' + components = duration_str.split(" ") + hours = 0 + minutes = 0 + seconds = 0 + for component in components: + milliseconds = 0 + for component in components: + if "h" in component: + hours = int(component[:-1]) + elif "ms" in component: + milliseconds = float(component[:-2]) + elif "m" in component: + minutes = int(component[:-1]) + elif "s" in component: + seconds = float(component[:-1]) + duration = timedelta(hours=hours, minutes=minutes, seconds=seconds).total_seconds() + return duration + +def join_trace (traces, result): + ''' + Join the Seqera (nextflow) trace with the scores + ''' + trace_dict = {} + for trace in traces: + id = trace["name"] + dataset_id = None + method_id = None + match = re.search(r'\((.*?)\)', id) + id_split = id.split(":") + if len(id_split)>4: + method_id = id_split[4] + if match: + group = match.group(1) + split_group = group.split(".") + if len(split_group)>1: + dataset_id = split_group[0] + if dataset_id is not None and method_id is not None: + dict_id = method_id + "_" + dataset_id + trace_dict[dict_id] = { + "duration_sec": trace["realtime"], + "cpu_pct": trace["%cpu"], + "peak_memory_mb": trace["peak_vmem"], + "disk_read_mb": trace["rchar"], + "disk_write_mb": trace["wchar"] + } + for score in result: + search_id = result[score]["method_id"] + "_" + result[score]["dataset_id"]+ "/" + result[score]["normalization_id"] + if search_id in trace_dict: + result[score]["resources"] = trace_dict[search_id] + return result + +print('Loading inputs', flush=True) +with open(par['input_scores'], 'r') as f: + scores = yaml.safe_load(f) +execution = read_csv(par['input_execution'], sep='\t') +method_info = load_meta(par['methods_meta']) +metric_info = load_meta(par['metrics_meta']) + +print('Organising scores', flush=True) +org_scores = organise_score(scores) + +print('Cleaning execution trace', flush=True) +execution = convert_size(execution, "rchar") +execution = convert_size(execution, "wchar") +execution = convert_size(execution, "peak_vmem") +execution["%cpu"].replace("%", "", regex=True, inplace=True) +execution["realtime"] = execution["realtime"].apply(convert_duration) + +print('Joining traces and scores', flush=True) +traces = execution.to_dict(orient="records") +org_scores = join_trace(traces, org_scores) + +print('Normalizing scores', flush=True) +org_scores = normalize_scores(org_scores, method_info, metric_info) +# fix NaN en inf +for dataset in org_scores.values(): + for scores in dataset: + scores["metric_values"] = fix_nan(scores["metric_values"]) + scores["scaled_scores"] = fix_nan_scaled(scores["scaled_scores"]) + scores["mean_score"] = np.array(list(scores["scaled_scores"].values())).mean() + +print('Writing results', flush=True) +result = [org_scores[id] for id in org_scores] + +result = list(np.concatenate(result).flat) + +with open (par['output'], 'w') as f: + json.dump(result, f, indent=4) \ No newline at end of file diff --git a/src/common/get_task_info/script.py b/src/common/get_task_info/script.py deleted file mode 100644 index f05eaef7bc..0000000000 --- a/src/common/get_task_info/script.py +++ /dev/null @@ -1,22 +0,0 @@ -from os import path -from yaml import load, CSafeLoader -import json - -## VIASH START -par = { - "input" : ".", - "task_id" : "denoising", - "output": "output/task.json", - -} -meta = { "functionality" : "foo" } - -## VIASH END - -task_info_path = path.join(par["input"], "src/tasks", par["task_id"], "api", "task_info.yaml") - -with open(task_info_path, "r") as f: - task_info = load(f, Loader=CSafeLoader ) - -with open(par["output"], "w") as out: - json.dump(task_info, out, indent=2) \ No newline at end of file diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index 3acb53bd50..0560b0ddff 100755 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -9,8 +9,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" +set -e + +DATASETS_DIR="resources_test/batch_integration" OUTPUT_DIR="resources_test/common/task_metadata" + if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" fi @@ -113,8 +117,20 @@ cat < $sha_file ] EOT -# Create a method info json -viash run src/common/get_method_info/config.vsh.yaml -- \ - --input . \ - --task_id "denoising" \ - --output "$OUTPUT_DIR/method_info.json" \ No newline at end of file +# Create all metadata +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -c src/wf_utils/labels_ci.config \ + -entry auto \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" + +# Copy task info +cp src/tasks/batch_integration/api/task_info.yaml "$OUTPUT_DIR/task_info.yaml" \ No newline at end of file diff --git a/src/common/workflows/transform_meta/config.vsh.yaml b/src/common/workflows/transform_meta/config.vsh.yaml new file mode 100644 index 0000000000..1b935050f9 --- /dev/null +++ b/src/common/workflows/transform_meta/config.vsh.yaml @@ -0,0 +1,84 @@ +functionality: + name: transform_meta + namespace: common/workflows + description: >- + This workflow transforms the meta information of the results into a format + that can be used by the website. + argument_groups: + - name: Inputs + arguments: + - name: "--input_scores" + type: file + required: true + direction: input + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--input_method_configs" + type: file + required: true + direction: input + example: method_configs.yaml + - name: "--input_metric_configs" + type: file + required: true + direction: input + example: metric_configs.yaml + - name: "--input_dataset_info" + type: file + required: true + direction: input + example: dataset_info.yaml + - name: "--input_execution" + type: file + required: true + direction: input + example: trace.txt + - name: "--input_task_info" + type: file + required: true + direction: input + example: task_info.yaml + - name: "--task_id" + type: string + required: true + direction: input + example: "batch_integration" + - name: Outputs + arguments: + - name: "--output_scores" + type: file + required: true + direction: output + description: A yaml file containing the scores of each of the methods + example: results.json + - name: "--output_method_info" + type: file + required: true + direction: output + example: method_info.json + - name: "--output_metric_info" + type: file + required: true + direction: output + example: metric_info.json + - name: "--output_dataset_info" + type: file + required: true + direction: output + example: dataset_info.json + - name: "--output_task_info" + type: file + required: true + direction: output + example: task_info.json + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/get_results + - name: common/get_method_info + - name: common/get_metric_info + - name: common/yaml_to_json +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/common/workflows/transform_meta/main.nf b/src/common/workflows/transform_meta/main.nf new file mode 100644 index 0000000000..39d99a0546 --- /dev/null +++ b/src/common/workflows/transform_meta/main.nf @@ -0,0 +1,90 @@ +// workflow auto { +// findStates(params, meta.config) +// | meta.workflow.run( +// auto: [publish: "state"] +// ) +// } + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + | get_method_info.run( + fromState: [ + "input": "input_method_configs", + "task_id" : "task_id", + "output": "output_method_info" + ], + toState: { id, output, state -> + state + [output_method: output.output] + } + ) + + | get_metric_info.run( + fromState: [ + "input": "input_metric_configs", + "task_id" : "task_id", + "output": "output_metric_info" + ], + toState: { id, output, state -> + state + [output_metric: output.output] + } + ) + + | yaml_to_json.run( + key: "dataset_info", + fromState: [ + "input": "input_dataset_info", + "output": "output_dataset_info" + ], + toState: { id, output, state -> + state + [output_dataset: output.output] + } + ) + + | yaml_to_json.run( + key: "task_info", + fromState: [ + "input": "input_task_info", + "output": "output_task_info" + ], + toState: { id, output, state -> + state + [output_task: output.output] + } + ) + + | get_results.run( + fromState: [ + "input_scores": "input_scores", + "input_execution" : "input_execution", + "methods_meta": "output_method", + "metrics_meta": "output_metric", + "task_id" : "task_id", + "output": "output_scores" + ], + toState: { id, output, state -> + state + [output_results: output.output] + } + ) + + | map{ id, state -> + def _meta = [join_id: id] + + def new_state = [ + output_scores: state.output_results, + output_method_info: state.output_method, + output_metric_info: state.output_metric, + output_dataset_info: state.output_dataset, + output_task_info: state.output_task, + _meta: _meta + ] + + ["output", new_state] + } + + emit: + output_ch +} \ No newline at end of file diff --git a/src/common/workflows/transform_meta/run_nf_tower_test.sh b/src/common/workflows/transform_meta/run_nf_tower_test.sh new file mode 100644 index 0000000000..c333630d22 --- /dev/null +++ b/src/common/workflows/transform_meta/run_nf_tower_test.sh @@ -0,0 +1,38 @@ +#!/bin/bash + +DATASETS_DIR="s3://openproblems-nextflow/output/v2/batch_integration" + +# try running on nf tower +cat > /tmp/params.yaml << HERE +id: batch_integration_transform +input_scores: "$DATASETS_DIR/output.run_benchmark.output_scores.yaml" +input_dataset_info: "$DATASETS_DIR/output.run_benchmark.output_dataset_info.yaml" +input_method_configs: "$DATASETS_DIR/output.run_benchmark.output_method_configs.yaml" +input_metric_configs: "$DATASETS_DIR/output.run_benchmark.output_metric_configs.yaml" +input_execution: "$DATASETS_DIR/trace.txt" +input_task_info: "$DATASETS_DIR/output.run_benchmark.task_info.yaml" +task_id: "batch_integration" +output_scores: "results.json" +output_method_info: "method_info.json" +output_metric_info: "metric_info.json" +output_dataset_info: "dataset_info.json" +output_task_info: "task_info.json" +publish_dir: $DATASETS_DIR +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} + + +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision integration_build \ + --pull-latest \ + --main-script target/nextflow/common/workflows/transform_meta/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/common/workflows/transform_meta/run_test.sh b/src/common/workflows/transform_meta/run_test.sh new file mode 100644 index 0000000000..e3f6d4d30a --- /dev/null +++ b/src/common/workflows/transform_meta/run_test.sh @@ -0,0 +1,50 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="output/temp" +OUTPUT_DIR="output/get_info" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 + +nextflow run . \ + -main-script target/nextflow/common/workflows/transform_meta/main.nf \ + -profile docker \ + -resume \ + --id "get_results_test" \ + --input_scores "$DATASETS_DIR/scores.yaml" \ + --input_dataset_info "$DATASETS_DIR/dataset_info.yaml" \ + --input_method_configs "$DATASETS_DIR/method_configs.yaml" \ + --input_metric_configs "$DATASETS_DIR/metric_configs.yaml" \ + --input_execution "$DATASETS_DIR/trace.txt" \ + --input_task_info "$DATASETS_DIR/task_info.yaml" \ + --task_id "batch_integration" \ + --output_scores "results.json"\ + --output_method_info "method_info.json"\ + --output_metric_info "metric_info.json"\ + --output_dataset_info "dataset_info.json"\ + --output_task_info "task_info.json" \ + --publish_dir "$OUTPUT_DIR" + + +# nextflow run . \ +# -main-script target/nextflow/common/workflows/transform_meta/main.nf \ +# -profile docker \ +# -resume \ +# -entry auto \ +# --input_states "$DATASETS_DIR/state.yaml" \ +# --rename_keys 'input_scores:output_scores,input_dataset_info:output_dataset_info, input_method_configs:output_method_configs, input_metric_configs:output_metric_configs, ' \ +# --settings '{"task_id": "batch_integration", "output_scores": "results.json", "output_method_info": "method_info.json", "output_metric_info": "metric_info.json", "output_dataset_info": "dataset_info.json", "output_task_info":"task_info.json"}' \ +# --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/common/get_task_info/config.vsh.yaml b/src/common/yaml_to_json/config.vsh.yaml similarity index 55% rename from src/common/get_task_info/config.vsh.yaml rename to src/common/yaml_to_json/config.vsh.yaml index 2822fa9443..b7bceb2488 100644 --- a/src/common/get_task_info/config.vsh.yaml +++ b/src/common/yaml_to_json/config.vsh.yaml @@ -1,11 +1,15 @@ __merge__: ../api/get_info.yaml functionality: - name: "get_task_info" + name: "yaml_to_json" namespace: "common" - description: "Extract task info" + description: "convert yaml file to json file" resources: - type: python_script path: script.py + test_resources: + - type: file + path: /resources_test/common/task_metadata/dataset_info.yaml + dest: test_file.yaml platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 diff --git a/src/common/yaml_to_json/script.py b/src/common/yaml_to_json/script.py new file mode 100644 index 0000000000..200d933c20 --- /dev/null +++ b/src/common/yaml_to_json/script.py @@ -0,0 +1,21 @@ +from os import path +import yaml +import json + +## VIASH START +par = { + "input" : ".", + "task_id" : "denoising", + "output": "output/task.json", + +} +meta = { "functionality" : "foo" } + +## VIASH END + +with open(par["input"], "r") as f: + yaml_file = yaml.safe_load(f) + + +with open(par["output"], "w") as out: + json.dump(yaml_file, out, indent=2) \ No newline at end of file diff --git a/src/datasets/api/file_normalized.yaml b/src/datasets/api/file_normalized.yaml index d53f5519f2..ea6f14e9fb 100644 --- a/src/datasets/api/file_normalized.yaml +++ b/src/datasets/api/file_normalized.yaml @@ -14,4 +14,9 @@ info: - type: double name: size_factors description: The size factors created by the normalisation method, if any. - required: false \ No newline at end of file + required: false + uns: + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/batch_integration/api/file_common_dataset.yaml b/src/tasks/batch_integration/api/file_common_dataset.yaml index 03c8ce4fb2..8a69bb4e2c 100644 --- a/src/tasks/batch_integration/api/file_common_dataset.yaml +++ b/src/tasks/batch_integration/api/file_common_dataset.yaml @@ -1,3 +1,6 @@ +# This file is based on the spec of the common dataset located at +# `src/datasets/api/file_common_dataset.yaml`. However, some fields +# such as obs.celltype and obs.batch are now required type: file example: "resources_test/common/pancreas/dataset.h5ad" info: @@ -46,14 +49,34 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true - type: string - name: normalization_id - description: "Which normalization was used" + name: data_url + description: Link to the original source of the dataset. + required: false + - name: data_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. required: false + - type: string + name: normalization_id + description: "Which normalization was used" + required: true - type: object name: knn description: Supplementary K nearest neighbors data. diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml index 10999fac2f..ac6fd88a42 100644 --- a/src/tasks/batch_integration/api/file_solution.yaml +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -46,14 +46,34 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true - type: string - name: normalization_id - description: "Which normalization was used" + name: data_url + description: Link to the original source of the dataset. + required: false + - name: data_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. required: false + - type: string + name: normalization_id + description: "Which normalization was used" + required: true - type: object name: knn description: Supplementary K nearest neighbors data. diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index f4ec46ec2c..ffd9f66fd0 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -1,19 +1,21 @@ import sys -import scib import anndata as ad ## VIASH START par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', 'hvgs': 2000, + 'obs_label': 'celltype', + 'obs_batch': 'batch', + 'subset_hvg': False, 'output': 'output.h5ad' } -meta = {} +meta = { + "config": "target/nextflow/batch_integration/process_dataset/.config.vsh.yaml", + "resources_dir": "src/common/helper_functions" +} ## VIASH END -# Remove this after upgrading to Viash 0.7.5 -sys.dont_write_bytecode = True - # import helper functions sys.path.append(meta['resources_dir']) from subset_anndata import read_config_slots_info, subset_anndata @@ -27,6 +29,7 @@ def compute_batched_hvg(adata, n_hvgs): if n_hvgs > adata.n_vars or n_hvgs <= 0: hvg_list = adata.var_names.tolist() else: + import scib hvg_list = scib.pp.hvg_batch( adata, batch_key='batch', diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 2b4089cb99..339c06eb4a 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -14,12 +14,27 @@ functionality: direction: input - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" type: file required: true direction: output - description: A TSV file containing the scores of each of the methods - example: scores.tsv + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true + direction: output + example: dataset_uns.yaml resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 4e9b10ed7e..fa0798f534 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -51,27 +51,23 @@ workflow run_wf { // process input parameter channel dataset_ch = input_ch - // store original id for later use - | map{ id, state -> - [id, state + [_meta: [join_id: id]]] - } - // extract the dataset metadata | check_dataset_schema.run( - fromState: [input: "input_dataset"], + fromState: [input: "input_solution"], toState: { id, output, state -> - state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [dataset_uns: dataset_uns] } ) - // run all methods + // run all methods method_out_ch1 = dataset_ch | runEach( components: methods, // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.normalization_id + def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -101,6 +97,9 @@ workflow run_wf { method_out_ch2 = method_out_ch1 | runEach( components: feature_to_embed, + id: { id, state, comp -> + id + "_f2e" + }, filter: { id, state, comp -> state.method_subtype == "feature"}, fromState: [ input: "method_output" ], toState: { id, output, state, comp -> @@ -116,6 +115,9 @@ workflow run_wf { method_out_ch3 = method_out_ch2 | runEach( components: embed_to_graph, + id: { id, state, comp -> + id + "_e2g" + }, filter: { id, state, comp -> state.method_subtype == "embedding"}, fromState: [ input: "method_output" ], toState: { id, output, state, comp -> @@ -128,9 +130,12 @@ workflow run_wf { | mix(method_out_ch2) // run metrics - output_ch = method_out_ch3 + score_ch = method_out_ch3 | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, filter: { id, state, comp -> state.method_subtype == comp.config.functionality.info.subtype }, @@ -146,25 +151,85 @@ workflow run_wf { } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta - ] - [new_id, new_state] - } - - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] - ) - - | setState(["output", "_meta"]) + // TODO: can we store everything below in a separate helper function? + + // extract the dataset metadata + dataset_meta_ch = dataset_ch + + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" + } + + | joinStates { ids, states -> + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + ["output", [output_dataset_info: dataset_uns_file]] + } + + // extract the scores + metric_uns_ch = score_ch + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + | joinStates { ids, states -> + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + ["output", [output_scores: score_uns_file]] + } + + // store the method and metric configs + comp_config_ch = input_ch + | map{ id, state -> + // store original id for later use + def _meta = [join_id: id] + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + _meta: _meta + ] + ["output", new_state] + } + + // merge all of the output data + // todo: add task info? + // todo: add trace log? + output_ch = comp_config_ch + | mix(metric_uns_ch, dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] + } emit: output_ch diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh index 43690c2475..b407308d29 100755 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh @@ -22,8 +22,10 @@ nextflow run . \ -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ -profile docker \ -resume \ + -c src/wf_utils/labels_ci.config \ -entry auto \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" \ No newline at end of file From 2dd376f5d51cf6ece0aa52c12557e0184f284a5f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Nov 2023 11:40:41 +0100 Subject: [PATCH 1060/1233] fix fallback normalization id (#288) Former-commit-id: 8ce1dea4823dbf9c73066d0268ce8797fdfe505c --- src/datasets/normalization/l1_sqrt/script.py | 2 +- src/datasets/normalization/log_cp/script.py | 2 +- src/datasets/normalization/sqrt_cp/script.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/datasets/normalization/l1_sqrt/script.py b/src/datasets/normalization/l1_sqrt/script.py index 84480bf14c..76c69cf897 100644 --- a/src/datasets/normalization/l1_sqrt/script.py +++ b/src/datasets/normalization/l1_sqrt/script.py @@ -23,7 +23,7 @@ print("Store output in adata", flush=True) adata.layers[par["layer_output"]] = l1_sqrt -adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) +adata.uns["normalization_id"] = par["normalization_id"] or meta['functionality_name'] print("Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/log_cp/script.py b/src/datasets/normalization/log_cp/script.py index 71fc3e3a66..905c91e976 100644 --- a/src/datasets/normalization/log_cp/script.py +++ b/src/datasets/normalization/log_cp/script.py @@ -28,7 +28,7 @@ print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) +adata.uns["normalization_id"] = par["normalization_id"] or meta['functionality_name'] print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/sqrt_cp/script.py b/src/datasets/normalization/sqrt_cp/script.py index 76c645d6e9..84afdaa19d 100644 --- a/src/datasets/normalization/sqrt_cp/script.py +++ b/src/datasets/normalization/sqrt_cp/script.py @@ -29,7 +29,7 @@ print(">> Store output in adata", flush=True) adata.layers[par["layer_output"]] = lognorm adata.obs[par["obs_size_factors"]] = norm["norm_factor"] -adata.uns["normalization_id"] = par.get("normalization_id", meta['functionality_name']) +adata.uns["normalization_id"] = par["normalization_id"] or meta['functionality_name'] print(">> Write data", flush=True) adata.write_h5ad(par['output'], compression="gzip") From 8496374baecab9402123b66e134075165052738a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Nov 2023 11:48:02 +0100 Subject: [PATCH 1061/1233] add retry strategy to check_url (#287) Former-commit-id: db9dae406b88bc42665d32ddf676a965067af611 --- src/common/comp_tests/check_method_config.py | 11 ++++++++++- src/common/comp_tests/check_metric_config.py | 11 ++++++++++- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index a2c2dde274..2389976518 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -25,8 +25,17 @@ def _load_bib(): def check_url(url): import requests + from urllib3.util.retry import Retry + from requests.adapters import HTTPAdapter - get = requests.head(url) + # configure retry strategy + session = requests.Session() + retry = Retry(connect=3, backoff_factor=0.5) + adapter = HTTPAdapter(max_retries=retry) + session.mount('http://', adapter) + session.mount('https://', adapter) + + get = session.head(url) if get.ok or get.status_code == 429: # 429 rejected, too many requests return True diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 487d89e8fd..d6dcd1472e 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -29,8 +29,17 @@ def _load_bib(): def check_url(url): import requests + from urllib3.util.retry import Retry + from requests.adapters import HTTPAdapter - get = requests.head(url) + # configure retry strategy + session = requests.Session() + retry = Retry(connect=3, backoff_factor=0.5) + adapter = HTTPAdapter(max_retries=retry) + session.mount('http://', adapter) + session.mount('https://', adapter) + + get = session.head(url) if get.ok or get.status_code == 429: # 429 rejected, too many requests return True From 2de86f991df20b8149970e70ab187f7d6b714fa5 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Nov 2023 12:58:09 +0100 Subject: [PATCH 1062/1233] remove batchelor workaround (#289) Former-commit-id: 3c9daec0dddf1ea20abb71b5e858baef17fa883b --- .../match_modalities/methods/fastmnn/config.vsh.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml index 01d04d881f..69ee306151 100644 --- a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -17,18 +17,13 @@ functionality: documentation_url: "https://github.com/LTLA/batchelor#readme" resources: - type: r_script - path: ./script.R + path: script.R platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - - type: apt - packages: git - type: r - cran: [Matrix, SingleCellExperiment] - script: - # Install batchelor from Bioconductor devel because the version on r2u is behind - - remotes::install_bioc("3.18/batchelor", upgrade = "always", type = "source") + bioc: batchelor - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] From b6d8e6ab2763d0f50a21d21e7f43a98c7641c1de Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 Nov 2023 14:54:49 +0100 Subject: [PATCH 1063/1233] update dependency (#290) Former-commit-id: b487ec1b5bdfbce731775898f5bd455d5a985699 --- src/tasks/predict_modality/metrics/correlation/config.vsh.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index 71dbea0b90..08b0cb21df 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -59,8 +59,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ proxyC, testthat] - github: dynverse/dynutils + cran: [ proxyC, testthat, dynutils ] - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] From 252d3b59360a16aa982307fc33a8379d2a30f46b Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 28 Nov 2023 12:39:53 +0100 Subject: [PATCH 1064/1233] Add cellxgene census query component (#282) * WIP cellxgene component * update to specific cellxgene version * Add initial cellxgene comp * small update * add source download componnent * update cellcensus query comp * remove cellcensus_source, rename cellxgene to query_cellxgene_census * use formatter * update component * add todo to test * fix test * remove filter function * Ali (#269) * wip attempt at storing metadata as part of the pipeline * extract scores as yaml * fix metadata storage * undo extract scores changes * make sure check_dataset_schema also works with np.ndarray and pd.core.series.Series * fix is_atomic * simplify types * require less resources * remove unnecessary changes * collect data in separate steps * revert andata import * add trace collectin for seqera platform * refactor get_results * update get_method info * update metric * refactor task_info * WIP workflow transform inf yamls * fix common workflow * remove local trace * update transform workflow cmd * remove view * WIP fix test * update res test scripts * fix test resource script * fix common tests * fix typo * disable api_info comp * add labelsto common configs * add nf_tower test * convert nan to none * wip add normalize results * add normalize function * update workflow * fix adding resources * fix errors in get_results output * add method info * reformat nextflow wf * ignore different normalization methods in the dataset meta * add missing uns fields * clean up script * use solution to check dataset uns * fix comment in script * flatten method info results --------- Co-authored-by: Kai Waldrant * change namespace * update component --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 73470cbb48115d4a0bc8ea0392144dc61512647d --- src/common/helper_functions/setup_logger.py | 12 ++ .../query_cellxgene_census/config.vsh.yaml | 88 ++++++++++++++ .../loaders/query_cellxgene_census/script.py | 113 ++++++++++++++++++ .../loaders/query_cellxgene_census/test.py | 38 ++++++ 4 files changed, 251 insertions(+) create mode 100644 src/common/helper_functions/setup_logger.py create mode 100644 src/datasets/loaders/query_cellxgene_census/config.vsh.yaml create mode 100644 src/datasets/loaders/query_cellxgene_census/script.py create mode 100644 src/datasets/loaders/query_cellxgene_census/test.py diff --git a/src/common/helper_functions/setup_logger.py b/src/common/helper_functions/setup_logger.py new file mode 100644 index 0000000000..ae71eb9611 --- /dev/null +++ b/src/common/helper_functions/setup_logger.py @@ -0,0 +1,12 @@ +def setup_logger(): + import logging + from sys import stdout + + logger = logging.getLogger() + logger.setLevel(logging.INFO) + console_handler = logging.StreamHandler(stdout) + logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s") + console_handler.setFormatter(logFormatter) + logger.addHandler(console_handler) + + return logger \ No newline at end of file diff --git a/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml b/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml new file mode 100644 index 0000000000..572b28f2a9 --- /dev/null +++ b/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml @@ -0,0 +1,88 @@ +functionality: + name: query_cellxgene_census + namespace: datasets/loaders + description: | + Query cells from a CellxGene Census or custom TileDBSoma object. + Aside from fetching the cells' RNA counts (`.X`), cell metadata + (`.obs`) and gene metadata (`.var`), this component also fetches + the dataset metadata and joins it into the cell metadata. + argument_groups: + - name: Input database + description: "Open CellxGene Census by version or URI." + arguments: + - name: "--input_uri" + type: string + description: "If specified, a URI containing the Census SOMA objects. If specified, will take precedence over the `--census_version` argument." + required: false + example: "s3://bucket/path" + - name: "--census_version" + description: "Which release of CellxGene census to use. Possible values are \"latest\", \"stable\", or the date of one of the releases (e.g. \"2023-07-25\"). For more information, check the documentation on [Census data releases](https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_data_release_info.html)." + type: string + example: "stable" + required: false + - name: Query + description: Arguments related to the query. + arguments: + - name: "--species" + type: string + description: The organism to query, usually one of `Homo sapiens` or `Mus musculus`. + required: false + default: "homo_sapiens" + multiple: false + - name: "--obs_value_filter" + type: string + description: "Filter for selecting the `obs` metadata (i.e. cells). Value is a filter query written in the SOMA `value_filter` syntax." + required: false + example: "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" + - name: "--cell_filter_grouping" + type: string + description: | + A subset of 'obs' columns by which to group the cells for filtering. + Only groups surpassing or equal to the `--cell_filter_minimum_count` + threshold will be retained. Take care not to introduce a selection + bias against cells with more fine-grained ontology annotations. + required: false + example: ["dataset_id", "tissue", "assay", "disease", "cell_type"] + multiple: true + - name: "--cell_filter_minimum_count" + type: double + description: | + A minimum number of cells per group to retain. If `--cell_filter_grouping` + is defined, this parameter should also be provided and vice versa. + required: false + example: 100 + - name: Outputs + description: Output arguments. + arguments: + - name: "--output" + type: file + description: Output h5ad file. + direction: output + required: true + example: output.h5ad + - name: "--output_compression" + type: string + choices: ["gzip", "lzf"] + required: false + example: "gzip" + resources: + - type: python_script + path: script.py + - path: /src/common/helper_functions/setup_logger.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - cellxgene-census~=1.2.0 + test_setup: + - type: python + packages: + - viashpy + - type: nextflow + directives: + label: [highmem, midcpu] \ No newline at end of file diff --git a/src/datasets/loaders/query_cellxgene_census/script.py b/src/datasets/loaders/query_cellxgene_census/script.py new file mode 100644 index 0000000000..1e0d284e89 --- /dev/null +++ b/src/datasets/loaders/query_cellxgene_census/script.py @@ -0,0 +1,113 @@ +import os +import sys +import cellxgene_census + +## VIASH START +par = { + "input_uri": None, + "census_version": "stable", + "species": "homo_sapiens", + "obs_value_filter": "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'", + "cell_filter_grouping": ["dataset_id", "tissue", "assay", "disease", "cell_type"], + "cell_filter_minimum_count": 100, + "output": "output.h5ad", + "output_compression": "gzip", +} +meta = {"resources_dir": "src/common/helper_functions"} +## VIASH END + +sys.path.append(meta["resources_dir"]) + +from setup_logger import setup_logger +logger = setup_logger() + +def connect_census(uri, census_version): + """ + Connect to CellxGene Census or user-provided TileDBSoma object + """ + ver = census_version or "stable" + logger.info("Connecting to CellxGene Census at %s", f"'{uri}'" if uri else f"version '{ver}'") + return cellxgene_census.open_soma(uri=uri, census_version=ver) + +def get_anndata(census_connection, obs_value_filter, species): + logger.info("Getting gene expression data based on %s query.", obs_value_filter) + return cellxgene_census.get_anndata( + census=census_connection, obs_value_filter=obs_value_filter, organism=species + ) + + +def add_cellcensus_metadata_obs(census_connection, query_data): + logger.info("Adding extented metadata to gene expression data.") + census_datasets = ( + census_connection["census_info"]["datasets"].read().concat().to_pandas() + ) + + query_data.obs.dataset_id = query_data.obs.dataset_id.astype("category") + + dataset_info = ( + census_datasets[ + census_datasets.dataset_id.isin(query_data.obs.dataset_id.cat.categories) + ][ + [ + "collection_id", + "collection_name", + "collection_doi", + "dataset_id", + "dataset_title", + ] + ] + .reset_index(drop=True) + .apply(lambda x: x.astype("category")) + ) + + return query_data.obs.merge(dataset_info, on="dataset_id", how="left") + + +def cellcensus_cell_filter(query_data, cell_filter_grouping, cell_filter_minimum_count): + t0 = query_data.shape + query_data = query_data[ + query_data.obs.groupby(cell_filter_grouping)["soma_joinid"].transform("count") + >= cell_filter_minimum_count + ] + t1 = query_data.shape + logger.info( + "Removed %s cells based on %s cell_filter_minimum_count of %s cell_filter_grouping." + % ((t0[0] - t1[0]), cell_filter_minimum_count, cell_filter_grouping) + ) + return query_data + + +def write_anndata(query_data, path, compression): + logger.info("Writing AnnData object to '%s'", path) + + query_data.write_h5ad(path, compression=compression) + + +def main(): + # check arguments + if (par["cell_filter_grouping"] is None) != (par["cell_filter_minimum_count"] is None): + raise NotImplementedError( + "You need to specify either both or none of the following parameters: cell_filter_grouping, cell_filter_minimum_count" + ) + + with connect_census(uri=par["input_uri"], census_version=par["census_version"]) as conn: + query_data = get_anndata(conn, par["obs_value_filter"], par["species"]) + + query_data.obs = add_cellcensus_metadata_obs(conn, query_data) + + if par["cell_filter_grouping"] is not None: + query_data = cellcensus_cell_filter( + query_data, + par["cell_filter_grouping"], + par["cell_filter_minimum_count"] + ) + + # use feature_id as var_names + query_data.var_names = query_data.var["feature_id"] + + # write output to file + write_anndata(query_data, par["output"], par["output_compression"]) + + +if __name__ == "__main__": + main() diff --git a/src/datasets/loaders/query_cellxgene_census/test.py b/src/datasets/loaders/query_cellxgene_census/test.py new file mode 100644 index 0000000000..9d887b83db --- /dev/null +++ b/src/datasets/loaders/query_cellxgene_census/test.py @@ -0,0 +1,38 @@ +import sys +import os +import pytest +import anndata as ad +import numpy as np + +## VIASH START +meta = { + 'resources_dir': './resources_test/', + 'executable': './target/docker/query/cellxgene_census', + 'config': '/home/di/code/openpipeline/src/query/cellxgene_census/config.vsh.yaml' +} +## VIASH END + +def test_cellxgene_extract_metadata_expression(run_component, tmp_path): + output_file = tmp_path / "output.h5ad" + + run_component([ + "--obs_value_filter", "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'", + "--output", output_file, + ]) + + # check whether file exists + assert os.path.exists(output_file), "Output file does not exist" + + component_data = ad.read(output_file) + var, obs = component_data.var, component_data.obs + assert not obs.empty, ".obs should not be empty" + assert "is_primary_data" in obs.columns + assert np.all(obs["is_primary_data"] == True) + assert "cell_type_ontology_term_id" in obs.columns + assert "disease" in obs.columns + assert "soma_joinid" in var.columns + assert "feature_id" in var.columns + assert component_data.n_obs + +if __name__ == '__main__': + sys.exit(pytest.main([__file__])) From 998ae2adb082e903f243118252424da4d99cae1f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 30 Nov 2023 17:44:34 +0100 Subject: [PATCH 1065/1233] create component for detecting obsolete ontology terms (#291) * create component for detecting obsolete ontology terms * make collection metadata optional * Add unit test to component * add test resources * add summary prints Former-commit-id: af54964d2f16d0a8eb2f42a51ce9707abecb614d --- .../check_obsolete_terms/config.vsh.yaml | 75 +++++++++++++++++++ .../ontology/check_obsolete_terms/script.R | 63 ++++++++++++++++ .../ontology/check_obsolete_terms/test.R | 54 +++++++++++++ .../query_cellxgene_census/config.vsh.yaml | 6 ++ .../loaders/query_cellxgene_census/script.py | 27 ++++++- .../resource_test_scripts/cellxgene_census.sh | 14 ++++ 6 files changed, 238 insertions(+), 1 deletion(-) create mode 100644 src/common/ontology/check_obsolete_terms/config.vsh.yaml create mode 100644 src/common/ontology/check_obsolete_terms/script.R create mode 100644 src/common/ontology/check_obsolete_terms/test.R create mode 100644 src/datasets/resource_test_scripts/cellxgene_census.sh diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml new file mode 100644 index 0000000000..025562c09f --- /dev/null +++ b/src/common/ontology/check_obsolete_terms/config.vsh.yaml @@ -0,0 +1,75 @@ +functionality: + name: check_obsolete_terms + namespace: common/ontology + description: | + Check for obsolete ontology terms in the dataset. + argument_groups: + - name: Inputs + arguments: + - name: "--input" + type: file + description: "Input h5ad file." + required: true + direction: input + example: dataset.h5ad + - name: "--struct" + type: string + description: "In which struct to look for the term." + required: true + direction: input + example: "obs" + - name: "--input_term" + type: string + description: "In which field to look for the term." + required: true + direction: input + example: "cell_type_ontology_term_id" + - name: Ontology + arguments: + - name: "--ontology" + type: file + description: "Ontology to check." + required: true + direction: input + example: cl.obo + - name: Arguments + arguments: + - name: "--obsolete_as_na" + type: boolean + description: "Whether to replace obsolete terms with NA." + default: true + - name: Outputs + arguments: + - name: "--output" + type: file + description: Output h5ad file. + direction: output + example: output.h5ad + - name: "--output_term" + type: string + description: "In which field to store the updated term." + required: true + example: "cell_type_ontology_term_id" + - name: "--output_name" + type: string + description: "In which field to store the updated term name." + required: true + example: "cell_type" + - name: "--output_obsolete" + type: string + description: "In which field to store whether a term is obsolete." + required: true + example: "cell_type_ontology_obsolete" + resources: + - type: r_script + path: script.R + test_resources: + - type: r_script + path: test.R + - path: /resources_test/common/cellxgene_census +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + packages: [ dplyr, tidyr, tibble, ontologyIndex, processx ] \ No newline at end of file diff --git a/src/common/ontology/check_obsolete_terms/script.R b/src/common/ontology/check_obsolete_terms/script.R new file mode 100644 index 0000000000..bc1ef0ccb7 --- /dev/null +++ b/src/common/ontology/check_obsolete_terms/script.R @@ -0,0 +1,63 @@ +library(dplyr, warn.conflicts = FALSE) +library(tidyr, warn.conflicts = FALSE) +library(tibble, warn.conflicts = FALSE) +library(ontologyIndex, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input = "resources_test/common/cellxgene_census/dataset.h5ad", + ontology = "resources_test/common/cellxgene_census/cl.obo", + input_term = "cell_type_ontology_term_id", + struct = "obs", + output = "output.h5ad", + output_term = "cell_type_ontology_term_id", + output_name = "cell_type", + output_obsolete = "cell_type_ontology_obsolete", + obsolete_as_na = TRUE +) +## VIASH END + +cat("Read ontology\n") +ont <- ontologyIndex::get_ontology( + par$ontology, + extract_tags = "everything" +) +ont_tib <- ont %>% + as.data.frame %>% + select(id, name, obsolete, replaced_by) %>% + as_tibble + +cat("Read anndata\n") +adata <- anndata::read_h5ad(par$input, backed = "r") + +cat("Find terms\n") +term_ids <- adata[[par$struct]][[par$input_term]] + +unique_term_ids <- as.character(unique(term_ids)) + +cat("Look for obsolete or replaced terms\n") +ont_map <- ont_tib %>% + slice(match(unique_term_ids, id)) %>% + transmute( + orig_id = id, + id = case_when( + !obsolete ~ id, + replaced_by != "" ~ replaced_by, + rep(par$obsolete_as_na, length(id)) ~ rep(NA_character_, length(id)), + TRUE ~ id + ) + ) %>% + left_join(ont_tib %>% select(id, name, obsolete), by = "id") + +cat("Store new columns in data structure\n") +new_data <- ont_map %>% slice(match(term_ids, orig_id)) +adata[[par$struct]][[par$output_term]] <- new_data$id +adata[[par$struct]][[par$output_name]] <- new_data$name +adata[[par$struct]][[par$output_obsolete]] <- ifelse( + !is.na(new_data$obsolete), + new_data$obsolete, + TRUE +) + +cat("Write to file\n") +anndata::write_h5ad(adata, par$output) diff --git a/src/common/ontology/check_obsolete_terms/test.R b/src/common/ontology/check_obsolete_terms/test.R new file mode 100644 index 0000000000..5e3c582021 --- /dev/null +++ b/src/common/ontology/check_obsolete_terms/test.R @@ -0,0 +1,54 @@ +library(assertthat) + +## VIASH START +meta <- list( + executable = "target/docker/common/ontology/check_obsolete_terms", + resources_dir = "resources_test/common/" +) +## VIASH END + +input_file <- paste0(meta$resources_dir, "/cellxgene_census/dataset.h5ad") +ontology_file <- paste0(meta$resources_dir, "/cellxgene_census/cl.obo") +temp_file <- tempfile(fileext = ".h5ad") +temp2_file <- tempfile(fileext = ".h5ad") + +# add obsolete terms to the dataset +input <- anndata::read_h5ad(input_file) +input$obs$cell_type_ontology_term_id <- as.character(input$obs$cell_type_ontology_term_id) +input$obs$cell_type_ontology_term_id[1:3] <- "CL:0000375" # obsolete, replaced by 'CL:0007010' +input$obs$cell_type_ontology_term_id[4:6] <- "CL:0000399" # obsolete, removed +input$obs$cell_type_ontology_term_id[7:9] <- "CL:0007011" # not obsolete +zzz <- input$write_h5ad(temp_file) + +# run component +zzz <- processx::run( + meta$executable, + c( + "--input", temp_file, + "--struct", "obs", + "--input_term", "cell_type_ontology_term_id", + "--ontology", ontology_file, + "--output", temp2_file, + "--output_term", "cell_type_ontology_term_id_new", + "--output_name", "cell_type_new", + "--output_obsolete", "cell_type_obsolete_new" + ), + echo = TRUE +) + +# check output +output <- anndata::read_h5ad(temp2_file) + +print(output$obs[1:10, , drop = FALSE]) + +assert_that( + all(output$obs$cell_type_ontology_term_id_new[1:3] == "CL:0007010"), + all(is.na(output$obs$cell_type_ontology_term_id_new[4:6])), + all(output$obs$cell_type_ontology_term_id_new[7:9] == "CL:0007011"), + all(output$obs$cell_type_new[1:3] == "preosteoblast"), + all(is.na(output$obs$cell_type_new[4:6])), + all(output$obs$cell_type_new[7:9] == "enteric neuron"), + all(!output$obs$cell_type_obsolete_new[1:3]), + all(output$obs$cell_type_obsolete_new[4:6]), + all(!output$obs$cell_type_obsolete_new[7:9]) +) diff --git a/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml b/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml index 572b28f2a9..85f6cf761b 100644 --- a/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml @@ -34,6 +34,12 @@ functionality: description: "Filter for selecting the `obs` metadata (i.e. cells). Value is a filter query written in the SOMA `value_filter` syntax." required: false example: "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" + - name: Arguments + description: Other arguments + arguments: + - name: "--add_collection_metadata" + type: boolean_true + description: Whether to add metadata to the obs related to the collection. - name: "--cell_filter_grouping" type: string description: | diff --git a/src/datasets/loaders/query_cellxgene_census/script.py b/src/datasets/loaders/query_cellxgene_census/script.py index 1e0d284e89..876e050871 100644 --- a/src/datasets/loaders/query_cellxgene_census/script.py +++ b/src/datasets/loaders/query_cellxgene_census/script.py @@ -82,6 +82,27 @@ def write_anndata(query_data, path, compression): query_data.write_h5ad(path, compression=compression) +def print_unique(adata, column): + formatted = "', '".join(adata.obs[column].unique()) + logger.info(f"Unique {column}: ['{formatted}']") + +def print_summary(query_data): + logger.info(f"Resulting dataset: {query_data}") + + logger.info("Summary of dataset:") + print_unique(query_data, "assay") + print_unique(query_data, "assay_ontology_term_id") + print_unique(query_data, "cell_type") + print_unique(query_data, "cell_type_ontology_term_id") + print_unique(query_data, "dataset_id") + print_unique(query_data, "development_stage") + print_unique(query_data, "development_stage_ontology_term_id") + print_unique(query_data, "disease") + print_unique(query_data, "disease_ontology_term_id") + print_unique(query_data, "tissue") + print_unique(query_data, "tissue_ontology_term_id") + print_unique(query_data, "tissue_general") + print_unique(query_data, "tissue_general_ontology_term_id") def main(): # check arguments @@ -93,7 +114,8 @@ def main(): with connect_census(uri=par["input_uri"], census_version=par["census_version"]) as conn: query_data = get_anndata(conn, par["obs_value_filter"], par["species"]) - query_data.obs = add_cellcensus_metadata_obs(conn, query_data) + if par["add_collection_metadata"]: + query_data.obs = add_cellcensus_metadata_obs(conn, query_data) if par["cell_filter_grouping"] is not None: query_data = cellcensus_cell_filter( @@ -105,6 +127,9 @@ def main(): # use feature_id as var_names query_data.var_names = query_data.var["feature_id"] + # print summary + print_summary(query_data) + # write output to file write_anndata(query_data, par["output"], par["output_compression"]) diff --git a/src/datasets/resource_test_scripts/cellxgene_census.sh b/src/datasets/resource_test_scripts/cellxgene_census.sh new file mode 100644 index 0000000000..45e4dd9e12 --- /dev/null +++ b/src/datasets/resource_test_scripts/cellxgene_census.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +DATASET_DIR="resources_test/common/cellxgene_census" + +[ ! -d "$DATASET_DIR" ] && mkdir -p "$DATASET_DIR" + +# download cell ontology obo file +wget https://github.com/obophenotype/cell-ontology/releases/download/v2023-02-15/cl.obo -O "$DATASET_DIR/cl.obo" + +# fetch dataset from cellxgene census +viash run src/datasets/loaders/query_cellxgene_census/config.vsh.yaml -- \ + --census_version 2023-07-25 \ + --obs_value_filter "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" \ + --output "$DATASET_DIR/dataset.h5ad" From a1b46e4302aaad27981c6d12d09381f48d4a01cf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 1 Dec 2023 15:28:28 +0100 Subject: [PATCH 1066/1233] Extend API for raw datasets based on the CELLxGENE Census schema (#293) * derive fields from the CELLxGENE schema * Rename celltype to cell_type * fix bmmc_x_starter script * fix label projection pancreas script * revert changes in openproblemsv1 script * fix pancreas script * add var to api * change raw h5ad uns specs * rename data_url and data_reference to dataset_* Former-commit-id: 7cebf6e90d76777f49d193cc30d8beab083233ba --- src/common/helper_functions/subset_anndata.py | 2 +- src/datasets/api/file_raw.yaml | 157 ++++++++++++++++-- .../loaders/openproblems_v1/config.vsh.yaml | 6 +- .../loaders/openproblems_v1/script.py | 14 +- src/datasets/loaders/openproblems_v1/test.py | 12 +- .../config.vsh.yaml | 6 +- .../openproblems_v1_multimodal/script.py | 16 +- .../openproblems_v1_multimodal/test.py | 16 +- .../processors/subsample/config.vsh.yaml | 2 +- src/datasets/processors/subsample/script.py | 14 +- .../processors/subsample/test_script.py | 2 +- .../resource_scripts/openproblems_v1.sh | 62 +++---- .../openproblems_v1_multimodal.sh | 16 +- .../resource_test_scripts/pancreas.sh | 8 +- .../scicar_cell_lines.sh | 6 +- .../process_openproblems_v1/config.vsh.yaml | 8 +- .../workflows/process_openproblems_v1/main.nf | 8 +- .../config.vsh.yaml | 8 +- .../main.nf | 8 +- .../api/comp_process_dataset.yaml | 2 +- .../api/file_common_dataset.yaml | 8 +- .../batch_integration/api/file_solution.yaml | 4 +- .../process_dataset/script.py | 2 +- .../api/file_common_dataset.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../process_dataset/script.py | 2 +- .../resources_test_scripts/pancreas.sh | 27 +-- .../resources_test_scripts/bmmc_x_starter.sh | 11 +- 28 files changed, 277 insertions(+), 154 deletions(-) diff --git a/src/common/helper_functions/subset_anndata.py b/src/common/helper_functions/subset_anndata.py index d183a02525..80bd160872 100644 --- a/src/common/helper_functions/subset_anndata.py +++ b/src/common/helper_functions/subset_anndata.py @@ -16,7 +16,7 @@ def read_config_slots_info(config_file, slot_mapping = {}): "counts": par["layer_counts"], }, "obs": { - "celltype": par["obs_celltype"], + "cell_type": par["obs_cell_type"], "batch": par["obs_batch"], } } diff --git a/src/datasets/api/file_raw.yaml b/src/datasets/api/file_raw.yaml index 877c7f2c43..2fd5475985 100644 --- a/src/datasets/api/file_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -2,7 +2,11 @@ type: file example: "resources_test/common/pancreas/raw.h5ad" info: label: "Raw dataset" - summary: "An unprocessed dataset as output by a dataset loader." + summary: An unprocessed dataset as output by a dataset loader. + description: | + This dataset contains raw counts and metadata as output by a dataset loader. + + The format of this file is derived from the [CELLxGENE schema v4.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md). slots: layers: - type: integer @@ -11,34 +15,166 @@ info: required: true obs: - type: string - name: celltype - description: Cell type information + name: dataset_id + description: Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes. required: false + - type: string - name: batch - description: Batch information + name: assay + description: Type of assay used to generate the cell data, indicating the methodology or technique employed. + required: false + + - type: string + name: assay_ontology_term_id + description: Experimental Factor Ontology (`EFO:`) term identifier for the assay, providing a standardized reference to the assay type. + required: false + + - type: string + name: cell_type + description: Classification of the cell type based on its characteristics and function within the tissue or organism. + required: false + + - type: string + name: cell_type_ontology_term_id + description: Cell Ontology (`CL:`) term identifier for the cell type, offering a standardized reference to the specific cell classification. + required: false + + - type: string + name: development_stage + description: Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase. + required: false + + - type: string + name: development_stage_ontology_term_id + description: | + Ontology term identifier for the developmental stage, providing a standardized reference to the organism's developmental phase. + + If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Developmental Stages (`HsapDv:`) ontology is used. + If the organism is mouse (`organism_ontology_term_id == 'NCBITaxon:10090'`), then the Mouse Developmental Stages (`MmusDv:`) ontology is used. + Otherwise, the Uberon (`UBERON:`) ontology is used. + required: false + + - type: string + name: disease + description: Information on any disease or pathological condition associated with the cell or donor. + required: false + + - type: string + name: disease_ontology_term_id + description: | + Ontology term identifier for the disease, enabling standardized disease classification and referencing. + + Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). + required: false + + - type: string + name: donor_id + description: Identifier for the donor from whom the cell sample is obtained. + required: false + + - type: boolean + name: is_primary_data + description: Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. + required: false + + - type: string + name: self_reported_ethnicity + description: Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. + required: false + + - type: string + name: self_reported_ethnicity_ontology_term_id + description: | + Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. + + If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. required: false + + - type: string + name: sex + description: Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. + required: false + + - type: string + name: sex_ontology_term_id + description: Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only `PATO:0000383`, `PATO:0000384` and `PATO:0001340` are allowed. + required: false + + - type: string + name: suspension_type + description: Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions. + required: false + - type: string name: tissue - description: Tissue information + description: Specific tissue from which the cells were derived, key for context and specificity in cell studies. + required: false + + - type: string + name: tissue_ontology_term_id + description: | + Ontology term identifier for the tissue, providing a standardized reference for the tissue type. + + For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). + For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. + required: false + + - type: string + name: tissue_general + description: General category or classification of the tissue, useful for broader grouping and comparison of cell data. + required: false + + - type: string + name: tissue_general_ontology_term_id + description: | + Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. + + For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). + For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. + required: false + + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: false + + - type: integer + name: soma_joinid + description: If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. + required: false + var: + - type: string + name: feature_id + description: Unique identifier for the feature, usually a ENSEMBL gene id. + required: false + + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + required: false + + - type: integer + name: soma_joinid + description: If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. required: false uns: - type: string name: dataset_id - description: "A unique identifier for the dataset" + description: A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived. required: true - name: dataset_name type: string - description: Nicely formatted name. + description: A human-readable name for the dataset. required: true - type: string - name: data_url + name: dataset_url description: Link to the original source of the dataset. required: false - - name: data_reference + - name: dataset_reference type: string description: Bibtex reference of the paper in which the dataset was published. required: false + multiple: true - name: dataset_summary type: string description: Short description of the dataset. @@ -51,3 +187,4 @@ info: type: string description: The organism of the sample in the dataset. required: false + multiple: true diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 0e8e75c428..58d495af8c 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--obs_celltype" + - name: "--obs_cell_type" type: "string" description: "Location of where to find the observation cell types." - name: "--obs_batch" @@ -32,11 +32,11 @@ functionality: type: string description: Nicely formatted name. required: true - - name: "--data_url" + - name: "--dataset_url" type: string description: Link to the original source of the dataset. required: false - - name: "--data_reference" + - name: "--dataset_reference" type: string description: Bibtex reference of the paper in which the dataset was published. required: false diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 927816780f..b08928e9c2 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { "dataset_id": "pancreas", - "obs_celltype": "celltype", + "obs_cell_type": "cell_type", "obs_batch": "tech", "obs_tissue": "tissue", "layer_counts": "counts", @@ -49,12 +49,12 @@ print(f"Setting .uns['{key}']", flush=True) adata.uns[key] = value -print("Setting .obs['celltype']", flush=True) -if par["obs_celltype"]: - if par["obs_celltype"] in adata.obs: - adata.obs["celltype"] = adata.obs[par["obs_celltype"]] +print("Setting .obs['cell_type']", flush=True) +if par["obs_cell_type"]: + if par["obs_cell_type"] in adata.obs: + adata.obs["cell_type"] = adata.obs[par["obs_cell_type"]] else: - print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.", flush=True) + print(f"Warning: key '{par['obs_cell_type']}' could not be found in adata.obs.", flush=True) print("Setting .obs['batch']", flush=True) if par["obs_batch"]: @@ -91,7 +91,7 @@ print("Add metadata to uns", flush=True) metadata_fields = [ - "dataset_id", "dataset_name", "data_url", "data_reference", + "dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism" ] uns_metadata = { diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index 1e50081b06..aa49864118 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -4,7 +4,7 @@ name = "pancreas" output = "dataset.h5ad" -obs_celltype = "celltype" +obs_cell_type = "celltype" obs_batch = "tech" print(">> Running script", flush=True) @@ -12,13 +12,13 @@ [ meta["executable"], "--dataset_id", name, - "--obs_celltype", obs_celltype, + "--obs_cell_type", obs_cell_type, "--obs_batch", obs_batch, "--layer_counts", "counts", "--output", output, "--dataset_name", "Pancreas", - "--data_url", "http://foo.org", - "--data_reference", "foo2000bar", + "--dataset_url", "http://foo.org", + "--dataset_reference", "foo2000bar", "--dataset_summary", "A short summary.", "--dataset_description", "A couple of paragraphs worth of text.", "--dataset_organism", "homo_sapiens", @@ -45,8 +45,8 @@ assert adata.X is None, "adata.X should be None/empty" assert "counts" in adata.layers, "Counts layer not found in output layers" assert adata.uns["dataset_id"] == name, f"Expected {name} as value" -if obs_celltype: - assert "celltype" in adata.obs.columns, "'celltype' column not found in obs of anndata output" +if obs_cell_type: + assert "cell_type" in adata.obs.columns, "'cell_type' column not found in obs of anndata output" if obs_batch: assert "batch" in adata.obs.columns, "'batch' column not found in obs of anndata output" diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 65cf2808a2..e593e11519 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--obs_celltype" + - name: "--obs_cell_type" type: "string" description: "Location of where to find the observation cell types." - name: "--obs_batch" @@ -32,11 +32,11 @@ functionality: type: string description: Nicely formatted name. required: true - - name: "--data_url" + - name: "--dataset_url" type: string description: Link to the original source of the dataset. required: false - - name: "--data_reference" + - name: "--dataset_reference" type: string description: Bibtex reference of the paper in which the dataset was published. required: false diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py index 8c0dbefa37..154e1400c9 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/script.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -7,7 +7,7 @@ ## VIASH START par = { "dataset_id": "scicar_mouse_kidney", - "obs_celltype": "celltype", + "obs_cell_type": "cell_type", "obs_batch": "replicate", "obs_tissue": None, "layer_counts": "counts", @@ -67,13 +67,13 @@ mod1.uns[key] = value mod2.uns[key] = value -print("Setting .obs['celltype']", flush=True) -if par["obs_celltype"]: - if par["obs_celltype"] in mod1.obs: - mod1.obs["celltype"] = mod1.obs[par["obs_celltype"]] - mod2.obs["celltype"] = mod2.obs[par["obs_celltype"]] +print("Setting .obs['cell_type']", flush=True) +if par["obs_cell_type"]: + if par["obs_cell_type"] in mod1.obs: + mod1.obs["cell_type"] = mod1.obs[par["obs_cell_type"]] + mod2.obs["cell_type"] = mod2.obs[par["obs_cell_type"]] else: - print(f"Warning: key '{par['obs_celltype']}' could not be found in adata.obs.", flush=True) + print(f"Warning: key '{par['obs_cell_type']}' could not be found in adata.obs.", flush=True) print("Setting .obs['batch']", flush=True) if par["obs_batch"]: @@ -117,7 +117,7 @@ print("Add metadata to uns", flush=True) metadata_fields = [ - "dataset_id", "dataset_name", "data_url", "data_reference", + "dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description" "dataset_organism" ] uns_metadata = { diff --git a/src/datasets/loaders/openproblems_v1_multimodal/test.py b/src/datasets/loaders/openproblems_v1_multimodal/test.py index e925817baa..26e8d9ff93 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/test.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/test.py @@ -3,7 +3,7 @@ import anndata as ad name = "scicar_mouse_kidney" -obs_celltype = "cell_name" +obs_cell_type = "cell_name" obs_batch = "replicate" obs_tissue = None @@ -15,14 +15,14 @@ [ meta["executable"], "--dataset_id", name, - "--obs_celltype", obs_celltype, + "--obs_cell_type", obs_cell_type, "--obs_batch", obs_batch, "--layer_counts", "counts", "--output_mod1", output_mod1_file, "--output_mod2", output_mod2_file, "--dataset_name", "Pancreas", - "--data_url", "http://foo.org", - "--data_reference", "foo2000bar", + "--dataset_url", "http://foo.org", + "--dataset_reference", "foo2000bar", "--dataset_summary", "A short summary.", "--dataset_description", "A couple of paragraphs worth of text.", "--dataset_organism", "homo_sapiens", @@ -52,8 +52,8 @@ assert output_mod1.X is None, ".X is not None/empty in mod 1 output" assert "counts" in output_mod1.layers, "'counts' not found in mod 1 output layers" assert output_mod1.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 1 output uns" -if obs_celltype: - assert "celltype" in output_mod1.obs.columns, "celltype column not found in mod 1 output obs" +if obs_cell_type: + assert "cell_type" in output_mod1.obs.columns, "cell_type column not found in mod 1 output obs" if obs_batch: assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" if obs_tissue: @@ -63,8 +63,8 @@ assert output_mod2.X is None, ".X is not None/empty in mod 2 output" assert "counts" in output_mod2.layers, "'counts' not found in mod 2 output layers" assert output_mod2.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 2 output uns" -if obs_celltype: - assert "celltype" in output_mod2.obs.columns, "celltype column not found in mod 2 output obs" +if obs_cell_type: + assert "cell_type" in output_mod2.obs.columns, "cell_type column not found in mod 2 output obs" if obs_batch: assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" if obs_tissue: diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index c0a7673eeb..9e2173e020 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: type: string multiple: true description: A list of genes to keep. - - name: "--keep_celltype_categories" + - name: "--keep_cell_type_categories" type: "string" multiple: true description: "Categories indexes to be selected" diff --git a/src/datasets/processors/subsample/script.py b/src/datasets/processors/subsample/script.py index c126c886ef..c2347349c0 100644 --- a/src/datasets/processors/subsample/script.py +++ b/src/datasets/processors/subsample/script.py @@ -8,10 +8,10 @@ "input_mod2": "resources_test/common/scicar_cell_lines/temp_mod2_full.h5ad", "n_obs": 600, "n_vars": 1500, - "keep_celltype_categories": None, + "keep_cell_type_categories": None, "keep_batch_categories": None, "keep_features": None, - "keep_celltype_categories": None, + "keep_cell_type_categories": None, "keep_batch_categories": None, "even": False, "output": "subsample_mod1.h5ad", @@ -49,14 +49,14 @@ print(">> Subsampling the observations", flush=True) obs_filt = np.ones(dtype=np.bool_, shape=adata_input.n_obs) -# subset by celltype -if par.get("keep_celltype_categories"): - print(f">> Selecting celltype_categories {par['keep_celltype_categories']}") - obs_filt = obs_filt & adata_input.obs["celltype"].isin(par["keep_celltype_categories"]) +# subset by cell_type +if par.get("keep_cell_type_categories"): + print(f">> Selecting cell_type_categories {par['keep_cell_type_categories']}") + obs_filt = obs_filt & adata_input.obs["cell_type"].isin(par["keep_cell_type_categories"]) # subset by batch if par.get("keep_batch_categories"): - print(f">> Selecting celltype_categories {par['keep_batch_categories']}") + print(f">> Selecting cell_type_categories {par['keep_batch_categories']}") obs_filt = obs_filt & adata_input.obs["batch"].isin(par["keep_batch_categories"]) # subsample evenly across batches or not diff --git a/src/datasets/processors/subsample/test_script.py b/src/datasets/processors/subsample/test_script.py index 44ff8cac69..80dde5d383 100644 --- a/src/datasets/processors/subsample/test_script.py +++ b/src/datasets/processors/subsample/test_script.py @@ -42,7 +42,7 @@ def test_keep_functionality(run_component): run_component([ "--input", input_path, - "--keep_celltype_categories", "acinar:beta", + "--keep_cell_type_categories", "acinar:beta", "--keep_batch_categories", "celseq:inDrop4:smarter", "--keep_features", ":".join(keep_features), "--output", output_path, diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 1c146b98df..7275f2ab1c 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -19,78 +19,78 @@ params_file="/tmp/datasets_openproblems_v1_params.yaml" cat > "$params_file" << 'HERE' param_list: - id: allen_brain_atlas - obs_celltype: label + obs_cell_type: label layer_counts: counts dataset_name: Mouse Brain Atlas - data_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 - data_reference: tasic2016adult + dataset_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 + dataset_reference: tasic2016adult dataset_summary: Adult mouse primary visual cortex dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). dataset_organism: mus_musculus - id: cengen - obs_celltype: cell_type + obs_cell_type: cell_type obs_batch: experiment_code obs_tissue: tissue layer_counts: counts dataset_name: CeNGEN - data_url: https://www.cengen.org - data_reference: hammarlund2018cengen + dataset_url: https://www.cengen.org + dataset_reference: hammarlund2018cengen dataset_summary: Complete Gene Expression Map of an Entire Nervous System dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. dataset_organism: caenorhabditis_elegans - id: immune_cells - obs_celltype: final_annotation + obs_cell_type: final_annotation obs_batch: batch obs_tissue: tissue layer_counts: counts dataset_name: Human immune - data_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html - data_reference: luecken2022benchmarking + dataset_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html + dataset_reference: luecken2022benchmarking dataset_summary: Human immune cells dataset from the scIB benchmarks dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). dataset_organism: homo_sapiens - id: mouse_blood_olsson_labelled - obs_celltype: celltype + obs_cell_type: celltype layer_counts: counts dataset_name: Mouse myeloid - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 - data_reference: olsson2016single + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 + dataset_reference: olsson2016single dataset_summary: Myeloid lineage differentiation from mouse blood dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. dataset_organism: mus_musculus - id: mouse_hspc_nestorowa2016 - obs_celltype: cell_type_label + obs_cell_type: cell_type_label layer_counts: counts dataset_name: Mouse HSPC - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 - data_reference: nestorowa2016single + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 + dataset_reference: nestorowa2016single dataset_summary: Haematopoeitic stem and progenitor cells from mouse bone marrow dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. dataset_organism: mus_musculus - id: pancreas - obs_celltype: celltype + obs_cell_type: celltype obs_batch: tech layer_counts: counts dataset_name: Human pancreas - data_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html - data_reference: luecken2022benchmarking + dataset_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html + dataset_reference: luecken2022benchmarking dataset_summary: Human pancreas cells dataset from the scIB benchmarks dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). dataset_organism: homo_sapiens # disabled as this is not working in openproblemsv1 # - id: tabula_muris_senis_droplet_lung - # obs_celltype: cell_type + # obs_cell_type: cell_type # obs_batch: donor_id # layer_counts: counts # dataset_name: Tabula Muris Senis Lung - # data_url: https://tabula-muris-senis.ds.czbiohub.org - # data_reference: tabula2020single + # dataset_url: https://tabula-muris-senis.ds.czbiohub.org + # dataset_reference: tabula2020single # dataset_summary: Aging mouse lung cells from Tabula Muris Senis # dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. # dataset_organism: mus_musculus @@ -98,8 +98,8 @@ param_list: - id: tenx_1k_pbmc layer_counts: counts dataset_name: 1k PBMCs - data_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 - data_reference: 10x2018pbmc + dataset_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 + dataset_reference: 10x2018pbmc dataset_summary: 1k peripheral blood mononuclear cells from a healthy donor dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. dataset_organism: homo_sapiens @@ -107,29 +107,29 @@ param_list: - id: tenx_5k_pbmc layer_counts: counts dataset_name: 5k PBMCs - data_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 - data_reference: 10x2019pbmc + dataset_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 + dataset_reference: 10x2019pbmc dataset_summary: 5k peripheral blood mononuclear cells from a healthy donor dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. dataset_organism: homo_sapiens - id: tnbc_wu2021 - obs_celltype: celltype_minor + obs_cell_type: celltype_minor layer_counts: counts dataset_name: Triple-Negative Breast Cancer - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 - data_reference: wu2021single + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 + dataset_reference: wu2021single dataset_summary: 1535 cells from six fresh triple-negative breast cancer tumors. dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). dataset_organism: homo_sapiens - id: zebrafish - obs_celltype: cell_type + obs_cell_type: cell_type obs_batch: lab layer_counts: counts dataset_name: Zebrafish embryonic cells - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 - data_reference: wagner2018single + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 + dataset_reference: wagner2018single dataset_summary: Single-cell mRNA sequencing of zebrafish embryonic cells. dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index f6e67dd12a..592de5521e 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -22,8 +22,8 @@ param_list: dataset_name: "CITE-Seq CBMC" dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." - data_reference: stoeckius2017simultaneous - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 + dataset_reference: stoeckius2017simultaneous + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 dataset_organism: homo_sapiens layer_counts: counts @@ -31,20 +31,20 @@ param_list: dataset_name: "sci-CAR Cell Lines" dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." - data_reference: cao2018joint - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_reference: cao2018joint + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 dataset_organism: "[homo_sapiens, mus_musculus]" - obs_celltype: cell_name + obs_cell_type: cell_name layer_counts: counts - id: scicar_mouse_kidney dataset_name: "sci-CAR Mouse Kidney" dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." - data_reference: cao2018joint - data_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_reference: cao2018joint + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 dataset_organism: mus_musculus - obs_celltype: cell_name + obs_cell_type: cell_name obs_batch: replicate layer_counts: counts diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 15d52aeb7d..61b12d59f1 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -25,16 +25,16 @@ nextflow run . \ -profile docker \ -resume \ --id pancreas \ - --obs_celltype "celltype" \ + --obs_cell_type "celltype" \ --obs_batch "tech" \ --layer_counts "counts" \ --dataset_name "Human pancreas" \ - --data_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ - --data_reference "luecken2022benchmarking" \ + --dataset_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ + --dataset_reference "luecken2022benchmarking" \ --dataset_summary "Human pancreas cells dataset from the scIB benchmarks" \ --dataset_description "Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq)." \ --dataset_organism "homo_sapiens" \ - --keep_celltype_categories "acinar:beta" \ + --keep_cell_type_categories "acinar:beta" \ --keep_batch_categories "celseq:inDrop4:smarter" \ --keep_features "$KEEP_FEATURES" \ --seed 123 \ diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index c0a07031fb..79413b93f4 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -23,11 +23,11 @@ nextflow run . \ --id scicar_cell_lines \ --obs_tissue "source" \ --layer_counts "counts" \ - --obs_celltype "cell_name" \ + --obs_cell_type "cell_name" \ --dataset_id scicar_cell_lines \ --dataset_name "sci-CAR cell lines" \ - --data_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ - --data_reference "cao2018joint" \ + --dataset_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ + --dataset_reference "cao2018joint" \ --dataset_summary "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells" \ --dataset_description "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells. Here, we use two sciCAR datasets that were obtained from the same study. The first dataset contains 4,825 cells from three cell lines (HEK293T cells, NIH/3T3 cells, and A549 cells) at multiple timepoints (0, 1 hour, 3 hours) after dexamethasone treatment. The second dataset contains 11,233 cells from wild-type adult mouse kidney." \ --dataset_organism "[homo_sapiens, mus_musculus]" \ diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 9575d690a1..5cdf080f93 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--obs_celltype" + - name: "--obs_cell_type" type: "string" description: "Location of where to find the observation cell types." - name: "--obs_batch" @@ -33,11 +33,11 @@ functionality: type: string description: Nicely formatted name. required: true - - name: "--data_url" + - name: "--dataset_url" type: string description: Link to the original source of the dataset. required: false - - name: "--data_reference" + - name: "--dataset_reference" type: string description: Bibtex reference of the paper in which the dataset was published. required: false @@ -71,7 +71,7 @@ functionality: type: string multiple: true description: A list of genes to keep. - - name: "--keep_celltype_categories" + - name: "--keep_cell_type_categories" type: "string" multiple: true description: "Categories indexes to be selected" diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 00411529e1..f9d2d42775 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -43,14 +43,14 @@ workflow run_wf { | openproblems_v1.run( fromState: [ "dataset_id": "id", - "obs_celltype": "obs_celltype", + "obs_cell_type": "obs_cell_type", "obs_batch": "obs_batch", "obs_tissue": "obs_tissue", "layer_counts": "layer_counts", "sparse": "sparse", "dataset_name": "dataset_name", - "data_url": "data_url", - "data_reference": "data_reference", + "dataset_url": "dataset_url", + "dataset_reference": "dataset_reference", "dataset_summary": "dataset_summary", "dataset_description": "dataset_description", "dataset_organism": "dataset_organism", @@ -66,7 +66,7 @@ workflow run_wf { "n_obs": "n_obs", "n_vars": "n_vars", "keep_features": "keep_features", - "keep_celltype_categories": "keep_celltype_categories", + "keep_cell_type_categories": "keep_cell_type_categories", "keep_batch_categories": "keep_batch_categories", "even": "even", "seed": "seed" diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 3f604e8b30..a6b4841bda 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: type: "string" description: "The ID of the dataset" required: true - - name: "--obs_celltype" + - name: "--obs_cell_type" type: "string" description: "Location of where to find the observation cell types." - name: "--obs_batch" @@ -33,11 +33,11 @@ functionality: type: string description: Nicely formatted name. required: true - - name: "--data_url" + - name: "--dataset_url" type: string description: Link to the original source of the dataset. required: false - - name: "--data_reference" + - name: "--dataset_reference" type: string description: Bibtex reference of the paper in which the dataset was published. required: false @@ -71,7 +71,7 @@ functionality: type: string multiple: true description: A list of genes to keep. - - name: "--keep_celltype_categories" + - name: "--keep_cell_type_categories" type: "string" multiple: true description: "Categories indexes to be selected" diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 00eb39d073..56c797985c 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -43,14 +43,14 @@ workflow run_wf { | openproblems_v1_multimodal.run( fromState: [ "dataset_id": "id", - "obs_celltype": "obs_celltype", + "obs_cell_type": "obs_cell_type", "obs_batch": "obs_batch", "obs_tissue": "obs_tissue", "layer_counts": "layer_counts", "sparse": "sparse", "dataset_name": "dataset_name", - "data_url": "data_url", - "data_reference": "data_reference", + "dataset_url": "dataset_url", + "dataset_reference": "dataset_reference", "dataset_summary": "dataset_summary", "dataset_description": "dataset_description", "dataset_organism": "dataset_organism" @@ -70,7 +70,7 @@ workflow run_wf { "n_obs": "n_obs", "n_vars": "n_vars", "keep_features": "keep_features", - "keep_celltype_categories": "keep_celltype_categories", + "keep_cell_type_categories": "keep_cell_type_categories", "keep_batch_categories": "keep_batch_categories", "even": "even", "seed": "seed" diff --git a/src/tasks/batch_integration/api/comp_process_dataset.yaml b/src/tasks/batch_integration/api/comp_process_dataset.yaml index 37706acdcf..715ef6d3c3 100644 --- a/src/tasks/batch_integration/api/comp_process_dataset.yaml +++ b/src/tasks/batch_integration/api/comp_process_dataset.yaml @@ -23,7 +23,7 @@ functionality: - name: "--obs_label" type: "string" description: "Which .obs slot to use as label." - default: "celltype" + default: "cell_type" - name: "--obs_batch" type: "string" description: "Which .obs slot to use as batch covariate." diff --git a/src/tasks/batch_integration/api/file_common_dataset.yaml b/src/tasks/batch_integration/api/file_common_dataset.yaml index 8a69bb4e2c..555a82b51d 100644 --- a/src/tasks/batch_integration/api/file_common_dataset.yaml +++ b/src/tasks/batch_integration/api/file_common_dataset.yaml @@ -1,6 +1,6 @@ # This file is based on the spec of the common dataset located at # `src/datasets/api/file_common_dataset.yaml`. However, some fields -# such as obs.celltype and obs.batch are now required +# such as obs.cell_type and obs.batch are now required type: file example: "resources_test/common/pancreas/dataset.h5ad" info: @@ -18,7 +18,7 @@ info: required: true obs: - type: string - name: celltype + name: cell_type description: Cell type information required: true - type: string @@ -54,10 +54,10 @@ info: description: Nicely formatted name. required: true - type: string - name: data_url + name: dataset_url description: Link to the original source of the dataset. required: false - - name: data_reference + - name: dataset_reference type: string description: Bibtex reference of the paper in which the dataset was published. required: false diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml index ac6fd88a42..463a82d50b 100644 --- a/src/tasks/batch_integration/api/file_solution.yaml +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -51,10 +51,10 @@ info: description: Nicely formatted name. required: true - type: string - name: data_url + name: dataset_url description: Link to the original source of the dataset. required: false - - name: data_reference + - name: dataset_reference type: string description: Bibtex reference of the paper in which the dataset was published. required: false diff --git a/src/tasks/batch_integration/process_dataset/script.py b/src/tasks/batch_integration/process_dataset/script.py index ffd9f66fd0..cf8af4c4b7 100644 --- a/src/tasks/batch_integration/process_dataset/script.py +++ b/src/tasks/batch_integration/process_dataset/script.py @@ -5,7 +5,7 @@ par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', 'hvgs': 2000, - 'obs_label': 'celltype', + 'obs_label': 'cell_type', 'obs_batch': 'batch', 'subset_hvg': False, 'output': 'output.h5ad' diff --git a/src/tasks/label_projection/api/file_common_dataset.yaml b/src/tasks/label_projection/api/file_common_dataset.yaml index 2cbd64b47f..e3b6741843 100644 --- a/src/tasks/label_projection/api/file_common_dataset.yaml +++ b/src/tasks/label_projection/api/file_common_dataset.yaml @@ -15,7 +15,7 @@ info: required: true obs: - type: string - name: celltype + name: cell_type description: Cell type information required: true - type: string diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 5f9b8f363b..8b4984bc40 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: - name: "--obs_label" type: "string" description: "Which .obs slot to use as label." - default: "celltype" + default: "cell_type" - name: "--obs_batch" type: "string" description: "Which .obs slot to use as batch covariate." diff --git a/src/tasks/label_projection/process_dataset/script.py b/src/tasks/label_projection/process_dataset/script.py index 6f1459da86..0f2c5482b6 100644 --- a/src/tasks/label_projection/process_dataset/script.py +++ b/src/tasks/label_projection/process_dataset/script.py @@ -9,7 +9,7 @@ 'method': 'batch', 'seed': None, 'obs_batch': 'batch', - 'obs_label': 'celltype', + 'obs_label': 'cell_type', 'output_train': 'train.h5ad', 'output_test': 'test.h5ad', 'output_solution': 'solution.h5ad' diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index cf7bcfe6f0..5a69340510 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -28,27 +28,12 @@ nextflow run . \ # run one method viash run src/tasks/label_projection/methods/knn/config.vsh.yaml -- \ - --input_train $DATASET_DIR/train.h5ad \ - --input_test $DATASET_DIR/test.h5ad \ - --output $DATASET_DIR/prediction.h5ad + --input_train $DATASET_DIR/pancreas/train.h5ad \ + --input_test $DATASET_DIR/pancreas/test.h5ad \ + --output $DATASET_DIR/pancreas/prediction.h5ad # run one metric viash run src/tasks/label_projection/metrics/accuracy/config.vsh.yaml -- \ - --input_prediction $DATASET_DIR/prediction.h5ad \ - --input_solution $DATASET_DIR/solution.h5ad \ - --output $DATASET_DIR/score.h5ad - -# # run benchmark -# export NXF_VER=22.04.5 - -# nextflow \ -# run . \ -# -main-script src/tasks/label_projection/workflows/run/main.nf \ -# -profile docker \ -# -resume \ -# --id pancreas \ -# --input_train $DATASET_DIR/train.h5ad \ -# --input_test $DATASET_DIR/test.h5ad \ -# --input_solution $DATASET_DIR/solution.h5ad \ -# --output scores.tsv \ -# --publish_dir $DATASET_DIR/ \ No newline at end of file + --input_prediction $DATASET_DIR/pancreas/prediction.h5ad \ + --input_solution $DATASET_DIR/pancreas/solution.h5ad \ + --output $DATASET_DIR/pancreas/score.h5ad diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh index 595045115e..5c8d31fd4a 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh @@ -13,6 +13,7 @@ OUTPUT_DIR="resources_test/predict_modality" export NXF_VER=22.04.5 +echo "Preprocess datasets" nextflow run . \ -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ -profile docker \ @@ -24,9 +25,9 @@ nextflow run . \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' - # run one method + echo "Run one method" viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $DATASET_DIR/train_mod1.h5ad \ - --input_train_mod2 $DATASET_DIR/train_mod2.h5ad \ - --input_test_mod1 $DATASET_DIR/test_mod1.h5ad \ - --output $DATASET_DIR/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/bmmc_cite_starter/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/bmmc_cite_starter/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/bmmc_cite_starter/test_mod1.h5ad \ + --output $OUTPUT_DIR/bmmc_cite_starter/prediction.h5ad From 3bc00f624122619eeacb681efc42e5ac47bfd8a8 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 6 Dec 2023 13:45:08 +0100 Subject: [PATCH 1067/1233] Fix website issues (#294) * store %cpu as numeric * update nf trace conversion * Update get_results to r script Co-authored-by: Robrecht Cannoodt * fix metrics info double listing * update bat_int task_info * rename metric_ids * #237 --------- Co-authored-by: Robrecht Cannoodt Co-authored-by: Robrecht Cannoodt Former-commit-id: fea5797c0f86d2ce18fec014ddff1aa17c916e7c --- src/common/get_metric_info/script.R | 6 + src/common/get_results/config.vsh.yaml | 21 +- src/common/get_results/script.R | 66 +++++ src/common/get_results/script.py | 246 ------------------ src/common/workflows/transform_meta/main.nf | 3 - .../transform_meta/run_nf_tower_test.sh | 12 +- .../workflows/transform_meta/run_test.sh | 5 +- .../batch_integration/api/task_info.yaml | 3 +- .../metrics/lisi/config.vsh.yaml | 1 + .../batch_integration/metrics/lisi/script.py | 2 +- .../workflows/run_benchmark/config.vsh.yaml | 1 - .../workflows/run_benchmark/main.nf | 1 - 12 files changed, 91 insertions(+), 276 deletions(-) create mode 100644 src/common/get_results/script.R delete mode 100644 src/common/get_results/script.py diff --git a/src/common/get_metric_info/script.R b/src/common/get_metric_info/script.R index 970604fc88..9ab6e34b1c 100644 --- a/src/common/get_metric_info/script.R +++ b/src/common/get_metric_info/script.R @@ -26,6 +26,12 @@ df <- map_df(configs, function(config) { metric_name = label, metric_summary = description, paper_reference = reference, + ) %>% + group_by(across(-paper_reference) + ) %>% + summarise( + paper_reference = paste(paper_reference, collapse = ", "), + .groups = "drop" ) jsonlite::write_json( diff --git a/src/common/get_results/config.vsh.yaml b/src/common/get_results/config.vsh.yaml index d9546c766c..711ce51c3c 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/get_results/config.vsh.yaml @@ -11,29 +11,20 @@ functionality: type: "file" example: resources/label_projection/benchmarks/openproblems_v1/trace.txt description: "Nextflow log file" - - name: "--methods_meta" - type: "file" - example: meta_methods.json - description: "File containing methods metadata" - - name: "--metrics_meta" - type: "file" - example: meta_metrics.json - description: "File containing metrics metadata" - - name: "--task_id" - type: "string" - example: "label_projection" - description: "Task id" - name: "--output" type: "file" direction: "output" default: "output.json" description: "Output json" resources: - - type: python_script - path: script.py + - type: r_script + path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [tidyverse, dynutils] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/get_results/script.R b/src/common/get_results/script.R new file mode 100644 index 0000000000..af0695e972 --- /dev/null +++ b/src/common/get_results/script.R @@ -0,0 +1,66 @@ +library(tidyverse) +library(rlang) + +## VIASH START +par <- list( + input_scores = "output/v2/batch_integration/scores.yaml", + input_execution = "output/v2/batch_integration/trace.txt", + output = "test.json" +) +## VIASH END + +# read scores +raw_scores <- yaml::yaml.load_file(par$input_scores) +score_df <- as_tibble(map_df(raw_scores, as.data.frame)) + +scores <- score_df %>% + complete(dataset_id, method_id, metric_ids, fill = list(metric_values = NA_real_), normalization_id) %>% + group_by(metric_ids, dataset_id) %>% + mutate( + scaled_score = dynutils::scale_minmax(metric_values) %|% 0 + ) %>% + group_by(dataset_id, method_id) %>% + summarise( + metric_values = list(as.list(setNames(metric_values, metric_ids))), + scaled_scores = list(as.list(setNames(scaled_score, metric_ids))), + mean_score = mean(scaled_score), + .groups = "drop" + ) + +# read nxf log +nxf_log <- read_tsv(par$input_execution) %>% + mutate( + id = name, + process_id = gsub(".*:(.*)_process.*", "\\1", id), + method_id = gsub(".*\\.([^)]*)\\)", "\\1", id) + ) %>% + filter(process_id == method_id) + + +# process execution info +execution_info <- nxf_log %>% + rowwise() %>% + transmute( + dataset_id = gsub(".*\\(([^/]*)\\/.*", "\\1", id), + normalization_id = gsub(".*\\/([^.]*)\\..*", "\\1", id), + method_id, + resources = list(list( + exit_code = exit, + duration_sec = as.numeric(lubridate::duration(toupper(realtime))), + cpu_pct = as.numeric(gsub("%", "", `%cpu`)), + peak_memory_mb = as.numeric(gsub(" *GB", "", peak_vmem)) * 1024, + disk_read_mb = as.numeric(gsub(" *MB", "", rchar)), + disk_write_mb = as.numeric(gsub(" *MB", "", wchar)) + )) + ) %>% + ungroup() + +df <- full_join(scores, execution_info, by = c("method_id", "dataset_id")) %>% + filter(!is.na(mean_score)) + +jsonlite::write_json( + purrr::transpose(df), + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file diff --git a/src/common/get_results/script.py b/src/common/get_results/script.py deleted file mode 100644 index 6216ad4f09..0000000000 --- a/src/common/get_results/script.py +++ /dev/null @@ -1,246 +0,0 @@ -import yaml -import json -from pandas import read_csv -from datetime import timedelta -import re -import numpy as np - -## VIASH START - -par = { - 'input_scores': 'output/v2/batch_integration/output.run_benchmark.output_scores.yaml', - 'input_execution': 'output/v2/batch_integration/trace.txt', - 'methods_meta': 'output/get_info/method_info.json', - 'metrics_meta': 'output/get_info/metric_info.json', - 'task_id': 'batch_integration', - 'output': 'output/temp/results.json' -} - -meta = { -} - -## VIASH END - -def load_meta (meta_file): - ''' - Load the meta information - ''' - with open(meta_file, 'r') as f: - meta = json.load(f) - return meta - -def get_info (id, type,meta_info): - ''' - Get the information of the method or metric - ''' - key = type + "_id" - for info in meta_info: - if info.get(key) == id: - return info - -def fix_values_scaled(metric_result): - for i, value in enumerate(metric_result): - if np.isnan(value): - metric_result[i] = 0.0 - return metric_result - -def fix_nan_scaled(metrics): - for metric in metrics: - if np.isnan(metrics[metric]) or np.isinf(metrics[metric]): - metrics[metric] = 0 - - return metrics - -def fix_nan (metrics): - for metric in metrics: - if np.isnan(metrics[metric]): - metrics[metric] = "NaN" - elif np.isneginf(metrics[metric]): - metrics[metric] = "-Inf" - elif np.isinf(metrics[metric]): - metrics[metric] = "Inf" - - return metrics - -def organise_score (scores): - ''' - combine all the metric values into one dictionary per method, dataset and normalization - ''' - score_temp = {} - for score in scores: - score_id = score["dataset_id"] + "_" + score["method_id"] + "_" + score["normalization_id"] - - if score.get("metric_values") is None: - score["metric_values"] = [None] * len(score["metric_ids"]) - # for i, value in enumerate(score["metric_values"]): - # if np.isnan(value): - # score["metric_values"][i] = None - comb_metric = zip(score["metric_ids"], score["metric_values"]) - score["metric_values"] = dict(comb_metric) - score["task_id"] = par["task_id"] - del score["metric_ids"] - if score_temp.get(score_id) is None: - score_temp[score_id] = score - else: - score_temp[score_id]["metric_values"].update(score["metric_values"]) - - return score_temp - -def normalize_scores (scores, method_info, metric_info): - """ - Normalize the scores - """ - - metric_names=list(set([metric["metric_id"] for metric in metric_info])) - - baseline_methods = [method["method_id"] for method in method_info if method["is_baseline"] ] - metric_not_maximize = [metric["metric_id"] for metric in metric_info if not metric["maximize"]] - per_dataset = {} - for id, score in scores.items(): - if per_dataset.get(score["dataset_id"]) is None: - per_dataset[score["dataset_id"]] = [] - - per_dataset[score["dataset_id"]].append(score) - - for id, dataset_results in per_dataset.items(): - for result in dataset_results: - result["scaled_scores"] = result["metric_values"].copy() - - for metric_name in metric_names: - metric_values = [] - baseline_values = [] - for result in dataset_results: - if metric_name in result["metric_values"]: - metric_values.append(result["metric_values"][metric_name]) - else: - result["metric_values"][metric_name]= float("nan") - metric_values.append(0.0) - if result["method_id"] in baseline_methods: - if metric_name in result["metric_values"]: - baseline_values.append(result["metric_values"][metric_name]) - - baseline_values = fix_values_scaled(baseline_values) - baseline_values = np.array(baseline_values) - baseline_min = np.nanmin(baseline_values) - baseline_range = np.nanmax(baseline_values) - baseline_min - metric_values = np.array(metric_values) - metric_values -= baseline_min - metric_values /= np.where(baseline_range != 0, baseline_range, 1) - - if metric_name in metric_not_maximize: - metric_values = 1 - metric_values - for result, score in zip(dataset_results,metric_values): - result["scaled_scores"][metric_name] = score - - return per_dataset - -def convert_size (df, col): - ''' - Convert the size to MB and to float type - ''' - mask_kb = df[col].str.contains("KB") - mask_mb = df[col].str.contains("MB") - mask_gb = df[col].str.contains("GB") - if mask_kb.any(): - df.loc[mask_kb, col] = df.loc[mask_kb, col].str.replace(" KB", "").astype(float)/1024 - - if mask_mb.any(): - df.loc[mask_mb, col] = df.loc[mask_mb, col].str.replace(" MB", "").astype(float) - - - if mask_gb.any(): - df.loc[mask_gb, col] = df.loc[mask_gb, col].str.replace(" GB", "").astype(float)*1024 - return df - -def convert_duration(duration_str): - ''' - Convert the duration to seconds - ''' - components = duration_str.split(" ") - hours = 0 - minutes = 0 - seconds = 0 - for component in components: - milliseconds = 0 - for component in components: - if "h" in component: - hours = int(component[:-1]) - elif "ms" in component: - milliseconds = float(component[:-2]) - elif "m" in component: - minutes = int(component[:-1]) - elif "s" in component: - seconds = float(component[:-1]) - duration = timedelta(hours=hours, minutes=minutes, seconds=seconds).total_seconds() - return duration - -def join_trace (traces, result): - ''' - Join the Seqera (nextflow) trace with the scores - ''' - trace_dict = {} - for trace in traces: - id = trace["name"] - dataset_id = None - method_id = None - match = re.search(r'\((.*?)\)', id) - id_split = id.split(":") - if len(id_split)>4: - method_id = id_split[4] - if match: - group = match.group(1) - split_group = group.split(".") - if len(split_group)>1: - dataset_id = split_group[0] - if dataset_id is not None and method_id is not None: - dict_id = method_id + "_" + dataset_id - trace_dict[dict_id] = { - "duration_sec": trace["realtime"], - "cpu_pct": trace["%cpu"], - "peak_memory_mb": trace["peak_vmem"], - "disk_read_mb": trace["rchar"], - "disk_write_mb": trace["wchar"] - } - for score in result: - search_id = result[score]["method_id"] + "_" + result[score]["dataset_id"]+ "/" + result[score]["normalization_id"] - if search_id in trace_dict: - result[score]["resources"] = trace_dict[search_id] - return result - -print('Loading inputs', flush=True) -with open(par['input_scores'], 'r') as f: - scores = yaml.safe_load(f) -execution = read_csv(par['input_execution'], sep='\t') -method_info = load_meta(par['methods_meta']) -metric_info = load_meta(par['metrics_meta']) - -print('Organising scores', flush=True) -org_scores = organise_score(scores) - -print('Cleaning execution trace', flush=True) -execution = convert_size(execution, "rchar") -execution = convert_size(execution, "wchar") -execution = convert_size(execution, "peak_vmem") -execution["%cpu"].replace("%", "", regex=True, inplace=True) -execution["realtime"] = execution["realtime"].apply(convert_duration) - -print('Joining traces and scores', flush=True) -traces = execution.to_dict(orient="records") -org_scores = join_trace(traces, org_scores) - -print('Normalizing scores', flush=True) -org_scores = normalize_scores(org_scores, method_info, metric_info) -# fix NaN en inf -for dataset in org_scores.values(): - for scores in dataset: - scores["metric_values"] = fix_nan(scores["metric_values"]) - scores["scaled_scores"] = fix_nan_scaled(scores["scaled_scores"]) - scores["mean_score"] = np.array(list(scores["scaled_scores"].values())).mean() - -print('Writing results', flush=True) -result = [org_scores[id] for id in org_scores] - -result = list(np.concatenate(result).flat) - -with open (par['output'], 'w') as f: - json.dump(result, f, indent=4) \ No newline at end of file diff --git a/src/common/workflows/transform_meta/main.nf b/src/common/workflows/transform_meta/main.nf index 39d99a0546..13bd00b552 100644 --- a/src/common/workflows/transform_meta/main.nf +++ b/src/common/workflows/transform_meta/main.nf @@ -60,9 +60,6 @@ workflow run_wf { fromState: [ "input_scores": "input_scores", "input_execution" : "input_execution", - "methods_meta": "output_method", - "metrics_meta": "output_metric", - "task_id" : "task_id", "output": "output_scores" ], toState: { id, output, state -> diff --git a/src/common/workflows/transform_meta/run_nf_tower_test.sh b/src/common/workflows/transform_meta/run_nf_tower_test.sh index c333630d22..835ccbbfe2 100644 --- a/src/common/workflows/transform_meta/run_nf_tower_test.sh +++ b/src/common/workflows/transform_meta/run_nf_tower_test.sh @@ -5,12 +5,12 @@ DATASETS_DIR="s3://openproblems-nextflow/output/v2/batch_integration" # try running on nf tower cat > /tmp/params.yaml << HERE id: batch_integration_transform -input_scores: "$DATASETS_DIR/output.run_benchmark.output_scores.yaml" -input_dataset_info: "$DATASETS_DIR/output.run_benchmark.output_dataset_info.yaml" -input_method_configs: "$DATASETS_DIR/output.run_benchmark.output_method_configs.yaml" -input_metric_configs: "$DATASETS_DIR/output.run_benchmark.output_metric_configs.yaml" +input_scores: "$DATASETS_DIR/scores.yaml" +input_dataset_info: "$DATASETS_DIR/dataset_info.yaml" +input_method_configs: "$DATASETS_DIR/method_configs.yaml" +input_metric_configs: "$DATASETS_DIR/metric_configs.yaml" input_execution: "$DATASETS_DIR/trace.txt" -input_task_info: "$DATASETS_DIR/output.run_benchmark.task_info.yaml" +input_task_info: "$DATASETS_DIR/task_info.yaml" task_id: "batch_integration" output_scores: "results.json" output_method_info: "method_info.json" @@ -29,7 +29,7 @@ process { HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision integration_build \ + --revision main_build \ --pull-latest \ --main-script target/nextflow/common/workflows/transform_meta/main.nf \ --workspace 53907369739130 \ diff --git a/src/common/workflows/transform_meta/run_test.sh b/src/common/workflows/transform_meta/run_test.sh index e3f6d4d30a..adf169cc1b 100644 --- a/src/common/workflows/transform_meta/run_test.sh +++ b/src/common/workflows/transform_meta/run_test.sh @@ -10,8 +10,8 @@ set -e # export TOWER_WORKSPACE_ID=53907369739130 -DATASETS_DIR="output/temp" -OUTPUT_DIR="output/get_info" +DATASETS_DIR="output/v2/batch_integration" +OUTPUT_DIR="/home/kai/Documents/openroblems/website/results/batch_integration_feature/data" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" @@ -23,6 +23,7 @@ nextflow run . \ -main-script target/nextflow/common/workflows/transform_meta/main.nf \ -profile docker \ -resume \ + -c src/wf_utils/labels_ci.config \ --id "get_results_test" \ --input_scores "$DATASETS_DIR/scores.yaml" \ --input_dataset_info "$DATASETS_DIR/dataset_info.yaml" \ diff --git a/src/tasks/batch_integration/api/task_info.yaml b/src/tasks/batch_integration/api/task_info.yaml index e76b641d5e..bc3a575029 100644 --- a/src/tasks/batch_integration/api/task_info.yaml +++ b/src/tasks/batch_integration/api/task_info.yaml @@ -19,7 +19,7 @@ description: | As input, methods require either normalised or unnormalised data with multiple batches and consistent cell type labels. The batch integrated output can be a feature matrix, a low dimensional embedding and/or a neighbourhood graph. The respective batch-integrated representation is then evaluated using sets of metrics that capture how well batch effects are removed and whether biological variance is conserved. - We have based this particular task on the latest, and most extensive benchmark of single-cell data integration methods [@luecken2022benchmarking]. + We have based this particular task on the latest, and most extensive benchmark of single-cell data integration methods. authors: - name: Michaela Mueller roles: [ maintainer, author ] @@ -29,6 +29,7 @@ authors: roles: [ contributor ] info: github: KaiWaldrant + orcid: "0009-0003-8555-1361" - name: Robrecht Cannoodt roles: [ contributor ] info: diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index 66531afcbd..e957434bd9 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -1,6 +1,7 @@ # use metric api spec __merge__: ../../api/comp_metric_graph.yaml functionality: + status: disabled name: lisi info: metrics: diff --git a/src/tasks/batch_integration/metrics/lisi/script.py b/src/tasks/batch_integration/metrics/lisi/script.py index 129389bff9..bdc9ed4e1a 100644 --- a/src/tasks/batch_integration/metrics/lisi/script.py +++ b/src/tasks/batch_integration/metrics/lisi/script.py @@ -55,7 +55,7 @@ 'dataset_id': input_solution.uns['dataset_id'], 'normalization_id': input_solution.uns['normalization_id'], 'method_id': input_integrated.uns['method_id'], - 'metric_ids': [ 'ilisi_graph', 'clisi_graph' ], + 'metric_ids': [ 'ilisi', 'clisi' ], 'metric_values': [ ilisi, clisi ] } ) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 339c06eb4a..ab061ba07e 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -71,7 +71,6 @@ functionality: - name: batch_integration/metrics/isolated_label_asw - name: batch_integration/metrics/isolated_label_f1 - name: batch_integration/metrics/kbet - - name: batch_integration/metrics/lisi - name: batch_integration/metrics/pcr platforms: - type: nextflow diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index fa0798f534..629ffe2b3b 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -44,7 +44,6 @@ workflow run_wf { isolated_label_asw, isolated_label_f1, kbet, - lisi, pcr ] From 3515a8a76c783c1fbbc5a6cec66aa2b6bde4d8b4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 6 Dec 2023 13:46:55 +0100 Subject: [PATCH 1068/1233] set label projection sampling method to random for the pancreas test data Former-commit-id: 2089322a7a3c6059cdebffde5854b4f58e2a2333 --- src/tasks/label_projection/resources_test_scripts/pancreas.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index 5a69340510..76d38f4978 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -21,7 +21,7 @@ nextflow run . \ -entry auto \ --input_states "$RAW_DATA/**/state.yaml" \ --rename_keys 'input:output_dataset' \ - --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad", "method": "random"}' \ --publish_dir "$DATASET_DIR" \ --output_state '$id/state.yaml' # output_state should be moved to settings once workaround is solved From 0fbeedbfeef17e122c4beefe9414daed431bbf6a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 6 Dec 2023 15:08:41 +0100 Subject: [PATCH 1069/1233] remove unused code (#297) * remove unused code * remove nextflow config in root Former-commit-id: a84c731b07ec0cfeb218a471ff4c61bf9f88c81c --- nextflow.config | 8 - .../process_openproblems_v1/nextflow.config | 16 - .../nextflow.config | 16 - .../process_datasets/nextflow.config | 16 - .../workflows/run_benchmark/nextflow.config | 16 - .../process_datasets/nextflow.config | 16 - .../workflows/run_benchmark/nextflow.config | 16 - .../workflows/run_benchmark/nextflow.config | 16 - src/wf_utils/BenchmarkHelper.nf | 429 --- src/wf_utils/WorkflowHelper.nf | 2769 ----------------- 10 files changed, 3318 deletions(-) delete mode 100644 nextflow.config delete mode 100644 src/datasets/workflows/process_openproblems_v1/nextflow.config delete mode 100644 src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config delete mode 100644 src/tasks/batch_integration/workflows/process_datasets/nextflow.config delete mode 100644 src/tasks/batch_integration/workflows/run_benchmark/nextflow.config delete mode 100644 src/tasks/denoising/workflows/process_datasets/nextflow.config delete mode 100644 src/tasks/denoising/workflows/run_benchmark/nextflow.config delete mode 100644 src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config delete mode 100644 src/wf_utils/BenchmarkHelper.nf delete mode 100644 src/wf_utils/WorkflowHelper.nf diff --git a/nextflow.config b/nextflow.config deleted file mode 100644 index 0fb77d8756..0000000000 --- a/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -manifest { - nextflowVersion = '!>=20.12.1-edge' -} - -includeConfig("./src/wf_utils/ProfilesHelper.config") -includeConfig("./src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/nextflow.config b/src/datasets/workflows/process_openproblems_v1/nextflow.config deleted file mode 100644 index 7b8ddab87d..0000000000 --- a/src/datasets/workflows/process_openproblems_v1/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'datasets/workflows/process_openproblems_v1' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Fetch and process legacy OpenProblems v1 datasets' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config b/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config deleted file mode 100644 index c90cc0589c..0000000000 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'datasets/workflows/process_openproblems_v1_multimodal' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Fetch and process legacy OpenProblems v1 multimodal datasets' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/tasks/batch_integration/workflows/process_datasets/nextflow.config b/src/tasks/batch_integration/workflows/process_datasets/nextflow.config deleted file mode 100644 index 150119dfa2..0000000000 --- a/src/tasks/batch_integration/workflows/process_datasets/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'batch_integration/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Batch integration' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config b/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config deleted file mode 100644 index 150119dfa2..0000000000 --- a/src/tasks/batch_integration/workflows/run_benchmark/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'batch_integration/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Batch integration' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/tasks/denoising/workflows/process_datasets/nextflow.config b/src/tasks/denoising/workflows/process_datasets/nextflow.config deleted file mode 100644 index 150119dfa2..0000000000 --- a/src/tasks/denoising/workflows/process_datasets/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'batch_integration/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Batch integration' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/tasks/denoising/workflows/run_benchmark/nextflow.config b/src/tasks/denoising/workflows/run_benchmark/nextflow.config deleted file mode 100644 index 2e537df35c..0000000000 --- a/src/tasks/denoising/workflows/run_benchmark/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'denoising/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Denoising' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config b/src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config deleted file mode 100644 index eadd1bd660..0000000000 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/nextflow.config +++ /dev/null @@ -1,16 +0,0 @@ -manifest { - name = 'dimensionality_reduction/workflows/run' - mainScript = 'main.nf' - nextflowVersion = '!>=22.04.5' - description = 'Dimensionality reduction' -} - -params { - rootDir = java.nio.file.Paths.get("$projectDir/../../../../../").toAbsolutePath().normalize().toString() -} - -// include common settings -includeConfig("${params.rootDir}/src/wf_utils/ProfilesHelper.config") -includeConfig("${params.rootDir}/src/wf_utils/labels.config") - -process.errorStrategy = 'ignore' diff --git a/src/wf_utils/BenchmarkHelper.nf b/src/wf_utils/BenchmarkHelper.nf deleted file mode 100644 index 57aefdbdd2..0000000000 --- a/src/wf_utils/BenchmarkHelper.nf +++ /dev/null @@ -1,429 +0,0 @@ -def runComponents(Map args) { - assert args.components: "runComponents should be passed a list of components to run" - - def components_ = args.components - if (components_ !instanceof List) { - components_ = [ components_ ] - } - assert components_.size() > 0: "pass at least one component to runComponents" - - def fromState_ = args.fromState - def toState_ = args.toState - def filter_ = args.filter - def id_ = args.id - - workflow runComponentsWf { - take: input_ch - main: - - // generate one channel per method - out_chs = components_.collect{ comp_ -> - def comp_config = comp_.config - - filter_ch = filter_ - ? input_ch | filter{tup -> - filter_(tup[0], tup[1], comp_config) - } - : input_ch - id_ch = id_ - ? filter_ch | map{tup -> - // def new_id = id_(tup[0], tup[1], comp_config) - def new_id = tup[0] - if (id_ instanceof String) { - new_id = id_ - } else if (id_ instanceof Closure) { - new_id = id_(new_id, tup[1], comp_config) - } - [new_id] + tup.drop(1) - } - : filter_ch - data_ch = id_ch | map{tup -> - def new_data = tup[1] - if (fromState_ instanceof Map) { - new_data = fromState_.collectEntries{ key0, key1 -> - [key0, new_data[key1]] - } - } else if (fromState_ instanceof List) { - new_data = fromState_.collectEntries{ key -> - [key, new_data[key]] - } - } else if (fromState_ instanceof Closure) { - new_data = fromState_(tup[0], new_data, comp_config) - } - tup.take(1) + [new_data] + tup.drop(1) - } - out_ch = data_ch - | comp_.run( - auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] - ) - post_ch = toState_ - ? out_ch | map{tup -> - def output = tup[1] - def old_state = tup[2] - if (toState_ instanceof Map) { - new_state = old_state + toState_.collectEntries{ key0, key1 -> - [key0, output[key1]] - } - } else if (toState_ instanceof List) { - new_state = old_state + toState_.collectEntries{ key -> - [key, output[key]] - } - } else if (toState_ instanceof Closure) { - new_state = toState_(tup[0], output, old_state, comp_config) - } - [tup[0], new_state] + tup.drop(3) - } - : out_ch - - post_ch - } - - // mix all results - output_ch = - (out_chs.size == 1) - ? out_chs[0] - : out_chs[0].mix(*out_chs.drop(1)) - - emit: output_ch - } - - return runComponentsWf -} - -def joinStates(Closure apply_) { - workflow joinStatesWf { - take: input_ch - main: - output_ch = input_ch - | toSortedList - | filter{ it.size() > 0 } - | map{ tups -> - def ids = tups.collect{it[0]} - def states = tups.collect{it[1]} - apply_(ids, states) - } - - emit: output_ch - } - return joinStatesWf -} - - -class CustomTraceObserver implements nextflow.trace.TraceObserver { - List traces - - CustomTraceObserver(List traces) { - this.traces = traces - } - - @Override - void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } - - @Override - void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } -} - -def initializeTracer() { - def traces = Collections.synchronizedList([]) - - // add custom trace observer which stores traces in the traces object - session.observers.add(new CustomTraceObserver(traces)) - - traces -} - -def writeJson(data, file) { - assert data: "writeJson: data should not be null" - assert file: "writeJson: file should not be null" - file.write(groovy.json.JsonOutput.toJson(data)) -} - -import org.yaml.snakeyaml.DumperOptions -import org.yaml.snakeyaml.Yaml -import org.yaml.snakeyaml.nodes.Node -import org.yaml.snakeyaml.nodes.Tag -import org.yaml.snakeyaml.representer.Representer -import org.yaml.snakeyaml.representer.Represent - - - -// Custom representer to modify how certain objects are represented in YAML -class CustomRepresenter extends Representer { - class RepresentFile implements Represent { - public Node representData(Object data) { - Path file = (Path) data; - String value = file.getFileName(); - Tag tag = new Tag("!file"); - return representScalar(tag, value); - } - } - CustomRepresenter(DumperOptions options) { - super(options) - this.representers.put(File, new RepresentFile()) - } -} - -String toTaggedYamlBlob(Map data) { - def options = new DumperOptions() - options.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK) - def representer = new CustomRepresenter(options) - def yaml = new Yaml(representer, options) - return yaml.dump(data) -} - - -import org.yaml.snakeyaml.TypeDescription -import org.yaml.snakeyaml.constructor.AbstractConstruct -import org.yaml.snakeyaml.constructor.Constructor - -// Custom constructor to modify how certain objects are parsed from YAML -class CustomConstructor extends Constructor { - Path root - - class ConstructFile extends AbstractConstruct { - public Object construct(Node node) { - String filename = (String) constructScalar(node); - if (root != null) { - return root.resolve(filename); - } - return java.nio.file.Paths.get(filename); - } - } - - CustomConstructor(Path root = null) { - super() - this.root = root - // Handling !file tag and parse it back to a File type - this.yamlConstructors.put(new Tag("!file"), new ConstructFile()) - } -} - -def readTaggedYaml(Path path) { - Constructor constructor = new CustomConstructor(path.getParent()) - Yaml yaml = new Yaml(constructor) - return yaml.load(path.text) -} - -def getPublishDir() { - return params.containsKey("publish_dir") ? params.publish_dir : - params.containsKey("publishDir") ? params.publishDir : - null -} - -process publishStatesProc { - // todo: check publishpath? - publishDir path: "${getPublishDir()}/${id}/", mode: "copy" - tag "$id" - input: - tuple val(id), val(yamlBlob), path(inputFiles) - output: - tuple val(id), path{["state.yaml"] + inputFiles} - script: - """ - echo '${yamlBlob}' > state.yaml - """ -} - -def collectFiles(obj) { - if (obj instanceof java.io.File || obj instanceof Path) { - return [obj] - } else if (obj instanceof List && obj !instanceof String) { - return obj.collectMany{item -> - collectFiles(item) - } - } else if (obj instanceof Map) { - return obj.collectMany{key, item -> - collectFiles(item) - } - } else { - return [] - } -} - - -def iterateMap(obj, fun) { - if (obj instanceof List && obj !instanceof String) { - return obj.collect{item -> - iterateMap(item, fun) - } - } else if (obj instanceof Map) { - return obj.collectEntries{key, item -> - [key.toString(), iterateMap(item, fun)] - } - } else { - return fun(obj) - } -} - -def convertPathsToFile(obj) { - iterateMap(obj, {x -> - if (x instanceof File) { - return x - } else if (x instanceof Path) { - return x.toFile() - } else { - return x - } - }) -} -def convertFilesToPath(obj) { - iterateMap(obj, {x -> - if (x instanceof Path) { - return x - } else if (x instanceof File) { - return x.toPath() - } else { - return x - } - }) -} - -def publishStates(Map args) { - workflow publishStatesWf { - take: input_ch - main: - input_ch - | map { tup -> - def id = tup[0] - def state = tup[1] - def files = collectFiles(state) - def yamlBlob = toTaggedYamlBlob([id: id] + state) - [id, yamlBlob, files] - } - | publishStatesProc - emit: input_ch - } - return publishStateWf -} - - -include { processConfig; helpMessage; channelFromParams; readYamlBlob } from "./WorkflowHelper.nf" - - -def findStates(Map params, Map config) { - // TODO: do a deep clone of config - def auto_config = config.clone() - auto_config.functionality = auto_config.functionality.clone() - // override arguments - auto_config.functionality.argument_groups = [] - auto_config.functionality.arguments = [ - [ - type: "string", - name: "--input_dir", - example: "/path/to/input/directory", - description: "Path to input directory containing the datasets to be integrated.", - required: true - ], - [ - type: "string", - name: "--filter", - example: "foo/.*/state.yaml", - description: "Regex to filter state files by path.", - required: false - ], - // to do: make this a yaml blob? - [ - type: "string", - name: "--rename_keys", - example: ["newKey1:oldKey1", "newKey2:oldKey2"], - description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", - required: false, - multiple: true, - multiple_sep: "," - ], - [ - type: "string", - name: "--settings", - example: '{"output_dataset": "dataset.h5ad", "k": 10}', - description: "Global arguments as a JSON glob to be passed to all components.", - required: false - ] - ] - - // run auto config through processConfig once more - auto_config = processConfig(auto_config) - - workflow findStatesWf { - helpMessage(auto_config) - - output_ch = - channelFromParams(params, auto_config) - | flatMap { autoId, args -> - - def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] - - // look for state files in input dir - def stateFiles = file("${args.input_dir}/**/state.yaml") - - // filter state files by regex - if (args.filter) { - stateFiles = stateFiles.findAll{ stateFile -> - def stateFileStr = stateFile.toString() - def matcher = stateFileStr =~ args.filter - matcher.matches()} - } - - // read in states - def states = stateFiles.collect { stateFile -> - def state_ = readTaggedYaml(stateFile) - [state_.id, state_] - } - - // construct renameMap - if (args.rename_keys) { - def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(":") - assert split.size() == 2: "Argument 'rename' should be of the form 'newKey:oldKey,newKey:oldKey'" - split - } - - // rename keys in state, only let states through which have all keys - // also add global settings - states = states.collectMany{id, state -> - def newState = [:] - - for (key in renameMap.keySet()) { - def origKey = renameMap[key] - if (!(state.containsKey(origKey))) { - return [] - } - newState[key] = state[origKey] - } - - [[id, globalSettings + newState]] - } - } - - states - } - emit: - output_ch - } - - return findStatesWf -} - -def setState(fun) { - workflow setStateWf { - take: input_ch - main: - output_ch = input_ch - | map { tup -> - def id = tup[0] - def state = tup[1] - def unfilteredState = fun(id, state) - def newState = unfilteredState.findAll{key, val -> val != null} - [id, newState] + tup.drop(2) - } - emit: output_ch - } - return setStateWf -} \ No newline at end of file diff --git a/src/wf_utils/WorkflowHelper.nf b/src/wf_utils/WorkflowHelper.nf deleted file mode 100644 index 6d79970d2d..0000000000 --- a/src/wf_utils/WorkflowHelper.nf +++ /dev/null @@ -1,2769 +0,0 @@ -//////////////////////////// -// VDSL3 helper functions // -//////////////////////////// - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgument.nf' -def _processArgument(arg) { - arg.multiple = arg.multiple != null ? arg.multiple : false - arg.required = arg.required != null ? arg.required : false - arg.direction = arg.direction != null ? arg.direction : "input" - arg.multiple_sep = arg.multiple_sep != null ? arg.multiple_sep : ":" - arg.plainName = arg.name.replaceAll("^-*", "") - - if (arg.type == "file") { - arg.must_exist = arg.must_exist != null ? arg.must_exist : true - arg.create_parent = arg.create_parent != null ? arg.create_parent : true - } - - // add default values to output files which haven't already got a default - if (arg.type == "file" && arg.direction == "output" && arg.default == null) { - def mult = arg.multiple ? "_*" : "" - def extSearch = "" - if (arg.default != null) { - extSearch = arg.default - } else if (arg.example != null) { - extSearch = arg.example - } - if (extSearch instanceof List) { - extSearch = extSearch[0] - } - def extSearchResult = extSearch.find("\\.[^\\.]+\$") - def ext = extSearchResult != null ? extSearchResult : "" - arg.default = "\$id.\$key.${arg.plainName}${mult}${ext}" - if (arg.multiple) { - arg.default = [arg.default] - } - } - - if (!arg.multiple) { - if (arg.default != null && arg.default instanceof List) { - arg.default = arg.default[0] - } - if (arg.example != null && arg.example instanceof List) { - arg.example = arg.example[0] - } - } - - if (arg.type == "boolean_true") { - arg.default = false - } - if (arg.type == "boolean_false") { - arg.default = true - } - - arg -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/_processArgumentGroup.nf' -def _processArgumentGroup(argumentGroups, name, arguments) { - def argNamesInGroups = argumentGroups.collectMany{it.arguments.findAll{it instanceof String}}.toSet() - - // Check if 'arguments' is in 'argumentGroups'. - def argumentsNotInGroup = arguments.findAll{arg -> !(argNamesInGroups.contains(arg.plainName))} - - // Check whether an argument group of 'name' exists. - def existing = argumentGroups.find{gr -> name == gr.name} - - // if there are no arguments missing from the argument group, just return the existing group (if any) - if (argumentsNotInGroup.isEmpty()) { - return existing == null ? [] : [existing] - - // if there are missing arguments and there is an existing group, add the missing arguments to it - } else if (existing != null) { - def newEx = existing.clone() - newEx.arguments.addAll(argumentsNotInGroup.findAll{it !instanceof String}) - return [newEx] - - // else create a new group - } else { - def newEx = [name: name, arguments: argumentsNotInGroup.findAll{it !instanceof String}] - return [newEx] - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/arguments/processInputsOutputs.nf' -def typeCheck(String stage, Map par, Object value, String id, String key) { - // expectedClass will only be != null if value is not of the expected type - def expectedClass = null - - if (!par.required && value == null) { - expectedClass = null - } else if (par.multiple) { - if (value instanceof List) { - try { - value = value.collect { listVal -> - typeCheck(stage, par + [multiple: false], listVal, id, key) - } - } catch (Exception e) { - expectedClass = "List[${par.type}]" - } - } else { - expectedClass = "List[${par.type}]" - } - } else if (par.type == "string") { - if (value instanceof GString) { - value = value.toString() - } - expectedClass = value instanceof String ? null : "String" - } else if (par.type == "integer") { - expectedClass = value instanceof Integer ? null : "Integer" - } else if (par.type == "long") { - if (value instanceof Integer) { - value = value.toLong() - } - expectedClass = value instanceof Long ? null : "Long" - } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") { - expectedClass = value instanceof Boolean ? null : "Boolean" - } else if (par.type == "file") { - if (stage == "output" || par.direction == "input") { - if (value instanceof File) { - value = value.toPath() - } - expectedClass = value instanceof Path ? null : "Path" - } else { // stage == "input" && par.direction == "output" - if (value instanceof GString) { - value = value.toString() - } - expectedClass = value instanceof String ? null : "String" - } - } else { - expectedClass = par.type - } - - if (expectedClass != null) { - error "Error in module '${key}' id '${id}': ${stage} argument '${par.plainName}' has the wrong type. " + - "Expected type: ${expectedClass}. Found type: ${value.getClass()}" - } - - return value -} - -Map processInputs(Map inputs, Map config, String id, String key) { - if (!workflow.stubRun) { - config.functionality.allArguments.each { arg -> - if (arg.required) { - assert inputs.containsKey(arg.plainName) && inputs.get(arg.plainName) != null : - "Error in module '${key}' id '${id}': required input argument '${arg.plainName}' is missing" - } - } - - inputs = inputs.collectEntries { name, value -> - def par = config.functionality.allArguments.find { it.plainName == name && (it.direction == "input" || it.type == "file") } - assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid input argument" - - value = typeCheck("input", par, value, id, key) - - [ name, value ] - } - } - return inputs -} - -Map processOutputs(Map outputs, Map config, String id, String key) { - if (!workflow.stubRun) { - config.functionality.allArguments.each { arg -> - if (arg.direction == "output" && arg.required) { - assert outputs.containsKey(arg.plainName) && outputs.get(arg.plainName) != null : - "Error in module '${key}' id '${id}': required output argument '${arg.plainName}' is missing" - } - } - - outputs = outputs.collectEntries { name, value -> - def par = config.functionality.allArguments.find { it.plainName == name && it.direction == "output" } - assert par != null : "Error in module '${key}' id '${id}': '${name}' is not a valid output argument" - - value = typeCheck("output", par, value, id, key) - - [ name, value ] - } - } - return outputs -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/IDChecker.nf' -class IDChecker { - final def items = [] as Set - - @groovy.transform.WithWriteLock - boolean observe(String item) { - if (items.contains(item)) { - return false - } else { - items << item - return true - } - } - - @groovy.transform.WithReadLock - boolean contains(String item) { - return items.contains(item) - } - - @groovy.transform.WithReadLock - Set getItems() { - return items.clone() - } -} -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_checkUniqueIds.nf' - -/** - * Check if the ids are unique across parameter sets - * - * @param parameterSets a list of parameter sets. - */ -private void _checkUniqueIds(List>> parameterSets) { - def ppIds = parameterSets.collect{it[0]} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_getChild.nf' - -// helper functions for reading params from file // -def _getChild(parent, child) { - if (child.contains("://") || java.nio.file.Paths.get(child).isAbsolute()) { - child - } else { - def parentAbsolute = java.nio.file.Paths.get(parent).toAbsolutePath().toString() - parentAbsolute.replaceAll('/[^/]*$', "/") + child - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_guessParamListFormat.nf' - -def _guessParamListFormat(params) { - if (!params.containsKey("param_list") || params.param_list == null) { - "none" - } else { - def param_list = params.param_list - - if (param_list !instanceof String) { - "asis" - } else if (param_list.endsWith(".csv")) { - "csv" - } else if (param_list.endsWith(".json") || param_list.endsWith(".jsn")) { - "json" - } else if (param_list.endsWith(".yaml") || param_list.endsWith(".yml")) { - "yaml" - } else { - "yaml_blob" - } - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/_splitParams.nf' -/** - * Split parameters for arguments that accept multiple values using their separator - * - * @param paramList A Map containing parameters to split. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A Map of parameters where the parameter values have been split into a list using - * their seperator. - */ -Map _splitParams(Map parValues, Map config){ - def parsedParamValues = parValues.collectEntries { parName, parValue -> - def parameterSettings = config.functionality.allArguments.find({it.plainName == parName}) - - if (!parameterSettings) { - // if argument is not found, do not alter - return [parName, parValue] - } - if (parameterSettings.multiple) { // Check if parameter can accept multiple values - if (parValue instanceof Collection) { - parValue = parValue.collect{it instanceof String ? it.split(parameterSettings.multiple_sep) : it } - } else if (parValue instanceof String) { - parValue = parValue.split(parameterSettings.multiple_sep) - } else if (parValue == null) { - parValue = [] - } else { - parValue = [ parValue ] - } - parValue = parValue.flatten() - } - // For all parameters check if multiple values are only passed for - // arguments that allow it. Quietly simplify lists of length 1. - if (!parameterSettings.multiple && parValue instanceof Collection) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] - } - [parName, parValue] - } - return parsedParamValues -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/applyConfig.nf' - -/** - * Apply the argument settings specified in a Viash config to a list of parameter sets. - * - Split the parameter values according to their seperator if - * the parameter accepts multiple values - * - Cast the parameters to their corect types. - * - Assertions: - * ~ Check if any unknown parameters are found - * ~ Check if the ID of the parameter set is unique across all sets. - * - * @return The input parameters that have been processed. - */ - -List applyConfig(List parameterSets, Map config){ - def processedparameterSets = parameterSets.collect({ parameterSet -> - def id = parameterSet[0] - def paramValues = parameterSet[1] - def passthrough = parameterSet.drop(2) - def processedSet = applyConfigToOneParameterSet(paramValues, config) - [id, processedSet] + passthrough - }) - - _checkUniqueIds(processedparameterSets) - return processedparameterSets -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/applyConfigToOneParameterSet.nf' -/** - * Cast parameters to the correct type as defined in the Viash config - * - * @param parValues A Map of input arguments. - * - * @return The input arguments that have been cast to the type from the viash config. - */ -private Map _castParamTypes(Map parValues, Map config) { - // Cast the input to the correct type according to viash config - def castParValues = parValues.collectEntries({ parName, parValue -> - def paramSettings = config.functionality.allArguments.find({it.plainName == parName}) - // dont parse parameters like publish_dir ( in which case paramSettings = null) - def parType = paramSettings ? paramSettings.get("type", null) : null - - // turn parValue into a list, if it isn't one already - if (parValue !instanceof Collection) { - parValue = [parValue] - } - - if (parType == "file" && paramSettings.get("direction", "input") == "input") { - parValue = parValue.collectMany{ parValueItem -> - if (parValueItem instanceof String) { - parValueItem = file(parValueItem) - } - if (parValueItem !instanceof Collection) { - parValueItem = [parValueItem] - } - parValueItem - } - // cast Paths to File? Or vice versa? - // parValue = parValue.collect{ - // if (path instanceof Path) { - // [path.toFile()] - // } else { - // [path] - // } - // } - } else if (parType == "integer") { - parValue = parValue.collect{it as Integer} - } else if (parType == "double") { - parValue = parValue.collect{it as Double} - } else if (parType == "boolean" || - parType == "boolean_true" || - parType == "boolean_false") { - parValue = parValue.collect{it as Boolean} - } - - // simplify list to value if need be - if (paramSettings && !paramSettings.multiple) { - assert parValue.size() == 1 : - "Error: argument ${parName} has too many values.\n" + - " Expected amount: 1. Found: ${parValue.size()}" - parValue = parValue[0] - } - - [parName, parValue] - }) - return castParValues -} - -/** - * Apply the argument settings specified in a Viash config to a single parameter set. - * - Split the parameter values according to their seperator if - * the parameter accepts multiple values - * - Cast the parameters to their corect types. - * - Assertions: - * ~ Check if any unknown parameters are found - * - * @param paramValues A Map of parameter to be processed. All parameters must - * also be specified in the Viash config. - * @param config: A Map of the Viash configuration. This Map can be generated from - * the config file using the readConfig() function. - * @return The input parameters that have been processed. - */ -Map applyConfigToOneParameterSet(Map paramValues, Map config){ - def splitParamValues = _splitParams(paramValues, config) - def castParamValues = _castParamTypes(splitParamValues, config) - - // Check if any unexpected arguments were passed - def knownParams = config.functionality.allArguments.collect({it.plainName}) + ["publishDir", "publish_dir"] - castParamValues.each({parName, parValue -> - assert parName in knownParams: "Unknown parameter. Parameter $parName should be in $knownParams" - }) - return castParamValues -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/channelFromParams.nf' -/** - * Resolve the file paths in the parameters relative to given path - * - * @param paramList A Map containing parameters to process. - * This function assumes that files are still of type String. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * @param relativeTo path of a file to resolve the parameters values to. - * - * @return A map of parameters where the location of the input file parameters have been resolved - * resolved relatively to the provided path. - */ -private Map _resolvePathsRelativeTo(Map paramList, Map config, String relativeTo) { - paramList.collectEntries { parName, parValue -> - argSettings = config.functionality.allArguments.find{it.plainName == parName} - if (argSettings && argSettings.type == "file" && argSettings.direction == "input") { - if (parValue instanceof Collection) { - parValue = parValue.collect({path -> - path !instanceof String ? path : file(_getChild(relativeTo, path)) - }) - } else { - parValue = parValue !instanceof String ? path : file(_getChild(relativeTo, parValue)) - } - } - [parName, parValue] - } -} - -/** - * Parse nextflow parameters based on settings defined in a viash config - * and return a nextflow channel. - * - * @param params Input parameters from nextflow. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A list of parameter sets that were parsed from the 'param_list' argument value. - */ -private List> _parseParamListArguments(Map params, Map config){ - // first try to guess the format (if not set in params) - def paramListFormat = _guessParamListFormat(params) - - // get the correct parser function for the detected params_list format - def paramListParsers = [ - "csv": {[it, readCsv(it)]}, - "json": {[it, readJson(it)]}, - "yaml": {[it, readYaml(it)]}, - "yaml_blob": {[null, readYamlBlob(it)]}, - "asis": {[null, it]}, - "none": {[null, [[:]]]} - ] - assert paramListParsers.containsKey(paramListFormat): - "Format of provided --param_list not recognised.\n" + - "You can use '--param_list_format' to manually specify the format.\n" + - "Found: '$paramListFormat'. Expected: one of 'csv', 'json', "+ - "'yaml', 'yaml_blob', 'asis' or 'none'" - def paramListParser = paramListParsers.get(paramListFormat) - - // fetch multi param inputs - def paramListOut = paramListParser(params.containsKey("param_list") ? params.param_list : "") - // multiFile is null if the value passed to param_list was not a file (e.g a blob) - // If the value was indeed a file, multiFile contains the location that file (used later). - def paramListFile = paramListOut[0] - def paramSets = paramListOut[1] // these are the actual parameters from reading the blob/file - - // data checks - assert paramSets instanceof List: "--param_list should contain a list of maps" - for (value in paramSets) { - assert value instanceof Map: "--param_list should contain a list of maps" - } - - // id is argument - def idIsArgument = config.functionality.allArguments.find({it.plainName == "id"}) != null - - // Reformat from List to List> by adding the ID as first element of a Tuple2 - paramSets = paramSets.collect({ paramValues -> - def paramId = paramValues.id - if (!idIsArgument) { - paramValues = paramValues.findAll{k, v -> k != "id"} - } - [paramId, paramValues] - }) - - // Split parameters with 'multiple: true' - paramSets = paramSets.collect({ id, paramValues -> - def splitParamValues = _splitParams(paramValues, config) - [id, splitParamValues] - }) - - // The paths of input files inside a param_list file may have been specified relatively to the - // location of the param_list file. These paths must be made absolute. - if (paramListFile){ - paramSets = paramSets.collect({ id, paramValues -> - def relativeParamValues = _resolvePathsRelativeTo(paramValues, config, paramListFile) - [id, relativeParamValues] - }) - } - - return paramSets -} - -/** - * Parse nextflow parameters based on settings defined in a viash config. - * Return a list of parameter sets, each parameter set corresponding to - * an event in a nextflow channel. The output from this function can be used - * with Channel.fromList to create a nextflow channel with Vdsl3 formatted - * events. - * - * This function performs: - * - A filtering of the params which can be found in the config file. - * - Process the params_list argument which allows a user to to initialise - * a Vsdl3 channel with multiple parameter sets. Possible formats are - * csv, json, yaml, or simply a yaml_blob. A csv should have column names - * which correspond to the different arguments of this pipeline. A json or a yaml - * file should be a list of maps, each of which has keys corresponding to the - * arguments of the pipeline. A yaml blob can also be passed directly as a parameter. - * When passing a csv, json or yaml, relative path names are relativized to the - * location of the parameter file. - * - Combine the parameter sets into a vdsl3 Channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A list of parameters with the first element of the event being - * the event ID and the second element containing a map of the parsed parameters. - */ - -private List>> _paramsToParamSets(Map params, Map config){ - /* parse regular parameters (not in param_list) */ - /*************************************************/ - def globalParams = config.functionality.allArguments - .findAll { params.containsKey(it.plainName) } - .collectEntries { [ it.plainName, params[it.plainName] ] } - def globalID = params.get("id", null) - def globalParamsValues = applyConfigToOneParameterSet(globalParams, config) - - /* process params_list arguments */ - /*********************************/ - def paramSets = _parseParamListArguments(params, config) - def parameterSetsWithConfigApplied = applyConfig(paramSets, config) - - /* combine arguments into channel */ - /**********************************/ - def processedParams = parameterSetsWithConfigApplied.indexed().collect{ index, paramSet -> - def id = paramSet[0] - def parValues = paramSet[1] - id = [id, globalID].find({it != null}) // first non-null element - - if (workflow.stubRun) { - // if stub run, explicitly add an id if missing - id = id ? id : "stub" + index - } - assert id != null: "Each parameter set should have at least an 'id'" - // Add regular parameters together with parameters passed with 'param_list' - def combinedArgsValues = globalParamsValues + parValues - - // Remove parameters which are null, if the default is also null - combinedArgsValues = combinedArgsValues.collectEntries{paramName, paramValue -> - parameterSettings = config.functionality.allArguments.find({it.plainName == paramName}) - if ( paramValue != null || parameterSettings.get("default", null) != null ) { - [paramName, paramValue] - } - } - [id, combinedArgsValues] - } - - // Check if ids (first element of each list) is unique - _checkUniqueIds(processedParams) - return processedParams -} - -/** - * Parse nextflow parameters based on settings defined in a viash config - * and return a nextflow channel. - * - * @param params Input parameters. Can optionaly contain a 'param_list' key that - * provides a list of arguments that can be split up into multiple events - * in the output channel possible formats of param_lists are: a csv file, - * json file, a yaml file or a yaml blob. Each parameters set (event) must - * have a unique ID. - * @param config A Map of the Viash configuration. This Map can be generated from the config file - * using the readConfig() function. - * - * @return A nextflow Channel with events. Events are formatted as a tuple that contains - * first contains the ID of the event and as second element holds a parameter map. - * - * - */ -def channelFromParams(Map params, Map config) { - processedParams = _paramsToParamSets(params, config) - return Channel.fromList(processedParams) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/checkUniqueIds.nf' -def checkUniqueIds(Map args) { - def stopOnError = args.stopOnError == null ? args.stopOnError : true - - def idChecker = new IDChecker() - - return filter { tup -> - if (!idChecker.observe(tup[0])) { - if (stopOnError) { - error "Duplicate id: ${tup[0]}" - } else { - log.warn "Duplicate id: ${tup[0]}, removing duplicate entry" - return false - } - } - return true - } -} -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/paramsToChannel.nf' -def paramsToChannel(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: paramsToChannel has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") - } - Channel.fromList(paramsToList(params, config)) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/paramsToList.nf' -viashChannelDeprecationWarningPrinted = false - -def paramsToList(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: paramsToList has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") - } - // fetch default params from functionality - def defaultArgs = config.functionality.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - - // fetch overrides in params - def paramArgs = config.functionality.allArguments - .findAll { params.containsKey(it.plainName) } - .collectEntries { [ it.plainName, params[it.plainName] ] } - - // check multi input params - // objects should be closures and not functions, thanks to FunctionDef - def multiParamFormat = _guessParamListFormat(params) - - def multiOptionFunctions = [ - "csv": {[it, readCsv(it)]}, - "json": {[it, readJson(it)]}, - "yaml": {[it, readYaml(it)]}, - "yaml_blob": {[null, readYamlBlob(it)]}, - "asis": {[null, it]}, - "none": {[null, [[:]]]} - ] - assert multiOptionFunctions.containsKey(multiParamFormat): - "Format of provided --param_list not recognised.\n" + - "You can use '--param_list_format' to manually specify the format.\n" + - "Found: '$multiParamFormat'. Expected: one of 'csv', 'json', 'yaml', 'yaml_blob', 'asis' or 'none'" - - // fetch multi param inputs - def multiOptionFun = multiOptionFunctions.get(multiParamFormat) - // todo: add try catch - def multiOptionOut = multiOptionFun(params.containsKey("param_list") ? params.param_list : "") - def paramList = multiOptionOut[1] - def multiFile = multiOptionOut[0] - - // data checks - assert paramList instanceof List: "--param_list should contain a list of maps" - for (value in paramList) { - assert value instanceof Map: "--param_list should contain a list of maps" - } - - // combine parameters - def processedParams = paramList.collect{ multiParam -> - // combine params - def combinedArgs = defaultArgs + paramArgs + multiParam - - if (workflow.stubRun) { - // if stub run, explicitly add an id if missing - combinedArgs = [id: "stub"] + combinedArgs - } else { - // else check whether required arguments exist - config.functionality.allArguments - .findAll { it.required } - .forEach { par -> - assert combinedArgs.containsKey(par.plainName): "Argument ${par.plainName} is required but does not have a value" - } - } - - // process arguments - def inputs = config.functionality.allArguments - .findAll{ par -> combinedArgs.containsKey(par.plainName) } - .collectEntries { par -> - // split on 'multiple_sep' - if (par.multiple) { - parData = combinedArgs[par.plainName] - if (parData instanceof List) { - parData = parData.collect{it instanceof String ? it.split(par.multiple_sep) : it } - } else if (parData instanceof String) { - parData = parData.split(par.multiple_sep) - } else if (parData == null) { - parData = [] - } else { - parData = [ parData ] - } - } else { - parData = [ combinedArgs[par.plainName] ] - } - - // flatten - parData = parData.flatten() - - // cast types - if (par.type == "file" && ((par.direction != null ? par.direction : "input") == "input")) { - parData = parData.collect{path -> - if (path !instanceof String) { - path - } else if (multiFile) { - file(_getChild(multiFile, path)) - } else { - file(path) - } - }.flatten() - } else if (par.type == "integer") { - parData = parData.collect{it as Integer} - } else if (par.type == "double") { - parData = parData.collect{it as Double} - } else if (par.type == "boolean" || par.type == "boolean_true" || par.type == "boolean_false") { - parData = parData.collect{it as Boolean} - } - // simplify list to value if need be - if (!par.multiple) { - assert parData.size() == 1 : - "Error: argument ${par.plainName} has too many values.\n" + - " Expected amount: 1. Found: ${parData.size()}" - parData = parData[0] - } - - // return pair - [ par.plainName, parData ] - } - // remove parameters which were explicitly set to null - .findAll{ par -> par != null } - } - - - // check processed params - processedParams.forEach { args -> - assert args.containsKey("id"): "Each argument set should have an 'id'. Argument set: $args" - } - def ppIds = processedParams.collect{it.id} - assert ppIds.size() == ppIds.unique().size() : "All argument sets should have unique ids. Detected ids: $ppIds" - - processedParams -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/preprocessInputs.nf' -// This helper file will be deprecated soon -preprocessInputsDeprecationWarningPrinted = false - -def preprocessInputsDeprecationWarning() { - if (!preprocessInputsDeprecationWarningPrinted) { - preprocessInputsDeprecationWarningPrinted = true - System.err.println("Warning: preprocessInputs() will be deprecated Viash 0.9.0.") - } -} - -/** - * Process a list of Vdsl3 formatted parameters and apply a Viash config to them: - * - Gather default parameters from the Viash config and make - * sure that they are correctly formatted (see applyConfig method). - * - Format the input parameters (also using the applyConfig method). - * - Apply the default parameter to the input parameters. - * - Do some assertions: - * ~ Check if the event IDs in the channel are unique. - * - * @param params A list of parameter sets as Tuples. The first element of the tuples - * must be a unique id of the parameter set, and the second element - * must contain the parameters themselves. Optional extra elements - * of the tuples will be passed to the output as is. - * @param config A Map of the Viash configuration. This Map can be generated from - * the config file using the readConfig() function. - * - * @return A list of processed parameters sets as tuples. - */ - -private List _preprocessInputsList(List params, Map config) { - // Get different parameter types (used throughout this function) - def defaultArgs = config.functionality.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - - // Apply config to default parameters - def parsedDefaultValues = applyConfigToOneParameterSet(defaultArgs, config) - - // Apply config to input parameters - def parsedInputParamSets = applyConfig(params, config) - - // Merge two parameter sets together - def parsedArgs = parsedInputParamSets.collect({ parsedInputParamSet -> - def id = parsedInputParamSet[0] - def parValues = parsedInputParamSet[1] - def passthrough = parsedInputParamSet.drop(2) - def parValuesWithDefault = parsedDefaultValues + parValues - [id, parValuesWithDefault] + passthrough - }) - _checkUniqueIds(parsedArgs) - - return parsedArgs -} - -/** - * Generate a nextflow Workflow that allows processing a channel of - * Vdsl3 formatted events and apply a Viash config to them: - * - Gather default parameters from the Viash config and make - * sure that they are correctly formatted (see applyConfig method). - * - Format the input parameters (also using the applyConfig method). - * - Apply the default parameter to the input parameters. - * - Do some assertions: - * ~ Check if the event IDs in the channel are unique. - * - * The events in the channel are formatted as tuples, with the - * first element of the tuples being a unique id of the parameter set, - * and the second element containg the the parameters themselves. - * Optional extra elements of the tuples will be passed to the output as is. - * - * @param args A map that must contain a 'config' key that points - * to a parsed config (see readConfig()). Optionally, a - * 'key' key can be provided which can be used to create a unique - * name for the workflow process. - * - * @return A workflow that allows processing a channel of Vdsl3 formatted events - * and apply a Viash config to them. - */ -def preprocessInputs(Map args) { - preprocessInputsDeprecationWarning() - - wfKey = args.key != null ? args.key : "preprocessInputs" - config = args.config - workflow preprocessInputsInstance { - take: - input_ch - - main: - assert config instanceof Map : - "Error in preprocessInputs: config must be a map. " + - "Expected class: Map. Found: config.getClass() is ${config.getClass()}" - - output_ch = input_ch - | toSortedList - | map { paramList -> _preprocessInputsList(paramList, config) } - | flatMap - emit: - output_ch - } - - return preprocessInputsInstance.cloneWithName(wfKey) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/runComponents.nf' -/** - * Run a list of components on a stream of data. - * - * @param components: list of Viash VDSL3 modules to run - * @param fromState: a closure, a map or a list of keys to extract from the input data. - * If a closure, it will be called with the id, the data and the component config. - * @param toState: a closure, a map or a list of keys to extract from the output data - * If a closure, it will be called with the id, the output data, the old state and the component config. - * @param filter: filter function to apply to the input. - * It will be called with the id, the data and the component config. - * @param id: id to use for the output data - * If a closure, it will be called with the id, the data and the component config. - * @param auto: auto options to pass to the components - * - * @return: a workflow that runs the components - **/ -def runComponents(Map args) { - assert args.components: "runComponents should be passed a list of components to run" - - def components_ = args.components - if (components_ !instanceof List) { - components_ = [ components_ ] - } - assert components_.size() > 0: "pass at least one component to runComponents" - - def fromState_ = args.fromState - def toState_ = args.toState - def filter_ = args.filter - def id_ = args.id - - workflow runComponentsWf { - take: input_ch - main: - - // generate one channel per method - out_chs = components_.collect{ comp_ -> - def comp_config = comp_.config - - filter_ch = filter_ - ? input_ch | filter{tup -> - filter_(tup[0], tup[1], comp_config) - } - : input_ch - id_ch = id_ - ? filter_ch | map{tup -> - // def new_id = id_(tup[0], tup[1], comp_config) - def new_id = tup[0] - if (id_ instanceof String) { - new_id = id_ - } else if (id_ instanceof Closure) { - new_id = id_(new_id, tup[1], comp_config) - } - [new_id] + tup.drop(1) - } - : filter_ch - data_ch = id_ch | map{tup -> - def new_data = tup[1] - if (fromState_ instanceof Map) { - new_data = fromState_.collectEntries{ key0, key1 -> - [key0, new_data[key1]] - } - } else if (fromState_ instanceof List) { - new_data = fromState_.collectEntries{ key -> - [key, new_data[key]] - } - } else if (fromState_ instanceof Closure) { - new_data = fromState_(tup[0], new_data, comp_config) - } - tup.take(1) + [new_data] + tup.drop(1) - } - out_ch = data_ch - | comp_.run( - auto: (args.auto ?: [:]) + [simplifyInput: false, simplifyOutput: false] - ) - post_ch = toState_ - ? out_ch | map{tup -> - def output = tup[1] - def old_state = tup[2] - if (toState_ instanceof Map) { - new_state = old_state + toState_.collectEntries{ key0, key1 -> - [key0, output[key1]] - } - } else if (toState_ instanceof List) { - new_state = old_state + toState_.collectEntries{ key -> - [key, output[key]] - } - } else if (toState_ instanceof Closure) { - new_state = toState_(tup[0], output, old_state, comp_config) - } - [tup[0], new_state] + tup.drop(3) - } - : out_ch - - post_ch - } - - // mix all results - output_ch = - (out_chs.size == 1) - ? out_chs[0] - : out_chs[0].mix(*out_chs.drop(1)) - - emit: output_ch - } - - return runComponentsWf -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/safeJoin.nf' -def safeJoin(targetChannel, sourceChannel, key) { - def sourceIDs = new IDChecker() - - def sourceCheck = sourceChannel - | map { tup -> - sourceIDs.observe(tup[0]) - tup - } - def targetCheck = targetChannel - | map { tup -> - def id = tup[0] - // def id = tup[1].containsKey("_meta").containsKey("join_id") ? tup[1]._meta.join_id : tup[0] - - if (!sourceIDs.contains(id)) { - error ( - "Error in module '${key}' when merging output with original state.\n" + - " Reason: output with id '${id}' could not be joined with source channel.\n" + - " If the IDs in the output channel differ from the input channel,\n" + - " please set `tup[1]._meta.join_id to the original ID.\n" + - " Original IDs in input channel: ['${sourceIDs.getItems().join("', '")}'].\n" + - " Unexpected ID in the output channel: '${id}'.\n" + - " Example input event: [\"id\", [input: file(...)]],\n" + - " Example output event: [\"newid\", [output: file(...), _meta: [join_id: \"id\"]]]" - ) - } - // TODO: add link to our documentation on how to fix this - - tup - } - targetCheck.join(sourceCheck) -} -// helper file: 'src/main/resources/io/viash/platforms/nextflow/channel/viashChannel.nf' - -def viashChannel(params, config) { - if (!viashChannelDeprecationWarningPrinted) { - viashChannelDeprecationWarningPrinted = true - System.err.println("Warning: viashChannel has deprecated in Viash 0.7.0. " + - "Please use a combination of channelFromParams and preprocessInputs.") - } - paramsToChannel(params, config) - | map{tup -> [tup.id, tup]} -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/addGlobalParams.nf' -def addGlobalArguments(config) { - def localConfig = [ - "functionality" : [ - "argument_groups": [ - [ - "name": "Nextflow input-output arguments", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "arguments" : [ - [ - 'name': '--publish_dir', - 'required': true, - 'type': 'string', - 'description': 'Path to an output directory.', - 'example': 'output/', - 'multiple': false - ], - [ - 'name': '--param_list', - 'required': false, - 'type': 'string', - 'description': '''Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob. - | - |* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ ['id': 'foo', 'input': 'foo.txt'], ['id': 'bar', 'input': 'bar.txt'] ]`. - |* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`. - |* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]`. - |* A yaml blob can also be passed directly as a string. Example: `--param_list "[ {'id': 'foo', 'input': 'foo.txt'}, {'id': 'bar', 'input': 'bar.txt'} ]"`. - | - |When passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.'''.stripMargin(), - 'example': 'my_params.yaml', - 'multiple': false, - 'hidden': true - ], - ] - ] - ] - ] - ] - - return processConfig(_mergeMap(config, localConfig)) -} - -def _mergeMap(Map lhs, Map rhs) { - return rhs.inject(lhs.clone()) { map, entry -> - if (map[entry.key] instanceof Map && entry.value instanceof Map) { - map[entry.key] = _mergeMap(map[entry.key], entry.value) - } else if (map[entry.key] instanceof Collection && entry.value instanceof Collection) { - map[entry.key] += entry.value - } else { - map[entry.key] = entry.value - } - return map - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/generateHelp.nf' -def _generateArgumentHelp(param) { - // alternatives are not supported - // def names = param.alternatives ::: List(param.name) - - def unnamedProps = [ - ["required parameter", param.required], - ["multiple values allowed", param.multiple], - ["output", param.direction.toLowerCase() == "output"], - ["file must exist", param.type == "file" && param.must_exist] - ].findAll{it[1]}.collect{it[0]} - - def dflt = null - if (param.default != null) { - if (param.default instanceof List) { - dflt = param.default.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - dflt = param.default.toString() - } - } - def example = null - if (param.example != null) { - if (param.example instanceof List) { - example = param.example.join(param.multiple_sep != null ? param.multiple_sep : ", ") - } else { - example = param.example.toString() - } - } - def min = param.min?.toString() - def max = param.max?.toString() - - def escapeChoice = { choice -> - def s1 = choice.replaceAll("\\n", "\\\\n") - def s2 = s1.replaceAll("\"", """\\\"""") - s2.contains(",") || s2 != choice ? "\"" + s2 + "\"" : s2 - } - def choices = param.choices == null ? - null : - "[ " + param.choices.collect{escapeChoice(it.toString())}.join(", ") + " ]" - - def namedPropsStr = [ - ["type", ([param.type] + unnamedProps).join(", ")], - ["default", dflt], - ["example", example], - ["choices", choices], - ["min", min], - ["max", max] - ] - .findAll{it[1]} - .collect{"\n " + it[0] + ": " + it[1].replaceAll("\n", "\\n")} - .join("") - - def descStr = param.description == null ? - "" : - _paragraphWrap("\n" + param.description.trim(), 80 - 8).join("\n ") - - "\n --" + param.plainName + - namedPropsStr + - descStr -} - -// Based on Helper.generateHelp() in Helper.scala -def _generateHelp(config) { - def fun = config.functionality - - // PART 1: NAME AND VERSION - def nameStr = fun.name + - (fun.version == null ? "" : " " + fun.version) - - // PART 2: DESCRIPTION - def descrStr = fun.description == null ? - "" : - "\n\n" + _paragraphWrap(fun.description.trim(), 80).join("\n") - - // PART 3: Usage - def usageStr = fun.usage == null ? - "" : - "\n\nUsage:\n" + fun.usage.trim() - - // PART 4: Options - def argGroupStrs = fun.allArgumentGroups.collect{argGroup -> - def name = argGroup.name - def descriptionStr = argGroup.description == null ? - "" : - "\n " + _paragraphWrap(argGroup.description.trim(), 80-4).join("\n ") + "\n" - def arguments = argGroup.arguments.collect{arg -> - arg instanceof String ? fun.allArguments.find{it.plainName == arg} : arg - }.findAll{it != null} - def argumentStrs = arguments.collect{param -> _generateArgumentHelp(param)} - - "\n\n$name:" + - descriptionStr + - argumentStrs.join("\n") - } - - // FINAL: combine - def out = nameStr + - descrStr + - usageStr + - argGroupStrs.join("") - - return out -} - -// based on Format._paragraphWrap -def _paragraphWrap(str, maxLength) { - def outLines = [] - str.split("\n").each{par -> - def words = par.split("\\s").toList() - - def word = null - def line = words.pop() - while(!words.isEmpty()) { - word = words.pop() - if (line.length() + word.length() + 1 <= maxLength) { - line = line + " " + word - } else { - outLines.add(line) - line = word - } - } - if (words.isEmpty()) { - outLines.add(line) - } - } - return outLines -} - -def helpMessage(config) { - if (params.containsKey("help") && params.help) { - def mergedConfig = addGlobalArguments(config) - def helpStr = _generateHelp(mergedConfig) - println(helpStr) - exit 0 - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/processConfig.nf' -def processConfig(config) { - // TODO: assert .functionality etc. - if (config.functionality.inputs) { - System.err.println("Warning: .functionality.inputs is deprecated. Please use .functionality.arguments instead.") - } - if (config.functionality.outputs) { - System.err.println("Warning: .functionality.outputs is deprecated. Please use .functionality.arguments instead.") - } - - // set defaults for inputs - config.functionality.inputs = - (config.functionality.inputs != null ? config.functionality.inputs : []).collect{arg -> - arg.type = arg.type != null ? arg.type : "file" - arg.direction = "input" - _processArgument(arg) - } - // set defaults for outputs - config.functionality.outputs = - (config.functionality.outputs != null ? config.functionality.outputs : []).collect{arg -> - arg.type = arg.type != null ? arg.type : "file" - arg.direction = "output" - _processArgument(arg) - } - // set defaults for arguments - config.functionality.arguments = - (config.functionality.arguments != null ? config.functionality.arguments : []).collect{arg -> - _processArgument(arg) - } - // set defaults for argument_group arguments - config.functionality.argument_groups = - (config.functionality.argument_groups != null ? config.functionality.argument_groups : []).collect{grp -> - grp.arguments = (grp.arguments != null ? grp.arguments : []).collect{arg -> - arg instanceof String ? arg.replaceAll("^-*", "") : _processArgument(arg) - } - grp - } - - // create combined arguments list - config.functionality.allArguments = - config.functionality.inputs + - config.functionality.outputs + - config.functionality.arguments + - config.functionality.argument_groups.collectMany{ group -> - group.arguments.findAll{ it !instanceof String } - } - - // add missing argument groups (based on Functionality::allArgumentGroups()) - def argGroups = config.functionality.argument_groups - def inputGroup = _processArgumentGroup(argGroups, "Inputs", config.functionality.inputs) - def outputGroup = _processArgumentGroup(argGroups, "Outputs", config.functionality.outputs) - def defaultGroup = _processArgumentGroup(argGroups, "Arguments", config.functionality.arguments) - def groupsFiltered = argGroups.findAll(gr -> !(["Inputs", "Outputs", "Arguments"].contains(gr.name))) - config.functionality.allArgumentGroups = inputGroup + outputGroup + defaultGroup + groupsFiltered - - config -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/config/readConfig.nf' - -def readConfig(file) { - def config = readYaml(file != null ? file : "$projectDir/config.vsh.yaml") - processConfig(config) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/collectTraces.nf' -class CustomTraceObserver implements nextflow.trace.TraceObserver { - List traces - - CustomTraceObserver(List traces) { - this.traces = traces - } - - @Override - void onProcessComplete(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } - - @Override - void onProcessCached(nextflow.processor.TaskHandler handler, nextflow.trace.TraceRecord trace) { - def trace2 = trace.store.clone() - trace2.script = null - traces.add(trace2) - } -} - -def collectTraces() { - def traces = Collections.synchronizedList([]) - - // add custom trace observer which stores traces in the traces object - session.observers.add(new CustomTraceObserver(traces)) - - traces -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/getPublishDir.nf' -def getPublishDir() { - return params.containsKey("publish_dir") ? params.publish_dir : - params.containsKey("publishDir") ? params.publishDir : - null -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/getRootDir.nf' - -// Recurse upwards until we find a '.build.yaml' file -def _findBuildYamlFile(path) { - def child = path.resolve(".build.yaml") - if (java.nio.file.Files.isDirectory(path) && java.nio.file.Files.exists(child)) { - return child - } else { - def parent = path.getParent() - if (parent == null) { - return null - } else { - return _findBuildYamlFile(parent) - } - } -} - -// get the root of the target folder -def getRootDir() { - def dir = _findBuildYamlFile(moduleDir.normalize()) - assert dir != null: "Could not find .build.yaml in the folder structure" - dir.getParent() -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/iterateMap.nf' -/** - * Recursively apply a function over the leaves of an object. - * @param obj The object to iterate over. - * @param fun The function to apply to each value. - * @return The object with the function applied to each value. - */ -def iterateMap(obj, fun) { - if (obj instanceof List && obj !instanceof String) { - return obj.collect{item -> - iterateMap(item, fun) - } - } else if (obj instanceof Map) { - return obj.collectEntries{key, item -> - [key.toString(), iterateMap(item, fun)] - } - } else { - return fun(obj) - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/functions/niceView.nf' -/** - * A view for printing the event of each channel as a YAML blob. - * This is useful for debugging. - */ -def niceView() { - workflow niceViewWf { - take: input - main: - output = input - | view{toYamlBlob(it)} - emit: output - } - return niceViewWf -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readCsv.nf' - -def readCsv(file_path) { - def output = [] - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - - // todo: allow escaped quotes in string - // todo: allow single quotes? - def splitRegex = java.util.regex.Pattern.compile(''',(?=(?:[^"]*"[^"]*")*[^"]*$)''') - def removeQuote = java.util.regex.Pattern.compile('''"(.*)"''') - - def br = java.nio.file.Files.newBufferedReader(inputFile) - - def row = -1 - def header = null - while (br.ready() && header == null) { - def line = br.readLine() - row++ - if (!line.startsWith("#")) { - header = splitRegex.split(line, -1).collect{field -> - m = removeQuote.matcher(field) - m.find() ? m.replaceFirst('$1') : field - } - } - } - assert header != null: "CSV file should contain a header" - - while (br.ready()) { - def line = br.readLine() - row++ - if (line == null) { - br.close() - break - } - - if (!line.startsWith("#")) { - def predata = splitRegex.split(line, -1) - def data = predata.collect{field -> - if (field == "") { - return null - } - m = removeQuote.matcher(field) - if (m.find()) { - return m.replaceFirst('$1') - } else { - return field - } - } - assert header.size() == data.size(): "Row $row should contain the same number as fields as the header" - - def dataMap = [header, data].transpose().collectEntries().findAll{it.value != null} - output.add(dataMap) - } - } - - output -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJson.nf' -def readJson(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - def jsonSlurper = new groovy.json.JsonSlurper() - jsonSlurper.parse(inputFile) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readJsonBlob.nf' -def readJsonBlob(str) { - def jsonSlurper = new groovy.json.JsonSlurper() - jsonSlurper.parseText(str) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readTaggedYaml.nf' -// Custom constructor to modify how certain objects are parsed from YAML -class CustomConstructor extends org.yaml.snakeyaml.constructor.Constructor { - Path root - - class ConstructPath extends org.yaml.snakeyaml.constructor.AbstractConstruct { - public Object construct(org.yaml.snakeyaml.nodes.Node node) { - String filename = (String) constructScalar(node); - if (root != null) { - return root.resolve(filename); - } - return java.nio.file.Paths.get(filename); - } - } - - CustomConstructor(org.yaml.snakeyaml.LoaderOptions options, Path root) { - super(options) - this.root = root - // Handling !file tag and parse it back to a File type - this.yamlConstructors.put(new org.yaml.snakeyaml.nodes.Tag("!file"), new ConstructPath()) - } -} - -def readTaggedYaml(Path path) { - def options = new org.yaml.snakeyaml.LoaderOptions() - def constructor = new CustomConstructor(options, path.getParent()) - def yaml = new org.yaml.snakeyaml.Yaml(constructor) - return yaml.load(path.text) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYaml.nf' -def readYaml(file_path) { - def inputFile = file_path !instanceof Path ? file(file_path) : file_path - def yamlSlurper = new org.yaml.snakeyaml.Yaml() - yamlSlurper.load(inputFile) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/readYamlBlob.nf' -def readYamlBlob(str) { - def yamlSlurper = new org.yaml.snakeyaml.Yaml() - yamlSlurper.load(str) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toJsonBlob.nf' -String toJsonBlob(data) { - return groovy.json.JsonOutput.toJson(data) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toTaggedYamlBlob.nf' -// Custom representer to modify how certain objects are represented in YAML -class CustomRepresenter extends org.yaml.snakeyaml.representer.Representer { - class RepresentPath implements org.yaml.snakeyaml.representer.Represent { - public String getFileName(Object obj) { - if (obj instanceof Path) { - def file = (Path) obj; - return file.getFileName().toString(); - } else if (obj instanceof File) { - def file = (File) obj; - return file.getName(); - } else { - throw new IllegalArgumentException("Object: " + obj + " is not a Path or File"); - } - } - - public org.yaml.snakeyaml.nodes.Node representData(Object data) { - String filename = getFileName(data); - def tag = new org.yaml.snakeyaml.nodes.Tag("!file"); - return representScalar(tag, filename); - } - } - CustomRepresenter(org.yaml.snakeyaml.DumperOptions options) { - super(options) - this.representers.put(sun.nio.fs.UnixPath, new RepresentPath()) - this.representers.put(Path, new RepresentPath()) - this.representers.put(File, new RepresentPath()) - } -} - -String toTaggedYamlBlob(data) { - def options = new org.yaml.snakeyaml.DumperOptions() - options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) - def representer = new CustomRepresenter(options) - def yaml = new org.yaml.snakeyaml.Yaml(representer, options) - return yaml.dump(data) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/toYamlBlob.nf' -String toYamlBlob(data) { - def options = new org.yaml.snakeyaml.DumperOptions() - options.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK) - options.setPrettyFlow(true) - def yaml = new org.yaml.snakeyaml.Yaml(options) - def cleanData = iterateMap(data, {it.toString()}) - return yaml.dump(data) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/writeJson.nf' -void writeJson(data, file) { - assert data: "writeJson: data should not be null" - assert file: "writeJson: file should not be null" - file.write(toJsonBlob(data)) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/readwrite/writeYaml.nf' -void writeYaml(data, file) { - assert data: "writeYaml: data should not be null" - assert file: "writeYaml: file should not be null" - file.write(toYamlBlob(data)) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/findStates.nf' -def findStates(Map params, Map config) { - // TODO: do a deep clone of config - def auto_config = config.clone() - auto_config.functionality = auto_config.functionality.clone() - // override arguments - auto_config.functionality.argument_groups = [] - auto_config.functionality.arguments = [ - [ - type: "file", - name: "--input_states", - example: "/path/to/input/directory/**/state.yaml", - description: "Path to input directory containing the datasets to be integrated.", - required: true, - multiple: true, - multiple_sep: ";" - ], - [ - type: "string", - name: "--filter", - example: "foo/.*/state.yaml", - description: "Regex to filter state files by path.", - required: false - ], - // to do: make this a yaml blob? - [ - type: "string", - name: "--rename_keys", - example: ["newKey1:oldKey1", "newKey2:oldKey2"], - description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.", - required: false, - multiple: true, - multiple_sep: "," - ], - [ - type: "string", - name: "--settings", - example: '{"output_dataset": "dataset.h5ad", "k": 10}', - description: "Global arguments as a JSON glob to be passed to all components.", - required: false - ] - ] - - // run auto config through processConfig once more - auto_config = processConfig(auto_config) - - workflow findStatesWf { - helpMessage(auto_config) - - output_ch = - channelFromParams(params, auto_config) - | flatMap { autoId, args -> - - def globalSettings = args.settings ? readYamlBlob(args.settings) : [:] - - // look for state files in input dir - def stateFiles = args.input_states - - // filter state files by regex - if (args.filter) { - stateFiles = stateFiles.findAll{ stateFile -> - def stateFileStr = stateFile.toString() - def matcher = stateFileStr =~ args.filter - matcher.matches()} - } - - // read in states - def states = stateFiles.collect { stateFile -> - def state_ = readTaggedYaml(stateFile) - [state_.id, state_] - } - - // construct renameMap - if (args.rename_keys) { - def renameMap = args.rename_keys.collectEntries{renameString -> - def split = renameString.split(":") - assert split.size() == 2: "Argument 'rename' should be of the form 'newKey:oldKey,newKey:oldKey'" - split - } - - // rename keys in state, only let states through which have all keys - // also add global settings - states = states.collectMany{id, state -> - def newState = [:] - - for (key in renameMap.keySet()) { - def origKey = renameMap[key] - if (!(state.containsKey(origKey))) { - return [] - } - newState[key] = state[origKey] - } - - [[id, globalSettings + newState]] - } - } - - states - } - emit: - output_ch - } - - return findStatesWf -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/publishStates.nf' -def collectFiles(obj) { - if (obj instanceof java.io.File || obj instanceof Path) { - return [obj] - } else if (obj instanceof List && obj !instanceof String) { - return obj.collectMany{item -> - collectFiles(item) - } - } else if (obj instanceof Map) { - return obj.collectMany{key, item -> - collectFiles(item) - } - } else { - return [] - } -} - -/** - * Recurse through a state and collect all input files and their target output filenames. - * @param obj The state to recurse through. - * @param prefix The prefix to prepend to the output filenames. - */ -def collectInputOutputPaths(obj, prefix) { - if (obj instanceof File || obj instanceof Path) { - def path = obj instanceof Path ? obj : obj.toPath() - def ext = path.getFileName().toString().find("\\.[^\\.]+\$") ?: "" - def newFilename = prefix + ext - return [[obj, newFilename]] - } else if (obj instanceof List && obj !instanceof String) { - return obj.withIndex().collectMany{item, ix -> - collectInputOutputPaths(item, prefix + "_" + ix) - } - } else if (obj instanceof Map) { - return obj.collectMany{key, item -> - collectInputOutputPaths(item, prefix + "." + key) - } - } else { - return [] - } -} - -def publishStates(Map args) { - def key_ = args.get("key") - - assert key_ != null : "publishStates: key must be specified" - - workflow publishStatesWf { - take: input_ch - main: - input_ch - | map { tup -> - def id_ = tup[0] - def state_ = tup[1] - - // the input files and the target output filenames - def inputOutputFiles_ = collectInputOutputPaths(state_, id_ + "." + key_).transpose() - def inputFiles_ = inputOutputFiles_[0] - def outputFiles_ = inputOutputFiles_[1] - - // convert state to yaml blob - def yamlBlob_ = toTaggedYamlBlob([id: id_] + state_) - - // adds a leading dot to the id (after any folder names) - // example: foo -> .foo, foo/bar -> foo/.bar - def idWithDot_ = id_.replaceAll("^(.+/)?([^/]+)", "\$1.\$2") - def yamlFile = '$id.$key.state.yaml' - .replaceAll('\\$id', idWithDot_) - .replaceAll('\\$key', key_) - - [id_, yamlBlob_, yamlFile, inputFiles_, outputFiles_] - } - | publishStatesProc - emit: input_ch - } - return publishStatesWf -} -process publishStatesProc { - // todo: check publishpath? - publishDir path: "${getPublishDir()}/", mode: "copy" - tag "$id" - input: - tuple val(id), val(yamlBlob), val(yamlFile), path(inputFiles, stageAs: "_inputfile?/*"), val(outputFiles) - output: - tuple val(id), path{[yamlFile] + outputFiles} - script: - def copyCommands = [ - inputFiles instanceof List ? inputFiles : [inputFiles], - outputFiles instanceof List ? outputFiles : [outputFiles] - ] - .transpose() - .collectMany{infile, outfile -> - if (infile.toString() != outfile.toString()) { - ["cp -r '${infile.toString()}' '${outfile.toString()}'"] - } else { - // no need to copy if infile is the same as outfile - [] - } - } - """ - mkdir -p "\$(dirname '${yamlFile}')" - echo "Storing state as yaml" - echo '${yamlBlob}' > '${yamlFile}' - echo "Copying output files to destination folder" - ${copyCommands.join("\n ")} - """ -} - - -// this assumes that the state contains no other values other than those specified in the config -def publishStatesByConfig(Map args) { - def config = args.get("config") - assert config != null : "publishStatesByConfig: config must be specified" - - def key_ = args.get("key", config.functionality.name) - assert key_ != null : "publishStatesByConfig: key must be specified" - - workflow publishStatesSimpleWf { - take: input_ch - main: - input_ch - | map { tup -> - def id_ = tup[0] - def state_ = tup[1] // e.g. [output: new File("myoutput.h5ad"), k: 10] - def origState_ = tup[2] // e.g. [output: '$id.$key.foo.h5ad'] - - // the processed state is a list of [key, value, srcPath, destPath] tuples, where - // - key, value is part of the state to be saved to disk - // - srcPath and destPath are lists of files to be copied from src to dest - def processedState = - config.functionality.allArguments - .findAll { it.direction == "output" } - .collectMany { par -> - def plainName_ = par.plainName - // if the state does not contain the key, it's an - // optional argument for which the component did - // not generate any output - if (!state_.containsKey(plainName_)) { - return [] - } - def value = state_[plainName_] - // if the parameter is not a file, it should be stored - // in the state as-is, but is not something that needs - // to be copied from the source path to the dest path - if (par.type != "file") { - return [[key: plainName_, value: value, srcPath: [], destPath: []]] - } - // if the orig state does not contain this filename, - // it's an optional argument for which the user specified - // that it should not be returned as a state - if (!origState_.containsKey(plainName_)) { - return [] - } - def filenameTemplate = origState_[plainName_] - // if the pararameter is multiple: true, fetch the template - if (par.multiple && filenameTemplate instanceof List) { - filenameTemplate = filenameTemplate[0] - } - // instantiate the template - filename = filenameTemplate - .replaceAll('\\$id', id_) - .replaceAll('\\$key', key_) - if (par.multiple) { - // if the parameter is multiple: true, the filename - // should contain a wildcard '*' that is replaced with - // the index of the file - assert filename.contains("*") : "Module '${key_}' id '${id_}': Multiple output files specified, but no wildcard '*' in the filename: ${filename}" - def outputPerFile = value.withIndex().collect{ val, ix -> - def destPath = filename.replace("*", ix.toString()) - def destFile = java.nio.file.Paths.get(destPath) - def srcPath = val instanceof File ? val.toPath() : val - [value: destFile, srcPath: srcPath, destPath: destPath] - } - def transposedOutputs = ["value", "srcPath", "destPath"].collectEntries{ key -> - [key, outputPerFile.collect{dic -> dic[key]}] - } - return [[key: plainName_] + transposedOutputs] - } else { - def destFile = java.nio.file.Paths.get(filename) - def srcPath = value instanceof File ? value.toPath() : value - return [[key: plainName_, value: destFile, srcPath: [srcPath], destPath: [filename]]] - } - } - - def updatedState_ = processedState.collectEntries{[it.key, it.value]} - def inputFiles_ = processedState.collectMany{it.srcPath} - def outputFiles_ = processedState.collectMany{it.destPath} - - // convert state to yaml blob - def yamlBlob_ = toTaggedYamlBlob([id: id_] + updatedState_) - - // adds a leading dot to the id (after any folder names) - // example: foo -> .foo, foo/bar -> foo/.bar - // TODO: allow defining the state.yaml template - def idWithDot_ = id_.replaceAll("^(.+/)?([^/]+)", "\$1.\$2") - def yamlFile = '$id.$key.state.yaml' - .replaceAll('\\$id', idWithDot_) - .replaceAll('\\$key', key_) - - [id_, yamlBlob_, yamlFile, inputFiles_, outputFiles_] - } - | publishStatesProc - emit: input_ch - } - return publishStatesSimpleWf -} -// helper file: 'src/main/resources/io/viash/platforms/nextflow/states/setState.nf' -def setState(fun) { - assert fun instanceof Closure || fun instanceof Map || fun instanceof List : - "Error in setState: Expected process argument to be a Closure, a Map, or a List. Found: class ${fun.getClass()}" - - // if fun is a List, convert to map - if (fun instanceof List) { - // check whether fun is a list[string] - assert fun.every{it instanceof CharSequence} : "Error in setState: argument is a List, but not all elements are Strings" - fun = fun.collectEntries{[it, it]} - } - - // if fun is a map, convert to closure - if (fun instanceof Map) { - // check whether fun is a map[string, string] - assert fun.values().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all values are Strings" - assert fun.keySet().every{it instanceof CharSequence} : "Error in setState: argument is a Map, but not all keys are Strings" - def funMap = fun.clone() - // turn the map into a closure to be used later on - fun = { id_, state_ -> - assert state_ instanceof Map : "Error in setState: the state is not a Map" - funMap.collectMany{newkey, origkey -> - if (state_.containsKey(origkey)) { - [[newkey, state_[origkey]]] - } else { - [] - } - }.collectEntries() - } - } - - map { tup -> - def id = tup[0] - def state = tup[1] - def unfilteredState = fun(id, state) - def newState = unfilteredState.findAll{key, val -> val != null} - [id, newState] + tup.drop(2) - } -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processAuto.nf' -// TODO: unit test processAuto -def processAuto(Map auto) { - // remove null values - auto = auto.findAll{k, v -> v != null} - - // check for unexpected keys - def expectedKeys = ["simplifyInput", "simplifyOutput", "transcript", "publish"] - def unexpectedKeys = auto.keySet() - expectedKeys - assert unexpectedKeys.isEmpty(), "unexpected keys in auto: '${unexpectedKeys.join("', '")}'" - - // check auto.simplifyInput - assert auto.simplifyInput instanceof Boolean, "auto.simplifyInput must be a boolean" - - // check auto.simplifyOutput - assert auto.simplifyOutput instanceof Boolean, "auto.simplifyOutput must be a boolean" - - // check auto.transcript - assert auto.transcript instanceof Boolean, "auto.transcript must be a boolean" - - // check auto.publish - assert auto.publish instanceof Boolean || auto.publish == "state", "auto.publish must be a boolean or 'state'" - - return auto.subMap(expectedKeys) -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processDirectives.nf' -def assertMapKeys(map, expectedKeys, requiredKeys, mapName) { - assert map instanceof Map : "Expected argument '$mapName' to be a Map. Found: class ${map.getClass()}" - map.forEach { key, val -> - assert key in expectedKeys : "Unexpected key '$key' in ${mapName ? mapName + " " : ""}map" - } - requiredKeys.forEach { requiredKey -> - assert map.containsKey(requiredKey) : "Missing required key '$key' in ${mapName ? mapName + " " : ""}map" - } -} - -// TODO: unit test processDirectives -def processDirectives(Map drctv) { - // remove null values - drctv = drctv.findAll{k, v -> v != null} - - // check for unexpected keys - def expectedKeys = [ - "accelerator", "afterScript", "beforeScript", "cache", "conda", "container", "containerOptions", "cpus", "disk", "echo", "errorStrategy", "executor", "machineType", "maxErrors", "maxForks", "maxRetries", "memory", "module", "penv", "pod", "publishDir", "queue", "label", "scratch", "storeDir", "stageInMode", "stageOutMode", "tag", "time" - ] - def unexpectedKeys = drctv.keySet() - expectedKeys - assert unexpectedKeys.isEmpty() : "Unexpected keys in process directive: '${unexpectedKeys.join("', '")}'" - - /* DIRECTIVE accelerator - accepted examples: - - [ limit: 4, type: "nvidia-tesla-k80" ] - */ - if (drctv.containsKey("accelerator")) { - assertMapKeys(drctv["accelerator"], ["type", "limit", "request", "runtime"], [], "accelerator") - } - - /* DIRECTIVE afterScript - accepted examples: - - "source /cluster/bin/cleanup" - */ - if (drctv.containsKey("afterScript")) { - assert drctv["afterScript"] instanceof CharSequence - } - - /* DIRECTIVE beforeScript - accepted examples: - - "source /cluster/bin/setup" - */ - if (drctv.containsKey("beforeScript")) { - assert drctv["beforeScript"] instanceof CharSequence - } - - /* DIRECTIVE cache - accepted examples: - - true - - false - - "deep" - - "lenient" - */ - if (drctv.containsKey("cache")) { - assert drctv["cache"] instanceof CharSequence || drctv["cache"] instanceof Boolean - if (drctv["cache"] instanceof CharSequence) { - assert drctv["cache"] in ["deep", "lenient"] : "Unexpected value for cache" - } - } - - /* DIRECTIVE conda - accepted examples: - - "bwa=0.7.15" - - "bwa=0.7.15 fastqc=0.11.5" - - ["bwa=0.7.15", "fastqc=0.11.5"] - */ - if (drctv.containsKey("conda")) { - if (drctv["conda"] instanceof List) { - drctv["conda"] = drctv["conda"].join(" ") - } - assert drctv["conda"] instanceof CharSequence - } - - /* DIRECTIVE container - accepted examples: - - "foo/bar:tag" - - [ registry: "reg", image: "im", tag: "ta" ] - is transformed to "reg/im:ta" - - [ image: "im" ] - is transformed to "im:latest" - */ - if (drctv.containsKey("container")) { - assert drctv["container"] instanceof Map || drctv["container"] instanceof CharSequence - if (drctv["container"] instanceof Map) { - def m = drctv["container"] - assertMapKeys(m, [ "registry", "image", "tag" ], ["image"], "container") - def part1 = - System.getenv('OVERRIDE_CONTAINER_REGISTRY') ? System.getenv('OVERRIDE_CONTAINER_REGISTRY') + "/" : - params.containsKey("override_container_registry") ? params["override_container_registry"] + "/" : // todo: remove? - m.registry ? m.registry + "/" : - "" - def part2 = m.image - def part3 = m.tag ? ":" + m.tag : ":latest" - drctv["container"] = part1 + part2 + part3 - } - } - - /* DIRECTIVE containerOptions - accepted examples: - - "--foo bar" - - ["--foo bar", "-f b"] - */ - if (drctv.containsKey("containerOptions")) { - if (drctv["containerOptions"] instanceof List) { - drctv["containerOptions"] = drctv["containerOptions"].join(" ") - } - assert drctv["containerOptions"] instanceof CharSequence - } - - /* DIRECTIVE cpus - accepted examples: - - 1 - - 10 - */ - if (drctv.containsKey("cpus")) { - assert drctv["cpus"] instanceof Integer - } - - /* DIRECTIVE disk - accepted examples: - - "1 GB" - - "2TB" - - "3.2KB" - - "10.B" - */ - if (drctv.containsKey("disk")) { - assert drctv["disk"] instanceof CharSequence - // assert drctv["disk"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") - // ^ does not allow closures - } - - /* DIRECTIVE echo - accepted examples: - - true - - false - */ - if (drctv.containsKey("echo")) { - assert drctv["echo"] instanceof Boolean - } - - /* DIRECTIVE errorStrategy - accepted examples: - - "terminate" - - "finish" - */ - if (drctv.containsKey("errorStrategy")) { - assert drctv["errorStrategy"] instanceof CharSequence - assert drctv["errorStrategy"] in ["terminate", "finish", "ignore", "retry"] : "Unexpected value for errorStrategy" - } - - /* DIRECTIVE executor - accepted examples: - - "local" - - "sge" - */ - if (drctv.containsKey("executor")) { - assert drctv["executor"] instanceof CharSequence - assert drctv["executor"] in ["local", "sge", "uge", "lsf", "slurm", "pbs", "pbspro", "moab", "condor", "nqsii", "ignite", "k8s", "awsbatch", "google-pipelines"] : "Unexpected value for executor" - } - - /* DIRECTIVE machineType - accepted examples: - - "n1-highmem-8" - */ - if (drctv.containsKey("machineType")) { - assert drctv["machineType"] instanceof CharSequence - } - - /* DIRECTIVE maxErrors - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxErrors")) { - assert drctv["maxErrors"] instanceof Integer - } - - /* DIRECTIVE maxForks - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxForks")) { - assert drctv["maxForks"] instanceof Integer - } - - /* DIRECTIVE maxRetries - accepted examples: - - 1 - - 3 - */ - if (drctv.containsKey("maxRetries")) { - assert drctv["maxRetries"] instanceof Integer - } - - /* DIRECTIVE memory - accepted examples: - - "1 GB" - - "2TB" - - "3.2KB" - - "10.B" - */ - if (drctv.containsKey("memory")) { - assert drctv["memory"] instanceof CharSequence - // assert drctv["memory"].matches("[0-9]+(\\.[0-9]*)? *[KMGTPEZY]?B") - // ^ does not allow closures - } - - /* DIRECTIVE module - accepted examples: - - "ncbi-blast/2.2.27" - - "ncbi-blast/2.2.27:t_coffee/10.0" - - ["ncbi-blast/2.2.27", "t_coffee/10.0"] - */ - if (drctv.containsKey("module")) { - if (drctv["module"] instanceof List) { - drctv["module"] = drctv["module"].join(":") - } - assert drctv["module"] instanceof CharSequence - } - - /* DIRECTIVE penv - accepted examples: - - "smp" - */ - if (drctv.containsKey("penv")) { - assert drctv["penv"] instanceof CharSequence - } - - /* DIRECTIVE pod - accepted examples: - - [ label: "key", value: "val" ] - - [ annotation: "key", value: "val" ] - - [ env: "key", value: "val" ] - - [ [label: "l", value: "v"], [env: "e", value: "v"]] - */ - if (drctv.containsKey("pod")) { - if (drctv["pod"] instanceof Map) { - drctv["pod"] = [ drctv["pod"] ] - } - assert drctv["pod"] instanceof List - drctv["pod"].forEach { pod -> - assert pod instanceof Map - // TODO: should more checks be added? - // See https://www.nextflow.io/docs/latest/process.html?highlight=directives#pod - // e.g. does it contain 'label' and 'value', or 'annotation' and 'value', or ...? - } - } - - /* DIRECTIVE publishDir - accepted examples: - - [] - - [ [ path: "foo", enabled: true ], [ path: "bar", enabled: false ] ] - - "/path/to/dir" - is transformed to [[ path: "/path/to/dir" ]] - - [ path: "/path/to/dir", mode: "cache" ] - is transformed to [[ path: "/path/to/dir", mode: "cache" ]] - */ - // TODO: should we also look at params["publishDir"]? - if (drctv.containsKey("publishDir")) { - def pblsh = drctv["publishDir"] - - // check different options - assert pblsh instanceof List || pblsh instanceof Map || pblsh instanceof CharSequence - - // turn into list if not already so - // for some reason, 'if (!pblsh instanceof List) pblsh = [ pblsh ]' doesn't work. - pblsh = pblsh instanceof List ? pblsh : [ pblsh ] - - // check elements of publishDir - pblsh = pblsh.collect{ elem -> - // turn into map if not already so - elem = elem instanceof CharSequence ? [ path: elem ] : elem - - // check types and keys - assert elem instanceof Map : "Expected publish argument '$elem' to be a String or a Map. Found: class ${elem.getClass()}" - assertMapKeys(elem, [ "path", "mode", "overwrite", "pattern", "saveAs", "enabled" ], ["path"], "publishDir") - - // check elements in map - assert elem.containsKey("path") - assert elem["path"] instanceof CharSequence - if (elem.containsKey("mode")) { - assert elem["mode"] instanceof CharSequence - assert elem["mode"] in [ "symlink", "rellink", "link", "copy", "copyNoFollow", "move" ] - } - if (elem.containsKey("overwrite")) { - assert elem["overwrite"] instanceof Boolean - } - if (elem.containsKey("pattern")) { - assert elem["pattern"] instanceof CharSequence - } - if (elem.containsKey("saveAs")) { - assert elem["saveAs"] instanceof CharSequence //: "saveAs as a Closure is currently not supported. Surround your closure with single quotes to get the desired effect. Example: '\{ foo \}'" - } - if (elem.containsKey("enabled")) { - assert elem["enabled"] instanceof Boolean - } - - // return final result - elem - } - // store final directive - drctv["publishDir"] = pblsh - } - - /* DIRECTIVE queue - accepted examples: - - "long" - - "short,long" - - ["short", "long"] - */ - if (drctv.containsKey("queue")) { - if (drctv["queue"] instanceof List) { - drctv["queue"] = drctv["queue"].join(",") - } - assert drctv["queue"] instanceof CharSequence - } - - /* DIRECTIVE label - accepted examples: - - "big_mem" - - "big_cpu" - - ["big_mem", "big_cpu"] - */ - if (drctv.containsKey("label")) { - if (drctv["label"] instanceof CharSequence) { - drctv["label"] = [ drctv["label"] ] - } - assert drctv["label"] instanceof List - drctv["label"].forEach { label -> - assert label instanceof CharSequence - // assert label.matches("[a-zA-Z0-9]([a-zA-Z0-9_]*[a-zA-Z0-9])?") - // ^ does not allow closures - } - } - - /* DIRECTIVE scratch - accepted examples: - - true - - "/path/to/scratch" - - '$MY_PATH_TO_SCRATCH' - - "ram-disk" - */ - if (drctv.containsKey("scratch")) { - assert drctv["scratch"] == true || drctv["scratch"] instanceof CharSequence - } - - /* DIRECTIVE storeDir - accepted examples: - - "/path/to/storeDir" - */ - if (drctv.containsKey("storeDir")) { - assert drctv["storeDir"] instanceof CharSequence - } - - /* DIRECTIVE stageInMode - accepted examples: - - "copy" - - "link" - */ - if (drctv.containsKey("stageInMode")) { - assert drctv["stageInMode"] instanceof CharSequence - assert drctv["stageInMode"] in ["copy", "link", "symlink", "rellink"] - } - - /* DIRECTIVE stageOutMode - accepted examples: - - "copy" - - "link" - */ - if (drctv.containsKey("stageOutMode")) { - assert drctv["stageOutMode"] instanceof CharSequence - assert drctv["stageOutMode"] in ["copy", "move", "rsync"] - } - - /* DIRECTIVE tag - accepted examples: - - "foo" - - '$id' - */ - if (drctv.containsKey("tag")) { - assert drctv["tag"] instanceof CharSequence - } - - /* DIRECTIVE time - accepted examples: - - "1h" - - "2days" - - "1day 6hours 3minutes 30seconds" - */ - if (drctv.containsKey("time")) { - assert drctv["time"] instanceof CharSequence - // todo: validation regex? - } - - return drctv -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/processWorkflowArgs.nf' -// depends on: thisConfig, thisDefaultWorkflowArgs -def processWorkflowArgs(Map args) { - // override defaults with args - def workflowArgs = thisDefaultWorkflowArgs + args - - // check whether 'key' exists - assert workflowArgs.containsKey("key") : "Error in module '${thisConfig.functionality.name}': key is a required argument" - - // if 'key' is a closure, apply it to the original key - if (workflowArgs["key"] instanceof Closure) { - workflowArgs["key"] = workflowArgs["key"](thisConfig.functionality.name) - } - def key = workflowArgs["key"] - assert key instanceof CharSequence : "Expected process argument 'key' to be a String. Found: class ${key.getClass()}" - assert key ==~ /^[a-zA-Z_]\w*$/ : "Error in module '$key': Expected process argument 'key' to consist of only letters, digits or underscores. Found: ${key}" - - // check for any unexpected keys - def expectedKeys = ["key", "directives", "auto", "map", "mapId", "mapData", "mapPassthrough", "filter", "fromState", "toState", "args", "renameKeys", "debug"] - def unexpectedKeys = workflowArgs.keySet() - expectedKeys - assert unexpectedKeys.isEmpty() : "Error in module '$key': unexpected arguments to the '.run()' function: '${unexpectedKeys.join("', '")}'" - - // check whether directives exists and apply defaults - assert workflowArgs.containsKey("directives") : "Error in module '$key': directives is a required argument" - assert workflowArgs["directives"] instanceof Map : "Error in module '$key': Expected process argument 'directives' to be a Map. Found: class ${workflowArgs['directives'].getClass()}" - workflowArgs["directives"] = processDirectives(thisDefaultWorkflowArgs.directives + workflowArgs["directives"]) - - // check whether directives exists and apply defaults - assert workflowArgs.containsKey("auto") : "Error in module '$key': auto is a required argument" - assert workflowArgs["auto"] instanceof Map : "Error in module '$key': Expected process argument 'auto' to be a Map. Found: class ${workflowArgs['auto'].getClass()}" - workflowArgs["auto"] = processAuto(thisDefaultWorkflowArgs.auto + workflowArgs["auto"]) - - // auto define publish, if so desired - if (workflowArgs.auto.publish == true && (workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : [:]).isEmpty()) { - // can't assert at this level thanks to the no_publish profile - // assert params.containsKey("publishDir") || params.containsKey("publish_dir") : - // "Error in module '${workflowArgs['key']}': if auto.publish is true, params.publish_dir needs to be defined.\n" + - // " Example: params.publish_dir = \"./output/\"" - def publishDir = getPublishDir() - - if (publishDir != null) { - workflowArgs.directives.publishDir = [[ - path: publishDir, - saveAs: "{ it.startsWith('.') ? null : it }", // don't publish hidden files, by default - mode: "copy" - ]] - } - } - - // auto define transcript, if so desired - if (workflowArgs.auto.transcript == true) { - // can't assert at this level thanks to the no_publish profile - // assert params.containsKey("transcriptsDir") || params.containsKey("transcripts_dir") || params.containsKey("publishDir") || params.containsKey("publish_dir") : - // "Error in module '${workflowArgs['key']}': if auto.transcript is true, either params.transcripts_dir or params.publish_dir needs to be defined.\n" + - // " Example: params.transcripts_dir = \"./transcripts/\"" - def transcriptsDir = - params.containsKey("transcripts_dir") ? params.transcripts_dir : - params.containsKey("transcriptsDir") ? params.transcriptsDir : - params.containsKey("publish_dir") ? params.publish_dir + "/_transcripts" : - params.containsKey("publishDir") ? params.publishDir + "/_transcripts" : - null - if (transcriptsDir != null) { - def timestamp = nextflow.Nextflow.getSession().getWorkflowMetadata().start.format('yyyy-MM-dd_HH-mm-ss') - def transcriptsPublishDir = [ - path: "$transcriptsDir/$timestamp/\${task.process.replaceAll(':', '-')}/\${id}/", - saveAs: "{ it.startsWith('.') ? it.replaceAll('^.', '') : null }", - mode: "copy" - ] - def publishDirs = workflowArgs.directives.publishDir != null ? workflowArgs.directives.publishDir : null ? workflowArgs.directives.publishDir : [] - workflowArgs.directives.publishDir = publishDirs + transcriptsPublishDir - } - } - - // if this is a stubrun, remove certain directives? - if (workflow.stubRun) { - workflowArgs.directives.keySet().removeAll(["publishDir", "cpus", "memory", "label"]) - } - - for (nam in ["map", "mapId", "mapData", "mapPassthrough", "filter"]) { - if (workflowArgs.containsKey(nam) && workflowArgs[nam]) { - assert workflowArgs[nam] instanceof Closure : "Error in module '$key': Expected process argument '$nam' to be null or a Closure. Found: class ${workflowArgs[nam].getClass()}" - } - } - - // TODO: should functions like 'map', 'mapId', 'mapData', 'mapPassthrough' be deprecated as well? - for (nam in ["renameKeys"]) { - if (workflowArgs.containsKey(nam) && workflowArgs[nam] != null) { - log.warn "module '$key': workflow argument '$nam' will be deprecated in Viash 0.9.0. Please use 'fromState' and 'toState' instead." - } - } - - // check fromState - workflowArgs["fromState"] = _processFromState(workflowArgs.get("fromState"), key, thisConfig) - - // check toState - workflowArgs["toState"] = _processToState(workflowArgs.get("toState"), key, thisConfig) - - // return output - return workflowArgs -} - -def _processFromState(fromState, key_, config_) { - assert fromState == null || fromState instanceof Closure || fromState instanceof Map || fromState instanceof List : - "Error in module '$key_': Expected process argument 'fromState' to be null, a Closure, a Map, or a List. Found: class ${fromState.getClass()}" - if (fromState == null) { - return null - } - - // if fromState is a List, convert to map - if (fromState instanceof List) { - // check whether fromstate is a list[string] - assert fromState.every{it instanceof CharSequence} : "Error in module '$key_': fromState is a List, but not all elements are Strings" - fromState = fromState.collectEntries{[it, it]} - } - - // if fromState is a map, convert to closure - if (fromState instanceof Map) { - // check whether fromstate is a map[string, string] - assert fromState.values().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all values are Strings" - assert fromState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': fromState is a Map, but not all keys are Strings" - def fromStateMap = fromState.clone() - def requiredInputNames = thisConfig.functionality.allArguments.findAll{it.required && it.direction == "Input"}.collect{it.plainName} - // turn the map into a closure to be used later on - fromState = { it -> - def state = it[1] - assert state instanceof Map : "Error in module '$key_': the state is not a Map" - def data = fromStateMap.collectMany{newkey, origkey -> - // check whether newkey corresponds to a required argument - if (state.containsKey(origkey)) { - [[newkey, state[origkey]]] - } else if (!requiredInputNames.contains(origkey)) { - [] - } else { - throw new Exception("Error in module '$key_': fromState key '$origkey' not found in current state") - } - }.collectEntries() - data - } - } - - return fromState -} - -def _processToState(toState, key_, config_) { - if (toState == null) { - toState = { tup -> tup[1] } - } - - // toState should be a closure, map[string, string], or list[string] - assert toState instanceof Closure || toState instanceof Map || toState instanceof List : - "Error in module '$key_': Expected process argument 'toState' to be a Closure, a Map, or a List. Found: class ${toState.getClass()}" - - // if toState is a List, convert to map - if (toState instanceof List) { - // check whether toState is a list[string] - assert toState.every{it instanceof CharSequence} : "Error in module '$key_': toState is a List, but not all elements are Strings" - toState = toState.collectEntries{[it, it]} - } - - // if toState is a map, convert to closure - if (toState instanceof Map) { - // check whether toState is a map[string, string] - assert toState.values().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all values are Strings" - assert toState.keySet().every{it instanceof CharSequence} : "Error in module '$key_': toState is a Map, but not all keys are Strings" - def toStateMap = toState.clone() - def requiredOutputNames = config_.functionality.allArguments.findAll{it.required && it.direction == "Output"}.collect{it.plainName} - // turn the map into a closure to be used later on - toState = { it -> - def output = it[1] - def state = it[2] - assert output instanceof Map : "Error in module '$key_': the output is not a Map" - assert state instanceof Map : "Error in module '$key_': the state is not a Map" - def extraEntries = toStateMap.collectMany{newkey, origkey -> - // check whether newkey corresponds to a required argument - if (output.containsKey(origkey)) { - [[newkey, output[origkey]]] - } else if (!requiredOutputNames.contains(origkey)) { - [] - } else { - throw new Exception("Error in module '$key_': toState key '$origkey' not found in current output") - } - }.collectEntries() - state + extraEntries - } - } - - return toState -} - -// helper file: 'src/main/resources/io/viash/platforms/nextflow/workflowFactory/workflowFactory.nf' -def _debug(workflowArgs, debugKey) { - if (workflowArgs.debug) { - view { "process '${workflowArgs.key}' $debugKey tuple: $it" } - } else { - map { it } - } -} - -// depends on: thisConfig, innerWorkflowFactory -def workflowFactory(Map args) { - def workflowArgs = processWorkflowArgs(args) - def key_ = workflowArgs["key"] - - workflow workflowInstance { - take: input_ - - main: - mid1_ = input_ - | checkUniqueIds([:]) - | _debug(workflowArgs, "input") - | map { tuple -> - tuple = tuple.clone() - - if (workflowArgs.map) { - tuple = workflowArgs.map(tuple) - } - if (workflowArgs.mapId) { - tuple[0] = workflowArgs.mapId(tuple[0]) - } - if (workflowArgs.mapData) { - tuple[1] = workflowArgs.mapData(tuple[1]) - } - if (workflowArgs.mapPassthrough) { - tuple = tuple.take(2) + workflowArgs.mapPassthrough(tuple.drop(2)) - } - - // check tuple - assert tuple instanceof List : - "Error in module '${key_}': element in channel should be a tuple [id, data, ...otherargs...]\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Expected class: List. Found: tuple.getClass() is ${tuple.getClass()}" - assert tuple.size() >= 2 : - "Error in module '${key_}': expected length of tuple in input channel to be two or greater.\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Found: tuple.size() == ${tuple.size()}" - - // check id field - assert tuple[0] instanceof CharSequence : - "Error in module '${key_}': first element of tuple in channel should be a String\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Found: ${tuple[0]}" - - // match file to input file - if (workflowArgs.auto.simplifyInput && (tuple[1] instanceof Path || tuple[1] instanceof List)) { - def inputFiles = thisConfig.functionality.allArguments - .findAll { it.type == "file" && it.direction == "input" } - - assert inputFiles.size() == 1 : - "Error in module '${key_}' id '${tuple[0]}'.\n" + - " Anonymous file inputs are only allowed when the process has exactly one file input.\n" + - " Expected: inputFiles.size() == 1. Found: inputFiles.size() is ${inputFiles.size()}" - - tuple[1] = [[ inputFiles[0].plainName, tuple[1] ]].collectEntries() - } - - // check data field - assert tuple[1] instanceof Map : - "Error in module '${key_}' id '${tuple[0]}': second element of tuple in channel should be a Map\n" + - " Example: [\"id\", [input: file('foo.txt'), arg: 10]].\n" + - " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" - - // rename keys of data field in tuple - if (workflowArgs.renameKeys) { - assert workflowArgs.renameKeys instanceof Map : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class: Map. Found: renameKeys.getClass() is ${workflowArgs.renameKeys.getClass()}" - assert tuple[1] instanceof Map : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Expected class: Map. Found: tuple[1].getClass() is ${tuple[1].getClass()}" - - // TODO: allow renameKeys to be a function? - workflowArgs.renameKeys.each { newKey, oldKey -> - assert newKey instanceof CharSequence : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class of newKey: String. Found: newKey.getClass() is ${newKey.getClass()}" - assert oldKey instanceof CharSequence : - "Error renaming data keys in module '${key_}' id '${tuple[0]}'.\n" + - " Example: renameKeys: ['new_key': 'old_key'].\n" + - " Expected class of oldKey: String. Found: oldKey.getClass() is ${oldKey.getClass()}" - assert tuple[1].containsKey(oldKey) : - "Error renaming data keys in module '${key}' id '${tuple[0]}'.\n" + - " Key '$oldKey' is missing in the data map. tuple[1].keySet() is '${tuple[1].keySet()}'" - tuple[1].put(newKey, tuple[1][oldKey]) - } - tuple[1].keySet().removeAll(workflowArgs.renameKeys.collect{ newKey, oldKey -> oldKey }) - } - tuple - } - - if (workflowArgs.filter) { - mid2_ = mid1_ - | filter{workflowArgs.filter(it)} - } else { - mid2_ = mid1_ - } - - if (workflowArgs.fromState) { - mid3_ = mid2_ - | map{ - def new_data = workflowArgs.fromState(it.take(2)) - [it[0], new_data] - } - } else { - mid3_ = mid2_ - } - - // fill in defaults - mid4_ = mid3_ - | map { tuple -> - def id_ = tuple[0] - def data_ = tuple[1] - - // TODO: could move fromState to here - - // fetch default params from functionality - def defaultArgs = thisConfig.functionality.allArguments - .findAll { it.containsKey("default") } - .collectEntries { [ it.plainName, it.default ] } - - // fetch overrides in params - def paramArgs = thisConfig.functionality.allArguments - .findAll { par -> - def argKey = key_ + "__" + par.plainName - params.containsKey(argKey) - } - .collectEntries { [ it.plainName, params[key_ + "__" + it.plainName] ] } - - // fetch overrides in data - def dataArgs = thisConfig.functionality.allArguments - .findAll { data_.containsKey(it.plainName) } - .collectEntries { [ it.plainName, data_[it.plainName] ] } - - // combine params - def combinedArgs = defaultArgs + paramArgs + workflowArgs.args + dataArgs - - // remove arguments with explicit null values - combinedArgs - .removeAll{_, val -> val == null || val == "viash_no_value" || val == "force_null"} - - combinedArgs = processInputs(combinedArgs, thisConfig, id_, key_) - - [id_, combinedArgs] + tuple.drop(2) - } - - // TODO: move some of the _meta.join_id wrangling to the safeJoin() function. - - out0_ = mid4_ - | _debug(workflowArgs, "processed") - // run workflow - | innerWorkflowFactory(workflowArgs) - // check output tuple - | map { id_, output_ -> - - // see if output map contains metadata - def meta_ = - output_ instanceof Map && output_.containsKey("_meta") ? - output_["_meta"] : - [:] - if (!meta_.containsKey("join_id")) { - meta_ = meta_ + ["join_id": id_] - } - - // remove metadata - output_ = output_.findAll{k, v -> k != "_meta"} - - output_ = processOutputs(output_, thisConfig, id_, key_) - - if (workflowArgs.auto.simplifyOutput && output_.size() == 1) { - output_ = output_.values()[0] - } - - [meta_.join_id, meta_, id_, output_] - } - // | view{"out0_: ${it.take(3)}"} - - // TODO: this join will fail if the keys changed during the innerWorkflowFactory - // join the output [join_id, meta, id, output] with the previous state [id, state, ...] - out1_ = safeJoin(out0_, mid2_, key_) - // input tuple format: [join_id, meta, id, output, prev_state, ...] - // output tuple format: [join_id, meta, id, new_state, ...] - | map{ tup -> - def new_state = workflowArgs.toState(tup.drop(2).take(3)) - tup.take(3) + [new_state] + tup.drop(5) - } - - if (workflowArgs.auto.publish == "state") { - out1pub_ = out1_ - // input tuple format: [join_id, meta, id, new_state, ...] - // output tuple format: [join_id, meta, id, new_state] - | map{ tup -> - tup.take(4) - } - - safeJoin(out1pub_, mid4_, key_) - // input tuple format: [join_id, meta, id, new_state, orig_state, ...] - // output tuple format: [id, new_state, orig_state] - | map { tup -> - tup.drop(2).take(3) - } - | publishStatesByConfig(key: key_, config: thisConfig) - } - - // remove join_id and meta - out2_ = out1_ - | map { tup -> - // input tuple format: [join_id, meta, id, new_state, ...] - // output tuple format: [id, new_state, ...] - tup.drop(2) - } - | _debug(workflowArgs, "output") - - out2_ - - emit: out2_ - } - - def wf = workflowInstance.cloneWithName(key_) - - // add factory function - wf.metaClass.run = { runArgs -> - workflowFactory(runArgs) - } - // add config to module for later introspection - wf.metaClass.config = thisConfig - - return wf -} From 8645e6391982806078038ceda06f0b2ac03a1999 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 6 Dec 2023 15:30:04 +0100 Subject: [PATCH 1070/1233] Fix component directive labels (#298) * Add nf-tower cli for dataset loader * add mising directive labels for dataset loader * add missing directive labels process datasets * remove space in file name Former-commit-id: 6ed72c793ae04eb3a14a7346fbf9cf3a96d0e585 --- .../loaders/openproblems_v1/config.vsh.yaml | 2 + .../config.vsh.yaml | 2 + src/datasets/processors/hvg/config.vsh.yaml | 2 + src/datasets/processors/knn/config.vsh.yaml | 2 + src/datasets/processors/pca/config.vsh.yaml | 2 + .../processors/subsample/config.vsh.yaml | 2 + src/datasets/processors/svd/config.vsh.yaml | 2 + .../openproblems_v1_multimodal_nf_tower.sh | 58 +++++++ .../openproblems_v1_nf_tower.sh | 154 ++++++++++++++++++ .../process_dataset/config.vsh.yaml | 2 + .../denoising/process_dataset/config.vsh.yaml | 2 + .../process_dataset/config.vsh.yaml | 2 + .../process_dataset/config.vsh.yaml | 2 + 13 files changed, 234 insertions(+) create mode 100755 src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh create mode 100755 src/datasets/resource_scripts/openproblems_v1_nf_tower.sh diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 58d495af8c..73874cbb4a 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -70,3 +70,5 @@ platforms: pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index e593e11519..d8c9fd1226 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -78,3 +78,5 @@ platforms: pip install --no-cache-dir -r /opt/openproblems/docker/openproblems/requirements.txt && \ pip install --no-cache-dir --editable /opt/openproblems - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index f0f5e87efe..f008be5e57 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -9,3 +9,5 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index ecc3bd6a82..c86f30373d 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -9,3 +9,5 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 5af00240cf..cbdfbc4288 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -13,3 +13,5 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 9e2173e020..6a5f5f4d69 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -47,3 +47,5 @@ platforms: packages: - viashpy - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index 5e97eab73f..e4a1f48d42 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -12,3 +12,5 @@ platforms: - type: python pypi: [scikit-learn] - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh new file mode 100755 index 0000000000..7028068f8e --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +params_file="/tmp/datasets_openproblems_v1_multimodal_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: citeseq_cbmc + dataset_name: "CITE-Seq CBMC" + dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" + dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." + dataset_reference: stoeckius2017simultaneous + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 + dataset_organism: homo_sapiens + layer_counts: counts + + - id: scicar_cell_lines + dataset_name: "sci-CAR Cell Lines" + dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" + dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." + dataset_reference: cao2018joint + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_organism: "[homo_sapiens, mus_musculus]" + obs_cell_type: cell_name + layer_counts: counts + + - id: scicar_mouse_kidney + dataset_name: "sci-CAR Mouse Kidney" + dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" + dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." + dataset_reference: cao2018joint + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 + dataset_organism: mus_musculus + obs_cell_type: cell_name + obs_batch: replicate + layer_counts: counts + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset_mod1: '$id/dataset_mod1.h5ad' +output_dataset_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' +output_state: '$id/state.yaml' +publish_dir: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file "$params_file" \ \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh new file mode 100755 index 0000000000..7ffe933674 --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh @@ -0,0 +1,154 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +params_file="/tmp/datasets_openproblems_v1_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: allen_brain_atlas + obs_cell_type: label + layer_counts: counts + dataset_name: Mouse Brain Atlas + dataset_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 + dataset_reference: tasic2016adult + dataset_summary: Adult mouse primary visual cortex + dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). + dataset_organism: mus_musculus + + - id: cengen + obs_cell_type: cell_type + obs_batch: experiment_code + obs_tissue: tissue + layer_counts: counts + dataset_name: CeNGEN + dataset_url: https://www.cengen.org + dataset_reference: hammarlund2018cengen + dataset_summary: Complete Gene Expression Map of an Entire Nervous System + dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. + dataset_organism: caenorhabditis_elegans + + - id: immune_cells + obs_cell_type: final_annotation + obs_batch: batch + obs_tissue: tissue + layer_counts: counts + dataset_name: Human immune + dataset_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html + dataset_reference: luecken2022benchmarking + dataset_summary: Human immune cells dataset from the scIB benchmarks + dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). + dataset_organism: homo_sapiens + + - id: mouse_blood_olsson_labelled + obs_cell_type: celltype + layer_counts: counts + dataset_name: Mouse myeloid + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 + dataset_reference: olsson2016single + dataset_summary: Myeloid lineage differentiation from mouse blood + dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. + dataset_organism: mus_musculus + + - id: mouse_hspc_nestorowa2016 + obs_cell_type: cell_type_label + layer_counts: counts + dataset_name: Mouse HSPC + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 + dataset_reference: nestorowa2016single + dataset_summary: Haematopoeitic stem and progenitor cells from mouse bone marrow + dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. + dataset_organism: mus_musculus + + - id: pancreas + obs_cell_type: celltype + obs_batch: tech + layer_counts: counts + dataset_name: Human pancreas + dataset_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html + dataset_reference: luecken2022benchmarking + dataset_summary: Human pancreas cells dataset from the scIB benchmarks + dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). + dataset_organism: homo_sapiens + + # disabled as this is not working in openproblemsv1 + # - id: tabula_muris_senis_droplet_lung + # obs_cell_type: cell_type + # obs_batch: donor_id + # layer_counts: counts + # dataset_name: Tabula Muris Senis Lung + # dataset_url: https://tabula-muris-senis.ds.czbiohub.org + # dataset_reference: tabula2020single + # dataset_summary: Aging mouse lung cells from Tabula Muris Senis + # dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. + # dataset_organism: mus_musculus + + - id: tenx_1k_pbmc + layer_counts: counts + dataset_name: 1k PBMCs + dataset_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 + dataset_reference: 10x2018pbmc + dataset_summary: 1k peripheral blood mononuclear cells from a healthy donor + dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. + dataset_organism: homo_sapiens + + - id: tenx_5k_pbmc + layer_counts: counts + dataset_name: 5k PBMCs + dataset_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 + dataset_reference: 10x2019pbmc + dataset_summary: 5k peripheral blood mononuclear cells from a healthy donor + dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. + dataset_organism: homo_sapiens + + - id: tnbc_wu2021 + obs_cell_type: celltype_minor + layer_counts: counts + dataset_name: Triple-Negative Breast Cancer + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 + dataset_reference: wu2021single + dataset_summary: 1535 cells from six fresh triple-negative breast cancer tumors. + dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). + dataset_organism: homo_sapiens + + - id: zebrafish + obs_cell_type: cell_type + obs_batch: lab + layer_counts: counts + dataset_name: Zebrafish embryonic cells + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 + dataset_reference: wagner2018single + dataset_summary: Single-cell mRNA sequencing of zebrafish embryonic cells. + dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. + dataset_organism: danio_rerio + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null +publish_dir: s3://openproblems-data/resources/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision integration_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file "$params_file" \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 5b8b7447a5..e751637511 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -14,3 +14,5 @@ platforms: pypi: - scib==1.1.3 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 057663cb29..41bea59011 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -33,3 +33,5 @@ platforms: - numpy - scipy - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 8b4984bc40..28e16f3cb6 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -27,3 +27,5 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] diff --git a/src/tasks/match_modalities/process_dataset/config.vsh.yaml b/src/tasks/match_modalities/process_dataset/config.vsh.yaml index 79b03ce982..9785c0d9ae 100644 --- a/src/tasks/match_modalities/process_dataset/config.vsh.yaml +++ b/src/tasks/match_modalities/process_dataset/config.vsh.yaml @@ -14,3 +14,5 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow + directives: + label: [ highmem, midcpu , midtime] From ce8252d12c550df1439980b1676a2a669c1898da Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 7 Dec 2023 23:24:37 +0100 Subject: [PATCH 1071/1233] Fix dataset wf (#300) * Add nf-tower cli for dataset loader * add mising directive labels for dataset loader * add missing directive labels process datasets * remove space in file name * update s3 bucket * increase yaml limit to 5mb * Fix dataset schema validation and remove unnecessary code to fix meta file size * Update dataset schema file path in config.vsh.yaml and main.nf * Add script for processing datasets on nf-tower in bat_int * Remove dataset_schema input from config.vsh.yaml * Add output_task_info to workflow configuration * Update publish directory in process_datasets.sh for bat_int * Update denoising process_datasets wf Former-commit-id: 82a6a4d06e69baf39df703e6ee0cbcfd9fa35c33 --- src/common/check_dataset_schema/script.py | 4 +-- .../openproblems_v1_multimodal_nf_tower.sh | 2 +- .../openproblems_v1_nf_tower.sh | 2 +- .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 2 +- .../nf_tower_scripts/run_test.sh | 2 +- .../process_datasets/config.vsh.yaml | 8 ++---- .../workflows/process_datasets/main.nf | 11 +++++--- .../workflows/run_benchmark/config.vsh.yaml | 7 ++++++ .../workflows/run_benchmark/main.nf | 4 +++ .../workflows/run_benchmark/run_test.sh | 2 +- .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 2 +- .../denoising/nf_tower_scripts/run_test.sh | 2 +- .../process_datasets/config.vsh.yaml | 9 ++----- .../workflows/process_datasets/main.nf | 11 +++++--- .../nf_tower_scripts/run_benchmark.sh | 2 +- .../nf_tower_scripts/run_test.sh | 2 +- 18 files changed, 90 insertions(+), 32 deletions(-) create mode 100644 src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh create mode 100755 src/tasks/denoising/nf_tower_scripts/process_datasets.sh diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index ef02af85c1..e70f990dcf 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -73,9 +73,9 @@ def to_dict_of_atomics(obj): for key, val in adata.uns.items(): if is_atomic(val): uns[key] = to_atomic(val) - elif is_list_of_atomics(val): + elif is_list_of_atomics(val) and len(val) <= 10: uns[key] = to_list_of_atomics(val) - elif is_dict_of_atomics(val): + elif is_dict_of_atomics(val) and len(val) <= 10: uns[key] = to_dict_of_atomics(val) structure = { struct: list(getattr(adata, struct).keys()) diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh index 7028068f8e..fa02f996e4 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh @@ -46,7 +46,7 @@ output_dataset_mod2: '$id/dataset_mod2.h5ad' output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' -publish_dir: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal +publish_dir: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh index 7ffe933674..381cd88768 100755 --- a/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh +++ b/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh @@ -135,7 +135,7 @@ output_normalized: force_null output_pca: force_null output_hvg: force_null output_knn: force_null -publish_dir: s3://openproblems-data/resources/datasets/openproblems_v1 +publish_dir: s3://openproblems-nextflow/resources/datasets/openproblems_v1 HERE cat > /tmp/nextflow.config << HERE diff --git a/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh b/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh new file mode 100644 index 0000000000..79f820c5a3 --- /dev/null +++ b/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: batch_integration_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/batch_integration/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh b/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh index ef527d8a82..fe6987e634 100644 --- a/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh @@ -4,7 +4,7 @@ # try running on nf tower cat > /tmp/params.yaml << HERE id: batch_integration -input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml +input_states: s3://openproblems-nextflow/resources/batch_integration/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output/v2/batch_integration diff --git a/src/tasks/batch_integration/nf_tower_scripts/run_test.sh b/src/tasks/batch_integration/nf_tower_scripts/run_test.sh index f9ee29fa4c..5c425be93a 100644 --- a/src/tasks/batch_integration/nf_tower_scripts/run_test.sh +++ b/src/tasks/batch_integration/nf_tower_scripts/run_test.sh @@ -5,7 +5,7 @@ DATASET_DIR=resources_test/batch_integration/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE id: batch_integration_test -input_states: s3://openproblems-data/resources_test/batch_integration/**/state.yaml +input_states: s3://openproblems-nextflow/resources_test/batch_integration/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration/ diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index c9bf906135..38701745dd 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -8,12 +8,6 @@ functionality: __merge__: "/src/tasks/batch_integration/api/file_common_dataset.yaml" required: true direction: input - - name: "--dataset_schema" - type: "file" - description: "The schema of the dataset to validate against" - required: true - default: "src/tasks/batch_integration/api/file_common_dataset.yaml" - direction: input - name: Outputs arguments: - name: "--output_dataset" @@ -28,6 +22,8 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/batch_integration/api/file_common_dataset.yaml" dependencies: - name: common/check_dataset_schema - name: batch_integration/process_dataset diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index 517db44bb7..d940182545 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -15,10 +15,13 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( - fromState: [ - "input": "input", - "schema": "dataset_schema" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + ] + }, args: [ "stop_on_error": false ], diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index ab061ba07e..586d912007 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -35,10 +35,17 @@ functionality: required: true direction: output example: dataset_uns.yaml + - name: "--output_task_info" + type: file + required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: /src/tasks/batch_integration/api/task_info.yaml dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 629ffe2b3b..101825c483 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -212,9 +212,12 @@ workflow run_wf { def metric_configs_file = tempFile("metric_configs.yaml") metric_configs_file.write(metric_configs_yaml_blob) + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, + output_task_info: task_info_file, _meta: _meta ] ["output", new_state] @@ -222,6 +225,7 @@ workflow run_wf { // merge all of the output data // todo: add task info? + // todo: add trace log? output_ch = comp_config_ch | mix(metric_uns_ch, dataset_meta_ch) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh index b407308d29..a24ebb706f 100755 --- a/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh +++ b/src/tasks/batch_integration/workflows/run_benchmark/run_test.sh @@ -26,6 +26,6 @@ nextflow run . \ -entry auto \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml"}' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state "state.yaml" \ No newline at end of file diff --git a/src/tasks/denoising/nf_tower_scripts/process_datasets.sh b/src/tasks/denoising/nf_tower_scripts/process_datasets.sh new file mode 100755 index 0000000000..d8ef8ed16f --- /dev/null +++ b/src/tasks/denoising/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: denoising_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_train": "train.h5ad", "output_test": "test.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/denoising/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh b/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh index 099b248244..afdd2157b6 100644 --- a/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh +++ b/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh @@ -5,7 +5,7 @@ DATASET_DIR=resources_test/denoising/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE id: denoising -input_states: s3://openproblems-data/resources/denoising/datasets/**/*state.yaml +input_states: s3://openproblems-nextflow/resources/denoising/datasets/**/*state.yaml rename_keys: 'input_train:output_train,input_test:output_test' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output/v2/denoising diff --git a/src/tasks/denoising/nf_tower_scripts/run_test.sh b/src/tasks/denoising/nf_tower_scripts/run_test.sh index a9b35a8d3e..2fa06943ed 100644 --- a/src/tasks/denoising/nf_tower_scripts/run_test.sh +++ b/src/tasks/denoising/nf_tower_scripts/run_test.sh @@ -5,7 +5,7 @@ DATASET_DIR=resources_test/denoising/pancreas # try running on nf tower cat > /tmp/params.yaml << HERE id: denoising_test -input_states: s3://openproblems-data/resources_test/denoising/pancreas/ +input_states: s3://openproblems-nextflow/resources_test/denoising/pancreas/ rename_keys: 'input_train:output_train,input_test:output_test' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output_test/v2/denoising/ diff --git a/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml index 1ce58796c5..5746c6247e 100644 --- a/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml @@ -8,13 +8,6 @@ functionality: required: true example: dataset.h5ad __merge__: "/src/tasks/denoising/api/file_common_dataset.yaml" - - name: Schemas - arguments: - - name: "--dataset_schema" - type: "file" - description: "The schema of the dataset to validate against" - required: true - default: "src/tasks/denoising/api/file_common_dataset.yaml" - name: Outputs arguments: - name: "--output_train" @@ -29,6 +22,8 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/denoising/api/file_common_dataset.yaml" dependencies: - name: common/check_dataset_schema - name: denoising/process_dataset diff --git a/src/tasks/denoising/workflows/process_datasets/main.nf b/src/tasks/denoising/workflows/process_datasets/main.nf index 8d52e1d81a..177ffc9e39 100644 --- a/src/tasks/denoising/workflows/process_datasets/main.nf +++ b/src/tasks/denoising/workflows/process_datasets/main.nf @@ -15,10 +15,13 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( - fromState: [ - "input": "input", - "schema": "dataset_schema" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + ] + }, args: [ "stop_on_error": false ], diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh index b6ae2b094f..acf0cd9391 100644 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh @@ -4,7 +4,7 @@ # try running on nf tower cat > /tmp/params.yaml << HERE id: dimensionality_reduction -input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets +input_states: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output/v2/dimensionality_reduction diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh index 9f3cdbfe9b..a9cf390032 100644 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh @@ -4,7 +4,7 @@ # try running on nf tower cat > /tmp/params.yaml << HERE id: dimensionality_reduction -input_states: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas +input_states: s3://openproblems-nextflow/resources_test/dimensionality_reduction/pancreas rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output_test/v2/dimensionality_reduction From f4cc5838f5eb48b11ce4b53d874306dc4f791ff1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 11 Dec 2023 14:41:24 +0100 Subject: [PATCH 1072/1233] Update process datasets wf (#301) * Add nf-tower cli for dataset loader * add mising directive labels for dataset loader * add missing directive labels process datasets * remove space in file name * update s3 bucket * increase yaml limit to 5mb * Fix dataset schema validation and remove unnecessary code to fix meta file size * Update dataset schema file path in config.vsh.yaml and main.nf * Add script for processing datasets on nf-tower in bat_int * Remove dataset_schema input from config.vsh.yaml * Add output_task_info to workflow configuration * Update publish directory in process_datasets.sh for bat_int * Update denoising process_datasets wf * Add dimensionality reduction dataset processing script and configuration files for nf-tower * Add label projection nf-tower scripts * add nf-tower scripts match_modalities * Add nf-tower scripts and configuration files for processing and running benchmark in predict_modality workflow * Add dataset info fields to benchmark API files Former-commit-id: cc1fd42875335d5ad3e7d799a513c3a2408fa2d2 --- .../denoising/api/file_common_dataset.yaml | 24 +++++++++++++++++ src/tasks/denoising/api/file_test.yaml | 26 +++++++++++++++++- .../api/file_common_dataset.yaml | 24 +++++++++++++++++ .../api/file_solution.yaml | 24 +++++++++++++++++ .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 2 +- .../process_datasets/config.vsh.yaml | 8 ++---- .../workflows/process_datasets/main.nf | 11 +++++--- .../api/file_common_dataset.yaml | 24 +++++++++++++++++ .../label_projection/api/file_solution.yaml | 24 +++++++++++++++++ .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 25 +++++++++++++++++ .../process_datasets/config.vsh.yaml | 8 ++---- .../workflows/process_datasets/main.nf | 11 +++++--- .../api/file_common_dataset_mod1.yaml | 24 +++++++++++++++++ .../api/file_common_dataset_mod2.yaml | 24 +++++++++++++++++ .../api/file_solution_mod1.yaml | 24 +++++++++++++++++ .../api/file_solution_mod2.yaml | 24 +++++++++++++++++ .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 25 +++++++++++++++++ .../resources_scripts/run_benchmark.sh | 6 ++--- .../process_datasets/config.vsh.yaml | 16 +++-------- .../workflows/process_datasets/main.nf | 22 +++++++++------ .../api/file_common_dataset_rna.yaml | 24 +++++++++++++++++ .../api/file_dataset_other_mod.yaml | 24 +++++++++++++++++ .../predict_modality/api/file_test_mod1.yaml | 20 ++++++++++++++ .../predict_modality/api/file_test_mod2.yaml | 20 ++++++++++++++ .../nf_tower_scripts/process_datasets.sh | 25 +++++++++++++++++ .../nf_tower_scripts/run_benchmark.sh | 27 +++++++++++++++++++ .../process_datasets/config.vsh.yaml | 16 +++-------- .../workflows/process_datasets/main.nf | 22 +++++++++------ 31 files changed, 564 insertions(+), 65 deletions(-) create mode 100755 src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh create mode 100755 src/tasks/label_projection/nf_tower_scripts/process_datasets.sh create mode 100755 src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh create mode 100755 src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh create mode 100755 src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh create mode 100755 src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh create mode 100755 src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh diff --git a/src/tasks/denoising/api/file_common_dataset.yaml b/src/tasks/denoising/api/file_common_dataset.yaml index 0f5551a4ca..ff913ce0de 100644 --- a/src/tasks/denoising/api/file_common_dataset.yaml +++ b/src/tasks/denoising/api/file_common_dataset.yaml @@ -14,3 +14,27 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false diff --git a/src/tasks/denoising/api/file_test.yaml b/src/tasks/denoising/api/file_test.yaml index eddfa7b95f..04d89251ce 100644 --- a/src/tasks/denoising/api/file_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -13,4 +13,28 @@ info: - type: string name: dataset_id description: "A unique identifier for the dataset" - required: true \ No newline at end of file + required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml index 8061f8f0c5..57af727c7c 100644 --- a/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml @@ -23,6 +23,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/dimensionality_reduction/api/file_solution.yaml b/src/tasks/dimensionality_reduction/api/file_solution.yaml index 02b376a78b..92d368508e 100644 --- a/src/tasks/dimensionality_reduction/api/file_solution.yaml +++ b/src/tasks/dimensionality_reduction/api/file_solution.yaml @@ -23,6 +23,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh new file mode 100755 index 0000000000..386df85ebf --- /dev/null +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: dimensionality_reduction_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh index acf0cd9391..31173c0add 100644 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh @@ -4,7 +4,7 @@ # try running on nf tower cat > /tmp/params.yaml << HERE id: dimensionality_reduction -input_states: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets +input_states: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' publish_dir: s3://openproblems-nextflow/output/v2/dimensionality_reduction diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml index bd80704db5..35e80f58ac 100644 --- a/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml @@ -8,12 +8,6 @@ functionality: __merge__: "/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" required: true direction: input - - name: "--dataset_schema" - type: "file" - required: true - direction: input - description: "The schema of the dataset to validate against" - default: "src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" - name: Outputs arguments: - name: "--output_dataset" @@ -28,6 +22,8 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" dependencies: - name: common/check_dataset_schema - name: dimensionality_reduction/process_dataset diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf index 38c35f072e..c01e356cd5 100644 --- a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf @@ -15,10 +15,13 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( - fromState: [ - "input": "input", - "schema": "dataset_schema" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + ] + }, args: [ "stop_on_error": false, "checks": null diff --git a/src/tasks/label_projection/api/file_common_dataset.yaml b/src/tasks/label_projection/api/file_common_dataset.yaml index e3b6741843..f5c50b7c5b 100644 --- a/src/tasks/label_projection/api/file_common_dataset.yaml +++ b/src/tasks/label_projection/api/file_common_dataset.yaml @@ -41,6 +41,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/label_projection/api/file_solution.yaml b/src/tasks/label_projection/api/file_solution.yaml index 78bc3243f6..f1ab136360 100644 --- a/src/tasks/label_projection/api/file_solution.yaml +++ b/src/tasks/label_projection/api/file_solution.yaml @@ -41,6 +41,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh b/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh new file mode 100755 index 0000000000..b61de64879 --- /dev/null +++ b/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: label_projection_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_train": "train.h5ad", "output_test": "test.h5ad", "output_solution": "solution.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/label_projection/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh b/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh new file mode 100755 index 0000000000..a5a1ceca4f --- /dev/null +++ b/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: label_projection +input_states: s3://openproblems-nextflow/resources/label_projection/datasets/**/state.yaml +rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/label_projection +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml index 77fb6fdbbe..c81309a9a9 100644 --- a/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml @@ -8,12 +8,6 @@ functionality: __merge__: "/src/tasks/label_projection/api/file_common_dataset.yaml" required: true direction: input - - name: "--dataset_schema" - type: "file" - description: "The schema of the dataset to validate against" - required: true - default: "src/tasks/label_projection/api/file_common_dataset.yaml" - direction: input - name: Outputs arguments: - name: "--output_train" @@ -32,6 +26,8 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/label_projection/api/file_common_dataset.yaml" dependencies: - name: common/check_dataset_schema - name: label_projection/process_dataset diff --git a/src/tasks/label_projection/workflows/process_datasets/main.nf b/src/tasks/label_projection/workflows/process_datasets/main.nf index 54675d9f9b..60b11ee39e 100644 --- a/src/tasks/label_projection/workflows/process_datasets/main.nf +++ b/src/tasks/label_projection/workflows/process_datasets/main.nf @@ -15,10 +15,13 @@ workflow run_wf { // TODO: check schema based on the values in `config` // instead of having to provide a separate schema file | check_dataset_schema.run( - fromState: [ - "input": "input", - "schema": "dataset_schema" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + ] + }, args: [ "stop_on_error": false ], diff --git a/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml b/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml index fec9d27fa9..cfb98e04ea 100644 --- a/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml +++ b/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml @@ -26,6 +26,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml b/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml index 9c63692c61..c42fbf525c 100644 --- a/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml +++ b/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml @@ -26,6 +26,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/match_modalities/api/file_solution_mod1.yaml b/src/tasks/match_modalities/api/file_solution_mod1.yaml index 2a9d52dc82..490e005e0a 100644 --- a/src/tasks/match_modalities/api/file_solution_mod1.yaml +++ b/src/tasks/match_modalities/api/file_solution_mod1.yaml @@ -28,6 +28,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/match_modalities/api/file_solution_mod2.yaml b/src/tasks/match_modalities/api/file_solution_mod2.yaml index 03009a7e1b..7cb21fef8e 100644 --- a/src/tasks/match_modalities/api/file_solution_mod2.yaml +++ b/src/tasks/match_modalities/api/file_solution_mod2.yaml @@ -28,6 +28,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: normalization_id description: "Which normalization was used" diff --git a/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh b/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh new file mode 100755 index 0000000000..7f5f2b5b03 --- /dev/null +++ b/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: match_modalities_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal/**/state.yaml +rename_keys: 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' +settings: '{"output_mod1": "output_mod1.h5ad", "output_mod2": "output_mod2.h5ad", "output_solution_mod1": "output_solution_mod1.h5ad", "output_solution_mod2": "output_solution_mod2.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/match_modalities/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config diff --git a/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh b/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh new file mode 100755 index 0000000000..898cd0d420 --- /dev/null +++ b/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: match_modalities +input_states: s3://openproblems-nextflow/resources/match_modalities/datasets/**/state.yaml +rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/match_modalities +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 19b3e61598..93d38aa38b 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -10,7 +10,7 @@ set -e # export TOWER_WORKSPACE_ID=53907369739130 -DATASETS_DIR="resources/label_projection" +DATASETS_DIR="resources/match_modalities" OUTPUT_DIR="output/test" if [ ! -d "$OUTPUT_DIR" ]; then @@ -19,13 +19,13 @@ fi export NXF_VER=22.04.5 nextflow run . \ - -main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + -main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ -profile docker \ -resume \ -entry auto \ -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_train:output_train,input_test:output_test,input_solution:output_solution' \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' \ --settings '{"output": "scores.tsv"}' \ --publish_dir "$OUTPUT_DIR"\ --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml index 0145373661..907b556f5d 100644 --- a/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml @@ -12,18 +12,6 @@ functionality: __merge__: "/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" required: true direction: input - - name: "--dataset_schema_mod1" - type: "file" - description: "The schema of the dataset mod1 to validate against" - required: true - default: "src/tasks/match_modalities/api/file_common_dataset_mod1.yaml" - direction: input - - name: "--dataset_schema_mod2" - type: "file" - description: "The schema of the dataset mod2 to validate against" - required: true - default: "src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" - direction: input - name: Outputs arguments: - name: "--output_mod1" @@ -46,6 +34,10 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml" + - type: file + path: "/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" dependencies: - name: common/check_dataset_schema - name: match_modalities/process_dataset diff --git a/src/tasks/match_modalities/workflows/process_datasets/main.nf b/src/tasks/match_modalities/workflows/process_datasets/main.nf index 9e6c9fea6c..50bd25b1fd 100644 --- a/src/tasks/match_modalities/workflows/process_datasets/main.nf +++ b/src/tasks/match_modalities/workflows/process_datasets/main.nf @@ -16,10 +16,13 @@ workflow run_wf { // instead of having to provide a separate schema file | check_dataset_schema.run( key: "check_dataset_schema_mod1", - fromState: [ - "input": "input_mod1", - "schema": "dataset_schema_mod1" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset_mod1.yaml") + ] + }, args: [ "stop_on_error": false ], @@ -29,10 +32,13 @@ workflow run_wf { ) | check_dataset_schema.run( key: "check_dataset_schema_mod2", - fromState: [ - "input": "input_mod2", - "schema": "dataset_schema_mod2" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset_mod2.yaml") + ] + }, args: [ "stop_on_error": false ], diff --git a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml index 92d4b5bc5b..a2801d3a1b 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml @@ -32,6 +32,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml index 8035d80019..15b2ac9fb4 100644 --- a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml +++ b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml @@ -32,6 +32,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index f0be88a16f..6e2d2d0c5e 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -32,6 +32,26 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index 217dfd8d61..414aab4228 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -32,6 +32,26 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. diff --git a/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh b/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh new file mode 100755 index 0000000000..9ebdb5a7ee --- /dev/null +++ b/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: predict_modality_process_datasets +input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal/**/state.yaml +rename_keys: 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' +settings: '{"output_train_mod1": "train_mod1.h5ad", "output_train_mod2": "train_mod2.h5ad", "output_test_mod1": "test_mod1.h5ad", "output_test_mod2": "test_mod2.h5ad"}' +publish_dir: s3://openproblems-nextflow/resources/predict_modality/datasets/openproblems_v1 +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh b/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh new file mode 100755 index 0000000000..9d56c45db7 --- /dev/null +++ b/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh @@ -0,0 +1,27 @@ +#!/bin/bash + +#!/bin/bash + +cat > /tmp/params.yaml << HERE +id: predict_modality +input_states: s3://openproblems-nextflow/resources/predict_modality/datasets/**/state.yaml +rename_keys: 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' +settings: '{"output": "scores.tsv"}' +publish_dir: s3://openproblems-nextflow/output/v2/predict_modality +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index b327ce5463..b2a0a9494c 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -12,18 +12,6 @@ functionality: __merge__: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" direction: input required: true - - name: "--dataset_schema_rna" - type: "file" - description: "The schema of the dataset to validate against" - required: true - default: "src/tasks/predict_modality/api/file_common_dataset_rna.yaml" - direction: input - - name: "--dataset_schema_other_mod" - type: "file" - description: "The schema of the dataset to validate against" - required: true - default: "src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" - direction: input - name: Outputs arguments: - name: "--output_train_mod1" @@ -46,6 +34,10 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/predict_modality/api/file_common_dataset_rna.yaml" + - type: file + path: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" dependencies: - name: common/check_dataset_schema - name: predict_modality/process_dataset diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index ae2c637070..64997c5597 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -16,10 +16,13 @@ workflow run_wf { // instead of having to provide a separate schema file | check_dataset_schema.run( key: "check_dataset_schema_rna", - fromState: [ - "input": "input_rna", - "schema": "dataset_schema_rna" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset_rna.yaml") + ] + }, args: [ "stop_on_error": false ], @@ -31,10 +34,13 @@ workflow run_wf { | check_dataset_schema.run( key: "check_dataset_schema_other_mod", - fromState: [ - "input": "input_other_mod", - "schema": "dataset_schema_other_mod" - ], + fromState: { id, state -> + // as a resource + [ + "input": state.input, + "schema": meta.resources_dir.resolve("file_common_dataset_other_mod.yaml") + ] + }, args: [ "stop_on_error": false ], From 26c44eb333a6276f50472d7e56f4011f99c4e58d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 Dec 2023 17:58:47 +0100 Subject: [PATCH 1073/1233] Fix dataset loaders and processors (#304) * fix opv1multimodal loader * fix processor Former-commit-id: f4c9eca860cf9ee58fa51fef4b7bf05ac058f0bd --- .../openproblems_v1_multimodal/script.py | 23 +++++++++++-------- .../openproblems_v1_multimodal/test.py | 18 +++++++++++---- .../workflows/process_datasets/main.nf | 4 ++-- 3 files changed, 29 insertions(+), 16 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py index 154e1400c9..4e19dd2e19 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/script.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -7,11 +7,16 @@ ## VIASH START par = { "dataset_id": "scicar_mouse_kidney", + "obs_tissue": "source", "obs_cell_type": "cell_type", - "obs_batch": "replicate", - "obs_tissue": None, "layer_counts": "counts", "output": "test_data.h5ad", + "dataset_name": "name", + "dataset_url": "https://some.url", + "dataset_reference": "reference", + "dataset_summary": "summary", + "dataset_description": "description", + "dataset_organism": "[homo_sapiens, mus_musculus]", } meta = { "resources_dir": "src/datasets/loaders/openproblems_v1/" @@ -118,15 +123,13 @@ print("Add metadata to uns", flush=True) metadata_fields = [ "dataset_id", "dataset_name", "dataset_url", "dataset_reference", - "dataset_summary", "dataset_description" "dataset_organism" + "dataset_summary", "dataset_description", "dataset_organism" ] -uns_metadata = { - id: par[id] - for id in metadata_fields - if id in par -} -mod1.uns.update(uns_metadata) -mod2.uns.update(uns_metadata) +for key in metadata_fields: + if key in par: + print(f" Setting .uns['{key}']", flush=True) + mod1.uns[key] = par[key] + mod2.uns[key] = par[key] print("Writing adata to file", flush=True) mod1.write_h5ad(par["output_mod1"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1_multimodal/test.py b/src/datasets/loaders/openproblems_v1_multimodal/test.py index 26e8d9ff93..36075814ff 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/test.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/test.py @@ -31,10 +31,10 @@ ) if out.stdout: - print(out.stdout) + print(out.stdout, flush=True) if out.returncode: - print(f"script: '{out.args}' exited with an error.") + print(f"script: '{out.args}' exited with an error.", flush=True) exit(out.returncode) print(">> Checking whether files exist", flush=True) @@ -51,23 +51,33 @@ print(">> Check that output mod1 fits expected API", flush=True) assert output_mod1.X is None, ".X is not None/empty in mod 1 output" assert "counts" in output_mod1.layers, "'counts' not found in mod 1 output layers" -assert output_mod1.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 1 output uns" if obs_cell_type: assert "cell_type" in output_mod1.obs.columns, "cell_type column not found in mod 1 output obs" if obs_batch: assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" if obs_tissue: assert "tissue" in output_mod1.obs.columns, "tissue column not found in mod 1 output obs" +assert output_mod1.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 1 output uns" +assert output_mod1.uns["dataset_name"] == "Pancreas", "Expected: Pancreas as value for dataset_name in mod 1 output uns" +assert output_mod1.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 1 output uns" +assert output_mod1.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 1 output uns" +assert output_mod1.uns["dataset_summary"] == "A short summary.", "Expected: A short summary. as value for dataset_summary in mod 1 output uns" +assert output_mod1.uns["dataset_description"] == "A couple of paragraphs worth of text.", "Expected: A couple of paragraphs worth of text. as value for dataset_description in mod 1 output uns" print(">> Check that output mod2 fits expected API", flush=True) assert output_mod2.X is None, ".X is not None/empty in mod 2 output" assert "counts" in output_mod2.layers, "'counts' not found in mod 2 output layers" -assert output_mod2.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 2 output uns" if obs_cell_type: assert "cell_type" in output_mod2.obs.columns, "cell_type column not found in mod 2 output obs" if obs_batch: assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" if obs_tissue: assert "tissue" in output_mod2.obs.columns, "tissue column not found in mod 2 output obs" +assert output_mod2.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 2 output uns" +assert output_mod2.uns["dataset_name"] == "Pancreas", "Expected: Pancreas as value for dataset_name in mod 2 output uns" +assert output_mod2.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 2 output uns" +assert output_mod2.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 2 output uns" +assert output_mod2.uns["dataset_summary"] == "A short summary.", "Expected: A short summary. as value for dataset_summary in mod 2 output uns" +assert output_mod2.uns["dataset_description"] == "A couple of paragraphs worth of text.", "Expected: A couple of paragraphs worth of text. as value for dataset_description in mod 2 output uns" print(">> All tests passed successfully", flush=True) diff --git a/src/tasks/match_modalities/workflows/process_datasets/main.nf b/src/tasks/match_modalities/workflows/process_datasets/main.nf index 50bd25b1fd..9f5466e370 100644 --- a/src/tasks/match_modalities/workflows/process_datasets/main.nf +++ b/src/tasks/match_modalities/workflows/process_datasets/main.nf @@ -19,7 +19,7 @@ workflow run_wf { fromState: { id, state -> // as a resource [ - "input": state.input, + "input": state.input_mod1, "schema": meta.resources_dir.resolve("file_common_dataset_mod1.yaml") ] }, @@ -35,7 +35,7 @@ workflow run_wf { fromState: { id, state -> // as a resource [ - "input": state.input, + "input": state.input_mod2, "schema": meta.resources_dir.resolve("file_common_dataset_mod2.yaml") ] }, From bc048339f65de99ddace0471d62b6216721e9b5e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 Dec 2023 22:16:50 +0100 Subject: [PATCH 1074/1233] fix component (#305) Former-commit-id: dbf67c52d073310cf4f2f5fdc9c4fbb1effa9579 --- src/tasks/denoising/process_dataset/script.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index 7f097490bf..d0eb9cf244 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -53,11 +53,12 @@ var=adata.var[[]], uns={"dataset_id": adata.uns["dataset_id"]} ) +test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"] output_test = ad.AnnData( layers={"counts": X_test.astype(float)}, obs=adata.obs[[]], var=adata.var[[]], - uns={"dataset_id": adata.uns["dataset_id"]} + uns={key: adata.uns[key] for key in test_uns_keys} ) # Remove no cells that do not have enough reads From 7c3e6ebbab747291628140a18b9611ab9097d647 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 06:38:32 +0100 Subject: [PATCH 1075/1233] update readmes (#302) * update readmes * update readmes Former-commit-id: d13f642ed11524ad1e283baed941a9952bdddbfe --- src/tasks/batch_integration/README.md | 77 ++++++++------ src/tasks/denoising/README.md | 91 ++++++++++------ src/tasks/dimensionality_reduction/README.md | 97 +++++++++++------ src/tasks/label_projection/README.md | 65 +++++++----- src/tasks/match_modalities/README.md | 103 ++++++++++++------- src/tasks/predict_modality/README.md | 84 +++++++++------ 6 files changed, 318 insertions(+), 199 deletions(-) diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 2d5ed3bbf3..0906460059 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -38,8 +38,7 @@ embedding and/or a neighbourhood graph. The respective batch-integrated representation is then evaluated using sets of metrics that capture how well batch effects are removed and whether biological variance is conserved. We have based this particular task on the latest, and most -extensive benchmark of single-cell data integration methods -\[@luecken2022benchmarking\]. +extensive benchmark of single-cell data integration methods. ## Authors & contributors @@ -115,12 +114,12 @@ Format:
AnnData object - obs: 'celltype', 'batch' + obs: 'cell_type', 'batch' var: 'hvg' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'knn'
@@ -128,20 +127,25 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | Cell type information. | -| `obs["batch"]` | `string` | Batch information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["cell_type"]` | `string` | Cell type information. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. |
@@ -161,7 +165,7 @@ Arguments: | `--input` | `file` | A subset of the common dataset. | | `--output_dataset` | `file` | (*Output*) Unintegrated AnnData HDF5 file. | | `--output_solution` | `file` | (*Output*) Solution dataset. | -| `--obs_label` | `string` | (*Optional*) Which .obs slot to use as label. Default: `celltype`. | +| `--obs_label` | `string` | (*Optional*) Which .obs slot to use as label. Default: `cell_type`. | | `--obs_batch` | `string` | (*Optional*) Which .obs slot to use as batch covariate. Default: `batch`. | | `--hvgs` | `integer` | (*Optional*) Number of highly variable genes. Default: `2000`. | | `--subset_hvg` | `boolean` | (*Optional*) Whether to subset to highly variable genes. Default: `FALSE`. | @@ -233,7 +237,7 @@ Format: obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'knn' @@ -241,20 +245,25 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["label"]` | `string` | label information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["label"]` | `string` | label information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. |
diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index fe16683e80..394a5f6df2 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -93,13 +93,13 @@ Format:
AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' + obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' + var: 'feature_id', 'feature_name', 'soma_joinid', 'hvg', 'hvg_score' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' varm: 'pca_loadings' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'pca_variance', 'knn'
@@ -107,29 +107,52 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | -| `obs["batch"]` | `string` | (*Optional*) Batch information. | -| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalised expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_name"]` | `string` | Nicely formatted name. | -| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | -| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | -| `uns["dataset_summary"]` | `string` | Short description of the dataset. | -| `uns["dataset_description"]` | `string` | Long description of the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["pca_variance"]` | `double` | The PCA variance objects. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:--------------------------------------------------|:----------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `obs["dataset_id"]` | `string` | (*Optional*) Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes. | +| `obs["assay"]` | `string` | (*Optional*) Type of assay used to generate the cell data, indicating the methodology or technique employed. | +| `obs["assay_ontology_term_id"]` | `string` | (*Optional*) Experimental Factor Ontology (`EFO:`) term identifier for the assay, providing a standardized reference to the assay type. | +| `obs["cell_type"]` | `string` | (*Optional*) Classification of the cell type based on its characteristics and function within the tissue or organism. | +| `obs["cell_type_ontology_term_id"]` | `string` | (*Optional*) Cell Ontology (`CL:`) term identifier for the cell type, offering a standardized reference to the specific cell classification. | +| `obs["development_stage"]` | `string` | (*Optional*) Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase. | +| `obs["development_stage_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Developmental Stages (`HsapDv:`) ontology is used. If the organism is mouse (`organism_ontology_term_id == 'NCBITaxon:10090'`), then the Mouse Developmental Stages (`MmusDv:`) ontology is used. Otherwise, the Uberon (`UBERON:`) ontology is used. | +| `obs["disease"]` | `string` | (*Optional*) Information on any disease or pathological condition associated with the cell or donor. | +| `obs["disease_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). | +| `obs["donor_id"]` | `string` | (*Optional*) Identifier for the donor from whom the cell sample is obtained. | +| `obs["is_primary_data"]` | `boolean` | (*Optional*) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. | +| `obs["self_reported_ethnicity"]` | `string` | (*Optional*) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. | +| `obs["self_reported_ethnicity_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. | +| `obs["sex"]` | `string` | (*Optional*) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. | +| `obs["sex_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only `PATO:0000383`, `PATO:0000384` and `PATO:0001340` are allowed. | +| `obs["suspension_type"]` | `string` | (*Optional*) Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions. | +| `obs["tissue"]` | `string` | (*Optional*) Specific tissue from which the cells were derived, key for context and specificity in cell studies. | +| `obs["tissue_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. | +| `obs["tissue_general"]` | `string` | (*Optional*) General category or classification of the tissue, useful for broader grouping and comparison of cell data. | +| `obs["tissue_general_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. | +| `obs["batch"]` | `string` | (*Optional*) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | +| `obs["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["feature_id"]` | `string` | (*Optional*) Unique identifier for the feature, usually a ENSEMBL gene id. | +| `var["feature_name"]` | `string` | (*Optional*) A human-readable name for the feature, usually a gene symbol. | +| `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived. | +| `uns["dataset_name"]` | `string` | A human-readable name for the dataset. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. |
@@ -199,7 +222,7 @@ Format: AnnData object layers: 'counts' - uns: 'dataset_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism' @@ -207,10 +230,16 @@ Slot description:
-| Slot | Type | Description | -|:--------------------|:----------|:-------------------------------------| -| `layers["counts"]` | `integer` | Raw counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. |
diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 01f7b4e15f..173b2907a7 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -85,13 +85,13 @@ Format:
AnnData object - obs: 'celltype', 'batch', 'tissue', 'size_factors' - var: 'hvg', 'hvg_score' + obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' + var: 'feature_id', 'feature_name', 'soma_joinid', 'hvg', 'hvg_score' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' varm: 'pca_loadings' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'data_url', 'data_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'pca_variance', 'knn' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'pca_variance', 'knn'
@@ -99,29 +99,52 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | (*Optional*) Cell type information. | -| `obs["batch"]` | `string` | (*Optional*) Batch information. | -| `obs["tissue"]` | `string` | (*Optional*) Tissue information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalised expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_name"]` | `string` | Nicely formatted name. | -| `uns["data_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | -| `uns["data_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | -| `uns["dataset_summary"]` | `string` | Short description of the dataset. | -| `uns["dataset_description"]` | `string` | Long description of the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["pca_variance"]` | `double` | The PCA variance objects. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:--------------------------------------------------|:----------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `obs["dataset_id"]` | `string` | (*Optional*) Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes. | +| `obs["assay"]` | `string` | (*Optional*) Type of assay used to generate the cell data, indicating the methodology or technique employed. | +| `obs["assay_ontology_term_id"]` | `string` | (*Optional*) Experimental Factor Ontology (`EFO:`) term identifier for the assay, providing a standardized reference to the assay type. | +| `obs["cell_type"]` | `string` | (*Optional*) Classification of the cell type based on its characteristics and function within the tissue or organism. | +| `obs["cell_type_ontology_term_id"]` | `string` | (*Optional*) Cell Ontology (`CL:`) term identifier for the cell type, offering a standardized reference to the specific cell classification. | +| `obs["development_stage"]` | `string` | (*Optional*) Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase. | +| `obs["development_stage_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Developmental Stages (`HsapDv:`) ontology is used. If the organism is mouse (`organism_ontology_term_id == 'NCBITaxon:10090'`), then the Mouse Developmental Stages (`MmusDv:`) ontology is used. Otherwise, the Uberon (`UBERON:`) ontology is used. | +| `obs["disease"]` | `string` | (*Optional*) Information on any disease or pathological condition associated with the cell or donor. | +| `obs["disease_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). | +| `obs["donor_id"]` | `string` | (*Optional*) Identifier for the donor from whom the cell sample is obtained. | +| `obs["is_primary_data"]` | `boolean` | (*Optional*) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. | +| `obs["self_reported_ethnicity"]` | `string` | (*Optional*) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. | +| `obs["self_reported_ethnicity_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. | +| `obs["sex"]` | `string` | (*Optional*) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. | +| `obs["sex_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only `PATO:0000383`, `PATO:0000384` and `PATO:0001340` are allowed. | +| `obs["suspension_type"]` | `string` | (*Optional*) Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions. | +| `obs["tissue"]` | `string` | (*Optional*) Specific tissue from which the cells were derived, key for context and specificity in cell studies. | +| `obs["tissue_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. | +| `obs["tissue_general"]` | `string` | (*Optional*) General category or classification of the tissue, useful for broader grouping and comparison of cell data. | +| `obs["tissue_general_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. | +| `obs["batch"]` | `string` | (*Optional*) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | +| `obs["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | +| `var["feature_id"]` | `string` | (*Optional*) Unique identifier for the feature, usually a ENSEMBL gene id. | +| `var["feature_name"]` | `string` | (*Optional*) A human-readable name for the feature, usually a gene symbol. | +| `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | +| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | +| `varm["pca_loadings"]` | `double` | The PCA loadings matrix. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalised expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived. | +| `uns["dataset_name"]` | `string` | A human-readable name for the dataset. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["pca_variance"]` | `double` | The PCA variance objects. | +| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. |
@@ -198,7 +221,7 @@ Format: AnnData object var: 'hvg_score' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -206,13 +229,19 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:-------------------------------------------------------------------------------------| -| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------------| +| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 4025ddcd7c..6ddc7b9bd8 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -87,11 +87,11 @@ Format:
AnnData object - obs: 'celltype', 'batch' + obs: 'cell_type', 'batch' var: 'hvg', 'hvg_score' obsm: 'X_pca' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id'
@@ -99,17 +99,23 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["celltype"]` | `string` | Cell type information. | -| `obs["batch"]` | `string` | Batch information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["cell_type"]` | `string` | Cell type information. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -233,7 +239,7 @@ Format: var: 'hvg', 'hvg_score' obsm: 'X_pca' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -241,17 +247,23 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["label"]` | `string` | Ground truth cell type labels. | -| `obs["batch"]` | `string` | Batch information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["label"]` | `string` | Ground truth cell type labels. | +| `obs["batch"]` | `string` | Batch information. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -350,8 +362,7 @@ Slot description: Metric score file -Example file: -`resources_test/label_projection/pancreas/score.h5ad` +Example file: `resources_test/label_projection/pancreas/score.h5ad` Description: diff --git a/src/tasks/match_modalities/README.md b/src/tasks/match_modalities/README.md index e9692e2b5b..b13299e86f 100644 --- a/src/tasks/match_modalities/README.md +++ b/src/tasks/match_modalities/README.md @@ -107,7 +107,7 @@ Format: AnnData object obsm: 'X_svd' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -115,13 +115,19 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:-------------------------------------| -| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -153,7 +159,7 @@ The first modality of a multimodal dataset. The cells of this dataset are randomly permuted. Example file: -`resources_test/common/scicar_cell_lines/dataset_mod1.h5ad` +`resources_test/match_modalities/scicar_cell_lines/dataset_mod1.h5ad` Description: @@ -190,7 +196,7 @@ The second modality of a multimodal dataset. The cells of this dataset are randomly permuted. Example file: -`resources_test/common/scicar_cell_lines/dataset_mod2.h5ad` +`resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad` Description: @@ -226,7 +232,7 @@ Slot description: The ground truth information for the first modality Example file: -`resources_test/common/scicar_cell_lines/solution_mod1.h5ad` +`resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad` Description: @@ -240,7 +246,7 @@ Format: obs: 'permutation_indices' obsm: 'X_svd' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -248,14 +254,20 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-----------------------------------------------------------| -| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | -| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -264,7 +276,7 @@ Slot description: The ground truth information for the second modality Example file: -`resources_test/common/scicar_cell_lines/solution_mod2.h5ad` +`resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad` Description: @@ -278,7 +290,7 @@ Format: obs: 'permutation_indices' obsm: 'X_svd' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -286,14 +298,20 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-----------------------------------------------------------| -| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | -| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["permutation_indices"]` | `integer` | Indices with which to revert the permutation of the cells. | +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -432,7 +450,8 @@ Slot description: Metric score file -Example file: `resources_test/match_modalities/score.h5ad` +Example file: +`resources_test/match_modalities/scicar_cell_lines/score.h5ad` Description: @@ -481,7 +500,7 @@ Format: AnnData object obsm: 'X_svd' layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -489,12 +508,18 @@ Slot description:
-| Slot | Type | Description | -|:--------------------------|:----------|:-------------------------------------| -| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:-------------------------------------------------------------------------------| +| `obsm["X_svd"]` | `double` | The resulting SVD PCA embedding. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index 9615286dc5..bb610644b2 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -248,7 +248,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' @@ -256,17 +256,22 @@ Slot description:
-| Slot | Type | Description | -|:---------------------------------|:----------|:-------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | -| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -290,7 +295,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' @@ -298,17 +303,22 @@ Slot description:
-| Slot | Type | Description | -|:---------------------------------|:----------|:-------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | -| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -458,7 +468,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts' - uns: 'dataset_id', 'gene_activity_var_names' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' @@ -466,14 +476,20 @@ Slot description:
-| Slot | Type | Description | -|:---------------------------------|:----------|:-------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | -| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | -| `layers["counts"]` | `integer` | Raw counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
From c783ce10776c73aa0337474d99d16703bf27fd64 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 06:52:26 +0100 Subject: [PATCH 1076/1233] Refactor components (#303) * move components related to processing the task results to separate namespace * remove unused code Former-commit-id: a56be44cf76b5c5f722f104ddb8a9e9906ec60f5 --- src/common/collect_data/script.sh | 58 ------------------- src/common/copy/config.vsh.yaml | 27 --------- src/common/copy/script.sh | 15 ----- src/common/copy/test.sh | 21 ------- .../api/get_info.yaml | 1 + .../get_api_info/config.vsh.yaml | 3 +- .../get_api_info/script.R | 0 .../get_method_info/config.vsh.yaml | 1 - .../get_method_info/script.R | 0 .../get_metric_info/config.vsh.yaml | 1 - .../get_metric_info/script.R | 0 .../get_results/config.vsh.yaml | 1 - .../get_results/script.R | 0 .../run}/config.vsh.yaml | 12 ++-- .../run}/main.nf | 0 .../run}/run_nf_tower_test.sh | 0 .../run}/run_test.sh | 0 .../yaml_to_json/config.vsh.yaml | 1 - .../yaml_to_json/script.py | 0 19 files changed, 8 insertions(+), 133 deletions(-) delete mode 100755 src/common/collect_data/script.sh delete mode 100644 src/common/copy/config.vsh.yaml delete mode 100644 src/common/copy/script.sh delete mode 100644 src/common/copy/test.sh rename src/common/{ => process_task_results}/api/get_info.yaml (93%) rename src/common/{ => process_task_results}/get_api_info/config.vsh.yaml (89%) rename src/common/{ => process_task_results}/get_api_info/script.R (100%) rename src/common/{ => process_task_results}/get_method_info/config.vsh.yaml (96%) rename src/common/{ => process_task_results}/get_method_info/script.R (100%) rename src/common/{ => process_task_results}/get_metric_info/config.vsh.yaml (96%) rename src/common/{ => process_task_results}/get_metric_info/script.R (100%) rename src/common/{ => process_task_results}/get_results/config.vsh.yaml (97%) rename src/common/{ => process_task_results}/get_results/script.R (100%) rename src/common/{workflows/transform_meta => process_task_results/run}/config.vsh.yaml (89%) rename src/common/{workflows/transform_meta => process_task_results/run}/main.nf (100%) rename src/common/{workflows/transform_meta => process_task_results/run}/run_nf_tower_test.sh (100%) rename src/common/{workflows/transform_meta => process_task_results/run}/run_test.sh (100%) rename src/common/{ => process_task_results}/yaml_to_json/config.vsh.yaml (95%) rename src/common/{ => process_task_results}/yaml_to_json/script.py (100%) diff --git a/src/common/collect_data/script.sh b/src/common/collect_data/script.sh deleted file mode 100755 index 70d2cd1e17..0000000000 --- a/src/common/collect_data/script.sh +++ /dev/null @@ -1,58 +0,0 @@ -#!/bin/bash - - - -# run a couple of components to generate experimental website view - -viash run src/common/list_git_shas/config.vsh.yaml -- \ - --input "../openproblems/" \ - --output "openproblems_git.json" - -# task_id="label_projection" -# task_id="dimensionality_reduction" -# task_id="denoising" -for task_id in label_projection dimensionality_reduction denoising; do - out_dir="../website-experimental/results_v2/$task_id/data" - - mkdir -p $out_dir - - # generate task info - viash run src/common/get_task_info/config.vsh.yaml -- \ - --input "../openproblems-v2" \ - --task_id $task_id \ - --output "$out_dir/task_info.json" - - # generate method info - viash run src/common/get_method_info/config.vsh.yaml -- \ - --input "../openproblems-v2" \ - --task_id $task_id \ - --output "$out_dir/temp_method_info.json" - viash run src/common/check_migration_status/config.vsh.yaml -- \ - --git_sha "openproblems_git.json" \ - --comp_info "$out_dir/temp_method_info.json" \ - --output "$out_dir/method_info.json" - rm "$out_dir/temp_method_info.json" - - # generate metric info - viash run src/common/get_metric_info/config.vsh.yaml -- \ - --input "../openproblems-v2" \ - --task_id $task_id \ - --output "$out_dir/temp_metric_info.json" - viash run src/common/check_migration_status/config.vsh.yaml -- \ - --git_sha "openproblems_git.json" \ - --comp_info "$out_dir/temp_metric_info.json" \ - --output "$out_dir/metric_info.json" - rm "$out_dir/temp_metric_info.json" - - # generate results - viash run src/common/get_results/config.vsh.yaml -- \ - --input_scores "resources/$task_id/benchmarks/openproblems_v1/combined.extract_scores.output.tsv" \ - --input_execution "resources/$task_id/benchmarks/openproblems_v1/nextflow_log.tsv" \ - --output "$out_dir/results.json" - - # generate api info - viash run src/common/get_api_info/config.vsh.yaml -- \ - --input "../openproblems-v2" \ - --task_id $task_id \ - --output "$out_dir/api.json" -done \ No newline at end of file diff --git a/src/common/copy/config.vsh.yaml b/src/common/copy/config.vsh.yaml deleted file mode 100644 index 150d36f181..0000000000 --- a/src/common/copy/config.vsh.yaml +++ /dev/null @@ -1,27 +0,0 @@ -functionality: - name: copy - namespace: "common" - description: Publish an artifact and optionally rename with parameters - arguments: - - name: "--input" - alternatives: ["-i"] - type: file - direction: input - required: true - description: Input filename - - name: "--output" - alternatives: ["-o"] - type: file - direction: output - required: true - description: Output filename - resources: - - type: bash_script - path: script.sh - test_resources: - - type: bash_script - path: test.sh -platforms: - - type: docker - image: ubuntu:22.04 - - type: nextflow diff --git a/src/common/copy/script.sh b/src/common/copy/script.sh deleted file mode 100644 index 1aeffceac0..0000000000 --- a/src/common/copy/script.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -set -eo pipefail - -## VIASH START -par_input="input.txt" -par_output="output.txt" -## VIASH END - -parent=`dirname "$par_output"` -if [[ ! -d "$parent" ]]; then - mkdir -p "$parent" -fi - -cp -r "$par_input" "$par_output" \ No newline at end of file diff --git a/src/common/copy/test.sh b/src/common/copy/test.sh deleted file mode 100644 index cb1f509c0c..0000000000 --- a/src/common/copy/test.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env bash -set -ex - -touch test_file.txt - -echo ">>> Testing if publish in local dir works" -"$meta_executable" \ - --input test_file.txt \ - --output another_file.txt - -[[ ! -f another_file.txt ]] && echo "It seems no output is generated" && exit 1 - -echo ">>> Testing if publish in local dir works" -"$meta_executable" \ - --input test_file.txt \ - --output adir/yadir/another_file.txt - -[[ ! -d adir ]] && echo "It seems no output is generated" && exit 1 -[[ ! -f adir/yadir/another_file.txt ]] && echo "It seems no output is generated" && exit 1 - -echo ">>> Test finished successfully" diff --git a/src/common/api/get_info.yaml b/src/common/process_task_results/api/get_info.yaml similarity index 93% rename from src/common/api/get_info.yaml rename to src/common/process_task_results/api/get_info.yaml index faf2351f44..117504cc75 100644 --- a/src/common/api/get_info.yaml +++ b/src/common/process_task_results/api/get_info.yaml @@ -1,4 +1,5 @@ functionality: + namespace: common/process_task_results arguments: - name: "--input" type: "file" diff --git a/src/common/get_api_info/config.vsh.yaml b/src/common/process_task_results/get_api_info/config.vsh.yaml similarity index 89% rename from src/common/get_api_info/config.vsh.yaml rename to src/common/process_task_results/get_api_info/config.vsh.yaml index 19a062e00b..26fa3d986c 100644 --- a/src/common/get_api_info/config.vsh.yaml +++ b/src/common/process_task_results/get_api_info/config.vsh.yaml @@ -1,8 +1,7 @@ __merge__: ../api/get_info.yaml functionality: status: disabled - name: "get_api_info" - namespace: "common" + name: get_api_info description: "Extract api info" resources: - type: r_script diff --git a/src/common/get_api_info/script.R b/src/common/process_task_results/get_api_info/script.R similarity index 100% rename from src/common/get_api_info/script.R rename to src/common/process_task_results/get_api_info/script.R diff --git a/src/common/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml similarity index 96% rename from src/common/get_method_info/config.vsh.yaml rename to src/common/process_task_results/get_method_info/config.vsh.yaml index d1fe3e99f6..ee425804b2 100644 --- a/src/common/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/get_info.yaml functionality: name: "get_method_info" - namespace: "common" description: "Extract method info" resources: - type: r_script diff --git a/src/common/get_method_info/script.R b/src/common/process_task_results/get_method_info/script.R similarity index 100% rename from src/common/get_method_info/script.R rename to src/common/process_task_results/get_method_info/script.R diff --git a/src/common/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml similarity index 96% rename from src/common/get_metric_info/config.vsh.yaml rename to src/common/process_task_results/get_metric_info/config.vsh.yaml index 443c22723a..d6d5426063 100644 --- a/src/common/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/get_info.yaml functionality: name: "get_metric_info" - namespace: "common" description: "Extract metric info" resources: - type: r_script diff --git a/src/common/get_metric_info/script.R b/src/common/process_task_results/get_metric_info/script.R similarity index 100% rename from src/common/get_metric_info/script.R rename to src/common/process_task_results/get_metric_info/script.R diff --git a/src/common/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml similarity index 97% rename from src/common/get_results/config.vsh.yaml rename to src/common/process_task_results/get_results/config.vsh.yaml index 711ce51c3c..fcdbeddb19 100644 --- a/src/common/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -1,6 +1,5 @@ functionality: name: "get_results" - namespace: "common" description: "Extract execution info" arguments: - name: "--input_scores" diff --git a/src/common/get_results/script.R b/src/common/process_task_results/get_results/script.R similarity index 100% rename from src/common/get_results/script.R rename to src/common/process_task_results/get_results/script.R diff --git a/src/common/workflows/transform_meta/config.vsh.yaml b/src/common/process_task_results/run/config.vsh.yaml similarity index 89% rename from src/common/workflows/transform_meta/config.vsh.yaml rename to src/common/process_task_results/run/config.vsh.yaml index 1b935050f9..309c2debbc 100644 --- a/src/common/workflows/transform_meta/config.vsh.yaml +++ b/src/common/process_task_results/run/config.vsh.yaml @@ -1,6 +1,6 @@ functionality: - name: transform_meta - namespace: common/workflows + name: run + namespace: common/process_task_results description: >- This workflow transforms the meta information of the results into a format that can be used by the website. @@ -76,9 +76,9 @@ functionality: path: main.nf entrypoint: run_wf dependencies: - - name: common/get_results - - name: common/get_method_info - - name: common/get_metric_info - - name: common/yaml_to_json + - name: common/process_task_results/get_results + - name: common/process_task_results/get_method_info + - name: common/process_task_results/get_metric_info + - name: common/process_task_results/yaml_to_json platforms: - type: nextflow \ No newline at end of file diff --git a/src/common/workflows/transform_meta/main.nf b/src/common/process_task_results/run/main.nf similarity index 100% rename from src/common/workflows/transform_meta/main.nf rename to src/common/process_task_results/run/main.nf diff --git a/src/common/workflows/transform_meta/run_nf_tower_test.sh b/src/common/process_task_results/run/run_nf_tower_test.sh similarity index 100% rename from src/common/workflows/transform_meta/run_nf_tower_test.sh rename to src/common/process_task_results/run/run_nf_tower_test.sh diff --git a/src/common/workflows/transform_meta/run_test.sh b/src/common/process_task_results/run/run_test.sh similarity index 100% rename from src/common/workflows/transform_meta/run_test.sh rename to src/common/process_task_results/run/run_test.sh diff --git a/src/common/yaml_to_json/config.vsh.yaml b/src/common/process_task_results/yaml_to_json/config.vsh.yaml similarity index 95% rename from src/common/yaml_to_json/config.vsh.yaml rename to src/common/process_task_results/yaml_to_json/config.vsh.yaml index b7bceb2488..4e24134d02 100644 --- a/src/common/yaml_to_json/config.vsh.yaml +++ b/src/common/process_task_results/yaml_to_json/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../api/get_info.yaml functionality: name: "yaml_to_json" - namespace: "common" description: "convert yaml file to json file" resources: - type: python_script diff --git a/src/common/yaml_to_json/script.py b/src/common/process_task_results/yaml_to_json/script.py similarity index 100% rename from src/common/yaml_to_json/script.py rename to src/common/process_task_results/yaml_to_json/script.py From 75ab1af45e4cdca834f20f7f370ab54fab5b6cbf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 07:00:08 +0100 Subject: [PATCH 1077/1233] fix missing namespace field Former-commit-id: f7086b1feaaf0f1f2a0cf26e8105e6f86c4bca5c --- src/common/process_task_results/get_results/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index fcdbeddb19..839ccfef6a 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -1,6 +1,7 @@ functionality: name: "get_results" description: "Extract execution info" + namespace: common/process_task_results arguments: - name: "--input_scores" type: "file" From 4e90337e9f5a8cae3e188f7271a9fb19abb414bf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 13:37:47 +0100 Subject: [PATCH 1078/1233] remove incorrect reference to /src/common/api in various components (#306) * remove incorrect reference to /src/common/api in various components * trigger full test #ci force Former-commit-id: 451f48e4b55edf8412092553f40dd2f665195bcc --- src/tasks/denoising/api/comp_method.yaml | 3 +-- src/tasks/label_projection/api/comp_method.yaml | 1 - src/tasks/match_modalities/api/comp_control_method.yaml | 3 +-- src/tasks/match_modalities/api/comp_method.yaml | 1 - src/tasks/predict_modality/api/comp_method.yaml | 3 +-- 5 files changed, 3 insertions(+), 8 deletions(-) diff --git a/src/tasks/denoising/api/comp_method.yaml b/src/tasks/denoising/api/comp_method.yaml index 9b263df2b4..517723772d 100644 --- a/src/tasks/denoising/api/comp_method.yaml +++ b/src/tasks/denoising/api/comp_method.yaml @@ -23,5 +23,4 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/denoising/pancreas dest: resources_test/denoising/pancreas - - path: /src/common/library.bib - - path: /src/common/api \ No newline at end of file + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/label_projection/api/comp_method.yaml b/src/tasks/label_projection/api/comp_method.yaml index 2650f839ac..1b7cb0dabc 100644 --- a/src/tasks/label_projection/api/comp_method.yaml +++ b/src/tasks/label_projection/api/comp_method.yaml @@ -29,4 +29,3 @@ functionality: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - path: /src/common/library.bib - - path: /src/common/api diff --git a/src/tasks/match_modalities/api/comp_control_method.yaml b/src/tasks/match_modalities/api/comp_control_method.yaml index 3610edbd3f..446ee8a41a 100644 --- a/src/tasks/match_modalities/api/comp_control_method.yaml +++ b/src/tasks/match_modalities/api/comp_control_method.yaml @@ -44,5 +44,4 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /src/common/library.bib - - path: /src/common/api \ No newline at end of file + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/match_modalities/api/comp_method.yaml b/src/tasks/match_modalities/api/comp_method.yaml index 57ff6a3318..37a5e90b0e 100644 --- a/src/tasks/match_modalities/api/comp_method.yaml +++ b/src/tasks/match_modalities/api/comp_method.yaml @@ -32,4 +32,3 @@ functionality: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - path: /src/common/library.bib - - path: /src/common/api diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index 59fe99ec28..42d836c82d 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -32,5 +32,4 @@ functionality: path: /src/common/comp_tests/run_and_check_adata.py - path: /resources_test/predict_modality/bmmc_cite_starter dest: resources_test/predict_modality/bmmc_cite_starter - - path: /src/common/library.bib - - path: /src/common/api \ No newline at end of file + - path: /src/common/library.bib \ No newline at end of file From 36ca4f99b6c2fa2babd9bfa4d2e5ed18505c9068 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 14:14:15 +0100 Subject: [PATCH 1079/1233] add temporary fix for PM task (#307) Former-commit-id: ccb90caaabb195dbba0110f33e2cc8b86e35cfec --- .../resource_test_scripts/bmmc_x_starter.sh | 54 +++++++++++++++++++ .../predict_modality/process_dataset/script.R | 7 +-- .../workflows/process_datasets/main.nf | 4 +- 3 files changed, 58 insertions(+), 7 deletions(-) diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh index 38d97831bb..db67188a68 100755 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ b/src/datasets/resource_test_scripts/bmmc_x_starter.sh @@ -1,5 +1,7 @@ #!/bin/bash +# TODO: replace this with a run of the correct dataset loader once it is available + NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" DATASET_DIR="resources_test/common" @@ -16,6 +18,32 @@ output_dataset_rna: !file dataset_rna.h5ad output_dataset_other_mod: !file dataset_adt.h5ad HERE +python - << HERE +import anndata as ad + +rna = ad.read_h5ad("$SUBDIR/dataset_rna.h5ad") +mod2 = ad.read_h5ad("$SUBDIR/dataset_adt.h5ad") + +rna.uns["dataset_id"] = "bmmc_cite_starter" +mod2.uns["dataset_id"] = "bmmc_cite_starter" +rna.uns["dataset_name"] = "BMMC Cite Starter" +mod2.uns["dataset_name"] = "BMMC Cite Starter" +rna.uns["dataset_url"] = "https://foo.bar" +mod2.uns["dataset_url"] = "https://foo.bar" +rna.uns["dataset_reference"] = "foo2001bar" +mod2.uns["dataset_reference"] = "foo2001bar" +rna.uns["dataset_summary"] = "summary" +mod2.uns["dataset_summary"] = "summary" +rna.uns["dataset_description"] = "description" +mod2.uns["dataset_description"] = "description" +rna.uns["dataset_organism"] = "homo_sapiens" +mod2.uns["dataset_organism"] = "homo_sapiens" + +rna.write_h5ad("$SUBDIR/dataset_rna.h5ad") +mod2.write_h5ad("$SUBDIR/dataset_adt.h5ad") +HERE + + SUBDIR="$DATASET_DIR/bmmc_multiome_starter" mkdir -p "$SUBDIR" wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ @@ -29,5 +57,31 @@ output_dataset_rna: !file dataset_rna.h5ad output_dataset_other_mod: !file dataset_atac.h5ad HERE + +python - << HERE +import anndata as ad + +rna = ad.read_h5ad("$SUBDIR/dataset_rna.h5ad") +mod2 = ad.read_h5ad("$SUBDIR/dataset_atac.h5ad") + +rna.uns["dataset_id"] = "bmmc_multiome_starter" +mod2.uns["dataset_id"] = "bmmc_multipme_starter" +rna.uns["dataset_name"] = "BMMC Multiome Starter" +mod2.uns["dataset_name"] = "BMMC Multiome Starter" +rna.uns["dataset_url"] = "https://foo.bar" +mod2.uns["dataset_url"] = "https://foo.bar" +rna.uns["dataset_reference"] = "foo2001bar" +mod2.uns["dataset_reference"] = "foo2001bar" +rna.uns["dataset_summary"] = "summary" +mod2.uns["dataset_summary"] = "summary" +rna.uns["dataset_description"] = "description" +mod2.uns["dataset_description"] = "description" +rna.uns["dataset_organism"] = "homo_sapiens" +mod2.uns["dataset_organism"] = "homo_sapiens" + +rna.write_h5ad("$SUBDIR/dataset_rna.h5ad") +mod2.write_h5ad("$SUBDIR/dataset_atac.h5ad") +HERE + # run task process dataset components src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index a9ece0b529..323a3a63f7 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -40,11 +40,8 @@ ad2_mod <- unique(ad2$var[["feature_types"]]) new_dataset_id <- paste0(ad1$uns[["dataset_id"]], "_", tolower(ad1_mod), "2", tolower(ad2_mod)) # determine new uns -ad1_uns <- ad2_uns <- list( - dataset_id = new_dataset_id, - # TODO: this should already be part of the source dataset - dataset_organism = "homo_sapiens" -) +uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism") +ad1_uns <- ad2_uns <- ad1$uns[uns_vars] ad1_uns$modality <- ad1_mod ad2_uns$modality <- ad2_mod diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 64997c5597..6aa9b70d43 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -19,7 +19,7 @@ workflow run_wf { fromState: { id, state -> // as a resource [ - "input": state.input, + "input": state.input_rna, "schema": meta.resources_dir.resolve("file_common_dataset_rna.yaml") ] }, @@ -37,7 +37,7 @@ workflow run_wf { fromState: { id, state -> // as a resource [ - "input": state.input, + "input": state.input_other_mod, "schema": meta.resources_dir.resolve("file_common_dataset_other_mod.yaml") ] }, From 14a57bc0e1ffcc594c82738710c7b66b0466832c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 15:55:26 +0100 Subject: [PATCH 1080/1233] Rework cellxgene census components (#299) * add extra data to cellxgene census component * add organism to spec * add cellxgene_census workflow, scripts and other updates * rework scripts * fix script * update script * update script * add workaround implementation for `get_anndata()` * update scripts * rename component * refactor workflows * add auto wf to dataset wfs * update directives * remove abstract * fix test * extend cxg census datasets Former-commit-id: d79099404f0212aa29901bf0c727783efd5e8a42 --- .../check_dataset_schema/config.vsh.yaml | 2 +- src/common/library.bib | 55 +++++ src/datasets/api/file_raw.yaml | 13 ++ .../config.vsh.yaml | 101 +++++++-- .../loaders/cellxgene_census/script.py | 200 ++++++++++++++++++ src/datasets/loaders/cellxgene_census/test.py | 61 ++++++ .../config.vsh.yaml | 130 ++++++++++++ .../script.py | 131 ++++++++++++ .../cellxgene_census_from_source_h5ad/test.py | 58 +++++ .../loaders/query_cellxgene_census/script.py | 138 ------------ .../loaders/query_cellxgene_census/test.py | 38 ---- .../normalization/l1_sqrt/config.vsh.yaml | 2 +- .../normalization/log_cp/config.vsh.yaml | 2 +- .../log_scran_pooling/config.vsh.yaml | 2 +- .../normalization/sqrt_cp/config.vsh.yaml | 2 +- src/datasets/processors/hvg/config.vsh.yaml | 2 +- src/datasets/processors/knn/config.vsh.yaml | 2 +- src/datasets/processors/pca/config.vsh.yaml | 2 +- .../processors/subsample/config.vsh.yaml | 2 +- src/datasets/processors/svd/config.vsh.yaml | 2 +- .../resource_scripts/cellxgene_census.sh | 32 +++ .../cellxgene_census_tower.sh | 86 ++++++++ .../process_cellxgene_census/config.vsh.yaml | 200 ++++++++++++++++++ .../process_cellxgene_census/main.nf | 143 +++++++++++++ .../workflows/process_openproblems_v1/main.nf | 24 +-- .../main.nf | 7 + 26 files changed, 1220 insertions(+), 217 deletions(-) rename src/datasets/loaders/{query_cellxgene_census => cellxgene_census}/config.vsh.yaml (52%) create mode 100644 src/datasets/loaders/cellxgene_census/script.py create mode 100644 src/datasets/loaders/cellxgene_census/test.py create mode 100644 src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml create mode 100644 src/datasets/loaders/cellxgene_census_from_source_h5ad/script.py create mode 100644 src/datasets/loaders/cellxgene_census_from_source_h5ad/test.py delete mode 100644 src/datasets/loaders/query_cellxgene_census/script.py delete mode 100644 src/datasets/loaders/query_cellxgene_census/test.py create mode 100755 src/datasets/resource_scripts/cellxgene_census.sh create mode 100755 src/datasets/resource_scripts/cellxgene_census_tower.sh create mode 100644 src/datasets/workflows/process_cellxgene_census/config.vsh.yaml create mode 100644 src/datasets/workflows/process_cellxgene_census/main.nf diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 2fe62151c4..610957e34e 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -54,4 +54,4 @@ platforms: packages: viashpy - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] + label: [ midtime, midmem, midcpu ] diff --git a/src/common/library.bib b/src/common/library.bib index 1621b97334..3e3475fdd6 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1462,3 +1462,58 @@ @article{zhang2021pydrmetrics doi = {10.1016/j.heliyon.2021.e06199}, url = {https://doi.org/10.1016/j.heliyon.2021.e06199} } + +@article {hrovatin2023delineating, + author = {Karin Hrovatin and Aim{\'e}e Bastidas-Ponce and Mostafa Bakhti and Luke Zappia and Maren B{\"u}ttner and Ciro Sallino and Michael Sterr and Anika B{\"o}ttcher and Adriana Migliorini and Heiko Lickert and Fabian J. Theis}, + title = {Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas}, + elocation-id = {2022.12.22.521557}, + year = {2023}, + doi = {10.1101/2022.12.22.521557}, + publisher = {Cold Spring Harbor Laboratory}, + URL = {https://www.biorxiv.org/content/early/2023/04/25/2022.12.22.521557}, + eprint = {https://www.biorxiv.org/content/early/2023/04/25/2022.12.22.521557.full.pdf}, + journal = {bioRxiv} +} + +@article{sikkema2023integrated, + title = {An integrated cell atlas of the lung in health and disease}, + volume = {29}, + ISSN = {1546-170X}, + url = {http://dx.doi.org/10.1038/s41591-023-02327-2}, + DOI = {10.1038/s41591-023-02327-2}, + number = {6}, + journal = {Nature Medicine}, + publisher = {Springer Science and Business Media LLC}, + author = {Sikkema, Lisa and Ramírez-Suástegui, Ciro and Strobl, Daniel C. and Gillett, Tessa E. and Zappia, Luke and Madissoon, Elo and Markov, Nikolay S. and Zaragosi, Laure-Emmanuelle and Ji, Yuge and Ansari, Meshal and Arguel, Marie-Jeanne and Apperloo, Leonie and Banchero, Martin and Bécavin, Christophe and Berg, Marijn and Chichelnitskiy, Evgeny and Chung, Mei-i and Collin, Antoine and Gay, Aurore C. 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F. and Chang, Charles A. and Chang, Stephen and Colville, Alex and Crasta, Sheela and Culver, Rebecca N. and Cvijović, Ivana and D’Amato, Gaetano and Ezran, Camille and Galdos, Francisco X. and Gillich, Astrid and Goodyer, William R. and Hang, Yan and Hayashi, Alyssa and Houshdaran, Sahar and Huang, Xianxi and Irwin, Juan C. and Jang, SoRi and Juanico, Julia Vallve and Kershner, Aaron M. and Kim, Soochi and Kiss, Bernhard and Kolluru, Saroja and Kong, William and Kumar, Maya E. and Kuo, Angera H. and Leylek, Rebecca and Li, Baoxiang and Loeb, Gabriel B. and Lu, Wan-Jin and Mantri, Sruthi and Markovic, Maxim and McAlpine, Patrick L. and de Morree, Antoine and Morri, Maurizio and Mrouj, Karim and Mukherjee, Shravani and Muser, Tyler and Neuh\"{o}fer, Patrick and Nguyen, Thi D. and Perez, Kimberly and Phansalkar, Ragini and Pisco, Angela Oliveira and Puluca, Nazan and Qi, Zhen and Rao, Poorvi and Raquer-McKay, Hayley and Schaum, Nicholas and Scott, Bronwyn and Seddighzadeh, Bobak and Segal, Joe and Sen, Sushmita and Sikandar, Shaheen and Spencer, Sean P. and Steffes, Lea C. and Subramaniam, Varun R. and Swarup, Aditi and Swift, Michael and Travaglini, Kyle J. and Van Treuren, Will and Trimm, Emily and Veizades, Stefan and Vijayakumar, Sivakamasundari and Vo, Kim Chi and Vorperian, Sevahn K. and Wang, Wanxin and Weinstein, Hannah N. W. and Winkler, Juliane and Wu, Timothy T. H. and Xie, Jamie and Yung, Andrea R. and Zhang, Yue and Detweiler, Angela M. and Mekonen, Honey and Neff, Norma F. and Sit, Rene V. and Tan, Michelle and Yan, Jia and Bean, Gregory R. and Charu, Vivek and Forgó, Erna and Martin, Brock A. and Ozawa, Michael G. and Silva, Oscar and Tan, Serena Y. and Toland, Angus and Vemuri, Venkata N. P. and Afik, Shaked and Awayan, Kyle and Botvinnik, Olga Borisovna and Byrne, Ashley and Chen, Michelle and Dehghannasiri, Roozbeh and Detweiler, Angela M. and Gayoso, Adam and Granados, Alejandro A. and Li, Qiqing and Mahmoudabadi, Gita and McGeever, Aaron and de Morree, Antoine and Olivieri, Julia Eve and Park, Madeline and Pisco, Angela Oliveira and Ravikumar, Neha and Salzman, Julia and Stanley, Geoff and Swift, Michael and Tan, Michelle and Tan, Weilun and Tarashansky, Alexander J. and Vanheusden, Rohan and Vorperian, Sevahn K. and Wang, Peter and Wang, Sheng and Xing, Galen and Xu, Chenling and Yosef, Nir and Alcántara-Hernández, Marcela and Antony, Jane and Chan, Charles K. F. and Chang, Charles A. and Colville, Alex and Crasta, Sheela and Culver, Rebecca and Dethlefsen, Les and Ezran, Camille and Gillich, Astrid and Hang, Yan and Ho, Po-Yi and Irwin, Juan C. and Jang, SoRi and Kershner, Aaron M. and Kong, William and Kumar, Maya E. and Kuo, Angera H. and Leylek, Rebecca and Liu, Shixuan and Loeb, Gabriel B. and Lu, Wan-Jin and Maltzman, Jonathan S. and Metzger, Ross J. and de Morree, Antoine and Neuh\"{o}fer, Patrick and Perez, Kimberly and Phansalkar, Ragini and Qi, Zhen and Rao, Poorvi and Raquer-McKay, Hayley and Sasagawa, Koki and Scott, Bronwyn and Sinha, Rahul and Song, Hanbing and Spencer, Sean P. and Swarup, Aditi and Swift, Michael and Travaglini, Kyle J. and Trimm, Emily and Veizades, Stefan and Vijayakumar, Sivakamasundari and Wang, Bruce and Wang, Wanxin and Winkler, Juliane and Xie, Jamie and Yung, Andrea R. and Artandi, Steven E. and Beachy, Philip A. and Clarke, Michael F. and Giudice, Linda C. and Huang, Franklin W. and Huang, Kerwyn Casey and Idoyaga, Juliana and Kim, Seung K. and Krasnow, Mark and Kuo, Christin S. and Nguyen, Patricia and Quake, Stephen R. and Rando, Thomas A. and Red-Horse, Kristy and Reiter, Jeremy and Relman, David A. and Sonnenburg, Justin L. and Wang, Bruce and Wu, Albert and Wu, Sean M. and Wyss-Coray, Tony}, + year = {2022}, + month = may +} + +@article{dominguez2022crosstissue, + title = {Cross-tissue immune cell analysis reveals tissue-specific features in humans}, + volume = {376}, + ISSN = {1095-9203}, + url = {http://dx.doi.org/10.1126/science.abl5197}, + DOI = {10.1126/science.abl5197}, + number = {6594}, + journal = {Science}, + publisher = {American Association for the Advancement of Science (AAAS)}, + author = {Domínguez Conde, C. and Xu, C. and Jarvis, L. B. and Rainbow, D. B. and Wells, S. B. and Gomes, T. and Howlett, S. K. and Suchanek, O. and Polanski, K. and King, H. W. and Mamanova, L. and Huang, N. and Szabo, P. A. and Richardson, L. and Bolt, L. and Fasouli, E. S. and Mahbubani, K. T. and Prete, M. and Tuck, L. and Richoz, N. and Tuong, Z. K. and Campos, L. and Mousa, H. S. and Needham, E. J. and Pritchard, S. and Li, T. and Elmentaite, R. and Park, J. and Rahmani, E. and Chen, D. and Menon, D. K. and Bayraktar, O. A. and James, L. K. and Meyer, K. B. and Yosef, N. and Clatworthy, M. R. and Sims, P. A. and Farber, D. L. and Saeb-Parsy, K. and Jones, J. L. and Teichmann, S. A.}, + year = {2022}, + month = may +} \ No newline at end of file diff --git a/src/datasets/api/file_raw.yaml b/src/datasets/api/file_raw.yaml index 2fd5475985..56ba539304 100644 --- a/src/datasets/api/file_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -77,6 +77,19 @@ info: description: Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. required: false + - type: string + name: organism + description: Organism from which the cell sample is obtained. + required: false + + - type: string + name: organism_ontology_term_id + description: | + Ontology term identifier for the organism, providing a standardized reference for the organism. + + Must be a term from the NCBI Taxonomy Ontology (`NCBITaxon:`) which is a child of `NCBITaxon:33208`. + required: false + - type: string name: self_reported_ethnicity description: Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. diff --git a/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml b/src/datasets/loaders/cellxgene_census/config.vsh.yaml similarity index 52% rename from src/datasets/loaders/query_cellxgene_census/config.vsh.yaml rename to src/datasets/loaders/cellxgene_census/config.vsh.yaml index 85f6cf761b..6593b91c1f 100644 --- a/src/datasets/loaders/query_cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census/config.vsh.yaml @@ -1,5 +1,5 @@ functionality: - name: query_cellxgene_census + name: cellxgene_census namespace: datasets/loaders description: | Query cells from a CellxGene Census or custom TileDBSoma object. @@ -20,26 +20,22 @@ functionality: type: string example: "stable" required: false - - name: Query + - name: Cell query description: Arguments related to the query. arguments: - name: "--species" type: string description: The organism to query, usually one of `Homo sapiens` or `Mus musculus`. - required: false - default: "homo_sapiens" - multiple: false + required: true + example: "homo_sapiens" - name: "--obs_value_filter" type: string description: "Filter for selecting the `obs` metadata (i.e. cells). Value is a filter query written in the SOMA `value_filter` syntax." - required: false + required: true example: "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" - - name: Arguments - description: Other arguments + - name: Filter cells by grouping + description: arguments: - - name: "--add_collection_metadata" - type: boolean_true - description: Whether to add metadata to the obs related to the collection. - name: "--cell_filter_grouping" type: string description: | @@ -51,12 +47,87 @@ functionality: example: ["dataset_id", "tissue", "assay", "disease", "cell_type"] multiple: true - name: "--cell_filter_minimum_count" - type: double + type: integer description: | A minimum number of cells per group to retain. If `--cell_filter_grouping` is defined, this parameter should also be provided and vice versa. required: false example: 100 + - name: Count filtering + description: Arguments related to filtering cells and genes by counts. + arguments: + - name: "--cell_filter_min_genes" + type: integer + description: Remove cells with less than this number of genes. + required: false + default: 50 + - name: "--cell_filter_min_counts" + type: integer + description: Remove cells with less than this number of counts. + required: false + default: 0 + - name: "--gene_filter_min_cells" + type: integer + description: Remove genes expressed in less than this number of cells. + required: false + default: 5 + - name: "--gene_filter_min_counts" + type: integer + description: Remove genes with less than this number of counts. + required: false + default: 0 + - name: Cell metadata + description: Cell metadata arguments + arguments: + - name: "--obs_batch" + type: string + description: | + Location of where to find the observation batch IDs. + + * If not specified, the `.obs["batch"]` field will not be included. + * If one or more values are specified, the `.obs["batch"]` field will be + set to the concatenated values of the specified fields, separated by + the `obs_batch_separator`. + required: false + multiple: true + multiple_sep: "," + example: ["batch"] + - name: "--obs_batch_separator" + type: string + description: Separator to use when concatenating the values of the `--obs_batch` fields. + required: false + default: "+" + - name: Dataset metadata + description: Information about the dataset that will be stored in the `.uns` slot. + arguments: + - name: "--dataset_id" + type: string + description: Unique identifier of the dataset. + required: true + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: true - name: Outputs description: Output arguments. arguments: @@ -80,11 +151,13 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + #image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: python:3.11 setup: - type: python packages: - - cellxgene-census~=1.2.0 + - cellxgene-census + - scanpy test_setup: - type: python packages: diff --git a/src/datasets/loaders/cellxgene_census/script.py b/src/datasets/loaders/cellxgene_census/script.py new file mode 100644 index 0000000000..8c2bcc7227 --- /dev/null +++ b/src/datasets/loaders/cellxgene_census/script.py @@ -0,0 +1,200 @@ +import sys +import cellxgene_census +import scanpy as sc +import tiledbsoma as soma + +## VIASH START +par = { + "input_uri": None, + "census_version": "stable", + "species": "mus_musculus", + "obs_value_filter": "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'", + "cell_filter_grouping": None, + "cell_filter_minimum_count": None, + "obs_batch": [ "donor_id" ], + "obs_batch_separator": "+", + "dataset_name": "pretty name", + "dataset_url": "url", + "dataset_reference": "ref", + "dataset_summary": "summ", + "dataset_description": "desc", + "dataset_organism": "mus_musculus", + "output": "output.h5ad", + "output_compression": "gzip", +} +meta = {"resources_dir": "src/common/helper_functions"} +## VIASH END + +sys.path.append(meta["resources_dir"]) + +from setup_logger import setup_logger +logger = setup_logger() + +def connect_census(uri, census_version): + """ + Connect to CellxGene Census or user-provided TileDBSoma object + """ + ver = census_version or "stable" + logger.info("Connecting to CellxGene Census at %s", f"'{uri}'" if uri else f"version '{ver}'") + return cellxgene_census.open_soma(uri=uri, census_version=ver) + +def get_anndata(census_connection, par): + logger.info("Getting gene expression data based on `%s` query.", par["obs_value_filter"]) + # workaround for https://github.com/chanzuckerberg/cellxgene-census/issues/891 + return cellxgene_census.get_anndata( + census=census_connection, + obs_value_filter=par["obs_value_filter"], + organism=par["species"] + ) + + # exp = census_connection["census_data"][par["species"]] + # query = exp.axis_query( + # "RNA", + # obs_query=soma.AxisQuery(value_filter=par["obs_value_filter"]), + # var_query=soma.AxisQuery(), + # ) + + # n_obs = query.n_obs + # n_vars = query.n_vars + # logger.info(f"Query yields {n_obs} cells and {n_vars} genes.") + + # logger.info("Fetching obs.") + # obs = query.obs().concat().to_pandas() + + # logger.info("Fetching var.") + # var = query.var().concat().to_pandas() + + # logger.info("Fetching X.") + # X = query.X("raw") + # Xcoo = X.coos().concat() + # Xcoos = Xcoo.to_scipy().tocsr() + # Xcoos_subset = Xcoos[obs["soma_joinid"]] + + # logger.info("Creating AnnData object.") + # return sc.AnnData( + # layers={"counts": Xcoos_subset}, + # obs=obs, + # var=var + # ) + +def filter_min_cells_per_group(adata, par): + t0 = adata.shape + cell_count = adata.obs \ + .groupby(par["cell_filter_grouping"])["soma_joinid"] \ + .transform("count") \ + + adata = adata[cell_count >= par["cell_filter_minimum_count"]] + t1 = adata.shape + logger.info( + "Removed %s cells based on %s cell_filter_minimum_count of %s cell_filter_grouping." + % ((t0[0] - t1[0]), par["cell_filter_minimum_count"], par["cell_filter_grouping"]) + ) + return adata + +def filter_by_counts(adata, par): + logger.info("Remove cells with few counts and genes with few counts.") + t0 = adata.shape + # remove cells with few counts and genes with few counts + if par["cell_filter_min_counts"]: + sc.pp.filter_cells(adata, min_counts=par["cell_filter_min_counts"]) + if par["cell_filter_min_genes"]: + sc.pp.filter_cells(adata, min_genes=par["cell_filter_min_genes"]) + if par["gene_filter_min_counts"]: + sc.pp.filter_genes(adata, min_counts=par["gene_filter_min_counts"]) + if par["gene_filter_min_cells"]: + sc.pp.filter_genes(adata, min_cells=par["gene_filter_min_cells"]) + t1 = adata.shape + logger.info("Removed %s cells and %s genes.", (t0[0] - t1[0]), (t0[1] - t1[1])) + +def move_x_to_layers(adata): + logger.info("Move .X to .layers['counts']") + adata.layers["counts"] = adata.X + adata.X = None + +def add_batch_to_obs(adata, par): + logger.info("Add batch to the AnnData object.") + if par["obs_batch"]: + # fetch batch columns from obs + cols = [adata.obs[key] for key in par["obs_batch"]] + + # join cols + obs_batch = [par["obs_batch_separator"].join(row) for row in zip(*cols)] + + # store in adata + adata.obs["batch"] = obs_batch + +def add_metadata_to_uns(adata, par): + logger.info("Add metadata to the AnnData object.") + for key in ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"]: + adata.uns[key] = par[key] + +def print_unique(adata, column): + formatted = "', '".join(adata.obs[column].unique()) + logger.info(f"Unique {column}: ['{formatted}']") + +def print_summary(adata): + logger.info(f"Resulting dataset: {adata}") + + logger.info("Summary of dataset:") + print_unique(adata, "assay") + print_unique(adata, "assay_ontology_term_id") + print_unique(adata, "cell_type") + print_unique(adata, "cell_type_ontology_term_id") + print_unique(adata, "dataset_id") + print_unique(adata, "development_stage") + print_unique(adata, "development_stage_ontology_term_id") + print_unique(adata, "disease") + print_unique(adata, "disease_ontology_term_id") + print_unique(adata, "tissue") + print_unique(adata, "tissue_ontology_term_id") + print_unique(adata, "tissue_general") + print_unique(adata, "tissue_general_ontology_term_id") + +def write_anndata(adata, par): + logger.info("Writing AnnData object to '%s'", par["output"]) + + adata.write_h5ad(par["output"], compression=par["output_compression"]) + +def main(par, meta): + # check arguments + if (par["cell_filter_grouping"] is None) != (par["cell_filter_minimum_count"] is None): + raise NotImplementedError( + "You need to specify either both or none of the following parameters: cell_filter_grouping, cell_filter_minimum_count" + ) + + with connect_census(uri=par["input_uri"], census_version=par["census_version"]) as conn: + adata = get_anndata(conn, par) + + print(f"AnnData: {adata}", flush=True) + + if par["cell_filter_grouping"] is not None: + adata = filter_min_cells_per_group(adata, par) + + # remove cells with few counts and genes with few counts + filter_by_counts(adata, par) + + # logger.log(f"Filtered AnnData: {adata}") + print(f"Filtered AnnData: {adata}", flush=True) + + # use feature_id as var_names + adata.var_names = adata.var["feature_id"] + + # not needed as long as we have our own implementation of `get_anndata` + # move .X to .layers["counts"] + move_x_to_layers(adata) + + # add batch to obs + add_batch_to_obs(adata, par) + + # add metadata to uns + add_metadata_to_uns(adata, par) + + # print summary + print_summary(adata) + + # write output to file + write_anndata(adata, par) + + +if __name__ == "__main__": + main(par, meta) diff --git a/src/datasets/loaders/cellxgene_census/test.py b/src/datasets/loaders/cellxgene_census/test.py new file mode 100644 index 0000000000..dba41bcc47 --- /dev/null +++ b/src/datasets/loaders/cellxgene_census/test.py @@ -0,0 +1,61 @@ +import sys +import os +import pytest +import anndata as ad +import numpy as np + +## VIASH START +meta = { + 'resources_dir': './resources_test/', + 'executable': './target/docker/query/cellxgene_census', + 'config': '/home/di/code/openpipeline/src/query/cellxgene_census/config.vsh.yaml' +} +## VIASH END + +def test_cellxgene_extract_metadata_expression(run_component, tmp_path): + output_file = tmp_path / "output.h5ad" + + run_component([ + "--species", "homo_sapiens", + "--obs_value_filter", "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'", + "--output", output_file, + "--obs_batch", "sex,sex", + "--dataset_id", "test_dataset_id", + "--dataset_name", "test_dataset_name", + "--dataset_url", "https://test_dataset_url.com", + "--dataset_reference", "test_dataset_reference", + "--dataset_summary", "test_dataset_summary", + "--dataset_description", "test_dataset_description", + "--dataset_organism", "test_homo_sapiens", + ]) + + # check whether file exists + assert os.path.exists(output_file), "Output file does not exist" + + adata = ad.read_h5ad(output_file) + + # check obs + assert not adata.obs.empty, ".obs should not be empty" + assert "is_primary_data" in adata.obs.columns + assert np.all(adata.obs["is_primary_data"] == True) + assert "cell_type_ontology_term_id" in adata.obs.columns + assert "disease" in adata.obs.columns + assert adata.n_obs > 10 + assert np.all([x in ["male+male", "female+female"] for x in adata.obs["batch"]]) + + # check var + assert "soma_joinid" in adata.var.columns + assert "feature_id" in adata.var.columns + + # check uns + assert adata.uns["dataset_id"] == "test_dataset_id", "Incorrect .uns['dataset_id']" + assert adata.uns["dataset_name"] == "test_dataset_name", "Incorrect .uns['dataset_name']" + assert adata.uns["dataset_url"] == "https://test_dataset_url.com", "Incorrect .uns['dataset_url']" + assert adata.uns["dataset_reference"] == "test_dataset_reference", "Incorrect .uns['dataset_reference']" + assert adata.uns["dataset_summary"] == "test_dataset_summary", "Incorrect .uns['dataset_summary']" + assert adata.uns["dataset_description"] == "test_dataset_description", "Incorrect .uns['dataset_description']" + assert adata.uns["dataset_organism"] == "test_homo_sapiens", "Incorrect .uns['dataset_organism']" + + +if __name__ == '__main__': + sys.exit(pytest.main([__file__])) diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml new file mode 100644 index 0000000000..1ccd1df18b --- /dev/null +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml @@ -0,0 +1,130 @@ +functionality: + name: cellxgene_census_from_source_h5ad + namespace: datasets/loaders + description: | + Query cells from a CellxGene Census or custom TileDBSoma object. + Aside from fetching the cells' RNA counts (`.X`), cell metadata + (`.obs`) and gene metadata (`.var`), this component also fetches + the dataset metadata and joins it into the cell metadata. + argument_groups: + - name: Input + description: Input arguments + arguments: + - name: "--input_id" + type: string + description: | + The dataset ID of the CellxGene Census dataset to query. + required: true + example: "a93eab58-3d82-4b61-8a2f-d7666dcdb7c4" + - name: Count filtering + description: Arguments related to filtering cells and genes by counts. + arguments: + - name: "--cell_filter_min_genes" + type: integer + description: Remove cells with less than this number of genes. + required: false + default: 50 + - name: "--cell_filter_min_counts" + type: integer + description: Remove cells with less than this number of counts. + required: false + default: 0 + - name: "--gene_filter_min_cells" + type: integer + description: Remove genes expressed in less than this number of cells. + required: false + default: 5 + - name: "--gene_filter_min_counts" + type: integer + description: Remove genes with less than this number of counts. + required: false + default: 0 + - name: Cell metadata + description: Cell metadata arguments + arguments: + - name: "--obs_batch" + type: string + description: | + Location of where to find the observation batch IDs. + + * If not specified, the `.obs["batch"]` field will not be included. + * If one or more values are specified, the `.obs["batch"]` field will be + set to the concatenated values of the specified fields, separated by + the `obs_batch_separator`. + required: false + multiple: true + multiple_sep: "," + example: ["batch"] + - name: "--obs_batch_separator" + type: string + description: Separator to use when concatenating the values of the `--obs_batch` fields. + required: false + default: "+" + - name: Dataset metadata + description: Information about the dataset that will be stored in the `.uns` slot. + arguments: + - name: "--dataset_id" + type: string + description: Unique identifier of the dataset. + required: true + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: true + - name: Outputs + description: Output arguments. + arguments: + - name: "--output" + type: file + description: Output h5ad file. + direction: output + required: true + example: output.h5ad + - name: "--output_compression" + type: string + choices: ["gzip", "lzf"] + required: false + example: "gzip" + resources: + - type: python_script + path: script.py + - path: /src/common/helper_functions/setup_logger.py + test_resources: + - type: python_script + path: test.py +platforms: + - type: docker + #image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: python:3.11 + setup: + - type: python + packages: + - cellxgene-census + - scanpy + test_setup: + - type: python + packages: + - viashpy + - type: nextflow + directives: + label: [highmem, midcpu] \ No newline at end of file diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/script.py b/src/datasets/loaders/cellxgene_census_from_source_h5ad/script.py new file mode 100644 index 0000000000..900232e6a4 --- /dev/null +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/script.py @@ -0,0 +1,131 @@ +import sys +import cellxgene_census +import scanpy as sc +import tempfile + +## VIASH START +par = { + "input_id": "0895c838-e550-48a3-a777-dbcd35d30272", + "obs_batch": [ "donor_id" ], + "obs_batch_separator": "+", + "dataset_name": "pretty name", + "dataset_url": "url", + "dataset_reference": "ref", + "dataset_summary": "summ", + "dataset_description": "desc", + "dataset_organism": "mus_musculus", + "output": "output.h5ad", + "output_compression": "gzip", +} +meta = {"resources_dir": "src/common/helper_functions"} +## VIASH END + +sys.path.append(meta["resources_dir"]) + +from setup_logger import setup_logger +logger = setup_logger() + +def get_anndata(par): + with tempfile.TemporaryDirectory() as tmp: + path = tmp + "/source.h5ad" + logger.info("Downloading source h5ad for dataset '%s' to '%s'.", par["input_id"], path) + cellxgene_census.download_source_h5ad(par["input_id"], path) + return sc.read_h5ad(path) + +def filter_by_counts(adata, par): + logger.info("Remove cells with few counts and genes with few counts.") + t0 = adata.shape + # remove cells with few counts and genes with few counts + if par["cell_filter_min_counts"]: + sc.pp.filter_cells(adata, min_counts=par["cell_filter_min_counts"]) + if par["cell_filter_min_genes"]: + sc.pp.filter_cells(adata, min_genes=par["cell_filter_min_genes"]) + if par["gene_filter_min_counts"]: + sc.pp.filter_genes(adata, min_counts=par["gene_filter_min_counts"]) + if par["gene_filter_min_cells"]: + sc.pp.filter_genes(adata, min_cells=par["gene_filter_min_cells"]) + t1 = adata.shape + logger.info("Removed %s cells and %s genes.", (t0[0] - t1[0]), (t0[1] - t1[1])) + +def move_x_to_layers(adata): + logger.info("Move .X to .layers['counts']") + adata.layers["counts"] = adata.X + adata.X = None + +def add_batch_to_obs(adata, par): + logger.info("Add batch to the AnnData object.") + if par["obs_batch"]: + # fetch batch columns from obs + cols = [adata.obs[key] for key in par["obs_batch"]] + + # join cols + obs_batch = [par["obs_batch_separator"].join(row) for row in zip(*cols)] + + # store in adata + adata.obs["batch"] = obs_batch + +def add_metadata_to_uns(adata, par): + logger.info("Add metadata to the AnnData object.") + for key in ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"]: + adata.uns[key] = par[key] + +def print_unique(adata, column): + if column not in adata.obs.columns: + logger.info(f"Column {column} not found in obs") + return + formatted = "', '".join(adata.obs[column].unique()) + logger.info(f"Unique {column}: ['{formatted}']") + +def print_summary(adata): + logger.info(f"Resulting dataset: {adata}") + + logger.info("Summary of dataset:") + print_unique(adata, "assay") + print_unique(adata, "assay_ontology_term_id") + print_unique(adata, "cell_type") + print_unique(adata, "cell_type_ontology_term_id") + print_unique(adata, "dataset_id") + print_unique(adata, "development_stage") + print_unique(adata, "development_stage_ontology_term_id") + print_unique(adata, "disease") + print_unique(adata, "disease_ontology_term_id") + print_unique(adata, "tissue") + print_unique(adata, "tissue_ontology_term_id") + print_unique(adata, "tissue_general") + print_unique(adata, "tissue_general_ontology_term_id") + +def write_anndata(adata, par): + logger.info("Writing AnnData object to '%s'", par["output"]) + + adata.write_h5ad(par["output"], compression=par["output_compression"]) + +def main(par, meta): + adata = get_anndata(par) + + logger.info("AnnData: %s", str(adata)) + + # remove cells with few counts and genes with few counts + filter_by_counts(adata, par) + + # this is not needed in source h5ads + # # use feature_id as var_names + # adata.var_names = adata.var["feature_id"] + + # move .X to .layers["counts"] + move_x_to_layers(adata) + + # add batch to obs + add_batch_to_obs(adata, par) + + # add metadata to uns + add_metadata_to_uns(adata, par) + + # print summary + print_summary(adata) + + # write output to file + write_anndata(adata, par) + + +if __name__ == "__main__": + main(par, meta) diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/test.py b/src/datasets/loaders/cellxgene_census_from_source_h5ad/test.py new file mode 100644 index 0000000000..098e8017a9 --- /dev/null +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/test.py @@ -0,0 +1,58 @@ +import sys +import os +import pytest +import anndata as ad +import numpy as np + +## VIASH START +meta = { + 'resources_dir': './resources_test/', + 'executable': './target/docker/datasets/loaders/cellxgene_census_from_source_h5ad/cellxgene_census_from_source_h5ad', + 'config': 'src/query/cellxgene_census/config.vsh.yaml' +} +## VIASH END + +def test_cellxgene_extract_metadata_expression(run_component, tmp_path): + output_file = tmp_path / "output.h5ad" + + run_component([ + "--input_id", "0895c838-e550-48a3-a777-dbcd35d30272", + "--output", output_file, + "--obs_batch", "donor_id", + "--dataset_id", "test_dataset_id", + "--dataset_name", "test_dataset_name", + "--dataset_url", "https://test_dataset_url.com", + "--dataset_reference", "test_dataset_reference", + "--dataset_summary", "test_dataset_summary", + "--dataset_description", "test_dataset_description", + "--dataset_organism", "test_homo_sapiens", + ]) + + # check whether file exists + assert os.path.exists(output_file), "Output file does not exist" + + adata = ad.read_h5ad(output_file) + + # check obs + assert not adata.obs.empty, ".obs should not be empty" + assert "is_primary_data" in adata.obs.columns + assert "cell_type_ontology_term_id" in adata.obs.columns + assert "disease" in adata.obs.columns + assert adata.n_obs > 10 + assert np.all([x in ["C41", "C58", "C70", "C72"] for x in adata.obs["batch"]]) + + # check var + assert "feature_name" in adata.var.columns + + # check uns + assert adata.uns["dataset_id"] == "test_dataset_id", "Incorrect .uns['dataset_id']" + assert adata.uns["dataset_name"] == "test_dataset_name", "Incorrect .uns['dataset_name']" + assert adata.uns["dataset_url"] == "https://test_dataset_url.com", "Incorrect .uns['dataset_url']" + assert adata.uns["dataset_reference"] == "test_dataset_reference", "Incorrect .uns['dataset_reference']" + assert adata.uns["dataset_summary"] == "test_dataset_summary", "Incorrect .uns['dataset_summary']" + assert adata.uns["dataset_description"] == "test_dataset_description", "Incorrect .uns['dataset_description']" + assert adata.uns["dataset_organism"] == "test_homo_sapiens", "Incorrect .uns['dataset_organism']" + + +if __name__ == '__main__': + sys.exit(pytest.main([__file__])) diff --git a/src/datasets/loaders/query_cellxgene_census/script.py b/src/datasets/loaders/query_cellxgene_census/script.py deleted file mode 100644 index 876e050871..0000000000 --- a/src/datasets/loaders/query_cellxgene_census/script.py +++ /dev/null @@ -1,138 +0,0 @@ -import os -import sys -import cellxgene_census - -## VIASH START -par = { - "input_uri": None, - "census_version": "stable", - "species": "homo_sapiens", - "obs_value_filter": "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'", - "cell_filter_grouping": ["dataset_id", "tissue", "assay", "disease", "cell_type"], - "cell_filter_minimum_count": 100, - "output": "output.h5ad", - "output_compression": "gzip", -} -meta = {"resources_dir": "src/common/helper_functions"} -## VIASH END - -sys.path.append(meta["resources_dir"]) - -from setup_logger import setup_logger -logger = setup_logger() - -def connect_census(uri, census_version): - """ - Connect to CellxGene Census or user-provided TileDBSoma object - """ - ver = census_version or "stable" - logger.info("Connecting to CellxGene Census at %s", f"'{uri}'" if uri else f"version '{ver}'") - return cellxgene_census.open_soma(uri=uri, census_version=ver) - -def get_anndata(census_connection, obs_value_filter, species): - logger.info("Getting gene expression data based on %s query.", obs_value_filter) - return cellxgene_census.get_anndata( - census=census_connection, obs_value_filter=obs_value_filter, organism=species - ) - - -def add_cellcensus_metadata_obs(census_connection, query_data): - logger.info("Adding extented metadata to gene expression data.") - census_datasets = ( - census_connection["census_info"]["datasets"].read().concat().to_pandas() - ) - - query_data.obs.dataset_id = query_data.obs.dataset_id.astype("category") - - dataset_info = ( - census_datasets[ - census_datasets.dataset_id.isin(query_data.obs.dataset_id.cat.categories) - ][ - [ - "collection_id", - "collection_name", - "collection_doi", - "dataset_id", - "dataset_title", - ] - ] - .reset_index(drop=True) - .apply(lambda x: x.astype("category")) - ) - - return query_data.obs.merge(dataset_info, on="dataset_id", how="left") - - -def cellcensus_cell_filter(query_data, cell_filter_grouping, cell_filter_minimum_count): - t0 = query_data.shape - query_data = query_data[ - query_data.obs.groupby(cell_filter_grouping)["soma_joinid"].transform("count") - >= cell_filter_minimum_count - ] - t1 = query_data.shape - logger.info( - "Removed %s cells based on %s cell_filter_minimum_count of %s cell_filter_grouping." - % ((t0[0] - t1[0]), cell_filter_minimum_count, cell_filter_grouping) - ) - return query_data - - -def write_anndata(query_data, path, compression): - logger.info("Writing AnnData object to '%s'", path) - - query_data.write_h5ad(path, compression=compression) - -def print_unique(adata, column): - formatted = "', '".join(adata.obs[column].unique()) - logger.info(f"Unique {column}: ['{formatted}']") - -def print_summary(query_data): - logger.info(f"Resulting dataset: {query_data}") - - logger.info("Summary of dataset:") - print_unique(query_data, "assay") - print_unique(query_data, "assay_ontology_term_id") - print_unique(query_data, "cell_type") - print_unique(query_data, "cell_type_ontology_term_id") - print_unique(query_data, "dataset_id") - print_unique(query_data, "development_stage") - print_unique(query_data, "development_stage_ontology_term_id") - print_unique(query_data, "disease") - print_unique(query_data, "disease_ontology_term_id") - print_unique(query_data, "tissue") - print_unique(query_data, "tissue_ontology_term_id") - print_unique(query_data, "tissue_general") - print_unique(query_data, "tissue_general_ontology_term_id") - -def main(): - # check arguments - if (par["cell_filter_grouping"] is None) != (par["cell_filter_minimum_count"] is None): - raise NotImplementedError( - "You need to specify either both or none of the following parameters: cell_filter_grouping, cell_filter_minimum_count" - ) - - with connect_census(uri=par["input_uri"], census_version=par["census_version"]) as conn: - query_data = get_anndata(conn, par["obs_value_filter"], par["species"]) - - if par["add_collection_metadata"]: - query_data.obs = add_cellcensus_metadata_obs(conn, query_data) - - if par["cell_filter_grouping"] is not None: - query_data = cellcensus_cell_filter( - query_data, - par["cell_filter_grouping"], - par["cell_filter_minimum_count"] - ) - - # use feature_id as var_names - query_data.var_names = query_data.var["feature_id"] - - # print summary - print_summary(query_data) - - # write output to file - write_anndata(query_data, par["output"], par["output_compression"]) - - -if __name__ == "__main__": - main() diff --git a/src/datasets/loaders/query_cellxgene_census/test.py b/src/datasets/loaders/query_cellxgene_census/test.py deleted file mode 100644 index 9d887b83db..0000000000 --- a/src/datasets/loaders/query_cellxgene_census/test.py +++ /dev/null @@ -1,38 +0,0 @@ -import sys -import os -import pytest -import anndata as ad -import numpy as np - -## VIASH START -meta = { - 'resources_dir': './resources_test/', - 'executable': './target/docker/query/cellxgene_census', - 'config': '/home/di/code/openpipeline/src/query/cellxgene_census/config.vsh.yaml' -} -## VIASH END - -def test_cellxgene_extract_metadata_expression(run_component, tmp_path): - output_file = tmp_path / "output.h5ad" - - run_component([ - "--obs_value_filter", "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'", - "--output", output_file, - ]) - - # check whether file exists - assert os.path.exists(output_file), "Output file does not exist" - - component_data = ad.read(output_file) - var, obs = component_data.var, component_data.obs - assert not obs.empty, ".obs should not be empty" - assert "is_primary_data" in obs.columns - assert np.all(obs["is_primary_data"] == True) - assert "cell_type_ontology_term_id" in obs.columns - assert "disease" in obs.columns - assert "soma_joinid" in var.columns - assert "feature_id" in var.columns - assert component_data.n_obs - -if __name__ == '__main__': - sys.exit(pytest.main([__file__])) diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 81e8ac9bdb..2be09a1216 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -24,4 +24,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index 858677d284..21285a2c30 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -15,4 +15,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 6ac7bcc811..1fd4e5cbab 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -15,4 +15,4 @@ platforms: pip: scanpy - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index be80374d67..fe001c0674 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -15,4 +15,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index f008be5e57..86c7d54171 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -10,4 +10,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [ midtime, highmem, midcpu ] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index c86f30373d..8084cc7791 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -10,4 +10,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [ midtime, highmem, midcpu ] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index cbdfbc4288..8fd788a357 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -14,4 +14,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [ midtime, highmem, midcpu ] diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 6a5f5f4d69..76cea7cf20 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -48,4 +48,4 @@ platforms: - viashpy - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [ midtime, highmem, midcpu ] diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index e4a1f48d42..61546777e1 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -13,4 +13,4 @@ platforms: pypi: [scikit-learn] - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [ midtime, highmem, midcpu ] diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh new file mode 100755 index 0000000000..58c63e8086 --- /dev/null +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -0,0 +1,32 @@ +#!/bin/bash + +cat > "/tmp/params.yaml" << 'HERE' +param_list: + - id: cxg_mm_pancreas_atlas + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" + obs_batch: donor_id + dataset_name: Mouse pancreatic islet atlas + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211799 + dataset_reference: hrovatin2023delineating + dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes + dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. + dataset_organism: mus_musculus + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null +publish_dir: output/temp +HERE + +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ + -profile docker \ + -params-file "/tmp/params.yaml" \ No newline at end of file diff --git a/src/datasets/resource_scripts/cellxgene_census_tower.sh b/src/datasets/resource_scripts/cellxgene_census_tower.sh new file mode 100755 index 0000000000..9f3eaf40d6 --- /dev/null +++ b/src/datasets/resource_scripts/cellxgene_census_tower.sh @@ -0,0 +1,86 @@ +#!/bin/bash + +cat > "/tmp/params.yaml" << 'HERE' +param_list: + - id: cxg_mouse_pancreas_atlas + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" + obs_batch: donor_id + dataset_name: Mouse pancreatic islet + dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes + dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. + dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 + dataset_reference: hrovatin2023delineating + dataset_organism: mus_musculus + - id: cxg_hcla + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '066943a2-fdac-4b29-b348-40cede398e4e'" + obs_batch: donor_id + dataset_name: Human Lung Cell Atlas + dataset_summary: An integrated cell atlas of the human lung in health and disease (core) + dataset_description: The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata. + dataset_url: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 + dataset_reference: sikkema2023integrated + dataset_organism: homo_sapiens + - id: cxg_tabula_sapiens + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '53d208b0-2cfd-4366-9866-c3c6114081bc'" + obs_batch: [donor_id, assay] + dataset_name: Tabula Sapiens + dataset_summary: A multiple-organ, single-cell transcriptomic atlas of humans + dataset_description: Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. + dataset_url: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 + dataset_reference: consortium2022tabula + dataset_organism: homo_sapiens + - id: cxg_immune_cell_atlas + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '1b9d8702-5af8-4142-85ed-020eb06ec4f6'" + obs_batch: donor_id + dataset_name: Immune Cell Atlas + dataset_summary: Cross-tissue immune cell analysis reveals tissue-specific features in humans + dataset_description: Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing. + dataset_url: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3 + dataset_reference: dominguez2022crosstissue + dataset_organism: homo_sapiens + # - id: cxg_ + # species: + # census_version: "2023-07-25" + # obs_value_filter: "dataset_id == ''" + # obs_batch: + # dataset_name: + # dataset_summary: + # dataset_description: + # dataset_url: + # dataset_reference: + # dataset_organism: + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null +publish_dir: s3://openproblems-nextflow/resources/datasets/cellxgene_census +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision 62e5f2edeb833e3c932d8ceb89842af79ea3dc1a \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ + --workspace 53907369739130 \ + --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --params-file "/tmp/params.yaml" \ + --config /tmp/nextflow.config diff --git a/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml b/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml new file mode 100644 index 0000000000..25fa8cbdf5 --- /dev/null +++ b/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml @@ -0,0 +1,200 @@ +functionality: + name: process_cellxgene_census + namespace: datasets/workflows + description: | + Fetch and process datasets originating from the CELLxGENE census. + argument_groups: + - name: Input database + description: "Open CellxGene Census by version or URI." + arguments: + - name: "--input_uri" + type: string + description: "If specified, a URI containing the Census SOMA objects. If specified, will take precedence over the `--census_version` argument." + required: false + example: "s3://bucket/path" + - name: "--census_version" + description: "Which release of CellxGene census to use. Possible values are \"latest\", \"stable\", or the date of one of the releases (e.g. \"2023-07-25\"). For more information, check the documentation on [Census data releases](https://chanzuckerberg.github.io/cellxgene-census/cellxgene_census_docsite_data_release_info.html)." + type: string + example: "stable" + required: false + - name: Cell query + description: Arguments related to the query. + arguments: + - name: "--species" + type: string + description: The organism to query, usually one of `Homo sapiens` or `Mus musculus`. + required: false + default: "homo_sapiens" + multiple: false + - name: "--obs_value_filter" + type: string + description: "Filter for selecting the `obs` metadata (i.e. cells). Value is a filter query written in the SOMA `value_filter` syntax." + required: false + example: "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" + - name: Cell filter + description: Filter the cells based on a minimum cell count per specified group + arguments: + - name: "--cell_filter_grouping" + type: string + description: | + A subset of 'obs' columns by which to group the cells for filtering. + Only groups surpassing or equal to the `--cell_filter_minimum_count` + threshold will be retained. Take care not to introduce a selection + bias against cells with more fine-grained ontology annotations. + required: false + example: ["dataset_id", "tissue", "assay", "disease", "cell_type"] + multiple: true + - name: "--cell_filter_minimum_count" + type: double + description: | + A minimum number of cells per group to retain. If `--cell_filter_grouping` + is defined, this parameter should also be provided and vice versa. + required: false + example: 100 + - name: Cell metadata + description: Cell metadata arguments + arguments: + - name: "--obs_batch" + type: string + description: | + Location of where to find the observation batch IDs. + + * If not specified, the `.obs["batch"]` field will not be included. + * If one or more values are specified, the `.obs["batch"]` field will be + set to the concatenated values of the specified fields, separated by + the `obs_batch_separator`. + required: false + multiple: true + multiple_sep: "," + example: ["batch"] + - name: "--obs_batch_separator" + type: string + description: Separator to use when concatenating the values of the `--obs_batch` fields. + required: false + default: "+" + - name: Dataset metadata + description: Information about the dataset that will be stored in the `.uns` slot. + arguments: + - name: "--id" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: true + - name: Sampling options + arguments: + - name: "--do_subsample" + type: boolean + default: false + description: "Whether or not to subsample the dataset" + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. + - name: "--keep_cell_type_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + - name: Normalization + arguments: + - name: "--normalization_methods" + type: string + multiple: true + choices: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt", "log_scran_pooling"] + default: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt"] + description: "Which normalization methods to run." + - name: Outputs + arguments: + - name: "--output_dataset" + __merge__: /src/datasets/api/file_common_dataset.yaml + direction: "output" + required: true + - name: "--output_meta" + direction: "output" + type: file + description: "Dataset metadata" + default: "dataset_metadata.yaml" + - name: "--output_raw" + __merge__: /src/datasets/api/file_raw.yaml + direction: "output" + required: false + - name: "--output_normalized" + __merge__: /src/datasets/api/file_normalized.yaml + direction: "output" + required: false + - name: "--output_pca" + __merge__: /src/datasets/api/file_pca.yaml + direction: "output" + required: false + - name: "--output_hvg" + __merge__: /src/datasets/api/file_hvg.yaml + direction: "output" + required: false + - name: "--output_knn" + __merge__: /src/datasets/api/file_knn.yaml + direction: "output" + required: false + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: datasets/loaders/cellxgene_census + - name: datasets/normalization/log_cp + - name: datasets/normalization/log_scran_pooling + - name: datasets/normalization/sqrt_cp + - name: datasets/normalization/l1_sqrt + - name: datasets/processors/subsample + - name: datasets/processors/pca + - name: datasets/processors/hvg + - name: datasets/processors/knn + - name: common/check_dataset_schema + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow diff --git a/src/datasets/workflows/process_cellxgene_census/main.nf b/src/datasets/workflows/process_cellxgene_census/main.nf new file mode 100644 index 0000000000..de0ba94752 --- /dev/null +++ b/src/datasets/workflows/process_cellxgene_census/main.nf @@ -0,0 +1,143 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + + // create different normalization methods by overriding the defaults + normalization_methods = [ + log_cp.run( + key: "log_cp10k", + args: [normalization_id: "log_cp10k", n_cp: 10000], + ), + log_cp.run( + key: "log_cpm", + args: [normalization_id: "log_cpm", n_cp: 1000000], + ), + sqrt_cp.run( + key: "sqrt_cp10k", + args: [normalization_id: "sqrt_cp10k", n_cp: 10000], + ), + sqrt_cp.run( + key: "sqrt_cpm", + args: [normalization_id: "sqrt_cpm", n_cp: 1000000], + ), + l1_sqrt.run( + key: "l1_sqrt", + args: [normalization_id: "l1_sqrt"], + ), + log_scran_pooling.run( + key: "log_scran_pooling", + args: [normalization_id: "log_scran_pooling"], + ) + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + + // fetch data from legacy openproblems + | cellxgene_census.run( + fromState: [ + "input_uri": "input_uri", + "census_version": "census_version", + "species": "species", + "obs_value_filter": "obs_value_filter", + "cell_filter_grouping": "cell_filter_grouping", + "cell_filter_minimum_count": "cell_filter_minimum_count", + "obs_batch": "obs_batch", + "obs_batch_separator": "obs_batch_separator", + "dataset_id": "id", + "dataset_name": "dataset_name", + "dataset_url": "dataset_url", + "dataset_reference": "dataset_reference", + "dataset_summary": "dataset_summary", + "dataset_description": "dataset_description", + "dataset_organism": "dataset_organism", + ], + toState: ["output_raw": "output"] + ) + + // subsample if so desired + | subsample.run( + runIf: { id, state -> state.do_subsample }, + fromState: [ + "input": "output_raw", + "n_obs": "n_obs", + "n_vars": "n_vars", + "keep_features": "keep_features", + "keep_cell_type_categories": "keep_cell_type_categories", + "keep_batch_categories": "keep_batch_categories", + "even": "even", + "seed": "seed" + ], + args: [output_mod2: null], + toState: ["output_raw": "output"] + ) + + | runEach( + components: normalization_methods, + id: { id, state, comp -> + if (state.normalization_methods.size() > 1) { + id + "/" + comp.name + } else { + id + } + }, + filter: { id, state, comp -> + comp.name in state.normalization_methods + }, + fromState: ["input": "output_raw"], + toState: { id, output, state, comp -> + state + [ + output_normalized: output.output, + normalization_id: comp.name + ] + } + ) + + | pca.run( + fromState: ["input": "output_normalized"], + toState: ["output_pca": "output" ] + ) + + | hvg.run( + fromState: ["input": "output_pca"], + toState: ["output_hvg": "output"] + ) + + | knn.run( + fromState: ["input": "output_hvg"], + toState: ["output_knn": "output"] + ) + + | check_dataset_schema.run( + fromState: ["input": "output_knn"], + toState: ["output_dataset": "output", "output_meta": "meta"] + ) + + // only output the files for which an output file was specified + | setState([ + "output_dataset", + "output_meta", + "output_raw", + "output_normalized", + "output_pca", + "output_hvg", + "output_knn", + "_meta" + ]) + + emit: + output_ch +} \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index f9d2d42775..66a90c7a43 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -1,3 +1,10 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + workflow run_wf { take: input_ch @@ -116,23 +123,6 @@ workflow run_wf { toState: ["output_dataset": "output", "output_meta": "meta"] ) - // TODO: remove this filter if we're sure the mismatch issue no longer occurs - | filter{ id, state -> - def uns = (new org.yaml.snakeyaml.Yaml().load(state.output_meta)).uns - def expected_id = state.normalization_methods.size() > 1 ? - "${uns.dataset_id}/${uns.normalization_id}" : - uns.dataset_id - expected_id = expected_id.replaceAll("_subsample", "") - - def is_ok = id == expected_id - - if (!is_ok) { - println("DETECTED ID MISMATCH: $id != $expected_id.\nTuple:\n${toYamlBlob([id, state])}\n") - } - - is_ok - } - // only output the files for which an output file was specified | setState([ "output_dataset", diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 56c797985c..d5a17ae6dc 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -1,3 +1,10 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + workflow run_wf { take: input_ch From cea289f3751bed9d0d1270b2f4b407ead20a9a88 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 16:15:55 +0100 Subject: [PATCH 1081/1233] add back nextflow.config Former-commit-id: c48ebd53c75809fe4df3a83589cca14ddfbc1616 --- nextflow.config | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 nextflow.config diff --git a/nextflow.config b/nextflow.config new file mode 100644 index 0000000000..a455cf74fa --- /dev/null +++ b/nextflow.config @@ -0,0 +1,8 @@ +manifest { + name = 'openproblems-bio/openproblems-v2' + mainScript = 'main.nf' + nextflowVersion = '!>=20.12.1-edge' + description = 'OpenProblems benchmarking pipeline' +} + +process.container = 'nextflow/bash:latest' From 93cc1b54b359430bd139c91ed4e5d8e24f4f30a2 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Dec 2023 16:42:34 +0100 Subject: [PATCH 1082/1233] clean up first Former-commit-id: e897ba9d6edcd1c10aea849765f7c181dd653cdb --- .../cellxgene_census_tower.sh | 48 ++----------------- 1 file changed, 3 insertions(+), 45 deletions(-) diff --git a/src/datasets/resource_scripts/cellxgene_census_tower.sh b/src/datasets/resource_scripts/cellxgene_census_tower.sh index 9f3eaf40d6..eb49c29278 100755 --- a/src/datasets/resource_scripts/cellxgene_census_tower.sh +++ b/src/datasets/resource_scripts/cellxgene_census_tower.sh @@ -2,50 +2,8 @@ cat > "/tmp/params.yaml" << 'HERE' param_list: - - id: cxg_mouse_pancreas_atlas - species: mus_musculus - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" - obs_batch: donor_id - dataset_name: Mouse pancreatic islet - dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes - dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. - dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 - dataset_reference: hrovatin2023delineating - dataset_organism: mus_musculus - - id: cxg_hcla - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '066943a2-fdac-4b29-b348-40cede398e4e'" - obs_batch: donor_id - dataset_name: Human Lung Cell Atlas - dataset_summary: An integrated cell atlas of the human lung in health and disease (core) - dataset_description: The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata. - dataset_url: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 - dataset_reference: sikkema2023integrated - dataset_organism: homo_sapiens - - id: cxg_tabula_sapiens - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '53d208b0-2cfd-4366-9866-c3c6114081bc'" - obs_batch: [donor_id, assay] - dataset_name: Tabula Sapiens - dataset_summary: A multiple-organ, single-cell transcriptomic atlas of humans - dataset_description: Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. - dataset_url: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 - dataset_reference: consortium2022tabula - dataset_organism: homo_sapiens - - id: cxg_immune_cell_atlas - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '1b9d8702-5af8-4142-85ed-020eb06ec4f6'" - obs_batch: donor_id - dataset_name: Immune Cell Atlas - dataset_summary: Cross-tissue immune cell analysis reveals tissue-specific features in humans - dataset_description: Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing. - dataset_url: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3 - dataset_reference: dominguez2022crosstissue - dataset_organism: homo_sapiens + + # template for adding new datasets # - id: cxg_ # species: # census_version: "2023-07-25" @@ -77,7 +35,7 @@ process { HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision 62e5f2edeb833e3c932d8ceb89842af79ea3dc1a \ + --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ --workspace 53907369739130 \ From c04a453647f3eac5656369acae51322dc2a31859 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 14 Dec 2023 10:05:36 +0100 Subject: [PATCH 1083/1233] Add more cellxgene datasets (#308) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * add cellxgene datasets Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com> * fix yaml formatting --------- Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com> Former-commit-id: 6cdba41787f894aa4d1ff6f4b8d00d866fefb62e --- src/common/library.bib | 69 +++++++++- .../resource_scripts/cellxgene_census.sh | 8 +- .../cellxgene_census_tower.sh | 127 ++++++++++++++++-- 3 files changed, 186 insertions(+), 18 deletions(-) diff --git a/src/common/library.bib b/src/common/library.bib index 3e3475fdd6..6055e3ecc2 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1516,4 +1516,71 @@ @article{dominguez2022crosstissue author = {Domínguez Conde, C. and Xu, C. and Jarvis, L. B. and Rainbow, D. B. and Wells, S. B. and Gomes, T. and Howlett, S. K. and Suchanek, O. and Polanski, K. and King, H. W. and Mamanova, L. and Huang, N. and Szabo, P. A. and Richardson, L. and Bolt, L. and Fasouli, E. S. and Mahbubani, K. T. and Prete, M. and Tuck, L. and Richoz, N. and Tuong, Z. K. and Campos, L. and Mousa, H. S. and Needham, E. J. and Pritchard, S. and Li, T. and Elmentaite, R. and Park, J. and Rahmani, E. and Chen, D. and Menon, D. K. and Bayraktar, O. A. and James, L. K. and Meyer, K. B. and Yosef, N. and Clatworthy, M. R. and Sims, P. A. and Farber, D. L. and Saeb-Parsy, K. and Jones, J. L. and Teichmann, S. A.}, year = {2022}, month = may -} \ No newline at end of file +} + +@article{eraslan2022singlenucleus, + title = {Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function}, + volume = {376}, + ISSN = {1095-9203}, + url = {http://dx.doi.org/10.1126/science.abl4290}, + DOI = {10.1126/science.abl4290}, + number = {6594}, + journal = {Science}, + publisher = {American Association for the Advancement of Science (AAAS)}, + author = {Eraslan, G\"{o}kcen and Drokhlyansky, Eugene and Anand, Shankara and Fiskin, Evgenij and Subramanian, Ayshwarya and Slyper, Michal and Wang, Jiali and Van Wittenberghe, Nicholas and Rouhana, John M. and Waldman, Julia and Ashenberg, Orr and Lek, Monkol and Dionne, Danielle and Win, Thet Su and Cuoco, Michael S. and Kuksenko, Olena and Tsankov, Alexander M. and Branton, Philip A. and Marshall, Jamie L. and Greka, Anna and Getz, Gad and Segrè, Ayellet V. and Aguet, Fran\c{c}ois and Rozenblatt-Rosen, Orit and Ardlie, Kristin G. and Regev, Aviv}, + year = {2022}, + month = may +} + +@article{li2023integrated, + title = {Integrated multi-omics single cell atlas of the human retina}, + url = {http://dx.doi.org/10.1101/2023.11.07.566105}, + DOI = {10.1101/2023.11.07.566105}, + publisher = {Cold Spring Harbor Laboratory}, + author = {Li, Jin and Wang, Jun and Ibarra, Ignacio L and Cheng, Xuesen and Luecken, Malte D and Lu, Jiaxiong and Monavarfeshani, Aboozar and Yan, Wenjun and Zheng, Yiqiao and Zuo, Zhen and Zayas Colborn, Samantha Lynn and Cortez, Berenice Sarahi and Owen, Leah A and Tran, Nicholas M and Shekhar, Karthik and Sanes, Joshua R and Stout, J Timothy and Chen, Shiming and Li, Yumei and DeAngelis, Margaret M and Theis, Fabian J and Chen, Rui}, + year = {2023}, + month = nov +} + +@article{wilson2022multimodal, + title = {Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression}, + volume = {13}, + ISSN = {2041-1723}, + url = {http://dx.doi.org/10.1038/s41467-022-32972-z}, + DOI = {10.1038/s41467-022-32972-z}, + number = {1}, + journal = {Nature Communications}, + publisher = {Springer Science and Business Media LLC}, + author = {Wilson, Parker C. and Muto, Yoshiharu and Wu, Haojia and Karihaloo, Anil and Waikar, Sushrut S. and Humphreys, Benjamin D.}, + year = {2022}, + month = sep +} + +@article{steuernagel2022hypomap, + title = {HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus}, + volume = {4}, + ISSN = {2522-5812}, + url = {http://dx.doi.org/10.1038/s42255-022-00657-y}, + DOI = {10.1038/s42255-022-00657-y}, + number = {10}, + journal = {Nature Metabolism}, + publisher = {Springer Science and Business Media LLC}, + author = {Steuernagel, Lukas and Lam, Brian Y. H. and Klemm, Paul and Dowsett, Georgina K. C. and Bauder, Corinna A. and Tadross, John A. and Hitschfeld, Tamara Sotelo and del Rio Martin, Almudena and Chen, Weiyi and de Solis, Alain J. and Fenselau, Henning and Davidsen, Peter and Cimino, Irene and Kohnke, Sara N. and Rimmington, Debra and Coll, Anthony P. and Beyer, Andreas and Yeo, Giles S. H. and Br\"{u}ning, Jens C.}, + year = {2022}, + month = oct, + pages = {1402–1419} +} + +@article{tian2023singlecell, + title = {Single-cell DNA methylation and 3D genome architecture in the human brain}, + volume = {382}, + ISSN = {1095-9203}, + url = {http://dx.doi.org/10.1126/science.adf5357}, + DOI = {10.1126/science.adf5357}, + number = {6667}, + journal = {Science}, + publisher = {American Association for the Advancement of Science (AAAS)}, + author = {Tian, Wei and Zhou, Jingtian and Bartlett, Anna and Zeng, Qiurui and Liu, Hanqing and Castanon, Rosa G. and Kenworthy, Mia and Altshul, Jordan and Valadon, Cynthia and Aldridge, Andrew and Nery, Joseph R. and Chen, Huaming and Xu, Jiaying and Johnson, Nicholas D. and Lucero, Jacinta and Osteen, Julia K. and Emerson, Nora and Rink, Jon and Lee, Jasper and Li, Yang E. and Siletti, Kimberly and Liem, Michelle and Claffey, Naomi and O’Connor, Carolyn and Yanny, Anna Marie and Nyhus, Julie and Dee, Nick and Casper, Tamara and Shapovalova, Nadiya and Hirschstein, Daniel and Ding, Song-Lin and Hodge, Rebecca and Levi, Boaz P. and Keene, C. Dirk and Linnarsson, Sten and Lein, Ed and Ren, Bing and Behrens, M. Margarita and Ecker, Joseph R.}, + year = {2023}, + month = oct +} diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index 58c63e8086..9a7d7a0f7a 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -2,16 +2,16 @@ cat > "/tmp/params.yaml" << 'HERE' param_list: - - id: cxg_mm_pancreas_atlas + - id: cxg_mouse_pancreas_atlas species: mus_musculus census_version: "2023-07-25" obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" obs_batch: donor_id - dataset_name: Mouse pancreatic islet atlas - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE211799 - dataset_reference: hrovatin2023delineating + dataset_name: Mouse Pancreatic Islet Atlas dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. + dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 + dataset_reference: hrovatin2023delineating dataset_organism: mus_musculus normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] diff --git a/src/datasets/resource_scripts/cellxgene_census_tower.sh b/src/datasets/resource_scripts/cellxgene_census_tower.sh index eb49c29278..18df311725 100755 --- a/src/datasets/resource_scripts/cellxgene_census_tower.sh +++ b/src/datasets/resource_scripts/cellxgene_census_tower.sh @@ -1,20 +1,121 @@ #!/bin/bash +# template for adding new datasets +# - id: cxg_ +# species: +# census_version: "2023-07-25" +# obs_value_filter: "dataset_id == ''" +# obs_batch: +# dataset_name: +# dataset_summary: +# dataset_description: +# dataset_url: +# dataset_reference: +# dataset_organism: + +# not sure which dataset ids to use +# - id: cxg_human_brain_atlas +# species: homo_sapiens +# census_version: "2023-07-25" +# obs_value_filter: "dataset_id == ''" # <--- ? +# obs_batch: donor_id +# dataset_name: Human Brain Atlas +# dataset_summary: Single-Cell DNA Methylation and 3D Genome Human Brain Atlas +# dataset_description: Delineating the gene regulatory programs underlying complex cell types is fundamental for understanding brain functions in health and disease. Here, we comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in over 500,000 cells from 46 brain regions. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. With these resources, we developed scMCodes that reliably predict brain cell types using their methylation status at select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell type-specific gene regulation in the adult human brain. +# dataset_url: https://cellxgene.cziscience.com/collections/fdebfda9-bb9a-4b4b-97e5-651097ea07b0 +# dataset_reference: tian2023singlecell +# dataset_organism: homo_sapiens + cat > "/tmp/params.yaml" << 'HERE' param_list: - - # template for adding new datasets - # - id: cxg_ - # species: - # census_version: "2023-07-25" - # obs_value_filter: "dataset_id == ''" - # obs_batch: - # dataset_name: - # dataset_summary: - # dataset_description: - # dataset_url: - # dataset_reference: - # dataset_organism: + - id: cxg_mouse_pancreas_atlas + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" + obs_batch: donor_id + dataset_name: Mouse Pancreatic Islet Atlas + dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes + dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. + dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 + dataset_reference: hrovatin2023delineating + dataset_organism: mus_musculus + - id: cxg_hcla + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '066943a2-fdac-4b29-b348-40cede398e4e'" + obs_batch: donor_id + dataset_name: Human Lung Cell Atlas + dataset_summary: An integrated cell atlas of the human lung in health and disease (core) + dataset_description: The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata. + dataset_url: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 + dataset_reference: sikkema2023integrated + dataset_organism: homo_sapiens + - id: cxg_tabula_sapiens + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '53d208b0-2cfd-4366-9866-c3c6114081bc'" + obs_batch: [donor_id, assay] + dataset_name: Tabula Sapiens + dataset_summary: A multiple-organ, single-cell transcriptomic atlas of humans + dataset_description: Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. + dataset_url: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 + dataset_reference: consortium2022tabula + dataset_organism: homo_sapiens + - id: cxg_immune_cell_atlas + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '1b9d8702-5af8-4142-85ed-020eb06ec4f6'" + obs_batch: donor_id + dataset_name: Immune Cell Atlas + dataset_summary: Cross-tissue immune cell analysis reveals tissue-specific features in humans + dataset_description: Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing. + dataset_url: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3 + dataset_reference: dominguez2022crosstissue + dataset_organism: homo_sapiens + - id: cxg_gtex_v9 + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '4ed927e9-c099-49af-b8ce-a2652d069333'" + obs_batch: donor_id + dataset_name: GTEX v9 + dataset_summary: Single-nucleus cross-tissue molecular reference maps to decipher disease gene function + dataset_description: Understanding the function of genes and their regulation in tissue homeostasis and disease requires knowing the cellular context in which genes are expressed in tissues across the body. Single cell genomics allows the generation of detailed cellular atlases in human tissues, but most efforts are focused on single tissue types. Here, we establish a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq), and apply it to 8 diverse, archived, frozen tissue types (three donors per tissue). We apply four snRNA-seq methods to each of 25 samples from 16 donors, generating a cross-tissue atlas of 209,126 nuclei profiles, and benchmark them vs. scRNA-seq of comparable fresh tissues. We use a conditional variational autoencoder (cVAE) to integrate an atlas across tissues, donors, and laboratory methods. We highlight shared and tissue-specific features of tissue-resident immune cells, identifying tissue-restricted and non-restricted resident myeloid populations. These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease. For rare, monogenic muscle diseases, we identify cell types that likely underlie the neuromuscular, metabolic, and immune components of these diseases, and biological processes involved in their pathology. For common complex diseases and traits analyzed by GWAS, we identify the cell types and gene modules that potentially underlie disease mechanisms. The experimental and analytical frameworks we describe will enable the generation of large-scale studies of how cellular and molecular processes vary across individuals and populations. + dataset_url: https://cellxgene.cziscience.com/collections/a3ffde6c-7ad2-498a-903c-d58e732f7470 + dataset_reference: eraslan2022singlenucleus + dataset_organism: homo_sapiens + - id: cxg_human_retina_cell_atlas + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == 'd6505c89-c43d-4c28-8c4f-7351a5fd5528'" + obs_batch: donor_id + dataset_name: Human Retina Cell Atlas + dataset_summary: Single cell atlas of the human retina + dataset_description: As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases. + dataset_url: https://cellxgene.cziscience.com/collections/4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e + dataset_reference: li2023integrated + dataset_organism: homo_sapiens + - id: cxg_dkd + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id in ['ad0bf220-dd49-4b71-bb5c-576fee675d2b', 'e067e5ca-e53e-485f-aa8e-efd5435229c8']" + obs_batch: donor_id + dataset_name: Diabetic Kidney Disease + dataset_summary: Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression + dataset_description: Multimodal single cell sequencing is a powerful tool for interrogating cell-specific changes in transcription and chromatin accessibility. We performed single nucleus RNA (snRNA-seq) and assay for transposase accessible chromatin sequencing (snATAC-seq) on human kidney cortex from donors with and without diabetic kidney disease (DKD) to identify altered signaling pathways and transcription factors associated with DKD. Both snRNA-seq and snATAC-seq had an increased proportion of VCAM1+ injured proximal tubule cells (PT_VCAM1) in DKD samples. PT_VCAM1 has a pro-inflammatory expression signature and transcription factor motif enrichment implicated NFkB signaling. We used stratified linkage disequilibrium score regression to partition heritability of kidney-function-related traits using publicly-available GWAS summary statistics. Cell-specific PT_VCAM1 peaks were enriched for heritability of chronic kidney disease (CKD), suggesting that genetic background may regulate chromatin accessibility and DKD progression. snATAC-seq found cell-specific differentially accessible regions (DAR) throughout the nephron that change accessibility in DKD and these regions were enriched for glucocorticoid receptor (GR) motifs. Changes in chromatin accessibility were associated with decreased expression of insulin receptor, increased gluconeogenesis, and decreased expression of the GR cytosolic chaperone, FKBP5, in the diabetic proximal tubule. Cleavage under targets and release using nuclease (CUT&RUN) profiling of GR binding in bulk kidney cortex and an in vitro model of the proximal tubule (RPTEC) showed that DAR co-localize with GR binding sites. CRISPRi silencing of GR response elements (GRE) in the FKBP5 gene body reduced FKBP5 expression in RPTEC, suggesting that reduced FKBP5 chromatin accessibility in DKD may alter cellular response to GR. We developed an open-source tool for single cell allele specific analysis (SALSA) to model the effect of genetic background on gene expression. Heterozygous germline single nucleotide variants (SNV) in proximal tubule ATAC peaks were associated with allele-specific chromatin accessibility and differential expression of target genes within cis-coaccessibility networks. Partitioned heritability of proximal tubule ATAC peaks with a predicted allele-specific effect was enriched for eGFR, suggesting that genetic background may modify DKD progression in a cell-specific manner. + dataset_url: https://cellxgene.cziscience.com/collections/b3e2c6e3-9b05-4da9-8f42-da38a664b45b + dataset_reference: wilson2022multimodal + dataset_organism: homo_sapiens + - id: cxg_hypomap + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == 'dbb4e1ed-d820-4e83-981f-88ef7eb55a35'" + obs_batch: donor_id + dataset_name: HypoMap + dataset_summary: A unified single cell gene expression atlas of the murine hypothalamus + dataset_description: The hypothalamus plays a key role in coordinating fundamental body functions. Despite recent progress in single-cell technologies, a unified catalogue and molecular characterization of the heterogeneous cell types and, specifically, neuronal subtypes in this brain region are still lacking. Here we present an integrated reference atlas “HypoMap” of the murine hypothalamus consisting of 384,925 cells, with the ability to incorporate new additional experiments. We validate HypoMap by comparing data collected from SmartSeq2 and bulk RNA sequencing of selected neuronal cell types with different degrees of cellular heterogeneity. + dataset_url: https://cellxgene.cziscience.com/collections/d86517f0-fa7e-4266-b82e-a521350d6d36 + dataset_reference: steuernagel2022hypomap + dataset_organism: mus_musculus normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset: '$id/dataset.h5ad' From 70fa9a12ea3ceaba3a2c57658afe81f6271e16ee Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 15 Dec 2023 09:51:45 +0100 Subject: [PATCH 1084/1233] openproblems_v1: Separate input_id from dataset_id (#311) * allow input ids to be different from the dataset ids * implement changes in the wf Former-commit-id: 298dcb15c19827bbd567d3cd251b38a3bad12946 --- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 8 ++++++-- src/datasets/loaders/openproblems_v1/script.py | 2 +- src/datasets/loaders/openproblems_v1/test.py | 8 +++++--- .../loaders/openproblems_v1_multimodal/config.vsh.yaml | 8 ++++++-- .../loaders/openproblems_v1_multimodal/script.py | 2 +- .../loaders/openproblems_v1_multimodal/test.py | 10 ++++++---- .../workflows/process_openproblems_v1/config.vsh.yaml | 6 +++++- src/datasets/workflows/process_openproblems_v1/main.nf | 3 ++- .../process_openproblems_v1_multimodal/config.vsh.yaml | 6 +++++- .../process_openproblems_v1_multimodal/main.nf | 3 ++- 10 files changed, 39 insertions(+), 17 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 73874cbb4a..5feab80c1b 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -5,9 +5,9 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--dataset_id" + - name: "--input_id" type: "string" - description: "The ID of the dataset" + description: "The ID of the dataset in OpenProblems v1" required: true - name: "--obs_cell_type" type: "string" @@ -28,6 +28,10 @@ functionality: description: Convert layers to a sparse CSR format. - name: Metadata arguments: + - name: "--dataset_id" + type: string + description: Unique identifier of the dataset. + required: true - name: "--dataset_name" type: string description: Nicely formatted name. diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index b08928e9c2..c09f7895bf 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -38,7 +38,7 @@ } # fetch dataset -dataset_fun, kwargs = dataset_funs[par["dataset_id"]] +dataset_fun, kwargs = dataset_funs[par["input_id"]] print("Fetch dataset", flush=True) adata = dataset_fun(**kwargs) diff --git a/src/datasets/loaders/openproblems_v1/test.py b/src/datasets/loaders/openproblems_v1/test.py index aa49864118..f1b0389837 100644 --- a/src/datasets/loaders/openproblems_v1/test.py +++ b/src/datasets/loaders/openproblems_v1/test.py @@ -2,7 +2,8 @@ import subprocess import anndata as ad -name = "pancreas" +input_id = "pancreas" +dataset_id = "openproblems_v1/" + input_id output = "dataset.h5ad" obs_cell_type = "celltype" obs_batch = "tech" @@ -11,7 +12,8 @@ out = subprocess.run( [ meta["executable"], - "--dataset_id", name, + "--input_id", input_id, + "--dataset_id", dataset_id, "--obs_cell_type", obs_cell_type, "--obs_batch", obs_batch, "--layer_counts", "counts", @@ -44,7 +46,7 @@ print(">> Check that output fits expected API", flush=True) assert adata.X is None, "adata.X should be None/empty" assert "counts" in adata.layers, "Counts layer not found in output layers" -assert adata.uns["dataset_id"] == name, f"Expected {name} as value" +assert adata.uns["dataset_id"] == dataset_id, f"Expected {dataset_id} as value" if obs_cell_type: assert "cell_type" in adata.obs.columns, "'cell_type' column not found in obs of anndata output" if obs_batch: diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index d8c9fd1226..585dfc4531 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -5,9 +5,9 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--dataset_id" + - name: "--input_id" type: "string" - description: "The ID of the dataset" + description: "The ID of the dataset in OpenProblems v1" required: true - name: "--obs_cell_type" type: "string" @@ -28,6 +28,10 @@ functionality: description: Convert layers to a sparse CSR format. - name: Metadata arguments: + - name: "--dataset_id" + type: string + description: Unique identifier of the dataset. + required: true - name: "--dataset_name" type: string description: Nicely formatted name. diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py index 4e19dd2e19..6a619ee93d 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/script.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -33,7 +33,7 @@ } # fetch dataset -dataset_fun, kwargs = dataset_funs[par["dataset_id"]] +dataset_fun, kwargs = dataset_funs[par["input_id"]] print("Fetch dataset", flush=True) adata = dataset_fun(**kwargs) diff --git a/src/datasets/loaders/openproblems_v1_multimodal/test.py b/src/datasets/loaders/openproblems_v1_multimodal/test.py index 36075814ff..d6ead5c88d 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/test.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/test.py @@ -2,7 +2,8 @@ import subprocess import anndata as ad -name = "scicar_mouse_kidney" +input_id = "scicar_mouse_kidney" +dataset_id = "openproblems_v1_multimodal/" + input_id obs_cell_type = "cell_name" obs_batch = "replicate" obs_tissue = None @@ -14,7 +15,8 @@ out = subprocess.run( [ meta["executable"], - "--dataset_id", name, + "--input_id", input_id, + "--dataset_id", dataset_id, "--obs_cell_type", obs_cell_type, "--obs_batch", obs_batch, "--layer_counts", "counts", @@ -57,7 +59,7 @@ assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" if obs_tissue: assert "tissue" in output_mod1.obs.columns, "tissue column not found in mod 1 output obs" -assert output_mod1.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 1 output uns" +assert output_mod1.uns["dataset_id"] == dataset_id, f"Expected: {dataset_id} as value for dataset_id in mod 1 output uns" assert output_mod1.uns["dataset_name"] == "Pancreas", "Expected: Pancreas as value for dataset_name in mod 1 output uns" assert output_mod1.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 1 output uns" assert output_mod1.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 1 output uns" @@ -73,7 +75,7 @@ assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" if obs_tissue: assert "tissue" in output_mod2.obs.columns, "tissue column not found in mod 2 output obs" -assert output_mod2.uns["dataset_id"] == name, f"Expected: {name} as value for dataset_id in mod 2 output uns" +assert output_mod2.uns["dataset_id"] == dataset_id, f"Expected: {dataset_id} as value for dataset_id in mod 2 output uns" assert output_mod2.uns["dataset_name"] == "Pancreas", "Expected: Pancreas as value for dataset_name in mod 2 output uns" assert output_mod2.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 2 output uns" assert output_mod2.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 2 output uns" diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 5cdf080f93..b6353da6fd 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -7,8 +7,12 @@ functionality: - name: Inputs arguments: - name: "--id" + type: string + description: Unique identifier of the dataset. + required: true + - name: "--input_id" type: "string" - description: "The ID of the dataset" + description: "The ID of the dataset in OpenProblems v1" required: true - name: "--obs_cell_type" type: "string" diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 66a90c7a43..0a9d98b3c5 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -49,12 +49,13 @@ workflow run_wf { // fetch data from legacy openproblems | openproblems_v1.run( fromState: [ - "dataset_id": "id", + "input_id": "input_id", "obs_cell_type": "obs_cell_type", "obs_batch": "obs_batch", "obs_tissue": "obs_tissue", "layer_counts": "layer_counts", "sparse": "sparse", + "dataset_id": "id", "dataset_name": "dataset_name", "dataset_url": "dataset_url", "dataset_reference": "dataset_reference", diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index a6b4841bda..69ce43ddf0 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -7,8 +7,12 @@ functionality: - name: Inputs arguments: - name: "--id" + type: string + description: Unique identifier of the dataset. + required: true + - name: "--input_id" type: "string" - description: "The ID of the dataset" + description: "The ID of the dataset in OpenProblems v1" required: true - name: "--obs_cell_type" type: "string" diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index d5a17ae6dc..0f8768ec1d 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -49,12 +49,13 @@ workflow run_wf { // fetch data from legacy openproblems | openproblems_v1_multimodal.run( fromState: [ - "dataset_id": "id", + "input_id": "input_id", "obs_cell_type": "obs_cell_type", "obs_batch": "obs_batch", "obs_tissue": "obs_tissue", "layer_counts": "layer_counts", "sparse": "sparse", + "dataset_id": "id", "dataset_name": "dataset_name", "dataset_url": "dataset_url", "dataset_reference": "dataset_reference", From 394369d706fa94fede7a0e530de0a7c7ee9072d4 Mon Sep 17 00:00:00 2001 From: sainirmayi <92786623+sainirmayi@users.noreply.github.com> Date: Sat, 16 Dec 2023 09:31:17 +0100 Subject: [PATCH 1085/1233] Add SIMLR (#312) * add SIMLR dimensionality reduction method * add description and reference * add SIMLR reference * change default n_dim and write output to file * Add SIMLR entry * Update documentation URL Co-authored-by: Kai Waldrant * Reformat code * Use explicit namespaces --------- Co-authored-by: Kai Waldrant Former-commit-id: bdbf261c9f70b98c6ceb7b6f0805e617aaf3c394 --- CHANGELOG.md | 2 + src/common/library.bib | 20 ++++++ .../methods/simlr/config.vsh.yaml | 57 ++++++++++++++++ .../methods/simlr/script.R | 67 +++++++++++++++++++ 4 files changed, 146 insertions(+) create mode 100644 src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/methods/simlr/script.R diff --git a/CHANGELOG.md b/CHANGELOG.md index 8773169a7b..857fa61a8d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -307,6 +307,8 @@ * `metrics/trustworthiness` should be removed because it is already included in `metrics/coranking`. +* `methods/simlr`: Added new SIMLR method. + ## match_modalities (PR #201) diff --git a/src/common/library.bib b/src/common/library.bib index 6055e3ecc2..a80290203b 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1348,6 +1348,26 @@ @article{wang2013target } +@article{wang2017visualization, + title = {Visualization and analysis of single-cell {RNA}-seq data by kernel-based similarity learning}, + volume = {14}, + copyright = {2017 Springer Nature America, Inc.}, + issn = {1548-7105}, + url = {https://www.nature.com/articles/nmeth.4207}, + doi = {10.1038/nmeth.4207}, + abstract = {The SIMLR software identifies similarities between cells across a range of single-cell RNA-seq data, enabling effective dimension reduction, clustering and visualization.}, + language = {en}, + number = {4}, + journal = {Nature Methods}, + author = {Wang, Bo and Zhu, Junjie and Pierson, Emma and Ramazzotti, Daniele and Batzoglou, Serafim}, + month = apr, + year = {2017}, + publisher = {Nature Publishing Group}, + keywords = {Gene expression, Genome informatics, Machine learning, Statistical methods}, + pages = {414--416}, +} + + @article{welch2019single, title = {Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity}, author = {Joshua D. Welch and Velina Kozareva and Ashley Ferreira and Charles Vanderburg and Carly Martin and Evan Z. Macosko}, diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml new file mode 100644 index 0000000000..9717025593 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -0,0 +1,57 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: simlr + + info: + label: SIMLR + summary: Multikernal-based learning of distance metrics from gene expression data for dimension reduction, clustering and visulaization. + description: | + Single-cell interpretation via multikernel learning (SIMLR) learns cell-to-cell similarity measures from single-cell RNA-seq data in using Gaussian kernels with various hyperparameters in order to perform dimension reduction, clustering and visualization. + SIMLR assumes that if C separable populations exist among the N cells, then the similarity matrix should have an approximate block-diagonal structure with C blocks whereby cells have larger similarities to other cells within the same subpopulations. Learned similarity between two cells should be small if the Euclidean distance between them is large. The cell-to-cell similarity is computed using an optimization framework over an N x N similarity matrix, a low-dimensional auxilary matrix enforcing low rank constraint on the similarity matrix, and the kernel weights. + Dimension reduction is achieved by the stochastic neighbor embedding methodology with the learned similarities as input. + preferred_normalization: log_cp10k + reference: "wang2017visualization" + documentation_url: https://github.com/BatzoglouLabSU/SIMLR/blob/SIMLR/README.md + repository_url: https://github.com/BatzoglouLabSU/SIMLR + + arguments: + - name: "--n_dim" + type: integer + description: Number of dimensions. + - name: "--n_clusters" + type: integer + description: Number of clusters to be estimated over the input dataset. + - name: "--tuning_param" + type: integer + default: 10 + description: Number of dimensions. + - name: "--impute" + type: boolean + default: false + description: Should the input data be transposed? + - name: "--normalize" + type: boolean + default: false + description: Should the input data be normalized? + - name: "--cores_ratio" + type: integer + default: 1 + description: Ratio of the number of cores to be used when computing the multi-kernel. + + resources: + - type: r_script + path: script.R + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + packages: [ grDevices ] + cran: [ Matrix, parallel, Rcpp, pracma, RcppAnnoy, RSpectra, igraph ] + bioc: [ SIMLR ] + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/simlr/script.R b/src/tasks/dimensionality_reduction/methods/simlr/script.R new file mode 100644 index 0000000000..49ffb44592 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/simlr/script.R @@ -0,0 +1,67 @@ +requireNamespace("anndata", quietly = TRUE) +requireNamespace("SIMLR", quietly = TRUE) + +## VIASH START +par <- list( + input = "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", + output = "output.h5ad", + n_clusters = NULL, + n_dim = NA, + tuning_param = 10, + impute = FALSE, + normalize = FALSE, + cores_ratio = 1 +) +meta <- list( + functionality_name = "simlr" +) +## VIASH END + +cat("Reading input files\n") +input <- anndata::read_h5ad(par$input) + +if (is.null(par$n_clusters)) { + cat("Estimating the number of clusters\n") + set.seed(1) + NUMC = 2:5 + estimates <- SIMLR::SIMLR_Estimate_Number_of_Clusters( + X = as.matrix(input$layers[["normalized"]]), + NUMC = NUMC, + cores.ratio = par$cores_ratio + ) + n_clusters <- NUMC[which.min(estimates$K2)] +} else { + n_clusters <- par$n_clusters +} + +if (is.null(par$n_dim)) { + n_dim <- NA +} else { + n_dim <- par$n_dim +} + +cat("Running SIMLR\n") +simlr_result <- SIMLR::SIMLR( + X = as.matrix(input$layers[["normalized"]]), + c = n_clusters, + no.dim = n_dim, + k = par$tuning_param, + if.impute = par$impute, + normalize = par$normalize, + cores.ratio = par$cores_ratio +) +obsm_X_emb <- simlr_result$ydata + +cat("Write output AnnData to file\n") +output <- anndata::AnnData( + uns = list( + dataset_id = input$uns[["dataset_id"]], + method_id = meta$functionality_name, + normalization_id = input$uns[["normalization_id"]] + ), + obsm = list( + X_emb = obsm_X_emb + ), + shape = input$shape +) +output$write_h5ad(par$output, compression = "gzip") From 48b703921d62543f706a47789508e553fb6360a4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 16 Dec 2023 09:37:00 +0100 Subject: [PATCH 1086/1233] rework dataset scripts (#310) * rework dataset scripts * fix scripts * Update src/tasks/dimensionality_reduction/resources_scripts/run_test.sh Co-authored-by: Kai Waldrant * fix scripts * change dataset_id to input_id * update dataset_id to input_id * Update compute environment in resource scripts --------- Co-authored-by: Kai Waldrant Former-commit-id: 35e065d0368c191db84031a67d6c06656832a549 --- .../process_task_results/get_results/script.R | 4 +- .../run/run_nf_tower_test.sh | 6 +- .../process_task_results/run/run_test.sh | 4 +- .../resource_scripts/cellxgene_census.sh | 125 +++++++++++++- .../resource_scripts/cellxgene_census_test.sh | 32 ++++ .../cellxgene_census_tower.sh | 145 ----------------- .../resource_scripts/openproblems_v1.sh | 65 ++++---- .../openproblems_v1_multimodal.sh | 33 ++-- .../openproblems_v1_multimodal_nf_tower.sh | 58 ------- .../openproblems_v1_multimodal_test.sh | 45 +++++ .../openproblems_v1_nf_tower.sh | 154 ------------------ .../resource_scripts/openproblems_v1_test.sh | 51 ++++++ .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 27 --- .../resources_scripts/process_datasets.sh | 43 +++-- .../resources_scripts/run_benchmark.sh | 48 +++--- .../run_test.sh | 10 +- .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 28 ---- .../resources_scripts/process_datasets.sh | 44 ++--- .../resources_scripts/run_benchmark.sh | 40 +++-- .../run_test.sh | 9 +- .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 27 --- .../resources_scripts/process_datasets.sh | 42 ++--- .../resources_scripts/run_benchmark.sh | 49 +++--- .../run_test.sh | 9 +- .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 25 --- .../resources_scripts/process_datasets.sh | 44 ++--- .../resources_scripts/run_benchmark.sh | 49 +++--- .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 25 --- .../resources_scripts/process_datasets.sh | 44 ++--- .../resources_scripts/run_benchmark.sh | 49 +++--- .../nf_tower_scripts/process_datasets.sh | 25 --- .../nf_tower_scripts/run_benchmark.sh | 27 --- .../resources_scripts/process_datasets.sh | 44 ++--- .../resources_scripts/run_benchmark.sh | 49 +++--- 39 files changed, 587 insertions(+), 1017 deletions(-) create mode 100755 src/datasets/resource_scripts/cellxgene_census_test.sh delete mode 100755 src/datasets/resource_scripts/cellxgene_census_tower.sh delete mode 100755 src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh create mode 100755 src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh delete mode 100755 src/datasets/resource_scripts/openproblems_v1_nf_tower.sh create mode 100755 src/datasets/resource_scripts/openproblems_v1_test.sh delete mode 100644 src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh delete mode 100644 src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh mode change 100755 => 100644 src/tasks/batch_integration/resources_scripts/process_datasets.sh mode change 100755 => 100644 src/tasks/batch_integration/resources_scripts/run_benchmark.sh rename src/tasks/batch_integration/{nf_tower_scripts => resources_scripts}/run_test.sh (68%) delete mode 100755 src/tasks/denoising/nf_tower_scripts/process_datasets.sh delete mode 100644 src/tasks/denoising/nf_tower_scripts/run_benchmark.sh mode change 100755 => 100644 src/tasks/denoising/resources_scripts/run_benchmark.sh rename src/tasks/denoising/{nf_tower_scripts => resources_scripts}/run_test.sh (72%) delete mode 100755 src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh delete mode 100644 src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh mode change 100755 => 100644 src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh rename src/tasks/dimensionality_reduction/{nf_tower_scripts => resources_scripts}/run_test.sh (70%) delete mode 100755 src/tasks/label_projection/nf_tower_scripts/process_datasets.sh delete mode 100755 src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh delete mode 100755 src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh delete mode 100755 src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh delete mode 100755 src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh delete mode 100755 src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index af0695e972..1f177775f7 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -3,8 +3,8 @@ library(rlang) ## VIASH START par <- list( - input_scores = "output/v2/batch_integration/scores.yaml", - input_execution = "output/v2/batch_integration/trace.txt", + input_scores = "resources/batch_integration/results/scores.yaml", + input_execution = "resources/batch_integration/results/trace.txt", output = "test.json" ) ## VIASH END diff --git a/src/common/process_task_results/run/run_nf_tower_test.sh b/src/common/process_task_results/run/run_nf_tower_test.sh index 835ccbbfe2..9d9a284a76 100644 --- a/src/common/process_task_results/run/run_nf_tower_test.sh +++ b/src/common/process_task_results/run/run_nf_tower_test.sh @@ -1,9 +1,9 @@ #!/bin/bash -DATASETS_DIR="s3://openproblems-nextflow/output/v2/batch_integration" +DATASETS_DIR="s3://openproblems-data/resources/batch_integration/results/" # try running on nf tower -cat > /tmp/params.yaml << HERE +cat > /tmp/params.yaml << 'HERE' id: batch_integration_transform input_scores: "$DATASETS_DIR/scores.yaml" input_dataset_info: "$DATASETS_DIR/dataset_info.yaml" @@ -33,6 +33,6 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/common/workflows/transform_meta/main.nf \ --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/common/process_task_results/run/run_test.sh b/src/common/process_task_results/run/run_test.sh index adf169cc1b..9457deffac 100644 --- a/src/common/process_task_results/run/run_test.sh +++ b/src/common/process_task_results/run/run_test.sh @@ -10,8 +10,8 @@ set -e # export TOWER_WORKSPACE_ID=53907369739130 -DATASETS_DIR="output/v2/batch_integration" -OUTPUT_DIR="/home/kai/Documents/openroblems/website/results/batch_integration_feature/data" +DATASETS_DIR="resources/batch_integration/results" +OUTPUT_DIR="../website/results/batch_integration_feature/data" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index 9a7d7a0f7a..f6371f0a0c 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -1,8 +1,34 @@ #!/bin/bash +# template for adding new datasets +# - id: cellxgene_census/ +# species: +# census_version: "2023-07-25" +# obs_value_filter: "dataset_id == ''" +# obs_batch: +# dataset_name: +# dataset_summary: +# dataset_description: +# dataset_url: +# dataset_reference: +# dataset_organism: + +# not sure which dataset ids to use +# - id: cellxgene_census/human_brain_atlas +# species: homo_sapiens +# census_version: "2023-07-25" +# obs_value_filter: "dataset_id == ''" # <--- ? +# obs_batch: donor_id +# dataset_name: Human Brain Atlas +# dataset_summary: Single-Cell DNA Methylation and 3D Genome Human Brain Atlas +# dataset_description: Delineating the gene regulatory programs underlying complex cell types is fundamental for understanding brain functions in health and disease. Here, we comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in over 500,000 cells from 46 brain regions. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. With these resources, we developed scMCodes that reliably predict brain cell types using their methylation status at select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell type-specific gene regulation in the adult human brain. +# dataset_url: https://cellxgene.cziscience.com/collections/fdebfda9-bb9a-4b4b-97e5-651097ea07b0 +# dataset_reference: tian2023singlecell +# dataset_organism: homo_sapiens + cat > "/tmp/params.yaml" << 'HERE' param_list: - - id: cxg_mouse_pancreas_atlas + - id: cellxgene_census/mouse_pancreas_atlas species: mus_musculus census_version: "2023-07-25" obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" @@ -13,6 +39,83 @@ param_list: dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 dataset_reference: hrovatin2023delineating dataset_organism: mus_musculus + - id: cellxgene_census/hcla + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '066943a2-fdac-4b29-b348-40cede398e4e'" + obs_batch: donor_id + dataset_name: Human Lung Cell Atlas + dataset_summary: An integrated cell atlas of the human lung in health and disease (core) + dataset_description: The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata. + dataset_url: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 + dataset_reference: sikkema2023integrated + dataset_organism: homo_sapiens + - id: cellxgene_census/tabula_sapiens + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '53d208b0-2cfd-4366-9866-c3c6114081bc'" + obs_batch: [donor_id, assay] + dataset_name: Tabula Sapiens + dataset_summary: A multiple-organ, single-cell transcriptomic atlas of humans + dataset_description: Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. + dataset_url: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 + dataset_reference: consortium2022tabula + dataset_organism: homo_sapiens + - id: cellxgene_census/immune_cell_atlas + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '1b9d8702-5af8-4142-85ed-020eb06ec4f6'" + obs_batch: donor_id + dataset_name: Immune Cell Atlas + dataset_summary: Cross-tissue immune cell analysis reveals tissue-specific features in humans + dataset_description: Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing. + dataset_url: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3 + dataset_reference: dominguez2022crosstissue + dataset_organism: homo_sapiens + - id: cellxgene_census/gtex_v9 + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '4ed927e9-c099-49af-b8ce-a2652d069333'" + obs_batch: donor_id + dataset_name: GTEX v9 + dataset_summary: Single-nucleus cross-tissue molecular reference maps to decipher disease gene function + dataset_description: Understanding the function of genes and their regulation in tissue homeostasis and disease requires knowing the cellular context in which genes are expressed in tissues across the body. Single cell genomics allows the generation of detailed cellular atlases in human tissues, but most efforts are focused on single tissue types. Here, we establish a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq), and apply it to 8 diverse, archived, frozen tissue types (three donors per tissue). We apply four snRNA-seq methods to each of 25 samples from 16 donors, generating a cross-tissue atlas of 209,126 nuclei profiles, and benchmark them vs. scRNA-seq of comparable fresh tissues. We use a conditional variational autoencoder (cVAE) to integrate an atlas across tissues, donors, and laboratory methods. We highlight shared and tissue-specific features of tissue-resident immune cells, identifying tissue-restricted and non-restricted resident myeloid populations. These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease. For rare, monogenic muscle diseases, we identify cell types that likely underlie the neuromuscular, metabolic, and immune components of these diseases, and biological processes involved in their pathology. For common complex diseases and traits analyzed by GWAS, we identify the cell types and gene modules that potentially underlie disease mechanisms. The experimental and analytical frameworks we describe will enable the generation of large-scale studies of how cellular and molecular processes vary across individuals and populations. + dataset_url: https://cellxgene.cziscience.com/collections/a3ffde6c-7ad2-498a-903c-d58e732f7470 + dataset_reference: eraslan2022singlenucleus + dataset_organism: homo_sapiens + - id: cellxgene_census/human_retina_cell_atlas + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id == 'd6505c89-c43d-4c28-8c4f-7351a5fd5528'" + obs_batch: donor_id + dataset_name: Human Retina Cell Atlas + dataset_summary: Single cell atlas of the human retina + dataset_description: As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases. + dataset_url: https://cellxgene.cziscience.com/collections/4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e + dataset_reference: li2023integrated + dataset_organism: homo_sapiens + - id: cellxgene_census/dkd + species: homo_sapiens + census_version: "2023-07-25" + obs_value_filter: "dataset_id in ['ad0bf220-dd49-4b71-bb5c-576fee675d2b', 'e067e5ca-e53e-485f-aa8e-efd5435229c8']" + obs_batch: donor_id + dataset_name: Diabetic Kidney Disease + dataset_summary: Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression + dataset_description: Multimodal single cell sequencing is a powerful tool for interrogating cell-specific changes in transcription and chromatin accessibility. We performed single nucleus RNA (snRNA-seq) and assay for transposase accessible chromatin sequencing (snATAC-seq) on human kidney cortex from donors with and without diabetic kidney disease (DKD) to identify altered signaling pathways and transcription factors associated with DKD. Both snRNA-seq and snATAC-seq had an increased proportion of VCAM1+ injured proximal tubule cells (PT_VCAM1) in DKD samples. PT_VCAM1 has a pro-inflammatory expression signature and transcription factor motif enrichment implicated NFkB signaling. We used stratified linkage disequilibrium score regression to partition heritability of kidney-function-related traits using publicly-available GWAS summary statistics. Cell-specific PT_VCAM1 peaks were enriched for heritability of chronic kidney disease (CKD), suggesting that genetic background may regulate chromatin accessibility and DKD progression. snATAC-seq found cell-specific differentially accessible regions (DAR) throughout the nephron that change accessibility in DKD and these regions were enriched for glucocorticoid receptor (GR) motifs. Changes in chromatin accessibility were associated with decreased expression of insulin receptor, increased gluconeogenesis, and decreased expression of the GR cytosolic chaperone, FKBP5, in the diabetic proximal tubule. Cleavage under targets and release using nuclease (CUT&RUN) profiling of GR binding in bulk kidney cortex and an in vitro model of the proximal tubule (RPTEC) showed that DAR co-localize with GR binding sites. CRISPRi silencing of GR response elements (GRE) in the FKBP5 gene body reduced FKBP5 expression in RPTEC, suggesting that reduced FKBP5 chromatin accessibility in DKD may alter cellular response to GR. We developed an open-source tool for single cell allele specific analysis (SALSA) to model the effect of genetic background on gene expression. Heterozygous germline single nucleotide variants (SNV) in proximal tubule ATAC peaks were associated with allele-specific chromatin accessibility and differential expression of target genes within cis-coaccessibility networks. Partitioned heritability of proximal tubule ATAC peaks with a predicted allele-specific effect was enriched for eGFR, suggesting that genetic background may modify DKD progression in a cell-specific manner. + dataset_url: https://cellxgene.cziscience.com/collections/b3e2c6e3-9b05-4da9-8f42-da38a664b45b + dataset_reference: wilson2022multimodal + dataset_organism: homo_sapiens + - id: cellxgene_census/hypomap + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == 'dbb4e1ed-d820-4e83-981f-88ef7eb55a35'" + obs_batch: donor_id + dataset_name: HypoMap + dataset_summary: A unified single cell gene expression atlas of the murine hypothalamus + dataset_description: The hypothalamus plays a key role in coordinating fundamental body functions. Despite recent progress in single-cell technologies, a unified catalogue and molecular characterization of the heterogeneous cell types and, specifically, neuronal subtypes in this brain region are still lacking. Here we present an integrated reference atlas “HypoMap” of the murine hypothalamus consisting of 384,925 cells, with the ability to incorporate new additional experiments. We validate HypoMap by comparing data collected from SmartSeq2 and bulk RNA sequencing of selected neuronal cell types with different degrees of cellular heterogeneity. + dataset_url: https://cellxgene.cziscience.com/collections/d86517f0-fa7e-4266-b82e-a521350d6d36 + dataset_reference: steuernagel2022hypomap + dataset_organism: mus_musculus normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset: '$id/dataset.h5ad' @@ -23,10 +126,20 @@ output_normalized: force_null output_pca: force_null output_hvg: force_null output_knn: force_null -publish_dir: output/temp +publish_dir: s3://openproblems-data/resources/datasets +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} HERE -nextflow run . \ - -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ - -profile docker \ - -params-file "/tmp/params.yaml" \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "/tmp/params.yaml" \ + --config /tmp/nextflow.config diff --git a/src/datasets/resource_scripts/cellxgene_census_test.sh b/src/datasets/resource_scripts/cellxgene_census_test.sh new file mode 100755 index 0000000000..b003c08d3c --- /dev/null +++ b/src/datasets/resource_scripts/cellxgene_census_test.sh @@ -0,0 +1,32 @@ +#!/bin/bash + +cat > "/tmp/params.yaml" << 'HERE' +param_list: + - id: cellxgene_census/mouse_pancreas_atlas + species: mus_musculus + census_version: "2023-07-25" + obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" + obs_batch: donor_id + dataset_name: Mouse Pancreatic Islet Atlas + dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes + dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. + dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 + dataset_reference: hrovatin2023delineating + dataset_organism: mus_musculus + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null +publish_dir: resources/datasets +HERE + +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ + -profile docker \ + -params-file "/tmp/params.yaml" \ No newline at end of file diff --git a/src/datasets/resource_scripts/cellxgene_census_tower.sh b/src/datasets/resource_scripts/cellxgene_census_tower.sh deleted file mode 100755 index 18df311725..0000000000 --- a/src/datasets/resource_scripts/cellxgene_census_tower.sh +++ /dev/null @@ -1,145 +0,0 @@ -#!/bin/bash - -# template for adding new datasets -# - id: cxg_ -# species: -# census_version: "2023-07-25" -# obs_value_filter: "dataset_id == ''" -# obs_batch: -# dataset_name: -# dataset_summary: -# dataset_description: -# dataset_url: -# dataset_reference: -# dataset_organism: - -# not sure which dataset ids to use -# - id: cxg_human_brain_atlas -# species: homo_sapiens -# census_version: "2023-07-25" -# obs_value_filter: "dataset_id == ''" # <--- ? -# obs_batch: donor_id -# dataset_name: Human Brain Atlas -# dataset_summary: Single-Cell DNA Methylation and 3D Genome Human Brain Atlas -# dataset_description: Delineating the gene regulatory programs underlying complex cell types is fundamental for understanding brain functions in health and disease. Here, we comprehensively examine human brain cell epigenomes by probing DNA methylation and chromatin conformation at single-cell resolution in over 500,000 cells from 46 brain regions. We identified 188 cell types and characterized their molecular signatures. Integrative analyses revealed concordant changes in DNA methylation, chromatin accessibility, chromatin organization, and gene expression across cell types, cortical areas, and basal ganglia structures. With these resources, we developed scMCodes that reliably predict brain cell types using their methylation status at select genomic sites. This multimodal epigenomic brain cell atlas provides new insights into the complexity of cell type-specific gene regulation in the adult human brain. -# dataset_url: https://cellxgene.cziscience.com/collections/fdebfda9-bb9a-4b4b-97e5-651097ea07b0 -# dataset_reference: tian2023singlecell -# dataset_organism: homo_sapiens - -cat > "/tmp/params.yaml" << 'HERE' -param_list: - - id: cxg_mouse_pancreas_atlas - species: mus_musculus - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" - obs_batch: donor_id - dataset_name: Mouse Pancreatic Islet Atlas - dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes - dataset_description: To better understand pancreatic β-cell heterogeneity we generated a mouse pancreatic islet atlas capturing a wide range of biological conditions. The atlas contains scRNA-seq datasets of over 300,000 mouse pancreatic islet cells, of which more than 100,000 are β-cells, from nine datasets with 56 samples, including two previously unpublished datasets. The samples vary in sex, age (ranging from embryonic to aged), chemical stress, and disease status (including T1D NOD model development and two T2D models, mSTZ and db/db) together with different diabetes treatments. Additional information about data fields is available in anndata uns field 'field_descriptions' and on https://github.com/theislab/mm_pancreas_atlas_rep/blob/main/resources/cellxgene.md. - dataset_url: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070 - dataset_reference: hrovatin2023delineating - dataset_organism: mus_musculus - - id: cxg_hcla - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '066943a2-fdac-4b29-b348-40cede398e4e'" - obs_batch: donor_id - dataset_name: Human Lung Cell Atlas - dataset_summary: An integrated cell atlas of the human lung in health and disease (core) - dataset_description: The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata. - dataset_url: https://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293 - dataset_reference: sikkema2023integrated - dataset_organism: homo_sapiens - - id: cxg_tabula_sapiens - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '53d208b0-2cfd-4366-9866-c3c6114081bc'" - obs_batch: [donor_id, assay] - dataset_name: Tabula Sapiens - dataset_summary: A multiple-organ, single-cell transcriptomic atlas of humans - dataset_description: Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects and allows detailed analysis and comparison of cell types that are shared between tissues. Our work creates a detailed portrait of cell types as well as their distribution and variation in gene expression across tissues and within the endothelial, epithelial, stromal and immune compartments. - dataset_url: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5 - dataset_reference: consortium2022tabula - dataset_organism: homo_sapiens - - id: cxg_immune_cell_atlas - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '1b9d8702-5af8-4142-85ed-020eb06ec4f6'" - obs_batch: donor_id - dataset_name: Immune Cell Atlas - dataset_summary: Cross-tissue immune cell analysis reveals tissue-specific features in humans - dataset_description: Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing. - dataset_url: https://cellxgene.cziscience.com/collections/62ef75e4-cbea-454e-a0ce-998ec40223d3 - dataset_reference: dominguez2022crosstissue - dataset_organism: homo_sapiens - - id: cxg_gtex_v9 - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == '4ed927e9-c099-49af-b8ce-a2652d069333'" - obs_batch: donor_id - dataset_name: GTEX v9 - dataset_summary: Single-nucleus cross-tissue molecular reference maps to decipher disease gene function - dataset_description: Understanding the function of genes and their regulation in tissue homeostasis and disease requires knowing the cellular context in which genes are expressed in tissues across the body. Single cell genomics allows the generation of detailed cellular atlases in human tissues, but most efforts are focused on single tissue types. Here, we establish a framework for profiling multiple tissues across the human body at single-cell resolution using single nucleus RNA-Seq (snRNA-seq), and apply it to 8 diverse, archived, frozen tissue types (three donors per tissue). We apply four snRNA-seq methods to each of 25 samples from 16 donors, generating a cross-tissue atlas of 209,126 nuclei profiles, and benchmark them vs. scRNA-seq of comparable fresh tissues. We use a conditional variational autoencoder (cVAE) to integrate an atlas across tissues, donors, and laboratory methods. We highlight shared and tissue-specific features of tissue-resident immune cells, identifying tissue-restricted and non-restricted resident myeloid populations. These include a cross-tissue conserved dichotomy between LYVE1- and HLA class II-expressing macrophages, and the broad presence of LAM-like macrophages across healthy tissues that is also observed in disease. For rare, monogenic muscle diseases, we identify cell types that likely underlie the neuromuscular, metabolic, and immune components of these diseases, and biological processes involved in their pathology. For common complex diseases and traits analyzed by GWAS, we identify the cell types and gene modules that potentially underlie disease mechanisms. The experimental and analytical frameworks we describe will enable the generation of large-scale studies of how cellular and molecular processes vary across individuals and populations. - dataset_url: https://cellxgene.cziscience.com/collections/a3ffde6c-7ad2-498a-903c-d58e732f7470 - dataset_reference: eraslan2022singlenucleus - dataset_organism: homo_sapiens - - id: cxg_human_retina_cell_atlas - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id == 'd6505c89-c43d-4c28-8c4f-7351a5fd5528'" - obs_batch: donor_id - dataset_name: Human Retina Cell Atlas - dataset_summary: Single cell atlas of the human retina - dataset_description: As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases. - dataset_url: https://cellxgene.cziscience.com/collections/4c6eaf5c-6d57-4c76-b1e9-60df8c655f1e - dataset_reference: li2023integrated - dataset_organism: homo_sapiens - - id: cxg_dkd - species: homo_sapiens - census_version: "2023-07-25" - obs_value_filter: "dataset_id in ['ad0bf220-dd49-4b71-bb5c-576fee675d2b', 'e067e5ca-e53e-485f-aa8e-efd5435229c8']" - obs_batch: donor_id - dataset_name: Diabetic Kidney Disease - dataset_summary: Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression - dataset_description: Multimodal single cell sequencing is a powerful tool for interrogating cell-specific changes in transcription and chromatin accessibility. We performed single nucleus RNA (snRNA-seq) and assay for transposase accessible chromatin sequencing (snATAC-seq) on human kidney cortex from donors with and without diabetic kidney disease (DKD) to identify altered signaling pathways and transcription factors associated with DKD. Both snRNA-seq and snATAC-seq had an increased proportion of VCAM1+ injured proximal tubule cells (PT_VCAM1) in DKD samples. PT_VCAM1 has a pro-inflammatory expression signature and transcription factor motif enrichment implicated NFkB signaling. We used stratified linkage disequilibrium score regression to partition heritability of kidney-function-related traits using publicly-available GWAS summary statistics. Cell-specific PT_VCAM1 peaks were enriched for heritability of chronic kidney disease (CKD), suggesting that genetic background may regulate chromatin accessibility and DKD progression. snATAC-seq found cell-specific differentially accessible regions (DAR) throughout the nephron that change accessibility in DKD and these regions were enriched for glucocorticoid receptor (GR) motifs. Changes in chromatin accessibility were associated with decreased expression of insulin receptor, increased gluconeogenesis, and decreased expression of the GR cytosolic chaperone, FKBP5, in the diabetic proximal tubule. Cleavage under targets and release using nuclease (CUT&RUN) profiling of GR binding in bulk kidney cortex and an in vitro model of the proximal tubule (RPTEC) showed that DAR co-localize with GR binding sites. CRISPRi silencing of GR response elements (GRE) in the FKBP5 gene body reduced FKBP5 expression in RPTEC, suggesting that reduced FKBP5 chromatin accessibility in DKD may alter cellular response to GR. We developed an open-source tool for single cell allele specific analysis (SALSA) to model the effect of genetic background on gene expression. Heterozygous germline single nucleotide variants (SNV) in proximal tubule ATAC peaks were associated with allele-specific chromatin accessibility and differential expression of target genes within cis-coaccessibility networks. Partitioned heritability of proximal tubule ATAC peaks with a predicted allele-specific effect was enriched for eGFR, suggesting that genetic background may modify DKD progression in a cell-specific manner. - dataset_url: https://cellxgene.cziscience.com/collections/b3e2c6e3-9b05-4da9-8f42-da38a664b45b - dataset_reference: wilson2022multimodal - dataset_organism: homo_sapiens - - id: cxg_hypomap - species: mus_musculus - census_version: "2023-07-25" - obs_value_filter: "dataset_id == 'dbb4e1ed-d820-4e83-981f-88ef7eb55a35'" - obs_batch: donor_id - dataset_name: HypoMap - dataset_summary: A unified single cell gene expression atlas of the murine hypothalamus - dataset_description: The hypothalamus plays a key role in coordinating fundamental body functions. Despite recent progress in single-cell technologies, a unified catalogue and molecular characterization of the heterogeneous cell types and, specifically, neuronal subtypes in this brain region are still lacking. Here we present an integrated reference atlas “HypoMap” of the murine hypothalamus consisting of 384,925 cells, with the ability to incorporate new additional experiments. We validate HypoMap by comparing data collected from SmartSeq2 and bulk RNA sequencing of selected neuronal cell types with different degrees of cellular heterogeneity. - dataset_url: https://cellxgene.cziscience.com/collections/d86517f0-fa7e-4266-b82e-a521350d6d36 - dataset_reference: steuernagel2022hypomap - dataset_organism: mus_musculus - -normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_dataset: '$id/dataset.h5ad' -output_meta: '$id/dataset_metadata.yaml' -output_state: '$id/state.yaml' -output_raw: force_null -output_normalized: force_null -output_pca: force_null -output_hvg: force_null -output_knn: force_null -publish_dir: s3://openproblems-nextflow/resources/datasets/cellxgene_census -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file "/tmp/params.yaml" \ - --config /tmp/nextflow.config diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 7275f2ab1c..84846dd9c7 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -6,21 +6,14 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -export TOWER_WORKSPACE_ID=53907369739130 - -OUTPUT_DIR="resources/datasets/openproblems_v1" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - params_file="/tmp/datasets_openproblems_v1_params.yaml" cat > "$params_file" << 'HERE' param_list: - - id: allen_brain_atlas + - id: openproblems_v1/allen_brain_atlas obs_cell_type: label layer_counts: counts + input_id: allen_brain_atlas dataset_name: Mouse Brain Atlas dataset_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 dataset_reference: tasic2016adult @@ -28,11 +21,12 @@ param_list: dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). dataset_organism: mus_musculus - - id: cengen + - id: openproblems_v1/cengen obs_cell_type: cell_type obs_batch: experiment_code obs_tissue: tissue layer_counts: counts + input_id: cengen dataset_name: CeNGEN dataset_url: https://www.cengen.org dataset_reference: hammarlund2018cengen @@ -40,11 +34,12 @@ param_list: dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. dataset_organism: caenorhabditis_elegans - - id: immune_cells + - id: openproblems_v1/immune_cells obs_cell_type: final_annotation obs_batch: batch obs_tissue: tissue layer_counts: counts + input_id: immune_cells dataset_name: Human immune dataset_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html dataset_reference: luecken2022benchmarking @@ -52,9 +47,10 @@ param_list: dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). dataset_organism: homo_sapiens - - id: mouse_blood_olsson_labelled + - id: openproblems_v1/mouse_blood_olsson_labelled obs_cell_type: celltype layer_counts: counts + input_id: mouse_blood_olsson_labelled dataset_name: Mouse myeloid dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 dataset_reference: olsson2016single @@ -62,9 +58,10 @@ param_list: dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. dataset_organism: mus_musculus - - id: mouse_hspc_nestorowa2016 + - id: openproblems_v1/mouse_hspc_nestorowa2016 obs_cell_type: cell_type_label layer_counts: counts + input_id: mouse_hspc_nestorowa2016 dataset_name: Mouse HSPC dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 dataset_reference: nestorowa2016single @@ -72,10 +69,11 @@ param_list: dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. dataset_organism: mus_musculus - - id: pancreas + - id: openproblems_v1/pancreas obs_cell_type: celltype obs_batch: tech layer_counts: counts + input_id: pancreas dataset_name: Human pancreas dataset_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html dataset_reference: luecken2022benchmarking @@ -84,10 +82,11 @@ param_list: dataset_organism: homo_sapiens # disabled as this is not working in openproblemsv1 - # - id: tabula_muris_senis_droplet_lung + # - id: openproblems_v1/tabula_muris_senis_droplet_lung # obs_cell_type: cell_type # obs_batch: donor_id # layer_counts: counts + # input_id: tabula_muris_senis_droplet_lung # dataset_name: Tabula Muris Senis Lung # dataset_url: https://tabula-muris-senis.ds.czbiohub.org # dataset_reference: tabula2020single @@ -95,8 +94,9 @@ param_list: # dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. # dataset_organism: mus_musculus - - id: tenx_1k_pbmc + - id: openproblems_v1/tenx_1k_pbmc layer_counts: counts + input_id: tenx_1k_pbmc dataset_name: 1k PBMCs dataset_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 dataset_reference: 10x2018pbmc @@ -104,8 +104,9 @@ param_list: dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. dataset_organism: homo_sapiens - - id: tenx_5k_pbmc + - id: openproblems_v1/tenx_5k_pbmc layer_counts: counts + input_id: tenx_5k_pbmc dataset_name: 5k PBMCs dataset_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 dataset_reference: 10x2019pbmc @@ -113,9 +114,10 @@ param_list: dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. dataset_organism: homo_sapiens - - id: tnbc_wu2021 + - id: openproblems_v1/tnbc_wu2021 obs_cell_type: celltype_minor layer_counts: counts + input_id: tnbc_wu2021 dataset_name: Triple-Negative Breast Cancer dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 dataset_reference: wu2021single @@ -123,10 +125,11 @@ param_list: dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). dataset_organism: homo_sapiens - - id: zebrafish + - id: openproblems_v1/zebrafish obs_cell_type: cell_type obs_batch: lab layer_counts: counts + input_id: zebrafish dataset_name: Zebrafish embryonic cells dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 dataset_reference: wagner2018single @@ -143,14 +146,20 @@ output_normalized: force_null output_pca: force_null output_hvg: force_null output_knn: force_null +publish_dir: s3://openproblems-data/resources/datasets +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} HERE -export NXF_VER=23.04.2 -nextflow run . \ - -main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ - -profile docker \ - -resume \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" - - # -with-tower +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision integration_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 592de5521e..c4b3896d70 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -6,19 +6,12 @@ REPO_ROOT=$(git rev-parse --show-toplevel) # ensure that the command below is run from the root of the repository cd "$REPO_ROOT" -export TOWER_WORKSPACE_ID=53907369739130 - -OUTPUT_DIR="resources/datasets/openproblems_v1_multimodal" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - params_file="/tmp/datasets_openproblems_v1_multimodal_params.yaml" cat > "$params_file" << 'HERE' param_list: - - id: citeseq_cbmc + - id: openproblems_v1_multimodal/citeseq_cbmc + input_id: citeseq_cbmc dataset_name: "CITE-Seq CBMC" dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." @@ -27,7 +20,8 @@ param_list: dataset_organism: homo_sapiens layer_counts: counts - - id: scicar_cell_lines + - id: openproblems_v1_multimodal/scicar_cell_lines + input_id: scicar_cell_lines dataset_name: "sci-CAR Cell Lines" dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." @@ -37,7 +31,8 @@ param_list: obs_cell_type: cell_name layer_counts: counts - - id: scicar_mouse_kidney + - id: openproblems_v1_multimodal/scicar_mouse_kidney + input_id: scicar_mouse_kidney dataset_name: "sci-CAR Mouse Kidney" dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." @@ -54,13 +49,13 @@ output_dataset_mod2: '$id/dataset_mod2.h5ad' output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' +publish_dir: s3://openproblems-data/resources/datasets HERE -export NXF_VER=22.04.5 -nextflow \ - run . \ - -main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ - -profile docker \ - -resume \ - -params-file "$params_file" \ - --publish_dir "$OUTPUT_DIR" +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh deleted file mode 100755 index fa02f996e4..0000000000 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal_nf_tower.sh +++ /dev/null @@ -1,58 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -params_file="/tmp/datasets_openproblems_v1_multimodal_params.yaml" - -cat > "$params_file" << 'HERE' -param_list: - - id: citeseq_cbmc - dataset_name: "CITE-Seq CBMC" - dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" - dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." - dataset_reference: stoeckius2017simultaneous - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 - dataset_organism: homo_sapiens - layer_counts: counts - - - id: scicar_cell_lines - dataset_name: "sci-CAR Cell Lines" - dataset_summary: "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)" - dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling for HEK293T cells, NIH/3T3 cells, A549 cells across three treatment conditions (DEX 0 hour, 1 hour and 3 hour treatment)." - dataset_reference: cao2018joint - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 - dataset_organism: "[homo_sapiens, mus_musculus]" - obs_cell_type: cell_name - layer_counts: counts - - - id: scicar_mouse_kidney - dataset_name: "sci-CAR Mouse Kidney" - dataset_summary: "sci-CAR profiles of 11k mouse kidney cells" - dataset_description: "Single cell RNA-seq and ATAC-seq co-profiling of 11k mouse kidney cells." - dataset_reference: cao2018joint - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089 - dataset_organism: mus_musculus - obs_cell_type: cell_name - obs_batch: replicate - layer_counts: counts - -normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_dataset_mod1: '$id/dataset_mod1.h5ad' -output_dataset_mod2: '$id/dataset_mod2.h5ad' -output_meta_mod1: '$id/dataset_metadata_mod1.yaml' -output_meta_mod2: '$id/dataset_metadata_mod2.yaml' -output_state: '$id/state.yaml' -publish_dir: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file "$params_file" \ \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh new file mode 100755 index 0000000000..d3a36cb5e1 --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh @@ -0,0 +1,45 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="resources/datasets" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="/tmp/datasets_openproblems_v1_multimodal_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_v1_multimodal/citeseq_cbmc + dataset_name: "CITE-Seq CBMC" + dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" + dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." + dataset_reference: stoeckius2017simultaneous + dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 + dataset_organism: homo_sapiens + layer_counts: counts + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset_mod1: '$id/dataset_mod1.h5ad' +output_dataset_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' +output_state: '$id/state.yaml' +HERE + +export NXF_VER=22.04.5 +nextflow \ + run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" diff --git a/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh b/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh deleted file mode 100755 index 381cd88768..0000000000 --- a/src/datasets/resource_scripts/openproblems_v1_nf_tower.sh +++ /dev/null @@ -1,154 +0,0 @@ -#!/bin/bash - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -params_file="/tmp/datasets_openproblems_v1_params.yaml" - -cat > "$params_file" << 'HERE' -param_list: - - id: allen_brain_atlas - obs_cell_type: label - layer_counts: counts - dataset_name: Mouse Brain Atlas - dataset_url: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71585 - dataset_reference: tasic2016adult - dataset_summary: Adult mouse primary visual cortex - dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). - dataset_organism: mus_musculus - - - id: cengen - obs_cell_type: cell_type - obs_batch: experiment_code - obs_tissue: tissue - layer_counts: counts - dataset_name: CeNGEN - dataset_url: https://www.cengen.org - dataset_reference: hammarlund2018cengen - dataset_summary: Complete Gene Expression Map of an Entire Nervous System - dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. - dataset_organism: caenorhabditis_elegans - - - id: immune_cells - obs_cell_type: final_annotation - obs_batch: batch - obs_tissue: tissue - layer_counts: counts - dataset_name: Human immune - dataset_url: https://theislab.github.io/scib-reproducibility/dataset_immune_cell_hum.html - dataset_reference: luecken2022benchmarking - dataset_summary: Human immune cells dataset from the scIB benchmarks - dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). - dataset_organism: homo_sapiens - - - id: mouse_blood_olsson_labelled - obs_cell_type: celltype - layer_counts: counts - dataset_name: Mouse myeloid - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70245 - dataset_reference: olsson2016single - dataset_summary: Myeloid lineage differentiation from mouse blood - dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. - dataset_organism: mus_musculus - - - id: mouse_hspc_nestorowa2016 - obs_cell_type: cell_type_label - layer_counts: counts - dataset_name: Mouse HSPC - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682 - dataset_reference: nestorowa2016single - dataset_summary: Haematopoeitic stem and progenitor cells from mouse bone marrow - dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. - dataset_organism: mus_musculus - - - id: pancreas - obs_cell_type: celltype - obs_batch: tech - layer_counts: counts - dataset_name: Human pancreas - dataset_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html - dataset_reference: luecken2022benchmarking - dataset_summary: Human pancreas cells dataset from the scIB benchmarks - dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). - dataset_organism: homo_sapiens - - # disabled as this is not working in openproblemsv1 - # - id: tabula_muris_senis_droplet_lung - # obs_cell_type: cell_type - # obs_batch: donor_id - # layer_counts: counts - # dataset_name: Tabula Muris Senis Lung - # dataset_url: https://tabula-muris-senis.ds.czbiohub.org - # dataset_reference: tabula2020single - # dataset_summary: Aging mouse lung cells from Tabula Muris Senis - # dataset_description: All lung cells from 10x profiles in Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. - # dataset_organism: mus_musculus - - - id: tenx_1k_pbmc - layer_counts: counts - dataset_name: 1k PBMCs - dataset_url: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0 - dataset_reference: 10x2018pbmc - dataset_summary: 1k peripheral blood mononuclear cells from a healthy donor - dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. - dataset_organism: homo_sapiens - - - id: tenx_5k_pbmc - layer_counts: counts - dataset_name: 5k PBMCs - dataset_url: https://www.10xgenomics.com/resources/datasets/5-k-peripheral-blood-mononuclear-cells-pbm-cs-from-a-healthy-donor-with-cell-surface-proteins-v-3-chemistry-3-1-standard-3-1-0 - dataset_reference: 10x2019pbmc - dataset_summary: 5k peripheral blood mononuclear cells from a healthy donor - dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. - dataset_organism: homo_sapiens - - - id: tnbc_wu2021 - obs_cell_type: celltype_minor - layer_counts: counts - dataset_name: Triple-Negative Breast Cancer - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118389 - dataset_reference: wu2021single - dataset_summary: 1535 cells from six fresh triple-negative breast cancer tumors. - dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). - dataset_organism: homo_sapiens - - - id: zebrafish - obs_cell_type: cell_type - obs_batch: lab - layer_counts: counts - dataset_name: Zebrafish embryonic cells - dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294 - dataset_reference: wagner2018single - dataset_summary: Single-cell mRNA sequencing of zebrafish embryonic cells. - dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. - dataset_organism: danio_rerio - -normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_dataset: '$id/dataset.h5ad' -output_meta: '$id/dataset_metadata.yaml' -output_state: '$id/state.yaml' -output_raw: force_null -output_normalized: force_null -output_pca: force_null -output_hvg: force_null -output_knn: force_null -publish_dir: s3://openproblems-nextflow/resources/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision integration_build \ - --pull-latest \ - --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file "$params_file" \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_test.sh b/src/datasets/resource_scripts/openproblems_v1_test.sh new file mode 100755 index 0000000000..a79545f052 --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_v1_test.sh @@ -0,0 +1,51 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="resources/datasets" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +params_file="/tmp/datasets_openproblems_v1_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_v1/pancreas + obs_cell_type: celltype + obs_batch: tech + layer_counts: counts + dataset_name: Human pancreas + dataset_url: https://theislab.github.io/scib-reproducibility/dataset_pancreas.html + dataset_reference: luecken2022benchmarking + dataset_summary: Human pancreas cells dataset from the scIB benchmarks + dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). + dataset_organism: homo_sapiens + +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_dataset: '$id/dataset.h5ad' +output_meta: '$id/dataset_metadata.yaml' +output_state: '$id/state.yaml' +output_raw: force_null +output_normalized: force_null +output_pca: force_null +output_hvg: force_null +output_knn: force_null +HERE + +export NXF_VER=23.04.2 +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "$OUTPUT_DIR" + + # -with-tower diff --git a/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh b/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh deleted file mode 100644 index 79f820c5a3..0000000000 --- a/src/tasks/batch_integration/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: batch_integration_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml -rename_keys: 'input:output_dataset' -settings: '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/batch_integration/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh b/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh deleted file mode 100644 index fe6987e634..0000000000 --- a/src/tasks/batch_integration/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - - -# try running on nf tower -cat > /tmp/params.yaml << HERE -id: batch_integration -input_states: s3://openproblems-nextflow/resources/batch_integration/datasets/**/state.yaml -rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/batch_integration -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh old mode 100755 new mode 100644 index 1ffe878348..a1c89a3b59 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -1,26 +1,25 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/batch_integration/datasets +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1" -OUTPUT_DIR="resources/batch_integration/datasets/openproblems_v1" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -resume \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input:output_dataset' \ - --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh old mode 100755 new mode 100644 index 979a16b87e..c908fe6460 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -1,31 +1,27 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +# try running on nf tower +cat > /tmp/params.yaml << 'HERE' +input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/batch_integration/results +HERE -set -e +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/batch_integration/datasets/openproblems_v1" -OUTPUT_DIR="resources/batch_integration/benchmarks/openproblems_v1" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -export NXF_VER=22.04.5 -nextflow run . \ - -main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ - -profile docker \ - -resume \ - -entry auto \ - --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/batch_integration/nf_tower_scripts/run_test.sh b/src/tasks/batch_integration/resources_scripts/run_test.sh similarity index 68% rename from src/tasks/batch_integration/nf_tower_scripts/run_test.sh rename to src/tasks/batch_integration/resources_scripts/run_test.sh index 5c425be93a..4e7ec2779e 100644 --- a/src/tasks/batch_integration/nf_tower_scripts/run_test.sh +++ b/src/tasks/batch_integration/resources_scripts/run_test.sh @@ -3,12 +3,12 @@ DATASET_DIR=resources_test/batch_integration/pancreas # try running on nf tower -cat > /tmp/params.yaml << HERE -id: batch_integration_test -input_states: s3://openproblems-nextflow/resources_test/batch_integration/**/state.yaml +cat > /tmp/params.yaml << 'HERE' +input_states: s3://openproblems-data/resources_test/batch_integration/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output_test/v2/batch_integration/ +output_state: "state.yaml" +publish_dir: s3://openproblems-nextflow/temp/batch_integration/ HERE cat > /tmp/nextflow.config << HERE @@ -22,6 +22,6 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script src/tasks/batch_integration/workflows/run/main.nf \ --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/nf_tower_scripts/process_datasets.sh b/src/tasks/denoising/nf_tower_scripts/process_datasets.sh deleted file mode 100755 index d8ef8ed16f..0000000000 --- a/src/tasks/denoising/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: denoising_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml -rename_keys: 'input:output_dataset' -settings: '{"output_train": "train.h5ad", "output_test": "test.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/denoising/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh b/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh deleted file mode 100644 index afdd2157b6..0000000000 --- a/src/tasks/denoising/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -DATASET_DIR=resources_test/denoising/pancreas - -# try running on nf tower -cat > /tmp/params.yaml << HERE -id: denoising -input_states: s3://openproblems-nextflow/resources/denoising/datasets/**/*state.yaml -rename_keys: 'input_train:output_train,input_test:output_test' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/denoising -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 213f6b0d4c..8cd173c137 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -1,26 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: denoising_process_datasets +input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/denoising/datasets/openproblems_v1 +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1" -OUTPUT_DIR="resources/denoising/datasets/openproblems_v1" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -resume \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input:output_dataset' \ - --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh old mode 100755 new mode 100644 index 635b9332f1..e03278abc3 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -1,21 +1,29 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +DATASET_DIR=resources_test/denoising/pancreas -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +# try running on nf tower +cat > /tmp/params.yaml << 'HERE' +id: denoising +input_states: s3://openproblems-data/resources/denoising/datasets/**/*state.yaml +rename_keys: 'input_train:output_train,input_test:output_test' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/denoising/results +HERE -set -e +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "resources/batch_integration/datasets/**/state.yaml" \ - --rename_keys 'input:output_dataset' \ - --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' \ - --publish_dir "resources/batch_integration/benchmarks/openproblems_v1" \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/denoising/nf_tower_scripts/run_test.sh b/src/tasks/denoising/resources_scripts/run_test.sh similarity index 72% rename from src/tasks/denoising/nf_tower_scripts/run_test.sh rename to src/tasks/denoising/resources_scripts/run_test.sh index 2fa06943ed..0b1a907db8 100644 --- a/src/tasks/denoising/nf_tower_scripts/run_test.sh +++ b/src/tasks/denoising/resources_scripts/run_test.sh @@ -3,12 +3,13 @@ DATASET_DIR=resources_test/denoising/pancreas # try running on nf tower -cat > /tmp/params.yaml << HERE +cat > /tmp/params.yaml << 'HERE' id: denoising_test -input_states: s3://openproblems-nextflow/resources_test/denoising/pancreas/ +input_states: s3://openproblems-data/resources_test/denoising/pancreas/ rename_keys: 'input_train:output_train,input_test:output_test' settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output_test/v2/denoising/ +output_state: "state.yaml" +publish_dir: s3://openproblems-nextflow/temp/denoising/ HERE cat > /tmp/nextflow.config << HERE @@ -22,7 +23,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh deleted file mode 100755 index 386df85ebf..0000000000 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: dimensionality_reduction_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml -rename_keys: 'input:output_dataset' -settings: '{"output_dataset": "dataset.h5ad", "output_solution": "solution.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh deleted file mode 100644 index 31173c0add..0000000000 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - - -# try running on nf tower -cat > /tmp/params.yaml << HERE -id: dimensionality_reduction -input_states: s3://openproblems-nextflow/resources/dimensionality_reduction/datasets/**/state.yaml -rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/dimensionality_reduction -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index e625796d42..38082e9907 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -1,24 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: dimensionality_reduction_process_datasets +input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/dimensionality_reduction/datasets/openproblems_v1 +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1" -OUTPUT_DIR="resources/dimensionality_reduction/datasets/openproblems_v1" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input:output_dataset' \ - --settings '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh old mode 100755 new mode 100644 index bda19a77e0..cab16d6538 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -1,31 +1,28 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +# try running on nf tower +cat > /tmp/params.yaml << 'HERE' +id: dimensionality_reduction +input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets/**/state.yaml +rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/dimensionality_reduction/results +HERE -set -e +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -# export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/dimensionality_reduction" -OUTPUT_DIR="output/test" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -export NXF_VER=22.04.5 -nextflow run . \ - -main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ - -profile docker \ - -resume \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR"\ - --output_state '$id/state.yaml' \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_test.sh similarity index 70% rename from src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh rename to src/tasks/dimensionality_reduction/resources_scripts/run_test.sh index a9cf390032..dd20094147 100644 --- a/src/tasks/dimensionality_reduction/nf_tower_scripts/run_test.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_test.sh @@ -2,12 +2,13 @@ # try running on nf tower -cat > /tmp/params.yaml << HERE +cat > /tmp/params.yaml << 'HERE' id: dimensionality_reduction -input_states: s3://openproblems-nextflow/resources_test/dimensionality_reduction/pancreas +input_states: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output_test/v2/dimensionality_reduction +output_state: "state.yaml" +s3://openproblems-nextflow/temp/dimensionality-reduction/ HERE cat > /tmp/nextflow.config << HERE @@ -21,7 +22,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh b/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh deleted file mode 100755 index b61de64879..0000000000 --- a/src/tasks/label_projection/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: label_projection_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1/**/state.yaml -rename_keys: 'input:output_dataset' -settings: '{"output_train": "train.h5ad", "output_test": "test.h5ad", "output_solution": "solution.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/label_projection/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh b/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh deleted file mode 100755 index a5a1ceca4f..0000000000 --- a/src/tasks/label_projection/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: label_projection -input_states: s3://openproblems-nextflow/resources/label_projection/datasets/**/state.yaml -rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/label_projection -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index 4cca9cb8de..3d1a8ebc22 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -1,26 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: label_projection_process_datasets +input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +rename_keys: 'input:output_dataset' +settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/label_projection/datasets/openproblems_v1 +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1" -OUTPUT_DIR="resources/label_projection/datasets/openproblems_v1" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -resume \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input:output_dataset' \ - --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 19b3e61598..ac53d89742 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -1,31 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: label_projection +input_states: s3://openproblems-data/resources/label_projection/datasets/**/state.yaml +rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/label_projection/results +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -# export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/label_projection" -OUTPUT_DIR="output/test" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -export NXF_VER=22.04.5 -nextflow run . \ - -main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ - -profile docker \ - -resume \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_train:output_train,input_test:output_test,input_solution:output_solution' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR"\ - --output_state '$id/state.yaml' \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh b/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh deleted file mode 100755 index 7f5f2b5b03..0000000000 --- a/src/tasks/match_modalities/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: match_modalities_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal/**/state.yaml -rename_keys: 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' -settings: '{"output_mod1": "output_mod1.h5ad", "output_mod2": "output_mod2.h5ad", "output_solution_mod1": "output_solution_mod1.h5ad", "output_solution_mod2": "output_solution_mod2.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/match_modalities/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config diff --git a/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh b/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh deleted file mode 100755 index 898cd0d420..0000000000 --- a/src/tasks/match_modalities/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: match_modalities -input_states: s3://openproblems-nextflow/resources/match_modalities/datasets/**/state.yaml -rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/match_modalities -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index f3a7acc797..552af342a6 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -1,26 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: match_modalities_process_datasets +input_states: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal/**/state.yaml +rename_keys: 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' +settings: '{"output_mod1": "$id/output_mod1.h5ad", "output_mod2": "$id/output_mod2.h5ad", "output_solution_mod1": "$id/output_solution_mod1.h5ad", "output_solution_mod2": "$id/output_solution_mod2.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/match_modalities/datasets/openproblems_v1_multimodal +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1_multimodal" -OUTPUT_DIR="resources/match_modalities/datasets/openproblems_v1_multimodal" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -resume \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ - --settings '{"output_mod1": "$id/output_mod1.h5ad", "output_mod2": "$id/output_mod2.h5ad", "output_solution_mod1": "$id/output_solution_mod1.h5ad", "output_solution_mod2": "$id/output_solution_mod2.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 93d38aa38b..4678111de0 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -1,31 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: match_modalities +input_states: s3://openproblems-data/resources/match_modalities/datasets/**/state.yaml +rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/match_modalities/results +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -# export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/match_modalities" -OUTPUT_DIR="output/test" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -export NXF_VER=22.04.5 -nextflow run . \ - -main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ - -profile docker \ - -resume \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR"\ - --output_state '$id/state.yaml' \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh b/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh deleted file mode 100755 index 9ebdb5a7ee..0000000000 --- a/src/tasks/predict_modality/nf_tower_scripts/process_datasets.sh +++ /dev/null @@ -1,25 +0,0 @@ -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: predict_modality_process_datasets -input_states: s3://openproblems-nextflow/resources/datasets/openproblems_v1_multimodal/**/state.yaml -rename_keys: 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' -settings: '{"output_train_mod1": "train_mod1.h5ad", "output_train_mod2": "train_mod2.h5ad", "output_test_mod1": "test_mod1.h5ad", "output_test_mod2": "test_mod2.h5ad"}' -publish_dir: s3://openproblems-nextflow/resources/predict_modality/datasets/openproblems_v1 -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh b/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh deleted file mode 100755 index 9d56c45db7..0000000000 --- a/src/tasks/predict_modality/nf_tower_scripts/run_benchmark.sh +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -#!/bin/bash - -cat > /tmp/params.yaml << HERE -id: predict_modality -input_states: s3://openproblems-nextflow/resources/predict_modality/datasets/**/state.yaml -rename_keys: 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' -settings: '{"output": "scores.tsv"}' -publish_dir: s3://openproblems-nextflow/output/v2/predict_modality -HERE - -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ - --workspace 53907369739130 \ - --compute-env 7IkB9ckC81O0dgNemcPJTD \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 4272b8b62f..8c69d24420 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -1,26 +1,26 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +cat > /tmp/params.yaml << 'HERE' +id: predict_modality_process_datasets +input_states: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal/**/state.yaml +rename_keys: 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' +settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/predict_modality/datasets/openproblems_v1 +HERE -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -set -e - -COMMON_DATASETS="resources/datasets/openproblems_v1_multimodal" -OUTPUT_DIR="resources/predict_modality/datasets/openproblems_v1_multimodal" - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -resume \ - --input_states "$COMMON_DATASETS/**/state.yaml" \ - --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ - --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' -# output_state should be moved to settings once workaround is solved \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index d4049b86d4..68183adaa7 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -1,31 +1,28 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -set -e - -# export TOWER_WORKSPACE_ID=53907369739130 +#!/bin/bash -DATASETS_DIR="resources_test/predict_modality" -OUTPUT_DIR="output/predict_modality" +cat > /tmp/params.yaml << 'HERE' +id: predict_modality +input_states: s3://openproblems-data/resources/predict_modality/datasets/**/state.yaml +rename_keys: 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-data/resources/predict_modality/results +HERE -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE -export NXF_VER=22.04.5 -nextflow run . \ - -main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ - -profile docker \ - -resume \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR"\ - --output_state '$id/state.yaml' \ No newline at end of file +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ No newline at end of file From e6cd9320d9353c774144f74592732e0c03767ef3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 19 Dec 2023 11:48:33 +0100 Subject: [PATCH 1087/1233] Add Neurips 2021 dataset loader (#309) * Add neurips2021 dataset loader * add test script * Add process_openproblems_neurips2021_bmmc workflow * Add resource_test script for processing NeurIPS 2021 BMMC dataset * Update predict_modality workflow and resource test script * Update neurips dataset loader * fix predict_modality to work with new data format * update neurips2021_bmmc.sh source path * force ci test * Add test resource file for openproblems_neurips2021_bmmc * download full dataset as tempfile * make fixes to the PM interface --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: cef0e5132b2d313a68f804480d77f8954a5bc495 --- src/common/library.bib | 12 ++ .../config.vsh.yaml | 70 +++++++ .../openproblems_neurips2021_bmmc/script.py | 106 +++++++++++ .../openproblems_neurips2021_bmmc/test.py | 70 +++++++ .../openproblems_neurips2021_multimodal.sh | 55 ++++++ .../resource_test_scripts/neurips2021_bmmc.sh | 58 ++++++ .../config.vsh.yaml | 135 ++++++++++++++ .../main.nf | 171 ++++++++++++++++++ .../api/comp_process_dataset.yaml | 8 +- .../api/file_common_dataset_other_mod.yaml | 34 +++- .../api/file_common_dataset_rna.yaml | 10 +- .../api/file_dataset_other_mod.yaml | 67 ------- .../api/file_dataset_rna.yaml | 43 ----- .../predict_modality/process_dataset/script.R | 34 ++-- ...{bmmc_x_starter.sh => neurips2021_bmmc.sh} | 2 +- 15 files changed, 735 insertions(+), 140 deletions(-) create mode 100644 src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml create mode 100644 src/datasets/loaders/openproblems_neurips2021_bmmc/script.py create mode 100644 src/datasets/loaders/openproblems_neurips2021_bmmc/test.py create mode 100644 src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh create mode 100755 src/datasets/resource_test_scripts/neurips2021_bmmc.sh create mode 100644 src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml create mode 100644 src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf delete mode 100644 src/tasks/predict_modality/api/file_dataset_other_mod.yaml delete mode 100644 src/tasks/predict_modality/api/file_dataset_rna.yaml rename src/tasks/predict_modality/resources_test_scripts/{bmmc_x_starter.sh => neurips2021_bmmc.sh} (92%) diff --git a/src/common/library.bib b/src/common/library.bib index a80290203b..9c711b3520 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -964,6 +964,18 @@ @article{nestorowa2016single url = {https://doi.org/10.1182/blood-2016-05-716480} } +@inproceedings{neurips, + author = {Luecken, Malte and Burkhardt, Daniel and Cannoodt, Robrecht and Lance, Christopher and Agrawal, Aditi and Aliee, Hananeh and Chen, Ann and Deconinck, Louise and Detweiler, Angela and Granados, Alejandro and Huynh, Shelly and Isacco, Laura and Kim, Yang and Klein, Dominik and DE KUMAR, BONY and Kuppasani, Sunil and Lickert, Heiko and McGeever, Aaron and Melgarejo, Joaquin and Mekonen, Honey and Morri, Maurizio and M\"{u}ller, Michaela and Neff, Norma and Paul, Sheryl and Rieck, Bastian and Schneider, Kaylie and Steelman, Scott and Sterr, Michael and Treacy, Daniel and Tong, Alexander and Villani, Alexandra-Chloe and Wang, Guilin and Yan, Jia and Zhang, Ce and Pisco, Angela and Krishnaswamy, Smita and Theis, Fabian and Bloom, Jonathan M}, + booktitle = {Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks}, + editor = {J. Vanschoren and S. Yeung}, + pages = {}, + publisher = {Curran}, + title = {A sandbox for prediction and integration of DNA, RNA, and proteins in single cells}, + url = {https://datasets-benchmarks-proceedings.neurips.cc/paper_files/paper/2021/file/158f3069a435b314a80bdcb024f8e422-Paper-round2.pdf}, + volume = {1}, + year = {2021} +} + @string{nov = {Nov.}} diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml new file mode 100644 index 0000000000..f63dbe29ae --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -0,0 +1,70 @@ +functionality: + name: "openproblems_neurips2021_bmmc" + namespace: "datasets/loaders" + description: "Fetch a dataset from the OpenProblems NeurIPS2021 competition" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + type: file + description: Processed h5ad file published at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122. + required: true + example: GSE194122_openproblems_neurips2021_cite_BMMC_processed.h5ad + - name: "--mod1" + type: string + description: Name of the first modality. + required: true + example: GEX + - name: "--mod2" + type: string + description: Name of the second modality. + required: true + example: ADT + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Outputs + arguments: + - name: "--output_mod1" + __merge__: ../../api/file_raw.yaml + direction: "output" + - name: "--output_mod2" + __merge__: ../../api/file_raw.yaml + direction: "output" + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: test.py + - type: file + path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + - type: nextflow + directives: + label: [ highmem, midcpu , midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py new file mode 100644 index 0000000000..7cae5abe0f --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -0,0 +1,106 @@ +import anndata as ad +import pandas as pd + + +## VIASH START +# The following code has been auto-generated by Viash. +par = { + "input": "resources/datasets/multimodal/cite_BMMC_processed.h5ad", + "mod1": "GEX", + "mod2": "ADT", + "dataset_name": "BMMC (CITE-seq)", + "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122", + "dataset_reference": "Neurips", + "dataset_summary": "value", + "dataset_description": "value", + "dataset_organism": "homo_sapiens", + "output_mod1": "output/mod1.h5ad", + "output_mod2": "output/mod2.h5ad" +} +meta = { + "functionality_name": "openproblems_neurips2021_bmmc", + "resources_dir": "/tmp/viash_inject_openproblems_neurips2021_bmmc14365472827677740971", +} + +## VIASH END + +def remove_other_mod_col (df, mod): + + df.drop(list(df.filter(like=mod)), axis=1, inplace=True) + + return df + +def remove_mod_prefix (df, mod): + + suffix = f"{mod}_" + df.columns = df.columns.str.removeprefix(suffix) + + return df + + +print("load dataset file", flush=True) +adata= ad.read_h5ad(par["input"]) + +# make var names unique +adata.var_names_make_unique() + +# Construct Modality datasets +print("Construct Mod datasets", flush=True) + +mask_mod1 = adata.var['feature_types'] == par["mod1"] +mask_mod2 = adata.var['feature_types'] == par["mod2"] + + +adata_mod1 = adata[:, mask_mod1] +adata_mod2 = adata[:, mask_mod2] + +# Remove other modality data from obs and var +mod1_var = pd.DataFrame(adata_mod1.var) +mod1_var = remove_other_mod_col(mod1_var, par["mod2"]) +mod1_var = remove_mod_prefix(mod1_var, par["mod1"]) + +mod1_obs = pd.DataFrame(adata_mod1.obs) +mod1_obs = remove_other_mod_col(mod1_obs, par["mod2"]) +mod1_obs = remove_mod_prefix(mod1_obs, par["mod1"]) + +adata_mod1.var = mod1_var +adata_mod1.obs = mod1_obs + +adata_mod1.uns = { key.replace(f"{par['mod1']}_", ""): value for key, value in adata.uns.items() if not key.startswith(par['mod2'])} +del adata_mod1.obsm +del adata_mod1.X + +mod2_var = pd.DataFrame(adata_mod2.var) +mod2_var = remove_other_mod_col(mod2_var, par["mod1"]) +mod2_var = remove_mod_prefix(mod2_var, par["mod2"]) + +mod2_obs = pd.DataFrame(adata_mod2.obs) +mod2_obs = remove_other_mod_col(mod2_obs, par["mod1"]) +mod2_obs = remove_mod_prefix(mod2_obs, par["mod2"]) + +adata_mod2.var = mod2_var +adata_mod2.obs = mod2_obs + +adata_mod2.uns = { key.replace(f"{par['mod2']}_", ""): value for key, value in adata.uns.items() if not key.startswith(par['mod1'])} +if par["mod2"] == "ATAC": + adata_mod2.obsm = { key.replace(f"{par['mod2']}_", ""): value for key, value in adata_mod2.uns.items() if key.startswith(par['mod2'])} +else: + del adata_mod2.obsm + + +del adata_mod2.X + +print("Add metadata to uns", flush=True) +metadata_fields = [ + "dataset_id", "dataset_name", "dataset_url", "dataset_reference", + "dataset_summary", "dataset_description", "dataset_organism" +] +for key in metadata_fields: + if key in par: + print(f" Setting .uns['{key}']", flush=True) + adata_mod1.uns[key] = par[key] + adata_mod2.uns[key] = par[key] + +print("Writing adata to file", flush=True) +adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py new file mode 100644 index 0000000000..ad884f2bc6 --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py @@ -0,0 +1,70 @@ +from os import path +import subprocess +import anndata as ad + +input = meta["resources_dir"] + "neurips2021_bmmc_cite.h5ad" +mod1 = "GEX" +mod2 = "ADT" + +output_mod1_file = "output_mod1.h5ad" +output_mod2_file = "output_mod2.h5ad" + +print(">> Running script", flush=True) +out = subprocess.run( + [ + meta["executable"], + "--input", input, + "--mod1", mod1, + "--mod2", mod2, + "--output_mod1", output_mod1_file, + "--output_mod2", output_mod2_file, + "--dataset_name", "BMMC (Multiome)", + "--dataset_url", "http://foo.org", + "--dataset_reference", "foo2000bar", + "--dataset_summary", "A short summary.", + "--dataset_description", "A couple of paragraphs worth of text.", + "--dataset_organism", "homo_sapiens", + ], + stderr=subprocess.STDOUT +) + +if out.stdout: + print(out.stdout, flush=True) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.", flush=True) + exit(out.returncode) + +print(">> Checking whether files exist", flush=True) +assert path.exists(output_mod1_file), "Output mod1 file does not exist" +assert path.exists(output_mod2_file), "Output mod2 file does not exist" + +print(">> Read output anndata", flush=True) +output_mod1 = ad.read_h5ad(output_mod1_file) +output_mod2 = ad.read_h5ad(output_mod2_file) + +print(f"output_mod1: {output_mod1}", flush=True) +print(f"output_mod2: {output_mod2}", flush=True) + +print(">> Check that output mod1 fits expected API", flush=True) +assert output_mod1.X is None, ".X is not None/empty in mod 1 output" +assert "counts" in output_mod1.layers, "'counts' not found in mod 1 output layers" +assert "cell_type" in output_mod1.obs.columns, "cell_type column not found in mod 1 output obs" +assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" +assert output_mod1.uns["dataset_name"] == "BMMC (Multiome)", "Expected: Pancreas as value for dataset_name in mod 1 output uns" +assert output_mod1.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 1 output uns" +assert output_mod1.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 1 output uns" +assert output_mod1.uns["dataset_summary"] == "A short summary.", "Expected: A short summary. as value for dataset_summary in mod 1 output uns" +assert output_mod1.uns["dataset_description"] == "A couple of paragraphs worth of text.", "Expected: A couple of paragraphs worth of text. as value for dataset_description in mod 1 output uns" + + +print(">> Check that output mod2 fits expected API", flush=True) +assert output_mod2.X is None, ".X is not None/empty in mod 2 output" +assert "counts" in output_mod2.layers, "'counts' not found in mod 2 output layers" +assert "cell_type" in output_mod2.obs.columns, "cell_type column not found in mod 2 output obs" +assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" +assert output_mod2.uns["dataset_name"] == "BMMC (Multiome)", "Expected: Pancreas as value for dataset_name in mod 2 output uns" +assert output_mod2.uns["dataset_url"] == "http://foo.org", "Expected: http://foo.org as value for dataset_url in mod 2 output uns" +assert output_mod2.uns["dataset_reference"] == "foo2000bar", "Expected: foo2000bar as value for dataset_reference in mod 2 output uns" +assert output_mod2.uns["dataset_summary"] == "A short summary.", "Expected: A short summary. as value for dataset_summary in mod 2 output uns" +assert output_mod2.uns["dataset_description"] == "A couple of paragraphs worth of text.", "Expected: A couple of paragraphs worth of text. as value for dataset_description in mod 2 output uns" \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh new file mode 100644 index 0000000000..96c07c758b --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -0,0 +1,55 @@ +#!/bin/bash + +wget "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" \ + -O "/tmp/neurips2021_bmmc_cite.h5ad.gz" + +gunzip "/tmp/neurips2021_bmmc_cite.h5ad.gz" + +wget "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" \ + -O "/tmp/neurips2021_bmmc_multiome.h5ad.gz" + +gunzip "/tmp/neurips2021_bmmc_multiome.h5ad.gz" + + + +params_file="/tmp/datasets_openproblems_nuerips2021_params.yaml" + + + +cat > "$params_file" << HERE +param_list: + - id: openproblems_neurips2021/bmmc_cite + input: "/tmp/neurips2021_bmmc_cite.h5ad" + mod1: GEX + mod2: ADT + dataset_name: bmmc (CITE-Seq) + dataset_organism: homo_sapiens + dataset_summary: "Short Summary." + dataset_description: "Full description." + + - id: openproblems_neurips2021/bmmc_multiome + input: "/tmp/neurips2021_bmmc_multiome.h5ad" + mod1: GEX + mod2: ATAC + dataset_name: bmmc (Multiome) + dataset_organism: homo_sapiens + dataset_summary: "Short Summary." + dataset_description: "Full description." + +dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" +dataset_reference: neurips +output_rna: '$id/dataset_rna.had' +output_other_mod: '$id/dataset_other_mod.h5ad' +output_meta_rna: '$id/dataset_metadata_rna.yaml' +output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_state: '$id/state.yaml +HERE + +export NXF_VER=23.04.2 +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" \ + --publish_dir "resources/datasets/openproblems_neurips2021" + diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh new file mode 100755 index 0000000000..a838f1bec7 --- /dev/null +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -0,0 +1,58 @@ +#!/bin/bash + +DATASET_DIR="resources_test/common" + +#make sure the following command has been executed +#viash ns build -q 'datasets|common' --parallel --setup cb + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# download full dataset as temp file +mkdir -p "$DATASET_DIR/neurips2021_bmmc_cite" + +INPUT="$DATASET_DIR/neurips2021_bmmc_cite/temp_neurips2021_bmmc_cite.h5ad" +INPUT_URL="https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" +if [ ! -f "$INPUT" ]; then + echo "Downloading neurips2021_bmmc_cite dataset" + + wget "$INPUT_URL" -O "${INPUT}.gz" + + gunzip "${INPUT}.gz" +fi + + +# download dataset +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + -resume \ + --id neurips2021_bmmc_cite \ + --input "$INPUT" \ + --mod1 "GEX" \ + --mod2 "ADT" \ + --dataset_name "bmcc (CITE-Seq)" \ + --dataset_url "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122" \ + --dataset_reference "Neurips" \ + --dataset_summary "neurips small summary" \ + --dataset_description "neurips big description" \ + --do_subsample true \ + --n_obs 600 \ + --n_vars 1500 \ + --seed 123 \ + --normalization_methods log_cp10k \ + --output_rna '$id/dataset_rna.h5ad' \ + --output_other_mod '$id/dataset_other_mod.h5ad' \ + --output_meta_rna '$id/dataset_metadata_rna.yaml' \ + --output_meta_other_mod '$id/dataset_metadata_other_mod.yaml' \ + --output_state '$id/state.yaml' \ + --publish_dir "$DATASET_DIR" + +# run task process dataset components +src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml new file mode 100644 index 0000000000..4d09936a4e --- /dev/null +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml @@ -0,0 +1,135 @@ +functionality: + name: process_openproblems_neurips2021_bmmc + namespace: datasets/workflows + description: | + Fetch and process Neurips 2021 multimodal datasets + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input" + type: "file" + description: "Path to the input dataset" + required: true + - name: "--mod1" + type: string + description: Name of the first modality. + required: true + example: GEX + - name: "--mod2" + type: string + description: Name of the second modality. + required: true + example: ADT + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Sampling options + arguments: + - name: "--do_subsample" + type: boolean + default: false + description: "Whether or not to subsample the dataset" + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. + - name: "--keep_cell_type_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + - name: Normalization + arguments: + - name: "--normalization_methods" + type: string + multiple: true + choices: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt", "log_scran_pooling"] + default: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt"] + description: "Which normalization methods to run." + - name: Outputs + arguments: + - name: "--output_rna" + direction: "output" + type: file + example: "dataset_rna.h5ad" + - name: "--output_other_mod" + direction: "output" + type: file + example: "dataset_other_mod.h5ad" + - name: "--output_meta_rna" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_rna.yaml" + - name: "--output_meta_other_mod" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_other_mod.yaml" + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: datasets/loaders/openproblems_neurips2021_bmmc + - name: datasets/normalization/log_cp + - name: datasets/normalization/log_scran_pooling + - name: datasets/normalization/sqrt_cp + - name: datasets/normalization/l1_sqrt + - name: datasets/processors/subsample + - name: datasets/processors/svd + - name: datasets/processors/hvg + - name: common/check_dataset_schema + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf new file mode 100644 index 0000000000..99800eacaa --- /dev/null +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -0,0 +1,171 @@ +workflow run_wf { + take: + input_ch + + main: + + // create different normalization methods by overriding the defaults + normalization_methods = [ + log_cp.run( + key: "log_cp10k", + args: [normalization_id: "log_cp10k", n_cp: 10000] + ), + log_cp.run( + key: "log_cpm", + args: [normalization_id: "log_cpm", n_cp: 1000000] + ), + sqrt_cp.run( + key: "sqrt_cp10k", + args: [normalization_id: "sqrt_cp10k", n_cp: 10000] + ), + sqrt_cp.run( + key: "sqrt_cpm", + args: [normalization_id: "sqrt_cpm", n_cp: 1000000] + ), + l1_sqrt.run( + key: "l1_sqrt", + args: [normalization_id: "l1_sqrt"] + ), + log_scran_pooling.run( + key: "log_scran_pooling", + args: [normalization_id: "log_scran_pooling"] + ) + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + + // process neurips downloaded dataset + | openproblems_neurips2021_bmmc.run( + fromState: [ + "input": "input", + "mod1": "mod1", + "mod2": "mod2", + "dataset_name": "dataset_name", + "dataset_url": "dataset_url", + "dataset_reference": "dataset_reference", + "dataset_summary": "dataset_summary", + "dataset_description": "dataset_description", + "dataset_organism": "dataset_organism" + ], + toState: [ + "raw_rna": "output_mod1", + "raw_other_mod": "output_mod2" + ] + ) + + // subsample if need be + | subsample.run( + runIf: { id, state -> state.do_subsample }, + fromState: [ + "input": "raw_rna", + "input_mod2": "raw_other_mod", + "n_obs": "n_obs", + "n_vars": "n_vars", + "keep_features": "keep_features", + "keep_cell_type_categories": "keep_cell_type_categories", + "keep_batch_categories": "keep_batch_categories", + "even": "even", + "seed": "seed" + ], + toState: [ + "raw_rna": "output", + "raw_other_mod": "output_mod2" + ] + ) + + // run normalization methods + | runEach( + components: normalization_methods, + id: { id, state, comp -> + if (state.normalization_methods.size() > 1) { + id + "/" + comp.name + } else { + id + } + }, + filter: { id, state, comp -> + comp.name in state.normalization_methods + }, + fromState: ["input": "raw_rna"], + toState: { id, output, state, comp -> + state + [ + "normalization_id": comp.name, + "normalized_rna": output.output + ] + } + ) + + // run normalization methods on second modality + | runEach( + components: normalization_methods, + filter: { id, state, comp -> + comp.name == state.normalization_id + }, + fromState: ["input": "raw_other_mod"], + toState: ["normalized_other_mod": "output"] + ) + + | svd.run( + fromState: [ + "input": "normalized_rna", + "input_mod2": "normalized_other_mod" + ], + toState: [ + "svd_rna": "output", + "svd_other_mod": "output_mod2" + ] + ) + + | hvg.run( + fromState: [ "input": "svd_rna" ], + toState: [ "hvg_rna": "output" ] + ) + + | hvg.run( + fromState: [ "input": "svd_other_mod" ], + toState: [ "hvg_other_mod": "output" ] + ) + + | check_dataset_schema.run( + fromState: { id, state -> + [ + "input": state.hvg_rna, + "checks": null + ] + }, + toState: [ + "output_rna": "output", + "output_meta_rna": "meta" + ] + ) + + | check_dataset_schema.run( + fromState: { id, state -> + [ + "input": state.hvg_other_mod, + "checks": null + ] + }, + toState: [ + "output_other_mod": "output", + "output_meta_other_mod": "meta" + ] + ) + + // only output the files for which an output file was specified + | setState([ + "output_rna", + "output_other_mod", + "output_meta_rna", + "output_meta_other_mod", + "_meta" + ]) + + emit: + output_ch +} diff --git a/src/tasks/predict_modality/api/comp_process_dataset.yaml b/src/tasks/predict_modality/api/comp_process_dataset.yaml index 844cf61c9f..14de13c3d1 100644 --- a/src/tasks/predict_modality/api/comp_process_dataset.yaml +++ b/src/tasks/predict_modality/api/comp_process_dataset.yaml @@ -9,11 +9,11 @@ functionality: A component for processing a Common Dataset into a task-specific dataset. arguments: - name: "--input_rna" - __merge__: file_dataset_rna.yaml + __merge__: file_common_dataset_rna.yaml direction: input required: true - name: "--input_other_mod" - __merge__: file_dataset_other_mod.yaml + __merge__: file_common_dataset_other_mod.yaml direction: input required: true - name: "--output_train_mod1" @@ -39,5 +39,5 @@ functionality: test_resources: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/common/bmmc_cite_starter - dest: resources_test/common/bmmc_cite_starter \ No newline at end of file + - path: /resources_test/common/neurips2021_bmmc_cite + dest: resources_test/common/neurips2021_bmmc_cite \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml index 8035d80019..90f8457322 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml @@ -1,18 +1,18 @@ type: file -example: "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad" +example: "resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad" info: label: "Raw dataset mod2" summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" slots: - X: - type: double - description: Normalized expression values - required: true layers: - type: integer name: counts description: Raw counts required: true + - type: double + name: normalized + description: Normalized expression values + required: true obs: - type: string name: batch @@ -32,6 +32,30 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml index a2801d3a1b..9802da2269 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml @@ -1,18 +1,18 @@ type: file -example: "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad" +example: "resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad" info: label: "Raw dataset RNA" summary: "The RNA modality of the raw dataset." slots: - X: - type: double - description: Normalized expression values - required: true layers: - type: integer name: counts description: Raw counts required: true + - type: double + name: normalized + description: Normalized expression values + required: true obs: - type: string name: batch diff --git a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_dataset_other_mod.yaml deleted file mode 100644 index 15b2ac9fb4..0000000000 --- a/src/tasks/predict_modality/api/file_dataset_other_mod.yaml +++ /dev/null @@ -1,67 +0,0 @@ -type: file -example: "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad" -info: - label: "Raw dataset mod2" - summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" - slots: - X: - type: double - description: Normalized expression values - required: true - layers: - - type: integer - name: counts - description: Raw counts - required: true - obs: - - type: string - name: batch - description: Batch information - required: true - - type: double - name: size_factors - description: The size factors of the cells prior to normalization. - required: false - var: - - type: string - name: gene_ids - description: The gene identifiers (if available) - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - name: dataset_name - type: string - description: Nicely formatted name. - required: true - - type: string - name: dataset_url - description: Link to the original source of the dataset. - required: false - - name: dataset_reference - type: string - description: Bibtex reference of the paper in which the dataset was published. - required: false - - name: dataset_summary - type: string - description: Short description of the dataset. - required: true - - name: dataset_description - type: string - description: Long description of the dataset. - required: true - - name: dataset_organism - type: string - description: The organism of the sample in the dataset. - required: false - - type: string - name: gene_activity_var_names - description: "Names of the gene activity matrix" - required: false - obsm: - - type: double - name: gene_activity - description: ATAC gene activity - required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_dataset_rna.yaml b/src/tasks/predict_modality/api/file_dataset_rna.yaml deleted file mode 100644 index 92d4b5bc5b..0000000000 --- a/src/tasks/predict_modality/api/file_dataset_rna.yaml +++ /dev/null @@ -1,43 +0,0 @@ -type: file -example: "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad" -info: - label: "Raw dataset RNA" - summary: "The RNA modality of the raw dataset." - slots: - X: - type: double - description: Normalized expression values - required: true - layers: - - type: integer - name: counts - description: Raw counts - required: true - obs: - - type: string - name: batch - description: Batch information - required: true - - type: double - name: size_factors - description: The size factors of the cells prior to normalization. - required: false - var: - - type: string - name: gene_ids - description: The gene identifiers (if available) - required: false - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true - - type: string - name: gene_activity_var_names - description: "Names of the gene activity matrix" - required: false - obsm: - - type: double - name: gene_activity - description: ATAC gene activity - required: false \ No newline at end of file diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 323a3a63f7..a3a40e1fce 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -4,12 +4,12 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( - input_rna = "resources_test/common/bmmc_cite_starter/dataset_rna.h5ad", - input_other_mod = "resources_test/common/bmmc_cite_starter/dataset_adt.h5ad.h5ad", - output_train_mod1 = "resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad", - output_train_mod2 = "resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad", - output_test_mod1 = "resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad", - output_test_mod2 = "resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad", + input_rna = "resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad", + input_other_mod = "resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad", + output_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", + output_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", + output_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", + output_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", swap = TRUE, seed = 1L ) @@ -53,7 +53,9 @@ ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids")), drop = FALSE] ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids")), drop = FALSE] if (ad1_mod == "ATAC") { - ad1$X@x <- (ad1$X@x > 0) + 0 + # binarize features + ad1$layers[["normalized"]]@x <- (ad1$layers[["normalized"]]@x > 0) + 0 + # copy gene activity in new object ad1_uns$gene_activity_var_names <- ad1$uns$gene_activity_var_names ad1_obsm$gene_activity <- as(ad1$obsm$gene_activity, "CsparseMatrix") @@ -62,12 +64,14 @@ if (ad1_mod == "ATAC") { if (ad2_mod == "ATAC") { # subset to make the task computationally feasible if (ncol(ad2) > 10000) { - poss_ix <- which(Matrix::colSums(ad2$X) > 0) + poss_ix <- which(Matrix::colSums(ad2$layers[["normalized"]]) > 0) sel_ix <- sort(sample(poss_ix, 10000)) ad2 <- ad2[, sel_ix]$copy() ad2_var <- ad2_var[sel_ix, , drop = FALSE] } - ad2$X@x <- (ad2$X@x > 0) + 0 + + # binarize features + ad2$layers[["normalized"]]@x <- (ad2$layers[["normalized"]]@x > 0) + 0 # copy gene activity in new object ad2_uns$gene_activity_var_names <- ad2$uns$gene_activity_var_names @@ -75,8 +79,8 @@ if (ad2_mod == "ATAC") { } cat("Creating train/test split\n") -is_train <- which(ad1$obs[["is_train"]]) -is_test <- which(!ad1$obs[["is_train"]]) +is_train <- which(ad1$obs[["is_train"]] == "train") +is_test <- which(!ad1$obs[["is_train"]] == "train") # sample cells if (length(is_test) > 1000) { @@ -98,14 +102,14 @@ subset_mats <- function(li, obs_filt) { cat("Create train objects\n") output_train_mod1 <- anndata::AnnData( - layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$X), is_train), + layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$layers[["normalized"]]), is_train), obsm = subset_mats(ad1_obsm, is_train), obs = train_obs, var = ad1_var, uns = ad1_uns ) output_train_mod2 <- anndata::AnnData( - layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$X), is_train), + layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$layers[["normalized"]]), is_train), obsm = subset_mats(ad2_obsm, is_train), obs = train_obs, var = ad2_var, @@ -114,14 +118,14 @@ output_train_mod2 <- anndata::AnnData( cat("Create test objects\n") output_test_mod1 <- anndata::AnnData( - layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$X), is_test), + layers = subset_mats(list(counts = ad1$layers[["counts"]], normalized = ad1$layers[["normalized"]]), is_test), obsm = subset_mats(ad1_obsm, is_test), obs = test_obs, var = ad1_var, uns = ad1_uns ) output_test_mod2 <- anndata::AnnData( - layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$X), is_test), + layers = subset_mats(list(counts = ad2$layers[["counts"]], normalized = ad2$layers[["normalized"]]), is_test), obsm = subset_mats(ad2_obsm, is_test), obs = test_obs, var = ad2_var, diff --git a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh similarity index 92% rename from src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh rename to src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 5c8d31fd4a..078d7398ee 100755 --- a/src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -20,7 +20,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ + --rename_keys 'input_rna:output_rna,input_other_mod:output_other_mod' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' From 233da0626828238b75b1fe4417b47981e6681e9d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Dec 2023 12:54:40 +0100 Subject: [PATCH 1088/1233] add custom config definitions (#314) Former-commit-id: e233515629e8ec6ad10fbdffc55bcf33b25fa92a --- src/datasets/resource_scripts/cellxgene_census.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index f6371f0a0c..c0555dbd2b 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -132,6 +132,13 @@ HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withLabel: highmem { + memory = '350GB' + } + withName: '.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } } HERE From 083f493bfeb18cf45db9fe4f501e0d25b7533e87 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 19 Dec 2023 12:57:34 +0100 Subject: [PATCH 1089/1233] Update benchmarking workflows (#313) * update denoising * WIP label_projection * update denoising process_datasets to store dataset nromaliztion_id Co-authored-by: sainirmayi * fix run_test typo denoising * fix wf alb_proj and denoising * add label_proj test * fix label_projection wf * update dim_red * update match_modalities * update process datasets * update predict_modality --------- Co-authored-by: sainirmayi Former-commit-id: 0a228033b6520e9404d0c84b1c8a149ed7c7787f --- .../resources_scripts/process_datasets.sh | 9 +- .../denoising/api/file_common_dataset.yaml | 4 + src/tasks/denoising/api/file_test.yaml | 6 +- src/tasks/denoising/process_dataset/script.py | 2 +- .../resources_scripts/process_datasets.sh | 11 ++- .../workflows/run_benchmark/config.vsh.yaml | 28 +++++- .../denoising/workflows/run_benchmark/main.nf | 88 ++++++++++++++----- .../workflows/run_benchmark/run_test.sh | 8 +- .../resources_scripts/process_datasets.sh | 11 ++- .../workflows/run_benchmark/config.vsh.yaml | 27 +++++- .../workflows/run_benchmark/main.nf | 82 +++++++++++++---- .../workflows/run_benchmark/run_test.sh | 4 +- .../resources_scripts/process_datasets.sh | 11 ++- .../workflows/run_benchmark/config.vsh.yaml | 28 +++++- .../workflows/run_benchmark/main.nf | 76 ++++++++++++---- .../workflows/run_benchmark/run_test.sh | 31 +++++++ .../resources_scripts/process_datasets.sh | 7 ++ .../workflows/run_benchmark/config.vsh.yaml | 28 +++++- .../workflows/run_benchmark/main.nf | 81 +++++++++++++---- .../workflows/run_benchmark/run_test.sh | 31 +++++++ .../workflows/run_benchmark/config.vsh.yaml | 28 +++++- .../workflows/run_benchmark/main.nf | 71 +++++++++++---- .../workflows/run_benchmark/run_test.sh | 6 +- 23 files changed, 549 insertions(+), 129 deletions(-) create mode 100644 src/tasks/label_projection/workflows/run_benchmark/run_test.sh create mode 100644 src/tasks/match_modalities/workflows/run_benchmark/run_test.sh diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index a1c89a3b59..6e83a9ef03 100644 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -1,7 +1,7 @@ #!/bin/bash cat > /tmp/params.yaml << 'HERE' -input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/state.yaml rename_keys: 'input:output_dataset' settings: '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' output_state: "$id/state.yaml" @@ -11,6 +11,13 @@ HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } } HERE diff --git a/src/tasks/denoising/api/file_common_dataset.yaml b/src/tasks/denoising/api/file_common_dataset.yaml index ff913ce0de..80760f0c62 100644 --- a/src/tasks/denoising/api/file_common_dataset.yaml +++ b/src/tasks/denoising/api/file_common_dataset.yaml @@ -38,3 +38,7 @@ info: type: string description: The organism of the sample in the dataset. required: false + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/tasks/denoising/api/file_test.yaml b/src/tasks/denoising/api/file_test.yaml index 04d89251ce..8ba63f7669 100644 --- a/src/tasks/denoising/api/file_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -37,4 +37,8 @@ info: - name: dataset_organism type: string description: The organism of the sample in the dataset. - required: false \ No newline at end of file + required: false + - type: string + name: normalization_id + description: "Which normalization was used" + required: true \ No newline at end of file diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index d0eb9cf244..29e067fb45 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -53,7 +53,7 @@ var=adata.var[[]], uns={"dataset_id": adata.uns["dataset_id"]} ) -test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"] +test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id"] output_test = ad.AnnData( layers={"counts": X_test.astype(float)}, obs=adata.obs[[]], diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 8cd173c137..9c20fe2a4d 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -2,16 +2,23 @@ cat > /tmp/params.yaml << 'HERE' id: denoising_process_datasets -input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/state.yaml rename_keys: 'input:output_dataset' settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' output_state: "$id/state.yaml" -publish_dir: s3://openproblems-data/resources/denoising/datasets/openproblems_v1 +publish_dir: s3://openproblems-data/resources/denoising/datasets HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } } HERE diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index e7d70583c1..83ec592191 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -14,16 +14,38 @@ functionality: direction: input - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" type: file required: true direction: output - description: A TSV file containing the scores of each of the methods - example: scores.tsv + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true + direction: output + example: dataset_uns.yaml + - name: "--output_task_info" + type: file + required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/denoising/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 37c46de440..12e04d205e 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -27,20 +27,17 @@ workflow run_wf { output_ch = input_ch - - // store original id for later use + | map{ id, state -> [id, state + [_meta: [join_id: id]]] } - // extract the dataset metadata | check_dataset_schema.run( - fromState: [ "input": "input_train" ], + fromState: [ "input": "input_test" ], toState: { id, output, state -> // load output yaml file - def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - // add metadata from file to state - state + metadata + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [dataset_uns: dataset_uns] } ) @@ -50,7 +47,7 @@ workflow run_wf { // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.normalization_id + def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -95,25 +92,68 @@ workflow run_wf { } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" + // extract the dataset metadata + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" + } + + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + + | joinStates { ids, states -> + + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + } + + // store the method and metric configs + | map{ id, state -> + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file ] - [new_id, new_state] + + ["output", state + new_state] } - - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] - ) - - | setState(["output", "_meta"]) emit: output_ch diff --git a/src/tasks/denoising/workflows/run_benchmark/run_test.sh b/src/tasks/denoising/workflows/run_benchmark/run_test.sh index 46f46f8eb2..da292a36c0 100755 --- a/src/tasks/denoising/workflows/run_benchmark/run_test.sh +++ b/src/tasks/denoising/workflows/run_benchmark/run_test.sh @@ -24,8 +24,8 @@ nextflow run . \ -resume \ -entry auto \ -c src/wf_utils/labels_ci.config \ - --id resources \ - --input_states "$DATASETS_DIR/**/.*state.yaml" \ + --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_train:output_train,input_test:output_test' \ - --settings '{"output": "scores.tsv"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index 38082e9907..f7bbecfa97 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -2,16 +2,23 @@ cat > /tmp/params.yaml << 'HERE' id: dimensionality_reduction_process_datasets -input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/state.yaml rename_keys: 'input:output_dataset' settings: '{"output_dataset": "$id/dataset.h5ad", "output_solution": "$id/solution.h5ad"}' output_state: "$id/state.yaml" -publish_dir: s3://openproblems-data/resources/dimensionality_reduction/datasets/openproblems_v1 +publish_dir: s3://openproblems-data/resources/dimensionality_reduction/datasets HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } } HERE diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 18efc35f98..c665b09a95 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -14,15 +14,38 @@ functionality: direction: input - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" type: file - example: output.tsv required: true direction: output + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true + direction: output + example: dataset_uns.yaml + - name: "--output_task_info" + type: file + required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/label_projection/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index 979143b66c..afe4f14ab2 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -40,9 +40,10 @@ workflow run_wf { // extract the dataset metadata | check_dataset_schema.run( - fromState: [input: "input_dataset"], + fromState: [input: "input_solution"], toState: { id, output, state -> - state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [dataset_uns: dataset_uns] } ) @@ -52,7 +53,7 @@ workflow run_wf { // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.normalization_id + def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -103,25 +104,68 @@ workflow run_wf { } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta - ] - [new_id, new_state] + // extract the dataset metadata + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" } - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] - ) + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + + | joinStates { ids, states -> + + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) - | setState(["output", "_meta"]) + ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + } + + // store the method and metric configs + | map{ id, state -> + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file + ] + + ["output", state + new_state] + } emit: output_ch diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh index 05f7294e22..82b8c5d2b8 100755 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh @@ -25,7 +25,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --id resources_test \ - --input_states "$DATASETS_DIR/**/*state.yaml" \ + --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output": "scores.tsv"}' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index 3d1a8ebc22..3fdb406dfd 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -2,16 +2,23 @@ cat > /tmp/params.yaml << 'HERE' id: label_projection_process_datasets -input_states: s3://openproblems-data/resources/datasets/openproblems_v1/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/state.yaml rename_keys: 'input:output_dataset' settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' output_state: "$id/state.yaml" -publish_dir: s3://openproblems-data/resources/label_projection/datasets/openproblems_v1 +publish_dir: s3://openproblems-data/resources/label_projection/datasets HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } } HERE diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 28feee8e9f..cd004ebae8 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -21,16 +21,38 @@ functionality: required: true - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" + type: file + required: true + direction: output + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true direction: output + example: dataset_uns.yaml + - name: "--output_task_info" type: file - example: output.tsv - description: A TSV file containing the scores of each of the methods required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/label_projection/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index aa458b08f9..39924aa0a9 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -33,19 +33,18 @@ workflow run_wf { output_ch = input_ch - // store original id for later use | map{ id, state -> [id, state + [_meta: [join_id: id]]] } // extract the dataset metadata | check_dataset_schema.run( - fromState: [ "input": "input_train" ], + fromState: [ "input": "input_solution" ], toState: { id, output, state -> // load output yaml file - def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state - state + metadata + state + [dataset_uns: dataset_uns] } ) @@ -55,7 +54,7 @@ workflow run_wf { // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.normalization_id + def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -105,23 +104,64 @@ workflow run_wf { } ) - // join all events into a new event - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta - ] - [new_id, new_state] + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" } - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } ) - | setState(["output", "_meta"]) + | joinStates { ids, states -> + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + ["output", [output_dataset_info: dataset_uns_file, output_scores: score_uns_file, _meta: states[0]._meta]] + } + + | map{ id, state -> + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file + ] + ["output", state + new_state] + } emit: diff --git a/src/tasks/label_projection/workflows/run_benchmark/run_test.sh b/src/tasks/label_projection/workflows/run_benchmark/run_test.sh new file mode 100644 index 0000000000..2f6f88dbdb --- /dev/null +++ b/src/tasks/label_projection/workflows/run_benchmark/run_test.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/label_projection" +OUTPUT_DIR="resources_test/label_projection/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_train:output_train,input_test:output_test,input_solution:output_solution' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index 552af342a6..c536fa6120 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -12,6 +12,13 @@ HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } } HERE diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index a3c4f2d8d5..d778530ecb 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -22,16 +22,38 @@ functionality: required: true - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" + type: file + required: true + direction: output + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true direction: output + example: dataset_uns.yaml + - name: "--output_task_info" type: file - example: output.tsv - description: A TSV file containing the scores of each of the methods required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/match_modalities/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index 65dfcb8cdb..6f49c63a29 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -36,12 +36,12 @@ workflow run_wf { // extract the dataset metadata | check_dataset_schema.run( - fromState: [ "input": "input_mod1" ], + fromState: [ "input": "input_solution_mod1" ], toState: { id, output, state -> // load output yaml file - def metadata = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns // add metadata from file to state - state + metadata + state + [dataset_uns: dataset_uns] } ) @@ -51,7 +51,7 @@ workflow run_wf { // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.normalization_id + def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -105,25 +105,68 @@ workflow run_wf { } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta - ] - [new_id, new_state] +// extract the dataset metadata + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" } - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } ) - | setState(["output", "_meta"]) + | joinStates { ids, states -> + + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + } + + // store the method and metric configs + | map{ id, state -> + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file + ] + + ["output", state + new_state] + } emit: output_ch diff --git a/src/tasks/match_modalities/workflows/run_benchmark/run_test.sh b/src/tasks/match_modalities/workflows/run_benchmark/run_test.sh new file mode 100644 index 0000000000..ee7c4c9909 --- /dev/null +++ b/src/tasks/match_modalities/workflows/run_benchmark/run_test.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +DATASETS_DIR="resources_test/match_modalities" +OUTPUT_DIR="resources_test/match_modalities/benchmarks/openproblems_v1" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --id resources_test \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index 7726f1708f..8bbc707ac9 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -22,16 +22,38 @@ functionality: direction: input - name: Outputs arguments: - - name: "--output" + - name: "--output_scores" type: file required: true direction: output - description: A TSV file containing the scores of each of the methods - example: scores.tsv + description: A yaml file containing the scores of each of the methods + example: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + example: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + example: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true + direction: output + example: dataset_uns.yaml + - name: "--output_task_info" + type: file + required: true + direction: output + example: task_info.yaml resources: - type: nextflow_script path: main.nf entrypoint: run_wf + - type: file + path: "/src/tasks/predict_modality/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 3b391d016b..a0915c2f47 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -41,7 +41,8 @@ workflow run_wf { | check_dataset_schema.run( fromState: [ "input": "input_train_mod1" ], toState: { id, output, state -> - state + (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [dataset_uns: dataset_uns] } ) @@ -102,26 +103,62 @@ workflow run_wf { } ) - // join all events into a new event where the new id is simply "output" and the new state consists of: - // - "input": a list of score h5ads - // - "output": the output argument of this workflow - | joinStates{ ids, states -> - def new_id = "output" - def new_state = [ - input: states.collect{it.metric_output}, - _meta: states[0]._meta - ] - [new_id, new_state] + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + + | joinStates { ids, states -> + + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] } - // convert to tsv and publish - | extract_scores.run( - fromState: ["input"], - toState: ["output"] - ) + // store the method and metric configs + | map{ id, state -> + + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) - | setState(["output", "_meta"]) + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file + ] + + ["output", state + new_state] + } emit: output_ch } \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index 7f96e00d0a..affe3247c2 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -8,7 +8,7 @@ cd "$REPO_ROOT" set -e -DATASETS_DIR="resources_test/predict_modality" +DATASETS_DIR="resources_test/predict_modality/neurips2021_bmmc_cite" OUTPUT_DIR="output/predict_modality" if [ ! -d "$OUTPUT_DIR" ]; then @@ -23,8 +23,8 @@ nextflow run . \ -resume \ -entry auto \ -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ + --input_states "$DATASETS_DIR/state.yaml" \ --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ - --settings '{"output": "scores.tsv"}' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' \ No newline at end of file From 9d5af980c485c966b6fc4aab312a73e22a4924c4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Dec 2023 14:00:24 +0100 Subject: [PATCH 1090/1233] Add components for extracting dataset info (#315) * add dataset comp * add get_dataset_info to workflow * commit * undo changes -- will be addressed in #314 * move get_dataset_info component * remove unnecessary dependencies * add component for extracting the dataset info * fix script * fix typo * fix script * update script * fix get_dataset_info --------- Co-authored-by: Kai Waldrant Former-commit-id: 17cc7cfd9310912351e02a4da6495881dad1e678 --- .../get_dataset_info/config.vsh.yaml | 20 +++++++ .../get_dataset_info/script.R | 28 ++++++++++ .../get_method_info/config.vsh.yaml | 4 -- .../get_metric_info/config.vsh.yaml | 4 -- .../process_task_results/run/config.vsh.yaml | 1 + src/common/process_task_results/run/main.nf | 3 +- .../yaml_to_json/script.py | 11 +--- .../resources_test_scripts/task_metadata.sh | 5 +- src/datasets/resource_scripts/dataset_info.sh | 40 +++++++++++++ .../extract_dataset_info/config.vsh.yaml | 34 +++++++++++ .../workflows/extract_dataset_info/main.nf | 56 +++++++++++++++++++ .../extract_dataset_info/run_test.sh | 32 +++++++++++ 12 files changed, 216 insertions(+), 22 deletions(-) create mode 100644 src/common/process_task_results/get_dataset_info/config.vsh.yaml create mode 100644 src/common/process_task_results/get_dataset_info/script.R create mode 100755 src/datasets/resource_scripts/dataset_info.sh create mode 100644 src/datasets/workflows/extract_dataset_info/config.vsh.yaml create mode 100644 src/datasets/workflows/extract_dataset_info/main.nf create mode 100755 src/datasets/workflows/extract_dataset_info/run_test.sh diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml new file mode 100644 index 0000000000..baa5c0a65d --- /dev/null +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -0,0 +1,20 @@ +__merge__: ../api/get_info.yaml +functionality: + name: "get_dataset_info" + description: "Extract dataset info and convert to expected format for website results" + resources: + - type: r_script + path: script.R + test_resources: + - type: file + path: /resources_test/common/task_metadata/dataset_info.yaml + dest: test_file.yaml +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [ purrr, dplyr, yaml, rlang, processx ] + - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_dataset_info/script.R b/src/common/process_task_results/get_dataset_info/script.R new file mode 100644 index 0000000000..c37e5f3bc2 --- /dev/null +++ b/src/common/process_task_results/get_dataset_info/script.R @@ -0,0 +1,28 @@ +library(purrr, warn.conflicts = FALSE) +library(dplyr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input = "resources_test/common/task_metadata/dataset_info.yaml", + output = "output/metric_info.json" +) +## VIASH END + +datasets <- yaml::yaml.load_file(par$input) + +df <- map_df(datasets, function(dataset) { + info <- as_tibble(map(dataset, as.data.frame)) +}) %>% + rename( + data_url = dataset_url, + data_reference = dataset_reference + ) + + +jsonlite::write_json( + purrr::transpose(df), + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file diff --git a/src/common/process_task_results/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml index ee425804b2..e683172c78 100644 --- a/src/common/process_task_results/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -15,10 +15,6 @@ platforms: setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] - - type: apt - packages: [ curl, default-jdk ] - - type: docker - run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml index d6d5426063..bbf0599d6e 100644 --- a/src/common/process_task_results/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -15,10 +15,6 @@ platforms: setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] - - type: apt - packages: [ curl, default-jdk ] - - type: docker - run: "curl -fsSL dl.viash.io | bash && mv viash /usr/bin/viash" - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/run/config.vsh.yaml b/src/common/process_task_results/run/config.vsh.yaml index 309c2debbc..00233084cb 100644 --- a/src/common/process_task_results/run/config.vsh.yaml +++ b/src/common/process_task_results/run/config.vsh.yaml @@ -79,6 +79,7 @@ functionality: - name: common/process_task_results/get_results - name: common/process_task_results/get_method_info - name: common/process_task_results/get_metric_info + - name: common/process_task_results/get_dataset_info - name: common/process_task_results/yaml_to_json platforms: - type: nextflow \ No newline at end of file diff --git a/src/common/process_task_results/run/main.nf b/src/common/process_task_results/run/main.nf index 13bd00b552..450b4bd18d 100644 --- a/src/common/process_task_results/run/main.nf +++ b/src/common/process_task_results/run/main.nf @@ -34,8 +34,7 @@ workflow run_wf { } ) - | yaml_to_json.run( - key: "dataset_info", + | get_dataset_info.run( fromState: [ "input": "input_dataset_info", "output": "output_dataset_info" diff --git a/src/common/process_task_results/yaml_to_json/script.py b/src/common/process_task_results/yaml_to_json/script.py index 200d933c20..45f6374515 100644 --- a/src/common/process_task_results/yaml_to_json/script.py +++ b/src/common/process_task_results/yaml_to_json/script.py @@ -1,21 +1,16 @@ -from os import path import yaml import json ## VIASH START par = { - "input" : ".", - "task_id" : "denoising", + "input": ".", + "task_id": "denoising", "output": "output/task.json", - } -meta = { "functionality" : "foo" } - ## VIASH END with open(par["input"], "r") as f: yaml_file = yaml.safe_load(f) - with open(par["output"], "w") as out: - json.dump(yaml_file, out, indent=2) \ No newline at end of file + json.dump(yaml_file, out, indent=2) diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index 0560b0ddff..ad6d547ded 100755 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -128,9 +128,6 @@ nextflow run . \ -entry auto \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml"}' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state "state.yaml" - -# Copy task info -cp src/tasks/batch_integration/api/task_info.yaml "$OUTPUT_DIR/task_info.yaml" \ No newline at end of file diff --git a/src/datasets/resource_scripts/dataset_info.sh b/src/datasets/resource_scripts/dataset_info.sh new file mode 100755 index 0000000000..95b8191e03 --- /dev/null +++ b/src/datasets/resource_scripts/dataset_info.sh @@ -0,0 +1,40 @@ +#!/bin/bash + +cat > "/tmp/params.yaml" << HERE +param_list: + - id: openproblems_v1 + input_states: "$DATASETS_DIR/openproblems_v1/**/log_cp10k/state.yaml" + rename_keys: 'input:output_dataset' + - id: openproblems_v1_multimodal + input_states: "$DATASETS_DIR/openproblems_v1_multimodal/**/log_cp10k/state.yaml" + rename_keys: 'input:output_dataset_mod1' + - id: cellxgene_census + input_states: "$DATASETS_DIR/cellxgene_census/**/log_cp10k/state.yaml" + rename_keys: 'input:output_dataset' +settings: '{"output": "dataset_info.yaml"}' +output_state: state.yaml +publish_dir: "$DATASETS_DIR" +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' + withLabel: highmem { + memory = '350GB' + } + withName: '.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --entry-name auto \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/extract_dataset_info/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "/tmp/params.yaml" \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/workflows/extract_dataset_info/config.vsh.yaml b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml new file mode 100644 index 0000000000..5397405086 --- /dev/null +++ b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml @@ -0,0 +1,34 @@ +functionality: + name: "extract_dataset_info" + namespace: "datasets/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __merge__: /src/datasets/api/file_raw.yaml + required: true + direction: input + - name: Filter arguments + arguments: + - name: "--filter_normalization_id" + type: string + required: false + direction: input + description: If defined, only the normalization with this ID will be included in the output. + multiple: true + default: [ log_cp10k ] + - name: Outputs + arguments: + - name: "--output" + type: file + required: true + direction: output + example: dataset_uns.yaml + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/check_dataset_schema +platforms: + - type: nextflow diff --git a/src/datasets/workflows/extract_dataset_info/main.nf b/src/datasets/workflows/extract_dataset_info/main.nf new file mode 100644 index 0000000000..6e942cbe4c --- /dev/null +++ b/src/datasets/workflows/extract_dataset_info/main.nf @@ -0,0 +1,56 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // extract the dataset metadata + | check_dataset_schema.run( + fromState: [input: "input"], + toState: { id, output, state -> + def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [dataset_uns: dataset_uns] + } + ) + + // only keep one of the normalization methods + | filter{ id, state -> + if (state.filter_normalization_id) { + state.filter_normalization_id.contains(state.dataset_uns.normalization_id) + } else { + true + } + } + + | joinStates { ids, states -> + // remove normalization id + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + + // store data as yaml + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + def new_state = [ + output: dataset_uns_file, + _meta: [join_id: ids[0]] + ] + ["output", new_state] + } + + + emit: + output_ch +} diff --git a/src/datasets/workflows/extract_dataset_info/run_test.sh b/src/datasets/workflows/extract_dataset_info/run_test.sh new file mode 100755 index 0000000000..9723de008a --- /dev/null +++ b/src/datasets/workflows/extract_dataset_info/run_test.sh @@ -0,0 +1,32 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="output/temp" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +DATASETS_DIR="resources_test/common" + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/datasets/workflows/extract_dataset_info/main.nf \ + -profile docker \ + -resume \ + -c src/wf_utils/labels_ci.config \ + -entry auto \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output": "dataset_info.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" \ No newline at end of file From f6cc8c2cb36988ae9aa310cbd21c564592809a1c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Dec 2023 20:13:38 +0100 Subject: [PATCH 1091/1233] Fix dataset info components (#316) * simplify get_dataset_info component * fix script * change default into example * fix script * fix script Former-commit-id: 4b7c0851a806685feb2599fb77a917c03663d43b --- .../get_dataset_info/config.vsh.yaml | 2 +- .../get_dataset_info/script.R | 23 ++++++++----------- src/datasets/resource_scripts/dataset_info.sh | 16 ++++++++++++- .../extract_dataset_info/config.vsh.yaml | 2 +- .../workflows/extract_dataset_info/main.nf | 1 + 5 files changed, 28 insertions(+), 16 deletions(-) diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml index baa5c0a65d..e9c4a0b0c6 100644 --- a/src/common/process_task_results/get_dataset_info/config.vsh.yaml +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -14,7 +14,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ purrr, dplyr, yaml, rlang, processx ] + cran: [ yaml, jsonlite ] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_dataset_info/script.R b/src/common/process_task_results/get_dataset_info/script.R index c37e5f3bc2..025624558b 100644 --- a/src/common/process_task_results/get_dataset_info/script.R +++ b/src/common/process_task_results/get_dataset_info/script.R @@ -1,27 +1,24 @@ -library(purrr, warn.conflicts = FALSE) -library(dplyr, warn.conflicts = FALSE) -library(rlang, warn.conflicts = FALSE) +requireNamespace("jsonlite", quietly = TRUE) +requireNamespace("yaml", quietly = TRUE) ## VIASH START par <- list( input = "resources_test/common/task_metadata/dataset_info.yaml", - output = "output/metric_info.json" + output = "output/dataset_info.json" ) ## VIASH END datasets <- yaml::yaml.load_file(par$input) -df <- map_df(datasets, function(dataset) { - info <- as_tibble(map(dataset, as.data.frame)) -}) %>% - rename( - data_url = dataset_url, - data_reference = dataset_reference - ) - +# transform into format expected by website +datasets_formatted <- lapply(datasets, function(dataset) { + dataset$data_url <- dataset$dataset_url + dataset$data_reference <- dataset$dataset_reference + dataset +}) jsonlite::write_json( - purrr::transpose(df), + datasets_formatted, par$output, auto_unbox = TRUE, pretty = TRUE diff --git a/src/datasets/resource_scripts/dataset_info.sh b/src/datasets/resource_scripts/dataset_info.sh index 95b8191e03..ecfa6e058a 100755 --- a/src/datasets/resource_scripts/dataset_info.sh +++ b/src/datasets/resource_scripts/dataset_info.sh @@ -1,5 +1,7 @@ #!/bin/bash +DATASETS_DIR="s3://openproblems-data/resources/datasets" + cat > "/tmp/params.yaml" << HERE param_list: - id: openproblems_v1 @@ -37,4 +39,16 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file "/tmp/params.yaml" \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config + + +# # run locally after the above has finished +# nextflow run . \ +# -main-script target/nextflow/common/process_task_results/get_dataset_info/main.nf \ +# -profile docker \ +# -resume \ +# --input "$DATASETS_DIR/dataset_info.yaml" \ +# --task_id "common" \ +# --output "dataset_info.json" \ +# --output_state state.yaml \ +# --publish_dir "../website/documentation/reference/datasets/data/" \ No newline at end of file diff --git a/src/datasets/workflows/extract_dataset_info/config.vsh.yaml b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml index 5397405086..452bf5429a 100644 --- a/src/datasets/workflows/extract_dataset_info/config.vsh.yaml +++ b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: direction: input description: If defined, only the normalization with this ID will be included in the output. multiple: true - default: [ log_cp10k ] + example: [ log_cp10k ] - name: Outputs arguments: - name: "--output" diff --git a/src/datasets/workflows/extract_dataset_info/main.nf b/src/datasets/workflows/extract_dataset_info/main.nf index 6e942cbe4c..9f847e8a2e 100644 --- a/src/datasets/workflows/extract_dataset_info/main.nf +++ b/src/datasets/workflows/extract_dataset_info/main.nf @@ -32,6 +32,7 @@ workflow run_wf { | joinStates { ids, states -> // remove normalization id + // TODO: make this optional through a parameter? def dataset_uns = states.collect{state -> def uns = state.dataset_uns.clone() uns.remove("normalization_id") From 3d8e26ea325b65fe79bdddb0f48387eabfe707db Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Dec 2023 20:21:12 +0100 Subject: [PATCH 1092/1233] Remove normalization from denoising (#318) * remove normalization from denoising task * remove unused api file Former-commit-id: 1930eb147b0844cd964dee4119279ea264878e69 --- .../denoising/api/file_common_dataset.yaml | 4 ---- src/tasks/denoising/api/file_dataset.yaml | 16 ---------------- src/tasks/denoising/api/file_test.yaml | 6 +----- src/tasks/denoising/process_dataset/script.py | 2 +- .../resources_scripts/process_datasets.sh | 2 +- .../denoising/workflows/run_benchmark/main.nf | 19 +------------------ 6 files changed, 4 insertions(+), 45 deletions(-) delete mode 100644 src/tasks/denoising/api/file_dataset.yaml diff --git a/src/tasks/denoising/api/file_common_dataset.yaml b/src/tasks/denoising/api/file_common_dataset.yaml index 80760f0c62..ff913ce0de 100644 --- a/src/tasks/denoising/api/file_common_dataset.yaml +++ b/src/tasks/denoising/api/file_common_dataset.yaml @@ -38,7 +38,3 @@ info: type: string description: The organism of the sample in the dataset. required: false - - type: string - name: normalization_id - description: "Which normalization was used" - required: true diff --git a/src/tasks/denoising/api/file_dataset.yaml b/src/tasks/denoising/api/file_dataset.yaml deleted file mode 100644 index 327e0d5e59..0000000000 --- a/src/tasks/denoising/api/file_dataset.yaml +++ /dev/null @@ -1,16 +0,0 @@ -type: file -example: "resources_test/common/pancreas/dataset.h5ad" -info: - label: "Preprocessed dataset" - summary: A dataset containing raw counts and a dataset id. - slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true - uns: - - type: string - name: dataset_id - description: "A unique identifier for the dataset" - required: true diff --git a/src/tasks/denoising/api/file_test.yaml b/src/tasks/denoising/api/file_test.yaml index 8ba63f7669..04d89251ce 100644 --- a/src/tasks/denoising/api/file_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -37,8 +37,4 @@ info: - name: dataset_organism type: string description: The organism of the sample in the dataset. - required: false - - type: string - name: normalization_id - description: "Which normalization was used" - required: true \ No newline at end of file + required: false \ No newline at end of file diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index 29e067fb45..d0eb9cf244 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -53,7 +53,7 @@ var=adata.var[[]], uns={"dataset_id": adata.uns["dataset_id"]} ) -test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id"] +test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"] output_test = ad.AnnData( layers={"counts": X_test.astype(float)}, obs=adata.obs[[]], diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 9c20fe2a4d..8fbb811c3b 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -2,7 +2,7 @@ cat > /tmp/params.yaml << 'HERE' id: denoising_process_datasets -input_states: s3://openproblems-data/resources/datasets/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/log_cp10k/state.yaml rename_keys: 'input:output_dataset' settings: '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad"}' output_state: "$id/state.yaml" diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 12e04d205e..250f659beb 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -45,15 +45,6 @@ workflow run_wf { | runEach( components: methods, - // use the 'filter' argument to only run a method on the normalisation the component is asking for - filter: { id, state, comp -> - def norm = state.dataset_uns.normalization_id - def pref = comp.config.functionality.info.preferred_normalization - // if the preferred normalisation is none at all, - // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref - }, - // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> id + "." + comp.config.functionality.name @@ -92,12 +83,6 @@ workflow run_wf { } ) - // extract the dataset metadata - // only keep one of the normalization methods - | filter{ id, state -> - state.dataset_uns.normalization_id == "log_cp10k" - } - // extract the scores | check_dataset_schema.run( key: "extract_scores", @@ -112,9 +97,7 @@ workflow run_wf { // store the dataset metadata in a file def dataset_uns = states.collect{state -> - def uns = state.dataset_uns.clone() - uns.remove("normalization_id") - uns + state.dataset_uns.clone() } def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) def dataset_uns_file = tempFile("dataset_uns.yaml") From 4dd8ab7be4957958acd131abbbeb8a3b050dc625 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 19 Dec 2023 20:40:46 +0100 Subject: [PATCH 1093/1233] remove multimodal starter dataset (#317) * remove multimodal starter dataset * fix indentation --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 2cf2a7352e6a0ebd36a4cfbc39bbdf6dedf4ae86 --- .../resource_test_scripts/bmmc_x_starter.sh | 87 ------------------- .../api/comp_control_method.yaml | 4 +- .../predict_modality/api/comp_method.yaml | 4 +- .../predict_modality/api/comp_metric.yaml | 4 +- .../predict_modality/api/file_prediction.yaml | 2 +- .../predict_modality/api/file_score.yaml | 2 +- .../predict_modality/api/file_test_mod1.yaml | 2 +- .../predict_modality/api/file_test_mod2.yaml | 2 +- .../predict_modality/api/file_train_mod1.yaml | 2 +- .../predict_modality/api/file_train_mod2.yaml | 2 +- .../control_methods/meanpergene/script.py | 8 +- .../control_methods/random_predict/script.R | 6 +- .../control_methods/solution/script.R | 2 +- .../control_methods/zeros/script.py | 6 +- .../methods/knnr_py/script.py | 6 +- .../methods/newwave_knnr/script.R | 4 +- .../metrics/correlation/script.R | 6 +- .../predict_modality/metrics/mse/script.py | 6 +- .../predict_modality/process_dataset/script.R | 12 +-- .../neurips2021_bmmc.sh | 12 +-- 20 files changed, 45 insertions(+), 134 deletions(-) delete mode 100755 src/datasets/resource_test_scripts/bmmc_x_starter.sh diff --git a/src/datasets/resource_test_scripts/bmmc_x_starter.sh b/src/datasets/resource_test_scripts/bmmc_x_starter.sh deleted file mode 100755 index db67188a68..0000000000 --- a/src/datasets/resource_test_scripts/bmmc_x_starter.sh +++ /dev/null @@ -1,87 +0,0 @@ -#!/bin/bash - -# TODO: replace this with a run of the correct dataset loader once it is available - -NEURIPS2021_URL="https://github.com/openproblems-bio/neurips2021_multimodal_viash/raw/main/resources_test/common" -DATASET_DIR="resources_test/common" - -SUBDIR="$DATASET_DIR/bmmc_cite_starter" -mkdir -p "$SUBDIR" -wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_rna.h5ad" \ - -O "$SUBDIR/dataset_rna.h5ad" -wget "$NEURIPS2021_URL/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter.output_mod2.h5ad" \ - -O "$SUBDIR/dataset_adt.h5ad" - -cat > "$SUBDIR/state.yaml" << HERE -id: bmmc_cite_starter -output_dataset_rna: !file dataset_rna.h5ad -output_dataset_other_mod: !file dataset_adt.h5ad -HERE - -python - << HERE -import anndata as ad - -rna = ad.read_h5ad("$SUBDIR/dataset_rna.h5ad") -mod2 = ad.read_h5ad("$SUBDIR/dataset_adt.h5ad") - -rna.uns["dataset_id"] = "bmmc_cite_starter" -mod2.uns["dataset_id"] = "bmmc_cite_starter" -rna.uns["dataset_name"] = "BMMC Cite Starter" -mod2.uns["dataset_name"] = "BMMC Cite Starter" -rna.uns["dataset_url"] = "https://foo.bar" -mod2.uns["dataset_url"] = "https://foo.bar" -rna.uns["dataset_reference"] = "foo2001bar" -mod2.uns["dataset_reference"] = "foo2001bar" -rna.uns["dataset_summary"] = "summary" -mod2.uns["dataset_summary"] = "summary" -rna.uns["dataset_description"] = "description" -mod2.uns["dataset_description"] = "description" -rna.uns["dataset_organism"] = "homo_sapiens" -mod2.uns["dataset_organism"] = "homo_sapiens" - -rna.write_h5ad("$SUBDIR/dataset_rna.h5ad") -mod2.write_h5ad("$SUBDIR/dataset_adt.h5ad") -HERE - - -SUBDIR="$DATASET_DIR/bmmc_multiome_starter" -mkdir -p "$SUBDIR" -wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad" \ - -O "$SUBDIR/dataset_rna.h5ad" -wget "$NEURIPS2021_URL/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_mod2.h5ad" \ - -O "$SUBDIR/dataset_atac.h5ad" - -cat > "$SUBDIR/state.yaml" << HERE -id: bmmc_multiome_starter -output_dataset_rna: !file dataset_rna.h5ad -output_dataset_other_mod: !file dataset_atac.h5ad -HERE - - -python - << HERE -import anndata as ad - -rna = ad.read_h5ad("$SUBDIR/dataset_rna.h5ad") -mod2 = ad.read_h5ad("$SUBDIR/dataset_atac.h5ad") - -rna.uns["dataset_id"] = "bmmc_multiome_starter" -mod2.uns["dataset_id"] = "bmmc_multipme_starter" -rna.uns["dataset_name"] = "BMMC Multiome Starter" -mod2.uns["dataset_name"] = "BMMC Multiome Starter" -rna.uns["dataset_url"] = "https://foo.bar" -mod2.uns["dataset_url"] = "https://foo.bar" -rna.uns["dataset_reference"] = "foo2001bar" -mod2.uns["dataset_reference"] = "foo2001bar" -rna.uns["dataset_summary"] = "summary" -mod2.uns["dataset_summary"] = "summary" -rna.uns["dataset_description"] = "description" -mod2.uns["dataset_description"] = "description" -rna.uns["dataset_organism"] = "homo_sapiens" -mod2.uns["dataset_organism"] = "homo_sapiens" - -rna.write_h5ad("$SUBDIR/dataset_rna.h5ad") -mod2.write_h5ad("$SUBDIR/dataset_atac.h5ad") -HERE - -# run task process dataset components -src/tasks/predict_modality/resources_test_scripts/bmmc_x_starter.sh \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml index 1adf1c18b1..8689478046 100644 --- a/src/tasks/predict_modality/api/comp_control_method.yaml +++ b/src/tasks/predict_modality/api/comp_control_method.yaml @@ -38,5 +38,5 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/bmmc_cite_starter - dest: resources_test/predict_modality/bmmc_cite_starter \ No newline at end of file + - path: /resources_test/predict_modality/neurips2021_bmmc_cite + dest: resources_test/predict_modality/neurips2021_bmmc_cite \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index 42d836c82d..db47e7ab3e 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -30,6 +30,6 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/bmmc_cite_starter - dest: resources_test/predict_modality/bmmc_cite_starter + - path: /resources_test/predict_modality/neurips2021_bmmc_cite + dest: resources_test/predict_modality/neurips2021_bmmc_cite - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml index d7abb273c5..bd75d423b8 100644 --- a/src/tasks/predict_modality/api/comp_metric.yaml +++ b/src/tasks/predict_modality/api/comp_metric.yaml @@ -25,6 +25,6 @@ functionality: path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/bmmc_cite_starter - dest: resources_test/predict_modality/bmmc_cite_starter + - path: /resources_test/predict_modality/neurips2021_bmmc_cite + dest: resources_test/predict_modality/neurips2021_bmmc_cite - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml index 3e27bc5822..85f6b0353b 100644 --- a/src/tasks/predict_modality/api/file_prediction.yaml +++ b/src/tasks/predict_modality/api/file_prediction.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/prediction.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad" info: label: "Prediction" summary: "A prediction of the mod2 expression values of the test cells" diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml index e7ef707e58..8f98054015 100644 --- a/src/tasks/predict_modality/api/file_score.yaml +++ b/src/tasks/predict_modality/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/score.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index 6e2d2d0c5e..8d047ae2da 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad" info: label: "Test mod1" summary: "The mod1 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index 414aab4228..32cf147a70 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad" info: label: "Test mod2" summary: "The mod2 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index c71332ed3c..d09e88e786 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad" info: label: "Train mod1" summary: "The mod1 expression values of the train cells." diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index fa5c73c0aa..3587ba4912 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad" +example: "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad" info: label: "Train mod2" summary: "The mod2 expression values of the train cells." diff --git a/src/tasks/predict_modality/control_methods/meanpergene/script.py b/src/tasks/predict_modality/control_methods/meanpergene/script.py index 038e6db9f6..12da162c5b 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/script.py +++ b/src/tasks/predict_modality/control_methods/meanpergene/script.py @@ -4,10 +4,10 @@ # VIASH START par = { - "input_train_mod1": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", - "input_test_mod1": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", - "input_train_mod2": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", - "output": "../../../../resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", + "input_train_mod1": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", + "input_test_mod1": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", + "input_train_mod2": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", + "output": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", } meta = { diff --git a/src/tasks/predict_modality/control_methods/random_predict/script.R b/src/tasks/predict_modality/control_methods/random_predict/script.R index b044ea2f08..c9783bb773 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/script.R +++ b/src/tasks/predict_modality/control_methods/random_predict/script.R @@ -4,9 +4,9 @@ library(Matrix, warn.conflicts = FALSE, quietly = TRUE) ## VIASH START par <- list( - input_train_mod1 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", - input_test_mod1 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", - input_train_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", + input_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", + input_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", + input_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", output = "output.h5ad" ) meta <- list(functionality_name = "foo") diff --git a/src/tasks/predict_modality/control_methods/solution/script.R b/src/tasks/predict_modality/control_methods/solution/script.R index fda1769695..c2a39c9acb 100644 --- a/src/tasks/predict_modality/control_methods/solution/script.R +++ b/src/tasks/predict_modality/control_methods/solution/script.R @@ -3,7 +3,7 @@ requireNamespace("anndata", quietly = TRUE) ## VIASH START par <- list( - input_test_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", + input_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", output = "output.h5ad" ) diff --git a/src/tasks/predict_modality/control_methods/zeros/script.py b/src/tasks/predict_modality/control_methods/zeros/script.py index 827a292b81..543512bbc5 100644 --- a/src/tasks/predict_modality/control_methods/zeros/script.py +++ b/src/tasks/predict_modality/control_methods/zeros/script.py @@ -4,9 +4,9 @@ # VIASH START par = { - "input_train_mod1": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod1.h5ad", - "input_test_mod1": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod1.h5ad", - "input_train_mod2": "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.train_mod2.h5ad", + "input_train_mod1": "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", + "input_test_mod1": "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", + "input_train_mod2": "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", "output": "output.h5ad", } diff --git a/src/tasks/predict_modality/methods/knnr_py/script.py b/src/tasks/predict_modality/methods/knnr_py/script.py index 3ba132d1b9..62a799a5f4 100644 --- a/src/tasks/predict_modality/methods/knnr_py/script.py +++ b/src/tasks/predict_modality/methods/knnr_py/script.py @@ -5,9 +5,9 @@ ## VIASH START par = { - 'input_train_mod1': 'resources_test/predict_modality/bmmc_cite_starter/cite_train_mod1.h5ad', - 'input_train_mod2': 'resources_test/predict_modality/bmmc_cite_starter/cite_train_mod2.h5ad', - 'input_test_mod1': 'resources_test/predict_modality/bmmc_cite_starter/cite_test_mod1.h5ad', + 'input_train_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad', 'distance_method': 'minkowski', 'output': 'output.h5ad', 'n_pcs': 4, diff --git a/src/tasks/predict_modality/methods/newwave_knnr/script.R b/src/tasks/predict_modality/methods/newwave_knnr/script.R index 2f1c7a36e0..4451f5cf11 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/script.R +++ b/src/tasks/predict_modality/methods/newwave_knnr/script.R @@ -6,9 +6,7 @@ requireNamespace("FNN", quietly = TRUE) requireNamespace("SingleCellExperiment", quietly = TRUE) ## VIASH START -path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" -path <- "resources_test/predict_modality/openproblems_bmmc_cite_starter/openproblems_bmmc_cite_starter." -path <- "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter." +path <- "resources_test/predict_modality/neurips2021_bmmc_cite/" par <- list( input_train_mod1 = paste0(path, "train_mod1.h5ad"), input_test_mod1 = paste0(path, "test_mod1.h5ad"), diff --git a/src/tasks/predict_modality/metrics/correlation/script.R b/src/tasks/predict_modality/metrics/correlation/script.R index a79620a350..c0d4e460e6 100644 --- a/src/tasks/predict_modality/metrics/correlation/script.R +++ b/src/tasks/predict_modality/metrics/correlation/script.R @@ -5,9 +5,9 @@ requireNamespace("anndata", quietly = TRUE) ## VIASH START par <- list( - input_test_mod2 = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", - input_prediction = "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", - output = "openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.scores.h5ad" + input_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", + input_prediction = "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", + output = "output/scores.h5ad" ) #/home/rcannood/workspace/openproblems/neurips2021_multimodal_viash/work/29/320fe1e10fcd323020345bcc8969c2/openproblems_bmmc_cite_mod2_dummy_mean_per_gene.correlation.output.h5ad ## VIASH END diff --git a/src/tasks/predict_modality/metrics/mse/script.py b/src/tasks/predict_modality/metrics/mse/script.py index 449b4970cb..fd98d93f34 100644 --- a/src/tasks/predict_modality/metrics/mse/script.py +++ b/src/tasks/predict_modality/metrics/mse/script.py @@ -4,9 +4,9 @@ ## VIASH START par = { - "input_test_mod2" : "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.test_mod2.h5ad", - "input_prediction" : "resources_test/predict_modality/openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.prediction.h5ad", - "output" : "openproblems_bmmc_multiome_starter/openproblems_bmmc_multiome_starter.scores.h5ad" + "input_test_mod2" : "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", + "input_prediction" : "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", + "output" : "output/scores.h5ad" } ## VIASH END diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index a3a40e1fce..18eb3d0dd1 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -14,12 +14,12 @@ par <- list( seed = 1L ) # par <- list( -# input_rna = "resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_rna.h5ad", -# input_other_mod = "resources_test/common/bmmc_multiome_starter/openproblems_bmmc_multiome_starter.output_atac.h5ad", -# output_train_mod1 = "resources_test/predict_modality/bmmc_multiome_starter/train_mod1.h5ad", -# output_train_mod2 = "resources_test/predict_modality/bmmc_multiome_starter/train_mod2.h5ad", -# output_test_mod1 = "resources_test/predict_modality/bmmc_multiome_starter/test_mod1.h5ad", -# output_test_mod2 = "resources_test/predict_modality/bmmc_multiome_starter/test_mod2.h5ad", +# input_rna = "resources_test/predict_modality/neurips2021_bmmc_mutliome/output_rna.h5ad", +# input_other_mod = "resources_test/predict_modality/neurips2021_bmmc_mutliome/output_atac.h5ad", +# output_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/train_mod1.h5ad", +# output_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/train_mod2.h5ad", +# output_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/test_mod1.h5ad", +# output_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/test_mod2.h5ad", # swap = TRUE, # seed = 1L # ) diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 078d7398ee..5756a9fd92 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -25,9 +25,9 @@ nextflow run . \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' - echo "Run one method" - viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/bmmc_cite_starter/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/bmmc_cite_starter/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/bmmc_cite_starter/test_mod1.h5ad \ - --output $OUTPUT_DIR/bmmc_cite_starter/prediction.h5ad +echo "Run one method" +viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ + --input_train_mod1 $OUTPUT_DIR/neurips2021_bmmc_cite/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/neurips2021_bmmc_cite/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/neurips2021_bmmc_cite/test_mod1.h5ad \ + --output $OUTPUT_DIR/neurips2021_bmmc_cite/prediction.h5ad From db30a41158b2f00bd45dccada6f5977097cdb21a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Dec 2023 20:44:27 +0100 Subject: [PATCH 1094/1233] update readmes (#319) Former-commit-id: 45e9e434a7c99ac8beaee17af84a37d99a7e41e2 --- src/tasks/denoising/README.md | 4 +- src/tasks/dimensionality_reduction/README.md | 4 +- src/tasks/predict_modality/README.md | 58 ++++++++++++-------- 3 files changed, 40 insertions(+), 26 deletions(-) diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 394a5f6df2..9012878a17 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -93,7 +93,7 @@ Format:
AnnData object - obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' + obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' var: 'feature_id', 'feature_name', 'soma_joinid', 'hvg', 'hvg_score' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' @@ -120,6 +120,8 @@ Slot description: | `obs["disease_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). | | `obs["donor_id"]` | `string` | (*Optional*) Identifier for the donor from whom the cell sample is obtained. | | `obs["is_primary_data"]` | `boolean` | (*Optional*) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. | +| `obs["organism"]` | `string` | (*Optional*) Organism from which the cell sample is obtained. | +| `obs["organism_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the organism, providing a standardized reference for the organism. Must be a term from the NCBI Taxonomy Ontology (`NCBITaxon:`) which is a child of `NCBITaxon:33208`. | | `obs["self_reported_ethnicity"]` | `string` | (*Optional*) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. | | `obs["self_reported_ethnicity_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. | | `obs["sex"]` | `string` | (*Optional*) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. | diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 173b2907a7..095191a4e0 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -85,7 +85,7 @@ Format:
AnnData object - obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' + obs: 'dataset_id', 'assay', 'assay_ontology_term_id', 'cell_type', 'cell_type_ontology_term_id', 'development_stage', 'development_stage_ontology_term_id', 'disease', 'disease_ontology_term_id', 'donor_id', 'is_primary_data', 'organism', 'organism_ontology_term_id', 'self_reported_ethnicity', 'self_reported_ethnicity_ontology_term_id', 'sex', 'sex_ontology_term_id', 'suspension_type', 'tissue', 'tissue_ontology_term_id', 'tissue_general', 'tissue_general_ontology_term_id', 'batch', 'soma_joinid', 'size_factors' var: 'feature_id', 'feature_name', 'soma_joinid', 'hvg', 'hvg_score' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' @@ -112,6 +112,8 @@ Slot description: | `obs["disease_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). | | `obs["donor_id"]` | `string` | (*Optional*) Identifier for the donor from whom the cell sample is obtained. | | `obs["is_primary_data"]` | `boolean` | (*Optional*) Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. | +| `obs["organism"]` | `string` | (*Optional*) Organism from which the cell sample is obtained. | +| `obs["organism_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the organism, providing a standardized reference for the organism. Must be a term from the NCBI Taxonomy Ontology (`NCBITaxon:`) which is a child of `NCBITaxon:33208`. | | `obs["self_reported_ethnicity"]` | `string` | (*Optional*) Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. | | `obs["self_reported_ethnicity_ontology_term_id"]` | `string` | (*Optional*) Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. | | `obs["sex"]` | `string` | (*Optional*) Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. | diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index bb610644b2..410633b674 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -50,7 +50,7 @@ the information about cellular state from one modality to the other. ``` mermaid flowchart LR - file_dataset_rna("Raw dataset RNA") + file_common_dataset_rna("Raw dataset RNA") comp_process_dataset[/"Data processor"/] file_train_mod1("Train mod1") file_train_mod2("Train mod2") @@ -61,8 +61,8 @@ flowchart LR comp_metric[/"Metric"/] file_prediction("Prediction") file_score("Score") - file_dataset_other_mod("Raw dataset mod2") - file_dataset_rna---comp_process_dataset + file_common_dataset_other_mod("Raw dataset mod2") + file_common_dataset_rna---comp_process_dataset comp_process_dataset-->file_train_mod1 comp_process_dataset-->file_train_mod2 comp_process_dataset-->file_test_mod1 @@ -79,14 +79,15 @@ flowchart LR comp_method-->file_prediction comp_metric-->file_score file_prediction---comp_metric - file_dataset_other_mod---comp_process_dataset + file_common_dataset_other_mod---comp_process_dataset ``` ## File format: Raw dataset RNA The RNA modality of the raw dataset. -Example file: `resources_test/common/bmmc_cite_starter/dataset_rna.h5ad` +Example file: +`resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad` Description: @@ -100,8 +101,8 @@ Format: obs: 'batch', 'size_factors' var: 'gene_ids' obsm: 'gene_activity' - layers: 'counts' - uns: 'dataset_id', 'gene_activity_var_names' + layers: 'counts', 'normalized' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names'
@@ -109,15 +110,22 @@ Slot description:
-| Slot | Type | Description | -|:---------------------------------|:----------|:-------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | -| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | -| `layers["counts"]` | `integer` | Raw counts. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | +| Slot | Type | Description | +|:---------------------------------|:----------|:-------------------------------------------------------------------------------| +| `obs["batch"]` | `string` | Batch information. | +| `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | +| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -149,7 +157,7 @@ Arguments: The mod1 expression values of the train cells. Example file: -`resources_test/predict_modality/bmmc_cite_starter/train_mod1.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad` Description: @@ -191,7 +199,7 @@ Slot description: The mod2 expression values of the train cells. Example file: -`resources_test/predict_modality/bmmc_cite_starter/train_mod2.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad` Description: @@ -233,7 +241,7 @@ Slot description: The mod1 expression values of the test cells. Example file: -`resources_test/predict_modality/bmmc_cite_starter/test_mod1.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad` Description: @@ -280,7 +288,7 @@ Slot description: The mod2 expression values of the test cells. Example file: -`resources_test/predict_modality/bmmc_cite_starter/test_mod2.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad` Description: @@ -387,7 +395,7 @@ Arguments: A prediction of the mod2 expression values of the test cells Example file: -`resources_test/predict_modality/bmmc_cite_starter/prediction.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad` Description: @@ -420,7 +428,7 @@ Slot description: Metric score file Example file: -`resources_test/predict_modality/bmmc_cite_starter/score.h5ad` +`resources_test/predict_modality/neurips2021_bmmc_cite/score.h5ad` Description: @@ -453,7 +461,8 @@ Slot description: The second modality of the raw dataset. Must be an ADT or an ATAC dataset -Example file: `resources_test/common/bmmc_cite_starter/dataset_adt.h5ad` +Example file: +`resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad` Description: @@ -467,7 +476,7 @@ Format: obs: 'batch', 'size_factors' var: 'gene_ids' obsm: 'gene_activity' - layers: 'counts' + layers: 'counts', 'normalized' uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names'
@@ -483,6 +492,7 @@ Slot description: | `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | | `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | | `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["dataset_name"]` | `string` | Nicely formatted name. | | `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | From d32c5c814913020b3b5051b72d4ec22819dafd1e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 20 Dec 2023 10:09:42 +0100 Subject: [PATCH 1095/1233] fix test scripts (#320) * fix test scripts * fix scripts * fix script * fix scripts Former-commit-id: 26f6239d88a4c148e64e198dc879f09e8d50cf4f --- .../resources_scripts/process_datasets.sh | 3 ++- .../resources_scripts/run_benchmark.sh | 5 ++-- .../{run_test.sh => run_benchmark_test.sh} | 9 +++---- .../resources_scripts/process_datasets.sh | 3 ++- .../resources_scripts/run_benchmark.sh | 9 +++---- .../{run_test.sh => run_benchmark_test.sh} | 9 +++---- .../resources_scripts/process_datasets.sh | 3 ++- .../resources_scripts/run_benchmark.sh | 6 ++--- .../{run_test.sh => run_benchmark_test.sh} | 10 +++---- .../resources_scripts/process_datasets.sh | 3 ++- .../resources_scripts/run_benchmark.sh | 4 +-- .../resources_scripts/run_benchmark_test.sh | 26 +++++++++++++++++++ 12 files changed, 54 insertions(+), 36 deletions(-) mode change 100644 => 100755 src/tasks/batch_integration/resources_scripts/process_datasets.sh mode change 100644 => 100755 src/tasks/batch_integration/resources_scripts/run_benchmark.sh rename src/tasks/batch_integration/resources_scripts/{run_test.sh => run_benchmark_test.sh} (77%) mode change 100644 => 100755 mode change 100644 => 100755 src/tasks/denoising/resources_scripts/run_benchmark.sh rename src/tasks/denoising/resources_scripts/{run_test.sh => run_benchmark_test.sh} (76%) mode change 100644 => 100755 mode change 100644 => 100755 src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh rename src/tasks/dimensionality_reduction/resources_scripts/{run_test.sh => run_benchmark_test.sh} (79%) mode change 100644 => 100755 create mode 100755 src/tasks/label_projection/resources_scripts/run_benchmark_test.sh diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh old mode 100644 new mode 100755 index 6e83a9ef03..139f7732b5 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -29,4 +29,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels batch_integration,process_datasets \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh old mode 100644 new mode 100755 index c908fe6460..8787840372 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -1,7 +1,5 @@ #!/bin/bash - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' @@ -24,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels batch_integration,full \ No newline at end of file diff --git a/src/tasks/batch_integration/resources_scripts/run_test.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh old mode 100644 new mode 100755 similarity index 77% rename from src/tasks/batch_integration/resources_scripts/run_test.sh rename to src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh index 4e7ec2779e..cfd7eccca8 --- a/src/tasks/batch_integration/resources_scripts/run_test.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh @@ -1,8 +1,5 @@ #!/bin/bash -DATASET_DIR=resources_test/batch_integration/pancreas - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/batch_integration/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' @@ -20,8 +17,10 @@ HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ - --main-script src/tasks/batch_integration/workflows/run/main.nf \ + --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ - --config /tmp/nextflow.config \ No newline at end of file + --entry-name auto \ + --config /tmp/nextflow.config \ + --labels batch_integration,test \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index 8fbb811c3b..d79fa70900 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -30,4 +30,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels denoising,process_datasets \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh old mode 100644 new mode 100755 index e03278abc3..edb3999a3d --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -1,11 +1,7 @@ #!/bin/bash -DATASET_DIR=resources_test/denoising/pancreas - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' -id: denoising -input_states: s3://openproblems-data/resources/denoising/datasets/**/*state.yaml +input_states: s3://openproblems-data/resources/denoising/datasets/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test' settings: '{"output": "scores.tsv"}' output_state: "state.yaml" @@ -26,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels denoising,full \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/run_test.sh b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh old mode 100644 new mode 100755 similarity index 76% rename from src/tasks/denoising/resources_scripts/run_test.sh rename to src/tasks/denoising/resources_scripts/run_benchmark_test.sh index 0b1a907db8..bae0ff6aed --- a/src/tasks/denoising/resources_scripts/run_test.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh @@ -1,11 +1,7 @@ #!/bin/bash -DATASET_DIR=resources_test/denoising/pancreas - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' -id: denoising_test -input_states: s3://openproblems-data/resources_test/denoising/pancreas/ +input_states: s3://openproblems-data/resources_test/denoising/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test' settings: '{"output": "scores.tsv"}' output_state: "state.yaml" @@ -26,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels denoising,test \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index f7bbecfa97..bbb064fb26 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -30,4 +30,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels dimensionality_reduction,process_datasets \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh old mode 100644 new mode 100755 index cab16d6538..d2dd6b951d --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -1,9 +1,6 @@ #!/bin/bash - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' -id: dimensionality_reduction input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' @@ -25,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels dimensionality_reduction,full \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_test.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh old mode 100644 new mode 100755 similarity index 79% rename from src/tasks/dimensionality_reduction/resources_scripts/run_test.sh rename to src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh index dd20094147..a98085f117 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_test.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh @@ -1,14 +1,11 @@ #!/bin/bash - -# try running on nf tower cat > /tmp/params.yaml << 'HERE' -id: dimensionality_reduction -input_states: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas +input_states: s3://openproblems-data/resources_test/dimensionality_reduction/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -s3://openproblems-nextflow/temp/dimensionality-reduction/ +publish_dir: s3://openproblems-nextflow/temp/dimensionality-reduction/ HERE cat > /tmp/nextflow.config << HERE @@ -25,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels dimensionality_reduction,test \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index 3fdb406dfd..2527c4950a 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -30,4 +30,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels label_projection,process_datasets \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index ac53d89742..a31f43e271 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -1,7 +1,6 @@ #!/bin/bash cat > /tmp/params.yaml << 'HERE' -id: label_projection input_states: s3://openproblems-data/resources/label_projection/datasets/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' settings: '{"output": "scores.tsv"}' @@ -23,4 +22,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels label_projection,full \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh new file mode 100755 index 0000000000..0d926dfd9a --- /dev/null +++ b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh @@ -0,0 +1,26 @@ +#!/bin/bash + +cat > /tmp/params.yaml << 'HERE' +input_states: s3://openproblems-data/resources_test/label_projection/**/state.yaml +rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' +settings: '{"output": "scores.tsv"}' +output_state: "state.yaml" +publish_dir: s3://openproblems-nextflow/temp/label_projection/ +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ + --labels label_projection,test \ No newline at end of file From fefcd16abe08359b3684be30285a414518309af6 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:23:42 +0100 Subject: [PATCH 1096/1233] update batch_int Former-commit-id: b69e226d2058bca5ebe8c3526ccfb1bf925a3bf9 --- .../resources_scripts/run_benchmark.sh | 16 +++++++++++++--- .../resources_scripts/run_benchmark_test.sh | 1 - .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 3 files changed, 18 insertions(+), 4 deletions(-) diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 8787840372..5362ce5eb6 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -1,19 +1,29 @@ #!/bin/bash -cat > /tmp/params.yaml << 'HERE' +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/dimensionality_reduction/results/${run_date}" + +cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/batch_integration/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE +cat /tmp/nextflow.config + tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh index cfd7eccca8..b328bdbc78 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh @@ -3,7 +3,6 @@ cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/batch_integration/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" publish_dir: s3://openproblems-nextflow/temp/batch_integration/ HERE diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 586d912007..137db5ecc9 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -20,26 +20,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From a4659ed23c13fff030467e57269f706ee29813f7 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:30:00 +0100 Subject: [PATCH 1097/1233] update denoising Former-commit-id: 02f1a7f952ee7b92413a5f55f6a9153d4ba3eb8d --- .../resources_scripts/run_benchmark.sh | 2 +- .../denoising/resources_scripts/run_benchmark.sh | 14 +++++++++++--- .../resources_scripts/run_benchmark_test.sh | 1 - .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 4 files changed, 17 insertions(+), 5 deletions(-) diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 5362ce5eb6..529613b4b1 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/dimensionality_reduction/results/${run_date}" +publish_dir="s3://openproblems-data/resources/batch_integration/results/${run_date}" cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index edb3999a3d..16f501767d 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -1,17 +1,25 @@ #!/bin/bash -cat > /tmp/params.yaml << 'HERE' +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/denoising/results/${run_date}" + +cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/denoising/datasets/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/denoising/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh index bae0ff6aed..ff0f3c166e 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh @@ -3,7 +3,6 @@ cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/denoising/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" publish_dir: s3://openproblems-nextflow/temp/denoising/ HERE diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index 83ec592191..f2e3d43c27 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -20,26 +20,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From c8adabbfde6f8fa8365f0cae2bfb144e7b650685 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:32:48 +0100 Subject: [PATCH 1098/1233] update label_projection Former-commit-id: 3c02f736c86cccab987983c3d25db81df5fc0aa0 --- .../resources_scripts/run_benchmark.sh | 14 +++++++++++--- .../resources_scripts/run_benchmark_test.sh | 1 - .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 3 files changed, 16 insertions(+), 4 deletions(-) diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index a31f43e271..1ab5b07930 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -1,17 +1,25 @@ #!/bin/bash -cat > /tmp/params.yaml << 'HERE' +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/label_projection/results/${run_date}" + +cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/label_projection/datasets/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/label_projection/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh index 0d926dfd9a..e61b82c336 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh @@ -3,7 +3,6 @@ cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/label_projection/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" publish_dir: s3://openproblems-nextflow/temp/label_projection/ HERE diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index cd004ebae8..7ae488c737 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -27,26 +27,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From 2273fa6ea30df61abbca9fa6595a1469f901af88 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:36:25 +0100 Subject: [PATCH 1099/1233] update dim_red Former-commit-id: 78497b89b3af95fe4ab6907dbc31666813fac980 --- .../resources_scripts/run_benchmark.sh | 14 +++++++++++--- .../resources_scripts/run_benchmark_test.sh | 1 - .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 3 files changed, 16 insertions(+), 4 deletions(-) diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index d2dd6b951d..d80f9d3ccd 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -1,17 +1,25 @@ #!/bin/bash -cat > /tmp/params.yaml << 'HERE' +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/dimensionality_reduction/results/${run_date}" + +cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/dimensionality_reduction/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh index a98085f117..d7a21b2757 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh @@ -3,7 +3,6 @@ cat > /tmp/params.yaml << 'HERE' input_states: s3://openproblems-data/resources_test/dimensionality_reduction/**/state.yaml rename_keys: 'input_dataset:output_dataset,input_solution:output_solution' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" publish_dir: s3://openproblems-nextflow/temp/dimensionality-reduction/ HERE diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index c665b09a95..48dc781f5c 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -20,26 +20,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From 5a164f6b02b66e08703fd729ee7ab7f03c3abc13 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:38:42 +0100 Subject: [PATCH 1100/1233] update MM Former-commit-id: 97336652c335bfc7a554a67fb108323dab3e0148 --- .../resources_scripts/run_benchmark.sh | 14 +++++++++++--- .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 2 files changed, 16 insertions(+), 3 deletions(-) diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 4678111de0..fec5e4cca8 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -1,18 +1,26 @@ #!/bin/bash -cat > /tmp/params.yaml << 'HERE' +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/match_modalities/results/${run_date}" + +cat > /tmp/params.yaml << HERE id: match_modalities input_states: s3://openproblems-data/resources/match_modalities/datasets/**/state.yaml rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2,input_solution_mod1:output_solution_mod1,input_solution_mod2:output_solution_mod2' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/match_modalities/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index d778530ecb..b81c631d53 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -28,26 +28,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From b02167afaa59472dcfb4f840ef7c5338a9603412 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 11:40:26 +0100 Subject: [PATCH 1101/1233] update PM Former-commit-id: 3ef2baad8c59d1a3fde20f11d9d61984fbe4e8a6 --- .../resources_scripts/run_benchmark.sh | 14 ++++++++++---- .../workflows/run_benchmark/config.vsh.yaml | 5 +++++ 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 68183adaa7..7c6e4b10d0 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -1,20 +1,26 @@ #!/bin/bash -#!/bin/bash +run_date=$(date +%Y%m%d) +publish_dir="s3://openproblems-data/resources/predict_modality/results/${run_date}" -cat > /tmp/params.yaml << 'HERE' +cat > /tmp/params.yaml << HERE id: predict_modality input_states: s3://openproblems-data/resources/predict_modality/datasets/**/state.yaml rename_keys: 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' -settings: '{"output": "scores.tsv"}' output_state: "state.yaml" -publish_dir: s3://openproblems-data/resources/predict_modality/results +publish_dir: "$publish_dir" HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' } + +trace { + enabled = true + overwrite = true + file = "$publish_dir/trace.txt" +} HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index 8bbc707ac9..d27be6c5aa 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -28,26 +28,31 @@ functionality: direction: output description: A yaml file containing the scores of each of the methods example: score_uns.yaml + default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output example: method_configs.yaml + default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output example: metric_configs.yaml + default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output example: dataset_uns.yaml + default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output example: task_info.yaml + default: task_info.yaml resources: - type: nextflow_script path: main.nf From f5af1001333bc23218f8669345d6f604c45119bc Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 20 Dec 2023 12:01:30 +0100 Subject: [PATCH 1102/1233] implement remarks Former-commit-id: 30c8b081546e5a0e049ba45bcc461f97a36d5765 --- .../batch_integration/resources_scripts/run_benchmark.sh | 2 -- .../workflows/run_benchmark/config.vsh.yaml | 5 ----- src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml | 5 ----- .../workflows/run_benchmark/config.vsh.yaml | 5 ----- .../label_projection/workflows/run_benchmark/config.vsh.yaml | 5 ----- .../match_modalities/workflows/run_benchmark/config.vsh.yaml | 5 ----- .../predict_modality/workflows/run_benchmark/config.vsh.yaml | 5 ----- 7 files changed, 32 deletions(-) diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 529613b4b1..6b81d7529e 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -22,8 +22,6 @@ trace { } HERE -cat /tmp/nextflow.config - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 137db5ecc9..79849696a9 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -19,31 +19,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index f2e3d43c27..5423b3cbc6 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -19,31 +19,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 48dc781f5c..12ce695181 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -19,31 +19,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 7ae488c737..1cbd3e00eb 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -26,31 +26,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index b81c631d53..a1e5660fee 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -27,31 +27,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index d27be6c5aa..a7f19f5972 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -27,31 +27,26 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: score_uns.yaml default: score_uns.yaml - name: "--output_method_configs" type: file required: true direction: output - example: method_configs.yaml default: method_configs.yaml - name: "--output_metric_configs" type: file required: true direction: output - example: metric_configs.yaml default: metric_configs.yaml - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_uns.yaml default: dataset_uns.yaml - name: "--output_task_info" type: file required: true direction: output - example: task_info.yaml default: task_info.yaml resources: - type: nextflow_script From 58b0de725ec7d5749aceb233f278976e10bd2711 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 20 Dec 2023 20:29:27 +0100 Subject: [PATCH 1103/1233] update bibtex and helper functions (#323) Former-commit-id: 6f6acccfdb7068a6c198b41e0d67d47552488b3b --- src/common/helper_functions/read_api_files.R | 74 ++++++++++++++++++++ src/common/library.bib | 14 ++++ 2 files changed, 88 insertions(+) diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index 67f5a1c550..1101f37f72 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -344,3 +344,77 @@ render_task_graph <- function(task_api, root = .task_graph_get_root(task_api)) { §``` §"), symbol = "§") } + + + +# Recursive function to process each property with indentation +.render_example_process_property <- function(prop, prop_name = NULL, indent_level = 0) { + if (is.null(prop_name)) { + prop_name <- "" + } + + out <- c() + + # define helper variables + indent_spaces <- strrep(" ", indent_level) + next_indent_spaces <- strrep(" ", indent_level + 2) + + # add comment if available + if ("description" %in% names(prop)) { + comment <- gsub("\n", paste0("\n", indent_spaces, "# "), stringr::str_trim(prop$description)) + out <- c(out, indent_spaces, "# ", comment, "\n") + } + + # add variable + out <- c(out, indent_spaces, prop_name, ": ") + + if (prop$type == "object" && "properties" %in% names(prop)) { + # Handle object with properties + prop_names <- setdiff(names(prop$properties), "additionalProperties") + sub_props <- unlist(lapply(prop_names, function(sub_prop_name) { + prop_out <- .render_example_process_property( + prop$properties[[sub_prop_name]], + sub_prop_name, + indent_level + 2 + ) + c(prop_out, "\n") + })) + c(out, "\n", sub_props[-length(sub_props)]) + } else if (prop$type == "array") { + if (is.list(prop$items) && "properties" %in% names(prop$items)) { + # Handle array of objects + array_items_yaml <- unlist(lapply(names(prop$items$properties), function(item_prop_name) { + prop_out <- .render_example_process_property( + prop$items$properties[[item_prop_name]], + item_prop_name, + indent_level + 4 + ) + c(prop_out, "\n") + })) + c(out, "\n", next_indent_spaces, "- ", array_items_yaml[-1]) + } else { + # Handle simple array + c(out, "[ ... ]") + } + } else { + c(out, "...") + } +} + +# Function for rendering an example yaml based on a JSON schema +render_example <- function(json_schema) { + if (!"properties" %in% names(json_schema)) { + return("") + } + text <- + unlist(lapply(names(json_schema$properties), function(prop_name) { + out <- .render_example_process_property( + json_schema$properties[[prop_name]], + prop_name, + 0 + ) + c(out, "\n") + })) + + paste(text, collapse = "") +} \ No newline at end of file diff --git a/src/common/library.bib b/src/common/library.bib index 9c711b3520..98a17ecd9d 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1616,3 +1616,17 @@ @article{tian2023singlecell year = {2023}, month = oct } + +@article{sonrel2023metaanalysis, + title = {Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability}, + volume = {24}, + ISSN = {1474-760X}, + url = {http://dx.doi.org/10.1186/s13059-023-02962-5}, + DOI = {10.1186/s13059-023-02962-5}, + number = {1}, + journal = {Genome Biology}, + publisher = {Springer Science and Business Media LLC}, + author = {Sonrel, Anthony and Luetge, Almut and Soneson, Charlotte and Mallona, Izaskun and Germain, Pierre-Luc and Knyazev, Sergey and Gilis, Jeroen and Gerber, Reto and Seurinck, Ruth and Paul, Dominique and Sonder, Emanuel and Crowell, Helena L. and Fanaswala, Imran and Al-Ajami, Ahmad and Heidari, Elyas and Schmeing, Stephan and Milosavljevic, Stefan and Saeys, Yvan and Mangul, Serghei and Robinson, Mark D.}, + year = {2023}, + month = may +} \ No newline at end of file From 0541b938504a867b15b68adabbbf6e1f10eb621e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 22 Dec 2023 22:15:44 +0100 Subject: [PATCH 1104/1233] Fix various issues with workflows and components (#324) * migrate qc script * fix get_info components * rework process_task_run component * fix broken reference * make sure DCA doesn't store anything in the uns * refactor batch int wf * fix issues with duplicate dataset info in denoising task * fix typo * fix duplicate dataset info and incorrect task info in dimred task * fix duplicate dataset info in label projection * commit script * change run id format Former-commit-id: 791546c6ce527177f6246e86e6218c0dd85b113b --- .../generate_qc/config.vsh.yaml | 39 +++ .../generate_qc/script.py | 287 ++++++++++++++++++ .../get_dataset_info/config.vsh.yaml | 2 +- .../get_dataset_info/script.R | 36 ++- .../get_method_info/config.vsh.yaml | 2 +- .../get_method_info/script.R | 75 +++-- .../get_metric_info/config.vsh.yaml | 2 +- .../get_metric_info/script.R | 77 +++-- .../get_results/config.vsh.yaml | 7 +- .../process_task_results/get_results/script.R | 136 +++++++-- .../get_task_info/config.vsh.yaml | 20 ++ .../get_task_info/script.R | 39 +++ .../process_task_results/run/config.vsh.yaml | 23 +- src/common/process_task_results/run/main.nf | 70 ++--- .../process_task_results/run/run_test.sh | 85 +++--- .../methods/liger/config.vsh.yaml | 2 +- .../methods/pyliger/config.vsh.yaml | 2 +- .../resources_scripts/run_benchmark.sh | 4 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 64 ++-- src/tasks/denoising/methods/dca/script.py | 8 +- .../resources_scripts/run_benchmark.sh | 7 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../denoising/workflows/run_benchmark/main.nf | 107 ++++--- .../workflows/run_benchmark/run_test.sh | 4 +- .../methods/simlr/config.vsh.yaml | 4 +- .../resources_scripts/run_benchmark.sh | 4 +- .../workflows/run_benchmark/config.vsh.yaml | 3 +- .../workflows/run_benchmark/main.nf | 88 ++++-- .../workflows/run_benchmark/run_test.sh | 8 +- .../resources_scripts/run_benchmark.sh | 4 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 86 ++++-- .../workflows/run_benchmark/run_test.sh | 2 +- .../resources_scripts/run_benchmark.sh | 4 +- .../resources_scripts/run_benchmark.sh | 4 +- 36 files changed, 954 insertions(+), 357 deletions(-) create mode 100644 src/common/process_task_results/generate_qc/config.vsh.yaml create mode 100644 src/common/process_task_results/generate_qc/script.py create mode 100644 src/common/process_task_results/get_task_info/config.vsh.yaml create mode 100644 src/common/process_task_results/get_task_info/script.R mode change 100644 => 100755 src/common/process_task_results/run/run_test.sh mode change 100644 => 100755 src/tasks/label_projection/workflows/run_benchmark/run_test.sh diff --git a/src/common/process_task_results/generate_qc/config.vsh.yaml b/src/common/process_task_results/generate_qc/config.vsh.yaml new file mode 100644 index 0000000000..1bcb0350c9 --- /dev/null +++ b/src/common/process_task_results/generate_qc/config.vsh.yaml @@ -0,0 +1,39 @@ +functionality: + name: "generate_qc" + description: "Generate task QC metrics" + namespace: common/process_task_results + arguments: + - name: "--task_info" + type: "file" + example: task_info.json + description: "Task info file" + - name: "--method_info" + type: "file" + example: method_info.json + description: "Method info file" + - name: "--metric_info" + type: "file" + example: metric_info.json + description: "Metric info file" + - name: "--dataset_info" + type: "file" + example: dataset_info.json + description: "Dataset info file" + - name: "--results" + type: "file" + example: results.json + description: "Results file" + - name: "--output" + type: "file" + direction: "output" + default: "output.json" + description: "Output json" + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/generate_qc/script.py b/src/common/process_task_results/generate_qc/script.py new file mode 100644 index 0000000000..a2f20979d1 --- /dev/null +++ b/src/common/process_task_results/generate_qc/script.py @@ -0,0 +1,287 @@ +import json +import numpy as np + +## VIASH START +## VIASH END + +EXPECTED_TASK_FIELDS = ["task_id", "task_name", "task_summary", "task_description"] +EXPECTED_METHOD_FIELDS = ["task_id", "commit_sha", "method_id", "method_name", "method_summary", "paper_reference", "is_baseline"] +EXPECTED_METRIC_FIELDS = ["task_id", "commit_sha", "metric_id", "metric_name", "metric_summary", "paper_reference", "maximize"] +EXPECTED_DATASET_FIELDS = ["task_id", "dataset_id", "dataset_name", "dataset_summary", "data_reference", "data_url"] + +def dump_json(obj, fp): + """Dump to JSON in a numpy-safe fashion.""" + json.dump( + obj, + fp, + indent=4, + sort_keys=False, + separators=(", ", ": "), + ensure_ascii=False, + ) + +def create_quality_control(task_info, dataset_info, method_info, metric_info, results): + """Quality control to detect anomalies in the results.""" + task_id = task_info["task_id"] + + result_qc = [] + + def add_qc( + category: str, + name: str, + value, + severity_value: float, + code: str, + message: str, + ) -> None: + "Add an entry to the result qc" + if severity_value <= 1: + severity = 0 + elif severity_value <= 2: + severity = 1 + elif severity_value <= 3: + severity = 2 + else: + severity = 3 + result_qc.append({ + "task_id": task_id, + "category": category, + "name": name, + "value": value, + "severity": severity, + "severity_value": severity_value, + "code": code, + "message": message + }) + + def percent_missing(list_of_dicts, field): + are_missing = [0.0 if field in item and item[field] is not None else 1.0 for item in list_of_dicts] + return np.mean(are_missing) + + # check task_info + for field in EXPECTED_TASK_FIELDS: + pct_missing = percent_missing([task_info], field) + add_qc( + "Task info", + f"Pct '{field}' missing", + pct_missing, + 3.0 if pct_missing > 0 else 0.0, + "percent_missing([task_info], field)", + f"Task metadata field '{field}' should be defined\n" + f" Task id: {task_id}\n" + f" Field: {field}\n" + ) + + # check method_info + for field in EXPECTED_METHOD_FIELDS: + pct_missing = percent_missing(method_info, field) + add_qc( + "Method info", + f"Pct '{field}' missing", + pct_missing, + 3.0 if pct_missing > 0 else 0.0, + "percent_missing(method_info, field)", + f"Method metadata field '{field}' should be defined\n" + f" Task id: {task_id}\n" + f" Field: {field}\n" + ) + + # check metric_info + for field in EXPECTED_METRIC_FIELDS: + pct_missing = percent_missing(metric_info, field) + add_qc( + "Metric info", + f"Pct '{field}' missing", + pct_missing, + 3.0 if pct_missing > 0 else 0.0, + "percent_missing(metric_info, field)", + f"Metric metadata field '{field}' should be defined\n" + f" Task id: {task_id}\n" + f" Field: {field}\n" + ) + + # check dataset_info + for field in EXPECTED_DATASET_FIELDS: + pct_missing = percent_missing(dataset_info, field) + add_qc( + "Dataset info", + f"Pct '{field}' missing", + pct_missing, + 3.0 if pct_missing > 0 else 0.0, + "percent_missing(dataset_info, field)", + f"Dataset metadata field '{field}' should be defined\n" + f" Task id: {task_id}\n" + f" Field: {field}\n" + ) + + # turn results into long format for easier processing + results_long = [ + { + "task_id": x["task_id"], + "method_id": x["method_id"], + "dataset_id": x["dataset_id"], + "metric_id": metric["metric_id"], + "metric_value" : x["metric_values"].get(metric["metric_id"]), + "scaled_score" : x["scaled_scores"].get(metric["metric_id"]), + } + for metric in metric_info + for x in results + ] + + # check percentage missing + pct_missing = 1 - len(results_long) / (len(method_info) * len(metric_info) * len(dataset_info)) + add_qc( + "Raw data", + "Number of results", + len(results), + pct_missing / .1, + "len(results) == len(method_info) * len(metric_info) * len(dataset_info)", + f"Number of results should be equal to #methods × #metrics × #datasets.\n" + f" Task id: {task_id}\n" + f" Number of results: {len(results)}\n" + f" Number of methods: {len(method_info)}\n" + f" Number of metrics: {len(metric_info)}\n" + f" Number of datasets: {len(dataset_info)}\n" + ) + + # QC per metric + for metric in metric_info: + metric_id = metric["metric_id"] + values = [ + res + for res in results_long + if res["metric_id"] == metric_id + and res["metric_value"] is not None + and np.isreal(res["metric_value"]) + ] + pct_missing = 1 - len(values) / len(dataset_info) / len(method_info) + + add_qc( + "Raw results", + f"Metric '{metric_id}' %missing", + pct_missing, + pct_missing / .1, + "pct_missing <= .1", + f"Percentage of missing results should be less than 10%.\n" + f" Task id: {task_id}\n" + f" Metric id: {metric_id}\n" + f" Percentage missing: {pct_missing*100:.0f}%\n" + ) + + # QC per method + for method in method_info: + method_id = method["method_id"] + values = [ + res + for res in results_long + if res["method_id"] == method_id + and res["metric_value"] is not None + and np.isreal(res["metric_value"]) + ] + pct_missing = 1 - len(values) / len(dataset_info) / len(metric_info) + + add_qc( + "Raw results", + f"Method '{method_id}' %missing", + pct_missing, + pct_missing / .1, + "pct_missing <= .1", + f"Percentage of missing results should be less than 10%.\n" + f" Task id: {task_id}\n" + f" method id: {method_id}\n" + f" Percentage missing: {pct_missing*100:.0f}%\n" + ) + + # QC per dataset + for dataset in dataset_info: + dataset_id = dataset["dataset_id"] + values = [ + res + for res in results_long + if res["dataset_id"] == dataset_id + and res["metric_value"] is not None + and np.isreal(res["metric_value"]) + ] + pct_missing = 1 - len(values) / len(metric_info) / len(method_info) + + add_qc( + "Raw results", + f"Dataset '{dataset_id}' %missing", + pct_missing, + pct_missing / .1, + "pct_missing <= .1", + f"Percentage of missing results should be less than 10%.\n" + f" Task id: {task_id}\n" + f" dataset id: {dataset_id}\n" + f" Percentage missing: {pct_missing*100:.0f}%\n" + ) + + + # QC per metric and method + for metric in metric_info: + for method in method_info: + metric_id = metric["metric_id"] + method_id = method["method_id"] + scores = [ + res["scaled_score"] + for res in results_long + if res["metric_id"] == metric_id + and res["method_id"] == method_id + and res["scaled_score"] is not None + and np.isreal(res["scaled_score"]) + ] + + if len(scores) >= 1: + worst_score = np.min(scores).item() + best_score = np.max(scores).item() + + add_qc( + "Scaling", + f"Worst score {method_id} {metric_id}", + worst_score, + worst_score / -1, + "worst_score >= -1", + f"Method {method_id} performs much worse than baselines.\n" + f" Task id: {task_id}\n" + f" Method id: {method_id}\n" + f" Metric id: {metric_id}\n" + f" Worst score: {worst_score}%\n" + ) + + add_qc( + "Scaling", + f"Best score {method_id} {metric_id}", + best_score, + best_score / 2, + "best_score <= 2", + f"Method {method_id} performs a lot better than baselines.\n" + f" Task id: {task_id}\n" + f" Method id: {method_id}\n" + f" Metric id: {metric_id}\n" + f" Best score: {best_score}%\n" + ) + + return result_qc + +def main(par): + # read data from files + with open(par["task_info"], "r", encoding="utf8") as file: + task_info = json.load(file) + with open(par["method_info"], "r", encoding="utf8") as file: + method_info = json.load(file) + with open(par["metric_info"], "r", encoding="utf8") as file: + metric_info = json.load(file) + with open(par["dataset_info"], "r", encoding="utf8") as file: + dataset_info = json.load(file) + with open(par["results"], "r", encoding="utf8") as file: + results = json.load(file) + + # create info objects + quality_control = create_quality_control(task_info, dataset_info, method_info, metric_info, results) + + # write data to files + with open(par["output"], "w", encoding="utf8") as file: + dump_json(quality_control, file) + +if __name__ == "__main__": + main(par) diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml index e9c4a0b0c6..8b5ff386fa 100644 --- a/src/common/process_task_results/get_dataset_info/config.vsh.yaml +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -14,7 +14,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ yaml, jsonlite ] + cran: [ purrr, yaml, rlang, processx ] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_dataset_info/script.R b/src/common/process_task_results/get_dataset_info/script.R index 025624558b..8a1f8d8696 100644 --- a/src/common/process_task_results/get_dataset_info/script.R +++ b/src/common/process_task_results/get_dataset_info/script.R @@ -1,9 +1,11 @@ requireNamespace("jsonlite", quietly = TRUE) requireNamespace("yaml", quietly = TRUE) +library(purrr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( - input = "resources_test/common/task_metadata/dataset_info.yaml", + input = "output/label_projection/dataset_uns.yaml", output = "output/dataset_info.json" ) ## VIASH END @@ -11,15 +13,35 @@ par <- list( datasets <- yaml::yaml.load_file(par$input) # transform into format expected by website -datasets_formatted <- lapply(datasets, function(dataset) { - dataset$data_url <- dataset$dataset_url - dataset$data_reference <- dataset$dataset_reference - dataset +outputs <- map(datasets, function(dataset) { + # ↑ the 'dataset' object could be used as the new format + + # TODO: it'd be nice if the s3 path was also included in the dataset info + + # construct v1 format + out <- list( + "task_id" = par$task_id, + "dataset_id" = dataset$dataset_id, + "dataset_name" = dataset$dataset_name, + "dataset_summary" = dataset$dataset_summary, + "data_reference" = dataset$dataset_reference %||% NA_character_, + "data_url" = dataset$dataset_url %||% NA_character_ + ) + + # show warning when certain data is missing and return null? + for (n in names(out)) { + if (is.null(out[[n]])) { + out_as_str <- jsonlite::toJSON(out, auto_unbox = TRUE, pretty = TRUE) + stop("missing value for value '", n, "' in ", out_as_str) + } + } + + out }) jsonlite::write_json( - datasets_formatted, + outputs, par$output, auto_unbox = TRUE, pretty = TRUE -) \ No newline at end of file +) diff --git a/src/common/process_task_results/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml index e683172c78..7caf98dbcb 100644 --- a/src/common/process_task_results/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -14,7 +14,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ purrr, dplyr, yaml, rlang, processx ] + cran: [ purrr, yaml, rlang, processx ] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_method_info/script.R b/src/common/process_task_results/get_method_info/script.R index a322050132..a923df4f39 100644 --- a/src/common/process_task_results/get_method_info/script.R +++ b/src/common/process_task_results/get_method_info/script.R @@ -1,67 +1,66 @@ +requireNamespace("jsonlite", quietly = TRUE) +requireNamespace("yaml", quietly = TRUE) library(purrr, warn.conflicts = FALSE) -library(dplyr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( input = "output/temp/method_configs.yaml", - task_id = "label_projection", output = "output/test/method_info.json" ) ## VIASH END configs <- yaml::yaml.load_file(par$input) -out <- map(configs, function(config) { - if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) +outputs <- map(configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") { + return(NULL) + } info <- config$functionality$info # add extra info - info$config_path <- gsub(".*\\./", "", config$info$config) - info$task_id <- par$task_id - info$method_id <- config$functionality$name + info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config) + info$task_id <- gsub("/.*", "", config$functionality$namespace) + info$id <- config$functionality$name info$namespace <- config$functionality$namespace - info$is_baseline <- grepl("control", info$type) info$commit_sha <- config$info$git_commit %||% "missing-sha" info$code_version <- "missing-version" + info$implementation_url <- paste0( + "https://github.com/openproblems-bio/openproblems-v2/tree/", + info$commit_sha, "/", + info$config_path + ) - # rename fields to v1 format - info$method_name <- info$label - info$label <- NULL - info$method_summary <- info$summary - info$summary <- NULL - info$method_description <- info$description - info$description <- NULL - info$paper_reference <- info$reference - info$reference <- NULL - info$code_url <- info$repository_url - info$repository_url <- NULL - info$v1.path <- info$v1$path - info$v1$path <- NULL - info$v1.commit <- info$v1$commit - info$v1$commit <- NULL - info$v1 <- NULL - info$type_info.label <- info$type_info$label - info$type_info$label <- NULL - info$type_info.summary <- info$type_info$summary - info$type_info$summary <- NULL - info$type_info.description <- info$type_info$description - info$type_info$description <- NULL - info$type_info <- NULL - if (length(info$variants) > 0) { - info$variants <- NULL - } - + # ↑ this could be used as the new format + # construct v1 format + out <- list( + task_id = info$task_id, + method_id = info$id, + method_name = info$label, + method_summary = info$summary, + is_baseline = grepl("control", info$type), + paper_reference = info$reference %||% NA_character_, + code_url = info$repository_url %||% NA_character_, + implementation_url = info$implementation_url %||% NA_character_, + code_version = NA_character_, + commit_sha = info$commit_sha + ) - # todo: show warning when certain data is missing and return null? + # show warning when certain data is missing and return null? + for (n in names(out)) { + if (is.null(out[[n]])) { + out_as_str <- jsonlite::toJSON(out, auto_unbox = TRUE, pretty = TRUE) + stop("missing value for value '", n, "' in ", out_as_str) + } + } # return output - info + out }) jsonlite::write_json( - out, + outputs, par$output, auto_unbox = TRUE, pretty = TRUE diff --git a/src/common/process_task_results/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml index bbf0599d6e..8ed18ad5b2 100644 --- a/src/common/process_task_results/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -14,7 +14,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ purrr, dplyr, yaml, rlang, processx ] + cran: [ purrr, yaml, rlang, processx ] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_metric_info/script.R b/src/common/process_task_results/get_metric_info/script.R index 9ab6e34b1c..9af0b6c852 100644 --- a/src/common/process_task_results/get_metric_info/script.R +++ b/src/common/process_task_results/get_metric_info/script.R @@ -1,41 +1,72 @@ +requireNamespace("jsonlite", quietly = TRUE) +requireNamespace("yaml", quietly = TRUE) library(purrr, warn.conflicts = FALSE) -library(dplyr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( input = "output/temp/metric_configs.yaml", - task_id = "batch_integration", output = "output/metric_info.json" ) ## VIASH END configs <- yaml::yaml.load_file(par$input) -df <- map_df(configs, function(config) { - if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") return(NULL) - info <- as_tibble(map_df(config$functionality$info$metrics, as.data.frame)) - info$config_path <- gsub(".*\\./", "", config$info$config) - info$task_id <- par$task_id - info$component_id <- config$functionality$name - info$namespace <- config$functionality$namespace - info -}) %>% - rename( - metric_id = name, - metric_name = label, - metric_summary = description, - paper_reference = reference, - ) %>% - group_by(across(-paper_reference) - ) %>% - summarise( - paper_reference = paste(paper_reference, collapse = ", "), - .groups = "drop" +outputs <- map(configs, function(config) { + if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") { + return(NULL) + } + + map( + config$functionality$info$metrics, + function(info) { + # add extra info + info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config) + info$task_id <- gsub("/.*", "", config$functionality$namespace) + info$id <- info$name + info$component_id <- config$functionality$name + info$namespace <- config$functionality$namespace + info$commit_sha <- config$info$git_commit %||% "missing-sha" + info$code_version <- "missing-version" + info$implementation_url <- paste0( + "https://github.com/openproblems-bio/openproblems-v2/tree/", + info$commit_sha, "/", + info$config_path + ) + + # ↑ this could be used as the new format + + # construct v1 format + out <- list( + task_id = info$task_id, + metric_id = info$id, + metric_name = info$label, + metric_summary = info$description, + paper_reference = info$reference %||% NA_character_, + implementation_url = info$implementation_url %||% NA_character_, + code_version = NA_character_, + commit_sha = info$commit_sha, + maximize = info$maximize + ) + + # show warning when certain data is missing and return null? + for (n in names(out)) { + if (is.null(out[[n]])) { + out_as_str <- jsonlite::toJSON(out, auto_unbox = TRUE, pretty = TRUE) + stop("missing value for value '", n, "' in ", out_as_str) + } + } + + # return output + out + } ) +}) + +outputs <- unlist(outputs, recursive = FALSE) jsonlite::write_json( - purrr::transpose(df), + outputs, par$output, auto_unbox = TRUE, pretty = TRUE diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index 839ccfef6a..9bd77c7f2b 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -3,6 +3,10 @@ functionality: description: "Extract execution info" namespace: common/process_task_results arguments: + - name: "--task_id" + type: "string" + example: "batch_integration" + description: "Task id" - name: "--input_scores" type: "file" example: resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.yaml @@ -24,8 +28,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [tidyverse, dynutils] + cran: [ purrr, yaml, rlang, dplyr, tidyr, readr, lubridate, dynutils, processx ] - type: nextflow directives: label: [lowmem, lowtime, lowcpu] - - type: native diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index 1f177775f7..ddfa30d37d 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -1,20 +1,37 @@ -library(tidyverse) -library(rlang) +requireNamespace("jsonlite", quietly = TRUE) +requireNamespace("yaml", quietly = TRUE) +requireNamespace("dynutils", quietly = TRUE) +requireNamespace("readr", quietly = TRUE) +requireNamespace("lubridate", quietly = TRUE) +library(dplyr, warn.conflicts = FALSE) +library(tidyr, warn.conflicts = FALSE) +library(purrr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) ## VIASH START par <- list( - input_scores = "resources/batch_integration/results/scores.yaml", - input_execution = "resources/batch_integration/results/trace.txt", - output = "test.json" + input_scores = "output/temp/score_uns.yaml", + input_execution = "output/temp/trace.txt", + output = "output/results.json" ) ## VIASH END # read scores -raw_scores <- yaml::yaml.load_file(par$input_scores) -score_df <- as_tibble(map_df(raw_scores, as.data.frame)) +raw_scores <- yaml::yaml.load_file(par$input_scores) %>% + map_df(function(x) { + as_tibble(as.data.frame( + x[c("dataset_id", "method_id", "metric_ids", "metric_values")] + )) + }) -scores <- score_df %>% - complete(dataset_id, method_id, metric_ids, fill = list(metric_values = NA_real_), normalization_id) %>% +# scale scores +scores <- raw_scores %>% + complete( + dataset_id, + method_id, + metric_ids, + fill = list(metric_values = NA_real_) + ) %>% group_by(metric_ids, dataset_id) %>% mutate( scaled_score = dynutils::scale_minmax(metric_values) %|% 0 @@ -27,40 +44,103 @@ scores <- score_df %>% .groups = "drop" ) -# read nxf log -nxf_log <- read_tsv(par$input_execution) %>% - mutate( +# read nxf log and process the task id +id_regex <- "^.*:(.*)_process \\((.*)/([^\\.]*)\\.(.*)\\)$" + +trace <- readr::read_tsv(par$input_execution) %>% + mutate( id = name, - process_id = gsub(".*:(.*)_process.*", "\\1", id), - method_id = gsub(".*\\.([^)]*)\\)", "\\1", id) + process_id = stringr::str_extract(id, id_regex, 1L), + dataset_id = stringr::str_extract(id, id_regex, 2L), + normalization_id = stringr::str_extract(id, id_regex, 3L), + method_id = stringr::str_extract(id, id_regex, 4L), ) %>% filter(process_id == method_id) +# parse strings into numbers +parse_exit <- function(x) { + if (is.na(x) || x == "-") { + NA_integer_ + } else { + as.integer(x) + } +} +parse_duration <- function(x) { + if (is.na(x) || x == "-") { + NA_real_ + } else { + as.numeric(lubridate::duration(toupper(x))) + } +} +parse_cpu <- function(x) { + if (is.na(x) || x == "-") { + NA_real_ + } else { + as.numeric(gsub(" *%", "", x)) + } +} +parse_size <- function(x) { + out <- + if (is.na(x) || x == "-") { + NA_integer_ + } else if (grepl("GB", x)) { + as.numeric(gsub(" *GB", "", x)) * 1024 + } else if (grepl("MB", x)) { + as.numeric(gsub(" *MB", "", x)) + } else if (grepl("KB", x)) { + as.numeric(gsub(" *KB", "", x)) / 1024 + } else if (grepl("B", x)) { + as.numeric(gsub(" *B", "", x)) / 1024 / 1024 + } else { + NA_integer_ + } + as.integer(ceiling(out)) +} -# process execution info -execution_info <- nxf_log %>% +execution_info <- trace %>% rowwise() %>% transmute( - dataset_id = gsub(".*\\(([^/]*)\\/.*", "\\1", id), - normalization_id = gsub(".*\\/([^.]*)\\..*", "\\1", id), + dataset_id, + normalization_id, method_id, resources = list(list( - exit_code = exit, - duration_sec = as.numeric(lubridate::duration(toupper(realtime))), - cpu_pct = as.numeric(gsub("%", "", `%cpu`)), - peak_memory_mb = as.numeric(gsub(" *GB", "", peak_vmem)) * 1024, - disk_read_mb = as.numeric(gsub(" *MB", "", rchar)), - disk_write_mb = as.numeric(gsub(" *MB", "", wchar)) + exit_code = parse_exit(exit), + duration_sec = parse_duration(realtime), + cpu_pct = parse_cpu(`%cpu`), + peak_memory_mb = parse_size(peak_vmem), + disk_read_mb = parse_size(rchar), + disk_write_mb = parse_size(wchar) )) ) %>% ungroup() -df <- full_join(scores, execution_info, by = c("method_id", "dataset_id")) %>% - filter(!is.na(mean_score)) +# combine scores with execution info +# fill up missing entries with NAs and 0s +metric_ids <- unique(raw_scores$metric_ids) +rep_names <- function(val) { + setNames( + as.list(rep(val, length(metric_ids))), + metric_ids + ) +} +out <- full_join( + scores, + execution_info, + by = c("method_id", "dataset_id") +) %>% + rowwise() %>% + mutate( + task_id = par$task_id, + metric_values = list(metric_values %||% rep_names(NA_real_)), + scaled_scores = list(scaled_scores %||% rep_names(0)), + mean_score = mean_score %|% 0, + ) %>% + ungroup() + jsonlite::write_json( - purrr::transpose(df), + purrr::transpose(out), par$output, auto_unbox = TRUE, pretty = TRUE -) \ No newline at end of file +) diff --git a/src/common/process_task_results/get_task_info/config.vsh.yaml b/src/common/process_task_results/get_task_info/config.vsh.yaml new file mode 100644 index 0000000000..6acdc65e1b --- /dev/null +++ b/src/common/process_task_results/get_task_info/config.vsh.yaml @@ -0,0 +1,20 @@ +__merge__: ../api/get_info.yaml +functionality: + name: "get_task_info" + description: "Extract task info" + resources: + - type: r_script + path: script.R + test_resources: + - type: file + path: /resources_test/common/task_metadata/task_info.yaml + dest: test_file.yaml +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [ purrr, yaml, rlang, processx ] + - type: nextflow + directives: + label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_task_info/script.R b/src/common/process_task_results/get_task_info/script.R new file mode 100644 index 0000000000..0848dd98bc --- /dev/null +++ b/src/common/process_task_results/get_task_info/script.R @@ -0,0 +1,39 @@ +requireNamespace("jsonlite", quietly = TRUE) +requireNamespace("yaml", quietly = TRUE) +library(purrr, warn.conflicts = FALSE) +library(rlang, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input = "output/temp/task_info.yaml", + output = "output/test/task_info.json" +) +## VIASH END + +info <- yaml::yaml.load_file(par$input) +# ↑ this could be used as the new format + +# construct v1 format +out <- list( + task_id = info$name, + commit_sha = NA_character_, + task_name = info$label, + task_summary = info$summary, + task_description = info$description, + repo = "openproblems-bio/openproblems-v2" +) + +# show warning when certain data is missing and return null? +for (n in names(out)) { + if (is.null(out[[n]])) { + out_as_str <- jsonlite::toJSON(out, auto_unbox = TRUE, pretty = TRUE) + stop("missing value for value '", n, "' in ", out_as_str) + } +} + +jsonlite::write_json( + out, + par$output, + auto_unbox = TRUE, + pretty = TRUE +) \ No newline at end of file diff --git a/src/common/process_task_results/run/config.vsh.yaml b/src/common/process_task_results/run/config.vsh.yaml index 00233084cb..d6b03a1b52 100644 --- a/src/common/process_task_results/run/config.vsh.yaml +++ b/src/common/process_task_results/run/config.vsh.yaml @@ -38,11 +38,6 @@ functionality: required: true direction: input example: task_info.yaml - - name: "--task_id" - type: string - required: true - direction: input - example: "batch_integration" - name: Outputs arguments: - name: "--output_scores" @@ -50,27 +45,32 @@ functionality: required: true direction: output description: A yaml file containing the scores of each of the methods - example: results.json + default: results.json - name: "--output_method_info" type: file required: true direction: output - example: method_info.json + default: method_info.json - name: "--output_metric_info" type: file required: true direction: output - example: metric_info.json + default: metric_info.json - name: "--output_dataset_info" type: file required: true direction: output - example: dataset_info.json + default: dataset_info.json - name: "--output_task_info" type: file required: true direction: output - example: task_info.json + default: task_info.json + - name: "--output_qc" + type: file + required: true + direction: output + default: quality_control.json resources: - type: nextflow_script path: main.nf @@ -80,6 +80,7 @@ functionality: - name: common/process_task_results/get_method_info - name: common/process_task_results/get_metric_info - name: common/process_task_results/get_dataset_info - - name: common/process_task_results/yaml_to_json + - name: common/process_task_results/get_task_info + - name: common/process_task_results/generate_qc platforms: - type: nextflow \ No newline at end of file diff --git a/src/common/process_task_results/run/main.nf b/src/common/process_task_results/run/main.nf index 450b4bd18d..3e33a5a2d0 100644 --- a/src/common/process_task_results/run/main.nf +++ b/src/common/process_task_results/run/main.nf @@ -12,73 +12,75 @@ workflow run_wf { main: output_ch = input_ch + | get_task_info.run( + key: "task_info", + fromState: [ + "input": "input_task_info" + ], + toState: ["output_task": "output"] + ) + + // extract task id from task info + | map { id, state -> + def task_id = readJson(state.output_task).task_id + [id, state + ["task_id": task_id]] + } + | get_method_info.run( fromState: [ "input": "input_method_configs", - "task_id" : "task_id", - "output": "output_method_info" + "task_id" : "task_id" ], - toState: { id, output, state -> - state + [output_method: output.output] - } + toState: ["output_method": "output"] ) | get_metric_info.run( fromState: [ "input": "input_metric_configs", - "task_id" : "task_id", - "output": "output_metric_info" + "task_id" : "task_id" ], - toState: { id, output, state -> - state + [output_metric: output.output] - } + toState: ["output_metric": "output"] ) | get_dataset_info.run( - fromState: [ + fromState: [ + "task_id" : "task_id", "input": "input_dataset_info", - "output": "output_dataset_info" ], - toState: { id, output, state -> - state + [output_dataset: output.output] - } + toState: ["output_dataset": "output"] ) - | yaml_to_json.run( - key: "task_info", + | get_results.run( fromState: [ - "input": "input_task_info", - "output": "output_task_info" + "task_id": "task_id", + "input_scores": "input_scores", + "input_execution" : "input_execution" ], - toState: { id, output, state -> - state + [output_task: output.output] - } + toState: ["output_results": "output"] ) - | get_results.run( - fromState: [ - "input_scores": "input_scores", - "input_execution" : "input_execution", - "output": "output_scores" + | generate_qc.run( + fromState: [ + "task_info": "output_task", + "method_info": "output_method", + "metric_info": "output_metric", + "dataset_info": "output_dataset", + "results": "output_results" ], - toState: { id, output, state -> - state + [output_results: output.output] - } + toState: ["output_qc": "output"] ) | map{ id, state -> - def _meta = [join_id: id] - def new_state = [ output_scores: state.output_results, output_method_info: state.output_method, output_metric_info: state.output_metric, output_dataset_info: state.output_dataset, output_task_info: state.output_task, - _meta: _meta + output_qc: state.output_qc ] - ["output", new_state] + [id, new_state] } emit: diff --git a/src/common/process_task_results/run/run_test.sh b/src/common/process_task_results/run/run_test.sh old mode 100644 new mode 100755 index 9457deffac..fa5067d6f1 --- a/src/common/process_task_results/run/run_test.sh +++ b/src/common/process_task_results/run/run_test.sh @@ -1,51 +1,44 @@ #!/bin/bash -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) +# fail on error +set -e -# ensure that the command below is run from the root of the repository +# ensure we're in the root of the repo +REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" -set -e - -# export TOWER_WORKSPACE_ID=53907369739130 - -DATASETS_DIR="resources/batch_integration/results" -OUTPUT_DIR="../website/results/batch_integration_feature/data" - -if [ ! -d "$OUTPUT_DIR" ]; then - mkdir -p "$OUTPUT_DIR" -fi - -export NXF_VER=22.04.5 - -nextflow run . \ - -main-script target/nextflow/common/workflows/transform_meta/main.nf \ - -profile docker \ - -resume \ - -c src/wf_utils/labels_ci.config \ - --id "get_results_test" \ - --input_scores "$DATASETS_DIR/scores.yaml" \ - --input_dataset_info "$DATASETS_DIR/dataset_info.yaml" \ - --input_method_configs "$DATASETS_DIR/method_configs.yaml" \ - --input_metric_configs "$DATASETS_DIR/metric_configs.yaml" \ - --input_execution "$DATASETS_DIR/trace.txt" \ - --input_task_info "$DATASETS_DIR/task_info.yaml" \ - --task_id "batch_integration" \ - --output_scores "results.json"\ - --output_method_info "method_info.json"\ - --output_metric_info "metric_info.json"\ - --output_dataset_info "dataset_info.json"\ - --output_task_info "task_info.json" \ - --publish_dir "$OUTPUT_DIR" - - -# nextflow run . \ -# -main-script target/nextflow/common/workflows/transform_meta/main.nf \ -# -profile docker \ -# -resume \ -# -entry auto \ -# --input_states "$DATASETS_DIR/state.yaml" \ -# --rename_keys 'input_scores:output_scores,input_dataset_info:output_dataset_info, input_method_configs:output_method_configs, input_metric_configs:output_metric_configs, ' \ -# --settings '{"task_id": "batch_integration", "output_scores": "results.json", "output_method_info": "method_info.json", "output_metric_info": "metric_info.json", "output_dataset_info": "dataset_info.json", "output_task_info":"task_info.json"}' \ -# --publish_dir "$OUTPUT_DIR" \ No newline at end of file +# settings +TASK="denoising" +TASK="dimensionality_reduction" +TASK="batch_integration" +TASK="label_projection" +DATE="20231220" + +for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_projection"; do + INPUT_DIR="s3://openproblems-data/resources/$TASK/results/$DATE" + OUTPUT_DIR="../website/results/$TASK/data" + + # # temp sync + # aws s3 sync $INPUT_DIR output/temp + + echo "Processing $TASK - $DATE" + + # start the run + NXF_VER=23.10.0 nextflow run . \ + -main-script target/nextflow/common/process_task_results/run/main.nf \ + -profile docker \ + -resume \ + -c src/wf_utils/labels_ci.config \ + --id "process" \ + --input_scores "$INPUT_DIR/score_uns.yaml" \ + --input_dataset_info "$INPUT_DIR/dataset_uns.yaml" \ + --input_method_configs "$INPUT_DIR/method_configs.yaml" \ + --input_metric_configs "$INPUT_DIR/metric_configs.yaml" \ + --input_execution "$INPUT_DIR/trace.txt" \ + --input_task_info "$INPUT_DIR/task_info.yaml" \ + --output_state "state.yaml" \ + --publish_dir "$OUTPUT_DIR" + + # cause quarto rerender to index page when in preview mode + touch ../website/results/$TASK/index.qmd +done \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index f262c931d5..7dd720bebc 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: deriving and implementing a novel coordinate descent algorithm to efficiently do the factorization. Joint clustering is performed and factor loadings are normalised. - reference: welch2019 + reference: welch2019single repository_url: https://github.com/welch-lab/liger documentation_url: https://github.com/welch-lab/liger preferred_normalization: log_cp10k diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index 8255a85a97..f26afdffbd 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: single-cell datasets, developed by the Macosko lab and maintained/extended by the Welch lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. - reference: welch2019 + reference: welch2019single repository_url: https://github.com/welch-lab/pyliger documentation_url: https://github.com/welch-lab/pyliger preferred_normalization: log_cp10k diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index 6b81d7529e..caf81eaf7b 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/batch_integration/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/batch_integration/results/${RUN_ID}" cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/batch_integration/datasets/**/state.yaml diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 79849696a9..976bd496d8 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: path: main.nf entrypoint: run_wf - type: file - path: /src/tasks/batch_integration/api/task_info.yaml + path: ../../api/task_info.yaml dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 101825c483..3e87a2703a 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -11,7 +11,7 @@ workflow run_wf { main: - // collect method list + // construct list of methods methods = [ bbknn, combat, @@ -33,7 +33,7 @@ workflow run_wf { random_integration ] - // collect metric list + // construct list of metrics metrics = [ asw_batch, asw_label, @@ -47,10 +47,15 @@ workflow run_wf { pcr ] - // process input parameter channel + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ dataset_ch = input_ch - - // extract the dataset metadata + // store join id + | map{ id, state -> + [id, state + ["_meta": [join_id: id]]] + } + // extract dataset metadata | check_dataset_schema.run( fromState: [input: "input_solution"], toState: { id, output, state -> @@ -59,6 +64,9 @@ workflow run_wf { } ) + /*************************** + * RUN METHODS AND METRICS * + ***************************/ // run all methods method_out_ch1 = dataset_ch | runEach( @@ -150,16 +158,18 @@ workflow run_wf { } ) + + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ // TODO: can we store everything below in a separate helper function? // extract the dataset metadata dataset_meta_ch = dataset_ch - // only keep one of the normalization methods | filter{ id, state -> state.dataset_uns.normalization_id == "log_cp10k" } - | joinStates { ids, states -> // store the dataset metadata in a file def dataset_uns = states.collect{state -> @@ -174,8 +184,8 @@ workflow run_wf { ["output", [output_dataset_info: dataset_uns_file]] } - // extract the scores - metric_uns_ch = score_ch + output_ch = score_ch + // extract scores | check_dataset_schema.run( key: "extract_scores", fromState: [input: "metric_output"], @@ -184,22 +194,8 @@ workflow run_wf { state + [score_uns: score_uns] } ) - | joinStates { ids, states -> - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_scores: score_uns_file]] - } - - // store the method and metric configs - comp_config_ch = input_ch - | map{ id, state -> - // store original id for later use - def _meta = [join_id: id] + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} def method_configs_yaml_blob = toYamlBlob(method_configs) @@ -212,23 +208,29 @@ workflow run_wf { def metric_configs_file = tempFile("metric_configs.yaml") metric_configs_file.write(metric_configs_yaml_blob) + // store the task info in a file def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + // create state def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, output_task_info: task_info_file, - _meta: _meta + output_scores: score_uns_file, + _meta: states[0]._meta ] + ["output", new_state] } - // merge all of the output data - // todo: add task info? - - // todo: add trace log? - output_ch = comp_config_ch - | mix(metric_uns_ch, dataset_meta_ch) + // merge all of the output data + | mix(dataset_meta_ch) | joinStates{ ids, states -> def mergedStates = states.inject([:]) { acc, m -> acc + m } [ids[0], mergedStates] diff --git a/src/tasks/denoising/methods/dca/script.py b/src/tasks/denoising/methods/dca/script.py index 2604f41574..b2a7ee99fa 100644 --- a/src/tasks/denoising/methods/dca/script.py +++ b/src/tasks/denoising/methods/dca/script.py @@ -17,14 +17,14 @@ input_train = ad.read_h5ad(par['input_train']) print("move layer to X", flush=True) -input_train.X = input_train.layers["counts"] +input_dca = ad.AnnData(X=input_train.layers["counts"]) +del input_train.X print("running dca", flush=True) -dca(input_train, epochs=par["epochs"]) +dca(input_dca, epochs=par["epochs"]) print("moving X back to layer", flush=True) -input_train.layers["denoised"] = scipy.sparse.csr_matrix(input_train.X) -del input_train.X +input_train.layers["denoised"] = scipy.sparse.csr_matrix(input_dca.X) print("Writing data", flush=True) input_train.uns["method_id"] = meta["functionality_name"] diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index 16f501767d..765e06ded7 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -1,10 +1,11 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/denoising/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/denoising/results/${RUN_ID}" +# make sure only log_cp10k is used cat > /tmp/params.yaml << HERE -input_states: s3://openproblems-data/resources/denoising/datasets/**/state.yaml +input_states: s3://openproblems-data/resources/denoising/datasets/**/log_cp10k/state.yaml rename_keys: 'input_train:output_train,input_test:output_test' output_state: "state.yaml" publish_dir: "$publish_dir" diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index 5423b3cbc6..cb741c20b8 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: path: main.nf entrypoint: run_wf - type: file - path: "/src/tasks/denoising/api/task_info.yaml" + path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 250f659beb..29c20372e2 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -10,7 +10,8 @@ workflow run_wf { input_ch main: - // construct a map of methods (id -> method_module) + + // construct list of methods methods = [ no_denoising, perfect_denoising, @@ -20,18 +21,21 @@ workflow run_wf { magic ] + // construct list of metrics metrics = [ mse, poisson ] - - - output_ch = input_ch - | map{ id, state -> - [id, state + [_meta: [join_id: id]]] + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch + // store join id + | map{ id, state -> + [id, state + ["_meta": [join_id: id]]] } - // extract the dataset metadata + // extract dataset metadata | check_dataset_schema.run( fromState: [ "input": "input_test" ], toState: { id, output, state -> @@ -40,23 +44,24 @@ workflow run_wf { state + [dataset_uns: dataset_uns] } ) + + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch // run all methods | runEach( components: methods, - // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> id + "." + comp.config.functionality.name }, - // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ - input_train: "input_train", - input_test: "input_test" - ], - - + input_train: "input_train", + input_test: "input_test" + ], // use 'toState' to publish that component's outputs to the overall state toState: { id, output, state, comp -> state + [ @@ -69,6 +74,9 @@ workflow run_wf { // run all metrics | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ input_test: "input_test", @@ -83,38 +91,46 @@ workflow run_wf { } ) - // extract the scores - | check_dataset_schema.run( - key: "extract_scores", - fromState: [input: "metric_output"], - toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] - } - ) - + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + // NOTE: the 'denoising' task doesn't use normalized data, + // so code related to normalization_ids is commented out + + // extract the dataset metadata + dataset_meta_ch = dataset_ch + // // only keep one of the normalization methods + // | filter{ id, state -> + // state.dataset_uns.normalization_id == "log_cp10k" + // } | joinStates { ids, states -> - // store the dataset metadata in a file def dataset_uns = states.collect{state -> - state.dataset_uns.clone() + def uns = state.dataset_uns.clone() + // uns.remove("normalization_id") + uns } def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) def dataset_uns_file = tempFile("dataset_uns.yaml") dataset_uns_file.write(dataset_uns_yaml_blob) - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + ["output", [output_dataset_info: dataset_uns_file]] } - // store the method and metric configs - | map{ id, state -> + output_ch = score_ch + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} def method_configs_yaml_blob = toYamlBlob(method_configs) @@ -129,13 +145,28 @@ workflow run_wf { def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, - output_task_info: task_info_file + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta ] - - ["output", state + new_state] + + ["output", new_state] + } + + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] } emit: diff --git a/src/tasks/denoising/workflows/run_benchmark/run_test.sh b/src/tasks/denoising/workflows/run_benchmark/run_test.sh index da292a36c0..9b31877c52 100755 --- a/src/tasks/denoising/workflows/run_benchmark/run_test.sh +++ b/src/tasks/denoising/workflows/run_benchmark/run_test.sh @@ -8,10 +8,8 @@ cd "$REPO_ROOT" set -e -# export TOWER_WORKSPACE_ID=53907369739130 - DATASETS_DIR="resources_test/denoising" -OUTPUT_DIR="resources_test/denoising/benchmarks/openproblems_v1" +OUTPUT_DIR="output/temp" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml index 9717025593..2cff2a4a65 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -5,9 +5,9 @@ functionality: info: label: SIMLR - summary: Multikernal-based learning of distance metrics from gene expression data for dimension reduction, clustering and visulaization. + summary: Multikernel-based learning of distance metrics from gene expression data for dimension reduction, clustering and visulaization. description: | - Single-cell interpretation via multikernel learning (SIMLR) learns cell-to-cell similarity measures from single-cell RNA-seq data in using Gaussian kernels with various hyperparameters in order to perform dimension reduction, clustering and visualization. + Single-cell Interpretation via Multikernel LeaRning (SIMLR) learns cell-to-cell similarity measures from single-cell RNA-seq data in using Gaussian kernels with various hyperparameters in order to perform dimension reduction, clustering and visualization. SIMLR assumes that if C separable populations exist among the N cells, then the similarity matrix should have an approximate block-diagonal structure with C blocks whereby cells have larger similarities to other cells within the same subpopulations. Learned similarity between two cells should be small if the Euclidean distance between them is large. The cell-to-cell similarity is computed using an optimization framework over an N x N similarity matrix, a low-dimensional auxilary matrix enforcing low rank constraint on the similarity matrix, and the kernel weights. Dimension reduction is achieved by the stochastic neighbor embedding methodology with the learned similarities as input. preferred_normalization: log_cp10k diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index d80f9d3ccd..facd4b0a02 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/dimensionality_reduction/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/dimensionality_reduction/results/${RUN_ID}" cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/dimensionality_reduction/datasets/**/state.yaml diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 12ce695181..575adb89c7 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: path: main.nf entrypoint: run_wf - type: file - path: "/src/tasks/label_projection/api/task_info.yaml" + path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores @@ -55,6 +55,7 @@ functionality: - name: dimensionality_reduction/methods/neuralee - name: dimensionality_reduction/methods/pca - name: dimensionality_reduction/methods/phate + - name: dimensionality_reduction/methods/simlr - name: dimensionality_reduction/methods/tsne - name: dimensionality_reduction/methods/umap - name: dimensionality_reduction/metrics/coranking diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index afe4f14ab2..7fb2f61ff3 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -11,7 +11,7 @@ workflow run_wf { main: - // collect method list + // construct list of methods methods = [ random_features, true_features, @@ -19,11 +19,12 @@ workflow run_wf { neuralee, pca, phate, + simlr, tsne, umap ] - // collect metric list + // construct list of metrics metrics = [ coranking, density_preservation, @@ -31,13 +32,15 @@ workflow run_wf { trustworthiness ] - output_ch = input_ch - // store original id for later use - | map{ id, state -> - [id, state + [_meta: [join_id: id]]] + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch + // store join id + | map{ id, state -> + [id, state + ["_meta": [join_id: id]]] } - // extract the dataset metadata | check_dataset_schema.run( fromState: [input: "input_solution"], @@ -47,6 +50,11 @@ workflow run_wf { } ) + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch + // run all methods | runEach( components: methods, @@ -88,6 +96,9 @@ workflow run_wf { // run all metrics | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: { id, state, comp -> [ @@ -104,24 +115,18 @@ workflow run_wf { } ) - // extract the dataset metadata + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + + // extract the dataset metadata + dataset_meta_ch = dataset_ch // only keep one of the normalization methods | filter{ id, state -> state.dataset_uns.normalization_id == "log_cp10k" } - - // extract the scores - | check_dataset_schema.run( - key: "extract_scores", - fromState: [input: "metric_output"], - toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] - } - ) - | joinStates { ids, states -> - // store the dataset metadata in a file def dataset_uns = states.collect{state -> def uns = state.dataset_uns.clone() @@ -132,18 +137,22 @@ workflow run_wf { def dataset_uns_file = tempFile("dataset_uns.yaml") dataset_uns_file.write(dataset_uns_yaml_blob) - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + ["output", [output_dataset_info: dataset_uns_file]] } - // store the method and metric configs - | map{ id, state -> + output_ch = score_ch + + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} def method_configs_yaml_blob = toYamlBlob(method_configs) @@ -158,13 +167,28 @@ workflow run_wf { def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, - output_task_info: task_info_file + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta ] - - ["output", state + new_state] + + ["output", new_state] + } + + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] } emit: diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh index 82b8c5d2b8..4bd2b01008 100755 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/run_test.sh @@ -8,10 +8,8 @@ cd "$REPO_ROOT" set -e -# export TOWER_WORKSPACE_ID=53907369739130 - DATASETS_DIR="resources_test/dimensionality_reduction" -OUTPUT_DIR="resources_test/dimensionality_reduction/benchmarks/openproblems_v1" +OUTPUT_DIR="output/temp" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" @@ -24,8 +22,8 @@ nextflow run . \ -resume \ -entry auto \ -c src/wf_utils/labels_ci.config \ - --id resources_test \ --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ - --publish_dir "$OUTPUT_DIR" \ No newline at end of file + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 1ab5b07930..29e9cdbbf4 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/label_projection/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/label_projection/results/${RUN_ID}" cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/label_projection/datasets/**/state.yaml diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 1cbd3e00eb..28c5261ef4 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -52,7 +52,7 @@ functionality: path: main.nf entrypoint: run_wf - type: file - path: "/src/tasks/label_projection/api/task_info.yaml" + path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - name: common/extract_scores diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index 39924aa0a9..4e9ba0c082 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -11,7 +11,7 @@ workflow run_wf { main: - // collect method list + // construct list of methods methods = [ true_labels, majority_vote, @@ -25,29 +25,35 @@ workflow run_wf { xgboost ] - // collect metric list + // construct list of metrics metrics = [ accuracy, f1 ] - output_ch = input_ch - - | map{ id, state -> - [id, state + [_meta: [join_id: id]]] + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch + // store join id + | map{ id, state -> + [id, state + ["_meta": [join_id: id]]] } - - // extract the dataset metadata + // extract dataset metadata | check_dataset_schema.run( fromState: [ "input": "input_solution" ], toState: { id, output, state -> // load output yaml file def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - // add metadata from file to state state + [dataset_uns: dataset_uns] } ) + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch + // run all methods | runEach( components: methods, @@ -90,6 +96,9 @@ workflow run_wf { // run all metrics | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ input_solution: "input_solution", @@ -104,21 +113,18 @@ workflow run_wf { } ) + + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + + // extract the dataset metadata + dataset_meta_ch = dataset_ch // only keep one of the normalization methods | filter{ id, state -> state.dataset_uns.normalization_id == "log_cp10k" } - - // extract the scores - | check_dataset_schema.run( - key: "extract_scores", - fromState: [input: "metric_output"], - toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] - } - ) - | joinStates { ids, states -> // store the dataset metadata in a file def dataset_uns = states.collect{state -> @@ -130,17 +136,22 @@ workflow run_wf { def dataset_uns_file = tempFile("dataset_uns.yaml") dataset_uns_file.write(dataset_uns_yaml_blob) - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_dataset_info: dataset_uns_file, output_scores: score_uns_file, _meta: states[0]._meta]] + ["output", [output_dataset_info: dataset_uns_file]] } - | map{ id, state -> + output_ch = score_ch + + // extract the scores + | check_dataset_schema.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns + state + [score_uns: score_uns] + } + ) + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} def method_configs_yaml_blob = toYamlBlob(method_configs) @@ -155,14 +166,29 @@ workflow run_wf { def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, - output_task_info: task_info_file + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta ] - ["output", state + new_state] + + ["output", new_state] } + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] + } emit: output_ch diff --git a/src/tasks/label_projection/workflows/run_benchmark/run_test.sh b/src/tasks/label_projection/workflows/run_benchmark/run_test.sh old mode 100644 new mode 100755 index 2f6f88dbdb..e9c712af48 --- a/src/tasks/label_projection/workflows/run_benchmark/run_test.sh +++ b/src/tasks/label_projection/workflows/run_benchmark/run_test.sh @@ -11,7 +11,7 @@ set -e # export TOWER_WORKSPACE_ID=53907369739130 DATASETS_DIR="resources_test/label_projection" -OUTPUT_DIR="resources_test/label_projection/benchmarks/openproblems_v1" +OUTPUT_DIR="output/temp" if [ ! -d "$OUTPUT_DIR" ]; then mkdir -p "$OUTPUT_DIR" diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index fec5e4cca8..44724d36e8 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/match_modalities/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/match_modalities/results/${RUN_ID}" cat > /tmp/params.yaml << HERE id: match_modalities diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 7c6e4b10d0..5ef1bee460 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -1,7 +1,7 @@ #!/bin/bash -run_date=$(date +%Y%m%d) -publish_dir="s3://openproblems-data/resources/predict_modality/results/${run_date}" +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/predict_modality/results/${RUN_ID}" cat > /tmp/params.yaml << HERE id: predict_modality From 251aa07f0fcd742ca8323c5b45ea5389abf56b75 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 22 Dec 2023 22:19:35 +0100 Subject: [PATCH 1105/1233] let script automatically detect latest results Former-commit-id: da928eba398fb3998c2961bbf1628709c1ec56a2 --- src/common/process_task_results/run/run_test.sh | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/src/common/process_task_results/run/run_test.sh b/src/common/process_task_results/run/run_test.sh index fa5067d6f1..045183a04e 100755 --- a/src/common/process_task_results/run/run_test.sh +++ b/src/common/process_task_results/run/run_test.sh @@ -7,15 +7,14 @@ set -e REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" -# settings -TASK="denoising" -TASK="dimensionality_reduction" -TASK="batch_integration" -TASK="label_projection" -DATE="20231220" - for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_projection"; do - INPUT_DIR="s3://openproblems-data/resources/$TASK/results/$DATE" +# for TASK in "label_projection"; do + BASE_DIR="s3://openproblems-data/resources/$TASK/results/" + + # find subdir in bucket with latest date + DATE=$(aws s3 ls $BASE_DIR | awk '{print $2}' | grep 'run_' | sort -r | head -n 1 | sed 's/\///') + + INPUT_DIR="$BASE_DIR/$DATE" OUTPUT_DIR="../website/results/$TASK/data" # # temp sync From 615489ef84d57d461c8facdd79fb1e1504241383 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 23 Dec 2023 20:56:52 +0100 Subject: [PATCH 1106/1233] Multiple fixes (#326) * fix typo in distance_correlation and output format * use trycatch to resolve any format issues Former-commit-id: c0dd4c4faae485938cadf7d9ca5635712b27c1dd --- .../process_task_results/get_results/script.R | 19 +++++++++++++------ .../metrics/distance_correlation/script.py | 10 +++++----- 2 files changed, 18 insertions(+), 11 deletions(-) diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index ddfa30d37d..c88b97f98c 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -9,19 +9,26 @@ library(purrr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START +dir <- "resources/dimensionality_reduction/results/run_2023-12-22_13-08-31" par <- list( - input_scores = "output/temp/score_uns.yaml", - input_execution = "output/temp/trace.txt", + input_scores = paste0(dir, "/score_uns.yaml"), + input_execution = paste0(dir, "/trace.txt"), output = "output/results.json" ) ## VIASH END # read scores -raw_scores <- yaml::yaml.load_file(par$input_scores) %>% +raw_scores <- + yaml::yaml.load_file(par$input_scores) %>% map_df(function(x) { - as_tibble(as.data.frame( - x[c("dataset_id", "method_id", "metric_ids", "metric_values")] - )) + tryCatch({ + as_tibble(as.data.frame( + x[c("dataset_id", "method_id", "metric_ids", "metric_values")] + )) + }, error = function(e) { + message("Encountered error while reading scores: ", e$message) + NULL + }) }) # scale scores diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py b/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py index d461f271b4..5d8e325126 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/script.py @@ -9,8 +9,8 @@ ## VIASH START par = { - "input_embedding": "resources_test/dimensionality_reduction/pancreas/reduced.h5ad", - "input_solution": "resources_test/dimensionality_reduction/pancreas/test.h5ad", + "input_embedding": "resources_test/dimensionality_reduction/pancreas/embedding.h5ad", + "input_solution": "resources_test/dimensionality_reduction/pancreas/solution.h5ad", "output": "score.h5ad", } ## VIASH END @@ -33,7 +33,7 @@ def _distance_correlation(X, X_emb): print("Compute NNLS residual after SVD", flush=True) n_svd = 500 svd_emb = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(high_dim) -dist_corr = _distance_correlation(svd_emb, X_emb) +dist_corr = _distance_correlation(svd_emb, X_emb).correlation #! Explicitly not changing it to use diffusion map method as this will have a positive effect on the diffusion map method for this specific metric. print("Compute NLSS residual after spectral embedding", flush=True) @@ -42,7 +42,7 @@ def _distance_correlation(X, X_emb): spectral_emb = umap.spectral.spectral_layout( high_dim, umap_graph, n_comps, random_state=np.random.default_rng() ) -dist_corr_spectral = _distance_correlation(spectral_emb, X_emb) +dist_corr_spectral = _distance_correlation(spectral_emb, X_emb).correlation print("Create output AnnData object", flush=True) output = ad.AnnData( @@ -50,7 +50,7 @@ def _distance_correlation(X, X_emb): "dataset_id": input_solution.uns["dataset_id"], "normalization_id": input_solution.uns["normalization_id"], "method_id": input_embedding.uns["method_id"], - "metric_ids": [ "distance correlation", "distance_correlation_spectral" ], + "metric_ids": [ "distance_correlation", "distance_correlation_spectral" ], "metric_values": [ dist_corr, dist_corr_spectral ] } ) From 83cb14cdd672aedf5fc0e4e7d8ae6e5337081b79 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 8 Jan 2024 11:55:27 +0100 Subject: [PATCH 1107/1233] also add motivation to the description (#327) Former-commit-id: ed44af5f1c12e7cea7712a0db5a18ee36b0ce2e4 --- src/common/process_task_results/get_task_info/script.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/process_task_results/get_task_info/script.R b/src/common/process_task_results/get_task_info/script.R index 0848dd98bc..16137707fb 100644 --- a/src/common/process_task_results/get_task_info/script.R +++ b/src/common/process_task_results/get_task_info/script.R @@ -19,7 +19,7 @@ out <- list( commit_sha = NA_character_, task_name = info$label, task_summary = info$summary, - task_description = info$description, + task_description = paste0(info$motivation, "\n\n", info$description), repo = "openproblems-bio/openproblems-v2" ) From 3fe75b5f432c9dcb9c64e81bc312d5b21787ea4f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 9 Jan 2024 10:36:24 +0100 Subject: [PATCH 1108/1233] Fix v2 quality control results (#329) * add exception for paper_reference in baseline methods * update pynndescent to atleast 0.5.11 * update pynndescent * set highmem for simlr method Former-commit-id: 164e45ab38ac201dae9d6797f14b1b9a5b84d811 --- src/common/process_task_results/generate_qc/script.py | 9 ++++++++- .../methods/densmap/config.vsh.yaml | 2 +- .../methods/simlr/config.vsh.yaml | 2 +- .../methods/umap/config.vsh.yaml | 2 +- .../metrics/density_preservation/config.vsh.yaml | 1 + .../metrics/distance_correlation/config.vsh.yaml | 1 + 6 files changed, 13 insertions(+), 4 deletions(-) diff --git a/src/common/process_task_results/generate_qc/script.py b/src/common/process_task_results/generate_qc/script.py index a2f20979d1..f15a877522 100644 --- a/src/common/process_task_results/generate_qc/script.py +++ b/src/common/process_task_results/generate_qc/script.py @@ -55,7 +55,14 @@ def add_qc( }) def percent_missing(list_of_dicts, field): - are_missing = [0.0 if field in item and item[field] is not None else 1.0 for item in list_of_dicts] + are_missing = [] + for item in list_of_dicts: + if field == 'paper_reference' and item.get('is_baseline', False): + are_missing.append(0.0) + elif field in item and item[field] is not None: + are_missing.append(0.0) + else: + are_missing.append(1.0) return np.mean(are_missing) # check task_info diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index ef539de6fb..cea27da3e0 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -38,7 +38,7 @@ platforms: - type: python packages: - umap-learn - - pynndescent==0.5.8 + - pynndescent==0.5.11 - type: native - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml index 2cff2a4a65..9157634498 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -54,4 +54,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 4de3253c9b..e5be09b66f 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -44,7 +44,7 @@ platforms: - type: python packages: - umap-learn - - pynndescent==0.5.8 + - pynndescent==0.5.11 - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 168531b210..0d0de7dfd6 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -37,6 +37,7 @@ platforms: - scipy - numpy - umap-learn + - pynndescent~=0.5.11 - type: nextflow directives: label: [ "midtime", lowmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index b7ff90bf28..9e005e22bd 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -43,6 +43,7 @@ platforms: - umap-learn - scikit-learn - numpy + - pynndescent~=0.5.11 - scipy - type: nextflow directives: From af7deb6300c51eac2525377a56d9a47169906371 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 17 Jan 2024 16:37:33 +0100 Subject: [PATCH 1109/1233] disable scanvi for now (#336) Former-commit-id: 27fa512d096c45c0d154bee5a76bcb6109769bf2 --- src/tasks/label_projection/methods/scanvi/config.vsh.yaml | 1 + .../label_projection/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/label_projection/workflows/run_benchmark/main.nf | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 3d29e25549..091766c6eb 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -1,6 +1,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" + status: disabled info: label: SCANVI summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 28c5261ef4..10520efdda 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -62,7 +62,7 @@ functionality: - name: label_projection/methods/knn - name: label_projection/methods/logistic_regression - name: label_projection/methods/mlp - - name: label_projection/methods/scanvi + # - name: label_projection/methods/scanvi - name: label_projection/methods/scanvi_scarches - name: label_projection/methods/xgboost - name: label_projection/metrics/accuracy diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index 4e9ba0c082..8df7cfa2df 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -19,7 +19,7 @@ workflow run_wf { knn, logistic_regression, mlp, - scanvi, + // scanvi, scanvi_scarches, // seurat_transferdata, xgboost From aa5920902d2a2503f7f2632fc3506bbffa0cbc14 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 17 Jan 2024 17:05:34 +0100 Subject: [PATCH 1110/1233] try to fix scanvi (#337) Former-commit-id: f4773e880a9f052245db70425efdc1bc64cbf176 --- src/tasks/label_projection/methods/scanvi/config.vsh.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 091766c6eb..43c031bfb4 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -1,7 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" - status: disabled info: label: SCANVI summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." @@ -33,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: nvcr.io/nvidia/pytorch:22.12-py3 + image: nvcr.io/nvidia/pytorch:23.12-py3 setup: - type: python packages: From 35bb82aa67efe607beec5c231cd24760acf93066 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 17 Jan 2024 17:06:00 +0100 Subject: [PATCH 1111/1233] fix neurips2021 wf and script (#333) * fix neurips2021 wf and script * refactor script Former-commit-id: 3a21a29a11985fc63821496ae64b3d44fdfc9ed6 --- src/common/decompress_gzip/config.vsh.yaml | 25 ++++++++ src/common/decompress_gzip/script.sh | 3 + src/common/decompress_gzip/test.sh | 22 +++++++ src/common/library.bib | 2 +- .../openproblems_neurips2021_bmmc/script.py | 47 +++++++-------- .../openproblems_neurips2021_multimodal.sh | 57 ++++++++----------- .../config.vsh.yaml | 1 + .../main.nf | 26 +++++++-- 8 files changed, 115 insertions(+), 68 deletions(-) create mode 100644 src/common/decompress_gzip/config.vsh.yaml create mode 100644 src/common/decompress_gzip/script.sh create mode 100644 src/common/decompress_gzip/test.sh mode change 100644 => 100755 src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh diff --git a/src/common/decompress_gzip/config.vsh.yaml b/src/common/decompress_gzip/config.vsh.yaml new file mode 100644 index 0000000000..751d31a162 --- /dev/null +++ b/src/common/decompress_gzip/config.vsh.yaml @@ -0,0 +1,25 @@ +functionality: + name: decompress_gzip + namespace: common + arguments: + - name: --input + type: file + description: Input file + example: /path/to/file.gz + - name: --output + type: file + description: Output file + example: /path/to/file + direction: output + resources: + - type: bash_script + path: script.sh + test_resources: + - type: bash_script + path: test.sh +platforms: + - type: docker + image: ubuntu:latest + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/common/decompress_gzip/script.sh b/src/common/decompress_gzip/script.sh new file mode 100644 index 0000000000..f0486b6068 --- /dev/null +++ b/src/common/decompress_gzip/script.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +gunzip "$par_input" -c > "$par_output" \ No newline at end of file diff --git a/src/common/decompress_gzip/test.sh b/src/common/decompress_gzip/test.sh new file mode 100644 index 0000000000..17bb20afbf --- /dev/null +++ b/src/common/decompress_gzip/test.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +set -e + +## VIASH START +## VIASH END + +echo "> Creating test file" +echo "Foo bar" > uncompressed.txt + +echo "> Compressing file" +gzip uncompressed.txt -c > compressed.txt.gz + +echo "> Decompressing file" +"$meta_executable" \ + --input "compressed.txt.gz" \ + --output "decompressed.txt" + +echo "> Comparing files" +diff uncompressed.txt decompressed.txt + +echo "> Test succeeded!" \ No newline at end of file diff --git a/src/common/library.bib b/src/common/library.bib index 98a17ecd9d..c3e35dfaa9 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -964,7 +964,7 @@ @article{nestorowa2016single url = {https://doi.org/10.1182/blood-2016-05-716480} } -@inproceedings{neurips, +@inproceedings{luecken2021neurips, author = {Luecken, Malte and Burkhardt, Daniel and Cannoodt, Robrecht and Lance, Christopher and Agrawal, Aditi and Aliee, Hananeh and Chen, Ann and Deconinck, Louise and Detweiler, Angela and Granados, Alejandro and Huynh, Shelly and Isacco, Laura and Kim, Yang and Klein, Dominik and DE KUMAR, BONY and Kuppasani, Sunil and Lickert, Heiko and McGeever, Aaron and Melgarejo, Joaquin and Mekonen, Honey and Morri, Maurizio and M\"{u}ller, Michaela and Neff, Norma and Paul, Sheryl and Rieck, Bastian and Schneider, Kaylie and Steelman, Scott and Sterr, Michael and Treacy, Daniel and Tong, Alexander and Villani, Alexandra-Chloe and Wang, Guilin and Yan, Jia and Zhang, Ce and Pisco, Angela and Krishnaswamy, Smita and Theis, Fabian and Bloom, Jonathan M}, booktitle = {Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks}, editor = {J. Vanschoren and S. Yeung}, diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index 7cae5abe0f..f24ea795a0 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -1,13 +1,11 @@ import anndata as ad import pandas as pd - ## VIASH START -# The following code has been auto-generated by Viash. par = { - "input": "resources/datasets/multimodal/cite_BMMC_processed.h5ad", + "input": "bmmc_multiome.decompress_gzip.h5ad", "mod1": "GEX", - "mod2": "ADT", + "mod2": "ATAC", "dataset_name": "BMMC (CITE-seq)", "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122", "dataset_reference": "Neurips", @@ -21,47 +19,38 @@ "functionality_name": "openproblems_neurips2021_bmmc", "resources_dir": "/tmp/viash_inject_openproblems_neurips2021_bmmc14365472827677740971", } - ## VIASH END -def remove_other_mod_col (df, mod): - +def remove_other_mod_col(df, mod): df.drop(list(df.filter(like=mod)), axis=1, inplace=True) - return df - -def remove_mod_prefix (df, mod): - +def remove_mod_prefix(df, mod): suffix = f"{mod}_" df.columns = df.columns.str.removeprefix(suffix) - return df - print("load dataset file", flush=True) -adata= ad.read_h5ad(par["input"]) - -# make var names unique -adata.var_names_make_unique() +adata = ad.read_h5ad(par["input"]) # Construct Modality datasets print("Construct Mod datasets", flush=True) - mask_mod1 = adata.var['feature_types'] == par["mod1"] mask_mod2 = adata.var['feature_types'] == par["mod2"] - adata_mod1 = adata[:, mask_mod1] adata_mod2 = adata[:, mask_mod2] # Remove other modality data from obs and var mod1_var = pd.DataFrame(adata_mod1.var) -mod1_var = remove_other_mod_col(mod1_var, par["mod2"]) -mod1_var = remove_mod_prefix(mod1_var, par["mod1"]) +remove_other_mod_col(mod1_var, par["mod2"]) +remove_mod_prefix(mod1_var, par["mod1"]) +mod1_var.index.name = "gene_symbol" +mod1_var.reset_index("gene_symbol", inplace=True) +mod1_var.set_index("gene_id", inplace=True) mod1_obs = pd.DataFrame(adata_mod1.obs) -mod1_obs = remove_other_mod_col(mod1_obs, par["mod2"]) -mod1_obs = remove_mod_prefix(mod1_obs, par["mod1"]) +remove_other_mod_col(mod1_obs, par["mod2"]) +remove_mod_prefix(mod1_obs, par["mod1"]) adata_mod1.var = mod1_var adata_mod1.obs = mod1_obs @@ -71,12 +60,16 @@ def remove_mod_prefix (df, mod): del adata_mod1.X mod2_var = pd.DataFrame(adata_mod2.var) -mod2_var = remove_other_mod_col(mod2_var, par["mod1"]) -mod2_var = remove_mod_prefix(mod2_var, par["mod2"]) +remove_other_mod_col(mod2_var, par["mod1"]) +remove_mod_prefix(mod2_var, par["mod2"]) +mod2_var.gene_id = mod2_var.index.values +mod2_var.index.name = "gene_symbol" +mod2_var.reset_index("gene_symbol", inplace=True) +mod2_var.set_index("gene_id", inplace=True) mod2_obs = pd.DataFrame(adata_mod2.obs) -mod2_obs = remove_other_mod_col(mod2_obs, par["mod1"]) -mod2_obs = remove_mod_prefix(mod2_obs, par["mod2"]) +remove_other_mod_col(mod2_obs, par["mod1"]) +remove_mod_prefix(mod2_obs, par["mod2"]) adata_mod2.var = mod2_var adata_mod2.obs = mod2_obs diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh old mode 100644 new mode 100755 index 96c07c758b..d5a04029da --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -1,55 +1,44 @@ #!/bin/bash -wget "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" \ - -O "/tmp/neurips2021_bmmc_cite.h5ad.gz" +params_file="/tmp/datasets_openproblems_neurips2021_params.yaml" -gunzip "/tmp/neurips2021_bmmc_cite.h5ad.gz" - -wget "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" \ - -O "/tmp/neurips2021_bmmc_multiome.h5ad.gz" - -gunzip "/tmp/neurips2021_bmmc_multiome.h5ad.gz" - - - -params_file="/tmp/datasets_openproblems_nuerips2021_params.yaml" - - - -cat > "$params_file" << HERE +cat > "$params_file" << 'HERE' param_list: - id: openproblems_neurips2021/bmmc_cite - input: "/tmp/neurips2021_bmmc_cite.h5ad" + # input: "/tmp/neurips2021_bmmc_cite.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" mod1: GEX mod2: ADT - dataset_name: bmmc (CITE-Seq) + dataset_name: OpenProblems NeurIPS2021 CITE-Seq dataset_organism: homo_sapiens - dataset_summary: "Short Summary." - dataset_description: "Full description." + dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." - id: openproblems_neurips2021/bmmc_multiome - input: "/tmp/neurips2021_bmmc_multiome.h5ad" + # input: "/tmp/neurips2021_bmmc_multiome.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" mod1: GEX mod2: ATAC - dataset_name: bmmc (Multiome) + dataset_name: OpenProblems NeurIPS2021 Multiome dataset_organism: homo_sapiens - dataset_summary: "Short Summary." - dataset_description: "Full description." + dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" -dataset_reference: neurips +dataset_reference: luecken2021neurips +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_rna: '$id/dataset_rna.had' output_other_mod: '$id/dataset_other_mod.h5ad' output_meta_rna: '$id/dataset_metadata_rna.yaml' output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' -output_state: '$id/state.yaml +output_state: '$id/state.yaml' +publish_dir: s3://openproblems-data/resources/datasets HERE -export NXF_VER=23.04.2 -nextflow run . \ - -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ - -profile docker \ - -resume \ - -params-file "$params_file" \ - --publish_dir "resources/datasets/openproblems_neurips2021" - +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml index 4d09936a4e..ee614f819c 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml @@ -127,6 +127,7 @@ functionality: - name: datasets/processors/svd - name: datasets/processors/hvg - name: common/check_dataset_schema + - name: common/decompress_gzip # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index 99800eacaa..cf9bb95e49 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -39,10 +39,15 @@ workflow run_wf { [id, state + [_meta: [join_id: id]]] } + | decompress_gzip.run( + fromState: ["input": "input"], + toState: ["input_decompressed": "output"] + ) + // process neurips downloaded dataset | openproblems_neurips2021_bmmc.run( fromState: [ - "input": "input", + "input": "input_decompressed", "mod1": "mod1", "mod2": "mod2", "dataset_name": "dataset_name", @@ -101,11 +106,17 @@ workflow run_wf { ) // run normalization methods on second modality - | runEach( - components: normalization_methods, - filter: { id, state, comp -> - comp.name == state.normalization_id - }, + | log_cp.run( + key: "log_cp10k_adt", + runIf: { id, state -> state.mod2 == "ADT" }, + args: [normalization_id: "log_cp10k", n_cp: 10000] + fromState: ["input": "raw_other_mod"], + toState: ["normalized_other_mod": "output"] + ) + | normalization_methods[0].run( // TODO: change this normalization method + key: "log_cp10k_atac", + runIf: { id, state -> state.mod2 == "ATAC" }, + args: [normalization_id: "log_cp10k", n_cp: 10000] fromState: ["input": "raw_other_mod"], toState: ["normalized_other_mod": "output"] ) @@ -126,7 +137,9 @@ workflow run_wf { toState: [ "hvg_rna": "output" ] ) + // TODO: should this only run on ATAC? or even not at all?s | hvg.run( + key: "hvg_other_mod", fromState: [ "input": "svd_other_mod" ], toState: [ "hvg_other_mod": "output" ] ) @@ -145,6 +158,7 @@ workflow run_wf { ) | check_dataset_schema.run( + key: "check_dataset_schema_other_mod", fromState: { id, state -> [ "input": state.hvg_other_mod, From 24261cd24776f14d6bbdf35757f3e27e7d1b3b2a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 17 Jan 2024 22:36:33 +0100 Subject: [PATCH 1112/1233] Bump actions/cache from 3 to 4 (#340) Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: dd7ec7738a2bba1db6543465d371cb0fe398edfc --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 4 ++-- .github/workflows/viash-test.yml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 59f8fb2d75..87c482649c 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -144,7 +144,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index b9c771838a..8452d28638 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -171,7 +171,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test @@ -207,7 +207,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 5 with: path: resources_test diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index a2b22dd142..03b90d2725 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -98,7 +98,7 @@ jobs: # use cache - name: Cache resources data - uses: actions/cache@v3 + uses: actions/cache@v4 timeout-minutes: 10 with: path: resources_test From af44bf2eb016866b64e882e946559c5d2a9e1d1f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 17 Jan 2024 22:37:02 +0100 Subject: [PATCH 1113/1233] Bump tj-actions/changed-files from 40 to 41 (#328) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 40 to 41. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v40...v41) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 112bcbf57ced16d81b3e6212776897d6a5621536 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 03b90d2725..6496d6ba06 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v40 + uses: tj-actions/changed-files@v41 with: separator: ";" diff_relative: true From 80909ee22bcc1bb1268bb50fcaeee6c0504aa3c9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 18 Jan 2024 11:43:32 +0100 Subject: [PATCH 1114/1233] fix neurips2021 wf Former-commit-id: cb7f74f2a8e85d66de8e9c1c70cf909dea5135a4 --- ...penproblems_neurips2021_multimodal_test.sh | 43 +++++++++++++++++++ .../main.nf | 7 +-- 2 files changed, 47 insertions(+), 3 deletions(-) create mode 100755 src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh new file mode 100755 index 0000000000..0aa5ba3228 --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +params_file="/tmp/datasets_openproblems_neurips2021_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_neurips2021/bmmc_cite + # input: "/tmp/neurips2021_bmmc_cite.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" + mod1: GEX + mod2: ADT + dataset_name: OpenProblems NeurIPS2021 CITE-Seq + dataset_organism: homo_sapiens + dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + + - id: openproblems_neurips2021/bmmc_multiome + # input: "/tmp/neurips2021_bmmc_multiome.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" + mod1: GEX + mod2: ATAC + dataset_name: OpenProblems NeurIPS2021 Multiome + dataset_organism: homo_sapiens + dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + +dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" +dataset_reference: luecken2021neurips +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_rna: '$id/dataset_rna.had' +output_other_mod: '$id/dataset_other_mod.h5ad' +output_meta_rna: '$id/dataset_metadata_rna.yaml' +output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_state: '$id/state.yaml' +publish_dir: resources/datasets/openproblems_neurips2021 +HERE + +export NXF_VER=23.10.1 +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + -profile docker \ + -resume \ + -params-file "$params_file" diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index cf9bb95e49..30bfd28ce3 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -106,17 +106,18 @@ workflow run_wf { ) // run normalization methods on second modality + // TODO: change this normalization method | log_cp.run( key: "log_cp10k_adt", runIf: { id, state -> state.mod2 == "ADT" }, - args: [normalization_id: "log_cp10k", n_cp: 10000] + args: [normalization_id: "log_cp10k", n_cp: 10000], fromState: ["input": "raw_other_mod"], toState: ["normalized_other_mod": "output"] ) - | normalization_methods[0].run( // TODO: change this normalization method + | log_cp.run( key: "log_cp10k_atac", runIf: { id, state -> state.mod2 == "ATAC" }, - args: [normalization_id: "log_cp10k", n_cp: 10000] + args: [normalization_id: "log_cp10k", n_cp: 10000], fromState: ["input": "raw_other_mod"], toState: ["normalized_other_mod": "output"] ) From baf693fa5c8795f0148ab84eddd1b64517491661 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 19 Jan 2024 09:58:53 +0100 Subject: [PATCH 1115/1233] fix workflow scripts Former-commit-id: 29b788e96e4e2db4b57677a6c3aeb431fe64082e --- .../openproblems_neurips2021_multimodal.sh | 12 +++++++++++- .../resources_scripts/process_datasets.sh | 13 +++++++++---- 2 files changed, 20 insertions(+), 5 deletions(-) diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index d5a04029da..57c8747452 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -35,10 +35,20 @@ output_state: '$id/state.yaml' publish_dir: s3://openproblems-data/resources/datasets HERE +cat > /tmp/nextflow.config << HERE +process { + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } +} +HERE + tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ - --params-file "$params_file" \ \ No newline at end of file + --params-file "$params_file" \ + --config /tmp/nextflow.config diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 8c69d24420..b80096a88a 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -2,16 +2,20 @@ cat > /tmp/params.yaml << 'HERE' id: predict_modality_process_datasets -input_states: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal/**/state.yaml -rename_keys: 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' +input_states: s3://openproblems-data/resources/datasets/**/state.yaml +rename_keys: 'input_rna:output_rna,input_other_mod:output_other_mod' settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' output_state: "$id/state.yaml" -publish_dir: s3://openproblems-data/resources/predict_modality/datasets/openproblems_v1 +publish_dir: s3://openproblems-data/resources/predict_modality/datasets HERE cat > /tmp/nextflow.config << HERE process { executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } } HERE @@ -23,4 +27,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels predict_modality,process_datasets \ No newline at end of file From 9f664b897a72a256b02fad2bba1103fd692d1fce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 23 Jan 2024 10:36:06 +0100 Subject: [PATCH 1116/1233] Bump nf-core/setup-nextflow from 1.4.0 to 1.5.0 (#343) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.4.0 to 1.5.0. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.4.0...v1.5.0) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 99fb3cce873533c810ed95a4ed60cb9ee7813961 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 87c482649c..b9863d1480 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -132,7 +132,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.4.0 + - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 8452d28638..99901cc88c 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -159,7 +159,7 @@ jobs: - uses: viash-io/viash-actions/setup@v4 - - uses: nf-core/setup-nextflow@v1.4.0 + - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from release branch, hopefully these are available From f4355350b723ec3abfecc1ebe4ed9f4770affbd5 Mon Sep 17 00:00:00 2001 From: Vishnuvasan Raghuraman <58689453+vishnu-vasan@users.noreply.github.com> Date: Tue, 23 Jan 2024 09:04:07 -0500 Subject: [PATCH 1117/1233] added new method: naive bayes (#334) Co-authored-by: vishnu-vasan Former-commit-id: 90c008aaf825950cf666a2c2758309652781a129 --- .../methods/naive_bayes/config.vsh.yaml | 33 +++++++++++++++++++ .../methods/naive_bayes/script.py | 28 ++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml create mode 100644 src/tasks/label_projection/methods/naive_bayes/script.py diff --git a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml new file mode 100644 index 0000000000..8989974c9d --- /dev/null +++ b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml @@ -0,0 +1,33 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: "naive_bayes" + info: + label: Naive Bayesian Classifier + summary: "Naive Bayes classification using feature probabilities to project cell type labels from a reference dataset." + description: | + Naive Bayes classification leverages probabilistic models based on Bayes' theorem + to classify cells into different types. In the context of single-cell datasets, this method + utilizes the probabilities of features to project cell type labels from a reference dataset + to new datasets. The algorithm assumes independence between features, making it computationally + efficient and well-suited for high-dimensional data. It is particularly useful for annotating + cells in atlas-scale datasets, ensuring consistency and alignment with existing reference annotations. + reference: "hosmer2013applied" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.naive_bayes.GaussianNB.html" + preferred_normalization: log_cp10k + variants: + naive_bayes_log_cp10k: + naive_bayes_scran: + preferred_normalization: log_scran_pooling + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: scikit-learn + - type: nextflow + directives: + label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/label_projection/methods/naive_bayes/script.py b/src/tasks/label_projection/methods/naive_bayes/script.py new file mode 100644 index 0000000000..542c088dca --- /dev/null +++ b/src/tasks/label_projection/methods/naive_bayes/script.py @@ -0,0 +1,28 @@ +import anndata as ad +import sklearn.naive_bayes + +## VIASH START +par = { + 'input_train': 'resources_test/label_projection/pancreas/train.h5ad', + 'input_test': 'resources_test/label_projection/pancreas/test.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'foo', +} +## VIASH END + +print("Load input data", flush=True) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) + +print("Fit to train data", flush=True) +classifier = sklearn.naive_bayes.GaussianNB() +classifier.fit(input_train.obsm["X_pca"], input_train.obs["label"].astype(str)) + +print("Predict on test data", flush=True) +input_test.obs["label_pred"] = classifier.predict(input_test.obsm["X_pca"]) + +print("Write output to file", flush=True) +input_test.uns["method_id"] = meta["functionality_name"] +input_test.write_h5ad(par['output'], compression="gzip") \ No newline at end of file From 22e2d562c111b12c86b4aad37a5d871303408ef6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 23 Jan 2024 15:23:42 +0100 Subject: [PATCH 1118/1233] Bump tj-actions/changed-files from 41 to 42 (#341) Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 41 to 42. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v41...v42) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 8ede5332243d2491ff8d68e96a2c14446329e601 --- .github/workflows/viash-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index 6496d6ba06..b128d6984d 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -52,7 +52,7 @@ jobs: - name: Get changed files id: changed-files - uses: tj-actions/changed-files@v41 + uses: tj-actions/changed-files@v42 with: separator: ";" diff_relative: true From e74fa2b907438ed6818c677636d16339b823cae4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 23 Jan 2024 15:23:59 +0100 Subject: [PATCH 1119/1233] time label should be `hightime` not `longtime`. (#344) Former-commit-id: 4e516f11dc3ed253f78d839f2b479a061e9c66a9 --- src/common/comp_tests/check_method_config.py | 2 +- src/common/comp_tests/check_metric_config.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index 2389976518..e20db55d6f 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -15,7 +15,7 @@ _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] -TIME_LABELS = ["lowtime", "midtime", "longtime"] +TIME_LABELS = ["lowtime", "midtime", "hightime"] MEM_LABELS = ["lowmem", "midmem", "highmem"] CPU_LABELS = ["lowcpu", "midcpu", "highcpu"] diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index d6dcd1472e..750caad8ec 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -17,7 +17,7 @@ _MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"] -TIME_LABELS = ["lowtime", "midtime", "longtime"] +TIME_LABELS = ["lowtime", "midtime", "hightime"] MEM_LABELS = ["lowmem", "midmem", "highmem"] CPU_LABELS = ["lowcpu", "midcpu", "highcpu"] From e7d56a15530fcd9b60cdfb0c4ffcd021bab996ea Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 24 Jan 2024 22:40:15 +0100 Subject: [PATCH 1120/1233] Predict modality/fix dataset (#342) * fix typo * fix atac typo * add shape to anndata outputs * update neurips2021 resource_test * fix var$gene_ids * set feature_id and feature_name to true * refactor var.gene_ id to var.feature_id/name * update intersect to feature_id * drop gene_id col * remove space * fix pd col creation * update index * Add workaround for dgCMatrix error Co-authored-by: Robrecht Cannoodt * add workaround to first mod * update test_resource sript predict_modality * refactor train/test set * restore Train/test split * Add train/test * Apply suggestions from code review --------- Co-authored-by: Robrecht Cannoodt Co-authored-by: Robrecht Cannoodt Former-commit-id: 8ac4d2583dd5d47e8925bc33f04850658a99da36 --- src/datasets/api/file_raw.yaml | 4 +- .../openproblems_neurips2021_bmmc/script.py | 33 ++++-- .../openproblems_neurips2021_multimodal.sh | 2 +- ...penproblems_neurips2021_multimodal_test.sh | 2 +- .../resource_test_scripts/neurips2021_bmmc.sh | 111 +++++++++--------- .../neurips2021_bmmc.sh | 16 ++- 6 files changed, 95 insertions(+), 73 deletions(-) diff --git a/src/datasets/api/file_raw.yaml b/src/datasets/api/file_raw.yaml index 56ba539304..76eb6ecaf2 100644 --- a/src/datasets/api/file_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -159,12 +159,12 @@ info: - type: string name: feature_id description: Unique identifier for the feature, usually a ENSEMBL gene id. - required: false + required: true - type: string name: feature_name description: A human-readable name for the feature, usually a gene symbol. - required: false + required: true - type: integer name: soma_joinid diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index f24ea795a0..49b5eb54e7 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -3,7 +3,7 @@ ## VIASH START par = { - "input": "bmmc_multiome.decompress_gzip.h5ad", + "input": "GSE194122_openproblems_neurips2021_cite_BMMC_processed.h5ad", "mod1": "GEX", "mod2": "ATAC", "dataset_name": "BMMC (CITE-seq)", @@ -32,6 +32,14 @@ def remove_mod_prefix(df, mod): print("load dataset file", flush=True) adata = ad.read_h5ad(par["input"]) +# Add is_train to obs +if "is_train" not in adata.obs.columns: + batch_info = adata.obs["batch"] + batch_categories = batch_info.dtype.categories + train = ["s1d1", "s2d1", "s2d4", "s3d6", "s3d1"] + adata.obs["is_train"] = [ x in train for x in batch_info ] + adata.obs["is_train"].replace([True, False], ["train", "test"]) + # Construct Modality datasets print("Construct Mod datasets", flush=True) mask_mod1 = adata.var['feature_types'] == par["mod1"] @@ -44,9 +52,12 @@ def remove_mod_prefix(df, mod): mod1_var = pd.DataFrame(adata_mod1.var) remove_other_mod_col(mod1_var, par["mod2"]) remove_mod_prefix(mod1_var, par["mod1"]) -mod1_var.index.name = "gene_symbol" -mod1_var.reset_index("gene_symbol", inplace=True) -mod1_var.set_index("gene_id", inplace=True) +mod1_var.index.name = "feature_name" +mod1_var["feature_id"] = mod1_var.gene_id +mod1_var.drop("gene_id", axis=1, inplace=True) +if not mod1_var.feature_id.hasnans: + mod1_var.reset_index("feature_name", inplace=True) + mod1_var.set_index("feature_id", drop=False, inplace=True) mod1_obs = pd.DataFrame(adata_mod1.obs) remove_other_mod_col(mod1_obs, par["mod2"]) @@ -62,10 +73,12 @@ def remove_mod_prefix(df, mod): mod2_var = pd.DataFrame(adata_mod2.var) remove_other_mod_col(mod2_var, par["mod1"]) remove_mod_prefix(mod2_var, par["mod2"]) -mod2_var.gene_id = mod2_var.index.values -mod2_var.index.name = "gene_symbol" -mod2_var.reset_index("gene_symbol", inplace=True) -mod2_var.set_index("gene_id", inplace=True) +mod2_var.index.name = "feature_name" +mod2_var["feature_id"] = mod2_var.gene_id +mod2_var.drop("gene_id", axis=1, inplace=True) +if not mod2_var.feature_id.hasnans: + mod2_var.reset_index("feature_name", inplace=True) + mod2_var.set_index("feature_id", drop=False, inplace=True) mod2_obs = pd.DataFrame(adata_mod2.obs) remove_other_mod_col(mod2_obs, par["mod1"]) @@ -76,9 +89,9 @@ def remove_mod_prefix(df, mod): adata_mod2.uns = { key.replace(f"{par['mod2']}_", ""): value for key, value in adata.uns.items() if not key.startswith(par['mod1'])} if par["mod2"] == "ATAC": - adata_mod2.obsm = { key.replace(f"{par['mod2']}_", ""): value for key, value in adata_mod2.uns.items() if key.startswith(par['mod2'])} + adata_mod2.obsm = { key.replace(f"{par['mod2']}_", ""): value for key, value in adata_mod2.obsm.items() if key.startswith(par['mod2'])} else: - del adata_mod2.obsm + del adata_mod2.obsm del adata_mod2.X diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index 57c8747452..97b592413b 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -27,7 +27,7 @@ param_list: dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" dataset_reference: luecken2021neurips normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_rna: '$id/dataset_rna.had' +output_rna: '$id/dataset_rna.h5ad' output_other_mod: '$id/dataset_other_mod.h5ad' output_meta_rna: '$id/dataset_metadata_rna.yaml' output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh index 0aa5ba3228..26631d43d8 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh @@ -27,7 +27,7 @@ param_list: dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" dataset_reference: luecken2021neurips normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_rna: '$id/dataset_rna.had' +output_rna: '$id/dataset_rna.h5ad' output_other_mod: '$id/dataset_other_mod.h5ad' output_meta_rna: '$id/dataset_metadata_rna.yaml' output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index a838f1bec7..af622c7454 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -1,58 +1,61 @@ #!/bin/bash -DATASET_DIR="resources_test/common" - -#make sure the following command has been executed -#viash ns build -q 'datasets|common' --parallel --setup cb - -# get the root of the directory -REPO_ROOT=$(git rev-parse --show-toplevel) - -# ensure that the command below is run from the root of the repository -cd "$REPO_ROOT" - -set -e - -# download full dataset as temp file -mkdir -p "$DATASET_DIR/neurips2021_bmmc_cite" - -INPUT="$DATASET_DIR/neurips2021_bmmc_cite/temp_neurips2021_bmmc_cite.h5ad" -INPUT_URL="https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122&format=file&file=GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" -if [ ! -f "$INPUT" ]; then - echo "Downloading neurips2021_bmmc_cite dataset" - - wget "$INPUT_URL" -O "${INPUT}.gz" - - gunzip "${INPUT}.gz" -fi - - -# download dataset -nextflow run . \ - -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ - -profile docker \ - -c src/wf_utils/labels_ci.config \ - -resume \ - --id neurips2021_bmmc_cite \ - --input "$INPUT" \ - --mod1 "GEX" \ - --mod2 "ADT" \ - --dataset_name "bmcc (CITE-Seq)" \ - --dataset_url "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE194122" \ - --dataset_reference "Neurips" \ - --dataset_summary "neurips small summary" \ - --dataset_description "neurips big description" \ - --do_subsample true \ - --n_obs 600 \ - --n_vars 1500 \ - --seed 123 \ - --normalization_methods log_cp10k \ - --output_rna '$id/dataset_rna.h5ad' \ - --output_other_mod '$id/dataset_other_mod.h5ad' \ - --output_meta_rna '$id/dataset_metadata_rna.yaml' \ - --output_meta_other_mod '$id/dataset_metadata_other_mod.yaml' \ - --output_state '$id/state.yaml' \ - --publish_dir "$DATASET_DIR" +params_file="/tmp/datasets_openproblems_neurips2021_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_neurips2021/bmmc_cite + # input: "/tmp/neurips2021_bmmc_cite.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" + mod1: GEX + mod2: ADT + dataset_name: OpenProblems NeurIPS2021 CITE-Seq + dataset_organism: homo_sapiens + dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + + - id: openproblems_neurips2021/bmmc_multiome + # input: "/tmp/neurips2021_bmmc_multiome.h5ad" + input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" + mod1: GEX + mod2: ATAC + dataset_name: OpenProblems NeurIPS2021 Multiome + dataset_organism: homo_sapiens + dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + +dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" +dataset_reference: luecken2021neurips +normalization_methods: [log_cp10k] +do_subsample: true +n_obs: 600 +n_vars: 1500 +output_rna: '$id/dataset_rna.h5ad' +output_other_mod: '$id/dataset_other_mod.h5ad' +output_meta_rna: '$id/dataset_metadata_rna.yaml' +output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_state: '$id/state.yaml' +publish_dir: s3://openproblems-data/resources_test/common +HERE + +cat > /tmp/nextflow.config << HERE +process { + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } +} +HERE + + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ + --config /tmp/nextflow.config \ + --labels predict_modality # run task process dataset components -src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh \ No newline at end of file +# src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 5756a9fd92..0879426660 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -19,7 +19,7 @@ nextflow run . \ -profile docker \ -entry auto \ -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/**/state.yaml" \ + --input_states "resources_test/common/openproblems_neurips2021/**/state.yaml" \ --rename_keys 'input_rna:output_rna,input_other_mod:output_other_mod' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ @@ -27,7 +27,13 @@ nextflow run . \ echo "Run one method" viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/neurips2021_bmmc_cite/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/neurips2021_bmmc_cite/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/neurips2021_bmmc_cite/test_mod1.h5ad \ - --output $OUTPUT_DIR/neurips2021_bmmc_cite/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/prediction.h5ad + +viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/prediction.h5ad From 41a8cebdc387f143f69d43365edce49bcb22c0fe Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 27 Jan 2024 06:27:18 +0100 Subject: [PATCH 1121/1233] Bump viash-io/viash-actions from 4 to 5 (#348) Bumps [viash-io/viash-actions](https://github.com/viash-io/viash-actions) from 4 to 5. - [Release notes](https://github.com/viash-io/viash-actions/releases) - [Changelog](https://github.com/viash-io/viash-actions/blob/main/CHANGELOG.md) - [Commits](https://github.com/viash-io/viash-actions/compare/v4...v5) --- updated-dependencies: - dependency-name: viash-io/viash-actions dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 1ddceb95ff08d0b8fad7373939788f557a0cec0d --- .github/workflows/integration-test.yml | 18 +++++++++--------- .github/workflows/main-build.yml | 12 ++++++------ .github/workflows/release-build.yml | 26 +++++++++++++------------- .github/workflows/viash-test.yml | 10 +++++----- 4 files changed, 33 insertions(+), 33 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index b9863d1480..54989e21be 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -17,9 +17,9 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5 id: cache with: s3_bucket: $s3_bucket @@ -31,7 +31,7 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v4 + - uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'integration_build' parallel: true @@ -45,7 +45,7 @@ jobs: exclude_assets: '' - id: ns_list - uses: viash-io/viash-actions/ns-list@v4 + uses: viash-io/viash-actions/ns-list@v5 with: platform: docker src: src @@ -87,10 +87,10 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - name: Build container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'integration_build' setup: build @@ -104,7 +104,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'integration_build' platform: docker @@ -130,14 +130,14 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from integration_build branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: ".functionality.version := 'integration_build'" parallel: true diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index b45aaafe29..ba1872afa8 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -16,14 +16,14 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - name: Remove target folder from .gitignore run: | # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v4 + - uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'main_build' parallel: true @@ -52,7 +52,7 @@ jobs: publish_branch: main_build - id: ns_list - uses: viash-io/viash-actions/ns-list@v4 + uses: viash-io/viash-actions/ns-list@v5 with: platform: docker src: src @@ -84,10 +84,10 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - name: Build container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -102,7 +102,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'main_build' platform: docker diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 99901cc88c..41983303b9 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -22,9 +22,9 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5 id: cache with: s3_bucket: $s3_bucket @@ -36,13 +36,13 @@ jobs: # allow publishing the target folder sed -i '/^target.*/d' .gitignore - - uses: viash-io/viash-actions/ns-build@v4 + - uses: viash-io/viash-actions/ns-build@v5 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true - name: Build nextflow schemas - uses: viash-io/viash-actions/pro/build-nextflow-schemas@v4 + uses: viash-io/viash-actions/pro/build-nextflow-schemas@v5 with: workflows: src components: src @@ -50,7 +50,7 @@ jobs: tools_version: 'main_build' - name: Build parameter files - uses: viash-io/viash-actions/pro/build-nextflow-params@v4 + uses: viash-io/viash-actions/pro/build-nextflow-params@v5 with: workflows: src components: src @@ -66,14 +66,14 @@ jobs: full_commit_message: "Deploy for release ${{ github.event.inputs.version_tag }} from ${{ github.sha }}" - id: ns_list_components - uses: viash-io/viash-actions/ns-list@v4 + uses: viash-io/viash-actions/ns-list@v5 with: platform: docker src: src format: json - id: ns_list_workflows - uses: viash-io/viash-actions/ns-list@v4 + uses: viash-io/viash-actions/ns-list@v5 with: src: workflows format: json @@ -113,10 +113,10 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - name: Build container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := 'main_build' platform: docker @@ -131,7 +131,7 @@ jobs: password: ${{ secrets.GTHB_PAT }} - name: Push container - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: .functionality.version := '${{ github.event.inputs.version_tag }}' platform: docker @@ -157,14 +157,14 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - uses: nf-core/setup-nextflow@v1.5.0 # build target dir # use containers from release branch, hopefully these are available - name: Build target dir - uses: viash-io/viash-actions/ns-build@v4 + uses: viash-io/viash-actions/ns-build@v5 with: config_mod: ".functionality.version := '${{ github.event.inputs.version_tag }}'" parallel: true @@ -203,7 +203,7 @@ jobs: steps: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 # use cache - name: Cache resources data diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index b128d6984d..bc4ba928ab 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -41,9 +41,9 @@ jobs: with: fetch-depth: 0 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 - - uses: viash-io/viash-actions/project/sync-and-cache-s3@v4 + - uses: viash-io/viash-actions/project/sync-and-cache-s3@v5 id: cache with: s3_bucket: $s3_bucket @@ -58,13 +58,13 @@ jobs: diff_relative: true - id: ns_list - uses: viash-io/viash-actions/ns-list@v4 + uses: viash-io/viash-actions/ns-list@v5 with: platform: docker format: json - id: ns_list_filtered - uses: viash-io/viash-actions/project/detect-changed-components@v4 + uses: viash-io/viash-actions/project/detect-changed-components@v5 with: input_file: "${{ steps.ns_list.outputs.output_file }}" @@ -94,7 +94,7 @@ jobs: - uses: actions/checkout@v4 - - uses: viash-io/viash-actions/setup@v4 + - uses: viash-io/viash-actions/setup@v5 # use cache - name: Cache resources data From bde12c487ccb8ccbdd8e0c26436dcd861d06d044 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 27 Jan 2024 07:18:03 +0100 Subject: [PATCH 1122/1233] run hvg before pca (#345) * run hvg before pca * kbb component shouldn't need an X * fix script Former-commit-id: 279fe54b17b57a4c942a9972cbbf2cda358f8d8b --- src/datasets/api/comp_processor_hvg.yaml | 2 +- src/datasets/api/comp_processor_knn.yaml | 2 +- src/datasets/api/comp_processor_pca.yaml | 6 +++++- src/datasets/api/comp_processor_svd.yaml | 2 +- src/datasets/processors/hvg/script.py | 6 +++--- src/datasets/processors/knn/script.py | 7 +------ src/datasets/processors/pca/script.py | 4 ++-- src/datasets/processors/svd/script.py | 10 +++++----- src/datasets/resource_test_scripts/pancreas.sh | 2 +- .../workflows/process_cellxgene_census/main.nf | 10 +++++----- src/datasets/workflows/process_openproblems_v1/main.nf | 10 +++++----- 11 files changed, 30 insertions(+), 31 deletions(-) diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index 8a1e263841..3935525f54 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -13,7 +13,7 @@ functionality: __merge__: file_pca.yaml required: true direction: input - - name: "--layer_input" + - name: "--input_layer" type: string default: "normalized" description: Which layer to use as input. diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index d432ed1d9d..1da86f9231 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -13,7 +13,7 @@ functionality: __merge__: file_hvg.yaml required: true direction: input - - name: "--layer_input" + - name: "--input_layer" type: string default: "normalized" description: Which layer to use as input. diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index a90a3efea2..f82419329c 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -13,10 +13,14 @@ functionality: __merge__: file_normalized.yaml required: true direction: input - - name: "--layer_input" + - name: "--input_layer" type: string default: "normalized" description: Which layer to use as input. + - name: "--input_var_features" + type: string + description: Column name in .var matrix that will be used to select which genes to run the PCA on. + default: hvg - name: "--output" direction: output __merge__: file_pca.yaml diff --git a/src/datasets/api/comp_processor_svd.yaml b/src/datasets/api/comp_processor_svd.yaml index 3f92376f8a..91413c2624 100644 --- a/src/datasets/api/comp_processor_svd.yaml +++ b/src/datasets/api/comp_processor_svd.yaml @@ -17,7 +17,7 @@ functionality: __merge__: file_normalized.yaml required: false direction: input - - name: "--layer_input" + - name: "--input_layer" type: string default: "normalized" description: Which layer to use as input. diff --git a/src/datasets/processors/hvg/script.py b/src/datasets/processors/hvg/script.py index dd16f41cf1..60af4317bb 100644 --- a/src/datasets/processors/hvg/script.py +++ b/src/datasets/processors/hvg/script.py @@ -4,7 +4,7 @@ ### VIASH START par = { 'input': 'work/ca/0751ff85df6f9478cb7bda5a705cad/zebrafish.sqrt_cpm.pca.output.h5ad', - 'layer_input': 'normalized', + 'input_layer': 'normalized', 'output': 'dataset.h5ad', 'var_hvg': 'hvg', 'var_hvg_score': 'hvg_score', @@ -16,12 +16,12 @@ adata = sc.read_h5ad(par['input']) print(">> Look for layer", flush=True) -layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] +layer = adata.X if not par['input_layer'] else adata.layers[par['input_layer']] print(">> Run HVG", flush=True) out = sc.pp.highly_variable_genes( adata, - layer=par["layer_input"], + layer=par["input_layer"], n_top_genes=par["num_features"], flavor='cell_ranger', inplace=False diff --git a/src/datasets/processors/knn/script.py b/src/datasets/processors/knn/script.py index 370c8ca2a8..ae364f6ba3 100644 --- a/src/datasets/processors/knn/script.py +++ b/src/datasets/processors/knn/script.py @@ -4,7 +4,7 @@ ### VIASH START par = { 'input': 'work/ca/0751ff85df6f9478cb7bda5a705cad/zebrafish.sqrt_cpm.pca.output.h5ad', - 'layer_input': 'normalized', + 'input_layer': 'normalized', 'output': 'dataset.h5ad', 'key_added': 'knn', 'n_neighbors': 15 @@ -14,9 +14,6 @@ print(">> Load data", flush=True) adata = sc.read(par['input']) -print(">> Look for layer", flush=True) -adata.X = adata.layers[par['layer_input']] - print(">> Run kNN", flush=True) sc.pp.neighbors( adata, @@ -25,8 +22,6 @@ n_neighbors=par['num_neighbors'] ) -del adata.X - print(">> Writing data", flush=True) adata.write_h5ad(par['output']) diff --git a/src/datasets/processors/pca/script.py b/src/datasets/processors/pca/script.py index 0990b97374..d56d376259 100644 --- a/src/datasets/processors/pca/script.py +++ b/src/datasets/processors/pca/script.py @@ -4,7 +4,7 @@ ### VIASH START par = { 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'layer_input': 'log_cp10k', + 'input_layer': 'log_cp10k', 'output': 'dataset.h5ad', 'obsm_embedding': 'X_pca', 'varm_loadings': 'pca_loadings', @@ -17,7 +17,7 @@ adata = sc.read(par['input']) print(">> Look for layer", flush=True) -layer = adata.X if not par['layer_input'] else adata.layers[par['layer_input']] +layer = adata.X if not par['input_layer'] else adata.layers[par['input_layer']] print(">> Run PCA", flush=True) X_pca, loadings, variance, variance_ratio = sc.tl.pca( diff --git a/src/datasets/processors/svd/script.py b/src/datasets/processors/svd/script.py index d474d732ff..8c94be407a 100644 --- a/src/datasets/processors/svd/script.py +++ b/src/datasets/processors/svd/script.py @@ -7,7 +7,7 @@ "input": "resources_test/common/scicar_cell_lines/normalized_mod1.h5ad", "input_mod2": "resources_test/common/scicar_cell_lines/normalized_mod2.h5ad", "output": "output.h5ad", - "layer_input": "normalized", + "input_layer": "normalized", "obsm_embedding": "X_svd", "num_components": 100, } @@ -19,18 +19,18 @@ adata2 = ad.read(par["input_mod2"]) print(">> check parameters", flush=True) -min_list = [par["num_components"], min(adata.layers[par["layer_input"]].shape) - 1] +min_list = [par["num_components"], min(adata.layers[par["input_layer"]].shape) - 1] if par["input_mod2"] is not None: - min_list.append(min(adata2.layers[par["layer_input"]].shape) - 1) + min_list.append(min(adata2.layers[par["input_layer"]].shape) - 1) n_svd = min(min_list) print(">> Run SVD", flush=True) -svd1 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.layers[par["layer_input"]]) +svd1 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata.layers[par["input_layer"]]) if par["input_mod2"] is not None: - svd2 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata2.layers[par["layer_input"]]) + svd2 = sklearn.decomposition.TruncatedSVD(n_svd).fit_transform(adata2.layers[par["input_layer"]]) print(">> Storing output", flush=True) adata.obsm[par["obsm_embedding"]] = svd1 diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 61b12d59f1..dbcbef4f57 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -42,8 +42,8 @@ nextflow run . \ --do_subsample true \ --output_raw '$id/raw.h5ad' \ --output_normalized '$id/normalized.h5ad' \ - --output_pca '$id/pca.h5ad' \ --output_hvg '$id/hvg.h5ad' \ + --output_pca '$id/pca.h5ad' \ --output_knn '$id/knn.h5ad' \ --output_dataset '$id/dataset.h5ad' \ --output_meta '$id/dataset_meta.yaml' \ diff --git a/src/datasets/workflows/process_cellxgene_census/main.nf b/src/datasets/workflows/process_cellxgene_census/main.nf index de0ba94752..886e28a5a0 100644 --- a/src/datasets/workflows/process_cellxgene_census/main.nf +++ b/src/datasets/workflows/process_cellxgene_census/main.nf @@ -106,16 +106,16 @@ workflow run_wf { } ) - | pca.run( - fromState: ["input": "output_normalized"], - toState: ["output_pca": "output" ] - ) - | hvg.run( fromState: ["input": "output_pca"], toState: ["output_hvg": "output"] ) + | pca.run( + fromState: ["input": "output_normalized"], + toState: ["output_pca": "output" ] + ) + | knn.run( fromState: ["input": "output_hvg"], toState: ["output_knn": "output"] diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 0a9d98b3c5..46511536d0 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -104,16 +104,16 @@ workflow run_wf { } ) - | pca.run( - fromState: ["input": "output_normalized"], - toState: ["output_pca": "output" ] - ) - | hvg.run( fromState: ["input": "output_pca"], toState: ["output_hvg": "output"] ) + | pca.run( + fromState: ["input": "output_normalized"], + toState: ["output_pca": "output" ] + ) + | knn.run( fromState: ["input": "output_hvg"], toState: ["output_knn": "output"] From 2d04517ed68206feef2f98bac82c31e9cf700b6d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Sat, 27 Jan 2024 07:21:29 +0100 Subject: [PATCH 1123/1233] return more struct info (#325) * return more struct info * create separte extract metadata comp * extract dataset metadata * overwrite var_names with gene symbols if available under .var["feature_name"] * Refactor file size and creation time in script.py * set feature_names and use for cell cycle score * add scripts for generating test data for cellxgene_census for batch integration task * extend run_an_check_adata.py to allow for more complex test setups (more input files only) * add dataset metadata wf * add description from schema if available * refactor `check_dataset_schema`: don't return metadata * deprecate `extract_scores` * use extract_metadata instead of check_dataset_schema where necessary * fetch argument schema from the config instead of a resource * simplify metadata wf * fix scripts * add missing commas * update extract_metadata so descriptions are included * fix test resource scripts * feature_name is now required * fix refactoring error * subset donor ids * Add script to extract datasets metadate file to website * fix when schema is not defined * Add multimodal dataset api file * remove merge * add method filter * only run on pancreas * if yaml * fix scicar workflow * various fixes * fix test_setup * fix unit test * fix PM test resources * fix scripts & tests * fix paths * remove print * make the `feature_id` column optional * make feature_name optional for now as well * fix loader * download input in test for now * fix paths --------- Co-authored-by: Kai Waldrant Co-authored-by: Michaela Mueller Former-commit-id: 40257613e2a45dba9e2b6afbdad5dd4915843068 --- .../check_dataset_schema/config.vsh.yaml | 18 +- src/common/check_dataset_schema/script.py | 120 +++------ src/common/check_dataset_schema/test.py | 7 +- src/common/comp_tests/run_and_check_adata.py | 107 ++++---- src/common/extract_metadata/config.vsh.yaml | 40 +++ src/common/extract_metadata/script.py | 206 +++++++++++++++ src/common/extract_metadata/test.py | 26 ++ src/common/extract_scores/config.vsh.yaml | 2 +- .../run/config.vsh.yaml | 29 +++ .../process_dataset_metadata/run/main.nf | 17 ++ .../process_dataset_metadata/run/run_test.sh | 40 +++ .../resources_test_scripts/task_metadata.sh | 4 +- src/datasets/api/file_multimodal_dataset.yaml | 243 ++++++++++++++++++ src/datasets/api/file_raw.yaml | 6 +- .../config.vsh.yaml | 4 +- .../openproblems_neurips2021_bmmc/script.py | 20 +- .../openproblems_neurips2021_bmmc/test.py | 24 +- .../loaders/openproblems_v1/script.py | 4 + .../resource_test_scripts/cellxgene_census.sh | 14 - .../cxg_mouse_pancreas_atlas.sh} | 15 +- .../resource_test_scripts/neurips2021_bmmc.sh | 42 +-- .../resource_test_scripts/pancreas.sh | 6 +- .../scicar_cell_lines.sh | 5 +- .../extract_dataset_info/config.vsh.yaml | 2 +- .../workflows/extract_dataset_info/main.nf | 7 +- .../extract_dataset_meta/config.vsh.yaml | 25 ++ .../workflows/extract_dataset_meta/main.nf | 20 ++ .../extract_dataset_meta/run_test.sh | 29 +++ .../process_cellxgene_census/config.vsh.yaml | 3 +- .../process_cellxgene_census/main.nf | 23 +- .../config.vsh.yaml | 9 +- .../main.nf | 42 +-- .../process_openproblems_v1/config.vsh.yaml | 3 +- .../workflows/process_openproblems_v1/main.nf | 23 +- .../config.vsh.yaml | 9 +- .../main.nf | 46 ++-- .../api/comp_metric_embedding.yaml | 15 +- .../metrics/cell_cycle_conservation/script.py | 6 +- .../{pancreas.sh => process.sh} | 35 ++- .../process_datasets/config.vsh.yaml | 3 +- .../workflows/process_datasets/main.nf | 24 +- .../workflows/run_benchmark/config.vsh.yaml | 8 +- .../workflows/run_benchmark/main.nf | 22 +- .../process_datasets/config.vsh.yaml | 3 +- .../workflows/process_datasets/main.nf | 24 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../denoising/workflows/run_benchmark/main.nf | 20 +- .../process_datasets/config.vsh.yaml | 3 +- .../workflows/process_datasets/main.nf | 22 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 15 +- .../process_datasets/config.vsh.yaml | 3 +- .../workflows/process_datasets/main.nf | 24 +- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 20 +- .../process_datasets/config.vsh.yaml | 5 +- .../workflows/process_datasets/main.nf | 47 ++-- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 18 +- .../api/comp_control_method.yaml | 4 +- .../predict_modality/api/comp_method.yaml | 4 +- .../predict_modality/api/comp_metric.yaml | 4 +- .../api/comp_process_dataset.yaml | 4 +- .../api/file_common_dataset_other_mod.yaml | 13 +- .../api/file_common_dataset_rna.yaml | 13 +- .../predict_modality/api/file_prediction.yaml | 2 +- .../predict_modality/api/file_score.yaml | 2 +- .../predict_modality/api/file_test_mod1.yaml | 2 +- .../predict_modality/api/file_test_mod2.yaml | 2 +- .../predict_modality/api/file_train_mod1.yaml | 2 +- .../predict_modality/api/file_train_mod2.yaml | 2 +- .../control_methods/meanpergene/script.py | 8 +- .../control_methods/random_predict/script.R | 6 +- .../control_methods/solution/script.R | 2 +- .../control_methods/zeros/script.py | 6 +- .../methods/knnr_py/script.py | 6 +- .../methods/newwave_knnr/script.R | 2 +- .../metrics/correlation/script.R | 5 +- .../predict_modality/metrics/mse/script.py | 4 +- .../process_dataset/config.vsh.yaml | 2 + .../predict_modality/process_dataset/script.R | 24 +- .../process_datasets/config.vsh.yaml | 5 +- .../workflows/process_datasets/main.nf | 49 ++-- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 16 +- .../workflows/run_benchmark/run_test.sh | 2 +- src/wf_utils/helper.nf | 14 + 87 files changed, 1277 insertions(+), 495 deletions(-) create mode 100644 src/common/extract_metadata/config.vsh.yaml create mode 100644 src/common/extract_metadata/script.py create mode 100644 src/common/extract_metadata/test.py create mode 100644 src/common/process_dataset_metadata/run/config.vsh.yaml create mode 100644 src/common/process_dataset_metadata/run/main.nf create mode 100644 src/common/process_dataset_metadata/run/run_test.sh create mode 100644 src/datasets/api/file_multimodal_dataset.yaml delete mode 100644 src/datasets/resource_test_scripts/cellxgene_census.sh rename src/datasets/{resource_scripts/cellxgene_census_test.sh => resource_test_scripts/cxg_mouse_pancreas_atlas.sh} (79%) create mode 100644 src/datasets/workflows/extract_dataset_meta/config.vsh.yaml create mode 100644 src/datasets/workflows/extract_dataset_meta/main.nf create mode 100755 src/datasets/workflows/extract_dataset_meta/run_test.sh rename src/tasks/batch_integration/resources_test_scripts/{pancreas.sh => process.sh} (51%) create mode 100644 src/wf_utils/helper.nf diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 610957e34e..7453da720f 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: description: A h5ad file. - name: --schema type: file - required: false + required: true description: A schema file for the h5ad object. - name: Arguments arguments: @@ -21,24 +21,12 @@ functionality: description: Whether or not to stop with exit code 1 if the input file does not adhere to the schema. - name: Output arguments: - - name: --checks + - name: --output type: file - required: false + required: true description: If specified, this file will contain a structured log of which checks succeeded (or not). example: checks.json direction: output - - name: --output - type: file - required: false - description: If specified, the output file will be a copy of the input file. - example: output.h5ad - direction: output - - name: --meta - type: file - required: false - description: If specified, the output file will contain metadata of the dataset. - example: output_meta.yaml - direction: output resources: - type: python_script path: script.py diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index e70f990dcf..b5a1c072c0 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -1,30 +1,30 @@ import anndata as ad import yaml -import shutil import json -import numpy as np -import pandas as pd ## VIASH START par = { - 'input': 'resources_test/common/pancreas/dataset.h5ad', - 'schema': 'src/tasks/denoising/api/file_common_dataset.yaml', + 'input': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/_viash_par/input_1/dataset.h5ad', + 'schema': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/_viash_par/schema_1/schema.yaml', 'stop_on_error': False, - 'checks': 'output/error.json', - 'output': 'output/output.h5ad', - 'meta': 'output/meta.json', + 'output': 'work/d4/f4fabc8aa4f2308841d4ab57bcff62/out.yaml', } ## VIASH END -def check_structure(slot_info, adata_slot): +def check_structure(slot, slot_info, adata_slot): missing = [] + if slot == "X": + slot_info["name"] = "X" + slot_info = [slot_info] for obj in slot_info: - if obj.get('required') and obj['name'] not in adata_slot: + adata_data = adata_slot.get(obj['name']) if slot != 'X' else adata_slot + if obj.get('required') and adata_data is None: missing.append(obj['name']) + # todo: check types return missing print('Load data', flush=True) -adata = ad.read_h5ad(par['input']).copy() +adata = ad.read_h5ad(par['input']) # create data structure out = { @@ -33,87 +33,27 @@ def check_structure(slot_info, adata_slot): "data_schema": "ok" } -def is_atomic(obj): - return isinstance(obj, str) or isinstance(obj, int) or isinstance(obj, bool) or isinstance(obj, float) +print("Check AnnData against schema", flush=True) +with open(par["schema"], "r") as f: + data_struct = yaml.safe_load(f) -def to_atomic(obj): - if isinstance(obj, np.float64): - return float(obj) - elif isinstance(obj, np.int64): - return int(obj) - elif isinstance(obj, np.bool_): - return bool(obj) - elif isinstance(obj, np.str_): - return str(obj) - return obj +def_slots = data_struct['info']['slots'] -def is_list_of_atomics(obj): - if not isinstance(obj, (list,pd.core.series.Series,np.ndarray)): - return False - return all(is_atomic(elem) for elem in obj) - -def to_list_of_atomics(obj): - if isinstance(obj, pd.core.series.Series): - obj = obj.to_numpy() - if isinstance(obj, np.ndarray): - obj = obj.tolist() - return [to_atomic(elem) for elem in obj] - -def is_dict_of_atomics(obj): - if not isinstance(obj, dict): - return False - return all(is_atomic(elem) for _, elem in obj.items()) - -def to_dict_of_atomics(obj): - return {k: to_atomic(v) for k, v in obj.items()} - -if par['meta'] is not None: - print("Extract metadata from object", flush=True) - uns = {} - for key, val in adata.uns.items(): - if is_atomic(val): - uns[key] = to_atomic(val) - elif is_list_of_atomics(val) and len(val) <= 10: - uns[key] = to_list_of_atomics(val) - elif is_dict_of_atomics(val) and len(val) <= 10: - uns[key] = to_dict_of_atomics(val) - structure = { - struct: list(getattr(adata, struct).keys()) - for struct - in ["obs", "var", "obsp", "varp", "obsm", "varm", "layers", "uns"] - } - meta = {"uns": uns, "structure": structure} - with open(par["meta"], "w") as f: - yaml.dump(meta, f, indent=2) - -if par['schema'] is not None: - print("Check AnnData against schema", flush=True) - with open(par["schema"], "r") as f: - data_struct = yaml.safe_load(f) - - def_slots = data_struct['info']['slots'] - - missing= [] - for slot in def_slots: - missing_x = False - if slot == "X": - if adata.X is None: - missing_x = True - continue - missing = check_structure(def_slots[slot], getattr(adata, slot)) - if missing_x: - missing.append("X") - if missing: - out['exit_code'] = 1 - out['data_schema'] = 'not ok' - out['error'][slot] = missing - - if par['checks'] is not None: - with open(par["checks"], "w") as f: - json.dump(out, f, indent=2) - -if par['output'] is not None and out["data_schema"] == "ok": - shutil.copyfile(par["input"], par["output"]) +out = { + "exit_code": 0, + "error": {}, + "data_schema": "ok" +} +for slot in def_slots: + print("Checking slot", slot, flush=True) + missing = check_structure(slot, def_slots[slot], getattr(adata, slot)) + if missing: + out['exit_code'] = 1 + out['data_schema'] = 'not ok' + out['error'][slot] = missing + +with open(par["output"], "w") as f: + json.dump(out, f, indent=2) if par['stop_on_error']: exit(out['exit_code']) diff --git a/src/common/check_dataset_schema/test.py b/src/common/check_dataset_schema/test.py index 9efb91e41b..1e7b5eb1e9 100644 --- a/src/common/check_dataset_schema/test.py +++ b/src/common/check_dataset_schema/test.py @@ -64,7 +64,7 @@ def error_schema(tmp_path): return schema def test_run(run_component, tmp_path, schema): - output_path = tmp_path / "output.h5ad" + output_path = tmp_path / "checks.json" run_component([ "--input", input_path, @@ -76,20 +76,17 @@ def test_run(run_component, tmp_path, schema): def test_error(run_component, tmp_path, error_schema): output_checks = tmp_path / "checks.json" - output_path = tmp_path / "output.h5ad" with pytest.raises(subprocess.CalledProcessError) as err: run_component([ "--input", input_path, "--schema", str(error_schema), "--stop_on_error", "true", - "--checks", str(output_checks), - "--output", str(output_path) + "--output", str(output_checks) ]) assert err.value.exitcode > 0 assert output_checks.exists(), "Output checks file does not exist" - assert not output_path.exists(), "Output path does not exist" with open(output_checks, "r") as f: out = json.load(f) diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py index 224c767694..f076cd3b19 100644 --- a/src/common/comp_tests/run_and_check_adata.py +++ b/src/common/comp_tests/run_and_check_adata.py @@ -13,11 +13,11 @@ ## VIASH END # helper functions -def check_slots(adata, slot_metadata): +def check_slots(adata, arg): """Check whether an AnnData file contains all for the required slots in the corresponding .info.slots field. """ - for struc_name, slot_items in slot_metadata.items(): + for struc_name, slot_items in arg["info"].get("slots", {}).items(): struc_x = getattr(adata, struc_name) if struc_name == "X": @@ -31,6 +31,42 @@ def check_slots(adata, slot_metadata): assert slot_item["name"] in struc_x,\ f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']" +def run_and_check(arguments, cmd): + print(">> Checking whether input files exist", flush=True) + for arg in arguments: + if arg["type"] == "file" and arg["direction"] == "input": + assert path.exists(arg["value"]), f"Input file '{arg['value']}' does not exist" + + print(f">> Running script as test", flush=True) + out = subprocess.run(cmd, stderr=subprocess.STDOUT) + + if out.stdout: + print(out.stdout) + + if out.returncode: + print(f"script: \'{' '.join(cmd)}\' exited with an error.") + exit(out.returncode) + + print(">> Checking whether output file exists", flush=True) + for arg in arguments: + if arg["type"] == "file" and arg["direction"] == "output": + assert path.exists(arg["value"]), f"Output file '{arg['value']}' does not exist" + + print(">> Reading h5ad files and checking formats", flush=True) + adatas = {} + for arg in arguments: + if arg["type"] == "file" and "slots" in arg["info"]: + print(f"Reading and checking {arg['clean_name']}", flush=True) + adata = ad.read_h5ad(arg["value"]) + + print(f" {adata}") + + check_slots(adata, arg) + + adatas[arg["clean_name"]] = adata + + print("All checks succeeded!", flush=True) + # read viash config with open(meta["config"], "r") as file: @@ -56,45 +92,30 @@ def check_slots(adata, slot_metadata): arguments.append(new_arg) -# construct command -cmd = [ meta["executable"] ] -for arg in arguments: - if arg["type"] == "file": - cmd.extend([arg["name"], arg["value"]]) - - -print(">> Checking whether input files exist", flush=True) -for arg in arguments: - if arg["type"] == "file" and arg["direction"] == "input": - assert path.exists(arg["value"]), f"Input file '{arg['value']}' does not exist" - -print(">> Running script as test", flush=True) -out = subprocess.run(cmd, stderr=subprocess.STDOUT) - -if out.stdout: - print(out.stdout) - -if out.returncode: - print(f"script: '{cmd}' exited with an error.") - exit(out.returncode) - -print(">> Checking whether output file exists", flush=True) -for arg in arguments: - if arg["type"] == "file" and arg["direction"] == "output": - assert path.exists(arg["value"]), f"Output file '{arg['value']}' does not exist" - -print(">> Reading h5ad files and checking formats", flush=True) -adatas = {} -for arg in arguments: - if arg["type"] == "file": - print(f"Reading and checking {arg['clean_name']}", flush=True) - adata = ad.read_h5ad(arg["value"]) - slots = arg["info"].get("slots") or {} - - print(f" {adata}") - - check_slots(adata, slots) - - adatas[arg["clean_name"]] = adata -print("All checks succeeded!", flush=True) +if "test_setup" not in config["functionality"]["info"]: + argument_sets = {"run": arguments} +else: + test_setup = config["functionality"]["info"]["test_setup"] + argument_sets = {} + for name, test_instance in test_setup.items(): + new_arguments = [] + for arg in arguments: + new_arg = arg.copy() + if arg["clean_name"] in test_instance: + val = test_instance[arg["clean_name"]] + if new_arg["type"] == "file" and new_arg["direction"] == "input": + val = f"{meta['resources_dir']}/{val}" + new_arg["value"] = val + new_arguments.append(new_arg) + argument_sets[name] = new_arguments + +for argset_name, argset_args in argument_sets.items(): + print(f">> Running test '{argset_name}'", flush=True) + # construct command + cmd = [ meta["executable"] ] + for arg in argset_args: + if arg["type"] == "file": + cmd.extend([arg["name"], arg["value"]]) + + run_and_check(argset_args, cmd) \ No newline at end of file diff --git a/src/common/extract_metadata/config.vsh.yaml b/src/common/extract_metadata/config.vsh.yaml new file mode 100644 index 0000000000..e131698433 --- /dev/null +++ b/src/common/extract_metadata/config.vsh.yaml @@ -0,0 +1,40 @@ +functionality: + name: extract_metadata + namespace: common + description: Extract the metadata from an h5ad file. + argument_groups: + - name: Inputs + arguments: + - name: --input + type: file + required: true + description: A h5ad file. + - name: --schema + type: file + required: false + description: An optional schema with which to annotate the output + - name: Output + arguments: + - name: --output + type: file + required: true + description: A yaml file containing the metadata. + example: output_meta.yaml + direction: output + resources: + - type: python_script + path: script.py + test_resources: + - path: /resources_test/common/pancreas + - path: /src/datasets/api/file_raw.yaml + - type: python_script + path: test.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + test_setup: + - type: python + packages: viashpy + - type: nextflow + directives: + label: [ midtime, midmem, midcpu ] diff --git a/src/common/extract_metadata/script.py b/src/common/extract_metadata/script.py new file mode 100644 index 0000000000..7a55b50e21 --- /dev/null +++ b/src/common/extract_metadata/script.py @@ -0,0 +1,206 @@ +import anndata as ad +import yaml +import numpy as np +import pandas as pd +import scipy +import os +import datetime + +## VIASH START +par = { + 'input': 'resources_test/common/pancreas/dataset.h5ad', + 'schema': 'src/datasets/api/file_raw.yaml', + 'output': 'output/meta.yaml', +} +## VIASH END + +print('Load data', flush=True) +adata = ad.read_h5ad(par['input']).copy() + +if par["schema"]: + print("Load schema", flush=True) + with open(par["schema"], "r") as f: + schema = yaml.safe_load(f) +else: + schema = None + +#################################################################################################### +## Helper functions for extracting the dataset metadata in uns ## +#################################################################################################### +def is_atomic(obj): + return isinstance(obj, str) or isinstance(obj, int) or isinstance(obj, bool) or isinstance(obj, float) + +def to_atomic(obj): + if isinstance(obj, np.float64): + return float(obj) + elif isinstance(obj, np.int64): + return int(obj) + elif isinstance(obj, np.bool_): + return bool(obj) + elif isinstance(obj, np.str_): + return str(obj) + return obj + +def is_list_of_atomics(obj): + if not isinstance(obj, (list,pd.core.series.Series,np.ndarray)): + return False + return all(is_atomic(elem) for elem in obj) + +def to_list_of_atomics(obj): + if isinstance(obj, pd.core.series.Series): + obj = obj.to_numpy() + if isinstance(obj, np.ndarray): + obj = obj.tolist() + return [to_atomic(elem) for elem in obj] + +def is_dict_of_atomics(obj): + if not isinstance(obj, dict): + return False + return all(is_atomic(elem) for _, elem in obj.items()) + +def to_dict_of_atomics(obj): + return {k: to_atomic(v) for k, v in obj.items()} + + +#################################################################################################### +## Helper functions for extracting metadata about the used data structures ## +#################################################################################################### +def get_structure_shape(obj) -> list: + if isinstance(obj, np.ndarray): + return list(obj.shape) + elif scipy.sparse.issparse(obj): + return list(obj.shape) + elif isinstance(obj, pd.core.frame.DataFrame): + return list(obj.shape) + elif isinstance(obj, pd.core.series.Series): + return list(obj.shape) + elif isinstance(obj, list): + return [len(obj)] + elif isinstance(obj, dict): + return [len(obj)] + elif is_atomic(obj): + return [1] + return None + +def get_structure_type(obj) -> str: + # return one of: atomic, dataFrame, vector, dict, denseMatrix, sparseMatrix + if is_atomic(obj): + return "atomic" + elif isinstance(obj, (list,pd.core.series.Series)): + return "vector" + elif isinstance(obj, dict): + return "dict" + elif isinstance(obj, pd.core.frame.DataFrame): + return "dataframe" + elif scipy.sparse.issparse(obj): + return "sparsematrix" + elif isinstance(obj, np.ndarray): + return "densematrix" + return "other: " + str(type(obj)) + +def get_structure_dtype(obj) -> str: + if isinstance(obj, np.ndarray): + return obj.dtype.name + elif isinstance(obj, pd.core.series.Series): + return obj.dtype.name + elif isinstance(obj, pd.core.frame.DataFrame): + return [dtype.name for dtype in obj.dtypes] + elif scipy.sparse.issparse(obj): + return obj.dtype.name + elif is_atomic(obj): + return type(obj).__name__ + return None + +def get_structure_schema_info(struct, key) -> dict: + if schema is None: + return {} + struct_args = schema.get("info", {}).get("slots", {}).get(struct, {}) + if struct_args is None: + return {} + if struct == "X": + return struct_args + + # look for item with the correct name + struct_results = [x for x in struct_args if x.get("name") == key] + + # return None if no match is found + if len(struct_results) != 1: + return {} + + return struct_results[0] + +def get_structure(adata, struct): + adata_struct = getattr(adata, struct) + + # turn `adata_struct` into a dict for `X` + if (struct == "X"): + adata_struct = {"X": adata_struct} if adata_struct is not None else {} + + output = [] + + for key, value in adata_struct.items(): + out = { + "name": key, + "type": get_structure_type(value), + "shape": get_structure_shape(value), + "dtype": get_structure_dtype(value), + } + + # see if the schema has information about this struct + schema_info = get_structure_schema_info(struct, key) + + if schema_info.get("description"): + out["description"] = schema_info.get("description") + if schema_info.get("type"): + out["schema_type"] = schema_info.get("type") + + output.append(out) + + return output + +#################################################################################################### +## Other helper functions ## +#################################################################################################### + +def get_file_size(path: str) -> int: + """Get the file size in bytes of the file at the given path.""" + return os.path.getsize(path) + +def get_file_creation_time(path: str) -> str: + """Get the creation time of the file at the given path.""" + # Get file creation time + creation_time = os.path.getctime(path) + # Convert creation time from seconds since epoch to a readable timestamp + creation_time = datetime.datetime.fromtimestamp(creation_time) + # Format the datetime object as 'DD-MM-YYYY' + creation_time = creation_time.strftime('%d-%m-%Y') + return str(creation_time) + + +print("Extract metadata from object", flush=True) +# Extract metadata about the adata object +uns = {} +for key, val in adata.uns.items(): + if is_atomic(val): + uns[key] = to_atomic(val) + elif is_list_of_atomics(val) and len(val) <= 10: + uns[key] = to_list_of_atomics(val) + elif is_dict_of_atomics(val) and len(val) <= 10: + uns[key] = to_dict_of_atomics(val) + +uns["file_size"] = get_file_size(par["input"]) +uns["date_created"] = get_file_creation_time(par["input"]) + +# Extract metadata about the data structures +structure = { + struct: get_structure(adata, struct) + for struct + in ["X", "obs", "var", "obsp", "varp", "obsm", "varm", "layers", "uns"] +} + +# ¢reate metadata object +meta = {"uns": uns, "structure": structure} + +print("Write metadata to file", flush=True) +with open(par["output"], "w") as f: + yaml.dump(meta, f, indent=2) diff --git a/src/common/extract_metadata/test.py b/src/common/extract_metadata/test.py new file mode 100644 index 0000000000..8af023d8f6 --- /dev/null +++ b/src/common/extract_metadata/test.py @@ -0,0 +1,26 @@ +import sys +import re +import pytest +import json +import subprocess + +## VIASH START +## VIASH END + +input_path = meta["resources_dir"] + "/pancreas/dataset.h5ad" +schema_path = meta["resources_dir"] + "/file_raw.yaml" + +def test_run(run_component, tmp_path): + output_path = tmp_path / "meta.yaml" + + run_component([ + "--input", input_path, + "--schema", schema_path, + "--output", str(output_path), + ]) + + assert output_path.exists(), "Output path does not exist" + + +if __name__ == "__main__": + sys.exit(pytest.main([__file__])) diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 40cabb5d39..45744d4048 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -1,7 +1,7 @@ functionality: name: "extract_scores" + status: disabled namespace: "common" - version: "dev" description: "Extract evaluation data frame on output" arguments: - name: "--input" diff --git a/src/common/process_dataset_metadata/run/config.vsh.yaml b/src/common/process_dataset_metadata/run/config.vsh.yaml new file mode 100644 index 0000000000..62396558b0 --- /dev/null +++ b/src/common/process_dataset_metadata/run/config.vsh.yaml @@ -0,0 +1,29 @@ +functionality: + name: run + namespace: common/process_dataset_metadata + description: >- + This workflow transforms the meta information of the datasets into a format + that can be used by the website. + argument_groups: + - name: Inputs + arguments: + - name: "--input" + type: file + required: true + direction: input + example: meta.yaml + - name: Outputs + arguments: + - name: "--output" + type: file + required: true + direction: output + default: $id.json + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/process_task_results/yaml_to_json +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/common/process_dataset_metadata/run/main.nf b/src/common/process_dataset_metadata/run/main.nf new file mode 100644 index 0000000000..2e453d5d52 --- /dev/null +++ b/src/common/process_dataset_metadata/run/main.nf @@ -0,0 +1,17 @@ +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + | yaml_to_json.run( + fromState: ["input"], + toState: ["output"] + ) + + | setState(["output"]) + + emit: + output_ch +} \ No newline at end of file diff --git a/src/common/process_dataset_metadata/run/run_test.sh b/src/common/process_dataset_metadata/run/run_test.sh new file mode 100644 index 0000000000..397b26f51e --- /dev/null +++ b/src/common/process_dataset_metadata/run/run_test.sh @@ -0,0 +1,40 @@ +#!/bin/bash + +# fail on error +set -e + +# ensure we're in the root of the repo +REPO_ROOT=$(git rev-parse --show-toplevel) +cd "$REPO_ROOT" + +# TODO: Add multimodal datasets +for LOADER in "cellxgene_census" "openproblems_v1"; do + BASE_DIR="s3://openproblems-data/resources/datasets/$LOADER/" + + for DATASET in $(aws s3 ls $BASE_DIR); do + + if [ "$DATASET" == "PRE" ]; then + continue + fi + + INPUT="${BASE_DIR%/}/${DATASET%/}/log_cp10k/dataset_metadata.yaml" + OUTPUT_DIR="../website/datasets/$LOADER/$DATASET" + + echo "Processing $LOADER - $DATASET : $INPUT" + # # temp sync + # aws s3 sync $INPUT_DIR output/temp + + # start the run + NXF_VER=23.10.0 nextflow run . \ + -main-script target/nextflow/common/process_dataset_metadata/run/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + --id "process" \ + --input "$INPUT" \ + --output_state "state.yaml" \ + --publish_dir "$OUTPUT_DIR" + +# cause quarto rerender to index page when in preview mode +# touch ../website/results/$TASK/index.qmd + done +done \ No newline at end of file diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index ad6d547ded..8c6afa39ac 100755 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -126,8 +126,8 @@ nextflow run . \ -resume \ -c src/wf_utils/labels_ci.config \ -entry auto \ - --input_states "$DATASETS_DIR/**/state.yaml" \ + --input_states "$DATASETS_DIR/pancreas/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ - --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml", "method_ids": ["bbknn", "mnnpy", "mnnr"]}' \ --publish_dir "$OUTPUT_DIR" \ --output_state "state.yaml" diff --git a/src/datasets/api/file_multimodal_dataset.yaml b/src/datasets/api/file_multimodal_dataset.yaml new file mode 100644 index 0000000000..1613993358 --- /dev/null +++ b/src/datasets/api/file_multimodal_dataset.yaml @@ -0,0 +1,243 @@ +type: file +example: "resources_test/common/pancreas/dataset.h5ad" +info: + label: "Common dataset" + summary: A dataset processed by the common dataset processing pipeline. + description: | + This dataset contains both raw counts and normalized data matrices, + as well as a SVD embedding and a HVG selection. + + The format of this file is derived from the [CELLxGENE schema v4.0.0](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/4.0.0/schema.md). + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + + - type: double + name: normalized + description: Normalised expression values + required: true + obs: + - type: string + name: dataset_id + description: Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes. + required: false + + - type: string + name: assay + description: Type of assay used to generate the cell data, indicating the methodology or technique employed. + required: false + + - type: string + name: assay_ontology_term_id + description: Experimental Factor Ontology (`EFO:`) term identifier for the assay, providing a standardized reference to the assay type. + required: false + + - type: string + name: cell_type + description: Classification of the cell type based on its characteristics and function within the tissue or organism. + required: false + + - type: string + name: cell_type_ontology_term_id + description: Cell Ontology (`CL:`) term identifier for the cell type, offering a standardized reference to the specific cell classification. + required: false + + - type: string + name: development_stage + description: Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase. + required: false + + - type: string + name: development_stage_ontology_term_id + description: | + Ontology term identifier for the developmental stage, providing a standardized reference to the organism's developmental phase. + + If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Developmental Stages (`HsapDv:`) ontology is used. + If the organism is mouse (`organism_ontology_term_id == 'NCBITaxon:10090'`), then the Mouse Developmental Stages (`MmusDv:`) ontology is used. + Otherwise, the Uberon (`UBERON:`) ontology is used. + required: false + + - type: string + name: disease + description: Information on any disease or pathological condition associated with the cell or donor. + required: false + + - type: string + name: disease_ontology_term_id + description: | + Ontology term identifier for the disease, enabling standardized disease classification and referencing. + + Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`). + required: false + + - type: string + name: donor_id + description: Identifier for the donor from whom the cell sample is obtained. + required: false + + - type: boolean + name: is_primary_data + description: Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data. + required: false + + - type: string + name: organism + description: Organism from which the cell sample is obtained. + required: false + + - type: string + name: organism_ontology_term_id + description: | + Ontology term identifier for the organism, providing a standardized reference for the organism. + + Must be a term from the NCBI Taxonomy Ontology (`NCBITaxon:`) which is a child of `NCBITaxon:33208`. + required: false + + - type: string + name: self_reported_ethnicity + description: Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits. + required: false + + - type: string + name: self_reported_ethnicity_ontology_term_id + description: | + Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. + + If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used. + required: false + + - type: string + name: sex + description: Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions. + required: false + + - type: string + name: sex_ontology_term_id + description: Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only `PATO:0000383`, `PATO:0000384` and `PATO:0001340` are allowed. + required: false + + - type: string + name: suspension_type + description: Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions. + required: false + + - type: string + name: tissue + description: Specific tissue from which the cells were derived, key for context and specificity in cell studies. + required: false + + - type: string + name: tissue_ontology_term_id + description: | + Ontology term identifier for the tissue, providing a standardized reference for the tissue type. + + For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). + For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. + required: false + + - type: string + name: tissue_general + description: General category or classification of the tissue, useful for broader grouping and comparison of cell data. + required: false + + - type: string + name: tissue_general_ontology_term_id + description: | + Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. + + For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). + For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`. + required: false + + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: false + + - type: integer + name: soma_joinid + description: If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. + required: false + + - type: double + name: size_factors + description: The size factors created by the normalisation method, if any. + required: false + var: + - type: string + name: feature_id + description: Unique identifier for the feature, usually a ENSEMBL gene id. + # TODO: make this required once openproblems_v1 dataloader supports it + required: false + + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + # TODO: make this required once the dataloader supports it + required: false + + - type: integer + name: soma_joinid + description: If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. + required: false + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + + obsm: + - type: double + name: X_svd + description: The resulting SVD embedding. + required: true + uns: + - type: string + name: dataset_id + description: A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived. + required: true + + - name: dataset_name + type: string + description: A human-readable name for the dataset. + required: true + + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + multiple: true + + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + multiple: true + + - type: string + name: normalization_id + description: "Which normalization was used" + required: true diff --git a/src/datasets/api/file_raw.yaml b/src/datasets/api/file_raw.yaml index 76eb6ecaf2..c4eaf1b17c 100644 --- a/src/datasets/api/file_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -159,12 +159,14 @@ info: - type: string name: feature_id description: Unique identifier for the feature, usually a ENSEMBL gene id. - required: true + # TODO: make this required once openproblems_v1 dataloader supports it + required: false - type: string name: feature_name description: A human-readable name for the feature, usually a gene symbol. - required: true + # TODO: make this required once the dataloader supports it + required: false - type: integer name: soma_joinid diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml index f63dbe29ae..32fbeecff4 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -60,8 +60,8 @@ functionality: test_resources: - type: python_script path: test.py - - type: file - path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad + # - type: file + # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index 49b5eb54e7..0b95f94af8 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -1,5 +1,6 @@ import anndata as ad import pandas as pd +import numpy as np ## VIASH START par = { @@ -32,13 +33,12 @@ def remove_mod_prefix(df, mod): print("load dataset file", flush=True) adata = ad.read_h5ad(par["input"]) -# Add is_train to obs +# Add is_train to obs if it is missing if "is_train" not in adata.obs.columns: batch_info = adata.obs["batch"] batch_categories = batch_info.dtype.categories train = ["s1d1", "s2d1", "s2d4", "s3d6", "s3d1"] - adata.obs["is_train"] = [ x in train for x in batch_info ] - adata.obs["is_train"].replace([True, False], ["train", "test"]) + adata.obs["is_train"] = [ "train" if x in train else "test" for x in batch_info ] # Construct Modality datasets print("Construct Mod datasets", flush=True) @@ -53,11 +53,10 @@ def remove_mod_prefix(df, mod): remove_other_mod_col(mod1_var, par["mod2"]) remove_mod_prefix(mod1_var, par["mod1"]) mod1_var.index.name = "feature_name" -mod1_var["feature_id"] = mod1_var.gene_id +mod1_var.reset_index("feature_name", inplace=True) +mod1_var["feature_id"] = np.where(mod1_var.gene_id.isna(), mod1_var.feature_name, mod1_var.gene_id.astype(str)) mod1_var.drop("gene_id", axis=1, inplace=True) -if not mod1_var.feature_id.hasnans: - mod1_var.reset_index("feature_name", inplace=True) - mod1_var.set_index("feature_id", drop=False, inplace=True) +mod1_var.set_index("feature_id", drop=False, inplace=True) mod1_obs = pd.DataFrame(adata_mod1.obs) remove_other_mod_col(mod1_obs, par["mod2"]) @@ -74,11 +73,10 @@ def remove_mod_prefix(df, mod): remove_other_mod_col(mod2_var, par["mod1"]) remove_mod_prefix(mod2_var, par["mod2"]) mod2_var.index.name = "feature_name" -mod2_var["feature_id"] = mod2_var.gene_id +mod2_var.reset_index("feature_name", inplace=True) +mod2_var["feature_id"] = np.where(mod2_var.gene_id.isna(), mod2_var.feature_name, mod2_var.gene_id.astype(str)) mod2_var.drop("gene_id", axis=1, inplace=True) -if not mod2_var.feature_id.hasnans: - mod2_var.reset_index("feature_name", inplace=True) - mod2_var.set_index("feature_id", drop=False, inplace=True) +mod2_var.set_index("feature_id", drop=False, inplace=True) mod2_obs = pd.DataFrame(adata_mod2.obs) remove_other_mod_col(mod2_obs, par["mod1"]) diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py index ad884f2bc6..c99abaddc3 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py @@ -2,13 +2,35 @@ import subprocess import anndata as ad -input = meta["resources_dir"] + "neurips2021_bmmc_cite.h5ad" +input = "neurips2021_bmmc_cite.h5ad" mod1 = "GEX" mod2 = "ADT" output_mod1_file = "output_mod1.h5ad" output_mod2_file = "output_mod2.h5ad" +input_url = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" + +# download input +print(">> Downloading input", flush=True) +out = subprocess.run( + [ + "wget", + "-O", input + ".gz", + input_url, + ], + stderr=subprocess.STDOUT +) +# unzip input +print(">> Unzipping input", flush=True) +out = subprocess.run( + [ + "gunzip", + input + ".gz", + ], + stderr=subprocess.STDOUT +) + print(">> Running script", flush=True) out = subprocess.run( [ diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index c09f7895bf..1d8226249c 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -5,6 +5,7 @@ ## VIASH START par = { + "input_id": "pancreas", "dataset_id": "pancreas", "obs_cell_type": "cell_type", "obs_batch": "tech", @@ -101,5 +102,8 @@ } adata.uns.update(uns_metadata) +# TODO: fix var annotation +# - add feature_id and feature_name + print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/resource_test_scripts/cellxgene_census.sh b/src/datasets/resource_test_scripts/cellxgene_census.sh deleted file mode 100644 index 45e4dd9e12..0000000000 --- a/src/datasets/resource_test_scripts/cellxgene_census.sh +++ /dev/null @@ -1,14 +0,0 @@ -#!/bin/bash - -DATASET_DIR="resources_test/common/cellxgene_census" - -[ ! -d "$DATASET_DIR" ] && mkdir -p "$DATASET_DIR" - -# download cell ontology obo file -wget https://github.com/obophenotype/cell-ontology/releases/download/v2023-02-15/cl.obo -O "$DATASET_DIR/cl.obo" - -# fetch dataset from cellxgene census -viash run src/datasets/loaders/query_cellxgene_census/config.vsh.yaml -- \ - --census_version 2023-07-25 \ - --obs_value_filter "is_primary_data == True and cell_type_ontology_term_id in ['CL:0000136', 'CL:1000311', 'CL:0002616'] and suspension_type == 'cell'" \ - --output "$DATASET_DIR/dataset.h5ad" diff --git a/src/datasets/resource_scripts/cellxgene_census_test.sh b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh similarity index 79% rename from src/datasets/resource_scripts/cellxgene_census_test.sh rename to src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh index b003c08d3c..df5dfa054d 100755 --- a/src/datasets/resource_scripts/cellxgene_census_test.sh +++ b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh @@ -1,11 +1,13 @@ #!/bin/bash +set -e + cat > "/tmp/params.yaml" << 'HERE' param_list: - - id: cellxgene_census/mouse_pancreas_atlas + - id: cxg_mouse_pancreas_atlas species: mus_musculus census_version: "2023-07-25" - obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8'" + obs_value_filter: "dataset_id == '49e4ffcc-5444-406d-bdee-577127404ba8' and donor_id in ['mouse_pancreatic_islet_atlas_Hrovatin__Fltp_2y__MUC13974', 'mouse_pancreatic_islet_atlas_Hrovatin__Fltp_2y__MUC13975', 'mouse_pancreatic_islet_atlas_Hrovatin__Fltp_2y__MUC13976']" obs_batch: donor_id dataset_name: Mouse Pancreatic Islet Atlas dataset_summary: Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes @@ -14,7 +16,7 @@ param_list: dataset_reference: hrovatin2023delineating dataset_organism: mus_musculus -normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +normalization_methods: [log_cp10k] output_dataset: '$id/dataset.h5ad' output_meta: '$id/dataset_metadata.yaml' output_state: '$id/state.yaml' @@ -23,10 +25,13 @@ output_normalized: force_null output_pca: force_null output_hvg: force_null output_knn: force_null -publish_dir: resources/datasets +publish_dir: resources_test/common +do_subsample: true HERE nextflow run . \ -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ -profile docker \ - -params-file "/tmp/params.yaml" \ No newline at end of file + -params-file "/tmp/params.yaml" + +# src/tasks/batch_integration/resources_test_scripts/process.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index af622c7454..13b4e7fdfa 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -35,27 +35,33 @@ output_other_mod: '$id/dataset_other_mod.h5ad' output_meta_rna: '$id/dataset_metadata_rna.yaml' output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' output_state: '$id/state.yaml' -publish_dir: s3://openproblems-data/resources_test/common +# publish_dir: s3://openproblems-data/resources_test/common HERE -cat > /tmp/nextflow.config << HERE -process { - withName:'.*publishStatesProc' { - memory = '16GB' - disk = '100GB' - } -} -HERE +# cat > /tmp/nextflow.config << HERE +# process { +# withName:'.*publishStatesProc' { +# memory = '16GB' +# disk = '100GB' +# } +# } +# HERE +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ + -profile docker \ + -resume \ + --publish_dir resources_test/common \ + -params-file "$params_file" -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ - --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ - --params-file "$params_file" \ - --config /tmp/nextflow.config \ - --labels predict_modality +# tw launch https://github.com/openproblems-bio/openproblems-v2.git \ +# --revision main_build \ +# --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ +# --workspace 53907369739130 \ +# --compute-env 1pK56PjjzeraOOC2LDZvN2 \ +# --params-file "$params_file" \ +# --config /tmp/nextflow.config \ +# --labels predict_modality # run task process dataset components -# src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh \ No newline at end of file +src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index dbcbef4f57..3c6de41303 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -1,7 +1,4 @@ #!/bin/bash -# -#make sure the following command has been executed -#viash_build -q 'label_projection|common' # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -25,6 +22,7 @@ nextflow run . \ -profile docker \ -resume \ --id pancreas \ + --input_id pancreas \ --obs_cell_type "celltype" \ --obs_batch "tech" \ --layer_counts "counts" \ @@ -53,7 +51,7 @@ nextflow run . \ rm -r $DATASET_DIR/temp_* # run task process dataset components -src/tasks/batch_integration/resources_test_scripts/pancreas.sh +src/tasks/batch_integration/resources_test_scripts/process.sh src/tasks/denoising/resources_test_scripts/pancreas.sh src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh src/tasks/label_projection/resources_test_scripts/pancreas.sh diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 79413b93f4..8f2c51067b 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -1,7 +1,4 @@ #!/bin/bash -# -#make sure the following command has been executed -#viash ns build -q 'datasets|common' --parallel --setup cb # get the root of the directory REPO_ROOT=$(git rev-parse --show-toplevel) @@ -21,10 +18,10 @@ nextflow run . \ -profile docker \ -resume \ --id scicar_cell_lines \ + --input_id scicar_cell_lines \ --obs_tissue "source" \ --layer_counts "counts" \ --obs_cell_type "cell_name" \ - --dataset_id scicar_cell_lines \ --dataset_name "sci-CAR cell lines" \ --dataset_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ --dataset_reference "cao2018joint" \ diff --git a/src/datasets/workflows/extract_dataset_info/config.vsh.yaml b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml index 452bf5429a..58433db567 100644 --- a/src/datasets/workflows/extract_dataset_info/config.vsh.yaml +++ b/src/datasets/workflows/extract_dataset_info/config.vsh.yaml @@ -29,6 +29,6 @@ functionality: path: main.nf entrypoint: run_wf dependencies: - - name: common/check_dataset_schema + - name: common/extract_metadata platforms: - type: nextflow diff --git a/src/datasets/workflows/extract_dataset_info/main.nf b/src/datasets/workflows/extract_dataset_info/main.nf index 9f847e8a2e..887812760e 100644 --- a/src/datasets/workflows/extract_dataset_info/main.nf +++ b/src/datasets/workflows/extract_dataset_info/main.nf @@ -13,11 +13,12 @@ workflow run_wf { output_ch = input_ch // extract the dataset metadata - | check_dataset_schema.run( + | extract_metadata.run( fromState: [input: "input"], toState: { id, output, state -> - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) diff --git a/src/datasets/workflows/extract_dataset_meta/config.vsh.yaml b/src/datasets/workflows/extract_dataset_meta/config.vsh.yaml new file mode 100644 index 0000000000..26041b1039 --- /dev/null +++ b/src/datasets/workflows/extract_dataset_meta/config.vsh.yaml @@ -0,0 +1,25 @@ +functionality: + name: "extract_dataset_meta" + namespace: "datasets/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __merge__: /src/datasets/api/file_raw.yaml + required: true + direction: input + - name: Outputs + arguments: + - name: "--output" + type: file + required: true + direction: output + example: meta.yaml + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + dependencies: + - name: common/extract_metadata +platforms: + - type: nextflow diff --git a/src/datasets/workflows/extract_dataset_meta/main.nf b/src/datasets/workflows/extract_dataset_meta/main.nf new file mode 100644 index 0000000000..cbac67b571 --- /dev/null +++ b/src/datasets/workflows/extract_dataset_meta/main.nf @@ -0,0 +1,20 @@ +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + // extract the dataset metadata + | extract_metadata.run( + fromState: [input: "input"], + toState: [output: "output"] + ) + + | setState([ + "output", + ]) + + emit: + output_ch +} diff --git a/src/datasets/workflows/extract_dataset_meta/run_test.sh b/src/datasets/workflows/extract_dataset_meta/run_test.sh new file mode 100755 index 0000000000..4792938fee --- /dev/null +++ b/src/datasets/workflows/extract_dataset_meta/run_test.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# export TOWER_WORKSPACE_ID=53907369739130 + +OUTPUT_DIR="output/temp" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +DATASETS_DIR="resources_test/common/pancreas/dataset.h5ad" + +export NXF_VER=22.04.5 +nextflow run . \ + -main-script target/nextflow/datasets/workflows/extract_dataset_meta/main.nf \ + -profile docker \ + -resume \ + -c src/wf_utils/labels_ci.config \ + --input $DATASETS_DIR \ + --output meta.yaml \ + --publish_dir "$OUTPUT_DIR" \ No newline at end of file diff --git a/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml b/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml index 25fa8cbdf5..3e1fd5263b 100644 --- a/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml +++ b/src/datasets/workflows/process_cellxgene_census/config.vsh.yaml @@ -181,6 +181,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - path: /src/wf_utils/helper.nf dependencies: - name: datasets/loaders/cellxgene_census - name: datasets/normalization/log_cp @@ -191,7 +192,7 @@ functionality: - name: datasets/processors/pca - name: datasets/processors/hvg - name: datasets/processors/knn - - name: common/check_dataset_schema + - name: common/extract_metadata # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_cellxgene_census/main.nf b/src/datasets/workflows/process_cellxgene_census/main.nf index 886e28a5a0..ea442143fe 100644 --- a/src/datasets/workflows/process_cellxgene_census/main.nf +++ b/src/datasets/workflows/process_cellxgene_census/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -121,9 +123,24 @@ workflow run_wf { toState: ["output_knn": "output"] ) - | check_dataset_schema.run( - fromState: ["input": "output_knn"], - toState: ["output_dataset": "output", "output_meta": "meta"] + // add synonym + | map{ id, state -> + [id, state + [output_dataset: state.output_knn]] + } + + | extract_metadata.run( + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_dataset") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) + [ + "input": state.output_dataset, + "schema": schemaYaml + ] + }, + toState: ["output_meta": "output"] ) // only output the files for which an output file was specified diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml index ee614f819c..5da6b740b5 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml @@ -97,12 +97,10 @@ functionality: arguments: - name: "--output_rna" direction: "output" - type: file - example: "dataset_rna.h5ad" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml - name: "--output_other_mod" direction: "output" - type: file - example: "dataset_other_mod.h5ad" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml - name: "--output_meta_rna" direction: "output" type: file @@ -117,6 +115,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - path: /src/wf_utils/helper.nf dependencies: - name: datasets/loaders/openproblems_neurips2021_bmmc - name: datasets/normalization/log_cp @@ -126,7 +125,7 @@ functionality: - name: datasets/processors/subsample - name: datasets/processors/svd - name: datasets/processors/hvg - - name: common/check_dataset_schema + - name: common/extract_metadata - name: common/decompress_gzip # test_resources: # - type: nextflow_script diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index 30bfd28ce3..3d3f2a83f4 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow run_wf { take: input_ch @@ -145,31 +147,41 @@ workflow run_wf { toState: [ "hvg_other_mod": "output" ] ) - | check_dataset_schema.run( + // add synonyms + | map{ id, state -> + [id, state + ["output_rna": state.hvg_rna, "output_other_mod": state.hvg_other_mod]] + } + + | extract_metadata.run( + key: "extract_metadata_rna", fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_rna") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ - "input": state.hvg_rna, - "checks": null + "input": state.output_rna, + "schema": schemaYaml ] }, - toState: [ - "output_rna": "output", - "output_meta_rna": "meta" - ] + toState: ["output_meta_rna": "output"] ) - | check_dataset_schema.run( - key: "check_dataset_schema_other_mod", + | extract_metadata.run( + key: "extract_metadata_other_mod", fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_other_mod") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ - "input": state.hvg_other_mod, - "checks": null + "input": state.output_other_mod, + "schema": schemaYaml ] }, - toState: [ - "output_other_mod": "output", - "output_meta_other_mod": "meta" - ] + toState: ["output_meta_other_mod": "output"] ) // only output the files for which an output file was specified diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index b6353da6fd..431ffe7b8d 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -135,6 +135,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - path: /src/wf_utils/helper.nf dependencies: - name: datasets/loaders/openproblems_v1 - name: datasets/normalization/log_cp @@ -145,7 +146,7 @@ functionality: - name: datasets/processors/pca - name: datasets/processors/hvg - name: datasets/processors/knn - - name: common/check_dataset_schema + - name: common/extract_metadata # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 46511536d0..90ec95e0f7 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -119,9 +121,24 @@ workflow run_wf { toState: ["output_knn": "output"] ) - | check_dataset_schema.run( - fromState: ["input": "output_knn"], - toState: ["output_dataset": "output", "output_meta": "meta"] + // add synonym + | map{ id, state -> + [id, state + [output_dataset: state.output_knn]] + } + + | extract_metadata.run( + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_dataset") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) + [ + "input": state.output_dataset, + "schema": schemaYaml + ] + }, + toState: ["output_meta": "output"] ) // only output the files for which an output file was specified diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 69ce43ddf0..1342df38c2 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -104,12 +104,10 @@ functionality: arguments: - name: "--output_dataset_mod1" direction: "output" - type: file - example: "dataset_mod1.h5ad" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml - name: "--output_dataset_mod2" direction: "output" - type: file - example: "dataset_mod2.h5ad" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml - name: "--output_meta_mod1" direction: "output" type: file @@ -124,6 +122,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf + - path: /src/wf_utils/helper.nf dependencies: - name: datasets/loaders/openproblems_v1_multimodal - name: datasets/normalization/log_cp @@ -133,7 +132,7 @@ functionality: - name: datasets/processors/subsample - name: datasets/processors/svd - name: datasets/processors/hvg - - name: common/check_dataset_schema + - name: common/extract_metadata # test_resources: # - type: nextflow_script # path: main.nf diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 0f8768ec1d..ef82b62cd7 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -142,32 +144,46 @@ workflow run_wf { toState: [ "hvg_mod2": "output" ] ) - | check_dataset_schema.run( + // add synonyms + | map{ id, state -> + [id, state + [ + "output_dataset_mod1": state.hvg_mod1, + "output_dataset_mod2": state.hvg_mod2 + ]] + } + + | extract_metadata.run( + key: "extract_metadata_mod1", fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_dataset_mod1") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ - "input": state.hvg_mod1, - "checks": null + "input": state.output_dataset_mod1, + "schema": schemaYaml ] }, - toState: [ - "output_dataset_mod1": "output", - "output_meta_mod1": "meta" - ] + toState: ["output_meta_mod1": "output"] ) - | check_dataset_schema.run( + | extract_metadata.run( + key: "extract_metadata_mod2", fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_dataset_mod2") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ - "input": state.hvg_mod2, - "checks": null + "input": state.output_dataset_mod2, + "schema": schemaYaml ] }, - toState: [ - "output_dataset_mod2": "output", - "output_meta_mod2": "meta" - ] + toState: ["output_meta_mod2": "output"] ) - + // only output the files for which an output file was specified | setState([ "output_dataset_mod1", diff --git a/src/tasks/batch_integration/api/comp_metric_embedding.yaml b/src/tasks/batch_integration/api/comp_metric_embedding.yaml index 6c23b2938d..7443fca8b4 100644 --- a/src/tasks/batch_integration/api/comp_metric_embedding.yaml +++ b/src/tasks/batch_integration/api/comp_metric_embedding.yaml @@ -8,6 +8,13 @@ functionality: summary: A batch integration embedding metric. description: | A metric for evaluating batch corrected embeddings. + test_setup: + pancreas: + input_integrated: resources_test/batch_integration/pancreas/integrated_embedding.h5ad + input_solution: resources_test/batch_integration/pancreas/solution.h5ad + cellxgene_census: + input_integrated: resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_embedding.h5ad + input_solution: resources_test/batch_integration/cxg_mouse_pancreas_atlas/solution.h5ad arguments: - name: --input_integrated __merge__: file_integrated_embedding.yaml @@ -22,10 +29,10 @@ functionality: direction: output required: true test_resources: - - path: /resources_test/batch_integration/pancreas - dest: resources_test/batch_integration/pancreas - - type: python_script - path: /src/common/comp_tests/check_metric_config.py + - path: /resources_test/batch_integration/ + dest: resources_test/batch_integration/ + # - type: python_script + # path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - path: /src/common/library.bib diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py index 3edc77ba88..6114defd81 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/script.py @@ -18,12 +18,16 @@ input_integrated = ad.read_h5ad(par['input_integrated']) input_solution.X = input_solution.layers['normalized'] +print('Use gene symbols for features', flush=True) +input_solution.var_names = input_solution.var['feature_name'] +input_integrated.var_names = input_integrated.var['feature_name'] + translator = { "homo_sapiens": "human", "mus_musculus": "mouse", } -print('compute score', flush=True) +print('Compute score', flush=True) if input_solution.uns['dataset_organism'] not in translator: score = np.nan else: diff --git a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh b/src/tasks/batch_integration/resources_test_scripts/process.sh similarity index 51% rename from src/tasks/batch_integration/resources_test_scripts/pancreas.sh rename to src/tasks/batch_integration/resources_test_scripts/process.sh index 5fa80a3bf1..3ab0dd2a4d 100755 --- a/src/tasks/batch_integration/resources_test_scripts/pancreas.sh +++ b/src/tasks/batch_integration/resources_test_scripts/process.sh @@ -26,17 +26,24 @@ nextflow run . \ --output_state '$id/state.yaml' # output_state should be moved to settings once workaround is solved -echo Running BBKNN -viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/dataset.h5ad \ - --output $DATASET_DIR/pancreas/integrated_graph.h5ad - -echo Running SCVI -viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/dataset.h5ad \ - --output $DATASET_DIR/pancreas/integrated_embedding.h5ad - -echo Running combat -viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ - --input $DATASET_DIR/pancreas/dataset.h5ad \ - --output $DATASET_DIR/pancreas/integrated_feature.h5ad \ No newline at end of file +for id in pancreas cxg_mouse_pancreas_atlas; do + if [ ! -f $DATASET_DIR/$id/dataset.h5ad ]; then + echo "Dataset $id not found" + exit 1 + fi + + echo Running BBKNN on $id + viash run src/tasks/batch_integration/methods/bbknn/config.vsh.yaml -- \ + --input $DATASET_DIR/$id/dataset.h5ad \ + --output $DATASET_DIR/$id/integrated_graph.h5ad + + echo Running SCVI on $id + viash run src/tasks/batch_integration/methods/scvi/config.vsh.yaml -- \ + --input $DATASET_DIR/$id/dataset.h5ad \ + --output $DATASET_DIR/$id/integrated_embedding.h5ad + + echo Running combat on $id + viash run src/tasks/batch_integration/methods/combat/config.vsh.yaml -- \ + --input $DATASET_DIR/$id/dataset.h5ad \ + --output $DATASET_DIR/$id/integrated_feature.h5ad +done \ No newline at end of file diff --git a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml index 38701745dd..3273e84165 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/process_datasets/config.vsh.yaml @@ -22,8 +22,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/batch_integration/api/file_common_dataset.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: batch_integration/process_dataset diff --git a/src/tasks/batch_integration/workflows/process_datasets/main.nf b/src/tasks/batch_integration/workflows/process_datasets/main.nf index d940182545..59cfee9f47 100644 --- a/src/tasks/batch_integration/workflows/process_datasets/main.nf +++ b/src/tasks/batch_integration/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -12,23 +14,23 @@ workflow run_wf { main: output_ch = input_ch - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file | check_dataset_schema.run( fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input, - "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset": "output", - "dataset_checks": "checks" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset": checks["exit_code"] == 0 ? state.input : null, + ] + } ) // remove datasets which didn't pass the schema check diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 976bd496d8..b430734e22 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -40,6 +40,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf @@ -48,7 +54,7 @@ functionality: path: ../../api/task_info.yaml dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: batch_integration/methods/bbknn - name: batch_integration/methods/combat - name: batch_integration/methods/fastmnn_embedding diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 3e87a2703a..6772a9bc4c 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -55,12 +55,14 @@ workflow run_wf { | map{ id, state -> [id, state + ["_meta": [join_id: id]]] } - // extract dataset metadata - | check_dataset_schema.run( + + // extract the dataset metadata + | extract_metadata.run( fromState: [input: "input_solution"], toState: { id, output, state -> - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -78,7 +80,10 @@ workflow run_wf { def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = state.method_ids.isEmpty() || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check }, // define a new 'id' by appending the method name to the dataset id @@ -186,12 +191,13 @@ workflow run_wf { output_ch = score_ch // extract scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml index 5746c6247e..6fc095704b 100644 --- a/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/denoising/workflows/process_datasets/config.vsh.yaml @@ -22,8 +22,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/denoising/api/file_common_dataset.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: denoising/process_dataset diff --git a/src/tasks/denoising/workflows/process_datasets/main.nf b/src/tasks/denoising/workflows/process_datasets/main.nf index 177ffc9e39..4437206b09 100644 --- a/src/tasks/denoising/workflows/process_datasets/main.nf +++ b/src/tasks/denoising/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -12,23 +14,23 @@ workflow run_wf { main: output_ch = input_ch - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file | check_dataset_schema.run( fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input, - "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset": "output", - "dataset_checks": "checks" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset": checks["exit_code"] == 0 ? state.input : null, + ] + } ) // remove datasets which didn't pass the schema check diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index cb741c20b8..b40e7a9e4b 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: denoising/control_methods/no_denoising - name: denoising/control_methods/perfect_denoising - name: denoising/methods/alra diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 29c20372e2..392af73246 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -35,13 +35,14 @@ workflow run_wf { | map{ id, state -> [id, state + ["_meta": [join_id: id]]] } - // extract dataset metadata - | check_dataset_schema.run( - fromState: [ "input": "input_test" ], + + // extract the dataset metadata + | extract_metadata.run( + fromState: [input: "input_test"], toState: { id, output, state -> - // load output yaml file - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -121,12 +122,13 @@ workflow run_wf { output_ch = score_ch // extract the scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml index 35e80f58ac..d6aa723b00 100644 --- a/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/config.vsh.yaml @@ -22,8 +22,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: dimensionality_reduction/process_dataset diff --git a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf index c01e356cd5..8d34f77e82 100644 --- a/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -12,21 +14,23 @@ workflow run_wf { main: output_ch = input_ch - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file | check_dataset_schema.run( fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input, - "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false, - "checks": null - ], - toState: ["dataset": "output"] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset": checks["exit_code"] == 0 ? state.input : null, + ] + } ) // remove datasets which didn't pass the schema check diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 575adb89c7..1f803bc5ea 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: dimensionality_reduction/control_methods/random_features - name: dimensionality_reduction/control_methods/true_features - name: dimensionality_reduction/methods/densmap diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index 7fb2f61ff3..9c9380fdac 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -41,12 +41,14 @@ workflow run_wf { | map{ id, state -> [id, state + ["_meta": [join_id: id]]] } + // extract the dataset metadata - | check_dataset_schema.run( + | extract_metadata.run( fromState: [input: "input_solution"], toState: { id, output, state -> - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -143,12 +145,13 @@ workflow run_wf { output_ch = score_ch // extract the scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml index c81309a9a9..09b2e9a829 100644 --- a/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/process_datasets/config.vsh.yaml @@ -26,8 +26,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/label_projection/api/file_common_dataset.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: label_projection/process_dataset diff --git a/src/tasks/label_projection/workflows/process_datasets/main.nf b/src/tasks/label_projection/workflows/process_datasets/main.nf index 60b11ee39e..88cf24935c 100644 --- a/src/tasks/label_projection/workflows/process_datasets/main.nf +++ b/src/tasks/label_projection/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -12,23 +14,23 @@ workflow run_wf { main: output_ch = input_ch - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file | check_dataset_schema.run( fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input, - "schema": meta.resources_dir.resolve("file_common_dataset.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset": "output", - "dataset_checks": "checks" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset": checks["exit_code"] == 0 ? state.input : null, + ] + } ) // remove datasets which didn't pass the schema check diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 10520efdda..39788910c9 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -55,7 +55,7 @@ functionality: path: "../../api/task_info.yaml" dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: label_projection/control_methods/true_labels - name: label_projection/control_methods/majority_vote - name: label_projection/control_methods/random_labels diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index 8df7cfa2df..58806bfdcf 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -39,13 +39,14 @@ workflow run_wf { | map{ id, state -> [id, state + ["_meta": [join_id: id]]] } - // extract dataset metadata - | check_dataset_schema.run( - fromState: [ "input": "input_solution" ], + + // extract the dataset metadata + | extract_metadata.run( + fromState: [input: "input_solution"], toState: { id, output, state -> - // load output yaml file - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -142,12 +143,13 @@ workflow run_wf { output_ch = score_ch // extract the scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml index 907b556f5d..5427343f9f 100644 --- a/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/process_datasets/config.vsh.yaml @@ -34,10 +34,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/match_modalities/api/file_common_dataset_mod1.yaml" - - type: file - path: "/src/tasks/match_modalities/api/file_common_dataset_mod2.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: match_modalities/process_dataset diff --git a/src/tasks/match_modalities/workflows/process_datasets/main.nf b/src/tasks/match_modalities/workflows/process_datasets/main.nf index 9f5466e370..ab5e9a83b0 100644 --- a/src/tasks/match_modalities/workflows/process_datasets/main.nf +++ b/src/tasks/match_modalities/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -11,42 +13,47 @@ workflow run_wf { main: output_ch = input_ch - - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file + | check_dataset_schema.run( key: "check_dataset_schema_mod1", fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input_mod1") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input_mod1, - "schema": meta.resources_dir.resolve("file_common_dataset_mod1.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset_mod1": "output" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset_mod1": checks["exit_code"] == 0 ? state.input_mod1 : null, + ] + } ) + | check_dataset_schema.run( key: "check_dataset_schema_mod2", fromState: { id, state -> - // as a resource + def schema = findArgumentSchema(meta.config, "input_mod2") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input_mod2, - "schema": meta.resources_dir.resolve("file_common_dataset_mod2.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset_mod2": "output" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset_mod2": checks["exit_code"] == 0 ? state.input_mod2 : null, + ] + } ) - + // remove datasets which didn't pass the schema check | filter { id, state -> state.dataset_mod1 != null && state.dataset_mod2 != null diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index a1e5660fee..df0971b8bc 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: path: "/src/tasks/match_modalities/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: match_modalities/control_methods/random_features - name: match_modalities/control_methods/true_features - name: match_modalities/methods/fastmnn diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index 6f49c63a29..d919104060 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -35,13 +35,12 @@ workflow run_wf { } // extract the dataset metadata - | check_dataset_schema.run( - fromState: [ "input": "input_solution_mod1" ], + | extract_metadata.run( + fromState: [input: "input_solution_mod1"], toState: { id, output, state -> - // load output yaml file - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - // add metadata from file to state - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -112,12 +111,13 @@ workflow run_wf { } // extract the scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml index 8689478046..5459e41adc 100644 --- a/src/tasks/predict_modality/api/comp_control_method.yaml +++ b/src/tasks/predict_modality/api/comp_control_method.yaml @@ -38,5 +38,5 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/neurips2021_bmmc_cite - dest: resources_test/predict_modality/neurips2021_bmmc_cite \ No newline at end of file + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index db47e7ab3e..f4810444fa 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -30,6 +30,6 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/neurips2021_bmmc_cite - dest: resources_test/predict_modality/neurips2021_bmmc_cite + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml index bd75d423b8..af6c71d9c5 100644 --- a/src/tasks/predict_modality/api/comp_metric.yaml +++ b/src/tasks/predict_modality/api/comp_metric.yaml @@ -25,6 +25,6 @@ functionality: path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/neurips2021_bmmc_cite - dest: resources_test/predict_modality/neurips2021_bmmc_cite + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_process_dataset.yaml b/src/tasks/predict_modality/api/comp_process_dataset.yaml index 14de13c3d1..37c85a6bcc 100644 --- a/src/tasks/predict_modality/api/comp_process_dataset.yaml +++ b/src/tasks/predict_modality/api/comp_process_dataset.yaml @@ -39,5 +39,5 @@ functionality: test_resources: - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/common/neurips2021_bmmc_cite - dest: resources_test/common/neurips2021_bmmc_cite \ No newline at end of file + - path: /resources_test/common/openproblems_neurips2021/bmmc_cite + dest: resources_test/common/openproblems_neurips2021/bmmc_cite \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml index 90f8457322..1b4e26c451 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad" +example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_other_mod.h5ad" info: label: "Raw dataset mod2" summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" @@ -24,8 +24,15 @@ info: required: false var: - type: string - name: gene_ids - description: The gene identifiers (if available) + name: feature_id + description: Unique identifier for the feature, usually a ENSEMBL gene id. + # TODO: make this required once openproblems_v1 dataloader supports it + required: true + + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + # TODO: make this required once the dataloader supports it required: false uns: - type: string diff --git a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml index 9802da2269..185c37c173 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_rna.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad" +example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_rna.h5ad" info: label: "Raw dataset RNA" summary: "The RNA modality of the raw dataset." @@ -24,8 +24,15 @@ info: required: false var: - type: string - name: gene_ids - description: The gene identifiers (if available) + name: feature_id + description: Unique identifier for the feature, usually a ENSEMBL gene id. + # TODO: make this required once openproblems_v1 dataloader supports it + required: true + + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + # TODO: make this required once the dataloader supports it required: false uns: - type: string diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml index 85f6b0353b..5cead0fc3b 100644 --- a/src/tasks/predict_modality/api/file_prediction.yaml +++ b/src/tasks/predict_modality/api/file_prediction.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad" info: label: "Prediction" summary: "A prediction of the mod2 expression values of the test cells" diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml index 8f98054015..f8b4757601 100644 --- a/src/tasks/predict_modality/api/file_score.yaml +++ b/src/tasks/predict_modality/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/score.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index 8d047ae2da..843c40cf44 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad" info: label: "Test mod1" summary: "The mod1 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index 32cf147a70..3e98f508c0 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad" info: label: "Test mod2" summary: "The mod2 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index d09e88e786..fc629448d6 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad" info: label: "Train mod1" summary: "The mod1 expression values of the train cells." diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index 3587ba4912..25e4b2425b 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad" info: label: "Train mod2" summary: "The mod2 expression values of the train cells." diff --git a/src/tasks/predict_modality/control_methods/meanpergene/script.py b/src/tasks/predict_modality/control_methods/meanpergene/script.py index 12da162c5b..043f19d42a 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/script.py +++ b/src/tasks/predict_modality/control_methods/meanpergene/script.py @@ -4,10 +4,10 @@ # VIASH START par = { - "input_train_mod1": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", - "input_test_mod1": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", - "input_train_mod2": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", - "output": "../../../../resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", + "input_train_mod1": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad", + "input_test_mod1": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad", + "input_train_mod2": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad", + "output": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad", } meta = { diff --git a/src/tasks/predict_modality/control_methods/random_predict/script.R b/src/tasks/predict_modality/control_methods/random_predict/script.R index c9783bb773..ab96dcc26a 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/script.R +++ b/src/tasks/predict_modality/control_methods/random_predict/script.R @@ -4,9 +4,9 @@ library(Matrix, warn.conflicts = FALSE, quietly = TRUE) ## VIASH START par <- list( - input_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", - input_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", - input_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", + input_train_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad", + input_test_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad", + input_train_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad", output = "output.h5ad" ) meta <- list(functionality_name = "foo") diff --git a/src/tasks/predict_modality/control_methods/solution/script.R b/src/tasks/predict_modality/control_methods/solution/script.R index c2a39c9acb..ae7c288e29 100644 --- a/src/tasks/predict_modality/control_methods/solution/script.R +++ b/src/tasks/predict_modality/control_methods/solution/script.R @@ -3,7 +3,7 @@ requireNamespace("anndata", quietly = TRUE) ## VIASH START par <- list( - input_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", + input_test_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad", output = "output.h5ad" ) diff --git a/src/tasks/predict_modality/control_methods/zeros/script.py b/src/tasks/predict_modality/control_methods/zeros/script.py index 543512bbc5..600b5c696c 100644 --- a/src/tasks/predict_modality/control_methods/zeros/script.py +++ b/src/tasks/predict_modality/control_methods/zeros/script.py @@ -4,9 +4,9 @@ # VIASH START par = { - "input_train_mod1": "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", - "input_test_mod1": "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", - "input_train_mod2": "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", + "input_train_mod1": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad", + "input_test_mod1": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad", + "input_train_mod2": "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad", "output": "output.h5ad", } diff --git a/src/tasks/predict_modality/methods/knnr_py/script.py b/src/tasks/predict_modality/methods/knnr_py/script.py index 62a799a5f4..f08c335ffe 100644 --- a/src/tasks/predict_modality/methods/knnr_py/script.py +++ b/src/tasks/predict_modality/methods/knnr_py/script.py @@ -5,9 +5,9 @@ ## VIASH START par = { - 'input_train_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad', - 'input_train_mod2': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad', - 'input_test_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad', + 'input_train_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad', 'distance_method': 'minkowski', 'output': 'output.h5ad', 'n_pcs': 4, diff --git a/src/tasks/predict_modality/methods/newwave_knnr/script.R b/src/tasks/predict_modality/methods/newwave_knnr/script.R index 4451f5cf11..3d1cb7b731 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/script.R +++ b/src/tasks/predict_modality/methods/newwave_knnr/script.R @@ -6,7 +6,7 @@ requireNamespace("FNN", quietly = TRUE) requireNamespace("SingleCellExperiment", quietly = TRUE) ## VIASH START -path <- "resources_test/predict_modality/neurips2021_bmmc_cite/" +path <- "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/" par <- list( input_train_mod1 = paste0(path, "train_mod1.h5ad"), input_test_mod1 = paste0(path, "test_mod1.h5ad"), diff --git a/src/tasks/predict_modality/metrics/correlation/script.R b/src/tasks/predict_modality/metrics/correlation/script.R index c0d4e460e6..585ec7c2b1 100644 --- a/src/tasks/predict_modality/metrics/correlation/script.R +++ b/src/tasks/predict_modality/metrics/correlation/script.R @@ -5,11 +5,10 @@ requireNamespace("anndata", quietly = TRUE) ## VIASH START par <- list( - input_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", - input_prediction = "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", + input_test_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad", + input_prediction = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad", output = "output/scores.h5ad" ) -#/home/rcannood/workspace/openproblems/neurips2021_multimodal_viash/work/29/320fe1e10fcd323020345bcc8969c2/openproblems_bmmc_cite_mod2_dummy_mean_per_gene.correlation.output.h5ad ## VIASH END cat("Reading solution file\n") diff --git a/src/tasks/predict_modality/metrics/mse/script.py b/src/tasks/predict_modality/metrics/mse/script.py index fd98d93f34..a5ae6bcc53 100644 --- a/src/tasks/predict_modality/metrics/mse/script.py +++ b/src/tasks/predict_modality/metrics/mse/script.py @@ -4,8 +4,8 @@ ## VIASH START par = { - "input_test_mod2" : "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", - "input_prediction" : "resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad", + "input_test_mod2" : "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad", + "input_prediction" : "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad", "output" : "output/scores.h5ad" } ## VIASH END diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index ece7137647..e972a31605 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -15,6 +15,8 @@ platforms: setup: - type: r cran: [ bit64 ] + # TODO: remove this when reticulate >= 1.35 is released + github: rstudio/reticulate - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 18eb3d0dd1..3c89d9afcc 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -4,22 +4,22 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( - input_rna = "resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad", - input_other_mod = "resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad", - output_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad", - output_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad", - output_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad", - output_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad", + input_rna = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_rna.h5ad", + input_other_mod = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_other_mod.h5ad", + output_train_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad", + output_train_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad", + output_test_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad", + output_test_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad", swap = TRUE, seed = 1L ) # par <- list( -# input_rna = "resources_test/predict_modality/neurips2021_bmmc_mutliome/output_rna.h5ad", -# input_other_mod = "resources_test/predict_modality/neurips2021_bmmc_mutliome/output_atac.h5ad", -# output_train_mod1 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/train_mod1.h5ad", -# output_train_mod2 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/train_mod2.h5ad", -# output_test_mod1 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/test_mod1.h5ad", -# output_test_mod2 = "resources_test/predict_modality/neurips2021_bmmc_mutliome/test_mod2.h5ad", +# input_rna = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_rna.h5ad", +# input_other_mod = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_atac.h5ad", +# output_train_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/train_mod1.h5ad", +# output_train_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/train_mod2.h5ad", +# output_test_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/test_mod1.h5ad", +# output_test_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/test_mod2.h5ad", # swap = TRUE, # seed = 1L # ) diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index b2a0a9494c..5ce0c95608 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -34,10 +34,7 @@ functionality: - type: nextflow_script path: main.nf entrypoint: run_wf - - type: file - path: "/src/tasks/predict_modality/api/file_common_dataset_rna.yaml" - - type: file - path: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" + - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema - name: predict_modality/process_dataset diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 6aa9b70d43..451f6f080a 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -1,3 +1,5 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + workflow auto { findStates(params, meta.config) | meta.workflow.run( @@ -12,43 +14,46 @@ workflow run_wf { main: output_ch = input_ch - // TODO: check schema based on the values in `config` - // instead of having to provide a separate schema file | check_dataset_schema.run( key: "check_dataset_schema_rna", - fromState: { id, state -> - // as a resource + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "input_rna") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input_rna, - "schema": meta.resources_dir.resolve("file_common_dataset_rna.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset_rna": "output", - "dataset_checks": "checks" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset_rna": checks["exit_code"] == 0 ? state.input_rna : null, + ] + } ) | check_dataset_schema.run( key: "check_dataset_schema_other_mod", - fromState: { id, state -> - // as a resource + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "input_other_mod") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) [ "input": state.input_other_mod, - "schema": meta.resources_dir.resolve("file_common_dataset_other_mod.yaml") + "schema": schemaYaml ] }, - args: [ - "stop_on_error": false - ], - toState: [ - "dataset_other_mod": "output", - "dataset_checks": "checks" - ] + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset_other_mod": checks["exit_code"] == 0 ? state.input_other_mod : null, + ] + } ) + | view{"test: ${it}"} // remove datasets which didn't pass the schema check | filter { id, state -> diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index a7f19f5972..fa77795ab8 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -56,7 +56,7 @@ functionality: path: "/src/tasks/predict_modality/api/task_info.yaml" dependencies: - name: common/check_dataset_schema - - name: common/extract_scores + - name: common/extract_metadata - name: predict_modality/control_methods/mean_per_gene - name: predict_modality/control_methods/random_predict - name: predict_modality/control_methods/zeros diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index a0915c2f47..4b03ac0a2a 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -38,11 +38,12 @@ workflow run_wf { } // extract the dataset metadata - | check_dataset_schema.run( - fromState: [ "input": "input_train_mod1" ], + | extract_metadata.run( + fromState: [input: "input_train_mod1"], toState: { id, output, state -> - def dataset_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [dataset_uns: dataset_uns] + state + [ + dataset_uns: readYaml(output.output).uns + ] } ) @@ -104,12 +105,13 @@ workflow run_wf { ) // extract the scores - | check_dataset_schema.run( + | extract_metadata.run( key: "extract_scores", fromState: [input: "metric_output"], toState: { id, output, state -> - def score_uns = (new org.yaml.snakeyaml.Yaml().load(output.meta)).uns - state + [score_uns: score_uns] + state + [ + score_uns: readYaml(output.output).uns + ] } ) diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index affe3247c2..ceb5066280 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -8,7 +8,7 @@ cd "$REPO_ROOT" set -e -DATASETS_DIR="resources_test/predict_modality/neurips2021_bmmc_cite" +DATASETS_DIR="resources_test/predict_modality/openproblems_neurips2021/bmmc_cite" OUTPUT_DIR="output/predict_modality" if [ ! -d "$OUTPUT_DIR" ]; then diff --git a/src/wf_utils/helper.nf b/src/wf_utils/helper.nf new file mode 100644 index 0000000000..7b3acd5b1c --- /dev/null +++ b/src/wf_utils/helper.nf @@ -0,0 +1,14 @@ +Map findArgumentSchema(Map config, String argument_id) { + def argument_groups = + (config.functionality.argument_groups ?: []) + + [ + arguments: config.functionality.arguments ?: [] + ] + + def schema_value = argument_groups.findResult{ gr -> + gr.arguments.find { arg -> + arg.name == ("--" + argument_id) + } + } + return schema_value +} From 331cbcccf1bf942f3e3d460ec6ada0c141e4ec83 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 1 Feb 2024 09:18:25 +0100 Subject: [PATCH 1124/1233] Update input parameters dataset workflows (#351) * update input parameters * add labels * add feature_name, feature_id * update param_list * update test_resources * fix failed test * Add .var.feature arguments to workflow config * make feature_name required in raw (unimodal) datasets #ci force * fix extraction of dataset metadata * add review suggestion * also set feature_name to true [ci force] * disable ontology comp * update task_meta resources_test script * CI force * uncomment scripts * CI force * rename _rna to _mod1 and _other_mod to _mod2 * ci force * add feature_name to api bat_int * redorder the API file input * ci force * don't set method to random * ci force * update MERGE files of datasets API * ci force * ci force * keep_features cxg_mouse resource_test * fix resources test script * ci force --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 3d286d04eff84565975975d5eabf654b3ba15809 --- src/common/create_task_readme/config.vsh.yaml | 2 +- .../check_obsolete_terms/config.vsh.yaml | 1 + .../run/config.vsh.yaml | 2 +- .../process_dataset_metadata/run/run_test.sh | 3 +- .../resources_test_scripts/task_metadata.sh | 6 ++ src/datasets/api/comp_processor_hvg.yaml | 2 +- src/datasets/api/comp_processor_knn.yaml | 2 +- src/datasets/api/comp_processor_pca.yaml | 2 +- src/datasets/api/file_hvg.yaml | 4 +- src/datasets/api/file_knn.yaml | 4 +- src/datasets/api/file_multimodal_dataset.yaml | 2 +- src/datasets/api/file_pca.yaml | 4 +- src/datasets/api/file_raw.yaml | 2 +- .../openproblems_neurips2021_bmmc/script.py | 10 +-- .../loaders/openproblems_v1/config.vsh.yaml | 8 +++ .../loaders/openproblems_v1/script.py | 19 +++++- .../config.vsh.yaml | 8 +++ .../openproblems_v1_multimodal/script.py | 29 ++++++++ .../resource_scripts/cellxgene_census.sh | 3 +- .../openproblems_neurips2021_multimodal.sh | 11 +-- ...penproblems_neurips2021_multimodal_test.sh | 8 +-- .../resource_scripts/openproblems_v1.sh | 21 +++++- .../openproblems_v1_multimodal.sh | 8 ++- .../cxg_mouse_pancreas_atlas.sh | 22 ++++-- .../resource_test_scripts/neurips2021_bmmc.sh | 8 +-- .../resource_test_scripts/pancreas.sh | 2 + .../scicar_cell_lines.sh | 2 + .../process_cellxgene_census/main.nf | 6 +- .../config.vsh.yaml | 12 ++-- .../main.nf | 68 +++++++++---------- .../process_openproblems_v1/config.vsh.yaml | 8 +++ .../workflows/process_openproblems_v1/main.nf | 6 +- .../config.vsh.yaml | 8 +++ .../api/file_common_dataset.yaml | 4 ++ .../batch_integration/api/file_dataset.yaml | 4 ++ .../batch_integration/api/file_solution.yaml | 4 ++ .../resources_test_scripts/pancreas.sh | 2 +- .../api/comp_process_dataset.yaml | 8 +-- ...rna.yaml => file_common_dataset_mod1.yaml} | 4 +- ...mod.yaml => file_common_dataset_mod2.yaml} | 4 +- .../predict_modality/methods/knnr_r/script.R | 2 +- .../predict_modality/methods/lm/script.R | 2 +- .../methods/random_forest/script.R | 2 +- .../predict_modality/process_dataset/script.R | 12 ++-- .../resources_scripts/process_datasets.sh | 2 +- .../neurips2021_bmmc.sh | 2 +- .../process_datasets/config.vsh.yaml | 8 +-- .../workflows/process_datasets/main.nf | 24 +++---- .../workflows/process_datasets/run_test.sh | 2 +- 49 files changed, 262 insertions(+), 127 deletions(-) rename src/tasks/predict_modality/api/{file_common_dataset_rna.yaml => file_common_dataset_mod1.yaml} (98%) rename src/tasks/predict_modality/api/{file_common_dataset_other_mod.yaml => file_common_dataset_mod2.yaml} (97%) diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index b869dbf5eb..ab9a0c8ebb 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -43,7 +43,7 @@ platforms: # download and install quarto-*-linux-amd64.deb from latest release run: | release_info=$(curl -s https://api.github.com/repos/quarto-dev/quarto-cli/releases/latest) && \ - download_url=$(echo "$release_info" | jq -r '.assets[] | select(.name | test("quarto-.*-linux-amd64.deb")) | .browser_download_url') && \ + download_url=$(printf "%s" "$release_info" | jq -r '.assets[] | select(.name | test("quarto-.*-linux-amd64.deb")) | .browser_download_url') && \ curl -sL "$download_url" -o /opt/quarto.deb && \ dpkg -i /opt/quarto.deb && \ rm /opt/quarto.deb diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml index 025562c09f..88bf830edf 100644 --- a/src/common/ontology/check_obsolete_terms/config.vsh.yaml +++ b/src/common/ontology/check_obsolete_terms/config.vsh.yaml @@ -1,4 +1,5 @@ functionality: + status: disabled name: check_obsolete_terms namespace: common/ontology description: | diff --git a/src/common/process_dataset_metadata/run/config.vsh.yaml b/src/common/process_dataset_metadata/run/config.vsh.yaml index 62396558b0..550b621ef6 100644 --- a/src/common/process_dataset_metadata/run/config.vsh.yaml +++ b/src/common/process_dataset_metadata/run/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: type: file required: true direction: output - default: $id.json + default: meta.json resources: - type: nextflow_script path: main.nf diff --git a/src/common/process_dataset_metadata/run/run_test.sh b/src/common/process_dataset_metadata/run/run_test.sh index 397b26f51e..3d5f829eee 100644 --- a/src/common/process_dataset_metadata/run/run_test.sh +++ b/src/common/process_dataset_metadata/run/run_test.sh @@ -29,8 +29,9 @@ for LOADER in "cellxgene_census" "openproblems_v1"; do -main-script target/nextflow/common/process_dataset_metadata/run/main.nf \ -profile docker \ -c src/wf_utils/labels_ci.config \ - --id "process" \ + --id "extract_metadata" \ --input "$INPUT" \ + --output meta.json \ --output_state "state.yaml" \ --publish_dir "$OUTPUT_DIR" diff --git a/src/common/resources_test_scripts/task_metadata.sh b/src/common/resources_test_scripts/task_metadata.sh index 8c6afa39ac..cd9072f443 100755 --- a/src/common/resources_test_scripts/task_metadata.sh +++ b/src/common/resources_test_scripts/task_metadata.sh @@ -125,9 +125,15 @@ nextflow run . \ -profile docker \ -resume \ -c src/wf_utils/labels_ci.config \ + -with-trace \ -entry auto \ --input_states "$DATASETS_DIR/pancreas/state.yaml" \ --rename_keys 'input_dataset:output_dataset,input_solution:output_solution' \ --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml", "method_ids": ["bbknn", "mnnpy", "mnnr"]}' \ --publish_dir "$OUTPUT_DIR" \ --output_state "state.yaml" + +cp trace.txt "$OUTPUT_DIR/trace.txt" + + +viash run src/common/process_task_results/get_method_info/config.vsh.yaml -- --input "$OUTPUT_DIR/method_configs.yaml" --output "$OUTPUT_DIR/method_info.json" diff --git a/src/datasets/api/comp_processor_hvg.yaml b/src/datasets/api/comp_processor_hvg.yaml index 3935525f54..2e24033aac 100644 --- a/src/datasets/api/comp_processor_hvg.yaml +++ b/src/datasets/api/comp_processor_hvg.yaml @@ -10,7 +10,7 @@ functionality: The resulting AnnData will contain both a boolean 'hvg' column in 'var', as well as a numerical 'hvg_score' in 'var'. arguments: - name: "--input" - __merge__: file_pca.yaml + __merge__: file_normalized.yaml required: true direction: input - name: "--input_layer" diff --git a/src/datasets/api/comp_processor_knn.yaml b/src/datasets/api/comp_processor_knn.yaml index 1da86f9231..b0e16f8fc4 100644 --- a/src/datasets/api/comp_processor_knn.yaml +++ b/src/datasets/api/comp_processor_knn.yaml @@ -10,7 +10,7 @@ functionality: The resulting AnnData will contain both the knn distances and the knn connectivities in 'obsp'. arguments: - name: "--input" - __merge__: file_hvg.yaml + __merge__: file_pca.yaml required: true direction: input - name: "--input_layer" diff --git a/src/datasets/api/comp_processor_pca.yaml b/src/datasets/api/comp_processor_pca.yaml index f82419329c..a7ca82bc07 100644 --- a/src/datasets/api/comp_processor_pca.yaml +++ b/src/datasets/api/comp_processor_pca.yaml @@ -10,7 +10,7 @@ functionality: The resulting AnnData will contain an embedding in obsm, as well as optional loadings in 'varm'. arguments: - name: "--input" - __merge__: file_normalized.yaml + __merge__: file_hvg.yaml required: true direction: input - name: "--input_layer" diff --git a/src/datasets/api/file_hvg.yaml b/src/datasets/api/file_hvg.yaml index 81cdac966f..0e9f05c30f 100644 --- a/src/datasets/api/file_hvg.yaml +++ b/src/datasets/api/file_hvg.yaml @@ -1,8 +1,8 @@ -__merge__: file_pca.yaml +__merge__: file_normalized.yaml type: file example: "resources_test/common/pancreas/hvg.h5ad" info: - label: "Dataset+PCA+HVG" + label: "Dataset+HVG" summary: "A normalised dataset with a PCA embedding and HVG selection." slots: var: diff --git a/src/datasets/api/file_knn.yaml b/src/datasets/api/file_knn.yaml index 497430369e..de7d2b8df5 100644 --- a/src/datasets/api/file_knn.yaml +++ b/src/datasets/api/file_knn.yaml @@ -1,8 +1,8 @@ -__merge__: file_hvg.yaml +__merge__: file_pca.yaml type: file example: "resources_test/common/pancreas/knn.h5ad" info: - label: "Dataset+PCA+HVG+kNN" + label: "Dataset+HVG+PCA+kNN" summary: "A normalised data with a PCA embedding, HVG selection and a kNN graph" slots: obsp: diff --git a/src/datasets/api/file_multimodal_dataset.yaml b/src/datasets/api/file_multimodal_dataset.yaml index 1613993358..950e9158f0 100644 --- a/src/datasets/api/file_multimodal_dataset.yaml +++ b/src/datasets/api/file_multimodal_dataset.yaml @@ -177,7 +177,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: false + required: true - type: integer name: soma_joinid diff --git a/src/datasets/api/file_pca.yaml b/src/datasets/api/file_pca.yaml index 267f00b6a7..daa26618e1 100644 --- a/src/datasets/api/file_pca.yaml +++ b/src/datasets/api/file_pca.yaml @@ -1,8 +1,8 @@ -__merge__: file_normalized.yaml +__merge__: file_hvg.yaml type: file example: "resources_test/common/pancreas/pca.h5ad" info: - label: "Dataset+PCA" + label: "Dataset+HVG+PCA" summary: "A normalised dataset with a PCA embedding" slots: obsm: diff --git a/src/datasets/api/file_raw.yaml b/src/datasets/api/file_raw.yaml index c4eaf1b17c..7ffab3b43e 100644 --- a/src/datasets/api/file_raw.yaml +++ b/src/datasets/api/file_raw.yaml @@ -166,7 +166,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: false + required: true - type: integer name: soma_joinid diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index 0b95f94af8..e573cd68de 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -22,7 +22,7 @@ } ## VIASH END -def remove_other_mod_col(df, mod): +def remove_mod_col(df, mod): df.drop(list(df.filter(like=mod)), axis=1, inplace=True) def remove_mod_prefix(df, mod): @@ -50,7 +50,7 @@ def remove_mod_prefix(df, mod): # Remove other modality data from obs and var mod1_var = pd.DataFrame(adata_mod1.var) -remove_other_mod_col(mod1_var, par["mod2"]) +remove_mod_col(mod1_var, par["mod2"]) remove_mod_prefix(mod1_var, par["mod1"]) mod1_var.index.name = "feature_name" mod1_var.reset_index("feature_name", inplace=True) @@ -59,7 +59,7 @@ def remove_mod_prefix(df, mod): mod1_var.set_index("feature_id", drop=False, inplace=True) mod1_obs = pd.DataFrame(adata_mod1.obs) -remove_other_mod_col(mod1_obs, par["mod2"]) +remove_mod_col(mod1_obs, par["mod2"]) remove_mod_prefix(mod1_obs, par["mod1"]) adata_mod1.var = mod1_var @@ -70,7 +70,7 @@ def remove_mod_prefix(df, mod): del adata_mod1.X mod2_var = pd.DataFrame(adata_mod2.var) -remove_other_mod_col(mod2_var, par["mod1"]) +remove_mod_col(mod2_var, par["mod1"]) remove_mod_prefix(mod2_var, par["mod2"]) mod2_var.index.name = "feature_name" mod2_var.reset_index("feature_name", inplace=True) @@ -79,7 +79,7 @@ def remove_mod_prefix(df, mod): mod2_var.set_index("feature_id", drop=False, inplace=True) mod2_obs = pd.DataFrame(adata_mod2.obs) -remove_other_mod_col(mod2_obs, par["mod1"]) +remove_mod_col(mod2_obs, par["mod1"]) remove_mod_prefix(mod2_obs, par["mod2"]) adata_mod2.var = mod2_var diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 5feab80c1b..584d79cd30 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -26,6 +26,14 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: "--var_feature_id" + type: "string" + description: "Location of where to find the feature IDs. Can be set to index if the feature IDs are the index." + example: gene_ids + - name: "--var_feature_name" + type: "string" + description: "Location of where to find the feature names. Can be set to index if the feature names are the index." + default: index - name: Metadata arguments: - name: "--dataset_id" diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 1d8226249c..1587719239 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -102,8 +102,23 @@ } adata.uns.update(uns_metadata) -# TODO: fix var annotation -# - add feature_id and feature_name +print("Setting .var['feature_name']", flush=True) +if par["var_feature_name"]: + if par["var_feature_name"] == "index": + adata.var["feature_name"] = adata.var.index + elif par["var_feature_name"] in adata.var: + adata.var["feature_name"] = adata.var[par["feature_name"]] + else: + print(f"Warning: key '{par['var_feature_name']}' could not be found in adata.var.", flush=True) + +print("Setting .var['feature_id']", flush=True) +if par["var_feature_id"]: + if par["var_feature_id"] == "index": + adata.var["feature_id"] = adata.var.index + elif par["var_feature_id"] in adata.var: + adata.var["feature_id"] = adata.var[par["feature_id"]] + else: + print(f"Warning: key '{par['var_feature_id']}' could not be found in adata.var.", flush=True) print("Writing adata to file", flush=True) adata.write_h5ad(par["output"], compression="gzip") diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index 585dfc4531..ee5cbd0607 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -26,6 +26,14 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: "--var_feature_id" + type: "string" + description: "Location of where to find the feature IDs. Can be set to index if the feature IDs are the index." + example: gene_ids + - name: "--var_feature_name" + type: "string" + description: "Location of where to find the feature names. Can be set to index if the feature names are the index." + default: index - name: Metadata arguments: - name: "--dataset_id" diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py index 6a619ee93d..959ec50d9e 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/script.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -120,6 +120,35 @@ del mod1.X del mod2.X +print("Setting .var['feature_name']", flush=True) +if par["var_feature_name"] == "index": + mod1.var["feature_name"] = mod1.var.index + mod2.var["feature_name"] = mod2.var.index +else: + if par["var_feature_name"] in mod1.var: + mod1.var["feature_name"] = mod1.var[par["feature_name"]] + else: + print(f"Warning: key '{par['var_feature_name']}' could not be found in adata_mod1.var.", flush=True) + if par["var_feature_name"] in mod2.var: + mod2.var["feature_name"] = mod2.var[par["feature_name"]] + else: + print(f"Warning: key '{par['var_feature_name']}' could not be found in adata_mod2.var.", flush=True) + +print("Setting .var['feature_id']", flush=True) +if par["var_feature_id"] == "index": + mod1.var["feature_id"] = mod1.var.index + mod2.var["feature_id"] = mod2.var.index +else: + if par["var_feature_id"] in mod1.var: + mod1.var["feature_id"] = mod1.var[par["feature_id"]] + else: + print(f"Warning: key '{par['var_feature_id']}' could not be found in adata_mod1.var.", flush=True) + if par["var_feature_id"] in mod2.var: + mod2.var["feature_id"] = mod2.var[par["feature_id"]] + else: + print(f"Warning: key '{par['var_feature_id']}' could not be found in adata_mod2.var.", flush=True) + + print("Add metadata to uns", flush=True) metadata_fields = [ "dataset_id", "dataset_name", "dataset_url", "dataset_reference", diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index c0555dbd2b..089600b5ef 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -149,4 +149,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file "/tmp/params.yaml" \ - --config /tmp/nextflow.config + --config /tmp/nextflow.config \ + --labels cellxgene_census,dataset_loader diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index 97b592413b..236ecf3c7c 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -27,10 +27,10 @@ param_list: dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" dataset_reference: luecken2021neurips normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_rna: '$id/dataset_rna.h5ad' -output_other_mod: '$id/dataset_other_mod.h5ad' -output_meta_rna: '$id/dataset_metadata_rna.yaml' -output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' publish_dir: s3://openproblems-data/resources/datasets HERE @@ -51,4 +51,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file "$params_file" \ - --config /tmp/nextflow.config + --config /tmp/nextflow.config \ + --labels openproblems_neurips2021_bmmc,dataset_loader \ diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh index 26631d43d8..be8444371b 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal_test.sh @@ -27,10 +27,10 @@ param_list: dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" dataset_reference: luecken2021neurips normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_rna: '$id/dataset_rna.h5ad' -output_other_mod: '$id/dataset_other_mod.h5ad' -output_meta_rna: '$id/dataset_metadata_rna.yaml' -output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' publish_dir: resources/datasets/openproblems_neurips2021 HERE diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index 84846dd9c7..cea09b2e65 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -20,6 +20,7 @@ param_list: dataset_summary: Adult mouse primary visual cortex dataset_description: A murine brain atlas with adjacent cell types as assumed benchmark truth, inferred from deconvolution proportion correlations using matching 10x Visium slides (see Dimitrov et al., 2022). dataset_organism: mus_musculus + var_feature_name: index - id: openproblems_v1/cengen obs_cell_type: cell_type @@ -33,6 +34,7 @@ param_list: dataset_summary: Complete Gene Expression Map of an Entire Nervous System dataset_description: 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. dataset_organism: caenorhabditis_elegans + var_feature_name: index - id: openproblems_v1/immune_cells obs_cell_type: final_annotation @@ -46,6 +48,7 @@ param_list: dataset_summary: Human immune cells dataset from the scIB benchmarks dataset_description: Human immune cells from peripheral blood and bone marrow taken from 5 datasets comprising 10 batches across technologies (10X, Smart-seq2). dataset_organism: homo_sapiens + var_feature_name: index - id: openproblems_v1/mouse_blood_olsson_labelled obs_cell_type: celltype @@ -57,6 +60,7 @@ param_list: dataset_summary: Myeloid lineage differentiation from mouse blood dataset_description: 660 FACS-isolated myeloid cells from 9 experiments sequenced using C1 Fluidigm and SMARTseq in 2016 by Olsson et al. dataset_organism: mus_musculus + var_feature_name: index - id: openproblems_v1/mouse_hspc_nestorowa2016 obs_cell_type: cell_type_label @@ -68,6 +72,9 @@ param_list: dataset_summary: Haematopoeitic stem and progenitor cells from mouse bone marrow dataset_description: 1656 hematopoietic stem and progenitor cells from mouse bone marrow. Sequenced by Smart-seq2. dataset_organism: mus_musculus + var_feature_name: name + var_feature_id: converted_alias + - id: openproblems_v1/pancreas obs_cell_type: celltype @@ -80,6 +87,7 @@ param_list: dataset_summary: Human pancreas cells dataset from the scIB benchmarks dataset_description: Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). dataset_organism: homo_sapiens + var_feature_name: index # disabled as this is not working in openproblemsv1 # - id: openproblems_v1/tabula_muris_senis_droplet_lung @@ -103,6 +111,7 @@ param_list: dataset_summary: 1k peripheral blood mononuclear cells from a healthy donor dataset_description: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in November 2018 by 10X Genomics. dataset_organism: homo_sapiens + var_feature_name: index - id: openproblems_v1/tenx_5k_pbmc layer_counts: counts @@ -113,6 +122,9 @@ param_list: dataset_summary: 5k peripheral blood mononuclear cells from a healthy donor dataset_description: 5k Peripheral Blood Mononuclear Cells (PBMCs) from a healthy donor. Sequenced on 10X v3 chemistry in July 2019 by 10X Genomics. dataset_organism: homo_sapiens + var_feature_name: index + var_feature_id: gene_ids + - id: openproblems_v1/tnbc_wu2021 obs_cell_type: celltype_minor @@ -124,6 +136,7 @@ param_list: dataset_summary: 1535 cells from six fresh triple-negative breast cancer tumors. dataset_description: 1535 cells from six TNBC donors by (Wu et al., 2021). This dataset includes cytokine activities, inferred using a multivariate linear model with cytokine-focused signatures, as assumed true cell-cell communication (Dimitrov et al., 2022). dataset_organism: homo_sapiens + var_feature_name: index - id: openproblems_v1/zebrafish obs_cell_type: cell_type @@ -136,6 +149,9 @@ param_list: dataset_summary: Single-cell mRNA sequencing of zebrafish embryonic cells. dataset_description: 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. dataset_organism: danio_rerio + var_feature_name: index + var_feature_id: index + normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset: '$id/dataset.h5ad' @@ -156,10 +172,11 @@ process { HERE tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision integration_build \ + --revision main_build \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file "$params_file" \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels openproblems_v1,dataset_loader \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index c4b3896d70..ed8e1a77e3 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -19,6 +19,7 @@ param_list: dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 dataset_organism: homo_sapiens layer_counts: counts + var_feature_name: index - id: openproblems_v1_multimodal/scicar_cell_lines input_id: scicar_cell_lines @@ -30,6 +31,8 @@ param_list: dataset_organism: "[homo_sapiens, mus_musculus]" obs_cell_type: cell_name layer_counts: counts + var_feature_id: index + var_feature_name: gene_short_name - id: openproblems_v1_multimodal/scicar_mouse_kidney input_id: scicar_mouse_kidney @@ -42,6 +45,8 @@ param_list: obs_cell_type: cell_name obs_batch: replicate layer_counts: counts + var_feature_id: index + var_feature_name: gene_short_name normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset_mod1: '$id/dataset_mod1.h5ad' @@ -58,4 +63,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ - --params-file "$params_file" \ \ No newline at end of file + --params-file "$params_file" \ + --labels openproblems_v1_multimodal,dataset_loader \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh index df5dfa054d..f6b5fc971c 100755 --- a/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh +++ b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh @@ -1,8 +1,15 @@ #!/bin/bash -set -e +DATASET_DIR=resources_test/common -cat > "/tmp/params.yaml" << 'HERE' + +mkdir -p $DATASET_DIR + +wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/g2m_genes_tirosh.txt -O $DATASET_DIR/temp_g2m_genes_tirosh_mm.txt +wget https://raw.githubusercontent.com/theislab/scib/c993ffd9ccc84ae0b1681928722ed21985fb91d1/scib/resources/s_genes_tirosh.txt -O $DATASET_DIR/temp_s_genes_tirosh_mm.txt +KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_mm.txt $DATASET_DIR/temp_s_genes_tirosh_mm.txt | paste -sd ":" -` + +cat > "/tmp/params.yaml" << HERE param_list: - id: cxg_mouse_pancreas_atlas species: mus_musculus @@ -17,16 +24,17 @@ param_list: dataset_organism: mus_musculus normalization_methods: [log_cp10k] -output_dataset: '$id/dataset.h5ad' -output_meta: '$id/dataset_metadata.yaml' -output_state: '$id/state.yaml' +output_dataset: '\$id/dataset.h5ad' +output_meta: '\$id/dataset_metadata.yaml' +output_state: '\$id/state.yaml' output_raw: force_null output_normalized: force_null output_pca: force_null output_hvg: force_null output_knn: force_null -publish_dir: resources_test/common +publish_dir: $DATASET_DIR do_subsample: true +keep_features: '$KEEP_FEATURES' HERE nextflow run . \ @@ -34,4 +42,6 @@ nextflow run . \ -profile docker \ -params-file "/tmp/params.yaml" +rm -r $DATASET_DIR/temp_* + # src/tasks/batch_integration/resources_test_scripts/process.sh \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 13b4e7fdfa..2e40f86734 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -30,10 +30,10 @@ normalization_methods: [log_cp10k] do_subsample: true n_obs: 600 n_vars: 1500 -output_rna: '$id/dataset_rna.h5ad' -output_other_mod: '$id/dataset_other_mod.h5ad' -output_meta_rna: '$id/dataset_metadata_rna.yaml' -output_meta_other_mod: '$id/dataset_metadata_other_mod.yaml' +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' # publish_dir: s3://openproblems-data/resources_test/common HERE diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 3c6de41303..9c0b1c5717 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -20,11 +20,13 @@ KEEP_FEATURES=`cat $DATASET_DIR/temp_g2m_genes_tirosh_hm.txt $DATASET_DIR/temp_s nextflow run . \ -main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ -profile docker \ + -c src/wf_utils/labels_ci.config \ -resume \ --id pancreas \ --input_id pancreas \ --obs_cell_type "celltype" \ --obs_batch "tech" \ + --var_feature_name "index" \ --layer_counts "counts" \ --dataset_name "Human pancreas" \ --dataset_url "https://theislab.github.io/scib-reproducibility/dataset_pancreas.html" \ diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 8f2c51067b..8aa67c556f 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -22,6 +22,8 @@ nextflow run . \ --obs_tissue "source" \ --layer_counts "counts" \ --obs_cell_type "cell_name" \ + --var_feature_id "index" \ + --var_feature_name "gene_short_name" \ --dataset_name "sci-CAR cell lines" \ --dataset_url "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089" \ --dataset_reference "cao2018joint" \ diff --git a/src/datasets/workflows/process_cellxgene_census/main.nf b/src/datasets/workflows/process_cellxgene_census/main.nf index ea442143fe..bd1fc813a9 100644 --- a/src/datasets/workflows/process_cellxgene_census/main.nf +++ b/src/datasets/workflows/process_cellxgene_census/main.nf @@ -109,17 +109,17 @@ workflow run_wf { ) | hvg.run( - fromState: ["input": "output_pca"], + fromState: ["input": "output_normalized"], toState: ["output_hvg": "output"] ) | pca.run( - fromState: ["input": "output_normalized"], + fromState: ["input": "output_hvg"], toState: ["output_pca": "output" ] ) | knn.run( - fromState: ["input": "output_hvg"], + fromState: ["input": "output_pca"], toState: ["output_knn": "output"] ) diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml index 5da6b740b5..aa991910bf 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml @@ -95,22 +95,22 @@ functionality: description: "Which normalization methods to run." - name: Outputs arguments: - - name: "--output_rna" + - name: "--output_mod1" direction: "output" __merge__: /src/datasets/api/file_multimodal_dataset.yaml - - name: "--output_other_mod" + - name: "--output_mod2" direction: "output" __merge__: /src/datasets/api/file_multimodal_dataset.yaml - - name: "--output_meta_rna" + - name: "--output_meta_mod1" direction: "output" type: file description: "Dataset metadata" - example: "dataset_metadata_rna.yaml" - - name: "--output_meta_other_mod" + example: "dataset_metadata_mod1.yaml" + - name: "--output_meta_mod2" direction: "output" type: file description: "Dataset metadata" - example: "dataset_metadata_other_mod.yaml" + example: "dataset_metadata_mod2.yaml" resources: - type: nextflow_script path: main.nf diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index 3d3f2a83f4..124cee9b9e 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -60,8 +60,8 @@ workflow run_wf { "dataset_organism": "dataset_organism" ], toState: [ - "raw_rna": "output_mod1", - "raw_other_mod": "output_mod2" + "raw_mod1": "output_mod1", + "raw_mod2": "output_mod2" ] ) @@ -69,8 +69,8 @@ workflow run_wf { | subsample.run( runIf: { id, state -> state.do_subsample }, fromState: [ - "input": "raw_rna", - "input_mod2": "raw_other_mod", + "input": "raw_mod1", + "input_mod2": "raw_mod2", "n_obs": "n_obs", "n_vars": "n_vars", "keep_features": "keep_features", @@ -80,8 +80,8 @@ workflow run_wf { "seed": "seed" ], toState: [ - "raw_rna": "output", - "raw_other_mod": "output_mod2" + "raw_mod1": "output", + "raw_mod2": "output_mod2" ] ) @@ -98,11 +98,11 @@ workflow run_wf { filter: { id, state, comp -> comp.name in state.normalization_methods }, - fromState: ["input": "raw_rna"], + fromState: ["input": "raw_mod1"], toState: { id, output, state, comp -> state + [ "normalization_id": comp.name, - "normalized_rna": output.output + "normalized_mod1": output.output ] } ) @@ -113,83 +113,83 @@ workflow run_wf { key: "log_cp10k_adt", runIf: { id, state -> state.mod2 == "ADT" }, args: [normalization_id: "log_cp10k", n_cp: 10000], - fromState: ["input": "raw_other_mod"], - toState: ["normalized_other_mod": "output"] + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] ) | log_cp.run( key: "log_cp10k_atac", runIf: { id, state -> state.mod2 == "ATAC" }, args: [normalization_id: "log_cp10k", n_cp: 10000], - fromState: ["input": "raw_other_mod"], - toState: ["normalized_other_mod": "output"] + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] ) | svd.run( fromState: [ - "input": "normalized_rna", - "input_mod2": "normalized_other_mod" + "input": "normalized_mod1", + "input_mod2": "normalized_mod2" ], toState: [ - "svd_rna": "output", - "svd_other_mod": "output_mod2" + "svd_mod1": "output", + "svd_mod2": "output_mod2" ] ) | hvg.run( - fromState: [ "input": "svd_rna" ], - toState: [ "hvg_rna": "output" ] + fromState: [ "input": "svd_mod1" ], + toState: [ "hvg_mod1": "output" ] ) // TODO: should this only run on ATAC? or even not at all?s | hvg.run( - key: "hvg_other_mod", - fromState: [ "input": "svd_other_mod" ], - toState: [ "hvg_other_mod": "output" ] + key: "hvg_mod2", + fromState: [ "input": "svd_mod2" ], + toState: [ "hvg_mod2": "output" ] ) // add synonyms | map{ id, state -> - [id, state + ["output_rna": state.hvg_rna, "output_other_mod": state.hvg_other_mod]] + [id, state + ["output_mod1": state.hvg_mod1, "output_mod2": state.hvg_mod2]] } | extract_metadata.run( - key: "extract_metadata_rna", + key: "extract_metadata_mod1", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "output_rna") + def schema = findArgumentSchema(meta.config, "output_mod1") // workaround: convert GString to String schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.output_rna, + "input": state.output_mod1, "schema": schemaYaml ] }, - toState: ["output_meta_rna": "output"] + toState: ["output_meta_mod1": "output"] ) | extract_metadata.run( - key: "extract_metadata_other_mod", + key: "extract_metadata_mod2", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "output_other_mod") + def schema = findArgumentSchema(meta.config, "output_mod2") // workaround: convert GString to String schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.output_other_mod, + "input": state.output_mod2, "schema": schemaYaml ] }, - toState: ["output_meta_other_mod": "output"] + toState: ["output_meta_mod2": "output"] ) // only output the files for which an output file was specified | setState([ - "output_rna", - "output_other_mod", - "output_meta_rna", - "output_meta_other_mod", + "output_mod1", + "output_mod2", + "output_meta_mod1", + "output_meta_mod2", "_meta" ]) diff --git a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml index 431ffe7b8d..fb0cd73a65 100644 --- a/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1/config.vsh.yaml @@ -31,6 +31,14 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: "--var_feature_id" + type: "string" + description: "Location of where to find the feature IDs. Can be set to index if the feature IDs are the index." + example: gene_ids + - name: "--var_feature_name" + type: "string" + description: "Location of where to find the feature names. Can be set to index if the feature names are the index." + default: index - name: Metadata arguments: - name: "--dataset_name" diff --git a/src/datasets/workflows/process_openproblems_v1/main.nf b/src/datasets/workflows/process_openproblems_v1/main.nf index 90ec95e0f7..ad57d63029 100644 --- a/src/datasets/workflows/process_openproblems_v1/main.nf +++ b/src/datasets/workflows/process_openproblems_v1/main.nf @@ -107,17 +107,17 @@ workflow run_wf { ) | hvg.run( - fromState: ["input": "output_pca"], + fromState: ["input": "output_normalized"], toState: ["output_hvg": "output"] ) | pca.run( - fromState: ["input": "output_normalized"], + fromState: ["input": "output_hvg"], toState: ["output_pca": "output" ] ) | knn.run( - fromState: ["input": "output_hvg"], + fromState: ["input": "output_pca"], toState: ["output_knn": "output"] ) diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index 1342df38c2..ad607c2229 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -31,6 +31,14 @@ functionality: type: boolean default: true description: Convert layers to a sparse CSR format. + - name: "--var_feature_id" + type: "string" + description: "Location of where to find the feature IDs. Can be set to index if the feature IDs are the index." + example: gene_ids + - name: "--var_feature_name" + type: "string" + description: "Location of where to find the feature names. Can be set to index if the feature names are the index." + default: index - name: Metadata arguments: - name: "--dataset_name" diff --git a/src/tasks/batch_integration/api/file_common_dataset.yaml b/src/tasks/batch_integration/api/file_common_dataset.yaml index 555a82b51d..66b7d14ecc 100644 --- a/src/tasks/batch_integration/api/file_common_dataset.yaml +++ b/src/tasks/batch_integration/api/file_common_dataset.yaml @@ -30,6 +30,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + required: true obsm: - type: double name: X_pca diff --git a/src/tasks/batch_integration/api/file_dataset.yaml b/src/tasks/batch_integration/api/file_dataset.yaml index 2ea6d0a94a..c53688aaf1 100644 --- a/src/tasks/batch_integration/api/file_dataset.yaml +++ b/src/tasks/batch_integration/api/file_dataset.yaml @@ -27,6 +27,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + required: true obsm: - type: double name: X_pca diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml index 463a82d50b..ea606cb22b 100644 --- a/src/tasks/batch_integration/api/file_solution.yaml +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -27,6 +27,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: string + name: feature_name + description: A human-readable name for the feature, usually a gene symbol. + required: true obsm: - type: double name: X_pca diff --git a/src/tasks/label_projection/resources_test_scripts/pancreas.sh b/src/tasks/label_projection/resources_test_scripts/pancreas.sh index 76d38f4978..5a69340510 100755 --- a/src/tasks/label_projection/resources_test_scripts/pancreas.sh +++ b/src/tasks/label_projection/resources_test_scripts/pancreas.sh @@ -21,7 +21,7 @@ nextflow run . \ -entry auto \ --input_states "$RAW_DATA/**/state.yaml" \ --rename_keys 'input:output_dataset' \ - --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad", "method": "random"}' \ + --settings '{"output_train": "$id/train.h5ad", "output_test": "$id/test.h5ad", "output_solution": "$id/solution.h5ad"}' \ --publish_dir "$DATASET_DIR" \ --output_state '$id/state.yaml' # output_state should be moved to settings once workaround is solved diff --git a/src/tasks/predict_modality/api/comp_process_dataset.yaml b/src/tasks/predict_modality/api/comp_process_dataset.yaml index 37c85a6bcc..c2c5feb2eb 100644 --- a/src/tasks/predict_modality/api/comp_process_dataset.yaml +++ b/src/tasks/predict_modality/api/comp_process_dataset.yaml @@ -8,12 +8,12 @@ functionality: description: | A component for processing a Common Dataset into a task-specific dataset. arguments: - - name: "--input_rna" - __merge__: file_common_dataset_rna.yaml + - name: "--input_mod1" + __merge__: file_common_dataset_mod1.yaml direction: input required: true - - name: "--input_other_mod" - __merge__: file_common_dataset_other_mod.yaml + - name: "--input_mod2" + __merge__: file_common_dataset_mod2.yaml direction: input required: true - name: "--output_train_mod1" diff --git a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml similarity index 98% rename from src/tasks/predict_modality/api/file_common_dataset_rna.yaml rename to src/tasks/predict_modality/api/file_common_dataset_mod1.yaml index 185c37c173..8bb39fb505 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_rna.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_rna.h5ad" +example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad" info: label: "Raw dataset RNA" summary: "The RNA modality of the raw dataset." @@ -33,7 +33,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: false + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml similarity index 97% rename from src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml rename to src/tasks/predict_modality/api/file_common_dataset_mod2.yaml index 1b4e26c451..dfa67d3898 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_other_mod.h5ad" +example: "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad" info: label: "Raw dataset mod2" summary: "The second modality of the raw dataset. Must be an ADT or an ATAC dataset" @@ -33,7 +33,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: false + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/methods/knnr_r/script.R b/src/tasks/predict_modality/methods/knnr_r/script.R index b7c20f6596..5679f8dd2d 100644 --- a/src/tasks/predict_modality/methods/knnr_r/script.R +++ b/src/tasks/predict_modality/methods/knnr_r/script.R @@ -3,7 +3,7 @@ requireNamespace("anndata", quietly = TRUE) library(Matrix, warn.conflicts = FALSE, quietly = TRUE) ## VIASH START -path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_mod1/openproblems_bmmc_multiome_phase1_mod1.censor_dataset.output_" par <- list( input_train_mod1 = paste0(path, "train_mod1.h5ad"), input_test_mod1 = paste0(path, "test_mod1.h5ad"), diff --git a/src/tasks/predict_modality/methods/lm/script.R b/src/tasks/predict_modality/methods/lm/script.R index 410b47f803..58d3febfb5 100644 --- a/src/tasks/predict_modality/methods/lm/script.R +++ b/src/tasks/predict_modality/methods/lm/script.R @@ -4,7 +4,7 @@ requireNamespace("pbapply", quietly = TRUE) library(Matrix, warn.conflicts = FALSE, quietly = TRUE) ## VIASH START -path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_mod1/openproblems_bmmc_multiome_phase1_mod1.censor_dataset.output_" par <- list( input_train_mod1 = paste0(path, "train_mod1.h5ad"), input_test_mod1 = paste0(path, "test_mod1.h5ad"), diff --git a/src/tasks/predict_modality/methods/random_forest/script.R b/src/tasks/predict_modality/methods/random_forest/script.R index 91612bbd48..e148eefbf7 100644 --- a/src/tasks/predict_modality/methods/random_forest/script.R +++ b/src/tasks/predict_modality/methods/random_forest/script.R @@ -4,7 +4,7 @@ requireNamespace("pbapply", quietly = TRUE) library(Matrix, warn.conflicts = FALSE, quietly = TRUE) ## VIASH START -path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_rna/openproblems_bmmc_multiome_phase1_rna.censor_dataset.output_" +path <- "output/datasets/predict_modality/openproblems_bmmc_multiome_phase1_mod1/openproblems_bmmc_multiome_phase1_mod1.censor_dataset.output_" par <- list( input_train_mod1 = paste0(path, "train_mod1.h5ad"), input_test_mod1 = paste0(path, "test_mod1.h5ad"), diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 3c89d9afcc..875429e348 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -4,8 +4,8 @@ library(Matrix, warn.conflicts = FALSE) ## VIASH START par <- list( - input_rna = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_rna.h5ad", - input_other_mod = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_other_mod.h5ad", + input_mod1 = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad", + input_mod2 = "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad", output_train_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad", output_train_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad", output_test_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad", @@ -14,8 +14,8 @@ par <- list( seed = 1L ) # par <- list( -# input_rna = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_rna.h5ad", -# input_other_mod = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_atac.h5ad", +# input_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_mod1.h5ad", +# input_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/output_atac.h5ad", # output_train_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/train_mod1.h5ad", # output_train_mod2 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/train_mod2.h5ad", # output_test_mod1 = "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/test_mod1.h5ad", @@ -29,8 +29,8 @@ cat("Using seed ", par$seed, "\n", sep = "") set.seed(par$seed) cat("Reading input data\n") -ad1 <- anndata::read_h5ad(if (!par$swap) par$input_rna else par$input_other_mod) -ad2 <- anndata::read_h5ad(if (!par$swap) par$input_other_mod else par$input_rna) +ad1 <- anndata::read_h5ad(if (!par$swap) par$input_mod1 else par$input_mod2) +ad2 <- anndata::read_h5ad(if (!par$swap) par$input_mod2 else par$input_mod1) # figure out modality types ad1_mod <- unique(ad1$var[["feature_types"]]) diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index b80096a88a..e41f9da9cd 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -3,7 +3,7 @@ cat > /tmp/params.yaml << 'HERE' id: predict_modality_process_datasets input_states: s3://openproblems-data/resources/datasets/**/state.yaml -rename_keys: 'input_rna:output_rna,input_other_mod:output_other_mod' +rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/predict_modality/datasets diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 0879426660..981871f2b4 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -20,7 +20,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --input_states "resources_test/common/openproblems_neurips2021/**/state.yaml" \ - --rename_keys 'input_rna:output_rna,input_other_mod:output_other_mod' \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index 5ce0c95608..fe4bee1e5a 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -4,12 +4,12 @@ functionality: argument_groups: - name: Inputs arguments: - - name: "--input_rna" - __merge__: "/src/tasks/predict_modality/api/file_common_dataset_rna.yaml" + - name: "--input_mod1" + __merge__: "/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml" required: true direction: input - - name: "--input_other_mod" - __merge__: "/src/tasks/predict_modality/api/file_common_dataset_other_mod.yaml" + - name: "--input_mod2" + __merge__: "/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml" direction: input required: true - name: Outputs diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 451f6f080a..601ec04181 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -15,13 +15,13 @@ workflow run_wf { output_ch = input_ch | check_dataset_schema.run( - key: "check_dataset_schema_rna", + key: "check_dataset_schema_mod1", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "input_rna") + def schema = findArgumentSchema(meta.config, "input_mod1") def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.input_rna, + "input": state.input_mod1, "schema": schemaYaml ] }, @@ -29,19 +29,19 @@ workflow run_wf { // read the output to see if dataset passed the qc def checks = readYaml(output.output) state + [ - "dataset_rna": checks["exit_code"] == 0 ? state.input_rna : null, + "dataset_mod1": checks["exit_code"] == 0 ? state.input_mod1 : null, ] } ) | check_dataset_schema.run( - key: "check_dataset_schema_other_mod", + key: "check_dataset_schema_mod2", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "input_other_mod") + def schema = findArgumentSchema(meta.config, "input_mod2") def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.input_other_mod, + "input": state.input_mod2, "schema": schemaYaml ] }, @@ -49,7 +49,7 @@ workflow run_wf { // read the output to see if dataset passed the qc def checks = readYaml(output.output) state + [ - "dataset_other_mod": checks["exit_code"] == 0 ? state.input_other_mod : null, + "dataset_mod2": checks["exit_code"] == 0 ? state.input_mod2 : null, ] } ) @@ -57,14 +57,14 @@ workflow run_wf { // remove datasets which didn't pass the schema check | filter { id, state -> - state.dataset_rna != null && - state.dataset_other_mod != null + state.dataset_mod1 != null && + state.dataset_mod2 != null } | process_dataset.run( fromState: [ - input_rna: "dataset_rna", - input_other_mod: "dataset_other_mod", + input_mod1: "dataset_mod1", + input_mod2: "dataset_mod2", output_train_mod1: "output_train_mod1", output_train_mod2: "output_train_mod2", output_test_mod1: "output_test_mod1", diff --git a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh index d7d4529e0c..e3c29c1ec8 100755 --- a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh +++ b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh @@ -22,7 +22,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_rna:output_dataset_rna,input_other_mod:output_dataset_other_mod' \ + --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' \ No newline at end of file From bea11fde61402e6defa25573e5ae932a7a58f0a4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Feb 2024 09:19:05 +0100 Subject: [PATCH 1125/1233] Bump nf-core/setup-nextflow from 1.5.0 to 1.5.1 (#352) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.5.0 to 1.5.1. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.5.0...v1.5.1) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: f1d9be5a9edb147ae48321f2b94453cf63bd24e8 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 54989e21be..722c8cf95c 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -132,7 +132,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.0 + - uses: nf-core/setup-nextflow@v1.5.1 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 41983303b9..0f40510e91 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -159,7 +159,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.0 + - uses: nf-core/setup-nextflow@v1.5.1 # build target dir # use containers from release branch, hopefully these are available From d5d058fc45d86bdb2f0b0a9899a295aa96aba098 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Thu, 1 Feb 2024 13:58:41 +0100 Subject: [PATCH 1126/1233] Porting predict_modality/guanlab_dengkw_pm from neurips2021_topmethods (#335) * port predict_modality/guanlab_dengkw_pm from neurips2021_topmethods * store `output.layers["normalized"]` as a csr matrix * Fill in summary and description --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: c096137fda6e272a3a7bc98f2e37b287ebab0d9c --- .../methods/guanlab_dengkw_pm/config.vsh.yaml | 49 ++++++ .../methods/guanlab_dengkw_pm/script.py | 140 ++++++++++++++++++ 2 files changed, 189 insertions(+) create mode 100644 src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml new file mode 100644 index 0000000000..030b3ba5b3 --- /dev/null +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -0,0 +1,49 @@ +# The API specifies which type of component this is. +__merge__: ../../api/comp_method.yaml + +functionality: + + name: guanlab_dengkw_pm + + info: + label: Guanlab-dengkw + summary: A kernel ridge regression method with RBF kernel. + description: | + This is a solution developed by Team Guanlab - dengkw in the Neurips 2021 competiton to predeict one modality from another using kernel ridge regression (KRR) with RBF kernel. Truncated SVD is applied on the combined training and test data from modality 1 followed by row-wise z-score normalization on the reduced matrix. The truncated SVD of modality 2 is predicted by training a KRR model on the normalized training matrix of modality 1. Predictions on the normalized test matrix are then re-mapped to the modality 2 feature space via the right singular vectors. + preferred_normalization: log_cp10k + reference: lance2022multimodal + documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw + repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw + + # Component-specific parameters (optional) + arguments: + - name: "--distance_method" + type: "string" + default: "minkowski" + description: The distance metric to use. Possible values include `euclidean` and `minkowski`. + choices: [euclidean, minkowski] + - name: "--n_pcs" + type: "integer" + default: 50 + description: Number of components to use for dimensionality reduction. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - scikit-learn + - pandas + - numpy + - scanpy + + - type: native + + - type: nextflow + directives: + label: [ "hightime", highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py new file mode 100644 index 0000000000..340e41c003 --- /dev/null +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -0,0 +1,140 @@ +import anndata as ad +import logging +import numpy as np +from scipy.sparse import csr_matrix +from sklearn.decomposition import TruncatedSVD +from sklearn.gaussian_process.kernels import RBF +from sklearn.kernel_ridge import KernelRidge +logging.basicConfig(level=logging.INFO) + +## VIASH START +par = { + 'input_train_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad', + 'output': 'output.h5ad', + 'distance_method': 'minkowski', + 'n_pcs': 50 +} +meta = { + 'functionality_name': 'guanlab_dengkw_pm' +} +## VIASH END + +print('Reading input files', flush=True) +input_train_mod1 = ad.read_h5ad(par['input_train_mod1']) +input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) +input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) + +pred_dimx = input_test_mod1.shape[0] +pred_dimy = input_train_mod2.shape[1] + +feature_obs = input_train_mod1.obs +gs_obs = input_train_mod2.obs + +batches = input_train_mod1.obs.batch.unique().tolist() +batch_len = len(batches) + +obs = input_test_mod1.obs +var = input_train_mod2.var +dataset_id = input_train_mod1.uns['dataset_id'] + +input_train = ad.concat( + {"train": input_train_mod1, "test": input_test_mod1}, + axis=0, + join="outer", + label="group", + fill_value=0, + index_unique="-" +) + +logging.info('Determine parameters by the modalities') +mod1_type = input_train_mod1.uns["modality"] +mod1_type = mod1_type.upper() +mod2_type = input_train_mod2.uns["modality"] +mod2_type = mod2_type.upper() +n_comp_dict = { + ("GEX", "ADT"): (300, 70, 10, 0.2), + ("ADT", "GEX"): (None, 50, 10, 0.2), + ("GEX", "ATAC"): (1000, 50, 10, 0.1), + ("ATAC", "GEX"): (100, 70, 10, 0.1) + } +logging.info(f"{mod1_type}, {mod2_type}") +n_mod1, n_mod2, scale, alpha = n_comp_dict[(mod1_type, mod2_type)] +logging.info(f"{n_mod1}, {n_mod2}, {scale}, {alpha}") + +# Perform PCA on the input data +logging.info('Models using the Truncated SVD to reduce the dimension') + +if n_mod1 is not None and n_mod1 < input_train.shape[1]: + embedder_mod1 = TruncatedSVD(n_components=n_mod1) + mod1_pca = embedder_mod1.fit_transform(input_train.layers["counts"]).astype(np.float32) + train_matrix = mod1_pca[input_train.obs['group'] == 'train'] + test_matrix = mod1_pca[input_train.obs['group'] == 'test'] +else: + train_matrix = input_train_mod1.to_df(layer="counts").values.astype(np.float32) + test_matrix = input_test_mod1.to_df(layer="counts").values.astype(np.float32) + +if n_mod2 is not None and n_mod2 < input_train_mod2.shape[1]: + embedder_mod2 = TruncatedSVD(n_components=n_mod2) + train_gs = embedder_mod2.fit_transform(input_train_mod2.layers["counts"]).astype(np.float32) +else: + train_gs = input_train_mod2.to_df(layer="counts").values.astype(np.float32) + +del input_train + +logging.info('Running normalization ...') +train_sd = np.std(train_matrix, axis=1).reshape(-1, 1) +train_sd[train_sd == 0] = 1 +train_norm = (train_matrix - np.mean(train_matrix, axis=1).reshape(-1, 1)) / train_sd +train_norm = train_norm.astype(np.float32) +del train_matrix + +test_sd = np.std(test_matrix, axis=1).reshape(-1, 1) +test_sd[test_sd == 0] = 1 +test_norm = (test_matrix - np.mean(test_matrix, axis=1).reshape(-1, 1)) / test_sd +test_norm = test_norm.astype(np.float32) +del test_matrix + +logging.info('Running KRR model ...') +y_pred = np.zeros((pred_dimx, pred_dimy), dtype=np.float32) +np.random.seed(1000) + +for _ in range(5): + np.random.shuffle(batches) + for batch in [batches[:batch_len//2], batches[batch_len//2:]]: + # for passing the test + if not batch: + batch = [batches[0]] + + logging.info(batch) + kernel = RBF(length_scale = scale) + krr = KernelRidge(alpha=alpha, kernel=kernel) + logging.info('Fitting KRR ... ') + krr.fit(train_norm[feature_obs.batch.isin(batch)], train_gs[gs_obs.batch.isin(batch)]) + y_pred += (krr.predict(test_norm) @ embedder_mod2.components_) + +np.clip(y_pred, a_min=0, a_max=None, out=y_pred) +if mod2_type == "ATAC": + np.clip(y_pred, a_min=0, a_max=1, out=y_pred) + +y_pred /= 10 + +# Store as sparse matrix to be efficient. +# Note that this might require different classifiers/embedders before-hand. +# Not every class is able to support such data structures. +y_pred = csr_matrix(y_pred) + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + layers = { + 'normalized': y_pred + }, + obs = obs, + var = var, + uns = { + 'dataset_id': input_train_mod1.uns['dataset_id'], + 'method_id': meta['functionality_name'] + } +) +output.write_h5ad(par['output'], compression='gzip') From 3e70d332e51fefa02e7825f465915c43d1e2b55c Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 1 Feb 2024 16:35:54 +0100 Subject: [PATCH 1127/1233] disable cell cycle conservation for now (#353) * disable cell cycle conservation for now * also disable cell_cycle_conservation metric in wfs --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 2e2ed4ced20f802b5b51481ddff4d4a1cb1bf53f --- .../metrics/cell_cycle_conservation/config.vsh.yaml | 1 + .../batch_integration/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/batch_integration/workflows/run_benchmark/main.nf | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 78bae7b655..cb1ef8bbae 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -1,6 +1,7 @@ # use metric api spec __merge__: ../../api/comp_metric_embedding.yaml functionality: + status: disabled name: cell_cycle_conservation info: metrics: diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index b430734e22..9525e736f5 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -77,7 +77,7 @@ functionality: - name: batch_integration/transformers/embed_to_graph - name: batch_integration/metrics/asw_batch - name: batch_integration/metrics/asw_label - - name: batch_integration/metrics/cell_cycle_conservation + # - name: batch_integration/metrics/cell_cycle_conservation - name: batch_integration/metrics/clustering_overlap - name: batch_integration/metrics/graph_connectivity - name: batch_integration/metrics/hvg_overlap diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 6772a9bc4c..9c15d3627f 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -37,7 +37,7 @@ workflow run_wf { metrics = [ asw_batch, asw_label, - cell_cycle_conservation, + // cell_cycle_conservation, clustering_overlap, graph_connectivity, hvg_overlap, From 1590e2c48375c831bc8a34200c63a2d871a4b413 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 2 Feb 2024 08:39:01 +0100 Subject: [PATCH 1128/1233] fix incorrect category of diffusion component (#354) Former-commit-id: a87afdcc861d948217081e243a2657ca5f45e369 --- .../methods/diffusion_map/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index 35ad00d903..bac586d8a2 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -1,4 +1,4 @@ -__merge__: ../../api/comp_control_method.yaml +__merge__: ../../api/comp_method.yaml functionality: name: "diffusion_maps" info: From d827e36c96e24b0530f27db5b0a5b1bfdd9a0fea Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Fri, 2 Feb 2024 09:47:04 +0100 Subject: [PATCH 1129/1233] Add Normalized Mutual Information metric (#332) * add SIMLR dimensionality reduction method * add description and reference * add SIMLR reference * change default n_dim and write output to file * Add SIMLR entry * Update documentation URL Co-authored-by: Kai Waldrant * Reformat code * Use explicit namespaces * Add new metric normalized_mutual_information * Add reference for adjusted rand index * change metric from normalized_mutual_information to clustering_performance * add .obs["cell type"] to slots * perform leiden clustering on embedding and compute NMI and ARI scores * fix typo * Compute neighbors if not already stored in input object Co-authored-by: Robrecht Cannoodt * Update src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py Use key_max to store best clustering Co-authored-by: Robrecht Cannoodt * Update src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py Co-authored-by: Robrecht Cannoodt * Update src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py Co-authored-by: Robrecht Cannoodt * Update src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py Co-authored-by: Robrecht Cannoodt * Make sure that the key is unique * add slot to common dataset * add key for cluster labels --------- Co-authored-by: Kai Waldrant Co-authored-by: Robrecht Cannoodt Former-commit-id: d9e44545337b90926df41f2f383e165eda6ef6fb --- CHANGELOG.md | 2 + src/common/library.bib | 32 ++++++++++ .../api/file_common_dataset.yaml | 5 ++ .../api/file_solution.yaml | 5 ++ .../clustering_performance/config.vsh.yaml | 61 ++++++++++++++++++ .../metrics/clustering_performance/script.py | 63 +++++++++++++++++++ 6 files changed, 168 insertions(+) create mode 100644 src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py diff --git a/CHANGELOG.md b/CHANGELOG.md index 857fa61a8d..b7fcc4e452 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -309,6 +309,8 @@ * `methods/simlr`: Added new SIMLR method. +* `metrics/clustering_performance`: Added new metric to assess clustering on the reduced dimensional embeddings using NMI and ARI. + ## match_modalities (PR #201) diff --git a/src/common/library.bib b/src/common/library.bib index c3e35dfaa9..9806965d00 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -400,6 +400,23 @@ @article{efremova2020cellphonedb } +@article{emmons2016analysis, + title = {Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale}, + volume = {11}, + ISSN = {1932-6203}, + url = {http://dx.doi.org/10.1371/journal.pone.0159161}, + doi = {10.1371/journal.pone.0159161}, + number = {7}, + journal = {PLOS ONE}, + publisher = {Public Library of Science (PLoS)}, + author = {Emmons, Scott and Kobourov, Stephen and Gallant, Mike and B\"{o}rner, Katy}, + editor = {Dovrolis, Constantine}, + year = {2016}, + month = jul, + pages = {e0159161} +} + + @article{eraslan2019single, title = {Single-cell {RNA}-seq denoising using a deep count autoencoder}, author = {G\"{o}kcen Eraslan and Lukas M. Simon and Maria Mircea and Nikola S. Mueller and Fabian J. Theis}, @@ -1091,6 +1108,21 @@ @article{rodriques2019slide } +@InProceedings{santos2009on, + author = {Santos, Jorge M. and Embrechts, Mark"}, + editor = {Alippi, Cesare and Polycarpou, Marios and Panayiotou, Christos and Ellinas, Georgios}, + title = {On the Use of the Adjusted Rand Index as a Metric for Evaluating Supervised Classification}, + booktitle = {Artificial Neural Networks -- ICANN 2009}, + year = {2009}, + publisher = {Springer Berlin Heidelberg}, + address = {Berlin, Heidelberg}, + pages = {175--184}, + isbn = {978-3-642-04277-5}, + doi = {10.1007/978-3-642-04277-5_18}, + url = {https://doi.org/10.1007/978-3-642-04277-5_18} +} + + @article{sarkar2021separating, title = {Separating measurement and expression models clarifies confusion in single-cell {RNA} sequencing analysis}, author = {Abhishek Sarkar and Matthew Stephens}, diff --git a/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml index 57af727c7c..dba599da9a 100644 --- a/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml +++ b/src/tasks/dimensionality_reduction/api/file_common_dataset.yaml @@ -13,6 +13,11 @@ info: name: normalized description: Normalized expression values required: true + obs: + - type: string + name: cell_type + description: Classification of the cell type based on its characteristics and function within the tissue or organism. + required: true var: - type: double name: hvg_score diff --git a/src/tasks/dimensionality_reduction/api/file_solution.yaml b/src/tasks/dimensionality_reduction/api/file_solution.yaml index 92d368508e..9d08f8fb7a 100644 --- a/src/tasks/dimensionality_reduction/api/file_solution.yaml +++ b/src/tasks/dimensionality_reduction/api/file_solution.yaml @@ -13,6 +13,11 @@ info: name: normalized description: Normalized expression values required: true + obs: + - type: string + name: cell_type + description: Classification of the cell type based on its characteristics and function within the tissue or organism. + required: true var: - type: double name: hvg_score diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml new file mode 100644 index 0000000000..643ebcb493 --- /dev/null +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml @@ -0,0 +1,61 @@ +__merge__: ../../api/comp_metric.yaml + +functionality: + name: clustering_performance + info: + metrics: + - name: normalized_mutual_information + label: NMI + summary: Normalized Mutual Information (NMI) is a measure of the concordance between clustering obtained from the reduced-dimensional embeddings and the cell labels. + description: | + The Normalized Mutual Information (NMI) is a measure of the similarity between cluster labels obtained from the clustering of dimensionality reduction embeddings and the true cell labels. It is a normalization of the Mutual Information (MI) score to scale the results between 0 (no mutual information) and 1 (perfect correlation). + Mutual Information quantifies the "amount of information" obtained about one random variable by observing the other random variable. Assuming two label assignments X and Y, it is given by: + $MI(X,Y) = \sum_{x=1}^{X}\sum_{y=1}^{Y}p(x,y)log(\frac{P(x,y)}{P(x)P'(y)})$, + where P(x,y) is the joint probability mass function of X and Y, and P(x), P'(y) are the marginal probability mass functions of X and Y respectively. The mutual information is normalized by some generalized mean of H(X) and H(Y). Therefore, Normalized Mutual Information can be defined as: + $NMI(X,Y) = \frac{MI(X,Y)}{mean(H(X),H(Y))}$, + where H(X) and H(Y) are the entropies of X and Y respectively. Higher NMI score suggests that the method is effective in preserving relevant information. + reference: emmons2016analysis + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.normalized_mutual_info_score.html + repository_url: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.normalized_mutual_info_score.html + min: 0 + max: 1 + maximize: true + - name: adjusted_rand_index + label: ARI + summary: Adjusted Rand Index (ARI) is a measure of the similarities between two cluster assignments of the reduced-dimensional embeddings and the true cell types. + description: | + Adjusted Rand Index (ARI) is a measure of similarity between two clusterings by considering all pairs of samples and counting pairs that are assigned in the same or different clusters in the predicted (from the reduced dimensional embeddings) and true clusterings (cell type labels). It is the Rand Index (RI) adjusted for chance. + Assuming the C as the cell type labels and K as the clustering of the reduced dimensional embedding, Rand Index can be defined as: + $RI = \frac{a + b}{{C}_{2}^{n_{samples}}}$, + where 'a' is the number of pairs of elements that are in the same set in C and in the same set in K, 'b' is the number of pairs of elements that are in different sets in C and in different sets in K, and ${C}_{2}^{n_{samples}}$ is the total number of possible pairs in the dataset. Random label assignments can be discounted as follows: + $ARI = \frac{RI - E[RI]}{max(RI) - E[RI]}$, + where E[RI] is the expected RI of random labellings. + reference: santos2009on + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.adjusted_rand_score.html#sklearn.metrics.adjusted_rand_score + repository_url: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.adjusted_rand_score.html#sklearn.metrics.adjusted_rand_score + min: 0 + max: 1 + maximize: true + + # Component-specific parameters + arguments: + - name: "--nmi_avg_method" + type: string + default: arithmetic + description: Method to compute normalizer in the denominator for normalized mutual information score calculation. + choices: [ min, geometric, arithmetic, max ] + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: [ scikit-learn, scanpy, leidenalg ] + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py b/src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py new file mode 100644 index 0000000000..eff2d5cd97 --- /dev/null +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/script.py @@ -0,0 +1,63 @@ +import anndata as ad +import scanpy as sc +from sklearn.cluster import KMeans +from sklearn.metrics import normalized_mutual_info_score +from sklearn.metrics import adjusted_rand_score + +## VIASH START +par = { + 'input_embedding': 'resources_test/dimensionality_reduction/pancreas/embedding.h5ad', + 'input_solution': 'resources_test/dimensionality_reduction/pancreas/solution.h5ad', + 'output': 'output.h5ad', + 'nmi_avg_method': 'arithmetic' +} +meta = { + 'functionality_name': 'clustering_performance' +} +## VIASH END + +print('Reading input files', flush=True) +input_embedding = ad.read_h5ad(par['input_embedding']) +input_solution = ad.read_h5ad(par['input_solution']) + +print('Compute metrics', flush=True) + +# Perform Leiden clustering on dimensionlity reduction embedding +n = 20 +resolutions = [2 * x / n for x in range(1, n + 1)] +score_max = 0 +res_max = resolutions[0] +key_max = None +score_all = [] + +if "neighbors" not in input_embedding.uns: + sc.pp.neighbors(input_embedding, use_rep="X_emb") + +for res in resolutions: + key_added = f"X_emb_leiden_{res}" + sc.tl.leiden(input_embedding, resolution=res, key_added=key_added) + score = normalized_mutual_info_score(input_solution.obs["cell_type"], input_embedding.obs[key_added], average_method = par['nmi_avg_method']) + score_all.append(score) + + if score_max < score: + score_max = score + res_max = res + key_max = key_added + +# Compute NMI scores +nmi = normalized_mutual_info_score(input_solution.obs["cell_type"], input_embedding.obs[key_max], average_method = par['nmi_avg_method']) + +# Compute ARI scores +ari = adjusted_rand_score(input_solution.obs["cell_type"], input_embedding.obs[key_max]) + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': input_embedding.uns['dataset_id'], + 'normalization_id': input_embedding.uns['normalization_id'], + 'method_id': input_embedding.uns['method_id'], + 'metric_ids': [ 'normalized_mutual_information', 'adjusted_rand_index' ], + 'metric_values': [ nmi, ari ] + } +) +output.write_h5ad(par['output'], compression='gzip') From ccf442b7a15dc594bd14a714e0a8e83e8dfb29d4 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 6 Feb 2024 10:01:21 +0100 Subject: [PATCH 1130/1233] fix exception when methods is null Former-commit-id: 9dc03fa34953250e0f35c6dafc92751c2f3490a1 --- src/tasks/batch_integration/workflows/run_benchmark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 9c15d3627f..91876737de 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -81,7 +81,7 @@ workflow run_wf { // if the preferred normalisation is none at all, // we can pass whichever dataset we want def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref - def method_check = state.method_ids.isEmpty() || state.method_ids.contains(comp.config.functionality.name) + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) method_check && norm_check }, From 17d0baae59b78b5112f816e3d4088c0ec0f71b94 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 10:03:02 +0100 Subject: [PATCH 1131/1233] Increase memory on fail (#346) * add nf memory usage * add custom config * remove from nextflow config Former-commit-id: 408e94ec97847e22a718fba8f130fc26fea7d24c --- src/wf_utils/labels_tw.config | 39 +++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 src/wf_utils/labels_tw.config diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config new file mode 100644 index 0000000000..691776ffaa --- /dev/null +++ b/src/wf_utils/labels_tw.config @@ -0,0 +1,39 @@ +process { + + executor = 'awsbatch' + + // Retry for exit codes that have something to do with memory issues + errorStrategy = { task.exitStatus in 137..143 ? 'retry' : 'ignore' } + maxRetries = 3 + maxMemory = null + + // Resource labels + withLabel: lowcpu { cpus = 5 } + withLabel: midcpu { cpus = 15 } + withLabel: highcpu { cpus = 30 } + + withLabel: lowmem { memory = { get_memory( 20.GB * task.attempt ) } } + withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } } + withLabel: highmem { memory = { get_memory( 100.GB * task.attempt ) } } +} + +def get_memory(to_compare) { + if (!process.containsKey("maxMemory") || !process.maxMemory) { + return to_compare + } + + try { + if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) { + return process.maxMemory + } + else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) { + return max_memory as nextflow.util.MemoryUnit + } + else { + return to_compare + } + } catch (all) { + println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!" + System.exit(1) + } +} \ No newline at end of file From 647b3e2d9fd71fb421d16ff83bb0038683b95f58 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 13:16:27 +0100 Subject: [PATCH 1132/1233] update Match_modalites Former-commit-id: a141df456b381e9a391039cd9207a7bbcd61799b --- .../workflows/run_benchmark/main.nf | 85 ++++++++++++------- 1 file changed, 55 insertions(+), 30 deletions(-) diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index d919104060..0f45c92c46 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -11,7 +11,7 @@ workflow run_wf { main: - // collect method list + // construct list of methods methods = [ random_features, true_features, @@ -21,17 +21,19 @@ workflow run_wf { procrustes ] - // collect metric list + // construct list of metrics metrics = [ knn_auc, mse ] - output_ch = input_ch - - // store original id for later use + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch + // store join id | map{ id, state -> - [id, state + [_meta: [join_id: id]]] + [id, state + ["_meta": [join_id: id]]] } // extract the dataset metadata @@ -44,6 +46,11 @@ workflow run_wf { } ) + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch + // run all methods | runEach( components: methods, @@ -88,6 +95,9 @@ workflow run_wf { // run all metrics | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ input_integrated_mod1: "method_output_mod1", @@ -104,25 +114,19 @@ workflow run_wf { } ) -// extract the dataset metadata + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + + // extract the dataset metadata + dataset_meta_ch = dataset_ch // only keep one of the normalization methods | filter{ id, state -> state.dataset_uns.normalization_id == "log_cp10k" } - // extract the scores - | extract_metadata.run( - key: "extract_scores", - fromState: [input: "metric_output"], - toState: { id, output, state -> - state + [ - score_uns: readYaml(output.output).uns - ] - } - ) - | joinStates { ids, states -> - // store the dataset metadata in a file def dataset_uns = states.collect{state -> def uns = state.dataset_uns.clone() @@ -133,17 +137,23 @@ workflow run_wf { def dataset_uns_file = tempFile("dataset_uns.yaml") dataset_uns_file.write(dataset_uns_yaml_blob) - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + ["output", [output_dataset_info: dataset_uns_file]] } - // store the method and metric configs - | map{ id, state -> + output_ch = score_ch + + // extract the scores + | extract_metadata.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + state + [ + score_uns: readYaml(output.output).uns + ] + } + ) + + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} @@ -159,13 +169,28 @@ workflow run_wf { def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, - output_task_info: task_info_file + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta ] - ["output", state + new_state] + ["output", new_state] + } + + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] } emit: From 41961124cdf44fdfbea014c45476d21fa2d5cea5 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 13:17:05 +0100 Subject: [PATCH 1133/1233] add labels Former-commit-id: b79ff08398c8fc5bf0dc420fbd02006310eec192 --- src/tasks/match_modalities/resources_scripts/run_benchmark.sh | 3 ++- src/tasks/predict_modality/resources_scripts/run_benchmark.sh | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 44724d36e8..f82e6acf35 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -31,4 +31,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels match_modalities,full \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 5ef1bee460..c595d2c862 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -31,4 +31,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ No newline at end of file + --config /tmp/nextflow.config \ + --labels predict_modality,full \ No newline at end of file From 1dd2d883c8ee5f3f1d8a7a3ec88de8d31e7a1478 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 13:23:29 +0100 Subject: [PATCH 1134/1233] update predict_modalities Former-commit-id: e3c59971146b6d022bdf73d3c3ebe366c6a4144b --- .../workflows/run_benchmark/main.nf | 83 +++++++++++++------ 1 file changed, 57 insertions(+), 26 deletions(-) diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 4b03ac0a2a..efd23657b2 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -11,7 +11,7 @@ workflow run_wf { main: - // collect method list + // construct list of methods methods = [ mean_per_gene, random_predict, @@ -24,17 +24,20 @@ workflow run_wf { random_forest ] - // collect metric list + // construct list of metrics metrics = [ correlation, mse ] - output_ch = input_ch + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch // store original id for later use | map{ id, state -> - [id, state + [_meta: [join_id: id]]] + [id, state + ["_meta": [join_id: id]]] } // extract the dataset metadata @@ -47,6 +50,11 @@ workflow run_wf { } ) + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch + // run all methods | runEach( components: methods, @@ -90,6 +98,9 @@ workflow run_wf { // run all metrics | runEach( components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, // use 'fromState' to fetch the arguments the component requires from the overall state fromState: [ input_test_mod2: "input_test_mod2", @@ -104,19 +115,18 @@ workflow run_wf { } ) - // extract the scores - | extract_metadata.run( - key: "extract_scores", - fromState: [input: "metric_output"], - toState: { id, output, state -> - state + [ - score_uns: readYaml(output.output).uns - ] - } - ) + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + // extract the dataset metadata + dataset_meta_ch = dataset_ch + // only keep one of the normalization methods + | filter{ id, state -> + state.dataset_uns.normalization_id == "log_cp10k" + } | joinStates { ids, states -> - // store the dataset metadata in a file def dataset_uns = states.collect{state -> def uns = state.dataset_uns.clone() @@ -127,18 +137,23 @@ workflow run_wf { def dataset_uns_file = tempFile("dataset_uns.yaml") dataset_uns_file.write(dataset_uns_yaml_blob) - // store the scores in a file - def score_uns = states.collect{it.score_uns} - def score_uns_yaml_blob = toYamlBlob(score_uns) - def score_uns_file = tempFile("score_uns.yaml") - score_uns_file.write(score_uns_yaml_blob) - - ["output", [output_scores: score_uns_file, output_dataset_info: dataset_uns_file, _meta: states[0]._meta]] + ["output", [output_dataset_info: dataset_uns_file]] } - // store the method and metric configs - | map{ id, state -> + output_ch = score_ch + // extract the scores + | extract_metadata.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + state + [ + score_uns: readYaml(output.output).uns + ] + } + ) + + | joinStates { ids, states -> // store the method configs in a file def method_configs = methods.collect{it.config} def method_configs_yaml_blob = toYamlBlob(method_configs) @@ -153,14 +168,30 @@ workflow run_wf { def task_info_file = meta.resources_dir.resolve("task_info.yaml") + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + def new_state = [ output_method_configs: method_configs_file, output_metric_configs: metric_configs_file, - output_task_info: task_info_file + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta ] - ["output", state + new_state] + ["output", new_state] + } + + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] } + emit: output_ch } \ No newline at end of file From 2c96734150d9aed7f8607d3ca2f67c97b486ba4f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 14:30:05 +0100 Subject: [PATCH 1135/1233] disable scot method temp Former-commit-id: 848c7d0127e588f7856d53b7877c3258d2ed7434 --- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 1 + src/tasks/match_modalities/workflows/run_benchmark/main.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index e6dddc9ccb..2b95429152 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -1,5 +1,6 @@ __merge__: ../../api/comp_method.yaml functionality: + status: disabled name: "scot" info: label: "Single Cell Optimal Transport" diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index 0f45c92c46..639e653c09 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -15,7 +15,7 @@ workflow run_wf { methods = [ random_features, true_features, - scot, + // scot, harmonic_alignment, fastmnn, procrustes From f5dedbfbb85c7f6fb2e110162042d10f8e7ca827 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 14:54:55 +0100 Subject: [PATCH 1136/1233] add normalization_id to .uns pred_mod Former-commit-id: f615d367b01397c1a2edad4bb40c86954b8dee47 --- src/tasks/predict_modality/process_dataset/script.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 875429e348..f1bcccb0ae 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -40,7 +40,7 @@ ad2_mod <- unique(ad2$var[["feature_types"]]) new_dataset_id <- paste0(ad1$uns[["dataset_id"]], "_", tolower(ad1_mod), "2", tolower(ad2_mod)) # determine new uns -uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism") +uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id") ad1_uns <- ad2_uns <- ad1$uns[uns_vars] ad1_uns$modality <- ad1_mod ad2_uns$modality <- ad2_mod From 2f504432c98723ef851c989edc39f074fe5d98b3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 15:00:46 +0100 Subject: [PATCH 1137/1233] remove view Former-commit-id: 8038b0235357bdd1bf63acda8ea9ccfae47bbd7e --- src/tasks/predict_modality/workflows/process_datasets/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 601ec04181..d777c322f5 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -53,7 +53,6 @@ workflow run_wf { ] } ) - | view{"test: ${it}"} // remove datasets which didn't pass the schema check | filter { id, state -> From 50cb29a8b24963a404ec17c5212a096817f149e2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 17:02:35 +0100 Subject: [PATCH 1138/1233] restore filter Former-commit-id: 23afa483465fe2cc5a518518c40ca8bef78e0508 --- .../workflows/run_benchmark/config.vsh.yaml | 2 +- .../workflows/run_benchmark/main.nf | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index df0971b8bc..db8bfb1f16 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: - name: match_modalities/control_methods/random_features - name: match_modalities/control_methods/true_features - name: match_modalities/methods/fastmnn - - name: match_modalities/methods/scot + # - name: match_modalities/methods/scot - name: match_modalities/methods/harmonic_alignment - name: match_modalities/methods/procrustes - name: match_modalities/metrics/knn_auc diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index efd23657b2..3a2b2b9dd4 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -60,13 +60,13 @@ workflow run_wf { components: methods, // // use the 'filter' argument to only run a method on the normalisation the component is asking for - // filter: { id, state, comp -> - // def norm = state.normalization_id - // def pref = comp.config.functionality.info.preferred_normalization - // // if the preferred normalisation is none at all, - // // we can pass whichever dataset we want - // (norm == "log_cp10k" && pref == "counts") || norm == pref - // }, + filter: { id, state, comp -> + def norm = state.dataset_uns.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + (norm == "log_cp10k" && pref == "counts") || norm == pref + }, // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> @@ -191,7 +191,7 @@ workflow run_wf { def mergedStates = states.inject([:]) { acc, m -> acc + m } [ids[0], mergedStates] } - + emit: output_ch } \ No newline at end of file From bf498384cae8d3e24df8f88878457c65c867345f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 17:09:02 +0100 Subject: [PATCH 1139/1233] enable scot Former-commit-id: 51aad699dce752b47699068ba36fd0c7a219571c --- src/tasks/match_modalities/methods/scot/config.vsh.yaml | 1 - .../match_modalities/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/match_modalities/workflows/run_benchmark/main.nf | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index 2b95429152..e6dddc9ccb 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -1,6 +1,5 @@ __merge__: ../../api/comp_method.yaml functionality: - status: disabled name: "scot" info: label: "Single Cell Optimal Transport" diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index db8bfb1f16..df0971b8bc 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -60,7 +60,7 @@ functionality: - name: match_modalities/control_methods/random_features - name: match_modalities/control_methods/true_features - name: match_modalities/methods/fastmnn - # - name: match_modalities/methods/scot + - name: match_modalities/methods/scot - name: match_modalities/methods/harmonic_alignment - name: match_modalities/methods/procrustes - name: match_modalities/metrics/knn_auc diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index 639e653c09..0f45c92c46 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -15,7 +15,7 @@ workflow run_wf { methods = [ random_features, true_features, - // scot, + scot, harmonic_alignment, fastmnn, procrustes From 776da37672c4658a495dcc9fa01ce0025af92876 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 6 Feb 2024 18:02:58 +0100 Subject: [PATCH 1140/1233] chore: Add branch naming convention to CONTRIBUTING.md Former-commit-id: 1228ba20a131ebb0578c36807da10faeea9219f9 --- CONTRIBUTING.qmd | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 4543aa8ec8..269d13b259 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -348,3 +348,42 @@ The [Viash reference docs](https://viash.io/reference/config/) page provides inf ```{bash, echo=FALSE} rm -r src/tasks/label_projection/methods/foo target/docker/label_projection/methods/foo ``` + +## Branch Naming Conventions + +### Category + +A git branch should start with a category. Pick one of these: feature, bugfix, hotfix, or test. + +* `feature` is for adding, refactoring or removing a feature +* `bugfix` is for fixing a bug +* `hotfix` is for changing code with a temporary solution and/or without following the usual process (usually because of an emergency) +* `test` is for experimenting outside of an issue/ticket +* `doc` is for adding, changing or removing documentation + +### Reference + +After the category, there should be a "`/`" followed by the reference of the issue/ticket/task you are working on. If there's no reference, just add no-ref. With task it is meant as benchmarking task e.g. batch_integration + +### Description + +After the reference, there should be another "`/`" followed by a description which sums up the purpose of this specific branch. This description should be short and "kebab-cased". + +By default, you can use the title of the issue/ticket you are working on. Just replace any special character by "`-`". + +### To sum up, follow this pattern when branching: + +```bash +git branch +``` + +### Examples + +* You need to add, refactor or remove a feature: `git branch feature/issue-42/create-new-button-component` +* You need to fix a bug: `git branch bugfix/issue-342/button-overlap-form-on-mobile` +* You need to fix a bug really fast (possibly with a temporary solution): `git branch hotfix/no-ref/registration-form-not-working` +* You need to experiment outside of an issue/ticket: `git branch test/no-ref/refactor-components-with-atomic-design` + +### References + +* [a-simplified-convention-for-naming-branches-and-commits-in-git](https://dev.to/varbsan/a-simplified-convention-for-naming-branches-and-commits-in-git-il4) \ No newline at end of file From 04f2706a9e048123704b6d715c1f6c5471808be0 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 7 Feb 2024 09:05:14 +0100 Subject: [PATCH 1141/1233] Update processing dataset metadata (#355) * Update with to accomodate multimodal data * rename bash script Former-commit-id: 3a811a7417ca8d97b531710dd83529b1d2ab27b4 --- .../process_dataset_metadata/run/run.sh | 53 +++++++++++++++++++ .../process_dataset_metadata/run/run_test.sh | 41 -------------- 2 files changed, 53 insertions(+), 41 deletions(-) create mode 100644 src/common/process_dataset_metadata/run/run.sh delete mode 100644 src/common/process_dataset_metadata/run/run_test.sh diff --git a/src/common/process_dataset_metadata/run/run.sh b/src/common/process_dataset_metadata/run/run.sh new file mode 100644 index 0000000000..4bd9fb34b6 --- /dev/null +++ b/src/common/process_dataset_metadata/run/run.sh @@ -0,0 +1,53 @@ +#!/bin/bash + +# fail on error +set -e + +# ensure we're in the root of the repo +REPO_ROOT=$(git rev-parse --show-toplevel) +cd "$REPO_ROOT" + +DATASET_DIR="s3://openproblems-data/resources/datasets/" + +for LOADER in $(aws s3 ls $DATASET_DIR); do + + if [ "$LOADER" == "PRE" ]; then + continue + fi + + BASE_DIR="${DATASET_DIR%/}/$LOADER" + + for DATASET in $(aws s3 ls $BASE_DIR); do + + if [ "$DATASET" == "PRE" ]; then + continue + fi + + FILE_DIR="${BASE_DIR%/}/${DATASET%/}/log_cp10k/" + FILES=$(aws s3 ls $FILE_DIR) + metafiles=$(echo "$FILES" | grep "meta" | awk '{print $NF}') + # metafiles=$(find $INPUT -type f -name "*meta*") + # echo $metafiles + + for metafile in $metafiles; do + INPUT="${FILE_DIR%/}/$metafile" + OUTPUT_DIR="../website/datasets/$LOADER/$DATASET" + OUTPUT_FILE="${metafile%.*}.json" + echo "Processing $LOADER - $DATASET : $INPUT" + + # start the + NXF_VER=23.10.0 nextflow run . \ + -main-script target/nextflow/common/process_dataset_metadata/run/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + --id "extract_metadata" \ + --input "$INPUT" \ + --output "$OUTPUT_FILE" \ + --output_state "state.yaml" \ + --publish_dir "$OUTPUT_DIR" + done + +# cause quarto rerender to index page when in preview mode +# touch ../website/results/$TASK/index.qmd + done +done \ No newline at end of file diff --git a/src/common/process_dataset_metadata/run/run_test.sh b/src/common/process_dataset_metadata/run/run_test.sh deleted file mode 100644 index 3d5f829eee..0000000000 --- a/src/common/process_dataset_metadata/run/run_test.sh +++ /dev/null @@ -1,41 +0,0 @@ -#!/bin/bash - -# fail on error -set -e - -# ensure we're in the root of the repo -REPO_ROOT=$(git rev-parse --show-toplevel) -cd "$REPO_ROOT" - -# TODO: Add multimodal datasets -for LOADER in "cellxgene_census" "openproblems_v1"; do - BASE_DIR="s3://openproblems-data/resources/datasets/$LOADER/" - - for DATASET in $(aws s3 ls $BASE_DIR); do - - if [ "$DATASET" == "PRE" ]; then - continue - fi - - INPUT="${BASE_DIR%/}/${DATASET%/}/log_cp10k/dataset_metadata.yaml" - OUTPUT_DIR="../website/datasets/$LOADER/$DATASET" - - echo "Processing $LOADER - $DATASET : $INPUT" - # # temp sync - # aws s3 sync $INPUT_DIR output/temp - - # start the run - NXF_VER=23.10.0 nextflow run . \ - -main-script target/nextflow/common/process_dataset_metadata/run/main.nf \ - -profile docker \ - -c src/wf_utils/labels_ci.config \ - --id "extract_metadata" \ - --input "$INPUT" \ - --output meta.json \ - --output_state "state.yaml" \ - --publish_dir "$OUTPUT_DIR" - -# cause quarto rerender to index page when in preview mode -# touch ../website/results/$TASK/index.qmd - done -done \ No newline at end of file From 2665238806e7c96d5aa6a98acab161da745e20fc Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 7 Feb 2024 09:05:47 +0100 Subject: [PATCH 1142/1233] Delete original feature_name/id .var fields (#356) * delete changed orig .var field * update labels Former-commit-id: df58d9643171d6bb73367735399c0493d87b9db8 --- .../loaders/openproblems_v1/script.py | 20 +++++++++++-------- .../openproblems_v1_multimodal/script.py | 4 ++++ .../resources_scripts/process_datasets.sh | 3 ++- 3 files changed, 18 insertions(+), 9 deletions(-) diff --git a/src/datasets/loaders/openproblems_v1/script.py b/src/datasets/loaders/openproblems_v1/script.py index 1587719239..2cdae43a74 100644 --- a/src/datasets/loaders/openproblems_v1/script.py +++ b/src/datasets/loaders/openproblems_v1/script.py @@ -103,20 +103,24 @@ adata.uns.update(uns_metadata) print("Setting .var['feature_name']", flush=True) -if par["var_feature_name"]: - if par["var_feature_name"] == "index": - adata.var["feature_name"] = adata.var.index - elif par["var_feature_name"] in adata.var: + +if par["var_feature_name"] == "index": + adata.var["feature_name"] = adata.var.index +else: + if par["var_feature_name"] in adata.var: adata.var["feature_name"] = adata.var[par["feature_name"]] + del adata.var[par["feature_name"]] else: print(f"Warning: key '{par['var_feature_name']}' could not be found in adata.var.", flush=True) print("Setting .var['feature_id']", flush=True) -if par["var_feature_id"]: - if par["var_feature_id"] == "index": - adata.var["feature_id"] = adata.var.index - elif par["var_feature_id"] in adata.var: + +if par["var_feature_id"] == "index": + adata.var["feature_id"] = adata.var.index +else: + if par["var_feature_id"] in adata.var: adata.var["feature_id"] = adata.var[par["feature_id"]] + del adata.var[par["feature_id"]] else: print(f"Warning: key '{par['var_feature_id']}' could not be found in adata.var.", flush=True) diff --git a/src/datasets/loaders/openproblems_v1_multimodal/script.py b/src/datasets/loaders/openproblems_v1_multimodal/script.py index 959ec50d9e..f70e92d048 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/script.py +++ b/src/datasets/loaders/openproblems_v1_multimodal/script.py @@ -127,10 +127,12 @@ else: if par["var_feature_name"] in mod1.var: mod1.var["feature_name"] = mod1.var[par["feature_name"]] + del mod1.var[par["feature_name"]] else: print(f"Warning: key '{par['var_feature_name']}' could not be found in adata_mod1.var.", flush=True) if par["var_feature_name"] in mod2.var: mod2.var["feature_name"] = mod2.var[par["feature_name"]] + del mod2.var[par["feature_name"]] else: print(f"Warning: key '{par['var_feature_name']}' could not be found in adata_mod2.var.", flush=True) @@ -141,10 +143,12 @@ else: if par["var_feature_id"] in mod1.var: mod1.var["feature_id"] = mod1.var[par["feature_id"]] + del mod1.var[par["feature_id"]] else: print(f"Warning: key '{par['var_feature_id']}' could not be found in adata_mod1.var.", flush=True) if par["var_feature_id"] in mod2.var: mod2.var["feature_id"] = mod2.var[par["feature_id"]] + del mod2.var[par["feature_id"]] else: print(f"Warning: key '{par['var_feature_id']}' could not be found in adata_mod2.var.", flush=True) diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index c536fa6120..27ba91ebbe 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -30,4 +30,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config + --config /tmp/nextflow.config \ + --labels match_modalities,process_datasets From 649b4e51f2b7851d75d765f72434dbf40461a6f6 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 7 Feb 2024 11:46:55 +0100 Subject: [PATCH 1143/1233] Update PR template (#363) * Update PR template * Update .github/PULL_REQUEST_TEMPLATE.md Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 3a63454fd651fdd13db86963f8892faedee17404 --- .github/PULL_REQUEST_TEMPLATE.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 43caae6b44..c48e62a4ac 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,4 +15,10 @@ Closes #xxxx (Replace xxxx with the GitHub issue number) - [ ] Proposed changes are described in the CHANGELOG.md -- [ ] CI Tests succeed and look good! \ No newline at end of file +- [ ] CI Tests succeed and look good! + +## Requirements after merging + +- [ ] Need to regenerate `common/` resources + +- [ ] Need to regenerate task-specific resources. Specify: \ No newline at end of file From 47c784313657e0c19fb1bd967a0aee9b112560f9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 8 Feb 2024 10:44:19 +0100 Subject: [PATCH 1144/1233] Bump nf-core/setup-nextflow from 1.5.1 to 1.5.2 (#368) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.5.1 to 1.5.2. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.5.1...v1.5.2) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 0baa112bb3609c7756f3272295f2b7e6ed4d05f9 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 722c8cf95c..4e6bf2f349 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -132,7 +132,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.1 + - uses: nf-core/setup-nextflow@v1.5.2 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 0f40510e91..e9c0115dff 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -159,7 +159,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.1 + - uses: nf-core/setup-nextflow@v1.5.2 # build target dir # use containers from release branch, hopefully these are available From 95a5913cd416239b2bfdc03bb12c4c6c3a2760e0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Feb 2024 10:44:31 +0100 Subject: [PATCH 1145/1233] fix descriptions in scripts (#367) Former-commit-id: 8b91c8fe427ebf98f10d9c8dcb4a8dd0d3c594ca --- src/datasets/resource_scripts/openproblems_v1_multimodal.sh | 2 +- .../resource_scripts/openproblems_v1_multimodal_test.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index ed8e1a77e3..7f5032f49d 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -14,7 +14,7 @@ param_list: input_id: citeseq_cbmc dataset_name: "CITE-Seq CBMC" dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" - dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." + dataset_description: "8k cord blood mononuclear cells profiled by CITEseq using a panel of 13 antibodies." dataset_reference: stoeckius2017simultaneous dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 dataset_organism: homo_sapiens diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh index d3a36cb5e1..5ffd3a4185 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh @@ -21,7 +21,7 @@ param_list: - id: openproblems_v1_multimodal/citeseq_cbmc dataset_name: "CITE-Seq CBMC" dataset_summary: "CITE-seq profiles of 8k Cord Blood Mononuclear Cells" - dataset_description: "8k cord blood mononuclear cells profiled by CITEsequsing a panel of 13 antibodies." + dataset_description: "8k cord blood mononuclear cells profiled by CITEseq using a panel of 13 antibodies." dataset_reference: stoeckius2017simultaneous dataset_url: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866 dataset_organism: homo_sapiens From aae2391ae978537285920143f5492315e955d544 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 8 Feb 2024 11:57:38 +0100 Subject: [PATCH 1146/1233] override dataset id (#369) * override dataset id * fix test Former-commit-id: 3e3fcd7e297ec9cd0cbe7ec478d4ec55b1a1ee6f --- .../loaders/openproblems_neurips2021_bmmc/config.vsh.yaml | 4 ++++ src/datasets/loaders/openproblems_neurips2021_bmmc/script.py | 1 + src/datasets/loaders/openproblems_neurips2021_bmmc/test.py | 1 + .../workflows/process_openproblems_neurips2021_bmmc/main.nf | 1 + 4 files changed, 7 insertions(+) diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml index 32fbeecff4..345788157f 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -22,6 +22,10 @@ functionality: example: ADT - name: Metadata arguments: + - name: "--dataset_id" + type: string + description: "A unique identifier for the dataset" + required: true - name: "--dataset_name" type: string description: Nicely formatted name. diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index e573cd68de..8ac734efff 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -7,6 +7,7 @@ "input": "GSE194122_openproblems_neurips2021_cite_BMMC_processed.h5ad", "mod1": "GEX", "mod2": "ATAC", + "dataset_id": "openproblems/neurips2021_bmmc", "dataset_name": "BMMC (CITE-seq)", "dataset_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122", "dataset_reference": "Neurips", diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py index c99abaddc3..b194a52fe4 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/test.py @@ -40,6 +40,7 @@ "--mod2", mod2, "--output_mod1", output_mod1_file, "--output_mod2", output_mod2_file, + "--dataset_id", "openproblems/neurips2021_bmmc", "--dataset_name", "BMMC (Multiome)", "--dataset_url", "http://foo.org", "--dataset_reference", "foo2000bar", diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index 124cee9b9e..a5bb6bf4ec 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -52,6 +52,7 @@ workflow run_wf { "input": "input_decompressed", "mod1": "mod1", "mod2": "mod2", + "dataset_id": "id", "dataset_name": "dataset_name", "dataset_url": "dataset_url", "dataset_reference": "dataset_reference", From 4fd52b1f367a4933df5496186cc09715b0743aeb Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 13 Feb 2024 17:16:31 +0100 Subject: [PATCH 1147/1233] Update multimodal tasks (#366) * update MM metrics * add multimodal task to process_task_result * set swap default to false * reticulate v1.35 has been released * proces metadata to data dir on website * readd github reticulate not yet publised on CRAN * Add swapped modality filter * run swapped modalities for Pred_mod * add normalization_id field to api files * Change dataset id (untested) * refactor new_dataset_id * readd defaullt value * fix typo * change dataset_name io id * update to param_list * fix typo Co-authored-by: Robrecht Cannoodt * add a new dataset_id depending on modality --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 4e1c139810ed6b0c4f90c9daf976bff9c0c68ac9 --- .../process_dataset_metadata/run/run.sh | 2 +- .../process_task_results/run/run_test.sh | 2 +- .../metrics/knn_auc/config.vsh.yaml | 6 +-- .../metrics/mse/config.vsh.yaml | 4 +- .../api/file_common_dataset_mod1.yaml | 4 ++ .../api/file_common_dataset_mod2.yaml | 4 ++ .../predict_modality/api/file_test_mod1.yaml | 8 ++++ .../predict_modality/api/file_test_mod2.yaml | 4 ++ .../predict_modality/api/file_train_mod1.yaml | 8 ++++ .../predict_modality/api/file_train_mod2.yaml | 8 ++++ src/tasks/predict_modality/api/task_info.yaml | 1 + .../process_dataset/config.vsh.yaml | 2 +- .../predict_modality/process_dataset/script.R | 11 +++-- .../resources_scripts/process_datasets.sh | 8 +++- .../neurips2021_bmmc.sh | 40 +++++++++++++++---- .../process_datasets/config.vsh.yaml | 5 +++ .../workflows/process_datasets/main.nf | 23 ++++++++++- .../workflows/run_benchmark/main.nf | 24 +++++++++-- .../workflows/run_benchmark/run_test.sh | 5 ++- 19 files changed, 140 insertions(+), 29 deletions(-) diff --git a/src/common/process_dataset_metadata/run/run.sh b/src/common/process_dataset_metadata/run/run.sh index 4bd9fb34b6..27ea225ed3 100644 --- a/src/common/process_dataset_metadata/run/run.sh +++ b/src/common/process_dataset_metadata/run/run.sh @@ -31,7 +31,7 @@ for LOADER in $(aws s3 ls $DATASET_DIR); do for metafile in $metafiles; do INPUT="${FILE_DIR%/}/$metafile" - OUTPUT_DIR="../website/datasets/$LOADER/$DATASET" + OUTPUT_DIR="../website/datasets/$LOADER/${DATASET%/}/data/" OUTPUT_FILE="${metafile%.*}.json" echo "Processing $LOADER - $DATASET : $INPUT" diff --git a/src/common/process_task_results/run/run_test.sh b/src/common/process_task_results/run/run_test.sh index 045183a04e..2477cb5362 100755 --- a/src/common/process_task_results/run/run_test.sh +++ b/src/common/process_task_results/run/run_test.sh @@ -7,7 +7,7 @@ set -e REPO_ROOT=$(git rev-parse --show-toplevel) cd "$REPO_ROOT" -for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_projection"; do +for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_projection" "match_modalities" "predict_modality"; do # for TASK in "label_projection"; do BASE_DIR="s3://openproblems-data/resources/$TASK/results/" diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index 16a66a4853..6207a6d5f9 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -3,12 +3,12 @@ functionality: name: "knn_auc" info: metrics: - - label: KNN AUC + - label: kNN Area Under the Curve name: knn_auc summary: "Compute the kNN Area Under the Curve" description: | - "Compute the kNN Area Under the Curve" - reference: "" + Let $f(i) \u2208 F$ be the scRNA-seq measurement of cell $i$, and $g(i) \u2208 G$ be the scATAC- seq measurement of cell $i$. kNN-AUC calculates the average percentage overlap of neighborhoods of $f(i)$ in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. + reference: "lance2022multimodal" min: 0 max: 1 maximize: true diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index 06fff957c8..6174ad8a4c 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -7,8 +7,8 @@ functionality: name: "mse" summary: Compute the mean squared error. description: | - The mean squared error (MSE) is a measure of the quality of an estimator. It is always non-negative, and values closer to zero are better. - reference: "" + Mean squared error (MSE) is the average distance between each pair of matched observations of the same cell in the learned latent space. Lower is better. + reference: "lance2022multimodal" maximize: true min: 0 max: "+.inf" diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml index 8bb39fb505..d893c0e27a 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml @@ -63,6 +63,10 @@ info: type: string description: The organism of the sample in the dataset. required: false + - name: normalization_id + type: string + description: The unique identifier of the normalization method used. + required: true - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml index dfa67d3898..d00c0e0cdc 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml @@ -63,6 +63,10 @@ info: type: string description: The organism of the sample in the dataset. required: false + - name: normalization_id + type: string + description: The unique identifier of the normalization method used. + required: true - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index 843c40cf44..3eea40432c 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -32,6 +32,10 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: common_dataset_id + description: "A common identifier for the dataset" + required: true - name: dataset_name type: string description: Nicely formatted name. @@ -56,6 +60,10 @@ info: type: string description: The organism of the sample in the dataset. required: false + - name: normalization_id + type: string + description: The unique identifier of the normalization method used. + required: true - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index 3e98f508c0..4abca6587c 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -32,6 +32,10 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: common_dataset_id + description: "A common identifier for the dataset" + required: true - name: dataset_name type: string description: Nicely formatted name. diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index fc629448d6..da3d064085 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -32,10 +32,18 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: common_dataset_id + description: "A common identifier for the dataset" + required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. required: false + - name: normalization_id + type: string + description: The unique identifier of the normalization method used. + required: true - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index 25e4b2425b..b5df6e17d1 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -32,10 +32,18 @@ info: name: dataset_id description: "A unique identifier for the dataset" required: true + - type: string + name: common_dataset_id + description: "A common identifier for the dataset" + required: true - name: dataset_organism type: string description: The organism of the sample in the dataset. required: false + - name: normalization_id + type: string + description: The unique identifier of the normalization method used. + required: true - type: string name: gene_activity_var_names description: "Names of the gene activity matrix" diff --git a/src/tasks/predict_modality/api/task_info.yaml b/src/tasks/predict_modality/api/task_info.yaml index 5ba57f5529..83d7582fed 100644 --- a/src/tasks/predict_modality/api/task_info.yaml +++ b/src/tasks/predict_modality/api/task_info.yaml @@ -27,6 +27,7 @@ authors: roles: [ contributor ] info: github: KaiWaldrant + orcid: "0009-0003-8555-1361" - name: Louise Deconinck roles: [ author ] info: diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index e972a31605..c6e7d493cc 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -5,7 +5,7 @@ functionality: - name: "--swap" type: "boolean" description: "Swap mod1 and mod2" - default: true + default: false resources: - type: r_script path: script.R diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index f1bcccb0ae..95eae6a920 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -36,15 +36,20 @@ ad2 <- anndata::read_h5ad(if (!par$swap) par$input_mod2 else par$input_mod1) ad1_mod <- unique(ad1$var[["feature_types"]]) ad2_mod <- unique(ad2$var[["feature_types"]]) -# determine new dataset id -new_dataset_id <- paste0(ad1$uns[["dataset_id"]], "_", tolower(ad1_mod), "2", tolower(ad2_mod)) - # determine new uns uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id") ad1_uns <- ad2_uns <- ad1$uns[uns_vars] ad1_uns$modality <- ad1_mod ad2_uns$modality <- ad2_mod +# Create new dataset id and name depending on the modality +ad1_uns[["common_dataset_id"]] <- ad2_uns[["common_dataset_id"]] <- ad1_uns$dataset_id +new_dataset_id <- paste0(ad1_uns$dataset_id, "_", ad1_mod, "2", ad2_mod) +ad1_uns$dataset_id <- ad2_uns$dataset_id <- new_dataset_id + +new_dataset_name <- paste0(ad1_uns$dataset_name, " (", ad1_mod, "2", ad2_mod, ")") +ad1_uns$dataset_name <- ad2_uns$dataset_name <- new_dataset_name + # determine new obsm ad1_obsm <- ad2_obsm <- list() diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index e41f9da9cd..1fc4490ede 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -1,10 +1,14 @@ #!/bin/bash cat > /tmp/params.yaml << 'HERE' -id: predict_modality_process_datasets +param_list: + - id: predict_modality_process_datasets + settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' + - id: predict_modality_process_datasets_swap + settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' + input_states: s3://openproblems-data/resources/datasets/**/state.yaml rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' -settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/predict_modality/datasets HERE diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 981871f2b4..d7ed2a4b27 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -25,15 +25,39 @@ nextflow run . \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' +# Swap the modalities +nextflow run . \ + -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "resources_test/common/openproblems_neurips2021/**/state.yaml" \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2' \ + --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state '$id/state.yaml' + echo "Run one method" viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/prediction.h5ad + +viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/prediction.h5ad + +viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/prediction.h5ad viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/prediction.h5ad diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index fe4bee1e5a..4b3153e789 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -12,6 +12,10 @@ functionality: __merge__: "/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml" direction: input required: true + - name: "--swap" + type: "boolean" + description: "Swap mod1 and mod2" + default: false - name: Outputs arguments: - name: "--output_train_mod1" @@ -37,6 +41,7 @@ functionality: - path: /src/wf_utils/helper.nf dependencies: - name: common/check_dataset_schema + - name: common/extract_metadata - name: predict_modality/process_dataset platforms: - type: nextflow diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index d777c322f5..ebb91d066c 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -67,7 +67,8 @@ workflow run_wf { output_train_mod1: "output_train_mod1", output_train_mod2: "output_train_mod2", output_test_mod1: "output_test_mod1", - output_test_mod2: "output_test_mod2" + output_test_mod2: "output_test_mod2", + swap: "swap" ], toState: [ "output_train_mod1", @@ -77,12 +78,30 @@ workflow run_wf { ] ) + // extract the dataset metadata + | extract_metadata.run( + key: "extract_metadata_mod1", + fromState: [input: "output_test_mod2"], + toState: { id, output, state -> + state + [ + dataset_id: readYaml(output.output).uns.dataset_id + ] + } + ) + + + | map { id, state -> + def new_id = state.dataset_id + [new_id, state + ["_meta": [join_id: id]]] + } + // only output the files for which an output file was specified | setState ([ "output_train_mod1", "output_train_mod2", "output_test_mod1", - "output_test_mod2" + "output_test_mod2", + "_meta" ]) emit: diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 3a2b2b9dd4..714339cb17 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -42,14 +42,30 @@ workflow run_wf { // extract the dataset metadata | extract_metadata.run( + key: "metadata_mod1", fromState: [input: "input_train_mod1"], toState: { id, output, state -> state + [ - dataset_uns: readYaml(output.output).uns + dataset_uns_mod1: readYaml(output.output).uns ] } ) + | extract_metadata.run( + key: "metadata_mod2", + fromState: [input: "input_test_mod2"], + toState: { id, output, state -> + state + [ + dataset_uns_mod2: readYaml(output.output).uns + ] + } + ) + + | map{ id, state -> + def rna_norm = state.dataset_uns_mod1.modality == "GEX" ? state.dataset_uns_mod1.normalization_id : state.dataset_uns_mod2.normalization_id + [id, state + [rna_norm: rna_norm]] + } + /*************************** * RUN METHODS AND METRICS * ***************************/ @@ -61,7 +77,7 @@ workflow run_wf { // // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.dataset_uns.normalization_id + def norm = state.rna_norm def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want @@ -124,12 +140,12 @@ workflow run_wf { dataset_meta_ch = dataset_ch // only keep one of the normalization methods | filter{ id, state -> - state.dataset_uns.normalization_id == "log_cp10k" + state.rna_norm == "log_cp10k" } | joinStates { ids, states -> // store the dataset metadata in a file def dataset_uns = states.collect{state -> - def uns = state.dataset_uns.clone() + def uns = state.dataset_uns_mod2.clone() uns.remove("normalization_id") uns } diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index ceb5066280..76a8e5b560 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -8,7 +8,7 @@ cd "$REPO_ROOT" set -e -DATASETS_DIR="resources_test/predict_modality/openproblems_neurips2021/bmmc_cite" +DATASETS_DIR="resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT" OUTPUT_DIR="output/predict_modality" if [ ! -d "$OUTPUT_DIR" ]; then @@ -22,9 +22,10 @@ nextflow run . \ -profile docker \ -resume \ -entry auto \ + -with-trace \ -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/state.yaml" \ --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' \ No newline at end of file + --output_state 'state.yaml' \ No newline at end of file From ce7d25ae2c99dc4e2fd46abecad3d5d699f77180 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 14 Feb 2024 09:13:32 +0100 Subject: [PATCH 1148/1233] restore new process id in nf workflow Former-commit-id: 3c7548a47cf375aff094a95e53ffec3c09c73228 --- .../workflows/process_datasets/main.nf | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index ebb91d066c..0437a9005d 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -81,17 +81,27 @@ workflow run_wf { // extract the dataset metadata | extract_metadata.run( key: "extract_metadata_mod1", - fromState: [input: "output_test_mod2"], + fromState: [input: "output_train_mod1"], toState: { id, output, state -> state + [ - dataset_id: readYaml(output.output).uns.dataset_id + modality_mod1: readYaml(output.output).uns.modality ] } ) + // extract the dataset metadata + | extract_metadata.run( + key: "extract_metadata_mod2", + fromState: [input: "output_train_mod2"], + toState: { id, output, state -> + state + [ + modality_mod2: readYaml(output.output).uns.modality + ] + } + ) | map { id, state -> - def new_id = state.dataset_id + def new_id = id + "_" + state.modality_mod1 + "2" + state.modality_mod2 [new_id, state + ["_meta": [join_id: id]]] } From 99384bfa249f9612f5365b00e94622b5bffbda3b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Feb 2024 15:11:40 +0100 Subject: [PATCH 1149/1233] update readmes (#371) Former-commit-id: 3494b86be0ca7e71a01e0b0c15e4b7ea48a4c4dc --- src/common/helper_functions/read_api_files.R | 20 ++++- src/tasks/batch_integration/README.md | 46 +++------- src/tasks/denoising/README.md | 14 +-- src/tasks/dimensionality_reduction/README.md | 46 ++++------ src/tasks/label_projection/README.md | 24 ------ src/tasks/match_modalities/README.md | 28 ------ src/tasks/predict_modality/README.md | 91 ++++++++------------ 7 files changed, 80 insertions(+), 189 deletions(-) diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index 1101f37f72..a2bfc35711 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -194,16 +194,28 @@ render_file <- function(spec) { spec$info$label <- basename(spec$info$example) } + example <- + if (is.null(spec$info$example) || is.na(spec$info$example)) { + "" + } else { + paste0("Example file: `", spec$info$example, "`") + } + + description <- + if (is.null(spec$info$description) || is.na(spec$info$description)) { + "" + } else { + paste0("Description:\n\n", spec$info$description) + } + strip_margin(glue::glue(" §## File format: {spec$info$label} § §{spec$info$summary %||% ''} § - §Example file: `{spec$info$example %|% ''}` - § - §Description: + §{example} § - §{spec$info$description %||% ''} + §{description} § §Format: § diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 0906460059..5a2fec741b 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -105,17 +105,13 @@ A subset of the common dataset. Example file: `resources_test/common/pancreas/dataset.h5ad` -Description: - -NA - Format:
AnnData object obs: 'cell_type', 'batch' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -132,6 +128,7 @@ Slot description: | `obs["cell_type"]` | `string` | Cell type information. | | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -178,17 +175,13 @@ Unintegrated AnnData HDF5 file. Example file: `resources_test/batch_integration/pancreas/dataset.h5ad` -Description: - -NA - Format:
AnnData object obs: 'batch', 'label' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -205,6 +198,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -223,17 +217,13 @@ Solution dataset Example file: `resources_test/batch_integration/pancreas/solution.h5ad` -Description: - -NA - Format:
AnnData object obs: 'batch', 'label' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -250,6 +240,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -421,17 +412,13 @@ An integrated AnnData HDF5 file. Example file: `resources_test/batch_integration/pancreas/integrated_embedding.h5ad` -Description: - -NA - Format:
AnnData object obs: 'batch', 'label' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca', 'X_emb' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -448,6 +435,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsm["X_emb"]` | `double` | integration embedding prediction. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | @@ -469,17 +457,13 @@ Integrated AnnData HDF5 file. Example file: `resources_test/batch_integration/pancreas/integrated_graph.h5ad` -Description: - -NA - Format:
AnnData object obs: 'batch', 'label' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities', 'connectivities', 'distances' layers: 'counts', 'normalized' @@ -496,6 +480,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -519,17 +504,13 @@ Integrated AnnData HDF5 file. Example file: `resources_test/batch_integration/pancreas/integrated_feature.h5ad` -Description: - -NA - Format:
AnnData object obs: 'batch', 'label' - var: 'hvg' + var: 'hvg', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized', 'corrected_counts' @@ -546,6 +527,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -566,10 +548,6 @@ Metric score file Example file: `score.h5ad` -Description: - -NA - Format:
diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 9012878a17..4dc1bbb895 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -135,7 +135,7 @@ Slot description: | `obs["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. | | `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | | `var["feature_id"]` | `string` | (*Optional*) Unique identifier for the feature, usually a ENSEMBL gene id. | -| `var["feature_name"]` | `string` | (*Optional*) A human-readable name for the feature, usually a gene symbol. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | @@ -183,10 +183,6 @@ The subset of molecules used for the training dataset Example file: `resources_test/denoising/pancreas/train.h5ad` -Description: - -NA - Format:
@@ -214,10 +210,6 @@ The subset of molecules used for the test dataset Example file: `resources_test/denoising/pancreas/test.h5ad` -Description: - -NA - Format:
@@ -307,10 +299,6 @@ A denoised dataset as output by a denoising method. Example file: `resources_test/denoising/pancreas/denoised.h5ad` -Description: - -NA - Format:
diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 095191a4e0..243ef80229 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -127,7 +127,7 @@ Slot description: | `obs["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell. | | `obs["size_factors"]` | `double` | (*Optional*) The size factors created by the normalisation method, if any. | | `var["feature_id"]` | `string` | (*Optional*) Unique identifier for the feature, usually a ENSEMBL gene id. | -| `var["feature_name"]` | `string` | (*Optional*) A human-readable name for the feature, usually a gene symbol. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | | `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | @@ -176,10 +176,6 @@ The dataset to pass to a method. Example file: `resources_test/dimensionality_reduction/pancreas/dataset.h5ad` -Description: - -NA - Format:
@@ -212,15 +208,12 @@ The data for evaluating a dimensionality reduction. Example file: `resources_test/dimensionality_reduction/pancreas/solution.h5ad` -Description: - -NA - Format:
AnnData object + obs: 'cell_type' var: 'hvg_score' layers: 'counts', 'normalized' uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id' @@ -231,19 +224,20 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------------------| -| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["dataset_name"]` | `string` | Nicely formatted name. | -| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | -| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | -| `uns["dataset_summary"]` | `string` | Short description of the dataset. | -| `uns["dataset_description"]` | `string` | Long description of the dataset. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | +| Slot | Type | Description | +|:-----------------------------|:----------|:---------------------------------------------------------------------------------------------------------| +| `obs["cell_type"]` | `string` | Classification of the cell type based on its characteristics and function within the tissue or organism. | +| `var["hvg_score"]` | `double` | High variability gene score (normalized dispersion). The greater, the more variable. | +| `layers["counts"]` | `integer` | Raw counts. | +| `layers["normalized"]` | `double` | Normalized expression values. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. |
@@ -310,10 +304,6 @@ A dataset with dimensionality reduction embedding. Example file: `resources_test/dimensionality_reduction/pancreas/embedding.h5ad` -Description: - -NA - Format:
@@ -344,10 +334,6 @@ Metric score file Example file: `resources_test/dimensionality_reduction/pancreas/score.h5ad` -Description: - -NA - Format:
diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index 6ddc7b9bd8..e58324b8b4 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -78,10 +78,6 @@ A subset of the common dataset. Example file: `resources_test/common/pancreas/dataset.h5ad` -Description: - -NA - Format:
@@ -145,10 +141,6 @@ The training data Example file: `resources_test/label_projection/pancreas/train.h5ad` -Description: - -NA - Format:
@@ -186,10 +178,6 @@ The test data (without labels) Example file: `resources_test/label_projection/pancreas/test.h5ad` -Description: - -NA - Format:
@@ -226,10 +214,6 @@ The solution for the test data Example file: `resources_test/label_projection/pancreas/solution.h5ad` -Description: - -NA - Format:
@@ -331,10 +315,6 @@ The prediction file Example file: `resources_test/label_projection/pancreas/prediction.h5ad` -Description: - -NA - Format:
@@ -364,10 +344,6 @@ Metric score file Example file: `resources_test/label_projection/pancreas/score.h5ad` -Description: - -NA - Format:
diff --git a/src/tasks/match_modalities/README.md b/src/tasks/match_modalities/README.md index b13299e86f..911977144b 100644 --- a/src/tasks/match_modalities/README.md +++ b/src/tasks/match_modalities/README.md @@ -161,10 +161,6 @@ are randomly permuted. Example file: `resources_test/match_modalities/scicar_cell_lines/dataset_mod1.h5ad` -Description: - -NA - Format:
@@ -198,10 +194,6 @@ are randomly permuted. Example file: `resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad` -Description: - -NA - Format:
@@ -234,10 +226,6 @@ The ground truth information for the first modality Example file: `resources_test/match_modalities/scicar_cell_lines/solution_mod1.h5ad` -Description: - -NA - Format:
@@ -278,10 +266,6 @@ The ground truth information for the second modality Example file: `resources_test/match_modalities/scicar_cell_lines/solution_mod2.h5ad` -Description: - -NA - Format:
@@ -385,10 +369,6 @@ The integrated embedding for the first modality Example file: `resources_test/match_modalities/scicar_cell_lines/integrated_mod1.h5ad` -Description: - -NA - Format:
@@ -419,10 +399,6 @@ The integrated embedding for the second modality Example file: `resources_test/match_modalities/scicar_cell_lines/integrated_mod2.h5ad` -Description: - -NA - Format:
@@ -453,10 +429,6 @@ Metric score file Example file: `resources_test/match_modalities/scicar_cell_lines/score.h5ad` -Description: - -NA - Format:
diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index 410633b674..537885fa56 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -50,7 +50,7 @@ the information about cellular state from one modality to the other. ``` mermaid flowchart LR - file_common_dataset_rna("Raw dataset RNA") + file_common_dataset_mod1("Raw dataset RNA") comp_process_dataset[/"Data processor"/] file_train_mod1("Train mod1") file_train_mod2("Train mod2") @@ -61,8 +61,8 @@ flowchart LR comp_metric[/"Metric"/] file_prediction("Prediction") file_score("Score") - file_common_dataset_other_mod("Raw dataset mod2") - file_common_dataset_rna---comp_process_dataset + file_common_dataset_mod2("Raw dataset mod2") + file_common_dataset_mod1---comp_process_dataset comp_process_dataset-->file_train_mod1 comp_process_dataset-->file_train_mod2 comp_process_dataset-->file_test_mod1 @@ -79,7 +79,7 @@ flowchart LR comp_method-->file_prediction comp_metric-->file_score file_prediction---comp_metric - file_common_dataset_other_mod---comp_process_dataset + file_common_dataset_mod2---comp_process_dataset ``` ## File format: Raw dataset RNA @@ -87,11 +87,7 @@ flowchart LR The RNA modality of the raw dataset. Example file: -`resources_test/common/neurips2021_bmmc_cite/dataset_rna.h5ad` - -Description: - -NA +`resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad` Format: @@ -99,10 +95,10 @@ Format: AnnData object obs: 'batch', 'size_factors' - var: 'gene_ids' + var: 'feature_id', 'feature_name' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'gene_activity_var_names'
@@ -114,7 +110,8 @@ Slot description: |:---------------------------------|:----------|:-------------------------------------------------------------------------------| | `obs["batch"]` | `string` | Batch information. | | `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `var["feature_id"]` | `string` | Unique identifier for the feature, usually a ENSEMBL gene id. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | @@ -125,6 +122,7 @@ Slot description: | `uns["dataset_summary"]` | `string` | Short description of the dataset. | | `uns["dataset_description"]` | `string` | Long description of the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -142,8 +140,8 @@ Arguments: | Name | Type | Description | |:----------------------|:----------|:---------------------------------------------------------------------------| -| `--input_rna` | `file` | The RNA modality of the raw dataset. | -| `--input_other_mod` | `file` | The second modality of the raw dataset. Must be an ADT or an ATAC dataset. | +| `--input_mod1` | `file` | The RNA modality of the raw dataset. | +| `--input_mod2` | `file` | The second modality of the raw dataset. Must be an ADT or an ATAC dataset. | | `--output_train_mod1` | `file` | (*Output*) The mod1 expression values of the train cells. | | `--output_train_mod2` | `file` | (*Output*) The mod2 expression values of the train cells. | | `--output_test_mod1` | `file` | (*Output*) The mod1 expression values of the test cells. | @@ -157,11 +155,7 @@ Arguments: The mod1 expression values of the train cells. Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad` Format: @@ -172,7 +166,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'common_dataset_id', 'dataset_organism', 'normalization_id', 'gene_activity_var_names'
@@ -189,7 +183,9 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -199,11 +195,7 @@ Slot description: The mod2 expression values of the train cells. Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad` Format: @@ -214,7 +206,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'common_dataset_id', 'dataset_organism', 'normalization_id', 'gene_activity_var_names'
@@ -231,7 +223,9 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -241,11 +235,7 @@ Slot description: The mod1 expression values of the test cells. Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad` Format: @@ -256,7 +246,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'common_dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'gene_activity_var_names'
@@ -273,12 +263,14 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | | `uns["dataset_name"]` | `string` | Nicely formatted name. | | `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | | `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | | `uns["dataset_summary"]` | `string` | Short description of the dataset. | | `uns["dataset_description"]` | `string` | Long description of the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
@@ -288,11 +280,7 @@ Slot description: The mod2 expression values of the test cells. Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/test_mod2.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad` Format: @@ -303,7 +291,7 @@ Format: var: 'gene_ids' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'common_dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names'
@@ -320,6 +308,7 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | | `uns["dataset_name"]` | `string` | Nicely formatted name. | | `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | | `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | @@ -395,11 +384,7 @@ Arguments: A prediction of the mod2 expression values of the test cells Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/prediction.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad` Format: @@ -428,11 +413,7 @@ Slot description: Metric score file Example file: -`resources_test/predict_modality/neurips2021_bmmc_cite/score.h5ad` - -Description: - -NA +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/score.h5ad` Format: @@ -462,11 +443,7 @@ The second modality of the raw dataset. Must be an ADT or an ATAC dataset Example file: -`resources_test/common/neurips2021_bmmc_cite/dataset_other_mod.h5ad` - -Description: - -NA +`resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad` Format: @@ -474,10 +451,10 @@ Format: AnnData object obs: 'batch', 'size_factors' - var: 'gene_ids' + var: 'feature_id', 'feature_name' obsm: 'gene_activity' layers: 'counts', 'normalized' - uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'gene_activity_var_names' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'normalization_id', 'gene_activity_var_names'
@@ -489,7 +466,8 @@ Slot description: |:---------------------------------|:----------|:-------------------------------------------------------------------------------| | `obs["batch"]` | `string` | Batch information. | | `obs["size_factors"]` | `double` | (*Optional*) The size factors of the cells prior to normalization. | -| `var["gene_ids"]` | `string` | (*Optional*) The gene identifiers (if available). | +| `var["feature_id"]` | `string` | Unique identifier for the feature, usually a ENSEMBL gene id. | +| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["gene_activity"]` | `double` | (*Optional*) ATAC gene activity. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | @@ -500,6 +478,7 @@ Slot description: | `uns["dataset_summary"]` | `string` | Short description of the dataset. | | `uns["dataset_description"]` | `string` | Long description of the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
From f9932a487f745a77dc2bb2ae0ed61023433ad146 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 14 Feb 2024 15:14:15 +0100 Subject: [PATCH 1150/1233] add thumbnail for the PM task (#372) * add thumbnail for the PM task * add thumbnail location to task_info --------- Co-authored-by: Kai Waldrant Former-commit-id: e4345be523e302ac9e54ddde32ad5064779ff19d --- src/tasks/predict_modality/api/task_info.yaml | 1 + src/tasks/predict_modality/api/thumbnail.svg | 666 ++++++++++++++++++ 2 files changed, 667 insertions(+) create mode 100644 src/tasks/predict_modality/api/thumbnail.svg diff --git a/src/tasks/predict_modality/api/task_info.yaml b/src/tasks/predict_modality/api/task_info.yaml index 83d7582fed..4d0c5596c4 100644 --- a/src/tasks/predict_modality/api/task_info.yaml +++ b/src/tasks/predict_modality/api/task_info.yaml @@ -1,6 +1,7 @@ name: predict_modality label: Predict Modality summary: "Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression)." +image: "thumbnail.svg" motivation: | Experimental techniques to measure multiple modalities within the same single cell are increasingly becoming available. The demand for these measurements is driven by the promise to provide a deeper insight into the state of a cell. diff --git a/src/tasks/predict_modality/api/thumbnail.svg b/src/tasks/predict_modality/api/thumbnail.svg new file mode 100644 index 0000000000..59436e6187 --- /dev/null +++ b/src/tasks/predict_modality/api/thumbnail.svg @@ -0,0 +1,666 @@ + + + + + + + + Gene + Expression + A + B + C + + + + + + True + Predicted + + + + + + + + + + + Chromatin Accessibility + Gene Expression + + Cell 1 + Cell 2 + + + + + + + + + + + + + + + Cell 3 + + + + + + + + A + B + C + Gene + + + + + + + + Task + Metric + Root mean square error + + + + + + + + + + + + + + A + B + C + Gene + + + + + + + + + + + + + + Ground-truth + Predicted + + Value Type + + + + + + Gene A + Genes + Gene B + Gene C + + From 48b71bf0cd7ad32b886c57a8401494e35d05b039 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 14 Feb 2024 15:23:51 +0100 Subject: [PATCH 1151/1233] [pred_mod] Update process datasets nf-tower script (#373) * add thumbnail for PM task * update readme * catch cases where description is not defined * refactor process_datasets nf-tower script --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: fe7b02e7b8b35ed2d9a6dd20cbc983e5b0828a37 --- .../resources_scripts/process_datasets.sh | 30 ++++++++++++++----- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 1fc4490ede..a20ce99963 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -1,13 +1,9 @@ #!/bin/bash cat > /tmp/params.yaml << 'HERE' -param_list: - - id: predict_modality_process_datasets - settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' - - id: predict_modality_process_datasets_swap - settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' - +id: predict_modality_process_datasets input_states: s3://openproblems-data/resources/datasets/**/state.yaml +settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/predict_modality/datasets @@ -32,4 +28,24 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ - --labels predict_modality,process_datasets \ No newline at end of file + --labels predict_modality,process_datasets + +cat > /tmp/params.yaml << 'HERE' +id: predict_modality_process_datasets_swap +input_states: s3://openproblems-data/resources/datasets/**/state.yaml +settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' +rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/predict_modality/datasets +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ + --labels predict_modality,process_datasets,swap_mod \ No newline at end of file From 9d96bfcdf35fee21780d3f6e2c2272361b0304a3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 14 Feb 2024 18:07:06 +0100 Subject: [PATCH 1152/1233] Update test_resources path (#375) Former-commit-id: e2cc44f636b954cd115e79d16d0a6983848c79a8 --- src/tasks/predict_modality/api/comp_control_method.yaml | 4 ++-- src/tasks/predict_modality/api/comp_method.yaml | 4 ++-- src/tasks/predict_modality/api/comp_metric.yaml | 4 ++-- src/tasks/predict_modality/api/file_prediction.yaml | 2 +- src/tasks/predict_modality/api/file_score.yaml | 2 +- src/tasks/predict_modality/api/file_test_mod1.yaml | 2 +- src/tasks/predict_modality/api/file_test_mod2.yaml | 2 +- src/tasks/predict_modality/api/file_train_mod1.yaml | 2 +- src/tasks/predict_modality/api/file_train_mod2.yaml | 2 +- .../resources_test_scripts/neurips2021_bmmc.sh | 1 + 10 files changed, 13 insertions(+), 12 deletions(-) diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml index 5459e41adc..ca478f4444 100644 --- a/src/tasks/predict_modality/api/comp_control_method.yaml +++ b/src/tasks/predict_modality/api/comp_control_method.yaml @@ -38,5 +38,5 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite \ No newline at end of file + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index f4810444fa..b7f91f0590 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -30,6 +30,6 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml index af6c71d9c5..73b2d2f5b0 100644 --- a/src/tasks/predict_modality/api/comp_metric.yaml +++ b/src/tasks/predict_modality/api/comp_metric.yaml @@ -25,6 +25,6 @@ functionality: path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml index 5cead0fc3b..08cc5f2f84 100644 --- a/src/tasks/predict_modality/api/file_prediction.yaml +++ b/src/tasks/predict_modality/api/file_prediction.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/prediction.h5ad" info: label: "Prediction" summary: "A prediction of the mod2 expression values of the test cells" diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml index f8b4757601..12927ffc7e 100644 --- a/src/tasks/predict_modality/api/file_score.yaml +++ b/src/tasks/predict_modality/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/score.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index 3eea40432c..d5c0b309c4 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod1.h5ad" info: label: "Test mod1" summary: "The mod1 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index 4abca6587c..a0d3012da8 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod2.h5ad" info: label: "Test mod2" summary: "The mod2 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index da3d064085..c675580a8e 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad" info: label: "Train mod1" summary: "The mod1 expression values of the train cells." diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index b5df6e17d1..f4a2eb01af 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad" info: label: "Train mod2" summary: "The mod2 expression values of the train cells." diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index d7ed2a4b27..1367e333ee 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -38,6 +38,7 @@ nextflow run . \ --output_state '$id/state.yaml' echo "Run one method" + viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad \ --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad \ From a6bf46c2db51a9bc570d79a1c3eceee8ab4a4696 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 15 Feb 2024 09:55:55 +0100 Subject: [PATCH 1153/1233] [pred_mod] fix uns output in process_datasets (#376) * Update get_dataset_info to include common_dataset_id * refactor copy of `.uns` * Update src/common/process_task_results/get_dataset_info/script.R Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 8d447db24ce90eae457ef0b54a9386243cd8e800 --- src/common/process_task_results/get_dataset_info/script.R | 4 ++++ src/tasks/predict_modality/process_dataset/script.R | 3 ++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/src/common/process_task_results/get_dataset_info/script.R b/src/common/process_task_results/get_dataset_info/script.R index 8a1f8d8696..17e3fb8afd 100644 --- a/src/common/process_task_results/get_dataset_info/script.R +++ b/src/common/process_task_results/get_dataset_info/script.R @@ -28,6 +28,10 @@ outputs <- map(datasets, function(dataset) { "data_url" = dataset$dataset_url %||% NA_character_ ) + if (!is.null(dataset[["common_dataset_id"]])) { + out[["common_dataset_id"]] <- dataset[["common_dataset_id"]] + } + # show warning when certain data is missing and return null? for (n in names(out)) { if (is.null(out[[n]])) { diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 95eae6a920..71658dfcab 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -38,7 +38,8 @@ ad2_mod <- unique(ad2$var[["feature_types"]]) # determine new uns uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id") -ad1_uns <- ad2_uns <- ad1$uns[uns_vars] +ad1_uns <- ad1$uns[uns_vars] +ad2_uns <- ad2$uns[uns_vars] ad1_uns$modality <- ad1_mod ad2_uns$modality <- ad2_mod From fd15d576305cf661e542dd0e4d2219f5351fb09f Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 15 Feb 2024 15:52:24 +0100 Subject: [PATCH 1154/1233] Update contributing and readme (#377) * WIP * Update contributing * Update README Former-commit-id: 5f3069e73d1941f1d8664f1e65dfe32201b6febe --- CONTRIBUTING.md | 395 +++++++++++++++++++++++++++++------------------ CONTRIBUTING.qmd | 36 +++-- README.md | 6 +- README.qmd | 2 +- 4 files changed, 270 insertions(+), 169 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d21edceda4..a57b23cbb0 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,25 +1,22 @@ -Contributing to OpenProblems -================ - -- Code of conduct -- Requirements -- Quick start -- Project - structure -- Adding a Viash component -- Running a component from CLI -- Building a - component -- Unit testing a component -- More - information +# Contributing to OpenProblems + + +- [Code of conduct](#code-of-conduct) +- [Requirements](#requirements) +- [Quick start](#quick-start) +- [Project structure](#project-structure) +- [Adding a Viash component](#adding-a-viash-component) +- [Running a component from CLI](#running-a-component-from-cli) +- [Building a component](#building-a-component) +- [Unit testing a component](#unit-testing-a-component) +- [More information](#more-information) +- [Branch Naming Conventions](#branch-naming-conventions) [OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). +You can find a full in depth guide on how to contribute to this project +on the [OpenProblems website](https://openproblems.bio/documentation/). ## Code of conduct @@ -55,7 +52,7 @@ modality alignment benchmark. Running the full pipeline is quite easy. **Step 0, fetch Viash and Nextflow** ``` bash -mkdir -p $HOME/bin +mkdir $HOME/bin curl -fsSL get.viash.io | bash -s -- --bin $HOME/bin --tools false curl -s https://get.nextflow.io | bash; mv nextflow $HOME/bin ``` @@ -68,8 +65,8 @@ viash -v nextflow -v ``` - viash 0.6.6 (c) 2020 Data Intuitive - nextflow version 22.10.4.5836 + viash 0.8.0 (c) 2020 Data Intuitive + nextflow version 23.04.1.5866 **Step 1, download test resources:** by running the following command. @@ -93,7 +90,7 @@ viash ns build --query 'label_projection|common' --parallel --setup cachedbuild ``` In development mode with 'dev'. - Exporting split_dataset (label_projection) =docker=> target/docker/label_projection/split_dataset + Exporting process_dataset (label_projection) =docker=> target/docker/label_projection/process_dataset Exporting accuracy (label_projection/metrics) =docker=> target/docker/label_projection/metrics/accuracy Exporting random_labels (label_projection/control_methods) =docker=> target/docker/label_projection/control_methods/random_labels [notice] Building container 'label_projection/control_methods_random_labels:dev' with Dockerfile @@ -113,7 +110,8 @@ The command might take a while to run, since it is building a docker container for each of the components. **Step 3, run the pipeline with nextflow.** To do so, run the bash -script located at `src/tasks/label_projection/workflows/run_nextflow.sh`: +script located at +`src/tasks/label_projection/workflows/run_nextflow.sh`: ``` bash src/tasks/label_projection/workflows/run/run_test.sh @@ -159,7 +157,7 @@ Detailed overview of a task folder (e.g. `src/tasks/label_projection`): ├── metrics Label projection metric components. ├── resources_scripts The scripts needed to run the benchmark. ├── resources_test_scripts The scripts needed to generate the test resources (which are needed for unit testing). - ├── split_dataset A component that masks a common dataset for use in the benchmark + ├── process_dataset A component that masks a common dataset for use in the benchmark └── workflows The benchmarking workflow. Detailed overview of the `src/datasets` folder: @@ -183,7 +181,8 @@ You can start creating a new component by [creating a Viash component](https://viash.io/guide/component/creation/docker.html). For example, to create a new Python-based method named `foo`, create a -Viash config at `src/tasks/label_projection/methods/foo/config.vsh.yaml`: +Viash config at +`src/tasks/label_projection/methods/foo/config.vsh.yaml`: ``` yaml __merge__: ../../api/comp_method.yaml @@ -198,29 +197,34 @@ functionality: # a short label of your method label: Foo - paper_doi: "10.1234/1234.5678.1234567890" + # A multiline description of your method. + description: "Todo: fill in" + + # A short summary of the method description. + summary: "Todo: fill in" + + # Add the bibtex reference to the "src/common/library.bib" if it is not already there. + reference: "cover1967nearest" - # if you don't have a Doi, you can specify a name, url and year manually: - # paper_name: "Nearest neighbor pattern classification" - # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" - # paper_year: 1967 - - code_url: "https://github.com/my_organisation/foo" + repository_url: "https://github.com/openproblems-bio/openproblems-v2" + documentation_url: "https://openproblems.bio/documentation/" + preferred_normalization: log_cp10k resources: - type: python_script path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python - packages: - - anndata~=0.8.0 - - scikit-learn + packages: [scikit-learn] - type: nextflow + directives: + label: [midtime, midmem, lowcpu] ``` -And create a script at `src/tasks/label_projection/methods/foo/script.py`: +And create a script at +`src/tasks/label_projection/methods/foo/script.py`: ``` python import anndata as ad @@ -267,19 +271,25 @@ viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help Arguments: --input_train - type: file, file must exist - example: training.h5ad - The training data + type: file, required parameter, file must exist + example: resources_test/label_projection/pancreas/train.h5ad --input_test - type: file, file must exist - example: test.h5ad - The test data (without labels) + type: file, required parameter, file must exist + example: resources_test/label_projection/pancreas/test.h5ad --output - type: file, output, file must exist - example: prediction.h5ad - The prediction file + type: file, required parameter, output, file must exist + example: resources_test/label_projection/pancreas/prediction.h5ad + +Before running a new component, youy will need to create the docker +container: + +``` bash +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- ---setup cachedbuild +``` + + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:dev' with Dockerfile You can **run the component** as follows: @@ -290,9 +300,6 @@ viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- \ --output resources_test/label_projection/pancreas/prediction.h5ad ``` - [notice] Checking if Docker image is available at 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev' - [warning] Could not pull from 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev'. Docker image doesn't exist or is not accessible. - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:dev' with Dockerfile Load data Create predictions Add method name to uns @@ -313,15 +320,11 @@ viash build src/tasks/label_projection/methods/foo/config.vsh.yaml \ -o target/docker/label_projection/methods/foo ``` -
- -> **Note** +> [!NOTE] > -> The `viash_build` component does a much better job of setting up a +> The `viash ns build` component does a much better job of setting up a > collection of components. -
- You can now view the same interface of the executable by running the executable with the `-h` parameter. @@ -335,19 +338,16 @@ target/docker/label_projection/methods/foo/foo -h Arguments: --input_train - type: file, file must exist - example: training.h5ad - The training data + type: file, required parameter, file must exist + example: resources_test/label_projection/pancreas/train.h5ad --input_test - type: file, file must exist - example: test.h5ad - The test data (without labels) + type: file, required parameter, file must exist + example: resources_test/label_projection/pancreas/test.h5ad --output - type: file, output, file must exist - example: prediction.h5ad - The prediction file + type: file, required parameter, output, file must exist + example: resources_test/label_projection/pancreas/prediction.h5ad Or **run the component** as follows: @@ -366,69 +366,85 @@ target/docker/label_projection/methods/foo/foo \ ## Unit testing a component The [method API -specifications](src/tasks/label_projection/api/comp_method.yaml) comes with a -generic unit test for free. This means you can unit test your component -using the **`viash test`** command. +specifications](src/tasks/label_projection/api/comp_method.yaml) comes +with a generic unit test for free. This means you can unit test your +component using the **`viash test`** command. ``` bash viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011' + Running tests in temporary directory: '/tmp/viash_test_foo11070556749764805852' + ==================================================================== + +/tmp/viash_test_foo11070556749764805852/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:test' with Dockerfile + [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods/foo:test /tmp/viash_test_foo11070556749764805852/build_executable -f /tmp/viash_test_foo11070556749764805852/build_executable/tmp/dockerbuild-foo-VMKj2u/Dockerfile' + #0 building with "default" instance using docker driver + + #1 [internal] load build definition from Dockerfile + #1 transferring dockerfile: 658B done + #1 DONE 0.1s + + #2 [internal] load .dockerignore + #2 transferring context: 2B done + #2 DONE 0.1s + + #3 [internal] load metadata for ghcr.io/openproblems-bio/base_python:1.0.2 + #3 DONE 0.3s + + #4 [1/2] FROM ghcr.io/openproblems-bio/base_python:1.0.2@sha256:65a577a3de37665b7a65548cb33c9153b6881742345593d33fe02919c8d66a20 + #4 DONE 0.0s + + #5 [2/2] RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "scikit-learn" + #5 CACHED + + #6 exporting to image + #6 exporting layers done + #6 writing image sha256:b5c134ce2ab91a0e616d7362f6bd168e6494c4a1bd7c643d62d7ad65d8678c5b done + #6 naming to ghcr.io/openproblems-bio/label_projection/methods/foo:test 0.0s done + #6 DONE 0.0s ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE' with Dockerfile - [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE /home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/build_executable/tmp/dockerbuild-foo-C7VuUU/Dockerfile' - Sending build context to Docker daemon 39.94kB - - Step 1/7 : FROM python:3.10 - ---> 465483cdaa4e - Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata~=0.8.0" "scikit-learn" - ---> Using cache - ---> 91f658ec0590 - Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" - ---> Using cache - ---> f1ace85a71b0 - Step 4/7 : LABEL org.opencontainers.image.created="2022-12-17T08:47:34+01:00" - ---> Running in 299ea3924905 - Removing intermediate container 299ea3924905 - ---> 6fc97da56de8 - Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2" - ---> Running in bf60068c5fe8 - Removing intermediate container bf60068c5fe8 - ---> 20ff545ec27a - Step 6/7 : LABEL org.opencontainers.image.revision="8a4877920fc79009dcb1e4bb16674b3b441c75ab" - ---> Running in c4410d3a7c78 - Removing intermediate container c4410d3a7c78 - ---> 1a57a0d9a7e5 - Step 7/7 : LABEL org.opencontainers.image.version="test_nGvjdE" - ---> Running in 81d7a66aa40a - Removing intermediate container 81d7a66aa40a - ---> 9d84592b1c1e - Successfully built 9d84592b1c1e - Successfully tagged ghcr.io/openproblems-bio/label_projection/methods_foo:test_nGvjdE + +/tmp/viash_test_foo11070556749764805852/test_check_method_config/test_executable + Load config data + Check general fields + Check info fields + Check platform fields + All checks succeeded! ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo17760509097337858011/test_generic_test/test_executable + +/tmp/viash_test_foo11070556749764805852/test_run_and_check_adata/test_executable + >> Running test 'run' + >> Checking whether input files exist >> Running script as test + Load data + Create predictions + Add method name to uns + Write output to file >> Checking whether output file exists - >> Reading h5ad files - input_test: AnnData object with n_obs × n_vars = 130 × 443 + >> Reading h5ad files and checking formats + Reading and checking input_train + AnnData object with n_obs × n_vars = 326 × 500 + obs: 'label', 'batch' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' + Reading and checking input_test + AnnData object with n_obs × n_vars = 174 × 500 obs: 'batch' var: 'hvg', 'hvg_score' uns: 'dataset_id', 'normalization_id' obsm: 'X_pca' layers: 'counts', 'normalized' - output: AnnData object with n_obs × n_vars = 130 × 443 + Reading and checking output + AnnData object with n_obs × n_vars = 174 × 500 obs: 'batch', 'label_pred' var: 'hvg', 'hvg_score' uns: 'dataset_id', 'method_id', 'normalization_id' obsm: 'X_pca' layers: 'counts', 'normalized' - >> Checking whether predictions were added - Checking whether data from input was copied properly to output All checks succeeded! ==================================================================== - SUCCESS! All 1 out of 1 test scripts succeeded! + SUCCESS! All 2 out of 2 test scripts succeeded! Cleaning up temporary directory Let’s introduce a bug in the script and try running the test again. For @@ -471,73 +487,95 @@ all of the required output slots. viash test src/tasks/label_projection/methods/foo/config.vsh.yaml ``` - Running tests in temporary directory: '/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128' + Running tests in temporary directory: '/tmp/viash_test_foo11839237358029204600' + ==================================================================== + +/tmp/viash_test_foo11839237358029204600/build_executable/foo ---verbosity 6 ---setup cachedbuild + [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/foo:test' with Dockerfile + [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods/foo:test /tmp/viash_test_foo11839237358029204600/build_executable -f /tmp/viash_test_foo11839237358029204600/build_executable/tmp/dockerbuild-foo-gPvc8b/Dockerfile' + #0 building with "default" instance using docker driver + + #1 [internal] load build definition from Dockerfile + #1 transferring dockerfile: 658B done + #1 DONE 0.1s + + #2 [internal] load .dockerignore + #2 transferring context: 2B done + #2 DONE 0.1s + + #3 [internal] load metadata for ghcr.io/openproblems-bio/base_python:1.0.2 + #3 DONE 0.3s + + #4 [1/2] FROM ghcr.io/openproblems-bio/base_python:1.0.2@sha256:65a577a3de37665b7a65548cb33c9153b6881742345593d33fe02919c8d66a20 + #4 DONE 0.0s + + #5 [2/2] RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "scikit-learn" + #5 CACHED + + #6 exporting to image + #6 exporting layers done + #6 writing image sha256:939f5846475192d821898f663f15872432e7a2c9033b38ac9b9522155270daf4 done + #6 naming to ghcr.io/openproblems-bio/label_projection/methods/foo:test 0.0s done + #6 DONE 0.0s ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable/foo ---verbosity 6 ---setup cachedbuild - [notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh' with Dockerfile - [info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh /home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable -f /home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/build_executable/tmp/dockerbuild-foo-VUcsWQ/Dockerfile' - Sending build context to Docker daemon 39.94kB - - Step 1/7 : FROM python:3.10 - ---> 465483cdaa4e - Step 2/7 : RUN pip install --upgrade pip && pip install --upgrade --no-cache-dir "anndata~=0.8.0" "scikit-learn" - ---> Using cache - ---> 91f658ec0590 - Step 3/7 : LABEL org.opencontainers.image.description="Companion container for running component label_projection/methods foo" - ---> Using cache - ---> f1ace85a71b0 - Step 4/7 : LABEL org.opencontainers.image.created="2022-12-17T08:47:52+01:00" - ---> Running in ae1e366b6410 - Removing intermediate container ae1e366b6410 - ---> 458c1b49e8b4 - Step 5/7 : LABEL org.opencontainers.image.source="https://github.com/openproblems-bio/openproblems-v2" - ---> Running in 06a244e7be1e - Removing intermediate container 06a244e7be1e - ---> cc48147df9e8 - Step 6/7 : LABEL org.opencontainers.image.revision="8a4877920fc79009dcb1e4bb16674b3b441c75ab" - ---> Running in 2372d2bddd3d - Removing intermediate container 2372d2bddd3d - ---> 7bcad47b5d1b - Step 7/7 : LABEL org.opencontainers.image.version="test_lnevgh" - ---> Running in 6499fcfa63af - Removing intermediate container 6499fcfa63af - ---> 2213de86e5bc - Successfully built 2213de86e5bc - Successfully tagged ghcr.io/openproblems-bio/label_projection/methods_foo:test_lnevgh + +/tmp/viash_test_foo11839237358029204600/test_check_method_config/test_executable + Load config data + Check general fields + Check info fields + Check platform fields + All checks succeeded! ==================================================================== - +/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/test_generic_test/test_executable - Traceback (most recent call last): + +/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/test_executable + >> Running test 'run' + >> Checking whether input files exist >> Running script as test + Load data + Not creating any predictions!!! + Not adding method name to uns!!! + Write output to file >> Checking whether output file exists - File "/viash_automount/home/rcannood/workspace/viash_temp/viash_test_foo4037451094287802128/test_generic_test/tmp//viash-run-foo-BVsf0m.py", line 57, in - >> Reading h5ad files - assert "label_pred" in output.obs - input_test: AnnData object with n_obs × n_vars = 130 × 443 - AssertionError + >> Reading h5ad files and checking formats + Reading and checking input_train + AnnData object with n_obs × n_vars = 326 × 500 + obs: 'label', 'batch' + var: 'hvg', 'hvg_score' + uns: 'dataset_id', 'normalization_id' + obsm: 'X_pca' + layers: 'counts', 'normalized' + Reading and checking input_test + AnnData object with n_obs × n_vars = 174 × 500 obs: 'batch' var: 'hvg', 'hvg_score' uns: 'dataset_id', 'normalization_id' obsm: 'X_pca' layers: 'counts', 'normalized' - output: AnnData object with n_obs × n_vars = 130 × 443 + Reading and checking output + AnnData object with n_obs × n_vars = 174 × 500 + Traceback (most recent call last): obs: 'batch' var: 'hvg', 'hvg_score' + File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 138, in uns: 'dataset_id', 'normalization_id' + run_and_check(argset_args, cmd) obsm: 'X_pca' + File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 81, in run_and_check layers: 'counts', 'normalized' - >> Checking whether predictions were added + check_slots(adata, arg) + File "/viash_automount/tmp/viash_test_foo11839237358029204600/test_run_and_check_adata/tmp//viash-run-foo-22aQh6.py", line 48, in check_slots + assert slot_item["name"] in struc_x,\ + AssertionError: File 'output.h5ad' is missing slot .obs['label_pred'] ==================================================================== - ERROR! Only 0 out of 1 test scripts succeeded! + ERROR! Only 1 out of 2 test scripts succeeded! Unexpected error occurred! If you think this is a bug, please post create an issue at https://github.com/viash-io/viash/issues containing a reproducible example and the stack trace below. - viash - 0.6.6 + viash - 0.8.0 Stacktrace: - java.lang.RuntimeException: Only 0 out of 1 test scripts succeeded! - at io.viash.ViashTest$.apply(ViashTest.scala:111) - at io.viash.Main$.internalMain(Main.scala:185) - at io.viash.Main$.main(Main.scala:77) + java.lang.RuntimeException: Only 1 out of 2 test scripts succeeded! + at io.viash.ViashTest$.apply(ViashTest.scala:134) + at io.viash.Main$.mainCLI(Main.scala:253) + at io.viash.Main$.mainCLIOrVersioned(Main.scala:123) + at io.viash.Main$.main(Main.scala:58) at io.viash.Main.main(Main.scala) ## More information @@ -548,3 +586,54 @@ and the [Guide](https://viash.io/guide/) will help you get started with creating components from scratch. + +## Branch Naming Conventions + +### Category + +A git branch should start with a category. Pick one of these: feature, +bugfix, hotfix, or test. + +- `feature` is for adding, refactoring or removing a feature +- `bugfix` is for fixing a bug +- `hotfix` is for changing code with a temporary solution and/or without + following the usual process (usually because of an emergency) +- `test` is for experimenting outside of an issue/ticket +- `doc` is for adding, changing or removing documentation + +### Reference + +After the category, there should be a “`/`” followed by the reference of +the issue/ticket/task you are working on. If there’s no reference, just +add no-ref. With task it is meant as benchmarking task +e.g. batch_integration + +### Description + +After the reference, there should be another “`/`” followed by a +description which sums up the purpose of this specific branch. This +description should be short and “kebab-cased”. + +By default, you can use the title of the issue/ticket you are working +on. Just replace any special character by “`-`”. + +### To sum up, follow this pattern when branching: + +``` bash +git branch +``` + +### Examples + +- You need to add, refactor or remove a feature: + `git branch feature/issue-42/create-new-button-component` +- You need to fix a bug: + `git branch bugfix/issue-342/button-overlap-form-on-mobile` +- You need to fix a bug really fast (possibly with a temporary + solution): `git branch hotfix/no-ref/registration-form-not-working` +- You need to experiment outside of an issue/ticket: + `git branch test/no-ref/refactor-components-with-atomic-design` + +### References + +- [a-simplified-convention-for-naming-branches-and-commits-in-git](https://dev.to/varbsan/a-simplified-convention-for-naming-branches-and-commits-in-git-il4) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index 269d13b259..a1c037c772 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -2,10 +2,11 @@ title: Contributing to OpenProblems format: gfm toc: true +toc-depth: 2 engine: knitr --- -[OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). +[OpenProblems](https://openproblems.bio) is a community effort, and everyone is welcome to contribute. This project is hosted on [github.com/openproblems-bio/openproblems-v2](https://github.com/openproblems-bio/openproblems-v2). You can find a full in depth guide on how to contribute to this project on the [OpenProblems website](https://openproblems.bio/documentation/). ## Code of conduct {#code-of-conduct} @@ -167,26 +168,30 @@ functionality: # a short label of your method label: Foo - paper_doi: "10.1234/1234.5678.1234567890" + # A multiline description of your method. + description: "Todo: fill in" - # if you don't have a Doi, you can specify a name, url and year manually: - # paper_name: "Nearest neighbor pattern classification" - # paper_url: "https://doi.org/10.1109/TIT.1967.1053964" - # paper_year: 1967 - - repository_url: "https://github.com/my_organisation/foo" + # A short summary of the method description. + summary: "Todo: fill in" + + # Add the bibtex reference to the "src/common/library.bib" if it is not already there. + reference: "cover1967nearest" + + repository_url: "https://github.com/openproblems-bio/openproblems-v2" + documentation_url: "https://openproblems.bio/documentation/" + preferred_normalization: log_cp10k resources: - type: python_script path: script.py platforms: - type: docker - image: "python:3.10" + image: ghcr.io/openproblems-bio/base_python:1.0.2 setup: - type: python - packages: - - anndata~=0.8.0 - - scikit-learn + packages: [scikit-learn] - type: nextflow + directives: + label: [midtime, midmem, lowcpu] HERE cat > src/tasks/label_projection/methods/foo/script.py << HERE @@ -241,6 +246,13 @@ You can view the interface of the executable by running the executable with the viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- --help ``` +Before running a new component, youy will need to create the docker container: + +```{bash} +viash run src/tasks/label_projection/methods/foo/config.vsh.yaml -- ---setup cachedbuild + +``` + You can **run the component** as follows: ```{bash} diff --git a/README.md b/README.md index 1dbb8d6abb..c51623f4ce 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ -OpenProblems v2 -================ +# OpenProblems v2 + Formalizing and benchmarking open problems in single-cell genomics. [**Visit the Open Problems Website.**](https://openproblems.bio/) To get started with developing a new method or metric, please see the -[Contribution guidelines](CONTRIBUTING.md). +[OpenProblems documentation](https://openproblems.bio/documentation/). ## Benefits of using Viash diff --git a/README.qmd b/README.qmd index 6d8bc5ea1d..63d294456a 100644 --- a/README.qmd +++ b/README.qmd @@ -9,7 +9,7 @@ Formalizing and benchmarking open problems in single-cell genomics. [**Visit the Open Problems Website.**](https://openproblems.bio/) -To get started with developing a new method or metric, please see the [Contribution guidelines](CONTRIBUTING.md). +To get started with developing a new method or metric, please see the [OpenProblems documentation](https://openproblems.bio/documentation/). ## Benefits of using Viash From 97402ee12e93fac889598da663c44a68db44b6fd Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 21 Feb 2024 10:14:17 +0100 Subject: [PATCH 1155/1233] [pred_mod] refactor dataset processing (#381) * Refactor new id * Update wf test * refactor modality swapping * add suggestion * Add suggestions Former-commit-id: 549152789a390af874d45737b7af1f918e2deb7f --- .../resources_scripts/process_datasets.sh | 22 +--------- .../neurips2021_bmmc.sh | 12 ----- .../process_datasets/config.vsh.yaml | 4 -- .../workflows/process_datasets/main.nf | 44 +++++++++++++------ .../workflows/process_datasets/run_test.sh | 2 +- 5 files changed, 32 insertions(+), 52 deletions(-) diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index a20ce99963..11da1b6ee6 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -28,24 +28,4 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ - --labels predict_modality,process_datasets - -cat > /tmp/params.yaml << 'HERE' -id: predict_modality_process_datasets_swap -input_states: s3://openproblems-data/resources/datasets/**/state.yaml -settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' -rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' -output_state: "$id/state.yaml" -publish_dir: s3://openproblems-data/resources/predict_modality/datasets -HERE - -tw launch https://github.com/openproblems-bio/openproblems-v2.git \ - --revision main_build \ - --pull-latest \ - --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ - --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ - --params-file /tmp/params.yaml \ - --entry-name auto \ - --config /tmp/nextflow.config \ - --labels predict_modality,process_datasets,swap_mod \ No newline at end of file + --labels predict_modality,process_datasets \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 1367e333ee..5f4321867d 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -25,18 +25,6 @@ nextflow run . \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' -# Swap the modalities -nextflow run . \ - -main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ - -profile docker \ - -entry auto \ - -c src/wf_utils/labels_ci.config \ - --input_states "resources_test/common/openproblems_neurips2021/**/state.yaml" \ - --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2' \ - --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad", "swap": true}' \ - --publish_dir "$OUTPUT_DIR" \ - --output_state '$id/state.yaml' - echo "Run one method" viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ diff --git a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml index 4b3153e789..66e5c5141b 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/process_datasets/config.vsh.yaml @@ -12,10 +12,6 @@ functionality: __merge__: "/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml" direction: input required: true - - name: "--swap" - type: "boolean" - description: "Swap mod1 and mod2" - default: false - name: Outputs arguments: - name: "--output_train_mod1" diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 0437a9005d..93b6d8ce1f 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -12,7 +12,25 @@ workflow run_wf { input_ch main: + + direction = Channel.of("normal", "swap") + output_ch = input_ch + + | combine(direction) + + // Add swap direction to the state and set new id + | map{id, state, dir -> + // Add direction (normal / swap) to id + // Note: this id is added before the normalisation id + // Example old id: dataset_loader/dataset_id/normalization_id + // Example new id: dataset_loader/dataset_id_direction/normalization_id + def id_split = id.tokenize("/") + def norm = id_split.takeRight(1)[0] + def new_id = id_split.dropRight(1).join("/") + "_" + dir + "/" + norm + + [new_id, state + [direction: dir, "_meta": [join_id: id]]] + } | check_dataset_schema.run( key: "check_dataset_schema_mod1", @@ -61,15 +79,18 @@ workflow run_wf { } | process_dataset.run( - fromState: [ - input_mod1: "dataset_mod1", - input_mod2: "dataset_mod2", - output_train_mod1: "output_train_mod1", - output_train_mod2: "output_train_mod2", - output_test_mod1: "output_test_mod1", - output_test_mod2: "output_test_mod2", - swap: "swap" - ], + fromState: { id, state -> + def swap_state = state.direction == "swap" ? true : false + [ + input_mod1: state.dataset_mod1, + input_mod2: state.dataset_mod2, + output_train_mod1: state.output_train_mod1, + output_train_mod2: state.output_train_mod2, + output_test_mod1: state.output_test_mod1, + output_test_mod2: state.output_test_mod2, + swap: swap_state + ] + }, toState: [ "output_train_mod1", "output_train_mod2", @@ -100,11 +121,6 @@ workflow run_wf { } ) - | map { id, state -> - def new_id = id + "_" + state.modality_mod1 + "2" + state.modality_mod2 - [new_id, state + ["_meta": [join_id: id]]] - } - // only output the files for which an output file was specified | setState ([ "output_train_mod1", diff --git a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh index e3c29c1ec8..4f921155e2 100755 --- a/src/tasks/predict_modality/workflows/process_datasets/run_test.sh +++ b/src/tasks/predict_modality/workflows/process_datasets/run_test.sh @@ -22,7 +22,7 @@ nextflow run . \ -entry auto \ -c src/wf_utils/labels_ci.config \ --input_states "$DATASETS_DIR/**/state.yaml" \ - --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2' \ --settings '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' \ --publish_dir "$OUTPUT_DIR" \ --output_state '$id/state.yaml' \ No newline at end of file From 299958aeacbb806f29b419a78319b5a687538450 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 21 Feb 2024 13:53:30 +0100 Subject: [PATCH 1156/1233] [pred_mod] Update test_resources path (#382) * Update test_resources path * rework process datasets workflow * fix wf * fix paths to test resources * #ci-force --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 636e8917cad1c68cccdc76e6f057bdf78aca4712 --- .../api/comp_control_method.yaml | 4 +- .../predict_modality/api/comp_method.yaml | 4 +- .../predict_modality/api/comp_metric.yaml | 4 +- .../predict_modality/api/file_prediction.yaml | 2 +- .../predict_modality/api/file_score.yaml | 2 +- .../predict_modality/api/file_test_mod1.yaml | 2 +- .../predict_modality/api/file_test_mod2.yaml | 2 +- .../predict_modality/api/file_train_mod1.yaml | 2 +- .../predict_modality/api/file_train_mod2.yaml | 2 +- .../neurips2021_bmmc.sh | 32 ++++---- .../workflows/process_datasets/main.nf | 81 +++++++++---------- 11 files changed, 64 insertions(+), 73 deletions(-) diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml index ca478f4444..82ab6e441f 100644 --- a/src/tasks/predict_modality/api/comp_control_method.yaml +++ b/src/tasks/predict_modality/api/comp_control_method.yaml @@ -38,5 +38,5 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT \ No newline at end of file + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index b7f91f0590..0855227a55 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -30,6 +30,6 @@ functionality: path: /src/common/comp_tests/check_method_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml index 73b2d2f5b0..c85f900e46 100644 --- a/src/tasks/predict_modality/api/comp_metric.yaml +++ b/src/tasks/predict_modality/api/comp_metric.yaml @@ -25,6 +25,6 @@ functionality: path: /src/common/comp_tests/check_metric_config.py - type: python_script path: /src/common/comp_tests/run_and_check_adata.py - - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT - dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT + - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap + dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml index 08cc5f2f84..0464b323d1 100644 --- a/src/tasks/predict_modality/api/file_prediction.yaml +++ b/src/tasks/predict_modality/api/file_prediction.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/prediction.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/prediction.h5ad" info: label: "Prediction" summary: "A prediction of the mod2 expression values of the test cells" diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml index 12927ffc7e..928e18eebf 100644 --- a/src/tasks/predict_modality/api/file_score.yaml +++ b/src/tasks/predict_modality/api/file_score.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/score.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/score.h5ad" info: label: "Score" summary: "Metric score file" diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index d5c0b309c4..fa8a770f08 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod1.h5ad" info: label: "Test mod1" summary: "The mod1 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index a0d3012da8..f1b12decd8 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod2.h5ad" info: label: "Test mod2" summary: "The mod2 expression values of the test cells." diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index c675580a8e..d9a0cda61c 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod1.h5ad" info: label: "Train mod1" summary: "The mod1 expression values of the train cells." diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index f4a2eb01af..a67092c8f0 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -1,5 +1,5 @@ type: file -example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad" +example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod2.h5ad" info: label: "Train mod2" summary: "The mod2 expression values of the train cells." diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh index 5f4321867d..534a3b5626 100755 --- a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh +++ b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh @@ -28,25 +28,25 @@ nextflow run . \ echo "Run one method" viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/normal/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/normal/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/normal/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite/normal/prediction.h5ad viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_ADT2GEX/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR//openproblems_neurips2021/bmmc_cite/swap/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR//openproblems_neurips2021/bmmc_cite/swap/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR//openproblems_neurips2021/bmmc_cite/swap/test_mod1.h5ad \ + --output $OUTPUT_DIR//openproblems_neurips2021/bmmc_cite/swap/prediction.h5ad viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_GEX2ATAC/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/normal/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/normal/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/normal/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/normal/prediction.h5ad viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \ - --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/train_mod1.h5ad \ - --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/train_mod2.h5ad \ - --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/test_mod1.h5ad \ - --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome_ATAC2GEX/prediction.h5ad + --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/swap/train_mod1.h5ad \ + --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/swap/train_mod2.h5ad \ + --input_test_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/swap/test_mod1.h5ad \ + --output $OUTPUT_DIR/openproblems_neurips2021/bmmc_multiome/swap/prediction.h5ad \ No newline at end of file diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 93b6d8ce1f..978942181a 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -13,25 +13,9 @@ workflow run_wf { main: - direction = Channel.of("normal", "swap") - output_ch = input_ch - | combine(direction) - - // Add swap direction to the state and set new id - | map{id, state, dir -> - // Add direction (normal / swap) to id - // Note: this id is added before the normalisation id - // Example old id: dataset_loader/dataset_id/normalization_id - // Example new id: dataset_loader/dataset_id_direction/normalization_id - def id_split = id.tokenize("/") - def norm = id_split.takeRight(1)[0] - def new_id = id_split.dropRight(1).join("/") + "_" + dir + "/" + norm - - [new_id, state + [direction: dir, "_meta": [join_id: id]]] - } - + // Check if the input datasets match the desired format -------------------------------- | check_dataset_schema.run( key: "check_dataset_schema_mod1", fromState: { id, state -> @@ -78,6 +62,35 @@ workflow run_wf { state.dataset_mod2 != null } + // Use datasets in both directions (mod1 -> mod2 and mod2 -> mod1) --------------------- + // extract the dataset metadata + | extract_metadata.run( + key: "extract_metadata", + fromState: [input: "dataset_mod1"], + toState: { id, output, state -> + def uns = readYaml(output.output).uns + state + [ + "dataset_id": uns.dataset_id, + "normalization_id": uns.normalization_id + ] + } + ) + + // Add swap direction to the state and set new id + | flatMap{id, state -> + ["normal", "swap"].collect { dir -> + // Add direction (normal / swap) to id + // Note: this id is added before the normalisation id + // Example old id: dataset_loader/dataset_id/normalization_id + // Example new id: dataset_loader/dataset_id/direction/normalization_id + def left = id.replaceAll("/${state.normalization_id}\$", "") + def right = id.replaceAll("^${left}", "") + def new_id = left + "/" + dir + right + + [new_id, state + [direction: dir, "_meta": [join_id: id]]] + } + } + | process_dataset.run( fromState: { id, state -> def swap_state = state.direction == "swap" ? true : false @@ -99,36 +112,14 @@ workflow run_wf { ] ) - // extract the dataset metadata - | extract_metadata.run( - key: "extract_metadata_mod1", - fromState: [input: "output_train_mod1"], - toState: { id, output, state -> - state + [ - modality_mod1: readYaml(output.output).uns.modality - ] - } - ) - - // extract the dataset metadata - | extract_metadata.run( - key: "extract_metadata_mod2", - fromState: [input: "output_train_mod2"], - toState: { id, output, state -> - state + [ - modality_mod2: readYaml(output.output).uns.modality - ] - } - ) - // only output the files for which an output file was specified | setState ([ - "output_train_mod1", - "output_train_mod2", - "output_test_mod1", - "output_test_mod2", - "_meta" - ]) + "output_train_mod1", + "output_train_mod2", + "output_test_mod1", + "output_test_mod2", + "_meta" + ]) emit: output_ch From adcdddaa1b864db2abc8b1f625d0b50df079c491 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 21 Feb 2024 14:17:27 +0100 Subject: [PATCH 1157/1233] Update denoising task components (#379) * update magic * refactor denoising methods * add id * store the train_sum in the test file * fix output * turn counts to float * fix alra * add SAVER * fix mse metric * remove unneeded script Former-commit-id: 94a696699e29d2fadd6292e56060beeec3062cbf --- src/common/library.bib | 15 ++++ src/tasks/denoising/api/file_denoised.yaml | 6 +- src/tasks/denoising/api/file_test.yaml | 6 +- .../denoising/methods/alra/config.vsh.yaml | 13 ++-- src/tasks/denoising/methods/alra/script.R | 44 ++++++++--- src/tasks/denoising/methods/dca/script.py | 30 +++++--- .../denoising/methods/knn_smoothing/script.py | 30 ++++++-- .../denoising/methods/magic/config.vsh.yaml | 6 +- src/tasks/denoising/methods/magic/script.py | 73 ++++++++++++------- .../denoising/methods/saver/config.vsh.yaml | 33 +++++++++ src/tasks/denoising/methods/saver/script.R | 39 ++++++++++ src/tasks/denoising/metrics/mse/script.py | 29 +++----- .../denoising/metrics/poisson/config.vsh.yaml | 5 +- src/tasks/denoising/metrics/poisson/script.py | 29 +++----- src/tasks/denoising/process_dataset/script.py | 11 ++- 15 files changed, 257 insertions(+), 112 deletions(-) create mode 100644 src/tasks/denoising/methods/saver/config.vsh.yaml create mode 100644 src/tasks/denoising/methods/saver/script.R diff --git a/src/common/library.bib b/src/common/library.bib index 9806965d00..03e9f411f4 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1661,4 +1661,19 @@ @article{sonrel2023metaanalysis author = {Sonrel, Anthony and Luetge, Almut and Soneson, Charlotte and Mallona, Izaskun and Germain, Pierre-Luc and Knyazev, Sergey and Gilis, Jeroen and Gerber, Reto and Seurinck, Ruth and Paul, Dominique and Sonder, Emanuel and Crowell, Helena L. and Fanaswala, Imran and Al-Ajami, Ahmad and Heidari, Elyas and Schmeing, Stephan and Milosavljevic, Stefan and Saeys, Yvan and Mangul, Serghei and Robinson, Mark D.}, year = {2023}, month = may +} + +@article{huang2018savergene, + title = {SAVER: gene expression recovery for single-cell RNA sequencing}, + volume = {15}, + ISSN = {1548-7105}, + url = {http://dx.doi.org/10.1038/s41592-018-0033-z}, + DOI = {10.1038/s41592-018-0033-z}, + number = {7}, + journal = {Nature Methods}, + publisher = {Springer Science and Business Media LLC}, + author = {Huang, Mo and Wang, Jingshu and Torre, Eduardo and Dueck, Hannah and Shaffer, Sydney and Bonasio, Roberto and Murray, John I. and Raj, Arjun and Li, Mingyao and Zhang, Nancy R.}, + year = {2018}, + month = jun, + pages = {539–542} } \ No newline at end of file diff --git a/src/tasks/denoising/api/file_denoised.yaml b/src/tasks/denoising/api/file_denoised.yaml index 3f8ebc6e59..fc79694028 100644 --- a/src/tasks/denoising/api/file_denoised.yaml +++ b/src/tasks/denoising/api/file_denoised.yaml @@ -4,11 +4,7 @@ info: label: "Denoised data" summary: A denoised dataset as output by a denoising method. slots: - layers: - - type: integer - name: counts - description: Raw counts - required: true + layers: - type: integer name: denoised description: denoised data diff --git a/src/tasks/denoising/api/file_test.yaml b/src/tasks/denoising/api/file_test.yaml index 04d89251ce..371b3054f7 100644 --- a/src/tasks/denoising/api/file_test.yaml +++ b/src/tasks/denoising/api/file_test.yaml @@ -37,4 +37,8 @@ info: - name: dataset_organism type: string description: The organism of the sample in the dataset. - required: false \ No newline at end of file + required: false + - name: train_sum + type: integer + description: The total number of counts in the training dataset. + required: true \ No newline at end of file diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index e9526009c0..f0e47c92e8 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -5,14 +5,14 @@ functionality: label: ALRA summary: "ALRA imputes missing values in scRNA-seq data by computing rank-k approximation, thresholding by gene, and rescaling the matrix." description: | - "Adaptively-thresholded Low Rank Approximation (ALRA). + Adaptively-thresholded Low Rank Approximation (ALRA). ALRA is a method for imputation of missing values in single cell RNA-sequencing data, described in the preprint, "Zero-preserving imputation of scRNA-seq data using low-rank approximation" available [here](https://www.biorxiv.org/content/early/2018/08/22/397588). Given a scRNA-seq expression matrix, ALRA first computes its rank-k approximation using randomized SVD. Next, each row (gene) is thresholded by the magnitude of the most negative value of that gene. - Finally, the matrix is rescaled." + Finally, the matrix is rescaled. reference: "linderman2018zero" repository_url: "https://github.com/KlugerLab/ALRA" documentation_url: https://github.com/KlugerLab/ALRA/blob/master/README.md @@ -23,10 +23,11 @@ functionality: alra: preferred_normalization: counts arguments: - - name: "--epochs" - type: "integer" - default: 300 - description: "Number of total epochs in training" + - name: "--norm" + type: string + choices: ["sqrt", "log"] + default: "log" + description: Normalization method resources: - type: r_script path: script.R diff --git a/src/tasks/denoising/methods/alra/script.R b/src/tasks/denoising/methods/alra/script.R index 6252cefffd..9a5b237c6f 100644 --- a/src/tasks/denoising/methods/alra/script.R +++ b/src/tasks/denoising/methods/alra/script.R @@ -1,29 +1,53 @@ - cat(">> Loading dependencies\n") library(anndata, warn.conflicts = FALSE) -library(Matrix, warn.conflicts = FALSE) library(ALRA, warn.conflicts = FALSE) ## VIASH START par <- list( input_train = "resources_test/denoising/pancreas/train.h5ad", - # input_train = "resources_test/common/pancreas/dataset.h5ad", + norm = "log", output = "output.h5ad" ) +meta <- list( + functionality_name = "alra" +) ## VIASH END cat(">> Load input data\n") -adata <- read_h5ad(par$input_train) +input_train <- read_h5ad(par$input_train, backed = "r") -counts <- t(adata$layers[["counts"]]) +cat(">> Set normalization method\n") +if (par$norm == "sqrt") { + norm_fn <- sqrt + denorm_fn <- function(x) x^2 +} else if (par$norm == "log") { + norm_fn <- log1p + denorm_fn <- expm1 +} else { + stop("Unknown normalization method: ", par$norm) +} + +cat(">> Normalize data\n") +data <- as.matrix(input_train$layers[["counts"]]) +totalPerCell <- rowSums(data) +data <- sweep(data, 1, totalPerCell, "/") +data <- norm_fn(data) cat(">> Run ALRA\n") -# alra doesn't work with sparce matrices -out <- alra(as.matrix(counts)) +data <- alra(data)$A_norm_rank_k_cor_sc +data <- denorm_fn(data) +data <- sweep(data, 1, totalPerCell, "*") cat(">> Store output\n") -adata$layers[["denoised"]] <- as(t(out$A_norm_rank_k_cor_sc), "CsparseMatrix") -adata$uns[["method_id"]] <- meta[["functionality_name"]] +output <- AnnData( + layers = list(denoised = data), + obs = input_train$obs[, c(), drop = FALSE], + var = input_train$var[, c(), drop = FALSE], + uns = list( + dataset_id = input_train$uns[["dataset_id"]], + method_id = meta$functionality_name + ) +) cat(">> Write output to file\n") -adata$write_h5ad(par$output, compression = "gzip") +output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/denoising/methods/dca/script.py b/src/tasks/denoising/methods/dca/script.py index b2a7ee99fa..d35f3c00a5 100644 --- a/src/tasks/denoising/methods/dca/script.py +++ b/src/tasks/denoising/methods/dca/script.py @@ -1,6 +1,5 @@ import anndata as ad from dca.api import dca -import scipy ## VIASH START par = { @@ -14,18 +13,27 @@ ## VIASH END print("load input data", flush=True) -input_train = ad.read_h5ad(par['input_train']) +input_train = ad.read_h5ad(par['input_train'], backed="r") -print("move layer to X", flush=True) -input_dca = ad.AnnData(X=input_train.layers["counts"]) -del input_train.X +print("Remove unneeded data", flush=True) +output = ad.AnnData( + X=input_train.layers["counts"], + obs=input_train.obs[[]], + var=input_train.var[[]], + uns={ + "dataset_id": input_train.uns["dataset_id"], + "method_id": meta["functionality_name"] + } +) -print("running dca", flush=True) -dca(input_dca, epochs=par["epochs"]) +del input_train -print("moving X back to layer", flush=True) -input_train.layers["denoised"] = scipy.sparse.csr_matrix(input_dca.X) +print("Run DCA", flush=True) +dca(output, epochs=par["epochs"]) + +print("Move output to correct location", flush=True) +output.layers["denoised"] = output.X +del output.X print("Writing data", flush=True) -input_train.uns["method_id"] = meta["functionality_name"] -input_train.write_h5ad(par["output"], compression="gzip") +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/denoising/methods/knn_smoothing/script.py b/src/tasks/denoising/methods/knn_smoothing/script.py index ec65960f42..450da2012a 100644 --- a/src/tasks/denoising/methods/knn_smoothing/script.py +++ b/src/tasks/denoising/methods/knn_smoothing/script.py @@ -1,7 +1,5 @@ import knn_smooth -import numpy as np import anndata as ad -import scipy ## VIASH START par = { @@ -14,12 +12,28 @@ ## VIASH END print("Load input data", flush=True) -input_train = ad.read_h5ad(par["input_train"]) +input_train = ad.read_h5ad(par["input_train"], backed="r") -print("process data", flush=True) -X = input_train.layers["counts"].transpose().toarray() -input_train.layers["denoised"] = scipy.sparse.csr_matrix((knn_smooth.knn_smoothing(X, k=10)).transpose()) +print("Remove unneeded data", flush=True) +X = input_train.layers["counts"].astype(float).transpose().toarray() + +# Create output AnnData for later use +output = ad.AnnData( + obs=input_train.obs[[]], + var=input_train.var[[]], + uns={ + "dataset_id": input_train.uns["dataset_id"], + "method_id": meta["functionality_name"] + } +) + +del input_train + +print("Run KNN smoothing", flush=True) +X = knn_smooth.knn_smoothing(X, k=10).transpose() + +print("Process data", flush=True) +output.layers["denoised"] = X print("Writing data", flush=True) -input_train.uns["method_id"] = meta["functionality_name"] -input_train.write_h5ad(par["output"], compression="gzip") +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 02b570f418..261d739ee7 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: magic: magic_approx: solver: approximate - knn_naive: + magic_knn_naive: norm: log decay: none t: 1 @@ -39,7 +39,7 @@ functionality: - name: "--norm" type: string choices: ["sqrt", "log"] - default: "sqrt" + default: "log" description: Normalization method - name: "--decay" type: integer @@ -60,4 +60,4 @@ platforms: pip: [scprep, magic-impute, scipy, scikit-learn<1.2] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/denoising/methods/magic/script.py b/src/tasks/denoising/methods/magic/script.py index 8f2ed4e566..075d2e21cd 100644 --- a/src/tasks/denoising/methods/magic/script.py +++ b/src/tasks/denoising/methods/magic/script.py @@ -7,49 +7,70 @@ ## VIASH START par = { - 'input_train': 'output_train.h5ad', - 'output': 'output_magic.h5ad', - 'solver': 'exact', - 'norm': 'sqrt', - 'decay': 1, - 't': 3, + "input_train": "resources_test/denoising/pancreas/train.h5ad", + "output": "output_magic.h5ad", + "solver": "exact", + "norm": "sqrt", + "decay": 1, + "t": 3, } meta = { - 'functionality_name': 'foo', + "functionality_name": "foo", } ## VIASH END +print("Load data", flush=True) +input_train = ad.read_h5ad(par["input_train"], backed="r") -print("load data", flush=True) -input_train = ad.read_h5ad(par['input_train']) - -normtype = par['norm'] - -if normtype == "sqrt": +print("Set normalization method", flush=True) +if par["norm"] == "sqrt": norm_fn = np.sqrt denorm_fn = np.square -elif normtype == "log": +elif par["norm"] == "log": norm_fn = np.log1p denorm_fn = np.expm1 +else: + raise ValueError("Unknown normalization method: " + par["norm"] + ".") -print("processing data", flush=True) +print("Remove unneeded data", flush=True) +X = input_train.layers["counts"] -X, libsize = scprep.normalize.library_size_normalize( - input_train.layers['counts'], rescale=1, return_library_size=True +# Create output AnnData for later use +output = ad.AnnData( + obs=input_train.obs[[]], + var=input_train.var[[]], + uns={ + "dataset_id": input_train.uns["dataset_id"], + "method_id": meta["functionality_name"] + } ) +del input_train + +print("Normalize data", flush=True) +X, libsize = scprep.normalize.library_size_normalize( + X, + rescale=1, + return_library_size=True +) X = scprep.utils.matrix_transform(X, norm_fn) -Y = MAGIC(solver=par['solver'], verbose=False, decay=par['decay'], t=par['t']).fit_transform( - X, genes="all_genes" + +print("Run MAGIC", flush=True) +magic = MAGIC( + solver=par["solver"], + decay=par["decay"], + t=par["t"], + verbose=False, ) +X = magic.fit_transform(X, genes="all_genes") -Y = scprep.utils.matrix_transform(Y, denorm_fn) -Y = scprep.utils.matrix_vector_elementwise_multiply(Y, libsize, axis=0) +print("Denormalizing data", flush=True) +X = scprep.utils.matrix_transform(X, denorm_fn) +X = scprep.utils.matrix_vector_elementwise_multiply(X, libsize, axis=0) -output_denoised = input_train.copy() -output_denoised.uns["method_id"] = meta["functionality_name"] -output_denoised.layers["denoised"] = scipy.sparse.csr_matrix(Y) +print("Create output AnnData", flush=True) +output.layers["denoised"] = X -print("Writing Data", flush=True) -output_denoised.write_h5ad(par['output'],compression="gzip") +print("Write Data", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/denoising/methods/saver/config.vsh.yaml b/src/tasks/denoising/methods/saver/config.vsh.yaml new file mode 100644 index 0000000000..b2fcc00b7a --- /dev/null +++ b/src/tasks/denoising/methods/saver/config.vsh.yaml @@ -0,0 +1,33 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: saver + status: disabled + info: + label: SAVER + summary: SAVER (Single-cell Analysis Via Expression Recovery) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile. + description: | + SAVER takes advantage of gene-to-gene relationships to recover the true expression level of each gene in each cell, + removing technical variation while retaining biological variation across cells (https://github.com/mohuangx/SAVER). + SAVER uses a post-quality-control scRNA-seq dataset with UMI counts as input. SAVER assumes that the count of each + gene in each cell follows a Poisson-gamma mixture, also known as a negative binomial model. Instead of specifying + the gamma prior, we estimate the prior parameters in an empirical Bayes-like approach with a Poisson LASSO regression, + using the expression of other genes as predictors. Once the prior parameters are estimated, SAVER outputs the + posterior distribution of the true expression, which quantifies estimation uncertainty, and the posterior mean is + used as the SAVER recovered expression value. + reference: huang2018savergene + repository_url: https://github.com/mohuangx/SAVER + documentation_url: https://mohuangx.github.io/SAVER/index.html + preferred_normalization: counts + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + # cran: [ bit64 ] + github: mohuangx/SAVER + - type: nextflow + directives: + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/denoising/methods/saver/script.R b/src/tasks/denoising/methods/saver/script.R new file mode 100644 index 0000000000..f6a44f4c3a --- /dev/null +++ b/src/tasks/denoising/methods/saver/script.R @@ -0,0 +1,39 @@ +cat(">> Loading dependencies\n") +library(anndata, warn.conflicts = FALSE) +library(SAVER, warn.conflicts = FALSE) +library(Matrix, warn.conflicts = FALSE) + +## VIASH START +par <- list( + input_train = "resources_test/denoising/pancreas/train.h5ad", + norm = "log", + output = "output.h5ad" +) +meta <- list( + functionality_name = "saver", + ncpus = 30 +) +## VIASH END + +cat(">> Load input data\n") +input_train <- read_h5ad(par$input_train, backed = "r") + +cat(">> Normalize data\n") +data <- as(t(input_train$layers[["counts"]]), "CsparseMatrix") + +cat(">> Run SAVER\n") +data <- t(saver(data, ncores = meta$ncpus, estimates.only = TRUE)) + +cat(">> Store output\n") +output <- AnnData( + layers = list(denoised = data), + obs = input_train$obs[, c(), drop = FALSE], + var = input_train$var[, c(), drop = FALSE], + uns = list( + dataset_id = input_train$uns[["dataset_id"]], + method_id = meta$functionality_name + ) +) + +cat(">> Write output to file\n") +output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/denoising/metrics/mse/script.py b/src/tasks/denoising/metrics/mse/script.py index 4635a8065a..eba964f132 100644 --- a/src/tasks/denoising/metrics/mse/script.py +++ b/src/tasks/denoising/metrics/mse/script.py @@ -3,7 +3,6 @@ import sklearn.metrics import scprep - ## VIASH START par = { 'input_test': 'resources_test/denoising/pancreas/test.h5ad', @@ -16,12 +15,11 @@ ## VIASH END print("Load data", flush=True) -input_denoised = ad.read_h5ad(par['input_denoised']) -input_test = ad.read_h5ad(par['input_test']) - +input_denoised = ad.read_h5ad(par['input_denoised'], backed="r") +input_test = ad.read_h5ad(par['input_test'], backed="r") -test_data = ad.AnnData(X=input_test.layers["counts"].toarray(), dtype="float") -denoised_data = ad.AnnData( X=input_denoised.layers["denoised"].toarray(), dtype="float") +test_data = ad.AnnData(X=input_test.layers["counts"], dtype="float") +denoised_data = ad.AnnData(X=input_denoised.layers["denoised"], dtype="float") print("Normalize data", flush=True) @@ -36,23 +34,18 @@ print("Compute mse value", flush=True) error = sklearn.metrics.mean_squared_error( - scprep.utils.toarray(test_data.X), denoised_data.X + scprep.utils.toarray(test_data.X), scprep.utils.toarray(denoised_data.X) ) print("Store mse value", flush=True) -output_metric = ad.AnnData( - layers={}, - obs=input_denoised.obs[[]], - var=input_denoised.var[[]], - uns={} +output = ad.AnnData( + uns={ key: val for key, val in input_test.uns.items() }, ) -for key in input_denoised.uns_keys(): - output_metric.uns[key] = input_denoised.uns[key] - -output_metric.uns["metric_ids"] = meta['functionality_name'] -output_metric.uns["metric_values"] = error +output.uns["method_id"] = input_denoised.uns["method_id"] +output.uns["metric_ids"] = meta['functionality_name'] +output.uns["metric_values"] = error print("Write adata to file", flush=True) -output_metric.write_h5ad(par['output'], compression="gzip") +output.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index 3160cf94ed..af02493367 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -5,9 +5,8 @@ functionality: metrics: - name: poisson label: Poisson Loss - summary: "The Poisson log lieklihood of the true counts observed in the distribution of denoised counts" - description: "The Poisson log likelihood of observing the true counts of the test dataset - given the distribution given in the denoised dataset." + summary: "The Poisson log likelihood of the true counts observed in the distribution of denoised counts" + description: "The Poisson log likelihood of observing the true counts of the test dataset given the distribution given in the denoised dataset." reference: batson2019molecular v1: path: openproblems/tasks/denoising/metrics/poisson.py diff --git a/src/tasks/denoising/metrics/poisson/script.py b/src/tasks/denoising/metrics/poisson/script.py index 98049825c7..537ccf0119 100644 --- a/src/tasks/denoising/metrics/poisson/script.py +++ b/src/tasks/denoising/metrics/poisson/script.py @@ -14,15 +14,15 @@ ## VIASH END print("Load Data", flush=True) -input_denoised = ad.read_h5ad(par['input_denoised']) -input_test = ad.read_h5ad(par['input_test']) +input_denoised = ad.read_h5ad(par['input_denoised'], backed="r") +input_test = ad.read_h5ad(par['input_test'], backed="r") -test_data = input_test.layers["counts"].toarray() -denoised_data = input_denoised.layers["denoised"].toarray() +test_data = scprep.utils.toarray(input_test.layers["counts"]) +denoised_data = scprep.utils.toarray(input_denoised.layers["denoised"]) print("Compute metric value", flush=True) # scaling -initial_sum = input_denoised.layers["counts"].sum() +initial_sum = input_test.uns["train_sum"] target_sum = test_data.sum() denoised_data = denoised_data * target_sum / initial_sum @@ -31,21 +31,16 @@ def poisson_nll_loss(y_pred: np.ndarray, y_true: np.ndarray) -> float: return (y_pred - y_true * np.log(y_pred + 1e-6)).mean() -error = poisson_nll_loss(scprep.utils.toarray(test_data), denoised_data) +error = poisson_nll_loss(test_data, denoised_data) print("Store poisson value", flush=True) -output_metric = ad.AnnData( - layers={}, - obs=input_denoised.obs[[]], - var=input_denoised.var[[]], - uns={} +output = ad.AnnData( + uns={ key: val for key, val in input_test.uns.items() }, ) -for key in input_denoised.uns_keys(): - output_metric.uns[key] = input_denoised.uns[key] - -output_metric.uns["metric_ids"] = meta['functionality_name'] -output_metric.uns["metric_values"] = error +output.uns["method_id"] = input_denoised.uns["method_id"] +output.uns["metric_ids"] = meta['functionality_name'] +output.uns["metric_values"] = error print("Write adata to file", flush=True) -output_metric.write_h5ad(par['output'], compression="gzip") +output.write_h5ad(par['output'], compression="gzip") diff --git a/src/tasks/denoising/process_dataset/script.py b/src/tasks/denoising/process_dataset/script.py index d0eb9cf244..94a5884046 100644 --- a/src/tasks/denoising/process_dataset/script.py +++ b/src/tasks/denoising/process_dataset/script.py @@ -11,7 +11,7 @@ 'seed': 0 } meta = { - "functionality_name": "split_data", + "functionality_name": "process_dataset", "resources_dir": "src/tasks/denoising/process_dataset" } ## VIASH END @@ -46,21 +46,24 @@ X_train.eliminate_zeros() X_test.eliminate_zeros() -# copy adata to train_set, test_set +# copy adata to train_set, test_set output_train = ad.AnnData( - layers={"counts": X_train.astype(float)}, + layers={"counts": X_train}, obs=adata.obs[[]], var=adata.var[[]], uns={"dataset_id": adata.uns["dataset_id"]} ) test_uns_keys = ["dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism"] output_test = ad.AnnData( - layers={"counts": X_test.astype(float)}, + layers={"counts": X_test}, obs=adata.obs[[]], var=adata.var[[]], uns={key: adata.uns[key] for key in test_uns_keys} ) +# add additional information for the train set +output_test.uns["train_sum"] = X_train.sum() + # Remove no cells that do not have enough reads is_missing = np.array(X_train.sum(axis=0) == 0) From a1eb36def3156d00f5267ae3563b4bb66bb9c197 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 21 Feb 2024 15:20:17 +0100 Subject: [PATCH 1158/1233] be more verbose when `create_task_readme` fails Former-commit-id: cd74c4bca8d153b36f66da85a01ec0e49aba6594 --- src/common/create_task_readme/script.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 4645020ea5..8c7d88586a 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -95,10 +95,10 @@ if (!dir.exists(meta$temp_dir)) { writeLines(qmd_content, qmd_file) cat("Render README.qmd to README.md\n") -md_content <- system( - paste0("quarto render ", qmd_file, " --output -"), - ignore.stderr = TRUE, - intern = TRUE +out <- processx::run( + command = "quarto", + args = c("render", qmd_file, "--output", "-"), + echo = TRUE ) -writeLines(md_content, par$output) \ No newline at end of file +writeLines(out$stdout, par$output) From bed99f00c2c57a5ab30fa18f13cfbf9e36d17fc6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 21 Feb 2024 15:21:29 +0100 Subject: [PATCH 1159/1233] add processx to dependencies Former-commit-id: 38e8b477aef4bd47dbfe0716a6a39f63ea42ef4e --- src/common/create_task_readme/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index ab9a0c8ebb..683c800403 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -36,7 +36,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64] + packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64, processx] - type: apt packages: [jq, curl] - type: docker From adc754498401cb16c67f245154887c3430ed449b Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 22 Feb 2024 13:17:55 +0100 Subject: [PATCH 1160/1233] refactor website results (#385) * Refactor to filter last retry * Update src/common/process_task_results/get_results/script.R --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 5848fb4a569a89b0a30c176feac0b90dd32a323a --- src/common/process_task_results/get_results/script.R | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index c88b97f98c..5f166b1263 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -12,7 +12,7 @@ library(rlang, warn.conflicts = FALSE) dir <- "resources/dimensionality_reduction/results/run_2023-12-22_13-08-31" par <- list( input_scores = paste0(dir, "/score_uns.yaml"), - input_execution = paste0(dir, "/trace.txt"), + input_execution ="resources_test/predict_modality/openproblems_neurips2021/results/trace.txt", output = "output/results.json" ) ## VIASH END @@ -61,9 +61,12 @@ trace <- readr::read_tsv(par$input_execution) %>% dataset_id = stringr::str_extract(id, id_regex, 2L), normalization_id = stringr::str_extract(id, id_regex, 3L), method_id = stringr::str_extract(id, id_regex, 4L), + submit = strptime(submit, "%Y-%m-%d %H:%M:%S"), ) %>% - filter(process_id == method_id) - + filter(process_id == method_id) %>% + arrange(desc(submit)) %>% + group_by(name) %>% + slice(1) # parse strings into numbers parse_exit <- function(x) { if (is.na(x) || x == "-") { From 7e29be72e1bd8e623bcd9d37023041d65ddc8ff9 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 23 Feb 2024 12:50:42 +0100 Subject: [PATCH 1161/1233] Use retries on tower (#384) * use retries * simplify * remove unused config settings * try to switch to ignore after retries * Update labels_tw.config Former-commit-id: ee8003152036251011d69e804e995974c905523f --- nextflow.config | 7 ------- .../resources_scripts/run_benchmark.sh | 14 +------------- .../denoising/resources_scripts/run_benchmark.sh | 14 +------------- .../resources_scripts/run_benchmark.sh | 14 +------------- .../resources_scripts/run_benchmark.sh | 14 +------------- .../resources_scripts/run_benchmark.sh | 14 +------------- .../resources_scripts/run_benchmark.sh | 14 +------------- src/wf_utils/labels_tw.config | 12 +++++++++--- 8 files changed, 15 insertions(+), 88 deletions(-) diff --git a/nextflow.config b/nextflow.config index a455cf74fa..6402ebf273 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,8 +1 @@ -manifest { - name = 'openproblems-bio/openproblems-v2' - mainScript = 'main.nf' - nextflowVersion = '!>=20.12.1-edge' - description = 'OpenProblems benchmarking pipeline' -} - process.container = 'nextflow/bash:latest' diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index caf81eaf7b..c8b40cfe53 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -10,18 +10,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -30,5 +18,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels batch_integration,full \ No newline at end of file diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index 765e06ded7..3d7e34e7b6 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -11,18 +11,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -31,5 +19,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels denoising,full \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index facd4b0a02..7d42c31176 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -10,18 +10,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -30,5 +18,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels dimensionality_reduction,full \ No newline at end of file diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index 29e9cdbbf4..cb859e5f56 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -10,18 +10,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -30,5 +18,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels label_projection,full \ No newline at end of file diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index f82e6acf35..77b9e8eb0b 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -11,18 +11,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -31,5 +19,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels match_modalities,full \ No newline at end of file diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index c595d2c862..279a579294 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -11,18 +11,6 @@ output_state: "state.yaml" publish_dir: "$publish_dir" HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' -} - -trace { - enabled = true - overwrite = true - file = "$publish_dir/trace.txt" -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -31,5 +19,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels predict_modality,full \ No newline at end of file diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 691776ffaa..50e9188e03 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -1,9 +1,8 @@ process { - executor = 'awsbatch' // Retry for exit codes that have something to do with memory issues - errorStrategy = { task.exitStatus in 137..143 ? 'retry' : 'ignore' } + errorStrategy = { task.attempt < 3 && task.exitStatus in ((130..145) + 104) ? 'retry' : 'ignore' } maxRetries = 3 maxMemory = null @@ -36,4 +35,11 @@ def get_memory(to_compare) { println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!" System.exit(1) } -} \ No newline at end of file +} + +// set tracing file +trace { + enabled = true + overwrite = true + file = "${params.publish_dir}/trace.txt" +} From 2f42636483157ca646a39611c0f5ddbb83d84ab1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 23 Feb 2024 21:37:34 +0100 Subject: [PATCH 1162/1233] [pred_mod] Refactor dataset_id (#387) * Add dataset_id arg * Add datased_id to workflow * set arg common dataset id to false Former-commit-id: c893d648a59409582b775234e4249f51c48d0dbd --- src/tasks/predict_modality/api/file_test_mod1.yaml | 2 +- src/tasks/predict_modality/api/file_test_mod2.yaml | 2 +- src/tasks/predict_modality/api/file_train_mod1.yaml | 2 +- src/tasks/predict_modality/api/file_train_mod2.yaml | 2 +- src/tasks/predict_modality/process_dataset/config.vsh.yaml | 4 ++++ src/tasks/predict_modality/process_dataset/script.R | 7 ++++--- .../predict_modality/workflows/process_datasets/main.nf | 1 + 7 files changed, 13 insertions(+), 7 deletions(-) diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index fa8a770f08..82925b0d49 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -35,7 +35,7 @@ info: - type: string name: common_dataset_id description: "A common identifier for the dataset" - required: true + required: false - name: dataset_name type: string description: Nicely formatted name. diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index f1b12decd8..dcff45087e 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -35,7 +35,7 @@ info: - type: string name: common_dataset_id description: "A common identifier for the dataset" - required: true + required: false - name: dataset_name type: string description: Nicely formatted name. diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index d9a0cda61c..393669263e 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -35,7 +35,7 @@ info: - type: string name: common_dataset_id description: "A common identifier for the dataset" - required: true + required: false - name: dataset_organism type: string description: The organism of the sample in the dataset. diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index a67092c8f0..34eeffb414 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -35,7 +35,7 @@ info: - type: string name: common_dataset_id description: "A common identifier for the dataset" - required: true + required: false - name: dataset_organism type: string description: The organism of the sample in the dataset. diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index c6e7d493cc..b303c7e50f 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -2,6 +2,10 @@ __merge__: ../api/comp_process_dataset.yaml functionality: name: "process_dataset" arguments: + - name: "--dataset_id" + type: "string" + description: "New dataset ID" + required: false - name: "--swap" type: "boolean" description: "Swap mod1 and mod2" diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 71658dfcab..cbaeb161dc 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -44,9 +44,10 @@ ad1_uns$modality <- ad1_mod ad2_uns$modality <- ad2_mod # Create new dataset id and name depending on the modality -ad1_uns[["common_dataset_id"]] <- ad2_uns[["common_dataset_id"]] <- ad1_uns$dataset_id -new_dataset_id <- paste0(ad1_uns$dataset_id, "_", ad1_mod, "2", ad2_mod) -ad1_uns$dataset_id <- ad2_uns$dataset_id <- new_dataset_id +if (!is.null(par$dataset_id)) { + ad1_uns[["common_dataset_id"]] <- ad2_uns[["common_dataset_id"]] <- ad1_uns$dataset_id + ad1_uns$dataset_id <- ad2_uns$dataset_id <- par$dataset_id +} new_dataset_name <- paste0(ad1_uns$dataset_name, " (", ad1_mod, "2", ad2_mod, ")") ad1_uns$dataset_name <- ad2_uns$dataset_name <- new_dataset_name diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 978942181a..92cf8039f1 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -95,6 +95,7 @@ workflow run_wf { fromState: { id, state -> def swap_state = state.direction == "swap" ? true : false [ + dataset_id: id, input_mod1: state.dataset_mod1, input_mod2: state.dataset_mod2, output_train_mod1: state.output_train_mod1, From 8ee42532f85dac9a68146c3b803eff70aa2c3e8c Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Feb 2024 11:37:52 +0100 Subject: [PATCH 1163/1233] add LMDS method (#388) * add LMDS method * fixes Former-commit-id: 524f3896da354d933456602890e367c8b03d6377 --- src/common/comp_tests/check_method_config.py | 2 +- src/common/comp_tests/check_metric_config.py | 2 +- src/common/library.bib | 20 ++++++++- .../methods/lmds/config.vsh.yaml | 44 +++++++++++++++++++ .../methods/lmds/script.R | 39 ++++++++++++++++ 5 files changed, 104 insertions(+), 3 deletions(-) create mode 100644 src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/methods/lmds/script.R diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py index e20db55d6f..04f3962bf3 100644 --- a/src/common/comp_tests/check_method_config.py +++ b/src/common/comp_tests/check_method_config.py @@ -53,7 +53,7 @@ def search_ref_bib(reference): if bib_entry: type_pattern = r"@(.*){" + reference - doi_pattern = r"(?=doi\s*=\s*{([^,}]+)})" + doi_pattern = r"(?=[Dd][Oo][Ii]\s*=\s*{([^,}]+)})" entry_type = re.search(type_pattern, bib_entry.group(1)) diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py index 750caad8ec..45fa1efc2b 100644 --- a/src/common/comp_tests/check_metric_config.py +++ b/src/common/comp_tests/check_metric_config.py @@ -57,7 +57,7 @@ def search_ref_bib(reference): if bib_entry: type_pattern = r"@(.*){" + reference - doi_pattern = r"(?=doi\s*=\s*{([^,}]+)})" + doi_pattern = r"(?=[Dd][Oo][Ii]\s*=\s*{([^,}]+)})" entry_type = re.search(type_pattern, bib_entry.group(1)) diff --git a/src/common/library.bib b/src/common/library.bib index 03e9f411f4..53113c84b6 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1649,6 +1649,7 @@ @article{tian2023singlecell month = oct } + @article{sonrel2023metaanalysis, title = {Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability}, volume = {24}, @@ -1663,6 +1664,23 @@ @article{sonrel2023metaanalysis month = may } + +@article{saelens2019comparison, + title = {A comparison of single-cell trajectory inference methods}, + volume = {37}, + ISSN = {1546-1696}, + url = {http://dx.doi.org/10.1038/s41587-019-0071-9}, + DOI = {10.1038/s41587-019-0071-9}, + number = {5}, + journal = {Nature Biotechnology}, + publisher = {Springer Science and Business Media LLC}, + author = {Saelens, Wouter and Cannoodt, Robrecht and Todorov, Helena and Saeys, Yvan}, + year = {2019}, + month = apr, + pages = {547–554} +} + + @article{huang2018savergene, title = {SAVER: gene expression recovery for single-cell RNA sequencing}, volume = {15}, @@ -1676,4 +1694,4 @@ @article{huang2018savergene year = {2018}, month = jun, pages = {539–542} -} \ No newline at end of file +} diff --git a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml new file mode 100644 index 0000000000..481bac5f86 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml @@ -0,0 +1,44 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: lmds + + info: + label: LMDS + summary: Landmark Multi-Dimensional Scaling + description: | + Landmark Multi-Dimensional Scaling (LMDS) is a method for dimensionality reduction that is based on the concept of multi-dimensional scaling. + LMDS is a non-linear dimensionality reduction method that is based on the concept of multi-dimensional scaling. + preferred_normalization: log_cp10k + reference: saelens2019comparison + documentation_url: https://dynverse.org/lmds/ + repository_url: https://github.com/dynverse/lmds + + arguments: + - name: "--n_dim" + type: integer + description: Number of dimensions. + default: 3 + - name: "--n_landmarks" + type: integer + description: Number of landmarks. + default: 1000 + - name: "--distance_method" + type: string + description: Number of clusters to be estimated over the input dataset. + choices: ["euclidean", "pearson", "spearman", "cosine", "chisquared", "hamming", "kullback", "manhattan", "maximum", "canberra", "minkowski"] + default: "pearson" + + resources: + - type: r_script + path: script.R + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [ Matrix, lmds ] + - type: nextflow + directives: + label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/lmds/script.R b/src/tasks/dimensionality_reduction/methods/lmds/script.R new file mode 100644 index 0000000000..ae9461c496 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/lmds/script.R @@ -0,0 +1,39 @@ +requireNamespace("anndata", quietly = TRUE) +requireNamespace("lmds", quietly = TRUE) + +## VIASH START +par <- list( + input = "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", + output = "output.h5ad", + n_dim = 3, + n_landmarks = 1000, + distance_method = "pearson" +) +## VIASH END + +cat("Reading input files\n") +input <- anndata::read_h5ad(par$input) + +# TODO: if we wanted to, we could compute the distance +# matrix in batches. This would be useful for large datasets. +cat("Running LMDS\n") +X_emb <- lmds::lmds( + input$layers[["normalized"]], + ndim = par$n_dim, + num_landmarks = par$n_landmarks, + distance_method = par$distance_method +) + +cat("Write output AnnData to file\n") +output <- anndata::AnnData( + uns = list( + dataset_id = input$uns[["dataset_id"]], + method_id = meta$functionality_name, + normalization_id = input$uns[["normalization_id"]] + ), + obsm = list( + X_emb = X_emb + ), + shape = input$shape +) +output$write_h5ad(par$output, compression = "gzip") From d2968fd4f3bd0bb812eaf02b4fc790fd06af6822 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 27 Feb 2024 12:40:05 +0100 Subject: [PATCH 1164/1233] [pred_mod] Update dataset id (#389) * Change id send to module * add method_ids arg ref #362 * Add suggestion Former-commit-id: a6bf60fc7feb259efe0029acebc22fe8f0b551b3 --- .../workflows/process_datasets/main.nf | 11 ++++++----- .../workflows/run_benchmark/config.vsh.yaml | 6 ++++++ .../predict_modality/workflows/run_benchmark/main.nf | 7 +++++-- .../workflows/run_benchmark/run_test.sh | 4 ++-- 4 files changed, 19 insertions(+), 9 deletions(-) diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index 92cf8039f1..d8a1f0250c 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -83,11 +83,12 @@ workflow run_wf { // Note: this id is added before the normalisation id // Example old id: dataset_loader/dataset_id/normalization_id // Example new id: dataset_loader/dataset_id/direction/normalization_id - def left = id.replaceAll("/${state.normalization_id}\$", "") - def right = id.replaceAll("^${left}", "") - def new_id = left + "/" + dir + right + def orig_dataset_id = id.replaceAll("/${state.normalization_id}$", "") + def normalization_id = id.replaceAll("^${orig_dataset_id}", "") + def new_dataset_id = orig_dataset_id + "/" + dir + def new_id = new_dataset_id + normalization_id - [new_id, state + [direction: dir, "_meta": [join_id: id]]] + [new_id, state + [dataset_id: new_dataset_id, direction: dir, "_meta": [join_id: id]]] } } @@ -95,7 +96,7 @@ workflow run_wf { fromState: { id, state -> def swap_state = state.direction == "swap" ? true : false [ - dataset_id: id, + dataset_id: state.dataset_id, input_mod1: state.dataset_mod1, input_mod2: state.dataset_mod2, output_train_mod1: state.output_train_mod1, diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index fa77795ab8..21becd3801 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -48,6 +48,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 714339cb17..747cf544e5 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -75,13 +75,16 @@ workflow run_wf { | runEach( components: methods, - // // use the 'filter' argument to only run a method on the normalisation the component is asking for + // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> def norm = state.rna_norm def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh index 76a8e5b560..93212af821 100755 --- a/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh +++ b/src/tasks/predict_modality/workflows/run_benchmark/run_test.sh @@ -8,7 +8,7 @@ cd "$REPO_ROOT" set -e -DATASETS_DIR="resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT" +DATASETS_DIR="resources_test/predict_modality/openproblems_neurips2021" OUTPUT_DIR="output/predict_modality" if [ ! -d "$OUTPUT_DIR" ]; then @@ -24,7 +24,7 @@ nextflow run . \ -entry auto \ -with-trace \ -c src/wf_utils/labels_ci.config \ - --input_states "$DATASETS_DIR/state.yaml" \ + --input_states "$DATASETS_DIR/**/state.yaml" \ --rename_keys 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' \ --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ --publish_dir "$OUTPUT_DIR" \ From ad99de291d6f669cd8439a493bf8f528966a971a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 4 Mar 2024 09:33:57 -0800 Subject: [PATCH 1165/1233] Bump nf-core/setup-nextflow from 1.5.2 to 2.0.0 (#394) Bumps [nf-core/setup-nextflow](https://github.com/nf-core/setup-nextflow) from 1.5.2 to 2.0.0. - [Release notes](https://github.com/nf-core/setup-nextflow/releases) - [Changelog](https://github.com/nf-core/setup-nextflow/blob/master/CHANGELOG.md) - [Commits](https://github.com/nf-core/setup-nextflow/compare/v1.5.2...v2.0.0) --- updated-dependencies: - dependency-name: nf-core/setup-nextflow dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: 28067c55104c5c9d30b1b5f9fe993ea7ed649b28 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/release-build.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 4e6bf2f349..9a68bfa543 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -132,7 +132,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.2 + - uses: nf-core/setup-nextflow@v2.0.0 # build target dir # use containers from integration_build branch, hopefully these are available diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index e9c0115dff..1d98b8e711 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -159,7 +159,7 @@ jobs: - uses: viash-io/viash-actions/setup@v5 - - uses: nf-core/setup-nextflow@v1.5.2 + - uses: nf-core/setup-nextflow@v2.0.0 # build target dir # use containers from release branch, hopefully these are available From 406df5518a69e1e276956511a6e7d52b35ab1ad0 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 6 Mar 2024 16:25:09 +0100 Subject: [PATCH 1166/1233] Increase subsample dimensions (#392) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Increase subsample dimensions Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com> * fix pancreas subsample error * force CI --------- Co-authored-by: Michaela Müller <51025211+mumichae@users.noreply.github.com> Former-commit-id: 69140a224584215bf30677f6d7bf05e5155caae3 --- .../resource_test_scripts/cxg_mouse_pancreas_atlas.sh | 3 +++ src/datasets/resource_test_scripts/pancreas.sh | 4 +++- .../metrics/cell_cycle_conservation/config.vsh.yaml | 1 - .../batch_integration/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/batch_integration/workflows/run_benchmark/main.nf | 2 +- 5 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh index f6b5fc971c..3b5d35ee5c 100755 --- a/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh +++ b/src/datasets/resource_test_scripts/cxg_mouse_pancreas_atlas.sh @@ -24,6 +24,8 @@ param_list: dataset_organism: mus_musculus normalization_methods: [log_cp10k] +n_obs: 600 +n_vars: 1500 output_dataset: '\$id/dataset.h5ad' output_meta: '\$id/dataset_metadata.yaml' output_state: '\$id/state.yaml' @@ -39,6 +41,7 @@ HERE nextflow run . \ -main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ + -c src/wf_utils/labels_ci.config \ -profile docker \ -params-file "/tmp/params.yaml" diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 9c0b1c5717..4c6f0b0ae9 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -40,6 +40,8 @@ nextflow run . \ --seed 123 \ --normalization_methods log_cp10k \ --do_subsample true \ + --n_obs 600 \ + --n_var 1500 \ --output_raw '$id/raw.h5ad' \ --output_normalized '$id/normalized.h5ad' \ --output_hvg '$id/hvg.h5ad' \ @@ -56,4 +58,4 @@ rm -r $DATASET_DIR/temp_* src/tasks/batch_integration/resources_test_scripts/process.sh src/tasks/denoising/resources_test_scripts/pancreas.sh src/tasks/dimensionality_reduction/resources_test_scripts/pancreas.sh -src/tasks/label_projection/resources_test_scripts/pancreas.sh +src/tasks/label_projection/resources_test_scripts/pancreas.sh \ No newline at end of file diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index cb1ef8bbae..78bae7b655 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -1,7 +1,6 @@ # use metric api spec __merge__: ../../api/comp_metric_embedding.yaml functionality: - status: disabled name: cell_cycle_conservation info: metrics: diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index 9525e736f5..b430734e22 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -77,7 +77,7 @@ functionality: - name: batch_integration/transformers/embed_to_graph - name: batch_integration/metrics/asw_batch - name: batch_integration/metrics/asw_label - # - name: batch_integration/metrics/cell_cycle_conservation + - name: batch_integration/metrics/cell_cycle_conservation - name: batch_integration/metrics/clustering_overlap - name: batch_integration/metrics/graph_connectivity - name: batch_integration/metrics/hvg_overlap diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 91876737de..5543ac91cd 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -37,7 +37,7 @@ workflow run_wf { metrics = [ asw_batch, asw_label, - // cell_cycle_conservation, + cell_cycle_conservation, clustering_overlap, graph_connectivity, hvg_overlap, From e7c930d236f7f1538b246a72cf9da27b21c07dac Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 7 Mar 2024 15:47:28 +0100 Subject: [PATCH 1167/1233] Fix CI failing tests (#395) * fix typo * transpose data in simlr method Former-commit-id: d3ecb1da3c76fe24ec21d7d4a1498647a2c26b73 --- .../resource_test_scripts/pancreas.sh | 2 +- .../methods/simlr/script.R | 26 ++++++++++--------- 2 files changed, 15 insertions(+), 13 deletions(-) diff --git a/src/datasets/resource_test_scripts/pancreas.sh b/src/datasets/resource_test_scripts/pancreas.sh index 4c6f0b0ae9..fb26f7ef30 100755 --- a/src/datasets/resource_test_scripts/pancreas.sh +++ b/src/datasets/resource_test_scripts/pancreas.sh @@ -41,7 +41,7 @@ nextflow run . \ --normalization_methods log_cp10k \ --do_subsample true \ --n_obs 600 \ - --n_var 1500 \ + --n_vars 1500 \ --output_raw '$id/raw.h5ad' \ --output_normalized '$id/normalized.h5ad' \ --output_hvg '$id/hvg.h5ad' \ diff --git a/src/tasks/dimensionality_reduction/methods/simlr/script.R b/src/tasks/dimensionality_reduction/methods/simlr/script.R index 49ffb44592..0622076c08 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/script.R +++ b/src/tasks/dimensionality_reduction/methods/simlr/script.R @@ -4,12 +4,12 @@ requireNamespace("SIMLR", quietly = TRUE) ## VIASH START par <- list( input = "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", - output = "output.h5ad", + output = "output.h5ad", n_clusters = NULL, n_dim = NA, tuning_param = 10, - impute = FALSE, - normalize = FALSE, + impute = FALSE, + normalize = FALSE, cores_ratio = 1 ) meta <- list( @@ -20,13 +20,15 @@ meta <- list( cat("Reading input files\n") input <- anndata::read_h5ad(par$input) +X <- t(as.matrix(input$layers[["normalized"]])) + if (is.null(par$n_clusters)) { cat("Estimating the number of clusters\n") set.seed(1) NUMC = 2:5 estimates <- SIMLR::SIMLR_Estimate_Number_of_Clusters( - X = as.matrix(input$layers[["normalized"]]), - NUMC = NUMC, + X = X, + NUMC = NUMC, cores.ratio = par$cores_ratio ) n_clusters <- NUMC[which.min(estimates$K2)] @@ -42,12 +44,12 @@ if (is.null(par$n_dim)) { cat("Running SIMLR\n") simlr_result <- SIMLR::SIMLR( - X = as.matrix(input$layers[["normalized"]]), - c = n_clusters, - no.dim = n_dim, - k = par$tuning_param, - if.impute = par$impute, - normalize = par$normalize, + X = X, + c = n_clusters, + no.dim = n_dim, + k = par$tuning_param, + if.impute = par$impute, + normalize = par$normalize, cores.ratio = par$cores_ratio ) obsm_X_emb <- simlr_result$ydata @@ -61,7 +63,7 @@ output <- anndata::AnnData( ), obsm = list( X_emb = obsm_X_emb - ), + ), shape = input$shape ) output$write_h5ad(par$output, compression = "gzip") From fd5ad23aca3767c1a5a412d26a7e5f19d00b29a8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 7 Mar 2024 10:37:09 -0800 Subject: [PATCH 1168/1233] Fix NewWave+KNNR component (#393) * installing newwave from github is no longer necessary * ensure that newwave input is a dgcMatrix * fix regex * convert matrix in neurips dataset loader * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Kai Waldrant Former-commit-id: 83fc635afcbd0309c1741f26608ffebada4b5ae0 --- .../openproblems_neurips2021_bmmc/script.py | 14 ++++++++++++++ .../methods/newwave_knnr/config.vsh.yaml | 2 -- .../predict_modality/methods/newwave_knnr/script.R | 11 ++++++++++- .../workflows/process_datasets/main.nf | 2 +- 4 files changed, 25 insertions(+), 4 deletions(-) diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index 8ac734efff..3a8342fbde 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -1,6 +1,7 @@ import anndata as ad import pandas as pd import numpy as np +from scipy import sparse ## VIASH START par = { @@ -30,10 +31,19 @@ def remove_mod_prefix(df, mod): suffix = f"{mod}_" df.columns = df.columns.str.removeprefix(suffix) +def convert_matrix(adata): + for key in adata: + if isinstance(adata[key], sparse.csr_matrix): + adata[key] = sparse.csc_matrix(adata[key]) + print("load dataset file", flush=True) adata = ad.read_h5ad(par["input"]) +# Convert to sparse csc_matrix +convert_matrix(adata.layers) +convert_matrix(adata.obsm) + # Add is_train to obs if it is missing if "is_train" not in adata.obs.columns: batch_info = adata.obs["batch"] @@ -109,3 +119,7 @@ def remove_mod_prefix(df, mod): print("Writing adata to file", flush=True) adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") + + + + diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index f3a37d053e..a9026f47cd 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -36,8 +36,6 @@ platforms: - type: r cran: [ lmds, FNN, proxy, proxyC] bioc: [ SingleCellExperiment, NewWave ] - - type: r - github: [Jiefei-Wang/SharedObject, fedeago/NewWave] - type: nextflow directives: label: [ "midtime", highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/script.R b/src/tasks/predict_modality/methods/newwave_knnr/script.R index 3d1cb7b731..84f8a0b469 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/script.R +++ b/src/tasks/predict_modality/methods/newwave_knnr/script.R @@ -34,8 +34,17 @@ input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) batch1 <- c(as.character(input_train_mod1$obs$batch), as.character(input_test_mod1$obs$batch)) batch2 <- as.character(input_train_mod1$obs$batch) +# create SummarizedExperiment object data1 <- SummarizedExperiment::SummarizedExperiment( - assays = list(counts = cbind(t(input_train_mod1$layers[["counts"]]), t(input_test_mod1$layers[["counts"]]))), + assays = list( + counts = as( + cbind( + t(input_train_mod1$layers[["counts"]]), + t(input_test_mod1$layers[["counts"]]) + ), + "CsparseMatrix" + ) + ), colData = data.frame(batch = factor(batch1)) ) data1 <- data1[Matrix::rowSums(SummarizedExperiment::assay(data1)) > 0, ] diff --git a/src/tasks/predict_modality/workflows/process_datasets/main.nf b/src/tasks/predict_modality/workflows/process_datasets/main.nf index d8a1f0250c..69d9949e41 100644 --- a/src/tasks/predict_modality/workflows/process_datasets/main.nf +++ b/src/tasks/predict_modality/workflows/process_datasets/main.nf @@ -83,7 +83,7 @@ workflow run_wf { // Note: this id is added before the normalisation id // Example old id: dataset_loader/dataset_id/normalization_id // Example new id: dataset_loader/dataset_id/direction/normalization_id - def orig_dataset_id = id.replaceAll("/${state.normalization_id}$", "") + def orig_dataset_id = id.replaceAll("/${state.normalization_id}", "") def normalization_id = id.replaceAll("^${orig_dataset_id}", "") def new_dataset_id = orig_dataset_id + "/" + dir def new_id = new_dataset_id + normalization_id From 747e461ea482574481a90edbc09fd3bca2dfc6d2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 12 Mar 2024 13:12:30 +0100 Subject: [PATCH 1169/1233] Add method_ids parameter to all tasks (#398) * Update denoising * Update dim_red * Upddate lab_proj * update match modalities Former-commit-id: 0ae327f0bc7f1171985bfc49a4efde9d2d7b3283 --- .../workflows/run_benchmark/config.vsh.yaml | 6 ++++++ src/tasks/denoising/workflows/run_benchmark/main.nf | 8 ++++++++ .../workflows/run_benchmark/config.vsh.yaml | 6 ++++++ .../workflows/run_benchmark/main.nf | 7 +++++-- .../workflows/run_benchmark/config.vsh.yaml | 6 ++++++ .../workflows/run_benchmark/main.nf | 5 ++++- .../workflows/run_benchmark/config.vsh.yaml | 6 ++++++ .../workflows/run_benchmark/main.nf | 13 ++++++++----- 8 files changed, 49 insertions(+), 8 deletions(-) diff --git a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml index b40e7a9e4b..5b1cf3dd04 100644 --- a/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/denoising/workflows/run_benchmark/config.vsh.yaml @@ -40,6 +40,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/denoising/workflows/run_benchmark/main.nf b/src/tasks/denoising/workflows/run_benchmark/main.nf index 392af73246..8b8f6ebd8d 100644 --- a/src/tasks/denoising/workflows/run_benchmark/main.nf +++ b/src/tasks/denoising/workflows/run_benchmark/main.nf @@ -54,6 +54,14 @@ workflow run_wf { // run all methods | runEach( components: methods, + + // use the 'filter' argument to only run a defined method or all methods + filter: { id, state, comp -> + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check + }, + // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> id + "." + comp.config.functionality.name diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 1f803bc5ea..882418a6d4 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -40,6 +40,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index 9c9380fdac..cea5936ca4 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -60,14 +60,17 @@ workflow run_wf { // run all methods | runEach( components: methods, - + // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> def norm = state.dataset_uns.normalization_id def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 39788910c9..159a7fe179 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -47,6 +47,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index 58806bfdcf..01c308575d 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -65,7 +65,10 @@ workflow run_wf { def pref = comp.config.functionality.info.preferred_normalization // if the preferred normalisation is none at all, // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check }, // define a new 'id' by appending the method name to the dataset id diff --git a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml index df0971b8bc..89da796600 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/match_modalities/workflows/run_benchmark/config.vsh.yaml @@ -48,6 +48,12 @@ functionality: required: true direction: output default: task_info.yaml + - name: Methods + arguments: + - name: "--method_ids" + type: string + multiple: true + description: A list of method ids to run. If not specified, all methods will be run. resources: - type: nextflow_script path: main.nf diff --git a/src/tasks/match_modalities/workflows/run_benchmark/main.nf b/src/tasks/match_modalities/workflows/run_benchmark/main.nf index 0f45c92c46..53753f3981 100644 --- a/src/tasks/match_modalities/workflows/run_benchmark/main.nf +++ b/src/tasks/match_modalities/workflows/run_benchmark/main.nf @@ -57,11 +57,14 @@ workflow run_wf { // use the 'filter' argument to only run a method on the normalisation the component is asking for filter: { id, state, comp -> - def norm = state.dataset_uns.normalization_id - def pref = comp.config.functionality.info.preferred_normalization - // if the preferred normalisation is none at all, - // we can pass whichever dataset we want - (norm == "log_cp10k" && pref == "counts") || norm == pref + def norm = state.dataset_uns.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check }, // define a new 'id' by appending the method name to the dataset id From b821f25cc8d0552f7c8f5587d49a5c9eb13d34c9 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 12 Mar 2024 15:49:51 +0100 Subject: [PATCH 1170/1233] [pred_mod] Refactor guanlab method (#399) * WIP refactor script * Add change comments * Add to workflow Former-commit-id: fbfebe255f1649f70f4cb1bcfbf3c5823cc9f366 --- .../methods/guanlab_dengkw_pm/config.vsh.yaml | 12 --- .../methods/guanlab_dengkw_pm/script.py | 88 +++++++------------ .../workflows/run_benchmark/config.vsh.yaml | 1 + .../workflows/run_benchmark/main.nf | 3 +- 4 files changed, 33 insertions(+), 71 deletions(-) diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index 030b3ba5b3..7e6ba58390 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -1,10 +1,6 @@ -# The API specifies which type of component this is. __merge__: ../../api/comp_method.yaml - functionality: - name: guanlab_dengkw_pm - info: label: Guanlab-dengkw summary: A kernel ridge regression method with RBF kernel. @@ -14,8 +10,6 @@ functionality: reference: lance2022multimodal documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw - - # Component-specific parameters (optional) arguments: - name: "--distance_method" type: "string" @@ -26,11 +20,9 @@ functionality: type: "integer" default: 50 description: Number of components to use for dimensionality reduction. - resources: - type: python_script path: script.py - platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 @@ -40,10 +32,6 @@ platforms: - scikit-learn - pandas - numpy - - scanpy - - - type: native - - type: nextflow directives: label: [ "hightime", highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py index 340e41c003..4c3d8f7897 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -1,11 +1,9 @@ import anndata as ad -import logging import numpy as np -from scipy.sparse import csr_matrix -from sklearn.decomposition import TruncatedSVD +import gc +from scipy.sparse import csc_matrix from sklearn.gaussian_process.kernels import RBF from sklearn.kernel_ridge import KernelRidge -logging.basicConfig(level=logging.INFO) ## VIASH START par = { @@ -21,11 +19,15 @@ } ## VIASH END + +## Removed PCA and normalization steps, as they arr already performed with the input data print('Reading input files', flush=True) input_train_mod1 = ad.read_h5ad(par['input_train_mod1']) input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) +dataset_id = input_train_mod1.uns['dataset_id'] + pred_dimx = input_test_mod1.shape[0] pred_dimy = input_train_mod2.shape[1] @@ -48,55 +50,24 @@ index_unique="-" ) -logging.info('Determine parameters by the modalities') -mod1_type = input_train_mod1.uns["modality"] -mod1_type = mod1_type.upper() -mod2_type = input_train_mod2.uns["modality"] -mod2_type = mod2_type.upper() -n_comp_dict = { - ("GEX", "ADT"): (300, 70, 10, 0.2), - ("ADT", "GEX"): (None, 50, 10, 0.2), - ("GEX", "ATAC"): (1000, 50, 10, 0.1), - ("ATAC", "GEX"): (100, 70, 10, 0.1) - } -logging.info(f"{mod1_type}, {mod2_type}") -n_mod1, n_mod2, scale, alpha = n_comp_dict[(mod1_type, mod2_type)] -logging.info(f"{n_mod1}, {n_mod2}, {scale}, {alpha}") - -# Perform PCA on the input data -logging.info('Models using the Truncated SVD to reduce the dimension') - -if n_mod1 is not None and n_mod1 < input_train.shape[1]: - embedder_mod1 = TruncatedSVD(n_components=n_mod1) - mod1_pca = embedder_mod1.fit_transform(input_train.layers["counts"]).astype(np.float32) - train_matrix = mod1_pca[input_train.obs['group'] == 'train'] - test_matrix = mod1_pca[input_train.obs['group'] == 'test'] -else: - train_matrix = input_train_mod1.to_df(layer="counts").values.astype(np.float32) - test_matrix = input_test_mod1.to_df(layer="counts").values.astype(np.float32) - -if n_mod2 is not None and n_mod2 < input_train_mod2.shape[1]: - embedder_mod2 = TruncatedSVD(n_components=n_mod2) - train_gs = embedder_mod2.fit_transform(input_train_mod2.layers["counts"]).astype(np.float32) -else: - train_gs = input_train_mod2.to_df(layer="counts").values.astype(np.float32) - -del input_train - -logging.info('Running normalization ...') -train_sd = np.std(train_matrix, axis=1).reshape(-1, 1) -train_sd[train_sd == 0] = 1 -train_norm = (train_matrix - np.mean(train_matrix, axis=1).reshape(-1, 1)) / train_sd -train_norm = train_norm.astype(np.float32) -del train_matrix - -test_sd = np.std(test_matrix, axis=1).reshape(-1, 1) -test_sd[test_sd == 0] = 1 -test_norm = (test_matrix - np.mean(test_matrix, axis=1).reshape(-1, 1)) / test_sd -test_norm = test_norm.astype(np.float32) -del test_matrix - -logging.info('Running KRR model ...') +print('Determine parameters by the modalities', flush=True) +mod1_type = input_train_mod1.uns["modality"].upper() +mod2_type = input_train_mod2.uns["modality"].upper() + +scale = 10 +alpha = 0.1 if (mod1_type == "ATAC" or mod2_type == "ATAC") else 0.2 + +train_norm = input_train_mod1.to_df(layer="normalized").values.astype(np.float32) +test_norm = input_test_mod1.to_df(layer="normalized").values.astype(np.float32) + +train_gs = input_train_mod2.to_df(layer="normalized").values.astype(np.float32) + +del input_train_mod1 +del input_test_mod1 +del input_train_mod2 +gc.collect() + +print('Running KRR model ...', flush=True) y_pred = np.zeros((pred_dimx, pred_dimy), dtype=np.float32) np.random.seed(1000) @@ -107,12 +78,12 @@ if not batch: batch = [batches[0]] - logging.info(batch) + print(batch, flush=True) kernel = RBF(length_scale = scale) krr = KernelRidge(alpha=alpha, kernel=kernel) - logging.info('Fitting KRR ... ') + print('Fitting KRR ... ', flush=True) krr.fit(train_norm[feature_obs.batch.isin(batch)], train_gs[gs_obs.batch.isin(batch)]) - y_pred += (krr.predict(test_norm) @ embedder_mod2.components_) + y_pred += krr.predict(test_norm) np.clip(y_pred, a_min=0, a_max=None, out=y_pred) if mod2_type == "ATAC": @@ -123,7 +94,8 @@ # Store as sparse matrix to be efficient. # Note that this might require different classifiers/embedders before-hand. # Not every class is able to support such data structures. -y_pred = csr_matrix(y_pred) +## Changed from csr to csc matrix as this is more supported. +y_pred = csc_matrix(y_pred) print("Write output AnnData to file", flush=True) output = ad.AnnData( @@ -133,7 +105,7 @@ obs = obs, var = var, uns = { - 'dataset_id': input_train_mod1.uns['dataset_id'], + 'dataset_id': dataset_id, 'method_id': meta['functionality_name'] } ) diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index 21becd3801..5f9eceb2c5 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -72,6 +72,7 @@ functionality: - name: predict_modality/methods/lm - name: predict_modality/methods/newwave_knnr - name: predict_modality/methods/random_forest + - name: predict_modality/methods/guanlab_dengkw_pm - name: predict_modality/metrics/correlation - name: predict_modality/metrics/mse platforms: diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 747cf544e5..8839cc18d4 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -21,7 +21,8 @@ workflow run_wf { knnr_r, lm, newwave_knnr, - random_forest + random_forest, + guanlab_dengkw_pm ] // construct list of metrics From a0c22e78a8a7bcb0442262e2b7a22b9e678518cb Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Mar 2024 09:51:27 +0100 Subject: [PATCH 1171/1233] add dask-expr as a dependency to pyliger (#400) Former-commit-id: 2201492c4d81f4c28013041c9e2f8edf22014eb1 --- src/tasks/batch_integration/methods/pyliger/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index f26afdffbd..a52aed6713 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -29,6 +29,7 @@ platforms: pypi: - umap-learn[plot] - pyliger + - dask-expr - type: nextflow directives: label: [ lowcpu, highmem, midtime ] From 692dacf3d5a881a8d6e52231df0c0803d27dfdcf Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 13 Mar 2024 10:32:49 +0100 Subject: [PATCH 1172/1233] Add disk labels (#390) * Add disk labels * Set disk label denoising * set disk storage to memory * remove disk label * refactor config * Update src/wf_utils/labels_tw.config --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: ee79ec8f6cddaa5f138232baa51dfa73527dd459 --- .../denoising/methods/alra/config.vsh.yaml | 2 +- .../methods/knn_smoothing/config.vsh.yaml | 2 +- .../methods/newwave_knnr/config.vsh.yaml | 2 +- src/wf_utils/labels_tw.config | 19 ++++++++++++++++--- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index f0e47c92e8..acf412233c 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -40,4 +40,4 @@ platforms: github: KlugerLab/ALRA - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu] diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index d872b8fdab..f84616f631 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index a9026f47cd..9984351b7d 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: bioc: [ SingleCellExperiment, NewWave ] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 50e9188e03..24380bdf1c 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -1,6 +1,9 @@ process { executor = 'awsbatch' + // Default disk space + disk = 50.GB + // Retry for exit codes that have something to do with memory issues errorStrategy = { task.attempt < 3 && task.exitStatus in ((130..145) + 104) ? 'retry' : 'ignore' } maxRetries = 3 @@ -11,9 +14,19 @@ process { withLabel: midcpu { cpus = 15 } withLabel: highcpu { cpus = 30 } - withLabel: lowmem { memory = { get_memory( 20.GB * task.attempt ) } } - withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } } - withLabel: highmem { memory = { get_memory( 100.GB * task.attempt ) } } + withLabel: lowmem { + memory = { get_memory( 20.GB * task.attempt ) } + disk = { 50.GB * task.attempt } + } + withLabel: midmem { + memory = { get_memory( 50.GB * task.attempt ) } + disk = { 100.GB * task.attempt } + } + withLabel: highmem { + memory = { get_memory( 100.GB * task.attempt ) } + disk = { 200.GB * task.attempt } + } + } def get_memory(to_compare) { From 93d26c23a60accad2c83b9300c1b50e274a1cd00 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 13 Mar 2024 11:30:26 +0100 Subject: [PATCH 1173/1233] Add a label for increasing the shared memory (#396) * WIP refactor script * increase shm_szie docker * fix typo * WIP * restore setup * Restore script * undo guanlab commit * remove empty line * Add shm-size to config * Update src/wf_utils/labels_tw.config Co-authored-by: Robrecht Cannoodt * Add sharedmem label to newwave --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 922d086d4cccba4b64f487a920d216528fc07622 --- .../methods/newwave_knnr/config.vsh.yaml | 2 +- src/wf_utils/labels_tw.config | 11 +++++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 9984351b7d..def16f755c 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: bioc: [ SingleCellExperiment, NewWave ] - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [ midtime, highmem, highcpu, highsharedmem ] diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 24380bdf1c..2af089636a 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -13,7 +13,6 @@ process { withLabel: lowcpu { cpus = 5 } withLabel: midcpu { cpus = 15 } withLabel: highcpu { cpus = 30 } - withLabel: lowmem { memory = { get_memory( 20.GB * task.attempt ) } disk = { 50.GB * task.attempt } @@ -26,7 +25,15 @@ process { memory = { get_memory( 100.GB * task.attempt ) } disk = { 200.GB * task.attempt } } - + withLabel: lowsharedmem { + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.05}mb" : ""} + } + withLabel: midsharedmem { + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.1}mb" : ""} + } + withLabel: highsharedmem { + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.25}mb" : ""} + } } def get_memory(to_compare) { From 912f3620611a08ed6571248503de2897e498fe74 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 13 Mar 2024 11:55:07 +0100 Subject: [PATCH 1174/1233] change special character (#402) Former-commit-id: 0aaef65e5acad35e2fbc0648f6375af4f61c732a --- src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index 6207a6d5f9..a6566ffd8a 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: name: knn_auc summary: "Compute the kNN Area Under the Curve" description: | - Let $f(i) \u2208 F$ be the scRNA-seq measurement of cell $i$, and $g(i) \u2208 G$ be the scATAC- seq measurement of cell $i$. kNN-AUC calculates the average percentage overlap of neighborhoods of $f(i)$ in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. + Let $f(i) \in F$ be the scRNA-seq measurement of cell $i$, and $g(i) \in G$ be the scATAC- seq measurement of cell $i$. kNN-AUC calculates the average percentage overlap of neighborhoods of $f(i)$ in $F$ with neighborhoods of $g(i)$ in $G$. Higher is better. reference: "lance2022multimodal" min: 0 max: 1 From 60b1f6b6bd4a62e430d33046782fe64e79f0cf13 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Mar 2024 17:02:25 +0100 Subject: [PATCH 1175/1233] Improve Dimensionality Reduction task (#401) * clean up configs * add pymde * add R-based implementation of diffusionmap * remove comment * change label * fix task description * add more methods and metrics to workflow * update authors * rename folder * fix filename * add workaround script.py * fix spectral features * update task info * add author info * set lmds dims to 2 Former-commit-id: 6272797468c6daac6f0479208a0ca4fbbdcd709f --- src/common/library.bib | 17 +++++ .../api/task_info.yaml | 67 ++++++++++++------- .../random_features/config.vsh.yaml | 2 +- .../spectral_features/config.vsh.yaml | 4 +- .../spectral_features}/script.py | 0 .../true_features/config.vsh.yaml | 2 +- .../methods/densmap/config.vsh.yaml | 2 +- .../methods/diffusion_map/config.vsh.yaml | 45 +++++-------- .../methods/diffusion_map/script.R | 37 ++++++++++ .../methods/ivis/config.vsh.yaml | 2 +- .../methods/lmds/config.vsh.yaml | 2 +- .../methods/neuralee/config.vsh.yaml | 2 +- .../methods/pca/config.vsh.yaml | 6 +- .../methods/phate/config.vsh.yaml | 2 +- .../methods/pymde/config.vsh.yaml | 41 ++++++++++++ .../methods/pymde/script.py | 59 ++++++++++++++++ .../methods/tsne/config.vsh.yaml | 2 +- .../methods/umap/config.vsh.yaml | 2 +- .../clustering_performance/config.vsh.yaml | 2 +- .../metrics/coranking/config.vsh.yaml | 2 +- .../density_preservation/config.vsh.yaml | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../workflows/run_benchmark/config.vsh.yaml | 5 ++ .../workflows/run_benchmark/main.nf | 8 +++ 24 files changed, 245 insertions(+), 70 deletions(-) rename src/tasks/dimensionality_reduction/{methods/diffusion_map => control_methods/spectral_features}/script.py (100%) create mode 100644 src/tasks/dimensionality_reduction/methods/diffusion_map/script.R create mode 100644 src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml create mode 100644 src/tasks/dimensionality_reduction/methods/pymde/script.py diff --git a/src/common/library.bib b/src/common/library.bib index 53113c84b6..50524c4b38 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -1695,3 +1695,20 @@ @article{huang2018savergene month = jun, pages = {539–542} } + + +@article{chari2023speciousart, + title = {The specious art of single-cell genomics}, + volume = {19}, + ISSN = {1553-7358}, + url = {http://dx.doi.org/10.1371/journal.pcbi.1011288}, + DOI = {10.1371/journal.pcbi.1011288}, + number = {8}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science (PLoS)}, + author = {Chari, Tara and Pachter, Lior}, + editor = {Papin, Jason A.}, + year = {2023}, + month = aug, + pages = {e1011288} +} diff --git a/src/tasks/dimensionality_reduction/api/task_info.yaml b/src/tasks/dimensionality_reduction/api/task_info.yaml index e202497c99..4f24ae9764 100644 --- a/src/tasks/dimensionality_reduction/api/task_info.yaml +++ b/src/tasks/dimensionality_reduction/api/task_info.yaml @@ -1,27 +1,38 @@ name: dimensionality_reduction -label: "Dimensionality reduction for visualization" +label: "Dimensionality reduction for 2D visualization" v1: path: openproblems/tasks/dimensionality_reduction/README.md commit: b353a462f6ea353e0fc43d0f9fcbbe621edc3a0b summary: Reduction of high-dimensional datasets to 2D for visualization & interpretation image: "thumbnail.svg" motivation: | - Dimensionality reduction is one of the key challenges in single-cell data representation. - Routine single-cell RNA sequencing (scRNA-seq) experiments measure cells in roughly - 20,000-30,000 dimensions (i.e., features - mostly gene transcripts but also other functional - elements encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq experiments have - been growing in terms of the number of cells measured. Originally, cutting-edge SmartSeq - experiments would yield a few hundred cells, at best. Now, it is not uncommon to see - experiments that yield over [100,000 cells]() - or even [> 1 million cells](https://doi.org/10.1126/science.aba7721). + Data visualisation is an important part of all stages of single-cell analysis, from + initial quality control to interpretation and presentation of final results. For bulk RNA-seq + studies, linear dimensionality reduction techniques such as PCA and MDS are commonly used + to visualise the variation between samples. While these methods are highly effective they + can only be used to show the first few components of variation which cannot fully represent + the increased complexity and number of observations in single-cell datasets. For this reason + non-linear techniques (most notably t-SNE and UMAP) have become the standard for visualising + single-cell studies. These methods attempt to compress a dataset into a two-dimensional space + while attempting to capture as much of the variance between observations as possible. Many + methods for solving this problem now exist. In general these methods try to preserve distances, + while some additionally consider aspects such as density within the embedded space or conservation + of continuous trajectories. Despite almost every single-cell study using one of these visualisations + there has been debate as to whether they can effectively capture the variation in single-cell + datasets [@chari2023speciousart]. description: | - Each *feature* in a dataset functions as a single dimension. While each of the ~30,000 - dimensions measured in each cell contribute to an underlying data structure, the overall - structure of the data is challenging to display in few dimensions due to data sparsity - and the [*"curse of dimensionality"*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) - (distances in high dimensional data don't distinguish data points well). Thus, we need to find - a way to [dimensionally reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) - the data for visualization and interpretation. + The dimensionality reduction task attempts to quantify the ability of methods to embed the + information present in complex single-cell studies into a two-dimensional space. Thus, this task + is specifically designed for dimensionality reduction for visualisation and does not consider other + uses of dimensionality reduction in standard single-cell workflows such as improving the + signal-to-noise ratio (and in fact several of the methods use PCA as a pre-processing step for this + reason). Unlike most tasks, methods for the dimensionality reduction task must accept a matrix + containing expression values normalised to 10,000 counts per cell and log transformed (log-10k) and + produce a two-dimensional coordinate for each cell. Pre-normalised matrices are required to + enforce consistency between the metric evaluation (which generally requires normalised data) and + the method runs. When these are not consistent, methods that use the same normalisation as used in + the metric tend to score more highly. For some methods we also evaluate the pre-processing + recommended by the method. authors: - name: Luke Zappia roles: [ maintainer, author ] @@ -31,7 +42,7 @@ authors: roles: [ author ] info: github: michalk8 - - name: "Scott Gigante" + - name: Scott Gigante roles: [ author ] info: github: scottgigante @@ -40,13 +51,23 @@ authors: roles: [ author ] info: github: bendemeo - - name: "Juan A. Cordero Varela" + - name: Robrecht Cannoodt + roles: [ author ] + info: + github: rcannood + orcid: 0000-0003-3641-729X + - name: Kai Waldrant roles: [ contributor ] info: - github: jacorvar - orcid: 0000-0002-7373-5433 - - name: Robrecht Cannoodt + github: KaiWaldrant + orcid: 0009-0003-8555-1361 + - name: Sai Nirmayi Yasa roles: [ contributor ] info: - github: rcannood - orcid: "0000-0003-3641-729X" + github: sainirmayi + orcid: 0009-0003-6319-9803 + - name: Juan A. Cordero Varela + roles: [ contributor ] + info: + github: jacorvar + orcid: 0000-0002-7373-5433 diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index bf2f1d61c4..8fa77a63af 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] \ No newline at end of file + label: [ midtime, highmem, highcpu ] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index 295b30c8f6..1fed7ff812 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: description: "Number of times to retry if the embedding fails, each time adding noise." resources: - type: python_script - path: /src/tasks/dimensionality_reduction/methods/diffusion_map/script.py + path: script.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.2 @@ -38,4 +38,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/script.py b/src/tasks/dimensionality_reduction/control_methods/spectral_features/script.py similarity index 100% rename from src/tasks/dimensionality_reduction/methods/diffusion_map/script.py rename to src/tasks/dimensionality_reduction/control_methods/spectral_features/script.py diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 5b534b356a..3a095d12e5 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -19,4 +19,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index cea27da3e0..532785519e 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -42,4 +42,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index bac586d8a2..2ad6ac887f 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -1,44 +1,31 @@ __merge__: ../../api/comp_method.yaml functionality: - name: "diffusion_maps" + name: diffusion_map info: - label: Diffusion maps - summary: "Positive control by Use 1000-dimensional diffusions maps as an embedding." - description: "This serves as a positive control since it uses 1000-dimensional diffusions maps as an embedding" + label: Diffusion Map + summary: Finding meaningful geometric descriptions of datasets using diffusion maps. + description: Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model. reference: coifman2006diffusion - documentation_url: https://github.com/openproblems-bio/openproblems - repository_url: https://github.com/openproblems-bio/openproblems + documentation_url: https://bioconductor.org/packages/release/bioc/html/destiny.html + repository_url: https://github.com/theislab/destiny v1: path: openproblems/tasks/dimensionality_reduction/methods/diffusion_map.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 preferred_normalization: log_cp10k - variants: - diffusion_map: + resources: + - type: r_script + path: script.R arguments: - - name: "--n_comps" - type: integer - default: 2 - description: "Number of components to use for the embedding." - - name: t + - name: "--n_dim" type: integer - default: 1 - description: "Number to power the eigenvalues by." - - name: n_retries - type: integer - default: 1 - description: "Number of times to retry if the embedding fails, each time adding noise." - resources: - - type: python_script - path: script.py + description: Number of dimensions. + default: 3 platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - - type: python - pypi: - - umap-learn - - scipy - - numpy + - type: r + bioc: destiny - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/script.R b/src/tasks/dimensionality_reduction/methods/diffusion_map/script.R new file mode 100644 index 0000000000..a9146c8db9 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/script.R @@ -0,0 +1,37 @@ +requireNamespace("anndata", quietly = TRUE) +requireNamespace("diffusionMap", quietly = TRUE) + +## VIASH START +par <- list( + input = "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", + output = "output.h5ad", + n_dim = 3 +) +## VIASH END + +cat("Reading input files\n") +input <- anndata::read_h5ad(par$input) + +cat("Running destiny diffusion map\n") +# create SummarizedExperiment object +sce <- SingleCellExperiment::SingleCellExperiment( + assays = list( + logcounts = t(as.matrix(input$layers[["normalized"]])) + ) +) +dm <- destiny::DiffusionMap(sce) +X_emb <- destiny::eigenvectors(dm)[, seq_len(par$n_dim)] + +cat("Write output AnnData to file\n") +output <- anndata::AnnData( + uns = list( + dataset_id = input$uns[["dataset_id"]], + normalization_id = input$uns[["normalization_id"]], + method_id = meta$functionality_name + ), + obsm = list( + X_emb = X_emb + ), + shape = input$shape +) +output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index d369c90298..b024fefb17 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -42,4 +42,4 @@ platforms: - ivis[cpu] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml index 481bac5f86..c6b1c4d0d3 100644 --- a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: - name: "--n_dim" type: integer description: Number of dimensions. - default: 3 + default: 2 - name: "--n_landmarks" type: integer description: Number of landmarks. diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index c665d23a12..ca802f29aa 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -52,4 +52,4 @@ platforms: - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index ea6565a461..5546509d1f 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -12,8 +12,8 @@ functionality: is calculated on the logCPM expression matrix with and without selecting 1000 HVGs. reference: pearson1901pca - repository_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" - documentation_url: "https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html" + repository_url: https://github.com/scikit-learn/scikit-learn + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html v1: path: openproblems/tasks/dimensionality_reduction/methods/pca.py commit: 154ccb9fd99113f3d28d9c3f139194539a0290f9 @@ -37,4 +37,4 @@ platforms: packages: scanpy - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 8b060e796c..36ec4d20d9 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -55,4 +55,4 @@ platforms: - "scikit-learn<1.2" - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml new file mode 100644 index 0000000000..ec3b39b402 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml @@ -0,0 +1,41 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: pymde + info: + label: PyMDE + summary: "A Python implementation of Minimum-Distortion Embedding" + description: | + PyMDE is a Python implementation of Minimum-Distortion Embedding. It is a non-linear + method that preserves distances between cells or neighbourhoods in the original space. + reference: agrawal2021mde + repository_url: https://github.com/cvxgrp/pymde + documentation_url: https://pymde.org + v1: + path: openproblems/tasks/dimensionality_reduction/methods/pymde.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + arguments: + - name: --embed_method + type: string + description: The method to use for embedding. Options are 'umap' and 'tsne'. + default: neighbors + choices: [ neighbors, distances ] + - name: --n_hvg + type: integer + description: Number of highly variable genes to subset to. If not specified, the input matrix will not be subset. + - name: --n_pca_dims + type: integer + description: Number of principal components to use for the initial PCA step. + default: 100 + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: pymde + - type: nextflow + directives: + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/pymde/script.py b/src/tasks/dimensionality_reduction/methods/pymde/script.py new file mode 100644 index 0000000000..612582d8c3 --- /dev/null +++ b/src/tasks/dimensionality_reduction/methods/pymde/script.py @@ -0,0 +1,59 @@ +import anndata as ad +import scanpy as sc +import pymde + +## VIASH START +par = { + "input": "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", + "output": "reduced.h5ad", + "embed_method": "neighbors", + "n_hvg": 1000, + "n_pca_dims": 50, +} +meta = { + "functionality_name": "foo", +} +## VIASH END + +if par["embed_method"] == "neighbors": + mde_fn = pymde.preserve_neighbors +elif par["embed_method"] == "distances": + mde_fn = pymde.preserve_distances +else: + raise ValueError(f"Unknown embedding method: {par['embed_method']}") + +print("Load input data", flush=True) +input = ad.read_h5ad(par["input"]) +X_mat = input.layers["normalized"] + +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = input.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + X_mat = X_mat[:, idx] + +print(f"Compute PCA", flush=True) +X_pca = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack") + +print(f"Run MDE", flush=True) +X_emb = ( + mde_fn(X_pca, embedding_dim=2, verbose=True) + .embed(verbose=True) + .detach() + .numpy() +) + +print("Create output AnnData", flush=True) +output = ad.AnnData( + obs=input.obs[[]], + obsm={ + "X_emb": X_emb + }, + uns={ + "dataset_id": input.uns["dataset_id"], + "normalization_id": input.uns["normalization_id"], + "method_id": meta["functionality_name"] + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 3502f49d01..81a2e0077c 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -46,4 +46,4 @@ platforms: - DmitryUlyanov/Multicore-TSNE - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index e5be09b66f..3f43794344 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -47,4 +47,4 @@ platforms: - pynndescent==0.5.11 - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml index 643ebcb493..b04f8698a2 100644 --- a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml @@ -58,4 +58,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [ midtime, midmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index eb23ba8ece..9852e9a739 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -163,4 +163,4 @@ platforms: cran: [ coRanking, bit64 ] - type: nextflow directives: - label: [ "midtime", highmem, midcpu ] + label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 0d0de7dfd6..8993ebf383 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -40,4 +40,4 @@ platforms: - pynndescent~=0.5.11 - type: nextflow directives: - label: [ "midtime", lowmem, midcpu ] + label: [ midtime, lowmem, midcpu ] diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index d320b8eb8f..83f10077c8 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -10,4 +10,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.2 - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index 882418a6d4..b398be5ed7 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -56,14 +56,19 @@ functionality: - name: common/check_dataset_schema - name: common/extract_metadata - name: dimensionality_reduction/control_methods/random_features + - name: dimensionality_reduction/control_methods/spectral_features - name: dimensionality_reduction/control_methods/true_features - name: dimensionality_reduction/methods/densmap + - name: dimensionality_reduction/methods/diffusionmap + - name: dimensionality_reduction/methods/ivis + - name: dimensionality_reduction/methods/lmds - name: dimensionality_reduction/methods/neuralee - name: dimensionality_reduction/methods/pca - name: dimensionality_reduction/methods/phate - name: dimensionality_reduction/methods/simlr - name: dimensionality_reduction/methods/tsne - name: dimensionality_reduction/methods/umap + - name: dimensionality_reduction/metrics/clustering_performance - name: dimensionality_reduction/metrics/coranking - name: dimensionality_reduction/metrics/density_preservation - name: dimensionality_reduction/metrics/distance_correlation diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index cea5936ca4..cbf5eef926 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -13,12 +13,19 @@ workflow run_wf { // construct list of methods methods = [ + // controls random_features, + spectral_features, true_features, + // methods densmap, + diffusionmap, + ivis, + lmds, neuralee, pca, phate, + pymde, simlr, tsne, umap @@ -26,6 +33,7 @@ workflow run_wf { // construct list of metrics metrics = [ + clustering_performance, coranking, density_preservation, distance_correlation, From a571c0d1a7affa5c1c74d87b3f4fad5a1dc35a89 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Mar 2024 22:39:45 +0100 Subject: [PATCH 1176/1233] Fix dimred components (#404) * fix workflow * reenable ivis Former-commit-id: 544e1b552b0a378846c681ae2c176ab9391395bb --- .../dimensionality_reduction/methods/ivis/config.vsh.yaml | 3 +-- src/tasks/dimensionality_reduction/methods/ivis/script.py | 4 ++-- .../workflows/run_benchmark/config.vsh.yaml | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index b024fefb17..bb6f88894e 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -2,8 +2,6 @@ __merge__: ../../api/comp_method.yaml functionality: - #Temporarily removed from OPv1 see commit 93d2161a08da3edf249abedff5111fb5ce527552 - status: disabled name: "ivis" info: label: "ivis" @@ -40,6 +38,7 @@ platforms: - type: python packages: - ivis[cpu] + - tensorflow<2.16 - type: nextflow directives: label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/dimensionality_reduction/methods/ivis/script.py b/src/tasks/dimensionality_reduction/methods/ivis/script.py index 704e56be6e..1eade8b74d 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/script.py +++ b/src/tasks/dimensionality_reduction/methods/ivis/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { - "input": "resources_test/dimensionality_reduction/pancreas/train.h5ad", + "input": "resources_test/dimensionality_reduction/pancreas/dataset.h5ad", "output": "reduced.h5ad", "n_hvg": 1000, "n_pca_dims": 50 @@ -26,7 +26,7 @@ X_mat = X_mat[:, idx] print(f"Running PCA with {par['n_pca_dims']} dimensions", flush=True) -X_pca = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack")[:, :2] +X_pca = sc.tl.pca(X_mat, n_comps=par["n_pca_dims"], svd_solver="arpack") print("Run ivis", flush=True) # parameters taken from: diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index b398be5ed7..da14aa65f5 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -59,7 +59,7 @@ functionality: - name: dimensionality_reduction/control_methods/spectral_features - name: dimensionality_reduction/control_methods/true_features - name: dimensionality_reduction/methods/densmap - - name: dimensionality_reduction/methods/diffusionmap + - name: dimensionality_reduction/methods/diffusion_map - name: dimensionality_reduction/methods/ivis - name: dimensionality_reduction/methods/lmds - name: dimensionality_reduction/methods/neuralee From 6339920d9b9996ff3fe1deec4692b9c578ec0a9e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Mar 2024 23:11:05 +0100 Subject: [PATCH 1177/1233] Fix DR workflow Former-commit-id: 121a5b75f10f761ec76bc01dfeef1d8dc9192511 --- .../dimensionality_reduction/workflows/run_benchmark/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf index cbf5eef926..1ba9251f9f 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/main.nf @@ -19,7 +19,7 @@ workflow run_wf { true_features, // methods densmap, - diffusionmap, + diffusion_map, ivis, lmds, neuralee, From 6347ed4142faf5bc04ebde45c075699346af79cf Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 13 Mar 2024 23:22:13 +0100 Subject: [PATCH 1178/1233] Fix DR workflow, 3rd attempt Former-commit-id: 2c2d6f0a7ecc3cac51fa23acc0eec036cee39446 --- .../workflows/run_benchmark/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml index da14aa65f5..aa751624d6 100644 --- a/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/workflows/run_benchmark/config.vsh.yaml @@ -65,6 +65,7 @@ functionality: - name: dimensionality_reduction/methods/neuralee - name: dimensionality_reduction/methods/pca - name: dimensionality_reduction/methods/phate + - name: dimensionality_reduction/methods/pymde - name: dimensionality_reduction/methods/simlr - name: dimensionality_reduction/methods/tsne - name: dimensionality_reduction/methods/umap From c20863627436701f4dcff4085952cfe55aae6ccc Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 14 Mar 2024 11:17:35 +0100 Subject: [PATCH 1179/1233] Update match_modalities (#403) * set maximize to false * fix typo * refactor mse * refactor true_features * undo mse changes Former-commit-id: 0891a3c0e7611c9536e55469b5ac2eade7407ff1 --- .../control_methods/true_features/script.py | 12 +++++++++++- .../match_modalities/metrics/mse/config.vsh.yaml | 3 ++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/src/tasks/match_modalities/control_methods/true_features/script.py b/src/tasks/match_modalities/control_methods/true_features/script.py index 2fd06b5a10..cf7abac8e5 100644 --- a/src/tasks/match_modalities/control_methods/true_features/script.py +++ b/src/tasks/match_modalities/control_methods/true_features/script.py @@ -1,4 +1,5 @@ import anndata as ad +import numpy as np ## VIASH START par = { @@ -18,6 +19,9 @@ adata_mod1 = ad.read_h5ad(par["input_mod1"]) adata_mod2 = ad.read_h5ad(par["input_mod2"]) +solution_mod1 = ad.read_h5ad(par["input_solution_mod1"]) +solution_mod2 = ad.read_h5ad(par["input_solution_mod2"]) + print("Storing true features", flush=True) output_mod1 = ad.AnnData( obs=adata_mod1.obs[[]], @@ -31,11 +35,17 @@ "method_id": meta["functionality_name"] } ) + +# Permutate mod1 according to mod2 +mod2_obsm = adata_mod1.obsm["X_svd"][solution_mod1.obs["permutation_indices"]] +reverse_indices_mod2 = np.argsort(solution_mod2.obs["permutation_indices"]) +mod2_obsm = mod2_obsm[reverse_indices_mod2] + output_mod2 = ad.AnnData( obs=adata_mod2.obs[[]], var=adata_mod2.var[[]], obsm={ - "integrated": adata_mod2.obsm["X_svd"] + "integrated": mod2_obsm }, uns={ "dataset_id": adata_mod2.uns["dataset_id"], diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index 6174ad8a4c..add2f42335 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -9,7 +9,7 @@ functionality: description: | Mean squared error (MSE) is the average distance between each pair of matched observations of the same cell in the learned latent space. Lower is better. reference: "lance2022multimodal" - maximize: true + maximize: false min: 0 max: "+.inf" v1: @@ -26,6 +26,7 @@ platforms: packages: - numpy - scipy + - scprep - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] From da713bd419627de87b7958ec5a8a733765ed15b1 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 18 Mar 2024 10:35:27 +0100 Subject: [PATCH 1180/1233] remove unnecessary step in ci (#407) Former-commit-id: d18504750fa21c3e9b2ccc9f5dc42638500bef03 --- .github/workflows/viash-test.yml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/.github/workflows/viash-test.yml b/.github/workflows/viash-test.yml index bc4ba928ab..e7ebcf4875 100644 --- a/.github/workflows/viash-test.yml +++ b/.github/workflows/viash-test.yml @@ -50,13 +50,6 @@ jobs: dest_path: resources_test cache_key_prefix: resources_test__ - - name: Get changed files - id: changed-files - uses: tj-actions/changed-files@v42 - with: - separator: ";" - diff_relative: true - - id: ns_list uses: viash-io/viash-actions/ns-list@v5 with: From 12440cc2aaf01f74d9d110076519ae8315cd021a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 18 Mar 2024 11:03:08 +0100 Subject: [PATCH 1181/1233] Fix results processing (#408) * fix scaling when metric maximise is true * also output metric execution info Former-commit-id: 31f6b555deae8c1df67ae472c45b8d7ba492fb95 --- .../get_results/config.vsh.yaml | 17 +- .../process_task_results/get_results/script.R | 152 ++++++++++++------ .../process_task_results/run/config.vsh.yaml | 5 + src/common/process_task_results/run/main.nf | 29 ++-- 4 files changed, 135 insertions(+), 68 deletions(-) diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index 9bd77c7f2b..fa3240404e 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -9,17 +9,26 @@ functionality: description: "Task id" - name: "--input_scores" type: "file" - example: resources/label_projection/benchmarks/openproblems_v1/combined.extract_scores.output.yaml + example: score_uns.yaml description: "Scores file" - name: "--input_execution" type: "file" - example: resources/label_projection/benchmarks/openproblems_v1/trace.txt + example: trace.txt description: "Nextflow log file" - - name: "--output" + - name: "--input_metric_info" + type: "file" + example: metric_info.json + description: "Metric info file" + - name: "--output_results" type: "file" direction: "output" - default: "output.json" + default: "results.json" description: "Output json" + - name: "--output_metric_execution_info" + type: "file" + direction: "output" + default: "metric_execution_info.json" + description: "Output metric execution info" resources: - type: r_script path: script.R diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index 5f166b1263..dc28c054f9 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -9,14 +9,58 @@ library(purrr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START -dir <- "resources/dimensionality_reduction/results/run_2023-12-22_13-08-31" par <- list( - input_scores = paste0(dir, "/score_uns.yaml"), - input_execution ="resources_test/predict_modality/openproblems_neurips2021/results/trace.txt", - output = "output/results.json" + input_scores = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_scores_1/score_uns.yaml", + input_execution = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_execution_1/trace.txt", + input_metric_info = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_metric_info_1/output.json", + output_results = "output/results.json", + output_metric_execution_info = "output/metric_execution_info.json" ) ## VIASH END +# --- helper functions --------------------------------------------------------- +cat("Loading helper functions\n") +parse_exit <- function(x) { + if (is.na(x) || x == "-") { + NA_integer_ + } else { + as.integer(x) + } +} +parse_duration <- function(x) { + if (is.na(x) || x == "-") { + NA_real_ + } else { + as.numeric(lubridate::duration(toupper(x))) + } +} +parse_cpu <- function(x) { + if (is.na(x) || x == "-") { + NA_real_ + } else { + as.numeric(gsub(" *%", "", x)) + } +} +parse_size <- function(x) { + out <- + if (is.na(x) || x == "-") { + NA_integer_ + } else if (grepl("GB", x)) { + as.numeric(gsub(" *GB", "", x)) * 1024 + } else if (grepl("MB", x)) { + as.numeric(gsub(" *MB", "", x)) + } else if (grepl("KB", x)) { + as.numeric(gsub(" *KB", "", x)) / 1024 + } else if (grepl("B", x)) { + as.numeric(gsub(" *B", "", x)) / 1024 / 1024 + } else { + NA_integer_ + } + as.integer(ceiling(out)) +} + +# --- read input files --------------------------------------------------------- +cat("Reading input files\n") # read scores raw_scores <- yaml::yaml.load_file(par$input_scores) %>% @@ -31,7 +75,11 @@ raw_scores <- }) }) -# scale scores +# read metric info +metric_info <- jsonlite::read_json(par$input_metric_info, simplifyVector = TRUE) + +# --- process scores and execution info ---------------------------------------- +cat("Processing scores and execution info\n") scores <- raw_scores %>% complete( dataset_id, @@ -39,9 +87,11 @@ scores <- raw_scores %>% metric_ids, fill = list(metric_values = NA_real_) ) %>% + left_join(metric_info %>% select(metric_ids = metric_id, maximize), by = "metric_ids") %>% group_by(metric_ids, dataset_id) %>% mutate( - scaled_score = dynutils::scale_minmax(metric_values) %|% 0 + scaled_score = dynutils::scale_minmax(metric_values) %|% 0, + scaled_score = ifelse(maximize, scaled_score, 1 - scaled_score) ) %>% group_by(dataset_id, method_id) %>% summarise( @@ -52,7 +102,7 @@ scores <- raw_scores %>% ) # read nxf log and process the task id -id_regex <- "^.*:(.*)_process \\((.*)/([^\\.]*)\\.(.*)\\)$" +id_regex <- "^.*:(.*)_process \\((.*)/([^\\.]*)(.[^\\.]*)?\\.(.*)\\)$" trace <- readr::read_tsv(par$input_execution) %>% mutate( @@ -60,54 +110,26 @@ trace <- readr::read_tsv(par$input_execution) %>% process_id = stringr::str_extract(id, id_regex, 1L), dataset_id = stringr::str_extract(id, id_regex, 2L), normalization_id = stringr::str_extract(id, id_regex, 3L), - method_id = stringr::str_extract(id, id_regex, 4L), + grp4 = gsub("^\\.", "", stringr::str_extract(id, id_regex, 4L)), + grp5 = stringr::str_extract(id, id_regex, 5L), submit = strptime(submit, "%Y-%m-%d %H:%M:%S"), ) %>% - filter(process_id == method_id) %>% + # detect whether entry is a metric or a method + mutate( + method_id = ifelse(is.na(grp4), grp5, grp4), + metric_id = ifelse(is.na(grp4), grp4, grp5) + ) %>% + select(-grp4, -grp5) %>% + filter(!is.na(method_id)) %>% + # take last entry for each run arrange(desc(submit)) %>% group_by(name) %>% - slice(1) -# parse strings into numbers -parse_exit <- function(x) { - if (is.na(x) || x == "-") { - NA_integer_ - } else { - as.integer(x) - } -} -parse_duration <- function(x) { - if (is.na(x) || x == "-") { - NA_real_ - } else { - as.numeric(lubridate::duration(toupper(x))) - } -} -parse_cpu <- function(x) { - if (is.na(x) || x == "-") { - NA_real_ - } else { - as.numeric(gsub(" *%", "", x)) - } -} -parse_size <- function(x) { - out <- - if (is.na(x) || x == "-") { - NA_integer_ - } else if (grepl("GB", x)) { - as.numeric(gsub(" *GB", "", x)) * 1024 - } else if (grepl("MB", x)) { - as.numeric(gsub(" *MB", "", x)) - } else if (grepl("KB", x)) { - as.numeric(gsub(" *KB", "", x)) / 1024 - } else if (grepl("B", x)) { - as.numeric(gsub(" *B", "", x)) / 1024 / 1024 - } else { - NA_integer_ - } - as.integer(ceiling(out)) -} + slice(1) %>% + ungroup() +# parse values execution_info <- trace %>% + filter(process_id == method_id) %>% # only keep method entries rowwise() %>% transmute( dataset_id, @@ -148,9 +170,39 @@ out <- full_join( ungroup() +# --- process metric execution info -------------------------------------------- +cat("Processing metric execution info\n") +metric_execution_info <- trace %>% + filter(process_id == metric_id) %>% # only keep metric entries + rowwise() %>% + transmute( + dataset_id, + normalization_id, + method_id, + metric_id, + resources = list(list( + exit_code = parse_exit(exit), + duration_sec = parse_duration(realtime), + cpu_pct = parse_cpu(`%cpu`), + peak_memory_mb = parse_size(peak_vmem), + disk_read_mb = parse_size(rchar), + disk_write_mb = parse_size(wchar) + )) + ) %>% + ungroup() + +# --- write output files ------------------------------------------------------- +cat("Writing output files\n") +# write output files jsonlite::write_json( purrr::transpose(out), - par$output, + par$output_results, + auto_unbox = TRUE, + pretty = TRUE +) +jsonlite::write_json( + purrr::transpose(metric_execution_info), + par$output_metric_execution_info, auto_unbox = TRUE, pretty = TRUE ) diff --git a/src/common/process_task_results/run/config.vsh.yaml b/src/common/process_task_results/run/config.vsh.yaml index d6b03a1b52..d746a54245 100644 --- a/src/common/process_task_results/run/config.vsh.yaml +++ b/src/common/process_task_results/run/config.vsh.yaml @@ -71,6 +71,11 @@ functionality: required: true direction: output default: quality_control.json + - name: "--output_metric_execution_info" + type: file + required: true + direction: output + default: metric_execution_info.json resources: - type: nextflow_script path: main.nf diff --git a/src/common/process_task_results/run/main.nf b/src/common/process_task_results/run/main.nf index 3e33a5a2d0..70836c37c3 100644 --- a/src/common/process_task_results/run/main.nf +++ b/src/common/process_task_results/run/main.nf @@ -54,9 +54,13 @@ workflow run_wf { fromState: [ "task_id": "task_id", "input_scores": "input_scores", - "input_execution" : "input_execution" + "input_execution": "input_execution", + "input_metric_info": "output_metric" ], - toState: ["output_results": "output"] + toState: [ + "output_results": "output_results", + "output_metric_execution_info": "output_metric_execution_info" + ] ) | generate_qc.run( @@ -70,18 +74,15 @@ workflow run_wf { toState: ["output_qc": "output"] ) - | map{ id, state -> - def new_state = [ - output_scores: state.output_results, - output_method_info: state.output_method, - output_metric_info: state.output_metric, - output_dataset_info: state.output_dataset, - output_task_info: state.output_task, - output_qc: state.output_qc - ] - - [id, new_state] - } + | setState([ + "output_scores": "output_results", + "output_method_info": "output_method", + "output_metric_info": "output_metric", + "output_dataset_info": "output_dataset", + "output_task_info": "output_task", + "output_qc": "output_qc", + "output_metric_execution_info": "output_metric_execution_info" + ]) emit: output_ch From fb71154bd58077aaf1e33ddb217dcdae715b16de Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 19 Mar 2024 10:16:28 +0100 Subject: [PATCH 1182/1233] fix shared mem config (#409) * fix shared mem config * docker test * update docker test * update docker test * fix docker test * undo docker test Former-commit-id: 282f0b389216bfb0c36dd51798b3a0f88ff6e1e0 --- src/wf_utils/labels_tw.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 2af089636a..6e19a98ee4 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -26,13 +26,13 @@ process { disk = { 200.GB * task.attempt } } withLabel: lowsharedmem { - containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.05}mb" : ""} + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size ${String.format("%.0f",task.memory.mega * 0.05)}" : ""} } withLabel: midsharedmem { - containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.1}mb" : ""} + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size ${String.format("%.0f",task.memory.mega * 0.1)}" : ""} } withLabel: highsharedmem { - containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size=${task.memory.mega * 0.25}mb" : ""} + containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size ${String.format("%.0f",task.memory.mega * 0.25)}" : ""} } } From 7b46edcaea7ce14cb38809ec87042f795fc5b9f7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 19 Mar 2024 11:48:45 +0100 Subject: [PATCH 1183/1233] Fix results scaling (#412) * fix scaling when metric maximise is true * also output metric execution info * fix score scaling * fix script * fix metric maximise value * fix script * fix score aggregation Former-commit-id: 1ce8070376c79ff448b9fdbc547527fa49941fef --- .../get_results/config.vsh.yaml | 8 +++++ .../process_task_results/get_results/script.R | 34 ++++++++++++++++--- src/common/process_task_results/run/main.nf | 2 ++ .../process_task_results/run/run_test.sh | 4 +-- .../distance_correlation/config.vsh.yaml | 4 +-- 5 files changed, 43 insertions(+), 9 deletions(-) diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index fa3240404e..84cc5f27bf 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -15,6 +15,14 @@ functionality: type: "file" example: trace.txt description: "Nextflow log file" + - name: "--input_dataset_info" + type: "file" + example: dataset_info.json + description: "Method info file" + - name: "--input_method_info" + type: "file" + example: method_info.json + description: "Method info file" - name: "--input_metric_info" type: "file" example: metric_info.json diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index dc28c054f9..492d8ca1e7 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -76,10 +76,36 @@ raw_scores <- }) # read metric info +dataset_info <- jsonlite::read_json(par$input_dataset_info, simplifyVector = TRUE) +method_info <- jsonlite::read_json(par$input_method_info, simplifyVector = TRUE) metric_info <- jsonlite::read_json(par$input_metric_info, simplifyVector = TRUE) # --- process scores and execution info ---------------------------------------- cat("Processing scores and execution info\n") +scale_scores <- function(values, is_control, maximize) { + control_values <- values[is_control & !is.na(values)] + if (length(control_values) < 2) { + return(NA_real_) + } + + min_control_value <- min(control_values) + max_control_value <- max(control_values) + + if (min_control_value == max_control_value) { + return(NA_real_) + } + + scaled <- (values - min_control_value) / (max_control_value - min_control_value) + + if (maximize) { + scaled + } else { + 1 - scaled + } +} +aggregate_scores <- function(scaled_score) { + mean(pmin(1, pmax(0, scaled_score)) %|% 0) +} scores <- raw_scores %>% complete( dataset_id, @@ -87,17 +113,15 @@ scores <- raw_scores %>% metric_ids, fill = list(metric_values = NA_real_) ) %>% + left_join(method_info %>% select(method_id, is_baseline), by = "method_id") %>% left_join(metric_info %>% select(metric_ids = metric_id, maximize), by = "metric_ids") %>% group_by(metric_ids, dataset_id) %>% - mutate( - scaled_score = dynutils::scale_minmax(metric_values) %|% 0, - scaled_score = ifelse(maximize, scaled_score, 1 - scaled_score) - ) %>% + mutate(scaled_score = scale_scores(metric_values, is_baseline, maximize[[1]]) %|% 0) %>% group_by(dataset_id, method_id) %>% summarise( metric_values = list(as.list(setNames(metric_values, metric_ids))), scaled_scores = list(as.list(setNames(scaled_score, metric_ids))), - mean_score = mean(scaled_score), + mean_score = aggregate_scores(scaled_score), .groups = "drop" ) diff --git a/src/common/process_task_results/run/main.nf b/src/common/process_task_results/run/main.nf index 70836c37c3..dadbcfa1f6 100644 --- a/src/common/process_task_results/run/main.nf +++ b/src/common/process_task_results/run/main.nf @@ -55,6 +55,8 @@ workflow run_wf { "task_id": "task_id", "input_scores": "input_scores", "input_execution": "input_execution", + "input_dataset_info": "output_dataset", + "input_method_info": "output_method", "input_metric_info": "output_metric" ], toState: [ diff --git a/src/common/process_task_results/run/run_test.sh b/src/common/process_task_results/run/run_test.sh index 2477cb5362..762785b754 100755 --- a/src/common/process_task_results/run/run_test.sh +++ b/src/common/process_task_results/run/run_test.sh @@ -12,9 +12,9 @@ for TASK in "denoising" "dimensionality_reduction" "batch_integration" "label_pr BASE_DIR="s3://openproblems-data/resources/$TASK/results/" # find subdir in bucket with latest date - DATE=$(aws s3 ls $BASE_DIR | awk '{print $2}' | grep 'run_' | sort -r | head -n 1 | sed 's/\///') + DATE=$(aws s3 ls $BASE_DIR --recursive | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#') - INPUT_DIR="$BASE_DIR/$DATE" + INPUT_DIR="$BASE_DIR/run_$DATE" OUTPUT_DIR="../website/results/$TASK/data" # # temp sync diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index 9e005e22bd..cb4d0cad8e 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: reference: kruskal1964mds min: 0 max: "+.inf" - maximize: false + maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/distance_correlation.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 @@ -22,7 +22,7 @@ functionality: reference: coifman2006diffusion min: 0 max: "+.inf" - maximize: false + maximize: true v1: path: openproblems/tasks/dimensionality_reduction/metrics/root_mean_square_error.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 From f99414b4905330740d55d24945c819df624cde07 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Tue, 19 Mar 2024 21:06:31 +0100 Subject: [PATCH 1184/1233] Add spatial decomposition (#365) * add spatial decomposition * Fix typo Co-authored-by: Robrecht Cannoodt * rename files * minor changes to api files * update * update input and output files * add motivation and flowchart * update docker image * update README * reformat * add resources_test_scripts * generate synthetic test datasets * update slot names * Keep .X empty * reformat code * update process_dataset * fix paths * resource_scripts and workflows * update paths and argument names * update structure description of returned anndata object * render task readme * change label masked to spatial masked * update process datasets workflow config * update process datasets * add cell2location method * update docker setup * add default detection alpha value * add batch and fix data type for 'cell_type' * add cell2location script * update info * use cxg_mouse_pancreas_atlas as test resource * update test resources in api * update description * add destvi * add file_common_dataset.yaml to api * add library.bib to test resources * update descriptions * minor updates * add NMFreg method * add NNLS method * force ci * delete run_benchmarks * add RCTD method * update process_dataset input * update test ressources paths * use compatible version of scvi-tools and dependencies * add stereoscope method * add tangram * update argument descriptions * add vanillanmf * add seurat method * avoid converting .obsm['coordinates'] slot to seurat object * Directly convert anndata to seurat * add control methods * add r2 metric * generate synthetic spatial dataset in process_dataset when required * run one method and metric * add workflows * update input example for process_dataset * update test resources path * update common dataset example path * remove unwanted import * provide default values to use when simulating spatial datasets * change preferred_normalization to counts * add variants * use default alpha 1.0 * minor fixes * update input arguments * update file descriptions * update task description * update commpn dataset example * update task description * re-render readme * add dataset simulator component * fix docker setup * separate dataset generation and splitting * update resource test script * update process dataset workflow * fix typo * add more info to config * add VIASH START and VIASH END comments * update test resources for process_dataset * Add variants * update changelog * add test resources to dataset simulator --------- Co-authored-by: Scott Gigante Co-authored-by: Scott Gigante <84813314+scottgigante-immunai@users.noreply.github.com> Co-authored-by: Robrecht Cannoodt Co-authored-by: Daniel Strobl <50872326+danielStrobl@users.noreply.github.com> Co-authored-by: Daniel Strobl Co-authored-by: Kai Waldrant Former-commit-id: 9d5fee4a6c6b49387a4018bdd6278a8ed7ff5c9a --- CHANGELOG.md | 51 ++- src/tasks/spatial_decomposition/README.md | 362 ++++++++++++++++++ .../api/comp_control_method.yaml | 38 ++ .../api/comp_method.yaml | 29 ++ .../api/comp_metric.yaml | 31 ++ .../api/comp_process_dataset.yaml | 33 ++ .../api/file_common_dataset.yaml | 75 ++++ .../api/file_output.yaml | 35 ++ .../spatial_decomposition/api/file_score.yaml | 25 ++ .../api/file_single_cell.yaml | 29 ++ .../api/file_solution.yaml | 29 ++ .../api/file_spatial_masked.yaml | 25 ++ .../spatial_decomposition/api/task_info.yaml | 23 ++ .../random_proportions/config.vsh.yaml | 25 ++ .../random_proportions/script.py | 42 ++ .../true_proportions/config.vsh.yaml | 22 ++ .../true_proportions/script.py | 40 ++ .../dataset_simulator/config.vsh.yaml | 201 ++++++++++ .../dataset_simulator/script.py | 195 ++++++++++ .../methods/cell2location/config.vsh.yaml | 86 +++++ .../methods/cell2location/script.py | 152 ++++++++ .../methods/destvi/config.vsh.yaml | 42 ++ .../methods/destvi/script.py | 62 +++ .../methods/nmfreg/config.vsh.yaml | 37 ++ .../methods/nmfreg/script.py | 101 +++++ .../methods/nnls/config.vsh.yaml | 30 ++ .../methods/nnls/script.py | 65 ++++ .../methods/rctd/config.vsh.yaml | 38 ++ .../methods/rctd/script.R | 94 +++++ .../methods/seurat/config.vsh.yaml | 39 ++ .../methods/seurat/script.R | 97 +++++ .../methods/stereoscope/config.vsh.yaml | 40 ++ .../methods/stereoscope/script.py | 61 +++ .../methods/tangram/config.vsh.yaml | 38 ++ .../methods/tangram/script.py | 84 ++++ .../methods/vanillanmf/config.vsh.yaml | 37 ++ .../methods/vanillanmf/script.py | 77 ++++ .../metrics/r2/config.vsh.yaml | 32 ++ .../metrics/r2/script.py | 39 ++ .../process_dataset/config.vsh.yaml | 13 + .../process_dataset/script.py | 42 ++ .../resources_scripts/process_datasets.sh | 0 .../resources_scripts/run_benchmark.sh | 0 .../resources_scripts/run_benchmark_test.sh | 0 .../cxg_mouse_pancreas_atlas.sh | 39 ++ .../resources_test_scripts/pancreas.sh | 43 +++ .../process_datasets/config.vsh.yaml | 43 +++ .../workflows/process_datasets/main.nf | 65 ++++ .../workflows/process_datasets/run_test.sh | 34 ++ .../workflows/run_benchmark/config.vsh.yaml | 68 ++++ .../workflows/run_benchmark/main.nf | 185 +++++++++ .../workflows/run_benchmark/run_test.sh | 28 ++ 52 files changed, 3120 insertions(+), 1 deletion(-) create mode 100644 src/tasks/spatial_decomposition/README.md create mode 100644 src/tasks/spatial_decomposition/api/comp_control_method.yaml create mode 100644 src/tasks/spatial_decomposition/api/comp_method.yaml create mode 100644 src/tasks/spatial_decomposition/api/comp_metric.yaml create mode 100644 src/tasks/spatial_decomposition/api/comp_process_dataset.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_common_dataset.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_output.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_score.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_single_cell.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_solution.yaml create mode 100644 src/tasks/spatial_decomposition/api/file_spatial_masked.yaml create mode 100644 src/tasks/spatial_decomposition/api/task_info.yaml create mode 100644 src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/control_methods/random_proportions/script.py create mode 100644 src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/control_methods/true_proportions/script.py create mode 100644 src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/dataset_simulator/script.py create mode 100644 src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/cell2location/script.py create mode 100644 src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/destvi/script.py create mode 100644 src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/nmfreg/script.py create mode 100644 src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/nnls/script.py create mode 100644 src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/rctd/script.R create mode 100644 src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/seurat/script.R create mode 100644 src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/stereoscope/script.py create mode 100644 src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/tangram/script.py create mode 100644 src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/methods/vanillanmf/script.py create mode 100644 src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/metrics/r2/script.py create mode 100644 src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/process_dataset/script.py create mode 100755 src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh create mode 100755 src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh create mode 100755 src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh create mode 100755 src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh create mode 100755 src/tasks/spatial_decomposition/resources_test_scripts/pancreas.sh create mode 100644 src/tasks/spatial_decomposition/workflows/process_datasets/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/workflows/process_datasets/main.nf create mode 100644 src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh create mode 100644 src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml create mode 100644 src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf create mode 100755 src/tasks/spatial_decomposition/workflows/run_benchmark/run_test.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index b7fcc4e452..675f9aa957 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -346,7 +346,6 @@ * `metrics/mse`: Migrated from v1. - ### Changes from V1 * `methods/scot`: Add new scot method. @@ -357,3 +356,53 @@ * The methods and metrics now take 2 modal datasets as input instead of 1. +## spatial_decomposition (PR #365) + +### NEW FUNCTIONALITY + +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the process, method and metric components. + +* `dataset_simulator`: Added a component to simulate spatial datasets with the required ground-truth. + +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. + +* `resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas` with `src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh`. + +* Added `variant` key to config files to store the different input parameter sets for components. + +* `workflows/run`: Added nf-tower test script. + +### V1 MIGRATION + +* `methods/cell2location`: Migrated from v1. + +* `methods/destvi`: Migrated from v1. + +* `methods/nmfreg`: Migrated from v1. + +* `methods/nnls`: Migrated and adapted from v1. + +* `methods/rctd`: Migrated and adapted from v1. + +* `methods/seurat`: Migrated and adapted from v1. + +* `methods/stereoscope`: Migrated from v1. + +* `methods/tangram`: Migrated from v1. + +* `methods/vanillanmf`: Migrated from v1. + +* `control_methods/random_proportions`: Migrated from v1. + +* `control_methods/true_proportions`: Migrated from v1. + +* `metric/r2`: Migrated from v1. + +### Changes from V1 + +* Raw counts and normalized expression data is stored in `.layers["counts"]` and `.layers["normalized"]`, respectively, + instead of in `.X`. + +* A `process_dataset` has been implemented to make a distinction between the data that a method or metric is allowed to see. diff --git a/src/tasks/spatial_decomposition/README.md b/src/tasks/spatial_decomposition/README.md new file mode 100644 index 0000000000..2ac66984b2 --- /dev/null +++ b/src/tasks/spatial_decomposition/README.md @@ -0,0 +1,362 @@ +# Spatial decomposition + + +Estimation of cell type proportions per spot in 2D space from spatial +transcriptomic data coupled with corresponding single-cell data + +Path: +[`src/tasks/spatial_decomposition`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/spatial_decomposition) + +## Motivation + +Spatial decomposition (also often referred to as Spatial deconvolution) +is applicable to spatial transcriptomics data where the transcription +profile of each capture location (spot, voxel, bead, etc.) do not share +a bijective relationship with the cells in the tissue, i.e., multiple +cells may contribute to the same capture location. The task of spatial +decomposition then refers to estimating the composition of cell +types/states that are present at each capture location. The cell +type/states estimates are presented as proportion values, representing +the proportion of the cells at each capture location that belong to a +given cell type. + +## Description + +We distinguish between *reference-based* decomposition and *de novo* +decomposition, where the former leverage external data (e.g., scRNA-seq +or scNuc-seq) to guide the inference process, while the latter only work +with the spatial data. We require that all datasets have an associated +reference single cell data set, but methods are free to ignore this +information. Due to the lack of real datasets with the necessary +ground-truth, this task makes use of a simulated dataset generated by +creating cell-aggregates by sampling from a Dirichlet distribution. The +ground-truth dataset consists of the spatial expression matrix, XY +coordinates of the spots, true cell-type proportions for each spot, and +the reference single-cell data (from which cell aggregated were +simulated). + +## Authors & contributors + +| name | roles | +|:-----------------|:-------------------| +| Giovanni Palla | author, maintainer | +| Scott Gigante | author | +| Sai Nirmayi Yasa | author | + +## API + +``` mermaid +flowchart LR + file_common_dataset("Common Dataset") + comp_process_dataset[/"Data processor"/] + file_single_cell("Single cell data") + file_spatial_masked("Spatial masked") + file_solution("Solution") + comp_control_method[/"Control method"/] + comp_method[/"Method"/] + comp_metric[/"Metric"/] + file_output("Output") + file_score("Score") + file_common_dataset---comp_process_dataset + comp_process_dataset-->file_single_cell + comp_process_dataset-->file_spatial_masked + comp_process_dataset-->file_solution + file_single_cell---comp_control_method + file_single_cell---comp_method + file_spatial_masked---comp_control_method + file_spatial_masked---comp_method + file_solution---comp_control_method + file_solution---comp_metric + comp_control_method-->file_output + comp_method-->file_output + comp_metric-->file_score + file_output---comp_metric +``` + +## File format: Common Dataset + +A subset of the common dataset. + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/dataset_simulated.h5ad` + +Format: + +
+ + AnnData object + obs: 'cell_type', 'batch' + var: 'hvg', 'hvg_score' + obsm: 'X_pca', 'coordinates', 'proportions_true' + layers: 'counts' + uns: 'cell_type_names', 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------------|:----------|:--------------------------------------------------------------------------------------------------------------------| +| `obs["cell_type"]` | `string` | Cell type label IDs. | +| `obs["batch"]` | `string` | A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | +| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | +| `obsm["coordinates"]` | `double` | (*Optional*) XY coordinates for each spot. | +| `obsm["proportions_true"]` | `double` | (*Optional*) True cell type proportions for each spot. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["cell_type_names"]` | `string` | (*Optional*) Cell type names corresponding to values in `cell_type`. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["dataset_name"]` | `string` | Nicely formatted name. | +| `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | +| `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | +| `uns["dataset_summary"]` | `string` | Short description of the dataset. | +| `uns["dataset_description"]` | `string` | Long description of the dataset. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | + +
+ +## Component type: Data processor + +Path: +[`src/spatial_decomposition`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition) + +A spatial decomposition dataset processor. + +Arguments: + +
+ +| Name | Type | Description | +|:--------------------------|:-------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------| +| `--input` | `file` | A subset of the common dataset. | +| `--output_single_cell` | `file` | (*Output*) The single-cell data file used as reference for the spatial data. | +| `--output_spatial_masked` | `file` | (*Output*) The spatial data file containing transcription profiles for each capture location, without cell-type proportions for each spot. | +| `--output_solution` | `file` | (*Output*) The spatial data file containing transcription profiles for each capture location, with true cell-type proportions for each spot / capture location. | + +
+ +## File format: Single cell data + +The single-cell data file used as reference for the spatial data + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad` + +Format: + +
+ + AnnData object + obs: 'cell_type', 'batch' + layers: 'counts' + uns: 'cell_type_names', 'dataset_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-------------------------|:----------|:---------------------------------------------------------------------------------------------------------------------------------| +| `obs["cell_type"]` | `string` | Cell type label IDs. | +| `obs["batch"]` | `string` | (*Optional*) A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["cell_type_names"]` | `string` | Cell type names corresponding to values in `cell_type`. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | + +
+ +## File format: Spatial masked + +The spatial data file containing transcription profiles for each capture +location, without cell-type proportions for each spot. + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad` + +Format: + +
+ + AnnData object + obsm: 'coordinates' + layers: 'counts' + uns: 'cell_type_names', 'dataset_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-------------------------|:----------|:--------------------------------------------------------------------------| +| `obsm["coordinates"]` | `double` | XY coordinates for each spot. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["cell_type_names"]` | `string` | Cell type names corresponding to columns of `proportions_pred` in output. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | + +
+ +## File format: Solution + +The spatial data file containing transcription profiles for each capture +location, with true cell-type proportions for each spot / capture +location. + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/solution.h5ad` + +Format: + +
+ + AnnData object + obsm: 'coordinates', 'proportions_true' + layers: 'counts' + uns: 'cell_type_names', 'dataset_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------|:----------|:-----------------------------------------------------------| +| `obsm["coordinates"]` | `double` | XY coordinates for each spot. | +| `obsm["proportions_true"]` | `double` | True cell type proportions for each spot. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["cell_type_names"]` | `string` | Cell type names corresponding to columns of `proportions`. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | + +
+ +## Component type: Control method + +Path: +[`src/spatial_decomposition/control_methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/control_methods) + +Quality control methods for verifying the pipeline. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------------|:-------|:-----------------------------------------------------------------------------------------------------------------------------------------------------| +| `--input_single_cell` | `file` | The single-cell data file used as reference for the spatial data. | +| `--input_spatial_masked` | `file` | The spatial data file containing transcription profiles for each capture location, without cell-type proportions for each spot. | +| `--input_solution` | `file` | The spatial data file containing transcription profiles for each capture location, with true cell-type proportions for each spot / capture location. | +| `--output` | `file` | (*Output*) Spatial data with estimated proportions. | + +
+ +## Component type: Method + +Path: +[`src/spatial_decomposition/methods`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/methods) + +A spatial composition method. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------------|:-------|:--------------------------------------------------------------------------------------------------------------------------------| +| `--input_single_cell` | `file` | The single-cell data file used as reference for the spatial data. | +| `--input_spatial_masked` | `file` | The spatial data file containing transcription profiles for each capture location, without cell-type proportions for each spot. | +| `--output` | `file` | (*Output*) Spatial data with estimated proportions. | + +
+ +## Component type: Metric + +Path: +[`src/spatial_decomposition/metrics`](https://github.com/openproblems-bio/openproblems-v2/tree/main/src/spatial_decomposition/metrics) + +A spatial decomposition metric. + +Arguments: + +
+ +| Name | Type | Description | +|:-------------------|:-------|:-----------------------------------------------------------------------------------------------------------------------------------------------------| +| `--input_method` | `file` | Spatial data with estimated proportions. | +| `--input_solution` | `file` | The spatial data file containing transcription profiles for each capture location, with true cell-type proportions for each spot / capture location. | +| `--output` | `file` | (*Output*) Metric score file. | + +
+ +## File format: Output + +Spatial data with estimated proportions. + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/output.h5ad` + +Description: + +Spatial data file with estimated cell type proportions. + +Format: + +
+ + AnnData object + obsm: 'coordinates', 'proportions_pred' + layers: 'counts' + uns: 'cell_type_names', 'dataset_id', 'method_id' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:---------------------------|:----------|:-----------------------------------------------------------| +| `obsm["coordinates"]` | `double` | XY coordinates for each spot. | +| `obsm["proportions_pred"]` | `double` | Estimated cell type proportions for each spot. | +| `layers["counts"]` | `integer` | Raw counts. | +| `uns["cell_type_names"]` | `string` | Cell type names corresponding to columns of `proportions`. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | + +
+ +## File format: Score + +Metric score file. + +Example file: +`resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/score.h5ad` + +Format: + +
+ + AnnData object + uns: 'dataset_id', 'method_id', 'metric_ids', 'metric_values' + +
+ +Slot description: + +
+ +| Slot | Type | Description | +|:-----------------------|:---------|:---------------------------------------------------------------------------------------------| +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["metric_ids"]` | `string` | One or more unique metric identifiers. | +| `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. | + +
+ diff --git a/src/tasks/spatial_decomposition/api/comp_control_method.yaml b/src/tasks/spatial_decomposition/api/comp_control_method.yaml new file mode 100644 index 0000000000..b92cd53051 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/comp_control_method.yaml @@ -0,0 +1,38 @@ +functionality: + namespace: "spatial_decomposition/control_methods" + info: + type: control_method + type_info: + label: Control method + summary: Quality control methods for verifying the pipeline. + description: | + Control methods have the same interface as the regular methods + but also receive the solution object as input. It serves as a + starting point to test the relative accuracy of new methods in + the task, and also as a quality control for the metrics defined + in the task. + arguments: + - name: "--input_single_cell" + __merge__: file_single_cell.yaml + direction: input + required: true + - name: "--input_spatial_masked" + __merge__: file_spatial_masked.yaml + direction: input + required: true + - name: "--input_solution" + __merge__: file_solution.yaml + direction: input + required: true + - name: "--output" + __merge__: file_output.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + - path: /src/common/library.bib diff --git a/src/tasks/spatial_decomposition/api/comp_method.yaml b/src/tasks/spatial_decomposition/api/comp_method.yaml new file mode 100644 index 0000000000..def4edae91 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/comp_method.yaml @@ -0,0 +1,29 @@ +functionality: + namespace: "spatial_decomposition/methods" + info: + type: method + type_info: + label: Method + summary: A spatial composition method. + description: "Method to estimate cell type proportions from spatial and single cell data" + arguments: + - name: "--input_single_cell" + __merge__: file_single_cell.yaml + direction: input + required: true + - name: "--input_spatial_masked" + __merge__: file_spatial_masked.yaml + direction: input + required: true + - name: "--output" + __merge__: file_output.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + - path: /src/common/library.bib \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/comp_metric.yaml b/src/tasks/spatial_decomposition/api/comp_metric.yaml new file mode 100644 index 0000000000..2cd5efd33a --- /dev/null +++ b/src/tasks/spatial_decomposition/api/comp_metric.yaml @@ -0,0 +1,31 @@ +functionality: + namespace: "spatial_decomposition/metrics" + info: + type: metric + type_info: + label: Metric + summary: A spatial decomposition metric. + description: | + A metric for evaluating accuracy of cell type proportion estimate + arguments: + - name: "--input_method" + __merge__: file_output.yaml + direction: input + required: true + - name: "--input_solution" + __merge__: file_solution.yaml + direction: input + required: true + - name: "--output" + __merge__: file_score.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_metric_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + - path: /src/common/library.bib + \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/comp_process_dataset.yaml b/src/tasks/spatial_decomposition/api/comp_process_dataset.yaml new file mode 100644 index 0000000000..336aa9866e --- /dev/null +++ b/src/tasks/spatial_decomposition/api/comp_process_dataset.yaml @@ -0,0 +1,33 @@ +functionality: + namespace: "spatial_decomposition" + info: + type: process_dataset + type_info: + label: Data processor + summary: A spatial decomposition dataset processor. + description: | + Prepare a common dataset for the spatial_decomposition task. + arguments: + - name: "--input" + __merge__: file_common_dataset.yaml + direction: input + required: true + - name: "--output_single_cell" + __merge__: file_single_cell.yaml + direction: output + required: true + - name: "--output_spatial_masked" + __merge__: file_spatial_masked.yaml + direction: output + required: true + - name: "--output_solution" + __merge__: file_solution.yaml + direction: output + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/common/cxg_mouse_pancreas_atlas + dest: resources_test/common/cxg_mouse_pancreas_atlas + - path: /resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas + dest: resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/file_common_dataset.yaml b/src/tasks/spatial_decomposition/api/file_common_dataset.yaml new file mode 100644 index 0000000000..c283d4d92b --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_common_dataset.yaml @@ -0,0 +1,75 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/dataset_simulated.h5ad" +info: + label: "Common Dataset" + summary: A subset of the common dataset. + slots: + layers: + - type: integer + name: counts + description: Raw counts. + required: true + obs: + - type: string + name: cell_type + description: Cell type label IDs. + required: true + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: true + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: true + - type: double + name: coordinates + description: XY coordinates for each spot. + required: false + - type: double + name: proportions_true + description: True cell type proportions for each spot + required: false + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to values in `cell_type` + required: false + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/file_output.yaml b/src/tasks/spatial_decomposition/api/file_output.yaml new file mode 100644 index 0000000000..4328ea5e80 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_output.yaml @@ -0,0 +1,35 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/output.h5ad" +info: + label: Output + summary: "Spatial data with estimated proportions." + description: "Spatial data file with estimated cell type proportions." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obsm: + - type: double + name: coordinates + description: XY coordinates for each spot + required: true + - type: double + name: proportions_pred + description: Estimated cell type proportions for each spot + required: true + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to columns of `proportions` + required: true + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/file_score.yaml b/src/tasks/spatial_decomposition/api/file_score.yaml new file mode 100644 index 0000000000..fea2d39e02 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_score.yaml @@ -0,0 +1,25 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/score.h5ad" +info: + label: "Score" + summary: Metric score file. + slots: + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: method_id + description: "A unique identifier for the method" + required: true + - type: string + name: metric_ids + description: "One or more unique metric identifiers" + multiple: true + required: true + - type: double + name: metric_values + description: "The metric values obtained for the given prediction. Must be of same length as 'metric_ids'." + multiple: true + required: true diff --git a/src/tasks/spatial_decomposition/api/file_single_cell.yaml b/src/tasks/spatial_decomposition/api/file_single_cell.yaml new file mode 100644 index 0000000000..0ec0a94156 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_single_cell.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad" +info: + label: "Single cell data" + summary: "The single-cell data file used as reference for the spatial data" + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obs: + - type: string + name: cell_type + description: Cell type label IDs + required: true + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: false + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to values in `cell_type` + required: true + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/file_solution.yaml b/src/tasks/spatial_decomposition/api/file_solution.yaml new file mode 100644 index 0000000000..bfe20e56f5 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_solution.yaml @@ -0,0 +1,29 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/solution.h5ad" +info: + label: Solution + summary: "The spatial data file containing transcription profiles for each capture location, with true cell-type proportions for each spot / capture location." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obsm: + - type: double + name: coordinates + description: XY coordinates for each spot + required: true + - type: double + name: proportions_true + description: True cell type proportions for each spot + required: true + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to columns of `proportions` + required: true + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/file_spatial_masked.yaml b/src/tasks/spatial_decomposition/api/file_spatial_masked.yaml new file mode 100644 index 0000000000..77632b59b6 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/file_spatial_masked.yaml @@ -0,0 +1,25 @@ +type: file +example: "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad" +info: + label: "Spatial masked" + summary: "The spatial data file containing transcription profiles for each capture location, without cell-type proportions for each spot." + slots: + layers: + - type: integer + name: counts + description: Raw counts + required: true + obsm: + - type: double + name: coordinates + description: XY coordinates for each spot + required: true + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to columns of `proportions_pred` in output + required: true + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/api/task_info.yaml b/src/tasks/spatial_decomposition/api/task_info.yaml new file mode 100644 index 0000000000..0fa3e16723 --- /dev/null +++ b/src/tasks/spatial_decomposition/api/task_info.yaml @@ -0,0 +1,23 @@ +name: spatial_decomposition +label: "Spatial decomposition" +summary: "Estimation of cell type proportions per spot in 2D space from spatial transcriptomic data coupled with corresponding single-cell data" +motivation: | + Spatial decomposition (also often referred to as Spatial deconvolution) is applicable to spatial transcriptomics data where the transcription profile of each capture location (spot, voxel, bead, etc.) do not share a bijective relationship with the cells in the tissue, i.e., multiple cells may contribute to the same capture location. The task of spatial decomposition then refers to estimating the composition of cell types/states that are present at each capture location. The cell type/states estimates are presented as proportion values, representing the proportion of the cells at each capture location that belong to a given cell type. +description: | + We distinguish between _reference-based_ decomposition and _de novo_ decomposition, where the former leverage external data (e.g., scRNA-seq or scNuc-seq) to guide the inference process, while the latter only work with the spatial data. We require that all datasets have an associated reference single cell data set, but methods are free to ignore this information. + Due to the lack of real datasets with the necessary ground-truth, this task makes use of a simulated dataset generated by creating cell-aggregates by sampling from a Dirichlet distribution. The ground-truth dataset consists of the spatial expression matrix, XY coordinates of the spots, true cell-type proportions for each spot, and the reference single-cell data (from which cell aggregated were simulated). +authors: + - name: "Giovanni Palla" + roles: [ author, maintainer ] + info: + github: giovp + - name: "Scott Gigante" + roles: [ author ] + info: + github: scottgigante + orcid: "0000-0002-4544-2764" + - name: "Sai Nirmayi Yasa" + roles: [ author ] + info: + github: sainirmayi + orcid: "0009-0003-6319-9803" \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml new file mode 100644 index 0000000000..e453dae5af --- /dev/null +++ b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml @@ -0,0 +1,25 @@ +__merge__: ../../api/comp_control_method.yaml + +functionality: + name: random_proportions + info: + label: Random Proportions + summary: "Negative control method that randomly assigns celltype proportions from a Dirichlet distribution." + description: | + A negative control method with random assignment of predicted celltype proportions from a Dirichlet distribution. + preferred_normalization: counts + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: numpy + - type: native + - type: nextflow + directives: + label: ["midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/random_proportions/script.py b/src/tasks/spatial_decomposition/control_methods/random_proportions/script.py new file mode 100644 index 0000000000..17af41d752 --- /dev/null +++ b/src/tasks/spatial_decomposition/control_methods/random_proportions/script.py @@ -0,0 +1,42 @@ +import anndata as ad +import numpy as np + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_solution': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/solution.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'random_proportions' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial_masked = ad.read_h5ad(par['input_spatial_masked']) +input_solution = ad.read_h5ad(par['input_solution']) + +print('Generate predictions', flush=True) +label_distribution = input_single_cell.obs["cell_type"].value_counts() +input_spatial_masked.obsm["proportions_pred"] = np.random.dirichlet(label_distribution, size=input_spatial_masked.shape[0]) + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial_masked.obs[[]], + var=input_spatial_masked.var[[]], + uns={ + 'cell_type_names': input_spatial_masked.uns['cell_type_names'], + 'dataset_id': input_spatial_masked.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial_masked.obsm['coordinates'], + 'proportions_pred': input_spatial_masked.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial_masked.layers['counts'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml new file mode 100644 index 0000000000..4c5f1a05ec --- /dev/null +++ b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml @@ -0,0 +1,22 @@ +__merge__: ../../api/comp_control_method.yaml + +functionality: + name: true_proportions + info: + label: True Proportions + summary: "Positive control method that assigns celltype proportions from the ground truth." + description: | + A positive control method with perfect assignment of predicted celltype proportions from the ground truth. + preferred_normalization: counts + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + - type: native + - type: nextflow + directives: + label: ["midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/true_proportions/script.py b/src/tasks/spatial_decomposition/control_methods/true_proportions/script.py new file mode 100644 index 0000000000..e4c47e31da --- /dev/null +++ b/src/tasks/spatial_decomposition/control_methods/true_proportions/script.py @@ -0,0 +1,40 @@ +import anndata as ad + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_solution': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/solution.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'true_proportions' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial_masked = ad.read_h5ad(par['input_spatial_masked']) +input_solution = ad.read_h5ad(par['input_solution']) + +print('Generate predictions', flush=True) +input_spatial_masked.obsm["proportions_pred"] = input_solution.obsm["proportions_true"] + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial_masked.obs[[]], + var=input_spatial_masked.var[[]], + uns={ + 'cell_type_names': input_spatial_masked.uns['cell_type_names'], + 'dataset_id': input_spatial_masked.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial_masked.obsm['coordinates'], + 'proportions_pred': input_spatial_masked.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial_masked.layers['counts'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml new file mode 100644 index 0000000000..67c85181f7 --- /dev/null +++ b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml @@ -0,0 +1,201 @@ +functionality: + name: "dataset_simulator" + namespace: "spatial_decomposition" + info: + type: dataset_simulator + type_info: + label: Dataset simulator + summary: Simulate cell aggregates from single-cell data. + description: | + The dataset simulator creates cell-aggregates from the single-cell dataset by sampling from a Dirichlet distribution. The simulated data consists of the the spatial expression matrix, the XY coordinates of the spots, the cell-type proportions in each spot, and the reference single-cell data. + variants: + alpha_1: + alpha: 1 + alpha_5: + alpha: 5 + alpha_0_5: + alpha: 0.5 + arguments: + - name: "--input" + type: file + description: Single-cell reference dataset + direction: input + example: "resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad" + info: + slots: + layers: + - type: integer + name: counts + description: Raw counts. + required: true + obs: + - type: string + name: cell_type + description: Cell type label IDs. + required: true + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: false + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: false + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: false + uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - name: "--alpha" + type: double + description: Alpha value to use for generating synthetic dataset + default: 1.0 + - name: "--n_obs" + type: integer + description: Number of spatial observations to generate. Default value is 100. + default: 100 + - name: "--cell_lb" + type: integer + description: Lower bound for number of cells at each spot. Default value is 10. + default: 10 + - name: "--cell_ub" + type: integer + description: Upper bound for number of cells at each spot. Default value is 30. + default: 30 + - name: "--umi_lb" + type: integer + description: Lower bound for number of cells at each spot. Default value is 1000. + default: 1000 + - name: "--umi_ub" + type: integer + description: Upper bound for number of UMIs at each spot. Default value is 5000. + default: 5000 + - name: "--simulated_data" + type: file + direction: output + description: Simulated dataset + required: false + example: dataset_simulated.h5ad + info: + slots: + layers: + - type: integer + name: counts + description: Raw counts. + required: true + obs: + - type: string + name: cell_type + description: Cell type label IDs. + required: true + - type: string + name: batch + description: A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. + required: true + var: + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: false + - type: integer + name: hvg_score + description: A ranking of the features by hvg. + required: false + obsm: + - type: double + name: X_pca + description: The resulting PCA embedding. + required: false + - type: double + name: coordinates + description: XY coordinates for each spot. + required: true + - type: double + name: proportions_true + description: True cell type proportions for each spot. + required: true + uns: + - type: string + name: cell_type_names + description: Cell type names corresponding to values in `cell_type`. + required: true + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + resources: + - type: python_script + path: script.py + test_resources: + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/common/cxg_mouse_pancreas_atlas + dest: resources_test/common/cxg_mouse_pancreas_atlas +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: [numpy, scanpy] + - type: nextflow + directives: + label: [ midtime, highmem, highcpu ] + - type: native diff --git a/src/tasks/spatial_decomposition/dataset_simulator/script.py b/src/tasks/spatial_decomposition/dataset_simulator/script.py new file mode 100644 index 0000000000..9fc09214de --- /dev/null +++ b/src/tasks/spatial_decomposition/dataset_simulator/script.py @@ -0,0 +1,195 @@ +from typing import Sequence +from typing import Union + +import anndata as ad +import numpy as np +import scanpy as sc + +## VIASH START +par = { + "input": "resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad", + "alpha": 1, + "n_obs": 100, + "cell_lb": 10, + "cell_ub": 30, + "umi_lb": 1000, + "umi_ub": 5000, + "simulated_data": "dataset_simulated.h5ad" +} +meta = { + "functionality_name": "dataset_simulator", + "resources_dir": "src/tasks/spatial_decomposition/dataset_simulator", +} +## VIASH END + +CELLTYPE_MIN_CELLS = 25 +# Reading input dataset +adata = ad.read_h5ad(par['input']) + +def generate_synthetic_dataset( + adata: ad.AnnData, + alpha: Union[float, Sequence] = 1.0, + n_obs: int = 1000, + cell_lb: int = 10, + cell_ub: int = 30, + umi_lb: int = 1000, + umi_ub: int = 5000, +) -> ad.AnnData: + """Create cell-aggregate samples for ground-truth spatial decomposition task. + + Parameters + ---------- + adata: AnnData + Anndata object. + type_column: str + name of column in `adata.obs` where cell type labels are given + alpha: Union[float,Sequence] + alpha value in dirichlet distribution. If single number then all alpha_i values + will be set to this value. Default value is 1. + n_obs: int + number of spatial observations to generate. Default value is 1000. + cell_lb: int + lower bound for number of cells at each spot. Default value is 10. + cell_ub: int + upper bound for number of cells at each spot. Default value is 30. + umi_lb: int + lower bound for number of UMIs at each spot. Default value is 10. + umi_ub: int + upper bound for number of UMIs at each spot. Default value is 30. + + Returns + ------- + AnnData with: + - `adata_merged.X`: simulated counts (aggregate of sc dataset). + - `adata_merged.obsm["proportions_true"]`: true proportion values. + - `adata_merged.obsm["coordinates"]`: coordinates of each spot. + - `adata_merged.obsm["n_cells"]`: number of cells from each type at every location. + + """ + + # remove rare celltypes + adata = filter_celltypes(adata) + + # set random generator seed + rng = np.random.default_rng(42) + + # get single cell expression data + counts = adata.layers['counts'] + # get cell annotations/labels + labels = adata.obs['cell_type'].values + # get unique labels + uni_labs = np.unique(labels) + # count number of labels + n_labs = len(uni_labs) + # get number of genes + n_genes = adata.shape[1] + + # create dict with indices of each label + label_indices = dict() + for label in uni_labs: + label_indices[label] = np.where(labels == label)[0] + + # adjust alpha to vector if single scalar + if not hasattr(alpha, "__len__"): + alpha = np.ones(n_labs) * alpha + else: + assert len(alpha) == n_labs, "alpha must be same size as number of cell types" + + # generate probability of sampling label at each spot + sp_props = rng.dirichlet(alpha, size=n_obs) + # number of cells present at each spot + n_cells = rng.integers(cell_lb, cell_ub, size=n_obs) + + # initialize spatial expression matrix + sp_x = np.zeros((n_obs, n_genes)) + # initialize spatial proportion matrix + sp_p = np.zeros((n_obs, n_labs)) + # initialize spatial cell number matrix + sp_c = np.zeros(sp_p.shape) + + # generate expression vector for each spot (s) + for s in range(n_obs): + # number of cells from each label at s + raw_s = rng.multinomial(n_cells[s], pvals=sp_props[s, :]) + # store number of cells from each type at s + sp_c[s, :] = raw_s + # compute proportion of each type at s + prop_s = raw_s / n_cells[s] + # store proportion of each type at s + sp_p[s, :] = prop_s + + # initialize transcript pool at s + pool_s = np.zeros(n_genes) + + # add molecules to transcript pool + for lab, n in enumerate(raw_s): + # get indices of cells from which transcripts should be added + idx_sl = rng.choice(label_indices[uni_labs[lab]], size=n) + # add molecules to pool + pool_s += counts[idx_sl, :].sum(axis=0).A.flatten() + + # number of UMIs at spot s + n_umis = rng.integers(umi_lb, umi_ub) + # compute probability of sampling UMI from gene + prob_pool_s = pool_s / pool_s.sum() + + # sample transcripts from pool + sp_x[s, :] = np.random.multinomial(n=n_umis, pvals=prob_pool_s) + + obs_names = ["spatial_{}".format(x) for x in range(n_obs)] + adata_spatial = ad.AnnData( + sp_x, + obs=dict(obs_names=obs_names), + var=dict(var_names=adata.var_names), + ) + + # fake coordinates + adata_spatial.obsm["coordinates"] = rng.random((adata_spatial.shape[0], 2)) + adata_spatial.obsm["proportions_true"] = sp_p + adata_spatial.obs["n_cells"] = n_cells + adata_spatial.obsm["n_cells"] = sp_c + + adata_merged = ad.concat( + {"sc": adata, "sp": adata_spatial}, + label="modality", + join="outer", + index_unique=None, + merge="unique", + uns_merge="unique" + ) + adata_merged.X[adata_merged.X == np.inf] = adata_merged.X.max() # remove inf + adata_merged.layers["counts"] = adata_merged.X + adata_merged.uns["cell_type_names"] = uni_labs + return adata_merged + +def filter_celltypes(adata, min_cells=CELLTYPE_MIN_CELLS): + """Filter rare celltypes from an AnnData""" + celltype_counts = adata.obs["cell_type"].value_counts() >= min_cells + keep_cells = np.isin(adata.obs["cell_type"], celltype_counts.index[celltype_counts]) + return adata[adata.obs.index[keep_cells]].copy() + +def filter_genes_cells(adata): + """Remove empty cells and genes.""" + if "var_names_all" not in adata.uns: + # fill in original var names before filtering + adata.uns["var_names_all"] = adata.var.index.to_numpy() + sc.pp.filter_genes(adata, min_cells=1) + sc.pp.filter_cells(adata, min_counts=2) + +adata.X = adata.layers["counts"] +sc.pp.filter_genes(adata, min_counts=10) +adata_merged = generate_synthetic_dataset(adata, + alpha=par['alpha'], + n_obs=par['n_obs'], + cell_lb=par['cell_lb'], + cell_ub=par['cell_ub'], + umi_lb=par['umi_lb'], + umi_ub=par['umi_ub'] +) +adata.uns["spatial_data_summary"] = f"Dirichlet alpha={par['alpha']}" +filter_genes_cells(adata_merged) +adata_merged.X = None +adata_merged.obs['is_primary_data'] = adata_merged.obs['is_primary_data'].fillna(False) + +print("Writing output to file") +adata_merged.write_h5ad(par["simulated_data"]) diff --git a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml new file mode 100644 index 0000000000..843c6932dc --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml @@ -0,0 +1,86 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: cell2location + + info: + label: Cell2Location + summary: "Cell2location uses a Bayesian model to resolve cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues." + description: | + Cell2location is a decomposition method based on Negative Binomial regression that is able to account for batch effects in estimating the single-cell gene expression signature used for the spatial decomposition step. + Note that when batch information is unavailable for this task, we can use either a hard-coded reference, or a negative-binomial learned reference without batch labels. The parameter alpha refers to the detection efficiency prior. + preferred_normalization: counts + variants: + cell2location_amortised_detection_alpha_20: + detection_alpha: 20 + amortised: true + cell2location_detection_alpha_1: + detection_alpha: 1 + cell2location_detection_alpha_20: + detection_alpha: 20 + cell2location_detection_alpha_20_nb: + detection_alpha: 20 + hard_coded_reference: false + cell2location_detection_alpha_200: + detection_alpha: 200 + reference: "kleshchevnikov2022cell2location" + documentation_url: https://cell2location.readthedocs.io/en/latest/ + repository_url: https://github.com/BayraktarLab/cell2location + + # Component-specific parameters (optional) + arguments: + - name: "--detection_alpha" + type: double + default: 20.0 + description: Hyperparameter controlling normalisation of within-experiment variation in RNA detection. + - name: "--n_cells_per_location" + type: integer + default: 20 + description: The expected average cell abundance. It is a tissue-dependent hyper-prior which can be estimated from histology images + - name: "--hard_coded_reference" + type: boolean + default: true + description: Whether to use hard-coded reference or negative binomial regression model to account for batch effects. Hard-coded reference used by default. + - name: "--amortised" + type: boolean + default: false + description: Whether to use amortised inference. + - name: "--num_samples" + type: integer + default: 1000 + description: Number of samples to use for summarising posterior distribution. + - name: "--sc_batch_size" + type: integer + default: 2500 + description: Batch size used to train regression model for estimation of reference single-cell gene expression signature. + - name: "--st_batch_size" + type: integer + description: Batch size used to train cell2location model for spatial mapping. + - name: "--max_epochs_sc" + type: integer + default: 250 + description: Maximum number of epochs to train regression model for estimation of reference single-cell gene expression signature. + - name: "--max_epochs_st" + type: integer + default: 30000 + description: Maximum number of epochs to train cell2location model for spatial mapping. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - scvi-tools==1.0.4 + - cell2location + - jax==0.4.23 + - jaxlib==0.4.23 + + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/cell2location/script.py b/src/tasks/spatial_decomposition/methods/cell2location/script.py new file mode 100644 index 0000000000..ea78421bd1 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/cell2location/script.py @@ -0,0 +1,152 @@ +import anndata as ad +import numpy as np +from cell2location.cluster_averages.cluster_averages import compute_cluster_averages +from cell2location.models import Cell2location +from cell2location.models import RegressionModel +from torch.nn import ELU + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'detection_alpha': 20.0, + 'n_cells_per_location': 20, + 'hard_coded_reference': True, + 'amortised': False, + 'num_samples': 1000, + 'sc_batch_size': 2500, + 'st_batch_size': None, + 'max_epochs_sc': 250, + 'max_epochs_st': 5000 +} +meta = { + 'functionality_name': 'cell2location' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +input_single_cell.X = input_single_cell.layers["counts"] +input_spatial.X = input_spatial.layers["counts"] + +if not par["hard_coded_reference"]: + if "batch" in input_single_cell.obs.columns: + input_single_cell.obs["batch_key"] = input_single_cell.obs["batch"].copy() + else: + input_single_cell.obs["batch_key"] = "all" + # REFERENCE SIGNATURE ESTIMATION FROM scRNA + # prepare anndata for the regression model + RegressionModel.setup_anndata( + adata=input_single_cell, + # 10X reaction / sample / batch + batch_key="batch_key", + # cell type, covariate used for constructing signatures + labels_key="cell_type", + ) + sc_model = RegressionModel(input_single_cell) + sc_model.train(max_epochs=par["max_epochs_sc"], batch_size=par["sc_batch_size"]) + # In this section, we export the estimated cell abundance + # (summary of the posterior distribution). + input_single_cell = sc_model.export_posterior( + input_single_cell, + sample_kwargs={"num_samples": par["num_samples"], "batch_size": par["sc_batch_size"]}, + ) + # export estimated expression in each cluster + try: + means_per_cluster = input_single_cell.varm["means_per_cluster_mu_fg"] + except KeyError: + # sometimes varm fails for unknown reason + means_per_cluster = input_single_cell.var + means_per_cluster = means_per_cluster[ + [ + f"means_per_cluster_mu_fg_{i}" + for i in input_single_cell.uns["mod"]["factor_names"] + ] + ].copy() + means_per_cluster.columns = input_single_cell.uns["mod"]["factor_names"] +else: + means_per_cluster = compute_cluster_averages( + input_single_cell, + labels="cell_type", + layer=None, + use_raw=False, + ) + +# SPATIAL MAPPING +# find shared genes and subset both anndata and reference signatures +intersect = np.intersect1d(input_spatial.var_names, means_per_cluster.index) +input_spatial = input_spatial[:, intersect].copy() +means_per_cluster = means_per_cluster.loc[intersect, :].copy() + +# prepare anndata for cell2location model +input_spatial.obs["sample"] = "all" +Cell2location.setup_anndata(adata=input_spatial, batch_key="sample") +cell2location_kwargs = dict( + cell_state_df=means_per_cluster, + # the expected average cell abundance: tissue-dependent hyper-prior which can be estimated from paired histology: + # here = average in the simulated dataset + N_cells_per_location=par["n_cells_per_location"], + # hyperparameter controlling normalisation of within-experiment variation in RNA detection: + detection_alpha=par["detection_alpha"], +) +if par["amortised"]: + cell2location_kwargs["amortised"] = True + cell2location_kwargs["encoder_mode"] = "multiple" + cell2location_kwargs["encoder_kwargs"] = { + "dropout_rate": 0.1, + "n_hidden": { + "single": 256, + "n_s_cells_per_location": 10, + "b_s_groups_per_location": 10, + "z_sr_groups_factors": 64, + "w_sf": 256, + "detection_y_s": 20, + }, + "use_batch_norm": False, + "use_layer_norm": True, + "n_layers": 1, + "activation_fn": ELU, + } +# create and train the model +st_model = Cell2location(input_spatial, **cell2location_kwargs) +st_model.train( + max_epochs=par["max_epochs_st"], + # train using full data (batch_size=None) + batch_size=par["st_batch_size"], + # use all data points in training because we need to estimate cell abundance at all locations + train_size=1, +) +# In this section, we export the estimated cell abundance (summary of the posterior distribution). +input_spatial = st_model.export_posterior( + input_spatial, + sample_kwargs={ + "num_samples": par["num_samples"], + "batch_size": par["st_batch_size"], + }, +) + +input_spatial.obsm["proportions_pred"] = input_spatial.obsm["q05_cell_abundance_w_sf"].values +input_spatial.obsm["proportions_pred"] /= input_spatial.obsm["proportions_pred"].sum(axis=1)[:, None] + +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + }, + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml new file mode 100644 index 0000000000..d4f71dc1cf --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -0,0 +1,42 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: destvi + + info: + label: DestVI + summary: "DestVI is a probabilistic method for multi-resolution analysis for spatial transcriptomics that explicitly models continuous variation within cell types" + description: | + Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI) is a spatial decomposition method that leverages a conditional generative model of spatial transcriptomics down to the sub-cell-type variation level, which is then used to decompose the cell-type proportions determining the spatial organization of a tissue. + preferred_normalization: counts + reference: "lopez2022destvi" + documentation_url: https://docs.scvi-tools.org/en/stable/user_guide/models/destvi.html + repository_url: https://github.com/scverse/scvi-tools + + arguments: + - name: "--max_epochs_sc" + type: integer + default: 500 + description: Number of epochs to train the Conditional version of single-cell Variational Inference (CondSCVI) model using MAP inference. + - name: "--max_epochs_sp" + type: integer + default: 10000 + description: Number of epochs to train the DestVI model using MAP inference. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - scvi-tools + - chex==0.1.85 + + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/destvi/script.py b/src/tasks/spatial_decomposition/methods/destvi/script.py new file mode 100644 index 0000000000..7a3cb82034 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/destvi/script.py @@ -0,0 +1,62 @@ +import anndata as ad +from scvi.model import CondSCVI +from scvi.model import DestVI + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'max_epochs_sc': 500, + 'max_epochs_sp': 5000 +} +meta = { + 'functionality_name': 'destvi' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +input_single_cell.X = input_single_cell.layers["counts"] +input_spatial.X = input_spatial.layers["counts"] + +CondSCVI.setup_anndata(input_single_cell, labels_key="cell_type") +sc_model = CondSCVI(input_single_cell, weight_obs=False) +sc_model.train( + max_epochs=par['max_epochs_sc'], + early_stopping=True, + train_size=0.9, + validation_size=0.1, + early_stopping_monitor="elbo_validation", +) + +DestVI.setup_anndata(input_spatial) +st_model = DestVI.from_rna_model(input_spatial, sc_model) +st_model.train( + max_epochs=par['max_epochs_sp'], + batch_size=min(int(input_spatial.n_obs / 20 + 3), 128), + plan_kwargs={"min_kl_weight": 3.0, "max_kl_weight": 3}, +) +input_spatial.obsm["proportions_pred"] = st_model.get_proportions().to_numpy() + +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml new file mode 100644 index 0000000000..2509287c99 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml @@ -0,0 +1,37 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: nmfreg + info: + label: NMFreg + summary: "NMFreg reconstructs gene expression as a weighted combination of cell type signatures defined by scRNA-seq." + description: | + Non-Negative Matrix Factorization regression (NMFreg) is a decomposition method that reconstructs expression of each spatial location as a weighted combination of cell-type signatures defined by scRNA-seq. It was originally developed for Slide-seq data. This is a re-implementation from https://github.com/tudaga/NMFreg_tutorial. + preferred_normalization: counts + reference: "rodriques2019slide" + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.NMF.html + repository_url: https://github.com/tudaga/NMFreg_tutorial/tree/master?tab=readme-ov-file + + arguments: + - name: "--n_components" + type: integer + default: 30 + description: Number of components to use for non-negative matrix factorization. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - numpy + - scipy + - scikit-learn + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/script.py b/src/tasks/spatial_decomposition/methods/nmfreg/script.py new file mode 100644 index 0000000000..dd3a104d8d --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/nmfreg/script.py @@ -0,0 +1,101 @@ +import anndata as ad +import numpy as np +from scipy.optimize import nnls +from scipy.sparse import issparse +from sklearn.decomposition import NMF +from sklearn.preprocessing import StandardScaler + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'n_components': 30 +} +meta = { + 'functionality_name': 'nmfreg' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +n_types = input_single_cell.obs["cell_type"].cat.categories.shape[0] + +# Learn from reference +if issparse(input_single_cell.layers['counts']): + X = input_single_cell.layers['counts'].toarray() +else: + X = input_single_cell.layers['counts'] +X_norm = X / X.sum(1)[:, np.newaxis] +X_scaled = StandardScaler(with_mean=False).fit_transform(X_norm) + +model = NMF( + n_components=par['n_components'], + init="random", + random_state=42 +) +Ha = model.fit_transform(X_scaled) +Wa = model.components_ + +cluster_df = input_single_cell.obs[["cell_type"]].copy() +cluster_df.loc[:, "factor"] = np.argmax(Ha, axis=1) +cluster_df.loc[:, "code"] = cluster_df.cell_type.values.codes +factor_to_cluster_map = np.array( + [ + np.histogram( + cluster_df.loc[cluster_df.factor == k, "code"], + bins=n_types, + range=(0, n_types), + )[0] + for k in range(par['n_components']) + ] +).T + +factor_to_best_celltype = np.argmax(factor_to_cluster_map, axis=0) + +factor_to_best_celltype_matrix = np.zeros((par['n_components'], n_types)) +for i, j in enumerate(factor_to_best_celltype): + factor_to_best_celltype_matrix[i, j] = 1 + +Ha_norm = StandardScaler(with_mean=False).fit_transform(Ha) +sc_deconv = np.dot(Ha_norm**2, factor_to_best_celltype_matrix) + +sc_deconv = sc_deconv / sc_deconv.sum(1)[:, np.newaxis] + +# Start run on actual spatial data +if issparse(input_spatial.layers['counts']): + X_sp = input_spatial.layers['counts'].toarray() +else: + X_sp = input_spatial.layers['counts'] +X_sp_norm = X_sp / X_sp.sum(1)[:, np.newaxis] +X_sp_scaled = StandardScaler(with_mean=False).fit_transform(X_sp_norm) + +bead_prop_soln = np.array( + [nnls(Wa.T, X_sp_scaled[b, :])[0] for b in range(X_sp_scaled.shape[0])] +) +bead_prop_soln = StandardScaler(with_mean=False).fit_transform(bead_prop_soln) +bead_prop = np.dot(bead_prop_soln, factor_to_best_celltype_matrix) + +prop = bead_prop / bead_prop.sum(1)[:, np.newaxis] +input_spatial.obsm["proportions_pred"] = prop + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + } +) +output.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml new file mode 100644 index 0000000000..07f3e73feb --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml @@ -0,0 +1,30 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: nnls + info: + label: NNLS + summary: "NNLS is a decomposition method based on Non-Negative Least Square Regression." + description: | + NonNegative Least Squares (NNLS), is a convex optimization problem with convex constraints. It was used by the AutoGeneS method to infer cellular proporrtions by solvong a multi-objective optimization problem. + preferred_normalization: counts + reference: "aliee2021autogenes" + documentation_url: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.nnls.html + repository_url: https://github.com/scipy/scipy + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - numpy + - scipy + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/nnls/script.py b/src/tasks/spatial_decomposition/methods/nnls/script.py new file mode 100644 index 0000000000..cbe86c3d51 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/nnls/script.py @@ -0,0 +1,65 @@ +import anndata as ad +import numpy as np +from scipy.optimize import nnls +from scipy.sparse import issparse + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad' +} +meta = { + 'functionality_name': 'nnls' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +# Compute means over each 'cell_type' +labels = input_single_cell.obs['cell_type'].cat.categories +n_var = input_single_cell.shape[1] +means = np.empty((labels.shape[0], n_var)) +for i, lab in enumerate(labels): + adata_lab = input_single_cell[input_single_cell.obs['cell_type'] == lab] + x_lab = adata_lab.layers['counts'] + means[i, :] = x_lab.mean(axis=0).flatten() +adata_means = ad.AnnData(means) +adata_means.obs_names = labels +adata_means.var_names = input_single_cell.var_names + +X = adata_means.X.T +y = input_spatial.layers['counts'].T +if issparse(y): + y = y.toarray() +res = np.zeros((y.shape[1], X.shape[1])) # (voxels, cells) +for i in range(y.shape[1]): + x, _ = nnls(X, y[:, i]) + res[i] = x + +# Normalize coefficients to sum to 1 +res[res < 0] = 0 +res = res / res.sum(axis=1, keepdims=1) + +input_spatial.obsm["proportions_pred"] = res + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml new file mode 100644 index 0000000000..b80c07a308 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -0,0 +1,38 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: rctd + info: + label: RCTD + summary: "RCTD learns cell type profiles from scRNA-seq to decompose cell type mixtures while correcting for differences across sequencing technologies." + description: | + RCTD (Robust Cell Type Decomposition) is a decomposition method that uses signatures learnt from single-cell data to decompose spatial expression of tissues. It is able to use a platform effect normalization step, which normalizes the scRNA-seq cell type profiles to match the platform effects of the spatial transcriptomics dataset. + preferred_normalization: counts + reference: cable2021robust + documentation_url: https://raw.githack.com/dmcable/spacexr/master/vignettes/spatial-transcriptomics.html + repository_url: https://github.com/dmcable/spacexr + + arguments: + - name: "--fc_cutoff" + type: double + default: 0.5 + description: Minimum log-fold-change (across cell types) for genes to be included in the platform effect normalization step. + - name: "--fc_cutoff_reg" + type: double + default: 0.75 + description: Minimum log-fold-change (across cell types) for genes to be included in the RCTD step. + resources: + - type: r_script + path: script.R + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [ Matrix ] + github: [ dmcable/spacexr ] + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/rctd/script.R b/src/tasks/spatial_decomposition/methods/rctd/script.R new file mode 100644 index 0000000000..814c41e874 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/rctd/script.R @@ -0,0 +1,94 @@ +library(anndata) +library(spacexr) +library(Matrix) + +## VIASH START +par <- list( + input_single_cell = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad", + input_spatial = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", + output = "output.h5ad", + fc_cutoff = 0.5, + fc_cutoff_reg = 0.75 +) +meta <- list( + functionality_name = "rctd", + cpus = 1 +) +## VIASH END + +cat("Reading input files\n") +input_single_cell <- anndata::read_h5ad(par$input_single_cell) +input_spatial <- anndata::read_h5ad(par$input_spatial) + +# set spatial coordinates for the single cell data +coordinates <- matrix(1, dim(input_single_cell)[1], 2) +rownames(coordinates) <- rownames(input_single_cell) +input_single_cell$obsm <- list(coordinates = coordinates) + +# remove rare cell types to prevent RCTD error +celltype_counts <- table(input_single_cell$obs$cell_type) +input_single_cell <- input_single_cell[input_single_cell$obs$cell_type %in% names(as.table(celltype_counts[celltype_counts > 25]))] + +# get single cell reference counts +sc_counts <- t(as.matrix(input_single_cell$layers['counts'])) +# get single cell reference labels +sc_cell_types <- factor(input_single_cell$obs$cell_type) +names(sc_cell_types) <- rownames(input_single_cell) +# construct reference object (specific for RCTD) +reference <- Reference(sc_counts, sc_cell_types) + +# get spatial data counts +sp_counts <- t(as.matrix(input_spatial$layers['counts'])) +# get spatial data coordinates +sp_coords <- as.data.frame(input_spatial$obsm['coordinates']) +colnames(sp_coords) <- c("x", "y") +rownames(sp_coords) <- rownames(input_spatial) +# create spatial object to use in RCTD +puck <- SpatialRNA(sp_coords, sp_counts) + +# create RCTD object from reference and spatialRNA objects +if (!is.null(meta$cpus)) { +max_cores <- meta$cpus +} else { +max_cores <- 1 +} +rctd <- create.RCTD( + puck, + reference, + max_cores = max_cores, + fc_cutoff = par$fc_cutoff, + fc_cutoff_reg = par$fc_cutoff_reg, + test_mode = FALSE, + UMI_min_sigma = 100, + CELL_MIN_INSTANCE = 1 +) + +# run analysis and get results +rctd <- run.RCTD(rctd) +results <- rctd@results +cell_type_names <- rctd@cell_type_info$info[[2]] + +# extract proportions and normalize them (to sum to one) +norm_weights <- sweep(results$weights, 1, rowSums(results$weights), "/") +norm_weights <- as.matrix(norm_weights) +coordinates <- as.matrix(sp_coords) + +cat("Write output AnnData to file\n") +output <- anndata::AnnData( + shape = input_spatial$shape, + obs = input_spatial$obs, + var = input_spatial$var, + uns = list( + cell_type_names = input_spatial$uns['cell_type_names'], + dataset_id = input_spatial$uns[["dataset_id"]], + method_id = meta[["functionality_name"]] + ), + obsm = list( + coordinates = coordinates, + proportions_pred = norm_weights + ), + layers = list( + counts = input_spatial$layers['counts'] + ) +) +output$write_h5ad(par[["output"]], compression = "gzip") diff --git a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml new file mode 100644 index 0000000000..fb947b634e --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml @@ -0,0 +1,39 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: seurat + info: + label: Seurat + summary: "Seurat method that is based on Canonical Correlation Analysis (CCA)." + description: | + This method applies the 'anchor'-based integration workflow introduced in Seurat v3, that enables the probabilistic transfer of annotations from a reference to a query set. First, mutual nearest neighbors (anchors) are identified from the reference scRNA-seq and query spatial datasets. Then, annotations are transfered from the single cell reference data to the sptial data along with prediction scores for each spot. + preferred_normalization: counts + reference: stuart2019comprehensive + documentation_url: https://satijalab.org/seurat/articles/spatial_vignette + repository_url: https://github.com/satijalab/seurat + + arguments: + - name: "--n_pcs" + type: integer + default: 30 + description: Number of principal components. + - name: "--sctransform_n_cells" + type: integer + default: 5000 + description: Number of cells sampled to build NB regression. + + resources: + - type: r_script + path: script.R + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.2 + setup: + - type: r + cran: [Matrix, Seurat] + + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/seurat/script.R b/src/tasks/spatial_decomposition/methods/seurat/script.R new file mode 100644 index 0000000000..df4ee0565f --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/seurat/script.R @@ -0,0 +1,97 @@ +library(anndata) +library(Seurat) + +## VIASH START +par <- list( + input_single_cell = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad", + input_spatial = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", + output = "output.h5ad", + n_pcs = 30, + sctransform_n_cells = 500 +) +meta <- list( + functionality_name = "seurat" +) +## VIASH END + +cat("Reading input files\n") +input_single_cell <- anndata::read_h5ad(par$input_single_cell) +input_spatial <- anndata::read_h5ad(par$input_spatial) + +cat(">> Converting AnnData to Seurat\n") +anndataToSeurat <- function(adata, assay) { + obj <- SeuratObject::CreateSeuratObject(counts = as(Matrix::t(adata$layers[["counts"]]), "CsparseMatrix"), assay = assay) + obj <- SeuratObject::AddMetaData(object = obj, metadata = adata$obs) + obj +} + +seurat_sc <- anndataToSeurat(input_single_cell, "RNA") +seurat_sp <- anndataToSeurat(input_spatial, "spatial") + +cat(">> Generate predictions\n") + +# Normalize and do dimred for spatial data +seurat_sp <- SCTransform( + seurat_sp, + assay = "spatial", + ncells = min(par$sctransform_n_cells, nrow(seurat_sp)), + verbose = TRUE +) + +seurat_sp <- RunPCA(seurat_sp, assay = "SCT", verbose = FALSE, n_pcs = par$n_pcs) + +# Normalize and do dimred for single cell data +seurat_sc <- SCTransform( + seurat_sc, + assay = "RNA", + ncells = min(par$sctransform_n_cells, nrow(seurat_sc)), + verbose = TRUE +) + +seurat_sc <- RunPCA(seurat_sc, verbose = FALSE, n_pcs = par$n_pcs) + +# find anchors (MNN's to compute adjustmen vectors) +anchors <- FindTransferAnchors( + reference = seurat_sc, + query = seurat_sp, + normalization.method = "SCT" +) + +# transfer labels from single cell data to spatial +predictions_assay <- TransferData( + anchorset = anchors, + refdata = as.factor(as.character(seurat_sc@meta.data$cell_type)), + prediction.assay = TRUE, + weight.reduction = seurat_sp[["pca"]], + dims = 1:par$n_pcs +) + +# format data and return results +predictions <- LayerData(predictions_assay, layer = "data") +predictions <- predictions[!(rownames(predictions) == "max"), ] +predictions <- t(predictions) + +sp_coords <- as.data.frame(input_spatial$obsm['coordinates']) +colnames(sp_coords) <- c("x", "y") +rownames(sp_coords) <- rownames(input_spatial) +sp_coords <- as.matrix(sp_coords) + +cat("Write output AnnData to file\n") +output <- anndata::AnnData( + shape = input_spatial$shape, + obs = input_spatial$obs, + var = input_spatial$var, + uns = list( + cell_type_names = input_spatial$uns['cell_type_names'], + dataset_id = input_spatial$uns[["dataset_id"]], + method_id = meta[["functionality_name"]] + ), + obsm = list( + coordinates = sp_coords, + proportions_pred = predictions + ), + layers = list( + counts = input_spatial$layers['counts'] + ) +) +output$write_h5ad(par[["output"]], compression = "gzip") diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml new file mode 100644 index 0000000000..655e644311 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -0,0 +1,40 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: stereoscope + + info: + label: Stereoscope + summary: "Stereoscope is a decomposition method based on Negative Binomial regression." + description: | + Stereoscope is a decomposition method based on Negative Binomial regression. It is similar in scope and implementation to cell2location but less flexible to incorporate additional covariates such as batch effects and other type of experimental design annotations. + preferred_normalization: counts + reference: andersson2020single + documentation_url: https://docs.scvi-tools.org/en/stable/user_guide/models/stereoscope.html + repository_url: https://github.com/scverse/scvi-tools + + arguments: + - name: "--max_epochs_sc" + type: integer + default: 100 + description: Number of of epochs to train RNAStereoscope model. + - name: "--max_epochs_sp" + type: integer + default: 1000 + description: Number of of epochs to train SpatialStereoscope model. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - scvi-tools + - type: native + - type: nextflow + directives: + label: [ "midtime", midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/script.py b/src/tasks/spatial_decomposition/methods/stereoscope/script.py new file mode 100644 index 0000000000..7965312e98 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/stereoscope/script.py @@ -0,0 +1,61 @@ +import anndata as ad +from scvi.external import RNAStereoscope +from scvi.external import SpatialStereoscope + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'max_epochs_sc': 100, + 'max_epochs_sp': 1000 +} +meta = { + 'functionality_name': 'stereoscope' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +input_single_cell.X = input_single_cell.layers["counts"] +input_spatial.X = input_spatial.layers["counts"] + +print('Generate predictions', flush=True) + +RNAStereoscope.setup_anndata(input_single_cell, labels_key="cell_type") +sc_model = RNAStereoscope(input_single_cell) +sc_model.train( + max_epochs=par["max_epochs_sc"], + # early_stopping=True, + # early_stopping_monitor="elbo_train" +) + +SpatialStereoscope.setup_anndata(input_spatial) +st_model = SpatialStereoscope.from_rna_model(input_spatial, sc_model) +st_model.train( + max_epochs=par["max_epochs_sp"], + # early_stopping=True, + # early_stopping_monitor="elbo_train" +) +input_spatial.obsm["proportions_pred"] = st_model.get_proportions().to_numpy() + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + }, + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml new file mode 100644 index 0000000000..a67596a8f4 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml @@ -0,0 +1,38 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: tangram + info: + label: Tangram + summary: "Tanagram maps single-cell gene expression data onto spatial gene expression data by fitting gene expression on shared genes" + description: | + Tangram is a method to map gene expression signatures from scRNA-seq data to spatial data. It performs the cell type mapping by learning a similarity matrix between single-cell and spatial locations based on gene expression profiles. + preferred_normalization: counts + reference: biancalani2021deep + documentation_url: https://tangram-sc.readthedocs.io/en/latest/index.html + repository_url: https://github.com/broadinstitute/Tangram + + arguments: + - name: "--num_epochs" + type: integer + default: 1000 + description: Number of epochs to use while mapping single cells to spatial locations. + - name: "--n_markers" + type: integer + default: 100 + description: Number of marker genes to use. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: tangram-sc + - type: native + - type: nextflow + directives: + label: [ "midtime",midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/tangram/script.py b/src/tasks/spatial_decomposition/methods/tangram/script.py new file mode 100644 index 0000000000..b24bc22b5f --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/tangram/script.py @@ -0,0 +1,84 @@ +import anndata as ad +import pandas as pd +import scanpy as sc +import tangram as tg +import torch + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'num_epochs': 1000, + 'n_markers': 100 +} +meta = { + 'functionality_name': 'tangram' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +print('Generate predictions', flush=True) +# analysis based on github.com/broadinstitute/Tangram/blob/master/tutorial_tangram_with_squidpy.ipynb +# using tangram from PyPi, not github version + +input_single_cell.X = input_single_cell.layers["counts"] +input_spatial.X = input_spatial.layers["counts"] + +# pre-process single cell data +sc.pp.normalize_total(input_single_cell, 1e4) +sc.pp.log1p(input_single_cell) +# identify marker genes +sc.tl.rank_genes_groups(input_single_cell, groupby="cell_type", use_raw=False) + +# extract marker genes to data frame +markers_df = pd.DataFrame(input_single_cell.uns["rank_genes_groups"]["names"]).iloc[0:par['n_markers'], :] + +# get union of all marker genes +markers = list(set(markers_df.melt().value.values)) + +# match genes between single cell and spatial data +tg.pp_adatas(input_single_cell, input_spatial, genes=markers) + +# get device +device = torch.device("cuda" if torch.cuda.is_available() else "cpu") + +# map single cells to spatial locations +ad_map = tg.map_cells_to_space( + input_single_cell, + input_spatial, + device=device, + num_epochs=par['num_epochs'], +) + +# transfer labels from mapped cells to spatial location +tg.project_cell_annotations(adata_map=ad_map, adata_sp=input_spatial, annotation="cell_type") + +# normalize scores +pred_props = input_spatial.obsm["tangram_ct_pred"].to_numpy() +input_spatial.obsm["proportions_pred"] = pred_props / pred_props.sum(axis=1)[:, None] + +# remove un-normalized predictions +del input_spatial.obsm["tangram_ct_pred"] + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + }, + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml new file mode 100644 index 0000000000..7bfd68e5b8 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml @@ -0,0 +1,37 @@ +__merge__: ../../api/comp_method.yaml + +functionality: + name: vanillanmf + info: + label: NMF + summary: "NMF reconstructs gene expression as a weighted combination of cell type signatures defined by scRNA-seq." + description: | + NMF is a decomposition method based on Non-negative Matrix Factorization (NMF) that reconstructs expression of each spatial location as a weighted combination of cell-type signatures defined by scRNA-seq. It is a simpler baseline than NMFreg as it only performs the NMF step based on mean expression signatures of cell types, returning the weights loading of the NMF as (normalized) cell type proportions, without the regression step. + preferred_normalization: counts + reference: cichocki2009fast + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.NMF.html + repository_url: https://github.com/scikit-learn/scikit-learn/blob/92c9b1866/sklearn/decomposition/ + + arguments: + - name: "--max_iter" + type: integer + default: 4000 + description: Maximum number of iterations before timing out. + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - numpy + - scipy + - scikit-learn + - type: native + - type: nextflow + directives: + label: [ "midtime",midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/script.py b/src/tasks/spatial_decomposition/methods/vanillanmf/script.py new file mode 100644 index 0000000000..9ca1302b55 --- /dev/null +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/script.py @@ -0,0 +1,77 @@ +import anndata as ad +import numpy as np +from scipy.sparse import issparse +from sklearn.decomposition import NMF + +## VIASH START +par = { + 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', + 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'output': 'output.h5ad', + 'max_iter': 4000 +} +meta = { + 'functionality_name': 'vanillanmf' +} +## VIASH END + +print('Reading input files', flush=True) +input_single_cell = ad.read_h5ad(par['input_single_cell']) +input_spatial = ad.read_h5ad(par['input_spatial_masked']) + +print('Generate predictions', flush=True) + +n_types = input_single_cell.obs["cell_type"].cat.categories.shape[0] +vanila_nmf_model = NMF( + n_components=n_types, + beta_loss="kullback-leibler", + solver="mu", + max_iter=par['max_iter'], + alpha_W=0.1, + alpha_H=0.1, + init="custom", + random_state=42, +) + +# Make profiles from single-cell expression dataset +# Compute means over each 'cell_type' +labels = input_single_cell.obs['cell_type'].cat.categories +n_var = input_single_cell.shape[1] +means = np.empty((labels.shape[0], n_var)) +for i, lab in enumerate(labels): + adata_lab = input_single_cell[input_single_cell.obs['cell_type'] == lab] + x_lab = adata_lab.layers['counts'] + means[i, :] = x_lab.mean(axis=0).flatten() +adata_means = ad.AnnData(means) +adata_means.obs_names = labels +adata_means.var_names = input_single_cell.var_names + +X = input_spatial.layers['counts'].toarray() + +Wa = vanila_nmf_model.fit_transform( + X.astype(adata_means.X.dtype), + H=adata_means.X, + W=np.ones((input_spatial.shape[0], n_types), dtype=adata_means.X.dtype), +) + +prop = Wa / Wa.sum(1)[:, np.newaxis] +input_spatial.obsm["proportions_pred"] = prop + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + obs=input_spatial.obs[[]], + var=input_spatial.var[[]], + uns={ + 'cell_type_names': input_spatial.uns['cell_type_names'], + 'dataset_id': input_spatial.uns['dataset_id'], + 'method_id': meta['functionality_name'] + }, + obsm={ + 'coordinates': input_spatial.obsm['coordinates'], + 'proportions_pred': input_spatial.obsm['proportions_pred'] + }, + layers={ + 'counts': input_spatial.layers['counts'] + } +) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml new file mode 100644 index 0000000000..06a3c62db3 --- /dev/null +++ b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml @@ -0,0 +1,32 @@ +__merge__: ../../api/comp_metric.yaml + +functionality: + name: r2 + info: + metrics: + - name: r2 + label: R2 + summary: "R2 represents the proportion of variance in the true proportions which is explained by the predicted proportions." + description: | + R2, or the “coefficient of determination”, reports the fraction of the true proportion values' variance that can be explained by the predicted proportion values. The best score, and upper bound, is 1.0. There is no fixed lower bound for the metric. The uniform/non-weighted average across all cell types/states is used to summarise performance. By default, cases resulting in a score of NaN (perfect predictions) or -Inf (imperfect predictions) are replaced with 1.0 (perfect predictions) or 0.0 (imperfect predictions) respectively. + reference: miles2005rsquared + documentation_url: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.r2_score.html + repository_url: https://github.com/scikit-learn/scikit-learn/tree/5c4aa5d0d90ba66247d675d4c3fc2fdfba3c39ff + min: -inf + max: 1 + maximize: true + + resources: + - type: python_script + path: script.py + +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: scikit-learn + - type: native + - type: nextflow + directives: + label: [ "midtime",midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/metrics/r2/script.py b/src/tasks/spatial_decomposition/metrics/r2/script.py new file mode 100644 index 0000000000..35420e021c --- /dev/null +++ b/src/tasks/spatial_decomposition/metrics/r2/script.py @@ -0,0 +1,39 @@ +import anndata as ad +import sklearn.metrics + +## VIASH START +par = { + 'input_method': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/output.h5ad', + 'input_solution': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/solution.h5ad', + 'output': 'score.h5ad' +} +meta = { + 'functionality_name': 'r2' +} +## VIASH END + +print('Reading input files', flush=True) +input_method = ad.read_h5ad(par['input_method']) +input_solution = ad.read_h5ad(par['input_solution']) + +print('Compute metrics', flush=True) +prop_true = input_solution.obsm["proportions_true"] +prop_pred = input_method.obsm["proportions_pred"] +r2_score = sklearn.metrics.r2_score( + prop_true, prop_pred, sample_weight=None, multioutput="uniform_average" +) + +uns_metric_ids = [ 'r2' ] +uns_metric_values = [ r2_score ] + +print("Write output AnnData to file", flush=True) +output = ad.AnnData( + uns={ + 'dataset_id': input_method.uns['dataset_id'], + 'method_id': input_method.uns['method_id'], + 'metric_ids': uns_metric_ids, + 'metric_values': uns_metric_values + } +) +output.write_h5ad(par['output'], compression='gzip') + diff --git a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml new file mode 100644 index 0000000000..83f10077c8 --- /dev/null +++ b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml @@ -0,0 +1,13 @@ +__merge__: ../api/comp_process_dataset.yaml +functionality: + name: "process_dataset" + resources: + - type: python_script + path: script.py + - path: /src/common/helper_functions/subset_anndata.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + - type: nextflow + directives: + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/spatial_decomposition/process_dataset/script.py b/src/tasks/spatial_decomposition/process_dataset/script.py new file mode 100644 index 0000000000..d944a99d42 --- /dev/null +++ b/src/tasks/spatial_decomposition/process_dataset/script.py @@ -0,0 +1,42 @@ +import anndata as ad +import sys + +## VIASH START +par = { + "input": "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/dataset_simulated.h5ad", + "output_spatial_masked": "spatial_masked.h5ad", + "output_single_cell": "single_cell_ref.h5ad", + "output_solution": "solution.h5ad", +} +meta = { + "functionality_name": "process_dataset", + "resources_dir": "src/tasks/spatial_decomposition/process_dataset", + "config": "target/nextflow/spatial_decomposition/process_dataset/.config.vsh.yaml" +} +## VIASH END + +sys.path.append(meta['resources_dir']) +from subset_anndata import read_config_slots_info, subset_anndata + +print(">> Load dataset", flush=True) +adata = ad.read_h5ad(par["input"]) + +print(">> Figuring out which data needs to be copied to which output file", flush=True) +slot_info = read_config_slots_info(meta["config"]) + +print(">> Split dataset by modality", flush=True) +is_sp = adata.obs["modality"] == "sp" +adata_sp = adata[is_sp, :].copy() +adata_sc = adata[~is_sp, :].copy() + +print(">> Create dataset for methods", flush=True) +output_spatial_masked = subset_anndata(adata_sp, slot_info['output_spatial_masked']) +output_single_cell = subset_anndata(adata_sc, slot_info['output_single_cell']) + +print(">> Create solution object for metrics", flush=True) +output_solution = subset_anndata(adata_sp, slot_info['output_solution']) + +print(">> Write to disk", flush=True) +output_spatial_masked.write_h5ad(par["output_spatial_masked"]) +output_single_cell.write_h5ad(par["output_single_cell"]) +output_solution.write_h5ad(par["output_solution"]) diff --git a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh b/src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh new file mode 100755 index 0000000000..fcbdaed3e0 --- /dev/null +++ b/src/tasks/spatial_decomposition/resources_test_scripts/cxg_mouse_pancreas_atlas.sh @@ -0,0 +1,39 @@ +#!/bin/bash + +# make sure the following command has been executed +# viash ns build -q 'spatial_decomposition|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common +DATASET_DIR=resources_test/spatial_decomposition + +mkdir -p $DATASET_DIR + +echo "Running process_dataset" +nextflow run . \ + -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$RAW_DATA/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad", "alpha": 1.0, "simulated_data": "$id/dataset_simulated.h5ad"}' \ + --publish_dir "$DATASET_DIR" \ + --output_state '$id/state.yaml' + +# run one method +viash run src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml -- \ + --input_single_cell $DATASET_DIR/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad \ + --input_spatial_masked $DATASET_DIR/cxg_mouse_pancreas_atlas/spatial_masked.h5ad \ + --output $DATASET_DIR/cxg_mouse_pancreas_atlas/output.h5ad + +# run one metric +viash run src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml -- \ + --input_method $DATASET_DIR/cxg_mouse_pancreas_atlas/output.h5ad \ + --input_solution $DATASET_DIR/cxg_mouse_pancreas_atlas/solution.h5ad \ + --output $DATASET_DIR/cxg_mouse_pancreas_atlas/score.h5ad diff --git a/src/tasks/spatial_decomposition/resources_test_scripts/pancreas.sh b/src/tasks/spatial_decomposition/resources_test_scripts/pancreas.sh new file mode 100755 index 0000000000..e4be381201 --- /dev/null +++ b/src/tasks/spatial_decomposition/resources_test_scripts/pancreas.sh @@ -0,0 +1,43 @@ +#!/bin/bash + +# make sure the following command has been executed +# viash ns build -q 'spatial_decomposition|common' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +RAW_DATA=resources_test/common/pancreas/dataset.h5ad +DATASET_DIR=resources_test/spatial_decomposition/pancreas + +if [ ! -f $RAW_DATA ]; then + echo "Error! Could not find raw data" + exit 1 +fi + +mkdir -p $DATASET_DIR + +# generate synthetic spatial data +SYNTHETIC_DATA=$DATASET_DIR/dataset_synthetic.h5ad +python3 src/tasks/spatial_decomposition/datasets/sample_datasets.py $RAW_DATA $SYNTHETIC_DATA + +# process dataset +viash run src/tasks/spatial_decomposition/process_dataset/config.vsh.yml -- \ + --input $SYNTHETIC_DATA \ + --output_spatial_masked $DATASET_DIR/spatial_masked.h5ad \ + --output_single_cell $DATASET_DIR/single_cell_ref.h5ad \ + --output_solution $DATASET_DIR/solution.h5ad + +# process dataset +# echo Running process_dataset +# nextflow run . \ +# -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ +# -profile docker \ +# -entry auto \ +# --input_states "$RAW_DATA/**/state.yaml" \ +# --rename_keys 'input:output_dataset' \ +# --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad"}' \ +# --publish_dir "$DATASET_DIR" \ +# --output_state '$id/state.yaml' \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/workflows/process_datasets/config.vsh.yaml b/src/tasks/spatial_decomposition/workflows/process_datasets/config.vsh.yaml new file mode 100644 index 0000000000..e99fd6787d --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/process_datasets/config.vsh.yaml @@ -0,0 +1,43 @@ +functionality: + name: "process_datasets" + namespace: "spatial_decomposition/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input" + __merge__: "/src/tasks/spatial_decomposition/api/file_common_dataset.yaml" + required: true + direction: input + - name: "--alpha" + type: double + required: false + direction: input + - name: Outputs + arguments: + - name: "--output_single_cell" + __merge__: /src/tasks/spatial_decomposition/api/file_single_cell.yaml + required: true + direction: output + - name: "--output_spatial_masked" + __merge__: /src/tasks/spatial_decomposition/api/file_spatial_masked.yaml + required: true + direction: output + - name: "--output_solution" + __merge__: /src/tasks/spatial_decomposition/api/file_solution.yaml + required: true + direction: output + - name: "--simulated_data" + type: file + required: false + direction: output + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + - path: /src/wf_utils/helper.nf + dependencies: + - name: common/check_dataset_schema + - name: spatial_decomposition/dataset_simulator + - name: spatial_decomposition/process_dataset +platforms: + - type: nextflow diff --git a/src/tasks/spatial_decomposition/workflows/process_datasets/main.nf b/src/tasks/spatial_decomposition/workflows/process_datasets/main.nf new file mode 100644 index 0000000000..4d53e5751e --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/process_datasets/main.nf @@ -0,0 +1,65 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + output_ch = input_ch + + | check_dataset_schema.run( + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "input") + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) + [ + "input": state.input, + "schema": schemaYaml + ] + }, + toState: { id, output, state -> + // read the output to see if dataset passed the qc + def checks = readYaml(output.output) + state + [ + "dataset": checks["exit_code"] == 0 ? state.input : null, + ] + } + ) + + // remove datasets which didn't pass the schema check + | filter { id, state -> + state.dataset != null + } + + | dataset_simulator.run( + runIf: {id, state -> state.alpha}, + fromState: [ + input: "dataset", + alpha: "alpha" + ], + toState: [ dataset: "simulated_data"], + auto: [publish: true] + ) + + | process_dataset.run( + fromState: [ input: "dataset" ], + toState: [ + output_single_cell: "output_single_cell", + output_spatial_masked: "output_spatial_masked", + output_solution: "output_solution" + ] + ) + + // only output the files for which an output file was specified + | setState(["output_single_cell", "output_spatial_masked", "output_solution"]) + + emit: + output_ch +} diff --git a/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh b/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh new file mode 100644 index 0000000000..e3a6bee7af --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh @@ -0,0 +1,34 @@ +#!/bin/bash + +# Run this prior to executing this script: +# bin/viash_build -q 'spatial_decomposition' + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +# nextflow run . \ +# -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ +# -profile docker \ +# -entry auto \ +# -c src/wf_utils/labels_ci.config \ +# --id run_test \ +# --input_states "resources_test/common/**/state.yaml" \ +# --rename_keys 'input:output_dataset' \ +# --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad"}' \ +# --publish_dir "resources_test/spatial_decomposition" + +# generate spatial dataset +nextflow run . \ + -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ + -profile docker \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "resources_test/common/**/state.yaml" \ + --rename_keys 'input:output_dataset' \ + --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad", "generate_dataset": true, "alpha": 1.0, "simulated_data": "$id/dataset_simulated.h5ad"}' \ + --publish_dir "resources_test/spatial_decomposition" \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml b/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml new file mode 100644 index 0000000000..ad2ab676b1 --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml @@ -0,0 +1,68 @@ +functionality: + name: "run_benchmark" + namespace: "spatial_decomposition/workflows" + argument_groups: + - name: Inputs + arguments: + - name: "--input_single_cell" + __merge__: "/src/tasks/spatial_decomposition/api/file_single_cell.yaml" + required: true + direction: input + - name: "--input_spatial_masked" + __merge__: "/src/tasks/spatial_decomposition/api/file_spatial_masked.yaml" + required: true + direction: input + - name: "--input_solution" + __merge__: "/src/tasks/spatial_decomposition/api/file_solution.yaml" + required: true + direction: input + - name: Outputs + arguments: + - name: "--output_scores" + type: file + required: true + direction: output + description: A yaml file containing the scores of each of the methods + default: score_uns.yaml + - name: "--output_method_configs" + type: file + required: true + direction: output + default: method_configs.yaml + - name: "--output_metric_configs" + type: file + required: true + direction: output + default: metric_configs.yaml + - name: "--output_dataset_info" + type: file + required: true + direction: output + default: dataset_uns.yaml + - name: "--output_task_info" + type: file + required: true + direction: output + default: task_info.yaml + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + - type: file + path: "../../api/task_info.yaml" + dependencies: + - name: common/check_dataset_schema + - name: common/extract_metadata + - name: spatial_decomposition/control_methods/random_proportions + - name: spatial_decomposition/control_methods/true_proportions + - name: spatial_decomposition/methods/cell2location + - name: spatial_decomposition/methods/destvi + - name: spatial_decomposition/methods/nmfreg + - name: spatial_decomposition/methods/rctd + - name: spatial_decomposition/methods/seurat + - name: spatial_decomposition/methods/stereoscope + - name: spatial_decomposition/methods/tangram + - name: spatial_decomposition/methods/vanillanmf + - name: spatial_decomposition/metrics/r2 +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf new file mode 100644 index 0000000000..509a13f0de --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf @@ -0,0 +1,185 @@ +workflow auto { + findStates(params, meta.config) + | meta.workflow.run( + auto: [publish: "state"] + ) +} + +workflow run_wf { + take: + input_ch + + main: + + // construct list of methods + methods = [ + random_proportions, + true_proportions, + cell2location, + destvi, + nmfreg, + rctd, + seurat, + stereoscope, + tangram, + vanillanmf + ] + + // construct list of metrics + metrics = [ + r2 + ] + + + /**************************** + * EXTRACT DATASET METADATA * + ****************************/ + dataset_ch = input_ch + // store join id + | map{ id, state -> + [id, state + ["_meta": [join_id: id]]] + } + + // extract the dataset metadata + | extract_metadata.run( + fromState: [input: "input_solution"], + toState: { id, output, state -> + state + [ + dataset_uns: readYaml(output.output).uns + ] + } + ) + + /*************************** + * RUN METHODS AND METRICS * + ***************************/ + score_ch = dataset_ch + + // run all methods + | runEach( + components: methods, + + // define a new 'id' by appending the method name to the dataset id + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, + + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, comp -> + def new_args = [ + input_single_cell: state.input_single_cell, + input_spatial_masked: state.input_spatial_masked + ] + if (comp.config.functionality.info.type == "control_method") { + new_args.input_solution = state.input_solution + } + new_args + }, + + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, state, comp -> + state + [ + method_id: comp.config.functionality.name, + method_output: output.output + ] + } + ) + + // run all metrics + | runEach( + components: metrics, + id: { id, state, comp -> + id + "." + comp.config.functionality.name + }, + // use 'fromState' to fetch the arguments the component requires from the overall state + fromState: { id, state, comp -> + [ + input_solution: state.input_solution, + input_method: state.method_output + ] + }, + // use 'toState' to publish that component's outputs to the overall state + toState: { id, output, state, comp -> + state + [ + metric_id: comp.config.functionality.name, + metric_output: output.output + ] + } + ) + + /****************************** + * GENERATE OUTPUT YAML FILES * + ******************************/ + // TODO: can we store everything below in a separate helper function? + + // extract the dataset metadata + dataset_meta_ch = dataset_ch + | joinStates { ids, states -> + // store the dataset metadata in a file + def dataset_uns = states.collect{state -> + def uns = state.dataset_uns.clone() + uns.remove("normalization_id") + uns + } + def dataset_uns_yaml_blob = toYamlBlob(dataset_uns) + def dataset_uns_file = tempFile("dataset_uns.yaml") + dataset_uns_file.write(dataset_uns_yaml_blob) + + ["output", [output_dataset_info: dataset_uns_file]] + } + + output_ch = score_ch + + // extract the scores + | extract_metadata.run( + key: "extract_scores", + fromState: [input: "metric_output"], + toState: { id, output, state -> + state + [ + score_uns: readYaml(output.output).uns + ] + } + ) + + | joinStates { ids, states -> + // store the method configs in a file + def method_configs = methods.collect{it.config} + def method_configs_yaml_blob = toYamlBlob(method_configs) + def method_configs_file = tempFile("method_configs.yaml") + method_configs_file.write(method_configs_yaml_blob) + + // store the metric configs in a file + def metric_configs = metrics.collect{it.config} + def metric_configs_yaml_blob = toYamlBlob(metric_configs) + def metric_configs_file = tempFile("metric_configs.yaml") + metric_configs_file.write(metric_configs_yaml_blob) + + def task_info_file = meta.resources_dir.resolve("task_info.yaml") + + // store the scores in a file + def score_uns = states.collect{it.score_uns} + def score_uns_yaml_blob = toYamlBlob(score_uns) + def score_uns_file = tempFile("score_uns.yaml") + score_uns_file.write(score_uns_yaml_blob) + + def new_state = [ + output_method_configs: method_configs_file, + output_metric_configs: metric_configs_file, + output_task_info: task_info_file, + output_scores: score_uns_file, + _meta: states[0]._meta + ] + + ["output", new_state] + } + + // merge all of the output data + | mix(dataset_meta_ch) + | joinStates{ ids, states -> + def mergedStates = states.inject([:]) { acc, m -> acc + m } + [ids[0], mergedStates] + } + + emit: + output_ch +} diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/run_test.sh b/src/tasks/spatial_decomposition/workflows/run_benchmark/run_test.sh new file mode 100755 index 0000000000..c48824bae5 --- /dev/null +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/run_test.sh @@ -0,0 +1,28 @@ +#!/bin/bash + +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +DATASETS_DIR="resources_test/spatial_decomposition" +OUTPUT_DIR="output/temp" + +if [ ! -d "$OUTPUT_DIR" ]; then + mkdir -p "$OUTPUT_DIR" +fi + +nextflow run . \ + -main-script target/nextflow/spatial_decomposition/workflows/run_benchmark/main.nf \ + -profile docker \ + -resume \ + -entry auto \ + -c src/wf_utils/labels_ci.config \ + --input_states "$DATASETS_DIR/**/state.yaml" \ + --rename_keys 'input_single_cell:output_single_cell,input_spatial_masked:output_spatial_masked,input_solution:output_solution' \ + --settings '{"output_scores": "scores.yaml", "output_dataset_info": "dataset_info.yaml", "output_method_configs": "method_configs.yaml", "output_metric_configs": "metric_configs.yaml", "output_task_info": "task_info.yaml"}' \ + --publish_dir "$OUTPUT_DIR" \ + --output_state "state.yaml" \ No newline at end of file From 12c37aaadced18100b2cdfaa30b714786b4083b1 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 21 Mar 2024 13:39:04 +0100 Subject: [PATCH 1185/1233] refactor knn metric according to v1 (#413) * refactor knn metric according to v1 * undo changes to viash block Former-commit-id: c759c9b8a94e63bee15f25ce11f5185bfa29c939 --- src/tasks/match_modalities/metrics/knn_auc/script.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/match_modalities/metrics/knn_auc/script.py b/src/tasks/match_modalities/metrics/knn_auc/script.py index 0af2c08566..cf5c14b473 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/script.py +++ b/src/tasks/match_modalities/metrics/knn_auc/script.py @@ -31,7 +31,7 @@ _, indices_true = ( sklearn.neighbors.NearestNeighbors(n_neighbors=n_neighbors) .fit(input_solution_mod1.obsm["X_svd"]) - .kneighbors(input_solution_mod2.obsm["X_svd"]) + .kneighbors(input_solution_mod1.obsm["X_svd"]) ) _, indices_pred = ( From a3047aa6040b03c1ef83bfb10fe6421c31c157d2 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 25 Mar 2024 11:52:06 +0100 Subject: [PATCH 1186/1233] Remove reticulate custom setup (#414) * Update setup * remove bit64 setup Former-commit-id: e76e11b98aa79d2c6780c36c76b9040a94c53111 --- src/common/create_task_readme/config.vsh.yaml | 4 ++-- src/datasets/normalization/log_scran_pooling/config.vsh.yaml | 2 +- src/tasks/denoising/methods/alra/config.vsh.yaml | 2 +- src/tasks/denoising/methods/saver/config.vsh.yaml | 1 - .../metrics/coranking/config.vsh.yaml | 2 +- .../methods/seurat_transferdata/config.vsh.yaml | 4 ++-- src/tasks/predict_modality/process_dataset/config.vsh.yaml | 5 ----- 7 files changed, 7 insertions(+), 13 deletions(-) diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index 683c800403..fba4f3a4d4 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -36,7 +36,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, bit64, processx] + packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, processx] - type: apt packages: [jq, curl] - type: docker @@ -50,5 +50,5 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [ midtime, lowmem, lowcpu ] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 1fd4e5cbab..87fd346fe5 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -10,7 +10,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ Matrix, rlang, bit64, scran, BiocParallel ] + cran: [ Matrix, rlang, scran, BiocParallel ] - type: python pip: scanpy - type: nextflow diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index acf412233c..76eda37a29 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -36,7 +36,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ Matrix, bit64, rsvd ] + cran: [ Matrix, rsvd ] github: KlugerLab/ALRA - type: nextflow directives: diff --git a/src/tasks/denoising/methods/saver/config.vsh.yaml b/src/tasks/denoising/methods/saver/config.vsh.yaml index b2fcc00b7a..af7fcadfc4 100644 --- a/src/tasks/denoising/methods/saver/config.vsh.yaml +++ b/src/tasks/denoising/methods/saver/config.vsh.yaml @@ -26,7 +26,6 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - # cran: [ bit64 ] github: mohuangx/SAVER - type: nextflow directives: diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 9852e9a739..526432a99f 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -160,7 +160,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ coRanking, bit64 ] + cran: [ coRanking ] - type: nextflow directives: label: [ midtime, highmem, midcpu ] diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 8c81554e21..78a8e140fd 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -30,7 +30,7 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: - type: r - cran: [ Matrix>=1.5.3, Seurat, rlang, bit64 ] + cran: [ Matrix>=1.5.3, Seurat, rlang ] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [ midtime, highmem, highcpu ] diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index b303c7e50f..b95c2f8308 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -16,11 +16,6 @@ functionality: platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 - setup: - - type: r - cran: [ bit64 ] - # TODO: remove this when reticulate >= 1.35 is released - github: rstudio/reticulate - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] From 0b610d78a74c30f04ac765cf96e535b885b12bb0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Apr 2024 17:18:12 +0200 Subject: [PATCH 1187/1233] fix hvg-related var slots (#419) Former-commit-id: 12d4837fc9116c10d2a6e3121d50bb04577e5b88 --- src/datasets/api/file_hvg.yaml | 4 ++-- src/datasets/api/file_multimodal_dataset.yaml | 2 +- src/tasks/batch_integration/api/file_common_dataset.yaml | 4 ++++ src/tasks/batch_integration/api/file_dataset.yaml | 4 ++++ src/tasks/batch_integration/api/file_solution.yaml | 4 ++++ src/tasks/label_projection/api/file_common_dataset.yaml | 2 +- src/tasks/label_projection/api/file_solution.yaml | 2 +- src/tasks/label_projection/api/file_test.yaml | 2 +- src/tasks/label_projection/api/file_train.yaml | 2 +- src/tasks/spatial_decomposition/api/file_common_dataset.yaml | 2 +- 10 files changed, 20 insertions(+), 8 deletions(-) diff --git a/src/datasets/api/file_hvg.yaml b/src/datasets/api/file_hvg.yaml index 0e9f05c30f..697be29e32 100644 --- a/src/datasets/api/file_hvg.yaml +++ b/src/datasets/api/file_hvg.yaml @@ -10,7 +10,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score - description: A ranking of the features by hvg. + description: A score for the feature indicating how highly variable it is. required: true diff --git a/src/datasets/api/file_multimodal_dataset.yaml b/src/datasets/api/file_multimodal_dataset.yaml index 950e9158f0..daac29d77b 100644 --- a/src/datasets/api/file_multimodal_dataset.yaml +++ b/src/datasets/api/file_multimodal_dataset.yaml @@ -189,7 +189,7 @@ info: description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true diff --git a/src/tasks/batch_integration/api/file_common_dataset.yaml b/src/tasks/batch_integration/api/file_common_dataset.yaml index 66b7d14ecc..097a6794a1 100644 --- a/src/tasks/batch_integration/api/file_common_dataset.yaml +++ b/src/tasks/batch_integration/api/file_common_dataset.yaml @@ -30,6 +30,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: double + name: hvg_score + description: A ranking of the features by hvg. + required: true - type: string name: feature_name description: A human-readable name for the feature, usually a gene symbol. diff --git a/src/tasks/batch_integration/api/file_dataset.yaml b/src/tasks/batch_integration/api/file_dataset.yaml index c53688aaf1..6d1eb928d8 100644 --- a/src/tasks/batch_integration/api/file_dataset.yaml +++ b/src/tasks/batch_integration/api/file_dataset.yaml @@ -27,6 +27,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: double + name: hvg_score + description: A ranking of the features by hvg. + required: true - type: string name: feature_name description: A human-readable name for the feature, usually a gene symbol. diff --git a/src/tasks/batch_integration/api/file_solution.yaml b/src/tasks/batch_integration/api/file_solution.yaml index ea606cb22b..7e8b07ea4c 100644 --- a/src/tasks/batch_integration/api/file_solution.yaml +++ b/src/tasks/batch_integration/api/file_solution.yaml @@ -27,6 +27,10 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true + - type: double + name: hvg_score + description: A ranking of the features by hvg. + required: true - type: string name: feature_name description: A human-readable name for the feature, usually a gene symbol. diff --git a/src/tasks/label_projection/api/file_common_dataset.yaml b/src/tasks/label_projection/api/file_common_dataset.yaml index f5c50b7c5b..eeb01ffd1e 100644 --- a/src/tasks/label_projection/api/file_common_dataset.yaml +++ b/src/tasks/label_projection/api/file_common_dataset.yaml @@ -27,7 +27,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true diff --git a/src/tasks/label_projection/api/file_solution.yaml b/src/tasks/label_projection/api/file_solution.yaml index f1ab136360..c7591678e0 100644 --- a/src/tasks/label_projection/api/file_solution.yaml +++ b/src/tasks/label_projection/api/file_solution.yaml @@ -27,7 +27,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true diff --git a/src/tasks/label_projection/api/file_test.yaml b/src/tasks/label_projection/api/file_test.yaml index 48eb3d98c5..9cb2177da5 100644 --- a/src/tasks/label_projection/api/file_test.yaml +++ b/src/tasks/label_projection/api/file_test.yaml @@ -23,7 +23,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true diff --git a/src/tasks/label_projection/api/file_train.yaml b/src/tasks/label_projection/api/file_train.yaml index 7f87e63e7d..d615fc5693 100644 --- a/src/tasks/label_projection/api/file_train.yaml +++ b/src/tasks/label_projection/api/file_train.yaml @@ -27,7 +27,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true diff --git a/src/tasks/spatial_decomposition/api/file_common_dataset.yaml b/src/tasks/spatial_decomposition/api/file_common_dataset.yaml index c283d4d92b..b5399a37c2 100644 --- a/src/tasks/spatial_decomposition/api/file_common_dataset.yaml +++ b/src/tasks/spatial_decomposition/api/file_common_dataset.yaml @@ -23,7 +23,7 @@ info: name: hvg description: Whether or not the feature is considered to be a 'highly variable gene' required: true - - type: integer + - type: double name: hvg_score description: A ranking of the features by hvg. required: true From 664202b89032d0514758103d781b594bb3b0d2e8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Apr 2024 17:40:44 +0200 Subject: [PATCH 1188/1233] simplify BI output format (#420) Former-commit-id: acd27f57e4ced023abf8bdb0c344276c62ed4270 --- src/tasks/batch_integration/README.md | 111 ++++++------------ .../api/file_integrated_embedding.yaml | 13 +- .../api/file_integrated_feature.yaml | 13 +- .../api/file_integrated_graph.yaml | 13 +- 4 files changed, 73 insertions(+), 77 deletions(-) diff --git a/src/tasks/batch_integration/README.md b/src/tasks/batch_integration/README.md index 5a2fec741b..7d525e9fc8 100644 --- a/src/tasks/batch_integration/README.md +++ b/src/tasks/batch_integration/README.md @@ -1,5 +1,6 @@ # Batch Integration + Remove unwanted batch effects from scRNA data while retaining biologically meaningful variation. @@ -111,7 +112,7 @@ Format: AnnData object obs: 'cell_type', 'batch' - var: 'hvg', 'feature_name' + var: 'hvg', 'hvg_score', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -128,6 +129,7 @@ Slot description: | `obs["cell_type"]` | `string` | Cell type information. | | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | @@ -181,7 +183,7 @@ Format: AnnData object obs: 'batch', 'label' - var: 'hvg', 'feature_name' + var: 'hvg', 'hvg_score', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -198,6 +200,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | @@ -223,7 +226,7 @@ Format: AnnData object obs: 'batch', 'label' - var: 'hvg', 'feature_name' + var: 'hvg', 'hvg_score', 'feature_name' obsm: 'X_pca' obsp: 'knn_distances', 'knn_connectivities' layers: 'counts', 'normalized' @@ -240,6 +243,7 @@ Slot description: | `obs["batch"]` | `string` | Batch information. | | `obs["label"]` | `string` | label information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | @@ -417,12 +421,8 @@ Format:
AnnData object - obs: 'batch', 'label' - var: 'hvg', 'feature_name' - obsm: 'X_pca', 'X_emb' - obsp: 'knn_distances', 'knn_connectivities' - layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id' + obsm: 'X_emb' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id'
@@ -430,23 +430,13 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["label"]` | `string` | label information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsm["X_emb"]` | `double` | integration embedding prediction. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | -| `uns["method_id"]` | `string` | A unique identifier for the method. | +| Slot | Type | Description | +|:--------------------------|:---------|:--------------------------------------------------------| +| `obsm["X_emb"]` | `double` | integration embedding prediction. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. |
@@ -462,12 +452,8 @@ Format:
AnnData object - obs: 'batch', 'label' - var: 'hvg', 'feature_name' - obsm: 'X_pca' - obsp: 'knn_distances', 'knn_connectivities', 'connectivities', 'distances' - layers: 'counts', 'normalized' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id', 'neighbors' + obsp: 'connectivities', 'distances' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id', 'neighbors'
@@ -475,25 +461,15 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["label"]` | `string` | label information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | -| `obsp["distances"]` | `double` | Neighbors connectivities matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | -| `uns["method_id"]` | `string` | A unique identifier for the method. | -| `uns["neighbors"]` | `object` | Supplementary K nearest neighbors data. | +| Slot | Type | Description | +|:--------------------------|:---------|:--------------------------------------------------------| +| `obsp["connectivities"]` | `double` | Neighbors connectivities matrix. | +| `obsp["distances"]` | `double` | Neighbors connectivities matrix. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. | +| `uns["neighbors"]` | `object` | Supplementary K nearest neighbors data. |
@@ -509,12 +485,8 @@ Format:
AnnData object - obs: 'batch', 'label' - var: 'hvg', 'feature_name' - obsm: 'X_pca' - obsp: 'knn_distances', 'knn_connectivities' - layers: 'counts', 'normalized', 'corrected_counts' - uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'knn', 'method_id' + layers: 'corrected_counts' + uns: 'dataset_id', 'normalization_id', 'dataset_organism', 'method_id'
@@ -522,23 +494,13 @@ Slot description:
-| Slot | Type | Description | -|:-----------------------------|:----------|:-------------------------------------------------------------------------| -| `obs["batch"]` | `string` | Batch information. | -| `obs["label"]` | `string` | label information. | -| `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | -| `obsm["X_pca"]` | `double` | The resulting PCA embedding. | -| `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | -| `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | -| `layers["counts"]` | `integer` | Raw counts. | -| `layers["normalized"]` | `double` | Normalized expression values. | -| `layers["corrected_counts"]` | `double` | Corrected counts after integration. | -| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["normalization_id"]` | `string` | Which normalization was used. | -| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | -| `uns["knn"]` | `object` | Supplementary K nearest neighbors data. | -| `uns["method_id"]` | `string` | A unique identifier for the method. | +| Slot | Type | Description | +|:-----------------------------|:---------|:--------------------------------------------------------| +| `layers["corrected_counts"]` | `double` | Corrected counts after integration. | +| `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | +| `uns["normalization_id"]` | `string` | Which normalization was used. | +| `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["method_id"]` | `string` | A unique identifier for the method. |
@@ -606,3 +568,4 @@ Arguments: | `--output` | `file` | (*Output*) An integrated AnnData HDF5 file. |
+ diff --git a/src/tasks/batch_integration/api/file_integrated_embedding.yaml b/src/tasks/batch_integration/api/file_integrated_embedding.yaml index cd9d021031..aa526abe71 100644 --- a/src/tasks/batch_integration/api/file_integrated_embedding.yaml +++ b/src/tasks/batch_integration/api/file_integrated_embedding.yaml @@ -1,4 +1,3 @@ -__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_embedding.h5ad" info: @@ -12,6 +11,18 @@ info: description: integration embedding prediction required: true uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: method_id description: "A unique identifier for the method" diff --git a/src/tasks/batch_integration/api/file_integrated_feature.yaml b/src/tasks/batch_integration/api/file_integrated_feature.yaml index 4e3979bedb..b89e16f907 100644 --- a/src/tasks/batch_integration/api/file_integrated_feature.yaml +++ b/src/tasks/batch_integration/api/file_integrated_feature.yaml @@ -1,4 +1,3 @@ -__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_feature.h5ad" info: @@ -12,6 +11,18 @@ info: description: Corrected counts after integration required: true uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: method_id description: "A unique identifier for the method" diff --git a/src/tasks/batch_integration/api/file_integrated_graph.yaml b/src/tasks/batch_integration/api/file_integrated_graph.yaml index 6af14980eb..8c09147d0d 100644 --- a/src/tasks/batch_integration/api/file_integrated_graph.yaml +++ b/src/tasks/batch_integration/api/file_integrated_graph.yaml @@ -1,4 +1,3 @@ -__merge__: "file_dataset.yaml" type: file example: "resources_test/batch_integration/pancreas/integrated_graph.h5ad" info: @@ -16,6 +15,18 @@ info: description: Neighbors connectivities matrix. required: true uns: + - type: string + name: dataset_id + description: "A unique identifier for the dataset" + required: true + - type: string + name: normalization_id + description: "Which normalization was used" + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false - type: string name: method_id description: "A unique identifier for the method" From 8a543a4a27d92c86cb7b7981e9490791e4abbb8d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Apr 2024 19:34:30 +0200 Subject: [PATCH 1189/1233] update to scib 1.1.5 (#422) Former-commit-id: 44e3590ac70ff4604db407efd4458d3354f48f49 --- src/common/create_component/script.py | 2 +- src/tasks/batch_integration/methods/bbknn/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/combat/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_embed/config.vsh.yaml | 2 +- .../batch_integration/methods/scanorama_feature/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scanvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml | 2 +- .../metrics/cell_cycle_conservation/config.vsh.yaml | 2 +- .../metrics/clustering_overlap/config.vsh.yaml | 2 +- .../metrics/graph_connectivity/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml | 2 +- .../metrics/isolated_label_asw/config.vsh.yaml | 2 +- .../batch_integration/metrics/isolated_label_f1/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/kbet/config.vsh.yaml | 2 +- src/tasks/batch_integration/metrics/pcr/config.vsh.yaml | 2 +- src/tasks/batch_integration/process_dataset/config.vsh.yaml | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 175d027382..482ec680b7 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -143,7 +143,7 @@ def generate_docker_platform(par) -> str: if par["language"] == "python": image_str = "ghcr.io/openproblems-bio/base_python:1.0.2" setup_type = "python" - package_example = "scib==1.1.3" + package_example = "scib==1.1.5" elif par["language"] == "r": image_str = "ghcr.io/openproblems-bio/base_r:1.0.2" setup_type = "r" diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 52217665c3..6b34c121f7 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -30,7 +30,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - bbknn - type: nextflow directives: diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index bd857f4e4a..572d978196 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -33,7 +33,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", highmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index 173c6fb11d..86aec82cd4 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -39,7 +39,7 @@ platforms: - pyyaml - requests - jsonschema - - scib==1.1.3 + - scib==1.1.5 github: - chriscainx/mnnpy - type: nextflow diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index 7bd2d56107..df64ef8449 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -29,7 +29,7 @@ platforms: - type: python pypi: - scanorama - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 2cec87c577..e691e5644a 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -29,7 +29,7 @@ platforms: - type: python pypi: - scanorama - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 7eaf674b26..f383faf269 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -38,7 +38,7 @@ platforms: - type: python pypi: - scvi-tools - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", lowmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 89af44209e..1458a0fe42 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -26,7 +26,7 @@ platforms: - type: python pypi: - scvi-tools - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index 14b47fc7b4..d9f9dff3ba 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -42,7 +42,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index f4d037f296..57ea6cd0f8 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -30,7 +30,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index 78bae7b655..de42057de1 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -39,7 +39,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index a9643660e6..60185ba12a 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -53,7 +53,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index cacda59b01..dbc6079e84 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -39,7 +39,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.4 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index a458636f27..a67a5ca1c5 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -38,7 +38,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.4 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index 5e81c2e303..16d2b3e2ad 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -32,7 +32,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.4 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index ad452e452f..2d4fce1e75 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -44,7 +44,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.4 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index 4a46752754..eb4bcf9f12 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -46,7 +46,7 @@ platforms: github: theislab/kBET - type: python pypi: - - scib==1.1.4 + - scib==1.1.5 - rpy2>=3 - anndata2ri - type: nextflow diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index 53c7307756..e1662b3ef9 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -36,7 +36,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ "midtime", midmem, lowcpu ] diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index e751637511..2b48e72359 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -12,7 +12,7 @@ platforms: setup: - type: python pypi: - - scib==1.1.3 + - scib==1.1.5 - type: nextflow directives: label: [ highmem, midcpu , midtime] From 4e458b571cd78ef662374b0af8b2328698c0cdea Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Apr 2024 19:35:08 +0200 Subject: [PATCH 1190/1233] update readmes (#421) Former-commit-id: d24d974c5a72d908639a76d58459fd050bb1e919 --- src/tasks/denoising/README.md | 10 +-- src/tasks/dimensionality_reduction/README.md | 64 +++++++++++++------- src/tasks/label_projection/README.md | 10 +-- src/tasks/match_modalities/README.md | 2 + src/tasks/predict_modality/README.md | 22 ++++--- src/tasks/spatial_decomposition/README.md | 2 +- 6 files changed, 68 insertions(+), 42 deletions(-) diff --git a/src/tasks/denoising/README.md b/src/tasks/denoising/README.md index 4dc1bbb895..da9d9b1912 100644 --- a/src/tasks/denoising/README.md +++ b/src/tasks/denoising/README.md @@ -1,5 +1,6 @@ # Denoising + Removing noise in sparse single-cell RNA-sequencing count data Path: @@ -138,7 +139,7 @@ Slot description: | `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A score for the feature indicating how highly variable it is. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -216,7 +217,7 @@ Format: AnnData object layers: 'counts' - uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism' + uns: 'dataset_id', 'dataset_name', 'dataset_url', 'dataset_reference', 'dataset_summary', 'dataset_description', 'dataset_organism', 'train_sum'
@@ -234,6 +235,7 @@ Slot description: | `uns["dataset_summary"]` | `string` | Short description of the dataset. | | `uns["dataset_description"]` | `string` | Long description of the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | +| `uns["train_sum"]` | `integer` | The total number of counts in the training dataset. |
@@ -304,7 +306,7 @@ Format:
AnnData object - layers: 'counts', 'denoised' + layers: 'denoised' uns: 'dataset_id', 'method_id'
@@ -315,7 +317,6 @@ Slot description: | Slot | Type | Description | |:---------------------|:----------|:-------------------------------------| -| `layers["counts"]` | `integer` | Raw counts. | | `layers["denoised"]` | `integer` | denoised data. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | | `uns["method_id"]` | `string` | A unique identifier for the method. | @@ -353,3 +354,4 @@ Slot description: | `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |
+ diff --git a/src/tasks/dimensionality_reduction/README.md b/src/tasks/dimensionality_reduction/README.md index 243ef80229..c18c5dc5ba 100644 --- a/src/tasks/dimensionality_reduction/README.md +++ b/src/tasks/dimensionality_reduction/README.md @@ -1,4 +1,5 @@ -# Dimensionality reduction for visualization +# Dimensionality reduction for 2D visualization + Reduction of high-dimensional datasets to 2D for visualization & interpretation @@ -8,29 +9,43 @@ Path: ## Motivation -Dimensionality reduction is one of the key challenges in single-cell -data representation. Routine single-cell RNA sequencing (scRNA-seq) -experiments measure cells in roughly 20,000-30,000 dimensions (i.e., -features - mostly gene transcripts but also other functional elements -encoded in mRNA such as lncRNAs). Since its inception,scRNA-seq -experiments have been growing in terms of the number of cells measured. -Originally, cutting-edge SmartSeq experiments would yield a few hundred -cells, at best. Now, it is not uncommon to see experiments that yield -over [100,000 cells](https://www.nature.com/articles/s41586-018-0590-4) -or even [\> 1 million cells](https://doi.org/10.1126/science.aba7721). +Data visualisation is an important part of all stages of single-cell +analysis, from initial quality control to interpretation and +presentation of final results. For bulk RNA-seq studies, linear +dimensionality reduction techniques such as PCA and MDS are commonly +used to visualise the variation between samples. While these methods are +highly effective they can only be used to show the first few components +of variation which cannot fully represent the increased complexity and +number of observations in single-cell datasets. For this reason +non-linear techniques (most notably t-SNE and UMAP) have become the +standard for visualising single-cell studies. These methods attempt to +compress a dataset into a two-dimensional space while attempting to +capture as much of the variance between observations as possible. Many +methods for solving this problem now exist. In general these methods try +to preserve distances, while some additionally consider aspects such as +density within the embedded space or conservation of continuous +trajectories. Despite almost every single-cell study using one of these +visualisations there has been debate as to whether they can effectively +capture the variation in single-cell datasets \[@chari2023speciousart\]. ## Description -Each *feature* in a dataset functions as a single dimension. While each -of the ~30,000 dimensions measured in each cell contribute to an -underlying data structure, the overall structure of the data is -challenging to display in few dimensions due to data sparsity and the -[*“curse of -dimensionality”*](https://en.wikipedia.org/wiki/Curse_of_dimensionality) -(distances in high dimensional data don’t distinguish data points well). -Thus, we need to find a way to [dimensionally -reduce](https://en.wikipedia.org/wiki/Dimensionality_reduction) the data -for visualization and interpretation. +The dimensionality reduction task attempts to quantify the ability of +methods to embed the information present in complex single-cell studies +into a two-dimensional space. Thus, this task is specifically designed +for dimensionality reduction for visualisation and does not consider +other uses of dimensionality reduction in standard single-cell workflows +such as improving the signal-to-noise ratio (and in fact several of the +methods use PCA as a pre-processing step for this reason). Unlike most +tasks, methods for the dimensionality reduction task must accept a +matrix containing expression values normalised to 10,000 counts per cell +and log transformed (log-10k) and produce a two-dimensional coordinate +for each cell. Pre-normalised matrices are required to enforce +consistency between the metric evaluation (which generally requires +normalised data) and the method runs. When these are not consistent, +methods that use the same normalisation as used in the metric tend to +score more highly. For some methods we also evaluate the pre-processing +recommended by the method. ## Authors & contributors @@ -40,8 +55,10 @@ for visualization and interpretation. | Michal Klein | author | | Scott Gigante | author | | Ben DeMeo | author | +| Robrecht Cannoodt | author | +| Kai Waldrant | contributor | +| Sai Nirmayi Yasa | contributor | | Juan A. Cordero Varela | contributor | -| Robrecht Cannoodt | contributor | ## API @@ -130,7 +147,7 @@ Slot description: | `var["feature_name"]` | `string` | A human-readable name for the feature, usually a gene symbol. | | `var["soma_joinid"]` | `integer` | (*Optional*) If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A score for the feature indicating how highly variable it is. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsp["knn_distances"]` | `double` | K nearest neighbors distance matrix. | | `obsp["knn_connectivities"]` | `double` | K nearest neighbors connectivities matrix. | @@ -356,3 +373,4 @@ Slot description: | `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |
+ diff --git a/src/tasks/label_projection/README.md b/src/tasks/label_projection/README.md index e58324b8b4..8981c503be 100644 --- a/src/tasks/label_projection/README.md +++ b/src/tasks/label_projection/README.md @@ -1,5 +1,6 @@ # Label projection + Automated cell type annotation from rich, labeled reference data Path: @@ -100,7 +101,7 @@ Slot description: | `obs["cell_type"]` | `string` | Cell type information. | | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | @@ -163,7 +164,7 @@ Slot description: | `obs["label"]` | `string` | Ground truth cell type labels. | | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized counts. | @@ -199,7 +200,7 @@ Slot description: |:--------------------------|:----------|:-------------------------------------------------------------------------| | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized counts. | @@ -236,7 +237,7 @@ Slot description: | `obs["label"]` | `string` | Ground truth cell type labels. | | `obs["batch"]` | `string` | Batch information. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized counts. | @@ -366,3 +367,4 @@ Slot description: | `uns["metric_values"]` | `double` | The metric values obtained for the given prediction. Must be of same length as ‘metric_ids’. |
+ diff --git a/src/tasks/match_modalities/README.md b/src/tasks/match_modalities/README.md index 911977144b..399c31ee92 100644 --- a/src/tasks/match_modalities/README.md +++ b/src/tasks/match_modalities/README.md @@ -1,5 +1,6 @@ # Match Modalities + Match cells across datasets of the same set of samples on different technologies / modalities. @@ -495,3 +496,4 @@ Slot description: | `uns["normalization_id"]` | `string` | Which normalization was used. |
+ diff --git a/src/tasks/predict_modality/README.md b/src/tasks/predict_modality/README.md index 537885fa56..add96684ce 100644 --- a/src/tasks/predict_modality/README.md +++ b/src/tasks/predict_modality/README.md @@ -1,5 +1,6 @@ # Predict Modality + Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression). @@ -155,7 +156,7 @@ Arguments: The mod1 expression values of the train cells. Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod1.h5ad` Format: @@ -183,7 +184,7 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | (*Optional*) A common identifier for the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | @@ -195,7 +196,7 @@ Slot description: The mod2 expression values of the train cells. Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod2.h5ad` Format: @@ -223,7 +224,7 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | (*Optional*) A common identifier for the dataset. | | `uns["dataset_organism"]` | `string` | (*Optional*) The organism of the sample in the dataset. | | `uns["normalization_id"]` | `string` | The unique identifier of the normalization method used. | | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. | @@ -235,7 +236,7 @@ Slot description: The mod1 expression values of the test cells. Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod1.h5ad` Format: @@ -263,7 +264,7 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | (*Optional*) A common identifier for the dataset. | | `uns["dataset_name"]` | `string` | Nicely formatted name. | | `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | | `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | @@ -280,7 +281,7 @@ Slot description: The mod2 expression values of the test cells. Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod2.h5ad` Format: @@ -308,7 +309,7 @@ Slot description: | `layers["counts"]` | `integer` | Raw counts. | | `layers["normalized"]` | `double` | Normalized expression values. | | `uns["dataset_id"]` | `string` | A unique identifier for the dataset. | -| `uns["common_dataset_id"]` | `string` | A common identifier for the dataset. | +| `uns["common_dataset_id"]` | `string` | (*Optional*) A common identifier for the dataset. | | `uns["dataset_name"]` | `string` | Nicely formatted name. | | `uns["dataset_url"]` | `string` | (*Optional*) Link to the original source of the dataset. | | `uns["dataset_reference"]` | `string` | (*Optional*) Bibtex reference of the paper in which the dataset was published. | @@ -384,7 +385,7 @@ Arguments: A prediction of the mod2 expression values of the test cells Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/prediction.h5ad` Format: @@ -413,7 +414,7 @@ Slot description: Metric score file Example file: -`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/score.h5ad` +`resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/score.h5ad` Format: @@ -482,3 +483,4 @@ Slot description: | `uns["gene_activity_var_names"]` | `string` | (*Optional*) Names of the gene activity matrix. |
+ diff --git a/src/tasks/spatial_decomposition/README.md b/src/tasks/spatial_decomposition/README.md index 2ac66984b2..0b3cfc85d9 100644 --- a/src/tasks/spatial_decomposition/README.md +++ b/src/tasks/spatial_decomposition/README.md @@ -102,7 +102,7 @@ Slot description: | `obs["cell_type"]` | `string` | Cell type label IDs. | | `obs["batch"]` | `string` | A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc. | | `var["hvg"]` | `boolean` | Whether or not the feature is considered to be a ‘highly variable gene’. | -| `var["hvg_score"]` | `integer` | A ranking of the features by hvg. | +| `var["hvg_score"]` | `double` | A ranking of the features by hvg. | | `obsm["X_pca"]` | `double` | The resulting PCA embedding. | | `obsm["coordinates"]` | `double` | (*Optional*) XY coordinates for each spot. | | `obsm["proportions_true"]` | `double` | (*Optional*) True cell type proportions for each spot. | From acfda972e0b93c42a9e69fcc78e932cfd9bb7611 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 2 Apr 2024 19:35:23 +0200 Subject: [PATCH 1191/1233] refactor liger (#415) * refactor liger * Update src/tasks/batch_integration/methods/liger/script.R --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 9fef3308ab86a148bc8bfbabda89abdccb983a65 --- .../methods/liger/config.vsh.yaml | 3 ++ .../batch_integration/methods/liger/script.R | 36 +++++++++++++------ 2 files changed, 29 insertions(+), 10 deletions(-) diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index 7dd720bebc..a68b06f8b4 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -21,8 +21,11 @@ platforms: - type: docker image: ghcr.io/openproblems-bio/base_r:1.0.2 setup: + - type: apt + packages: cmake - type: r cran: rliger + github: welch-lab/RcppPlanc - type: nextflow directives: label: [ lowcpu, highmem, midtime ] diff --git a/src/tasks/batch_integration/methods/liger/script.R b/src/tasks/batch_integration/methods/liger/script.R index be9f6351e5..a0ef9e9f42 100644 --- a/src/tasks/batch_integration/methods/liger/script.R +++ b/src/tasks/batch_integration/methods/liger/script.R @@ -26,27 +26,39 @@ anndataToLiger <- function(adata) { }) names(raw_data) <- batch_names - rliger::createLiger(raw.data = raw_data, remove.missing = FALSE) + rliger::createLiger(rawData = raw_data, removeMissing = FALSE) } addNormalizedDataToLiger <- function(adata, lobj) { - norm_data <- lapply(names(lobj@raw.data), function(name) { + norm_data <- lapply(names(rliger::rawData(lobj)), function(name) { norm <- adata$layers[["normalized"]] + # subset + col_names <- colnames(rliger::rawData(lobj)[[name]]) + row_names <- rownames(rliger::rawData(lobj)[[name]]) + prefix <- paste0(name, "_") + col_names <- sub(prefix, "", col_names) + norm <- norm[ - colnames(lobj@raw.data[[name]]), - rownames(lobj@raw.data[[name]]), + col_names, + row_names, drop = FALSE ] + + # add prefix + rownames(norm) <- paste0(prefix, rownames(norm)) + # transpose norm <- Matrix::t(norm) # turn into dgcMatrix as(as(norm, "denseMatrix"), "CsparseMatrix") }) - names(norm_data) <- names(lobj@raw.data) + names(norm_data) <- names(rliger::rawData(lobj)) - lobj@norm.data <- norm_data + for (name in names(rliger::rawData(lobj))) { + lobj@datasets[[name]]@normData <- norm_data[[name]] + } lobj } @@ -63,18 +75,22 @@ lobj <- addNormalizedDataToLiger(adata, lobj) cat(">> Select genes\n") # lobj <- rliger::selectGenes(lobj) # overwrite gene selection to include all genes -lobj@var.genes <- adata$var_names +lobj@varFeatures <- adata$var_names cat(">> Perform scaling\n") -lobj <- rliger::scaleNotCenter(lobj, remove.missing = FALSE) +lobj <- rliger::scaleNotCenter(lobj, removeMissing = FALSE) cat(">> Joint Matrix Factorization\n") -lobj <- rliger::optimizeALS(lobj, k = 20) +lobj <- rliger::runIntegration(lobj, k = 20) cat(">> Quantile normalization\n") -lobj <- rliger::quantile_norm(lobj) +lobj <- rliger::quantileNorm(lobj) cat(">> Store dimred in adata\n") +# remove dataset names from rownames +for (name in names(rliger::rawData(lobj))) { + rownames(lobj@H.norm) <- sub(paste0(name, "_"), "", rownames(lobj@H.norm)) +} adata$obsm[["X_emb"]] <- lobj@H.norm[rownames(adata), , drop = FALSE] adata$uns[["method_id"]] <- meta$functionality_name From 6c1b5f4fe72d998b4a0214d99300abb78adf4445 Mon Sep 17 00:00:00 2001 From: Martin Kim <46072231+martinkim0@users.noreply.github.com> Date: Wed, 3 Apr 2024 00:58:50 -0700 Subject: [PATCH 1192/1233] refactor scvi-tools based methods (#416) * lower bound scvi-tools, other fixes * add release notes * Refactor scvi without scib * remove comments * switch to pytorch_nvidia image * only output necessary data * add more arguments to component * add more params to scanvi * Apply suggestions from code review Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com> * Apply more suggestions from code review * Use counts --------- Co-authored-by: Kai Waldrant Co-authored-by: Robrecht Cannoodt Former-commit-id: 05cfabe9f4562e99296172caeed748d16d4fec4f --- CHANGELOG.md | 12 ++++ .../methods/scanvi/config.vsh.yaml | 54 +++++++++------- .../methods/scanvi/script.py | 63 ++++++++++++++----- .../methods/scvi/config.vsh.yaml | 36 ++++++++--- .../batch_integration/methods/scvi/script.py | 53 ++++++++++++---- .../methods/scanvi/config.vsh.yaml | 15 +++-- .../label_projection/methods/scanvi/script.py | 36 +++++++---- .../methods/scanvi_scarches/config.vsh.yaml | 20 +----- .../methods/destvi/config.vsh.yaml | 9 ++- .../methods/stereoscope/config.vsh.yaml | 6 +- 10 files changed, 204 insertions(+), 100 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 675f9aa957..a3196f4bf9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -67,6 +67,8 @@ * Add library.bib file check to component unit test (PR #167) +* Lower bound scvi-tools to 1.1.0 for all methods using the package (PR #416). + ### BUG FIXES * fix typos in metric and common defenition schemas (PR #212) @@ -106,6 +108,12 @@ ## batch_integration +### MINOR CHANGES + +* Updated `methods/scanvi` to use `counts` as `preferred_normalization` + +* Updated `methods/scvi` to use `counts` as `preferred_normalization` + ### NEW FUNCTIONALITY * `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. @@ -168,6 +176,10 @@ ## label_projection +### MINOR CHANGES + +* Updated `methods/scanvi` to use `counts` as `preferred_normalization` + ### NEW FUNCTIONALITY * `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index f383faf269..72e82cf7dd 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -1,44 +1,56 @@ -# The API specifies which type of component this is. -# It contains specifications for: -# - The input/output files -# - Common parameters -# - A unit test __merge__: ../../api/comp_method_embedding.yaml functionality: - # A unique identifier for your component (required). - # Can contain only lowercase letters or underscores. name: scanvi - - # Metadata for your component info: - # A relatively short label, used when rendering visualisarions (required) - label: ScanVI - # A one sentence summary of how this method works (required). Used when - # rendering summary tables. - summary: "ScanVI is a deep learning method that considers cell type labels." + label: scANVI + summary: "scANVI is a deep learning method that considers cell type labels." description : | scANVI (single-cell ANnotation using Variational Inference; Python class SCANVI) is a semi-supervised model for single-cell transcriptomics data. In a sense, it can be seen as a scVI extension that can leverage the cell type knowledge for a subset of the cells present in the data sets to infer the states of the rest of the cells. reference: "lopez2018deep" - repository_url: "https://github.com/YosefLab/scvi-tools" - documentation_url: "https://github.com/YosefLab/scvi-tools#readme" + repository_url: "https://github.com/scverse/scvi-tools" + documentation_url: "https://docs.scvi-tools.org/en/stable/user_guide/models/scanvi.html" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scanvi.py commit: 29803b95c88b4ec5921df2eec7111fd5d1a95daf - preferred_normalization: log_cp10k + preferred_normalization: counts variants: scanvi_full_unscaled: + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. + - name: --n_latent + type: integer + default: 30 + description: Number of latent dimensions. + - name: --n_hidden + type: integer + default: 128 + description: Number of hidden units. + - name: --n_layers + type: integer + default: 2 + description: Number of layers. + - name: --max_epochs_scvi + type: integer + example: 400 + description: Maximum number of training epochs for scVI. + - name: --max_epochs_scanvi + type: integer + example: 10 + description: Maximum number of training epochs for scANVI. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python pypi: - - scvi-tools - - scib==1.1.5 + - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [ midtime, lowmem, lowcpu, gpu ] diff --git a/src/tasks/batch_integration/methods/scanvi/script.py b/src/tasks/batch_integration/methods/scanvi/script.py index e812191e6e..9c0886816d 100644 --- a/src/tasks/batch_integration/methods/scanvi/script.py +++ b/src/tasks/batch_integration/methods/scanvi/script.py @@ -1,30 +1,65 @@ -import yaml import anndata as ad -from scib.integration import scanvi +from scvi.model import SCVI, SCANVI ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/dataset.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'n_hvg': 2000, + 'n_latent': 30, + 'n_hidden': 128, + 'n_layers': 2, + 'max_epochs_scvi': 20, + 'max_epochs_scanvi': 20 } meta = { - 'functionality_name' : 'foo', - 'config': 'bar' + 'functionality_name' : 'scanvi', } ## VIASH END - - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + adata = adata[:, idx].copy() + +print("Processing data", flush=True) +SCVI.setup_anndata(adata, layer="counts", batch_key="batch") + +print("Run scVI", flush=True) +model_kwargs = { + key: par[key] + for key in ["n_latent", "n_hidden", "n_layers"] + if par[key] is not None +} + +vae = SCVI(adata, **model_kwargs) -print('Run scanvi', flush=True) -adata.X = adata.layers['normalized'] -adata = scanvi(adata, batch='batch', labels='label') -del adata.X +vae.train(max_epochs=par["max_epochs_scvi"], train_size=1.0) + +print('Run SCANVI', flush=True) +scanvae = SCANVI.from_scvi_model( + scvi_model=vae, + labels_key="label", + unlabeled_category="UnknownUnknown", # pick anything definitely not in a dataset +) +scanvae.train(max_epochs=par["max_epochs_scanvi"], train_size=1.0) print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + obsm={ + "X_emb": scanvae.get_latent_representation(), + }, + uns={ + "dataset_id": adata.uns["dataset_id"], + "normalization_id": adata.uns["normalization_id"], + "method_id": meta["functionality_name"], + }, +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 1458a0fe42..03362da69c 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -8,25 +8,47 @@ functionality: description: | scVI combines a variational autoencoder with a hierarchical Bayesian model. It uses the negative binomial distribution to describe gene expression of each cell, conditioned on unobserved factors and the batch variable. ScVI is run as implemented in Luecken et al. reference: "lopez2018deep" - repository_url: "https://github.com/YosefLab/scvi-tools" - documentation_url: "https://github.com/YosefLab/scvi-tools#readme" + repository_url: "https://github.com/scverse/scvi-tools" + documentation_url: "https://docs.scvi-tools.org/en/stable/user_guide/models/scvi.html" v1: path: openproblems/tasks/_batch_integration/batch_integration_graph/methods/scvi.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cp10k + preferred_normalization: counts variants: scvi_full_unscaled: + # defaults are derived from te scvi tutorial: + # https://docs.scvi-tools.org/en/stable/tutorials/notebooks/scrna/harmonization.html + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. + - name: --n_latent + type: integer + default: 30 + description: Number of latent dimensions. + - name: --n_hidden + type: integer + default: 128 + description: Number of hidden units. + - name: --n_layers + type: integer + default: 2 + description: Number of layers. + - name: --max_epochs + type: integer + example: 400 + description: Maximum number of epochs. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python pypi: - - scvi-tools - - scib==1.1.5 + - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [ midtime, midmem, lowcpu, gpu ] diff --git a/src/tasks/batch_integration/methods/scvi/script.py b/src/tasks/batch_integration/methods/scvi/script.py index f9811c10ac..3c5feb6f9c 100644 --- a/src/tasks/batch_integration/methods/scvi/script.py +++ b/src/tasks/batch_integration/methods/scvi/script.py @@ -1,27 +1,56 @@ -import yaml import anndata as ad -from scib.integration import scvi +from scvi.model import SCVI ## VIASH START par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'input': 'resources_test/batch_integration/pancreas/dataset.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'n_hvg': 2000, + 'n_latent': 30, + 'n_hidden': 128, + 'n_layers': 2, + 'max_epochs': 400 } meta = { - 'functionality_name' : 'foo', - 'config': 'bar' + 'functionality_name' : 'scvi', } ## VIASH END print('Read input', flush=True) adata = ad.read_h5ad(par['input']) -print('Run scvi', flush=True) -adata.X = adata.layers['normalized'] -adata = scvi(adata, batch='batch') -del adata.X +if par["n_hvg"]: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var["hvg_score"].to_numpy().argsort()[::-1][:par["n_hvg"]] + adata = adata[:, idx].copy() + +print("Processing data", flush=True) +SCVI.setup_anndata(adata, layer="counts", batch_key="batch") + +print("Run scVI", flush=True) +model_kwargs = { + key: par[key] + for key in ["n_latent", "n_hidden", "n_layers"] + if par[key] is not None +} + +vae = SCVI(adata, **model_kwargs) + +vae.train(max_epochs=par["max_epochs"], train_size=1.0) print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + obsm={ + "X_emb": vae.get_latent_representation(), + }, + uns={ + "dataset_id": adata.uns["dataset_id"], + "normalization_id": adata.uns["normalization_id"], + "method_id": meta["functionality_name"], + }, +) + +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 43c031bfb4..01e6e1ea36 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -2,8 +2,8 @@ __merge__: ../../api/comp_method.yaml functionality: name: "scanvi" info: - label: SCANVI - summary: "ScANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." + label: scANVI + summary: "scANVI predicts cell type labels for unlabelled test data by leveraging cell type labels, modelling uncertainty and using deep neural networks with stochastic optimization." description: | single-cell ANnotation using Variational Inference is a semi-supervised variant of the scVI(Lopez et al. 2018) algorithm. Like scVI, @@ -13,12 +13,12 @@ functionality: in the generative modelling. In this approach, scANVI is used to predict the cell type labels of the unlabelled test data. reference: "lotfollahi2020query" - repository_url: "https://github.com/YosefLab/scvi-tools" + repository_url: "https://github.com/scverse/scvi-tools" documentation_url: https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html v1: path: openproblems/tasks/label_projection/methods/scvi_tools.py commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 - preferred_normalization: log_cp10k + preferred_normalization: counts variants: scanvi_all_genes: scanvi_hvg: @@ -32,13 +32,12 @@ functionality: path: script.py platforms: - type: docker - image: nvcr.io/nvidia/pytorch:23.12-py3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python packages: - - pyyaml - - "anndata~=0.8.0" - scarches + - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ "midtime", midmem, highcpu, gpu ] + label: [ midtime, midmem, highcpu, gpu ] diff --git a/src/tasks/label_projection/methods/scanvi/script.py b/src/tasks/label_projection/methods/scanvi/script.py index d9834bdca6..d34fccd932 100644 --- a/src/tasks/label_projection/methods/scanvi/script.py +++ b/src/tasks/label_projection/methods/scanvi/script.py @@ -1,5 +1,6 @@ import anndata as ad import scarches as sca +import pandas as pd # followed procedure from here: # https://scarches.readthedocs.io/en/latest/scanvi_surgery_pipeline.html @@ -17,30 +18,28 @@ ## VIASH END print("Load input data", flush=True) -input_train_orig = ad.read_h5ad(par['input_train']) -input_test_orig = ad.read_h5ad(par['input_test']) +input_train = ad.read_h5ad(par['input_train']) +input_test = ad.read_h5ad(par['input_test']) if par["num_hvg"]: print("Subsetting to HVG", flush=True) - hvg_idx = input_train_orig.var['hvg_score'].to_numpy().argsort()[:par["num_hvg"]] - input_train = input_train_orig[:,hvg_idx] - input_test = input_test_orig[:,hvg_idx] -else: - input_train = input_train_orig - input_test = input_test_orig + hvg_idx = input_train.var['hvg_score'].to_numpy().argsort()[:par["num_hvg"]] + input_train = input_train[:,hvg_idx] + input_test = input_test[:,hvg_idx] print("Concatenating train and test data", flush=True) input_train.obs['is_test'] = False input_test.obs['is_test'] = True input_test.obs['label'] = "Unknown" adata = ad.concat([input_train, input_test], merge = "same") +del input_train print("Create SCANVI model and train it on fully labelled reference dataset", flush=True) sca.models.SCVI.setup_anndata( adata, batch_key="batch", labels_key="label", - layer="normalized" + layer="counts" ) vae = sca.models.SCVI( @@ -60,9 +59,20 @@ print("Make predictions", flush=True) preds = scanvae.predict(adata) -input_test_orig.obs["label_pred"] = preds[adata.obs['is_test'].values] -print("Write output to file", flush=True) -input_test_orig.uns["method_id"] = meta["functionality_name"] -input_test_orig.write_h5ad(par['output'], compression="gzip") +print("Store outputs", flush=True) +output = ad.AnnData( + obs=pd.DataFrame( + {"label_pred": preds[adata.obs['is_test'].values]}, + index=input_test.obs.index, + ), + var=input_test.var[[]], + uns={ + "dataset_id": input_test.uns["dataset_id"], + "normalization_id": input_test.uns["normalization_id"], + "method_id": meta["functionality_name"], + }, +) +print("Write output to file", flush=True) +output.write_h5ad(par["output"], compression="gzip") diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 039f256e47..284ab3da91 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -1,14 +1,7 @@ -# The API specifies which type of component this is. -# It contains specifications for: -# - The input/output files -# - Common parameters -# - A unit test __merge__: ../../api/comp_method.yaml functionality: name: scanvi_scarches - - # Metadata for your component (required) info: label: scANVI+scArches summary: 'Query to reference single-cell integration with transfer learning with scANVI and scArches' @@ -22,9 +15,6 @@ functionality: commit: e3be930c6d4bbd656ab1e656badb52bb50e6cdd6 variants: scanvi_scarches: - #! TODO: add other scanvi_scarches variants - - # Component-specific parameters (optional) arguments: - name: "--n_latent" type: "integer" @@ -46,19 +36,15 @@ functionality: type: "integer" default: 2 description: "Maximum number of training epochs" - - # Resources required to run the component resources: - # The script of your component - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 - # Add custom dependencies here + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python - pypi: scvi-tools + pypi: scvi-tools>=1.1.0 - type: nextflow directives: - label: [ "midtime",midmem, midcpu] + label: [ midtime, midmem, midcpu, gpu ] diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index d4f71dc1cf..2637b39668 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: description: Number of epochs to train the Conditional version of single-cell Variational Inference (CondSCVI) model using MAP inference. - name: "--max_epochs_sp" type: integer - default: 10000 + default: 2000 description: Number of epochs to train the DestVI model using MAP inference. resources: @@ -29,14 +29,13 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python packages: - - scvi-tools - - chex==0.1.85 + - scvi-tools>=1.1.0 - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [ midtime, midmem, midcpu, gpu ] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index 655e644311..88a1fd3faa 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -29,12 +29,12 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 setup: - type: python packages: - - scvi-tools + - scvi-tools>=1.1.0 - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [ midtime, midmem, midcpu, gpu ] From 550c3e602163af0227ab1d906821ea84ff2ea48b Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Wed, 3 Apr 2024 17:13:08 +0200 Subject: [PATCH 1193/1233] [bat_int] refactor methods (#423) * refactor bbknn * refactor combat * refactor mnnpy * refactor mnnpy * Update bbknn * Update Combat * refactor scanorama_embed * Refactor scanorama feature * refactor output pyliger * refactor scalex_embed * refactor scalex_feature * refactor mnn_correct * Update Liger * refactor fastmnn * Update src/tasks/batch_integration/methods/fastmnn_feature/script.R Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 3861275cc48e4c561db38658adecce98e4902a41 --- .../methods/bbknn/config.vsh.yaml | 18 +++++- .../batch_integration/methods/bbknn/script.py | 41 +++++++++--- .../methods/combat/config.vsh.yaml | 13 ++-- .../methods/combat/script.py | 28 +++++++-- .../methods/fastmnn_embedding/config.vsh.yaml | 4 +- .../methods/fastmnn_feature/config.vsh.yaml | 5 +- .../methods/fastmnn_feature/script.R | 18 ++++-- .../methods/liger/config.vsh.yaml | 2 +- .../batch_integration/methods/liger/script.R | 20 ++++-- .../methods/mnn_correct/config.vsh.yaml | 4 +- .../methods/mnn_correct/script.R | 22 +++++-- .../methods/mnnpy/config.vsh.yaml | 9 ++- .../batch_integration/methods/mnnpy/script.py | 38 +++++++++-- .../methods/pyliger/config.vsh.yaml | 2 +- .../methods/pyliger/script.py | 20 ++++-- .../methods/scalex_embed/config.vsh.yaml | 19 ++---- .../methods/scalex_embed/script.py | 25 ++++++-- .../methods/scalex_feature/config.vsh.yaml | 20 ++---- .../methods/scalex_feature/script.py | 29 ++++++--- .../methods/scanorama_embed/config.vsh.yaml | 10 ++- .../methods/scanorama_embed/script.py | 63 ++++++++++++++++--- .../methods/scanorama_feature/config.vsh.yaml | 10 ++- .../methods/scanorama_feature/script.py | 60 +++++++++++++++--- 23 files changed, 360 insertions(+), 120 deletions(-) diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 6b34c121f7..60d6414a35 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -21,17 +21,29 @@ functionality: bbknn_full_unscaled: bbknn_full_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --annoy_n_trees + type: integer + default: 10 + description: Number of trees to use in the annoy forrest. + - name: --neighbors_within_batch + type: integer + default: 3 + description: Number of neighbors to report within each batch. + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: - - scib==1.1.5 - bbknn - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [ midtime, midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/bbknn/script.py b/src/tasks/batch_integration/methods/bbknn/script.py index e47655a87e..d2a6e464ae 100644 --- a/src/tasks/batch_integration/methods/bbknn/script.py +++ b/src/tasks/batch_integration/methods/bbknn/script.py @@ -1,12 +1,13 @@ -import yaml import anndata as ad -from scib.integration import bbknn +import bbknn ## VIASH START par = { 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'annoy_n_trees': 10, + 'neighbors_within_batch': 3, + 'n_hvg': 2000, } meta = { 'functionality_name': 'foo', @@ -15,13 +16,35 @@ ## VIASH END print('Read input', flush=True) -input = ad.read_h5ad(par['input']) +adata = ad.read_h5ad(par['input']) + +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() print('Run BBKNN', flush=True) -input.X = input.layers['normalized'] -input = bbknn(input, batch='batch') -del input.X +kwargs = dict(batch_key='batch', copy=True) +kwargs['annoy_n_trees'] = par['annoy_n_trees'] +kwargs['neighbors_within_batch'] = par['neighbors_within_batch'] + +ad_bbknn = bbknn.bbknn(adata, **kwargs) + +print("Store output", flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + obsp={ + 'connectivities': ad_bbknn.obsp['connectivities'], + 'distances': ad_bbknn.obsp['distances'], + }, + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + 'neighbors': ad_bbknn.uns['neighbors'] + } +) print("Store outputs", flush=True) -input.uns['method_id'] = meta['functionality_name'] -input.write_h5ad(par['output'], compression='gzip') +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 572d978196..5511dd769c 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -24,16 +24,17 @@ functionality: combat_full_unscaled: combat_full_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 - setup: - - type: python - pypi: - - scib==1.1.5 + image: ghcr.io/openproblems-bio/base_python:1.0.3 - type: nextflow directives: - label: [ "midtime", highmem, lowcpu ] + label: [ midtime, highmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/combat/script.py b/src/tasks/batch_integration/methods/combat/script.py index 6cd90fc28f..c5f0ed8dd5 100644 --- a/src/tasks/batch_integration/methods/combat/script.py +++ b/src/tasks/batch_integration/methods/combat/script.py @@ -1,4 +1,3 @@ -import yaml import scanpy as sc from scipy.sparse import csr_matrix @@ -6,7 +5,7 @@ par = { 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', - 'hvg': True + 'n_hvg': 2000, } meta = { @@ -19,13 +18,30 @@ print('Read input', flush=True) adata = sc.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + + print('Run Combat', flush=True) adata.X = adata.layers['normalized'] adata.X = sc.pp.combat(adata, key='batch', inplace=False) -adata.layers['corrected_counts'] = csr_matrix(adata.X) -del(adata.X) + +print("Store output", flush=True) +output = sc.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + }, + layers={ + 'corrected_counts': csr_matrix(adata.X), + } +) print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index 3a06155602..07622a548c 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -26,11 +26,11 @@ functionality: path: ../fastmnn_feature/script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.3 setup: - type: r bioc: - batchelor - type: nextflow directives: - label: [ "midtime", lowcpu, highmem ] + label: [ midtime, lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index 186e190647..5c706da9ff 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -1,4 +1,3 @@ -# use method api spec __merge__: ../../api/comp_method_feature.yaml functionality: name: fastmnn_feature @@ -26,10 +25,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.3 setup: - type: r bioc: batchelor - type: nextflow directives: - label: [ "midtime", lowcpu, highmem ] + label: [ midtime, lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/script.R b/src/tasks/batch_integration/methods/fastmnn_feature/script.R index 7da33bc9cc..dbccd52d29 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/script.R +++ b/src/tasks/batch_integration/methods/fastmnn_feature/script.R @@ -30,14 +30,22 @@ cat("Reformat output\n") # reusing the same script for fastmnn_embed and fastmnn_feature return_type <- gsub("fastmnn_", "", meta[["functionality_name"]]) +output <- anndata::AnnData( + shape = adata$shape, + uns = list( + dataset_id = adata$uns[["dataset_id"]], + normalization_id = adata$uns[["normalization_id"]], + method_id = meta$functionality_name + ) +) + if (return_type == "feature") { layer <- as(SummarizedExperiment::assay(out, "reconstructed"), "sparseMatrix") - adata$layers[["corrected_counts"]] <- t(layer) + output$layers[["corrected_counts"]] <- t(layer) } else if (return_type == "embedding") { obsm <- SingleCellExperiment::reducedDim(out, "corrected") - adata$obsm[["X_emb"]] <- obsm + output$obsm[["X_emb"]] <- obsm } -cat("Store outputs\n") -adata$uns[["method_id"]] <- meta$functionality_name -zzz <- adata$write_h5ad(par$output, compression = "gzip") +cat("Write output to file\n") +zzz <- output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index a68b06f8b4..f43697e2e7 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.3 setup: - type: apt packages: cmake diff --git a/src/tasks/batch_integration/methods/liger/script.R b/src/tasks/batch_integration/methods/liger/script.R index a0ef9e9f42..b7159063ff 100644 --- a/src/tasks/batch_integration/methods/liger/script.R +++ b/src/tasks/batch_integration/methods/liger/script.R @@ -86,13 +86,23 @@ lobj <- rliger::runIntegration(lobj, k = 20) cat(">> Quantile normalization\n") lobj <- rliger::quantileNorm(lobj) -cat(">> Store dimred in adata\n") +cat(">> Store output\n") # remove dataset names from rownames for (name in names(rliger::rawData(lobj))) { rownames(lobj@H.norm) <- sub(paste0(name, "_"), "", rownames(lobj@H.norm)) } -adata$obsm[["X_emb"]] <- lobj@H.norm[rownames(adata), , drop = FALSE] -adata$uns[["method_id"]] <- meta$functionality_name -cat(">> Write AnnData to disk\n") -zzz <- adata$write_h5ad(par$output, compression = "gzip") +output <- anndata::AnnData( + uns = list( + dataset_id = adata$uns[["dataset_id"]], + normalization_id = adata$uns[["normalization_id"]], + method_id = meta$functionality_name + ), + obsm = list( + X_emb = lobj@H.norm[rownames(adata), , drop = FALSE] + ), + shape = adata$shape +) + +cat(">> Write AnnData to file\n") +zzz <- output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 7cbf7e82f6..3284514982 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -17,11 +17,11 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.3 setup: - type: r bioc: - batchelor - type: nextflow directives: - label: [ "midtime", lowcpu, highmem ] + label: [ midtime, lowcpu, highmem ] diff --git a/src/tasks/batch_integration/methods/mnn_correct/script.R b/src/tasks/batch_integration/methods/mnn_correct/script.R index 3f3476d7d4..0e6dfa2606 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/script.R +++ b/src/tasks/batch_integration/methods/mnn_correct/script.R @@ -7,7 +7,7 @@ suppressPackageStartupMessages({ }) ## VIASH START par <- list( - input = 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + input = 'resources_test/batch_integration/pancreas/dataset.h5ad', output = 'output.h5ad' ) meta <- list( @@ -26,8 +26,22 @@ out <- suppressWarnings(batchelor::mnnCorrect( cat("Reformat output\n") layer <- SummarizedExperiment::assay(out, "corrected") -adata$layers[["corrected_counts"]] <- as(t(layer), "sparseMatrix") +as(t(layer), "sparseMatrix") + + cat("Store outputs\n") -adata$uns[["method_id"]] <- meta$functionality_name -zzz <- adata$write_h5ad(par$output, compression = "gzip") +output <- anndata::AnnData( + uns = list( + dataset_id = adata$uns[["dataset_id"]], + normalization_id = adata$uns[["normalization_id"]], + method_id = meta$functionality_name + ), + layers = list( + corrected_counts = as(t(layer), "sparseMatrix") + ), + shape = adata$shape +) + +cat("Write output to file\n") +zzz <- output$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index 86aec82cd4..2c5075534b 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -22,10 +22,16 @@ functionality: mnn_full_unscaled: mnn_full_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: + # Due to a [ gcc-8 ] dependency in the mnnpy package, we need to use a python:3.8 image - type: docker image: python:3.8 setup: @@ -39,9 +45,8 @@ platforms: - pyyaml - requests - jsonschema - - scib==1.1.5 github: - chriscainx/mnnpy - type: nextflow directives: - label: [ "midtime", lowcpu, lowmem ] + label: [ midtime, lowcpu, lowmem ] diff --git a/src/tasks/batch_integration/methods/mnnpy/script.py b/src/tasks/batch_integration/methods/mnnpy/script.py index 0fdae66a0a..34e726133e 100644 --- a/src/tasks/batch_integration/methods/mnnpy/script.py +++ b/src/tasks/batch_integration/methods/mnnpy/script.py @@ -1,11 +1,11 @@ import anndata as ad -from scib.integration import mnn +import mnnpy ## VIASH START par = { 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'n_hvg': 2000, } meta = { 'functionality_name': 'foo', @@ -16,12 +16,38 @@ print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + print('Run mnn', flush=True) adata.X = adata.layers['normalized'] -adata.layers['corrected_counts'] = mnn(adata, batch='batch').X +split = [] +batch_categories = adata.obs['batch'].cat.categories +for i in batch_categories: + split.append(adata[adata.obs['batch'] == i].copy()) +corrected, _, _ = mnnpy.mnn_correct( + *split, + batch_key='batch', + batch_categories=batch_categories, + index_unique=None + ) + +print("Store outputs", flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + }, + layers={ + 'corrected_counts': corrected.X, + } +) -del adata.X print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index a52aed6713..fd124c05ec 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/pyliger/script.py b/src/tasks/batch_integration/methods/pyliger/script.py index 59cb2b895c..aa2250a857 100644 --- a/src/tasks/batch_integration/methods/pyliger/script.py +++ b/src/tasks/batch_integration/methods/pyliger/script.py @@ -64,9 +64,19 @@ print('>> Concatenate outputs', flush=True) ad_out = ad.concat(lobj.adata_list) -print('>> Store output', flush=True) -adata.obsm['X_emb'] = ad_out[adata.obs_names, :].obsm['H_norm'] -adata.uns['method_id'] = meta['functionality_name'] +print('Store output', flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + obsm={ + 'X_emb': ad_out[adata.obs_names, :].obsm['H_norm'] + }, + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + } +) -print("Write output to disk", flush=True) -adata.write_h5ad(par['output'], compression='gzip') +print("Write output to file", flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index 0ee13aa2d1..3fea89f30e 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -1,20 +1,8 @@ -# The API specifies which type of component this is. -# It contains specifications for: -# - The input/output files -# - Common parameters -# - A unit test __merge__: ../../api/comp_method_embedding.yaml - functionality: - # A unique identifier for your component (required). - # Can contain only lowercase letters or underscores. name: scalex_embed - # Metadata for your component info: - # A relatively short label, used when rendering visualisarions (required) label: SCALEX (embedding) - # A one sentence summary of how this method works (required). Used when - # rendering summary tables. summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space description : | SCALEX is a method for integrating heterogeneous single-cell data online using a VAE framework. Its generalised encoder disentangles batch-related components from batch-invariant biological components, which are then projected into a common cell-embedding space. @@ -29,12 +17,17 @@ functionality: scalex_feature_unscaled: scanorama_feature_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_embed/script.py b/src/tasks/batch_integration/methods/scalex_embed/script.py index 52f4d09428..1259fd130a 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/script.py +++ b/src/tasks/batch_integration/methods/scalex_embed/script.py @@ -1,5 +1,4 @@ import anndata as ad -import scanpy as sc import scalex ## VIASH START @@ -14,11 +13,14 @@ } ## VIASH END - - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + print('Run SCALEX', flush=True) adata.X = adata.layers['normalized'] adata = scalex.SCALEX( @@ -37,5 +39,18 @@ adata.obsm["X_emb"] = adata.obsm["latent"] print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + obsm={ + 'X_emb': adata.obsm['latent'], + }, + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 340b72b704..2cc484ab70 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -1,21 +1,8 @@ -# The API specifies which type of component this is. -# It contains specifications for: -# - The input/output files -# - Common parameters -# - A unit test __merge__: ../../api/comp_method_feature.yaml - functionality: - # A unique identifier for your component (required). - # Can contain only lowercase letters or underscores. name: scalex_feature - - # Metadata for your component info: - # A relatively short label, used when rendering visualisarions (required) label: SCALEX (feature) - # A one sentence summary of how this method works (required). Used when - # rendering summary tables. summary: Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space description : | SCALEX is a method for integrating heterogeneous single-cell data online using a VAE framework. Its generalised encoder disentangles batch-related components from batch-invariant biological components, which are then projected into a common cell-embedding space. @@ -30,12 +17,17 @@ functionality: scalex_feature_unscaled: scanorama_feature_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: diff --git a/src/tasks/batch_integration/methods/scalex_feature/script.py b/src/tasks/batch_integration/methods/scalex_feature/script.py index b67c85c932..ef33ee2a43 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/script.py +++ b/src/tasks/batch_integration/methods/scalex_feature/script.py @@ -6,7 +6,7 @@ par = { 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'n_hvg': 2000, } meta = { 'functionality_name' : 'foo', @@ -14,11 +14,14 @@ } ## VIASH END - - print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + print('Run SCALEX', flush=True) adata.X = adata.layers['normalized'] adata = scalex.SCALEX( @@ -34,8 +37,20 @@ outdir=None, gpu=0, ) -adata.layers['corrected_counts'] = adata.layers["impute"] -print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +print("Store output", flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + layers={ + 'corrected_counts': adata.layers["impute"], + }, + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + } +) + +print("Write output to file", flush=True) +output.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index df64ef8449..fda846438f 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -19,17 +19,21 @@ functionality: scanorama_embed_full_unscaled: scanorama_embed_full_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: - scanorama - - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] \ No newline at end of file + label: [ midtime, midmem, lowcpu ] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/scanorama_embed/script.py b/src/tasks/batch_integration/methods/scanorama_embed/script.py index 321d3163fb..950aa3b193 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/script.py +++ b/src/tasks/batch_integration/methods/scanorama_embed/script.py @@ -1,12 +1,11 @@ -import yaml import anndata as ad -from scib.integration import scanorama +import scanorama ## VIASH START par = { 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', 'output': 'output.h5ad', - 'hvg': True, + 'n_hvg': 2000, } meta = { 'functionality_name': 'foo', @@ -14,14 +13,62 @@ } ## VIASH END +# based on scib +# -> https://github.com/theislab/scib/blob/59ae6eee5e611d9d3db067685ec96c28804e9127/scib/utils.py#L51C1-L72C62 +def merge_adata(*adata_list, **kwargs): + """Merge adatas from list while remove duplicated ``obs`` and ``var`` columns + + :param adata_list: ``anndata`` objects to be concatenated + :param kwargs: arguments to be passed to ``anndata.AnnData.concatenate`` + """ + + if len(adata_list) == 1: + return adata_list[0] + + # Make sure that adatas do not contain duplicate columns + for _adata in adata_list: + for attr in ("obs", "var"): + df = getattr(_adata, attr) + dup_mask = df.columns.duplicated() + if dup_mask.any(): + print( + f"Deleting duplicated keys `{list(df.columns[dup_mask].unique())}` from `adata.{attr}`." + ) + setattr(_adata, attr, df.loc[:, ~dup_mask]) + + return ad.AnnData.concatenate(*adata_list, **kwargs) + + print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + print('Run scanorama', flush=True) adata.X = adata.layers['normalized'] -adata.obsm['X_emb'] = scanorama(adata, batch='batch').obsm['X_emb'] -del adata.X +split = [] +batch_categories = adata.obs['batch'].cat.categories +for i in batch_categories: + split.append(adata[adata.obs['batch'] == i].copy()) +corrected = scanorama.correct_scanpy(split, return_dimred=True) +corrected = merge_adata(*corrected, batch_key='batch', batch_categories=batch_categories, index_unique=None) + +print("Store output", flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + }, + obsm={ + 'X_emb': corrected.obsm["X_scanorama"], + } +) -print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write(par['output'], compression='gzip') +print("Write output to file", flush=True) +output.write(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index e691e5644a..86a3fe1d72 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -19,17 +19,21 @@ functionality: scanorama_feature_full_unscaled: scanorama_feature_full_scaled: preferred_normalization: log_cp10k_scaled + arguments: + - name: --n_hvg + type: integer + default: 2000 + description: Number of highly variable genes to use. resources: - type: python_script path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python pypi: - scanorama - - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [ midtime, midmem, lowcpu ] diff --git a/src/tasks/batch_integration/methods/scanorama_feature/script.py b/src/tasks/batch_integration/methods/scanorama_feature/script.py index b7ad5a8a08..614180ec99 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/script.py +++ b/src/tasks/batch_integration/methods/scanorama_feature/script.py @@ -1,6 +1,5 @@ -import yaml import anndata as ad -from scib.integration import scanorama +import scanorama ## VIASH START par = { @@ -14,15 +13,62 @@ } ## VIASH END +# based on scib +# -> https://github.com/theislab/scib/blob/59ae6eee5e611d9d3db067685ec96c28804e9127/scib/utils.py#L51C1-L72C62 +def merge_adata(*adata_list, **kwargs): + """Merge adatas from list while remove duplicated ``obs`` and ``var`` columns + + :param adata_list: ``anndata`` objects to be concatenated + :param kwargs: arguments to be passed to ``anndata.AnnData.concatenate`` + """ + + if len(adata_list) == 1: + return adata_list[0] + + # Make sure that adatas do not contain duplicate columns + for _adata in adata_list: + for attr in ("obs", "var"): + df = getattr(_adata, attr) + dup_mask = df.columns.duplicated() + if dup_mask.any(): + print( + f"Deleting duplicated keys `{list(df.columns[dup_mask].unique())}` from `adata.{attr}`." + ) + setattr(_adata, attr, df.loc[:, ~dup_mask]) + + return ad.AnnData.concatenate(*adata_list, **kwargs) + + print('Read input', flush=True) adata = ad.read_h5ad(par['input']) +if par['n_hvg']: + print(f"Select top {par['n_hvg']} high variable genes", flush=True) + idx = adata.var['hvg_score'].to_numpy().argsort()[::-1][:par['n_hvg']] + adata = adata[:, idx].copy() + print('Run scanorama', flush=True) adata.X = adata.layers['normalized'] -adata.layers['corrected_counts'] = scanorama(adata, batch='batch').X +split = [] +batch_categories = adata.obs['batch'].cat.categories +for i in batch_categories: + split.append(adata[adata.obs['batch'] == i].copy()) +corrected = scanorama.correct_scanpy(split, return_dimred=True) +corrected = merge_adata(*corrected, batch_key='batch', batch_categories=batch_categories, index_unique=None) -del adata.X +print("Store output", flush=True) +output = ad.AnnData( + obs=adata.obs[[]], + var=adata.var[[]], + uns={ + 'dataset_id': adata.uns['dataset_id'], + 'normalization_id': adata.uns['normalization_id'], + 'method_id': meta['functionality_name'], + }, + layers={ + 'corrected_counts': corrected.X, + } +) -print("Store outputs", flush=True) -adata.uns['method_id'] = meta['functionality_name'] -adata.write_h5ad(par['output'], compression='gzip') +print("Write output to file", flush=True) +output.write_h5ad(par['output'], compression='gzip') From 434c8b9868f8f49ad5b0c9f9127cb4acbf3151b0 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 11 Apr 2024 08:12:50 +0200 Subject: [PATCH 1194/1233] Update nextflow error strategy (#424) * Update nextflow error strategy * Update relevant exit code Former-commit-id: a1c27c78a13bfd0b9c91f8fbfd28c2b6b6303fdf --- src/wf_utils/labels_tw.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 6e19a98ee4..161a23573e 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -5,7 +5,7 @@ process { disk = 50.GB // Retry for exit codes that have something to do with memory issues - errorStrategy = { task.attempt < 3 && task.exitStatus in ((130..145) + 104) ? 'retry' : 'ignore' } + errorStrategy = { task.attempt < 3 && task.exitStatus in (137) ? 'retry' : 'ignore' } maxRetries = 3 maxMemory = null From 1c188824fc079af7663305a1bfa986e174295a9b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 11 Apr 2024 12:58:42 +0200 Subject: [PATCH 1195/1233] Finetune task readme (#427) * allow to finetune the task readme * fix dangling slash * restructure arguments * fix test Former-commit-id: aa12980c865d559cba9a70b7f7407a19d06ab4f7 --- src/common/create_task_readme/config.vsh.yaml | 45 ++++++++++++------- src/common/create_task_readme/render_all.sh | 2 + src/common/create_task_readme/script.R | 25 ++++++++--- src/common/create_task_readme/test.R | 11 ++--- 4 files changed, 57 insertions(+), 26 deletions(-) diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index fba4f3a4d4..6967466c0c 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -3,21 +3,36 @@ functionality: namespace: common description: | Create a README for the task. - arguments: - - type: string - name: --task - description: Which task the component will be added to. - example: denoising - - type: file - name: --output - direction: output - description: Path to the component directory. Suggested location is `src//README.md`. - default: src/tasks/${VIASH_PAR_TASK}/README.md - - type: file - name: --viash_yaml - description: | - Path to the project config file. Needed for knowing the relative location of a file to the project root. - default: "_viash.yaml" + argument_groups: + - name: Inputs + arguments: + - type: string + name: --task + description: Which task the component will be added to. + example: denoising + required: false + - type: file + name: --task_dir + description: Path to the task directory. + default: src/tasks/${VIASH_PAR_TASK} + required: false + - type: file + name: --viash_yaml + description: | + Path to the project config file. Needed for knowing the relative location of a file to the project root. + default: "_viash.yaml" + - type: string + name: --github_url + description: | + URL to the GitHub repository. Needed for linking to the source code. + default: "https://github.com/openproblems-bio/openproblems-v2/tree/main/" + - name: Outputs + arguments: + - type: file + name: --output + direction: output + description: Path to the component directory. Suggested location is `src/tasks//README.md`. + default: src/tasks/${VIASH_PAR_TASK}/README.md resources: - type: r_script path: script.R diff --git a/src/common/create_task_readme/render_all.sh b/src/common/create_task_readme/render_all.sh index 00dc2a8db0..e44195c1ed 100755 --- a/src/common/create_task_readme/render_all.sh +++ b/src/common/create_task_readme/render_all.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -e + TASK_IDS=`ls src/tasks` for task_id in $TASK_IDS; do diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 8c7d88586a..9f74d52b4c 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -5,8 +5,10 @@ library(dplyr, quietly = TRUE, warn.conflicts = FALSE) ## VIASH START par <- list( "task" = "batch_integration", + "task_dir" = "src/tasks/batch_integration", "output" = "src/tasks/batch_integration/README.md", - "viash_yaml" = "_viash.yaml" + "viash_yaml" = "_viash.yaml", + "github_url" = "https://github.com/openproblems-bio/openproblems-v2/tree/main/" ) meta <- list( "resources_dir" = "src/common/helper_functions", @@ -14,15 +16,23 @@ meta <- list( ) ## VIASH END +if (is.null(par$task) && is.null(par$task_dir)) { + stop("Either 'task' or 'task_dir' must be provided") +} +if (is.null(par$viash_yaml)) { + stop("Argument 'viash_yaml' must be provided") +} +if (is.null(par$output)) { + stop("Argument 'output' must be provided") +} + # import helper function source(paste0(meta["resources_dir"], "/read_and_merge_yaml.R")) source(paste0(meta["resources_dir"], "/strip_margin.R")) source(paste0(meta["resources_dir"], "/read_api_files.R")) cat("Read task info\n") -task_dir <- paste0(dirname(par[["viash_yaml"]]), "/src/tasks/", par[["task"]]) %>% - gsub("^\\./", "", .) -task_api <- read_task_api(task_dir) +task_api <- read_task_api(par[["task_dir"]]) # determine ordering root <- .task_graph_get_root(task_api) @@ -55,7 +65,10 @@ authors_str <- } cat("Generate qmd content\n") -task_dir_short <- gsub(".*openproblems-v2/", "", task_dir) +relative_path <- par[["task_dir"]] %>% + gsub(paste0(dirname(par[["viash_yaml"]]), "/*"), "", .) %>% + gsub("/*$", "", .) +source_url <- paste0(par[["github_url"]], relative_path) qmd_content <- strip_margin(glue::glue(" §--- §title: \"{task_api$task_info$label}\" @@ -64,7 +77,7 @@ qmd_content <- strip_margin(glue::glue(" § §{task_api$task_info$summary} § - §Path: [`{task_dir_short}`](https://github.com/openproblems-bio/openproblems-v2/tree/main/{task_dir_short}) + §Path: [`{relative_path}`]({source_url}) § §## Motivation § diff --git a/src/common/create_task_readme/test.R b/src/common/create_task_readme/test.R index abf3f4521f..9af1fe9738 100644 --- a/src/common/create_task_readme/test.R +++ b/src/common/create_task_readme/test.R @@ -1,6 +1,6 @@ +requireNamespace("assertthat", quietly = TRUE) ## VIASH START - ## VIASH END opv2 <- paste0(meta$resources_dir, "/openproblems-v2") @@ -8,10 +8,11 @@ output_path <- "output.md" cat(">> Running the script as test\n") system(paste( - meta["executable"], - "--task", "label_projection", - "--output", output_path, - "--viash_yaml", paste0(opv2, "/_viash.yaml") + meta["executable"], + "--task", "label_projection", + "--output", output_path, + "--task_dir", paste0(opv2, "/src/tasks/label_projection"), + "--viash_yaml", paste0(opv2, "/_viash.yaml") )) cat(">> Checking whether output files exist\n") From fd7cddb6152825999e68e87ec7f8d63c5215eb59 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 12 Apr 2024 09:42:40 +0200 Subject: [PATCH 1196/1233] Use CLR and TFIDF for ADT and ATAC normalisation (#428) * add normalisation methods for atac and adt * use normalisation methods in multimodal workflows * use from_layer to_layer * fix tfidf * fix inconsistency Former-commit-id: 31d2c2c9d0dce283d83c4d79dee1110b4829efd5 --- .../normalization/atac_tfidf/config.vsh.yaml | 22 +++++++++++++++ .../normalization/atac_tfidf/script.py | 26 +++++++++++++++++ .../normalization/prot_clr/config.vsh.yaml | 26 +++++++++++++++++ src/datasets/normalization/prot_clr/script.py | 28 +++++++++++++++++++ .../resource_test_scripts/neurips2021_bmmc.sh | 2 ++ .../config.vsh.yaml | 2 ++ .../main.nf | 14 ++++------ .../config.vsh.yaml | 2 ++ .../main.nf | 15 ++++++---- 9 files changed, 124 insertions(+), 13 deletions(-) create mode 100644 src/datasets/normalization/atac_tfidf/config.vsh.yaml create mode 100644 src/datasets/normalization/atac_tfidf/script.py create mode 100644 src/datasets/normalization/prot_clr/config.vsh.yaml create mode 100644 src/datasets/normalization/prot_clr/script.py diff --git a/src/datasets/normalization/atac_tfidf/config.vsh.yaml b/src/datasets/normalization/atac_tfidf/config.vsh.yaml new file mode 100644 index 0000000000..83c152101a --- /dev/null +++ b/src/datasets/normalization/atac_tfidf/config.vsh.yaml @@ -0,0 +1,22 @@ +__merge__: ../../api/comp_normalization.yaml +functionality: + name: "atac_tfidf" + description: | + Transform peak counts with TF-IDF (Term Frequency - Inverse Document Frequency). + + TF: peak counts are normalised by total number of counts per cell DF: total number of counts for each peak IDF: number of cells divided by DF + + By default, log(TF) * log(IDF) is returned. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - muon + - type: nextflow + directives: + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/normalization/atac_tfidf/script.py b/src/datasets/normalization/atac_tfidf/script.py new file mode 100644 index 0000000000..ecb772bd64 --- /dev/null +++ b/src/datasets/normalization/atac_tfidf/script.py @@ -0,0 +1,26 @@ +import anndata as ad +from muon import atac as ac + +## VIASH START +par = { + 'input': "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad", + 'output': "output_norm.h5ad" +} +meta = { + 'functionality_name': "tfidf" +} +## VIASH END + +print("Load data", flush=True) +adata = ad.read_h5ad(par['input']) + +print("Normalize data", flush=True) +input_adata = ad.AnnData(X=adata.layers["counts"]) +normalized_counts = ac.pp.tfidf(input_adata, inplace=False) + +print("Store output in adata", flush=True) +adata.layers[par["layer_output"]] = normalized_counts +adata.uns["normalization_id"] = par["normalization_id"] or meta['functionality_name'] + +print("Write data", flush=True) +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/normalization/prot_clr/config.vsh.yaml b/src/datasets/normalization/prot_clr/config.vsh.yaml new file mode 100644 index 0000000000..c12c8afdbc --- /dev/null +++ b/src/datasets/normalization/prot_clr/config.vsh.yaml @@ -0,0 +1,26 @@ +__merge__: ../../api/comp_normalization.yaml +functionality: + name: "prot_clr" + description: | + Perform center log ratio (CLR) normalization on input CITE-seq data (Stoeckius et al. 2017). + + The CLR transformation is defined as: + + $$ + x_{\text{clr}} = \log\left(\frac{x}{g(x)}\right) + $$ + + where $\(g(x)\)$ is the geometric mean of the row $\(x\)$. + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.2 + setup: + - type: python + packages: + - muon + - type: nextflow + directives: + label: [ midtime, midmem, midcpu ] diff --git a/src/datasets/normalization/prot_clr/script.py b/src/datasets/normalization/prot_clr/script.py new file mode 100644 index 0000000000..3f0a2fb3fd --- /dev/null +++ b/src/datasets/normalization/prot_clr/script.py @@ -0,0 +1,28 @@ +import anndata as ad +from muon import prot as pt + +## VIASH START +par = { + 'input': "resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad", + 'output': "output_norm.h5ad" +} +meta = { + 'functionality_name': "clr" +} +## VIASH END + +print("Load data", flush=True) +adata = ad.read_h5ad(par['input']) + +print("Normalize data", flush=True) +input_adata = ad.AnnData(X=adata.layers["counts"]) +normalized_counts = pt.pp.clr(input_adata, inplace=False) +if not normalized_counts: + raise RuntimeError("CLR failed to return the requested output layer") + +print("Store output in adata", flush=True) +adata.layers[par["layer_output"]] = normalized_counts.X +adata.uns["normalization_id"] = par["normalization_id"] or meta['functionality_name'] + +print("Write data", flush=True) +adata.write_h5ad(par['output'], compression="gzip") diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 2e40f86734..9def39d9c9 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -1,5 +1,7 @@ #!/bin/bash +set -e + params_file="/tmp/datasets_openproblems_neurips2021_params.yaml" cat > "$params_file" << 'HERE' diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml index aa991910bf..8d3ca51d0b 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/config.vsh.yaml @@ -122,6 +122,8 @@ functionality: - name: datasets/normalization/log_scran_pooling - name: datasets/normalization/sqrt_cp - name: datasets/normalization/l1_sqrt + - name: datasets/normalization/prot_clr + - name: datasets/normalization/atac_tfidf - name: datasets/processors/subsample - name: datasets/processors/svd - name: datasets/processors/hvg diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index a5bb6bf4ec..1d73ab4429 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -86,7 +86,7 @@ workflow run_wf { ] ) - // run normalization methods + // run mod1 normalization methods | runEach( components: normalization_methods, id: { id, state, comp -> @@ -109,18 +109,16 @@ workflow run_wf { ) // run normalization methods on second modality - // TODO: change this normalization method - | log_cp.run( - key: "log_cp10k_adt", + // TODO: can we change this to DSB? + | prot_clr.run( runIf: { id, state -> state.mod2 == "ADT" }, - args: [normalization_id: "log_cp10k", n_cp: 10000], + args: [normalization_id: "prot_clr"], fromState: ["input": "raw_mod2"], toState: ["normalized_mod2": "output"] ) - | log_cp.run( - key: "log_cp10k_atac", + | atac_tfidf.run( runIf: { id, state -> state.mod2 == "ATAC" }, - args: [normalization_id: "log_cp10k", n_cp: 10000], + args: [normalization_id: "atac_tfidf"], fromState: ["input": "raw_mod2"], toState: ["normalized_mod2": "output"] ) diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index ad607c2229..d9de5d0728 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -137,6 +137,8 @@ functionality: - name: datasets/normalization/log_scran_pooling - name: datasets/normalization/sqrt_cp - name: datasets/normalization/l1_sqrt + - name: datasets/normalization/prot_clr + - name: datasets/normalization/atac_tfidf - name: datasets/processors/subsample - name: datasets/processors/svd - name: datasets/processors/hvg diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index ef82b62cd7..6143b43ec9 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -114,11 +114,16 @@ workflow run_wf { ) // run normalization methods on second modality - | runEach( - components: normalization_methods, - filter: { id, state, comp -> - comp.name == state.normalization_id - }, + // TODO: can we change this to DSB? + | prot_clr.run( + runIf: { id, state -> state.mod2 == "ADT" }, + args: [normalization_id: "prot_clr"], + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] + ) + | atac_tfidf.run( + runIf: { id, state -> state.mod2 == "ATAC" }, + args: [normalization_id: "atac_tfidf"], fromState: ["input": "raw_mod2"], toState: ["normalized_mod2": "output"] ) From 5efcba456340193022eaf601caefd7ad9d62ed14 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 12 Apr 2024 13:13:30 +0200 Subject: [PATCH 1197/1233] add configs Former-commit-id: da84b3620f23a191f1fcbe1ba396ae8c30c0918e --- .../resource_scripts/openproblems_v1_multimodal.sh | 14 +++++++++++++- .../resource_test_scripts/neurips2021_bmmc.sh | 3 ++- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 7f5032f49d..573a47c817 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -57,6 +57,17 @@ output_state: '$id/state.yaml' publish_dir: s3://openproblems-data/resources/datasets HERE + +cat > /tmp/nextflow.config << HERE +process { + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + errorStrategy = "ignore" +} +HERE + tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -64,4 +75,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --workspace 53907369739130 \ --compute-env 1pK56PjjzeraOOC2LDZvN2 \ --params-file "$params_file" \ - --labels openproblems_v1_multimodal,dataset_loader \ No newline at end of file + --labels openproblems_v1_multimodal,dataset_loader \ + --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 9def39d9c9..189969617e 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -54,7 +54,8 @@ nextflow run . \ -profile docker \ -resume \ --publish_dir resources_test/common \ - -params-file "$params_file" + -params-file "$params_file" \ + -c src/wf_utils/labels.config # tw launch https://github.com/openproblems-bio/openproblems-v2.git \ # --revision main_build \ From 6f7ef2c1a451f9bd5e0fd7addb1702d6bee9daa3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Tue, 16 Apr 2024 13:27:20 +0200 Subject: [PATCH 1198/1233] Add mod params (#430) Former-commit-id: 2f43dd753ce8af73a9b93cfe4c9fd4b84ba164c3 --- .../resource_scripts/openproblems_v1_multimodal.sh | 6 ++++++ .../resource_test_scripts/scicar_cell_lines.sh | 2 ++ .../process_openproblems_v1_multimodal/config.vsh.yaml | 10 ++++++++++ .../process_openproblems_v1_multimodal/main.nf | 1 + 4 files changed, 19 insertions(+) diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 573a47c817..1fb8b2adf0 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -20,6 +20,8 @@ param_list: dataset_organism: homo_sapiens layer_counts: counts var_feature_name: index + mod1: GEX + mod2: ADT - id: openproblems_v1_multimodal/scicar_cell_lines input_id: scicar_cell_lines @@ -33,6 +35,8 @@ param_list: layer_counts: counts var_feature_id: index var_feature_name: gene_short_name + mod1: GEX + mod2: ATAC - id: openproblems_v1_multimodal/scicar_mouse_kidney input_id: scicar_mouse_kidney @@ -47,6 +51,8 @@ param_list: layer_counts: counts var_feature_id: index var_feature_name: gene_short_name + mod1: GEX + mod2: ATAC normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] output_dataset_mod1: '$id/dataset_mod1.h5ad' diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 8aa67c556f..895cde58cb 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -30,6 +30,8 @@ nextflow run . \ --dataset_summary "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells" \ --dataset_description "sciCAR is a combinatorial indexing-based assay that jointly measures cellular transcriptomes and the accessibility of cellular chromatin in the same cells. Here, we use two sciCAR datasets that were obtained from the same study. The first dataset contains 4,825 cells from three cell lines (HEK293T cells, NIH/3T3 cells, and A549 cells) at multiple timepoints (0, 1 hour, 3 hours) after dexamethasone treatment. The second dataset contains 11,233 cells from wild-type adult mouse kidney." \ --dataset_organism "[homo_sapiens, mus_musculus]" \ + --mod1 GEX \ + --mod2 ATAC \ --do_subsample true \ --n_obs 600 \ --n_vars 1500 \ diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index d9de5d0728..b21bb34482 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -39,6 +39,16 @@ functionality: type: "string" description: "Location of where to find the feature names. Can be set to index if the feature names are the index." default: index + - name: "--mod1" + type: string + description: Name of the first modality. + required: true + example: GEX + - name: "--mod2" + type: string + description: Name of the second modality. + required: true + example: ADT - name: Metadata arguments: - name: "--dataset_name" diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index 6143b43ec9..da4d34ef5f 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -145,6 +145,7 @@ workflow run_wf { ) | hvg.run( + key: "hvg_mod2", fromState: [ "input": "svd_mod2" ], toState: [ "hvg_mod2": "output" ] ) From c69889587bb5b80e59dd3506a5fb44a7086611b9 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Tue, 16 Apr 2024 18:21:58 +0530 Subject: [PATCH 1199/1233] Update spatial decomposition resource scripts (#429) * add resource scripts * add spatial data summary to simulated dataset * add simulated dataset properties in comment * update id * remove id from params.yaml Co-authored-by: Kai Waldrant * add label highmem to config * check if .obs contains key is_primary_data --------- Co-authored-by: Kai Waldrant Former-commit-id: 949427cd2a6927a19a61ffc2f94d6cdd0be3cac2 --- .../dataset_simulator/script.py | 5 +-- .../resources_scripts/process_datasets.sh | 36 +++++++++++++++++++ .../resources_scripts/run_benchmark.sh | 22 ++++++++++++ .../resources_scripts/run_benchmark_test.sh | 0 .../workflows/process_datasets/run_test.sh | 11 ------ 5 files changed, 61 insertions(+), 13 deletions(-) delete mode 100755 src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh diff --git a/src/tasks/spatial_decomposition/dataset_simulator/script.py b/src/tasks/spatial_decomposition/dataset_simulator/script.py index 9fc09214de..48daafd374 100644 --- a/src/tasks/spatial_decomposition/dataset_simulator/script.py +++ b/src/tasks/spatial_decomposition/dataset_simulator/script.py @@ -186,10 +186,11 @@ def filter_genes_cells(adata): umi_lb=par['umi_lb'], umi_ub=par['umi_ub'] ) -adata.uns["spatial_data_summary"] = f"Dirichlet alpha={par['alpha']}" +adata_merged.uns["spatial_data_summary"] = f"Dirichlet alpha={par['alpha']}" filter_genes_cells(adata_merged) adata_merged.X = None -adata_merged.obs['is_primary_data'] = adata_merged.obs['is_primary_data'].fillna(False) +if "is_primary_data" in adata_merged.obs: + adata_merged.obs['is_primary_data'] = adata_merged.obs['is_primary_data'].fillna(False) print("Writing output to file") adata_merged.write_h5ad(par["simulated_data"]) diff --git a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh index e69de29bb2..b435a8eeb8 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh @@ -0,0 +1,36 @@ +#!/bin/bash + +# Simulating spot-resolution spatial data with alpha = 1 + +cat > /tmp/params.yaml << 'HERE' +id: spatial_decomposition_process_datasets +input_states: s3://openproblems-data/resources/datasets/**/state.yaml +settings: '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad", "alpha": 1.0, "simulated_data": "$id/dataset_simulated.h5ad"}' +rename_keys: 'input:output_dataset' +output_state: "$id/state.yaml" +publish_dir: s3://openproblems-data/resources/spatial_decomposition/datasets +HERE + +cat > /tmp/nextflow.config << HERE +process { + executor = 'awsbatch' + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } + withLabel:highmem { + memory = '350GB' + } +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config /tmp/nextflow.config \ + # --labels spatial_decomposition,process_datasets diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh index e69de29bb2..a87f0c889c 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" +publish_dir="s3://openproblems-data/resources/spatial_decomposition/results/${RUN_ID}" + +cat > /tmp/params.yaml << HERE +input_states: s3://openproblems-data/resources/spatial_decomposition/datasets/**/state.yaml +rename_keys: 'input_single_cell:output_single_cell,input_spatial_masked:output_spatial_masked,input_solution:output_solution' +output_state: "state.yaml" +publish_dir: "$publish_dir" +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/spatial_decomposition/workflows/run_benchmark/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file /tmp/params.yaml \ + --entry-name auto \ + --config src/wf_utils/labels_tw.config \ + --labels spatial_decomposition,full \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark_test.sh deleted file mode 100755 index e69de29bb2..0000000000 diff --git a/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh b/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh index e3a6bee7af..432c924789 100644 --- a/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh +++ b/src/tasks/spatial_decomposition/workflows/process_datasets/run_test.sh @@ -11,17 +11,6 @@ cd "$REPO_ROOT" set -e -# nextflow run . \ -# -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ -# -profile docker \ -# -entry auto \ -# -c src/wf_utils/labels_ci.config \ -# --id run_test \ -# --input_states "resources_test/common/**/state.yaml" \ -# --rename_keys 'input:output_dataset' \ -# --settings '{"output_spatial_masked": "$id/spatial_masked.h5ad", "output_single_cell": "$id/single_cell_ref.h5ad", "output_solution": "$id/solution.h5ad"}' \ -# --publish_dir "resources_test/spatial_decomposition" - # generate spatial dataset nextflow run . \ -main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ From f073e7bf2c0f732a77f35547c8f31f4025e7ee57 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Wed, 17 Apr 2024 16:39:52 +0530 Subject: [PATCH 1200/1233] FIx dataset simulator (#431) * explicitly convert non-string objects in .obs slots to categoricals * Add info about fix in comments Former-commit-id: 624c44219ad04e350e5eb38ab2beb4b2c9179a03 --- .../dataset_simulator/script.py | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/src/tasks/spatial_decomposition/dataset_simulator/script.py b/src/tasks/spatial_decomposition/dataset_simulator/script.py index 48daafd374..901d7def5f 100644 --- a/src/tasks/spatial_decomposition/dataset_simulator/script.py +++ b/src/tasks/spatial_decomposition/dataset_simulator/script.py @@ -23,9 +23,11 @@ ## VIASH END CELLTYPE_MIN_CELLS = 25 + # Reading input dataset adata = ad.read_h5ad(par['input']) + def generate_synthetic_dataset( adata: ad.AnnData, alpha: Union[float, Sequence] = 1.0, @@ -162,12 +164,14 @@ def generate_synthetic_dataset( adata_merged.uns["cell_type_names"] = uni_labs return adata_merged + def filter_celltypes(adata, min_cells=CELLTYPE_MIN_CELLS): """Filter rare celltypes from an AnnData""" celltype_counts = adata.obs["cell_type"].value_counts() >= min_cells keep_cells = np.isin(adata.obs["cell_type"], celltype_counts.index[celltype_counts]) return adata[adata.obs.index[keep_cells]].copy() + def filter_genes_cells(adata): """Remove empty cells and genes.""" if "var_names_all" not in adata.uns: @@ -176,6 +180,7 @@ def filter_genes_cells(adata): sc.pp.filter_genes(adata, min_cells=1) sc.pp.filter_cells(adata, min_counts=2) + adata.X = adata.layers["counts"] sc.pp.filter_genes(adata, min_counts=10) adata_merged = generate_synthetic_dataset(adata, @@ -189,8 +194,15 @@ def filter_genes_cells(adata): adata_merged.uns["spatial_data_summary"] = f"Dirichlet alpha={par['alpha']}" filter_genes_cells(adata_merged) adata_merged.X = None -if "is_primary_data" in adata_merged.obs: - adata_merged.obs['is_primary_data'] = adata_merged.obs['is_primary_data'].fillna(False) + +# Convert non-string objects to categoricals to avoid +# TypeError: Can't implicitly convert non-string objects to strings +# In this case, the error is raised when there are NA values in .obs columns with dtype object (boolean). +# The resulting anndata object cannot be written to a file. +# This conversion is handled in later versions of anndata (0.10) +for col in adata_merged.obs: + if adata_merged.obs[col].dtype == 'object': + adata_merged.obs[col] = adata_merged.obs[col].astype('category') print("Writing output to file") adata_merged.write_h5ad(par["simulated_data"]) From 2b18e331e37c570a039d23a010212291c6626f73 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 17 Apr 2024 21:41:59 +0200 Subject: [PATCH 1201/1233] update readme component Former-commit-id: 80824d9d5d07b0d0721c6a7495e2110f3a533547 --- src/common/create_task_readme/script.R | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 9f74d52b4c..6a38201952 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -75,9 +75,16 @@ qmd_content <- strip_margin(glue::glue(" §format: gfm §--- § + § + § §{task_api$task_info$summary} § - §Path: [`{relative_path}`]({source_url}) + §Path to source: [`{relative_path}`]({source_url}) + § + §{task_api$task_info$readme} § §## Motivation § From 67c310a6b915be91ec81269d6238e415ac49e5df Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 18 Apr 2024 12:03:31 +0200 Subject: [PATCH 1202/1233] fix readme Former-commit-id: 4ec99374d27374ab8261f77a535e6ca326ce5c43 --- src/common/create_task_readme/script.R | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/common/create_task_readme/script.R b/src/common/create_task_readme/script.R index 6a38201952..55388ea7ed 100644 --- a/src/common/create_task_readme/script.R +++ b/src/common/create_task_readme/script.R @@ -63,6 +63,16 @@ authors_str <- } else { "" } +readme_str <- + if (is.null(task_api$task_info$readme) || is.na(task_api$task_info$readme)) { + "" + } else { + paste0( + "\n## README\n\n", + task_api$task_info$readme, + "\n" + ) + } cat("Generate qmd content\n") relative_path <- par[["task_dir"]] %>% @@ -84,7 +94,7 @@ qmd_content <- strip_margin(glue::glue(" § §Path to source: [`{relative_path}`]({source_url}) § - §{task_api$task_info$readme} + §{readme_str} § §## Motivation § From 9d237f673debcc08e3e12f0536ac5ee7b64e2fa7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 18 Apr 2024 15:54:44 +0200 Subject: [PATCH 1203/1233] fix regex to allow optional normalisation Former-commit-id: 388b1094059592e77cd21edee13d1d171bab112a --- .../process_task_results/get_results/script.R | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index 492d8ca1e7..111eb8a2d5 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -9,10 +9,14 @@ library(purrr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START +dir <- "/home/rcannood/workspace/openproblems-bio/task-dge-perturbation-prediction/work/8f/1ee60cd1fbfddd98eadcc11f3fb1d0/_viash_par" par <- list( - input_scores = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_scores_1/score_uns.yaml", - input_execution = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_execution_1/trace.txt", - input_metric_info = "work/0b/80ef7640d545eecbb7f5656bf3981b/_viash_par/input_metric_info_1/output.json", + task_id = "task_1", + input_scores = paste0(dir, "/input_scores_1/score_uns.yaml"), + input_execution = paste0(dir, "/input_execution_1/trace.txt"), + input_dataset_info = paste0(dir, "/input_dataset_info_1/output.json"), + input_method_info = paste0(dir, "/input_method_info_1/output.json"), + input_metric_info = paste0(dir, "/input_metric_info_1/output.json"), output_results = "output/results.json", output_metric_execution_info = "output/metric_execution_info.json" ) @@ -126,14 +130,14 @@ scores <- raw_scores %>% ) # read nxf log and process the task id -id_regex <- "^.*:(.*)_process \\((.*)/([^\\.]*)(.[^\\.]*)?\\.(.*)\\)$" +id_regex <- "^.*:(.*)_process \\((.*)(/[^\\.]*)?(.[^\\.]*)?\\.(.*)\\)$" trace <- readr::read_tsv(par$input_execution) %>% mutate( id = name, process_id = stringr::str_extract(id, id_regex, 1L), dataset_id = stringr::str_extract(id, id_regex, 2L), - normalization_id = stringr::str_extract(id, id_regex, 3L), + normalization_id = gsub("^/", "", stringr::str_extract(id, id_regex, 3L)), grp4 = gsub("^\\.", "", stringr::str_extract(id, id_regex, 4L)), grp5 = stringr::str_extract(id, id_regex, 5L), submit = strptime(submit, "%Y-%m-%d %H:%M:%S"), From a6b96686e5af9fb26c92b4dc06f349b4113dc37d Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 19 Apr 2024 11:30:20 +0200 Subject: [PATCH 1204/1233] Restore original script (#432) Former-commit-id: b3a00b3b5c2918c50399a9980f5b3942bfb2868b --- .../methods/guanlab_dengkw_pm/config.vsh.yaml | 4 +- .../methods/guanlab_dengkw_pm/script.py | 64 ++++++++++++++----- 2 files changed, 50 insertions(+), 18 deletions(-) diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index 7e6ba58390..cfd891969a 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.3 setup: - type: python packages: @@ -34,4 +34,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "hightime", highmem, highcpu] + label: [ midtime, highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py index 4c3d8f7897..fb4d38529f 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -2,6 +2,7 @@ import numpy as np import gc from scipy.sparse import csc_matrix +from sklearn.decomposition import TruncatedSVD from sklearn.gaussian_process.kernels import RBF from sklearn.kernel_ridge import KernelRidge @@ -51,21 +52,52 @@ ) print('Determine parameters by the modalities', flush=True) -mod1_type = input_train_mod1.uns["modality"].upper() -mod2_type = input_train_mod2.uns["modality"].upper() - -scale = 10 -alpha = 0.1 if (mod1_type == "ATAC" or mod2_type == "ATAC") else 0.2 - -train_norm = input_train_mod1.to_df(layer="normalized").values.astype(np.float32) -test_norm = input_test_mod1.to_df(layer="normalized").values.astype(np.float32) - -train_gs = input_train_mod2.to_df(layer="normalized").values.astype(np.float32) - -del input_train_mod1 -del input_test_mod1 -del input_train_mod2 -gc.collect() +mod1_type = input_train_mod1.uns["modality"] +mod1_type = mod1_type.upper() +mod2_type = input_train_mod2.uns["modality"] +mod2_type = mod2_type.upper() +n_comp_dict = { + ("GEX", "ADT"): (300, 70, 10, 0.2), + ("ADT", "GEX"): (None, 50, 10, 0.2), + ("GEX", "ATAC"): (1000, 50, 10, 0.1), + ("ATAC", "GEX"): (100, 70, 10, 0.1) + } +print(f"{mod1_type}, {mod2_type}", flush=True) +n_mod1, n_mod2, scale, alpha = n_comp_dict[(mod1_type, mod2_type)] +print(f"{n_mod1}, {n_mod2}, {scale}, {alpha}", flush=True) + +# Perform PCA on the input data +print('Models using the Truncated SVD to reduce the dimension', flush=True) + +if n_mod1 is not None and n_mod1 < input_train.shape[1]: + embedder_mod1 = TruncatedSVD(n_components=n_mod1) + mod1_pca = embedder_mod1.fit_transform(input_train.layers["counts"]).astype(np.float32) + train_matrix = mod1_pca[input_train.obs['group'] == 'train'] + test_matrix = mod1_pca[input_train.obs['group'] == 'test'] +else: + train_matrix = input_train_mod1.to_df(layer="counts").values.astype(np.float32) + test_matrix = input_test_mod1.to_df(layer="counts").values.astype(np.float32) + +if n_mod2 is not None and n_mod2 < input_train_mod2.shape[1]: + embedder_mod2 = TruncatedSVD(n_components=n_mod2) + train_gs = embedder_mod2.fit_transform(input_train_mod2.layers["counts"]).astype(np.float32) +else: + train_gs = input_train_mod2.to_df(layer="counts").values.astype(np.float32) + +del input_train + +print('Running normalization ...', flush=True) +train_sd = np.std(train_matrix, axis=1).reshape(-1, 1) +train_sd[train_sd == 0] = 1 +train_norm = (train_matrix - np.mean(train_matrix, axis=1).reshape(-1, 1)) / train_sd +train_norm = train_norm.astype(np.float32) +del train_matrix + +test_sd = np.std(test_matrix, axis=1).reshape(-1, 1) +test_sd[test_sd == 0] = 1 +test_norm = (test_matrix - np.mean(test_matrix, axis=1).reshape(-1, 1)) / test_sd +test_norm = test_norm.astype(np.float32) +del test_matrix print('Running KRR model ...', flush=True) y_pred = np.zeros((pred_dimx, pred_dimy), dtype=np.float32) @@ -83,7 +115,7 @@ krr = KernelRidge(alpha=alpha, kernel=kernel) print('Fitting KRR ... ', flush=True) krr.fit(train_norm[feature_obs.batch.isin(batch)], train_gs[gs_obs.batch.isin(batch)]) - y_pred += krr.predict(test_norm) + y_pred += (krr.predict(test_norm) @ embedder_mod2.components_) np.clip(y_pred, a_min=0, a_max=None, out=y_pred) if mod2_type == "ATAC": From c0cd3c404a3c20505222d77998d7efed37e7795b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 22 Apr 2024 13:08:53 +0200 Subject: [PATCH 1205/1233] Bump base images to 1.0.4 (#434) * bump to 1.0.4 * fix dca * fix cell2location * uniformize directives Former-commit-id: 4b059e43143960fc68621d268b1a535263697e87 --- CONTRIBUTING.qmd | 2 +- src/common/check_dataset_schema/config.vsh.yaml | 4 ++-- src/common/check_yaml_schema/config.vsh.yaml | 2 +- src/common/create_component/script.py | 6 +++--- src/common/create_task_readme/config.vsh.yaml | 4 ++-- src/common/decompress_gzip/config.vsh.yaml | 2 +- src/common/extract_metadata/config.vsh.yaml | 4 ++-- src/common/extract_scores/config.vsh.yaml | 4 ++-- .../ontology/check_obsolete_terms/config.vsh.yaml | 2 +- .../process_task_results/generate_qc/config.vsh.yaml | 2 +- .../process_task_results/get_api_info/config.vsh.yaml | 2 +- .../get_dataset_info/config.vsh.yaml | 2 +- .../get_method_info/config.vsh.yaml | 2 +- .../get_metric_info/config.vsh.yaml | 2 +- .../process_task_results/get_results/config.vsh.yaml | 2 +- .../get_task_info/config.vsh.yaml | 2 +- .../process_task_results/yaml_to_json/config.vsh.yaml | 2 +- src/datasets/loaders/cellxgene_census/config.vsh.yaml | 2 +- .../cellxgene_census_from_source_h5ad/config.vsh.yaml | 2 +- .../openproblems_neurips2021_bmmc/config.vsh.yaml | 4 ++-- src/datasets/loaders/openproblems_v1/config.vsh.yaml | 4 ++-- .../openproblems_v1_multimodal/config.vsh.yaml | 4 ++-- src/datasets/normalization/atac_tfidf/config.vsh.yaml | 4 ++-- src/datasets/normalization/l1_sqrt/config.vsh.yaml | 4 ++-- src/datasets/normalization/log_cp/config.vsh.yaml | 4 ++-- .../normalization/log_scran_pooling/config.vsh.yaml | 4 ++-- src/datasets/normalization/prot_clr/config.vsh.yaml | 4 ++-- src/datasets/normalization/sqrt_cp/config.vsh.yaml | 4 ++-- src/datasets/processors/hvg/config.vsh.yaml | 4 ++-- src/datasets/processors/knn/config.vsh.yaml | 4 ++-- src/datasets/processors/pca/config.vsh.yaml | 4 ++-- src/datasets/processors/subsample/config.vsh.yaml | 4 ++-- src/datasets/processors/svd/config.vsh.yaml | 4 ++-- src/migration/check_migration_status/config.vsh.yaml | 2 +- src/migration/list_git_shas/config.vsh.yaml | 2 +- src/migration/update_bibtex/config.vsh.yaml | 2 +- .../no_integration_batch/config.vsh.yaml | 4 ++-- .../control_methods/random_embed_cell/config.vsh.yaml | 4 ++-- .../random_embed_cell_jitter/config.vsh.yaml | 4 ++-- .../random_integration/config.vsh.yaml | 4 ++-- .../batch_integration/methods/bbknn/config.vsh.yaml | 4 ++-- .../batch_integration/methods/combat/config.vsh.yaml | 4 ++-- .../methods/fastmnn_embedding/config.vsh.yaml | 4 ++-- .../methods/fastmnn_feature/config.vsh.yaml | 4 ++-- .../batch_integration/methods/liger/config.vsh.yaml | 4 ++-- .../methods/mnn_correct/config.vsh.yaml | 4 ++-- .../batch_integration/methods/mnnpy/config.vsh.yaml | 2 +- .../batch_integration/methods/pyliger/config.vsh.yaml | 4 ++-- .../methods/scalex_embed/config.vsh.yaml | 4 ++-- .../methods/scalex_feature/config.vsh.yaml | 4 ++-- .../methods/scanorama_embed/config.vsh.yaml | 4 ++-- .../methods/scanorama_feature/config.vsh.yaml | 4 ++-- .../batch_integration/methods/scanvi/config.vsh.yaml | 4 ++-- .../batch_integration/methods/scvi/config.vsh.yaml | 4 ++-- .../metrics/asw_batch/config.vsh.yaml | 4 ++-- .../metrics/asw_label/config.vsh.yaml | 4 ++-- .../metrics/cell_cycle_conservation/config.vsh.yaml | 4 ++-- .../metrics/clustering_overlap/config.vsh.yaml | 4 ++-- .../metrics/graph_connectivity/config.vsh.yaml | 4 ++-- .../metrics/hvg_overlap/config.vsh.yaml | 4 ++-- .../metrics/isolated_label_asw/config.vsh.yaml | 4 ++-- .../metrics/isolated_label_f1/config.vsh.yaml | 4 ++-- .../batch_integration/metrics/kbet/config.vsh.yaml | 4 ++-- .../batch_integration/metrics/lisi/config.vsh.yaml | 4 ++-- .../batch_integration/metrics/pcr/config.vsh.yaml | 4 ++-- .../batch_integration/process_dataset/config.vsh.yaml | 4 ++-- .../transformers/embed_to_graph/config.vsh.yaml | 4 ++-- .../transformers/feature_to_embed/config.vsh.yaml | 4 ++-- .../control_methods/no_denoising/config.vsh.yaml | 4 ++-- .../control_methods/perfect_denoising/config.vsh.yaml | 4 ++-- src/tasks/denoising/methods/alra/config.vsh.yaml | 4 ++-- src/tasks/denoising/methods/dca/config.vsh.yaml | 11 +++++++++-- .../denoising/methods/knn_smoothing/config.vsh.yaml | 4 ++-- src/tasks/denoising/methods/magic/config.vsh.yaml | 2 +- src/tasks/denoising/methods/saver/config.vsh.yaml | 4 ++-- src/tasks/denoising/metrics/mse/config.vsh.yaml | 4 ++-- src/tasks/denoising/metrics/poisson/config.vsh.yaml | 4 ++-- src/tasks/denoising/process_dataset/config.vsh.yaml | 4 ++-- .../control_methods/random_features/config.vsh.yaml | 4 ++-- .../control_methods/spectral_features/config.vsh.yaml | 4 ++-- .../control_methods/true_features/config.vsh.yaml | 4 ++-- .../methods/densmap/config.vsh.yaml | 4 ++-- .../methods/diffusion_map/config.vsh.yaml | 4 ++-- .../methods/ivis/config.vsh.yaml | 4 ++-- .../methods/lmds/config.vsh.yaml | 4 ++-- .../methods/neuralee/config.vsh.yaml | 4 ++-- .../methods/pca/config.vsh.yaml | 4 ++-- .../methods/phate/config.vsh.yaml | 4 ++-- .../methods/pymde/config.vsh.yaml | 4 ++-- .../methods/simlr/config.vsh.yaml | 4 ++-- .../methods/tsne/config.vsh.yaml | 4 ++-- .../methods/umap/config.vsh.yaml | 4 ++-- .../metrics/clustering_performance/config.vsh.yaml | 4 ++-- .../metrics/coranking/config.vsh.yaml | 4 ++-- .../metrics/density_preservation/config.vsh.yaml | 4 ++-- .../metrics/distance_correlation/config.vsh.yaml | 4 ++-- .../metrics/trustworthiness/config.vsh.yaml | 4 ++-- .../process_dataset/config.vsh.yaml | 4 ++-- .../control_methods/majority_vote/config.vsh.yaml | 4 ++-- .../control_methods/random_labels/config.vsh.yaml | 4 ++-- .../control_methods/true_labels/config.vsh.yaml | 4 ++-- .../label_projection/methods/knn/config.vsh.yaml | 4 ++-- .../methods/logistic_regression/config.vsh.yaml | 4 ++-- .../label_projection/methods/mlp/config.vsh.yaml | 4 ++-- .../methods/naive_bayes/config.vsh.yaml | 4 ++-- .../label_projection/methods/scanvi/config.vsh.yaml | 4 ++-- .../methods/scanvi_scarches/config.vsh.yaml | 4 ++-- .../methods/seurat_transferdata/config.vsh.yaml | 4 ++-- .../label_projection/methods/xgboost/config.vsh.yaml | 4 ++-- .../label_projection/metrics/accuracy/config.vsh.yaml | 2 +- src/tasks/label_projection/metrics/f1/config.vsh.yaml | 2 +- .../label_projection/process_dataset/config.vsh.yaml | 4 ++-- .../control_methods/random_features/config.vsh.yaml | 4 ++-- .../control_methods/true_features/config.vsh.yaml | 4 ++-- .../match_modalities/methods/fastmnn/config.vsh.yaml | 4 ++-- .../methods/harmonic_alignment/config.vsh.yaml | 4 ++-- .../methods/procrustes/config.vsh.yaml | 4 ++-- .../match_modalities/methods/scot/config.vsh.yaml | 4 ++-- .../match_modalities/metrics/knn_auc/config.vsh.yaml | 4 ++-- .../match_modalities/metrics/mse/config.vsh.yaml | 4 ++-- .../match_modalities/process_dataset/config.vsh.yaml | 4 ++-- .../control_methods/meanpergene/config.vsh.yaml | 4 ++-- .../control_methods/random_predict/config.vsh.yaml | 4 ++-- .../control_methods/solution/config.vsh.yaml | 4 ++-- .../control_methods/zeros/config.vsh.yaml | 4 ++-- .../methods/guanlab_dengkw_pm/config.vsh.yaml | 4 ++-- .../predict_modality/methods/knnr_py/config.vsh.yaml | 4 ++-- .../predict_modality/methods/knnr_r/config.vsh.yaml | 4 ++-- src/tasks/predict_modality/methods/lm/config.vsh.yaml | 4 ++-- .../methods/newwave_knnr/config.vsh.yaml | 4 ++-- .../methods/random_forest/config.vsh.yaml | 4 ++-- .../metrics/correlation/config.vsh.yaml | 4 ++-- .../predict_modality/metrics/mse/config.vsh.yaml | 4 ++-- .../predict_modality/process_dataset/config.vsh.yaml | 4 ++-- .../random_proportions/config.vsh.yaml | 4 ++-- .../control_methods/true_proportions/config.vsh.yaml | 4 ++-- .../dataset_simulator/config.vsh.yaml | 4 ++-- .../methods/cell2location/config.vsh.yaml | 5 +++-- .../methods/destvi/config.vsh.yaml | 4 ++-- .../methods/nmfreg/config.vsh.yaml | 4 ++-- .../methods/nnls/config.vsh.yaml | 4 ++-- .../methods/rctd/config.vsh.yaml | 4 ++-- .../methods/seurat/config.vsh.yaml | 4 ++-- .../methods/stereoscope/config.vsh.yaml | 4 ++-- .../methods/tangram/config.vsh.yaml | 4 ++-- .../methods/vanillanmf/config.vsh.yaml | 4 ++-- .../spatial_decomposition/metrics/r2/config.vsh.yaml | 4 ++-- .../process_dataset/config.vsh.yaml | 4 ++-- 148 files changed, 284 insertions(+), 276 deletions(-) diff --git a/CONTRIBUTING.qmd b/CONTRIBUTING.qmd index a1c037c772..995c02d361 100644 --- a/CONTRIBUTING.qmd +++ b/CONTRIBUTING.qmd @@ -185,7 +185,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: [scikit-learn] diff --git a/src/common/check_dataset_schema/config.vsh.yaml b/src/common/check_dataset_schema/config.vsh.yaml index 7453da720f..d25bf5766e 100644 --- a/src/common/check_dataset_schema/config.vsh.yaml +++ b/src/common/check_dataset_schema/config.vsh.yaml @@ -36,10 +36,10 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 test_setup: - type: python packages: viashpy - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/common/check_yaml_schema/config.vsh.yaml b/src/common/check_yaml_schema/config.vsh.yaml index 44922bdf50..40a62fd2c8 100644 --- a/src/common/check_yaml_schema/config.vsh.yaml +++ b/src/common/check_yaml_schema/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: diff --git a/src/common/create_component/script.py b/src/common/create_component/script.py index 482ec680b7..822d0eac87 100644 --- a/src/common/create_component/script.py +++ b/src/common/create_component/script.py @@ -62,7 +62,7 @@ def create_config(par, component_type, pretty_name, script_path) -> str: | # Allows turning the component into a Nextflow module / pipeline. | - type: nextflow | directives: - | label: [ "midtime",midmem, midcpu] + | label: [midtime,midmem, midcpu] |''' ) @@ -141,11 +141,11 @@ def generate_resources(par, script_path) -> str: def generate_docker_platform(par) -> str: """Set up the docker platform for Python.""" if par["language"] == "python": - image_str = "ghcr.io/openproblems-bio/base_python:1.0.2" + image_str = "ghcr.io/openproblems-bio/base_python:1.0.4" setup_type = "python" package_example = "scib==1.1.5" elif par["language"] == "r": - image_str = "ghcr.io/openproblems-bio/base_r:1.0.2" + image_str = "ghcr.io/openproblems-bio/base_r:1.0.4" setup_type = "r" package_example = "tidyverse" return strip_margin(f'''\ diff --git a/src/common/create_task_readme/config.vsh.yaml b/src/common/create_task_readme/config.vsh.yaml index 6967466c0c..6ba0a726c7 100644 --- a/src/common/create_task_readme/config.vsh.yaml +++ b/src/common/create_task_readme/config.vsh.yaml @@ -48,7 +48,7 @@ functionality: dest: openproblems-v2/_viash.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r packages: [dplyr, purrr, rlang, glue, yaml, fs, cli, igraph, rmarkdown, processx] @@ -65,5 +65,5 @@ platforms: - type: native - type: nextflow directives: - label: [ midtime, lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/common/decompress_gzip/config.vsh.yaml b/src/common/decompress_gzip/config.vsh.yaml index 751d31a162..2716dc554d 100644 --- a/src/common/decompress_gzip/config.vsh.yaml +++ b/src/common/decompress_gzip/config.vsh.yaml @@ -22,4 +22,4 @@ platforms: image: ubuntu:latest - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] + label: [midtime, lowmem, lowcpu] diff --git a/src/common/extract_metadata/config.vsh.yaml b/src/common/extract_metadata/config.vsh.yaml index e131698433..0636812619 100644 --- a/src/common/extract_metadata/config.vsh.yaml +++ b/src/common/extract_metadata/config.vsh.yaml @@ -31,10 +31,10 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 test_setup: - type: python packages: viashpy - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/common/extract_scores/config.vsh.yaml b/src/common/extract_scores/config.vsh.yaml index 45744d4048..46fb174924 100644 --- a/src/common/extract_scores/config.vsh.yaml +++ b/src/common/extract_scores/config.vsh.yaml @@ -26,10 +26,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ tidyverse ] - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] + label: [midtime, lowmem, lowcpu] diff --git a/src/common/ontology/check_obsolete_terms/config.vsh.yaml b/src/common/ontology/check_obsolete_terms/config.vsh.yaml index 88bf830edf..dbb0506098 100644 --- a/src/common/ontology/check_obsolete_terms/config.vsh.yaml +++ b/src/common/ontology/check_obsolete_terms/config.vsh.yaml @@ -70,7 +70,7 @@ functionality: - path: /resources_test/common/cellxgene_census platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r packages: [ dplyr, tidyr, tibble, ontologyIndex, processx ] \ No newline at end of file diff --git a/src/common/process_task_results/generate_qc/config.vsh.yaml b/src/common/process_task_results/generate_qc/config.vsh.yaml index 1bcb0350c9..9b3b07dc01 100644 --- a/src/common/process_task_results/generate_qc/config.vsh.yaml +++ b/src/common/process_task_results/generate_qc/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: label: [lowmem, lowtime, lowcpu] diff --git a/src/common/process_task_results/get_api_info/config.vsh.yaml b/src/common/process_task_results/get_api_info/config.vsh.yaml index 26fa3d986c..2026c007ab 100644 --- a/src/common/process_task_results/get_api_info/config.vsh.yaml +++ b/src/common/process_task_results/get_api_info/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, dplyr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_dataset_info/config.vsh.yaml b/src/common/process_task_results/get_dataset_info/config.vsh.yaml index 8b5ff386fa..75f4952738 100644 --- a/src/common/process_task_results/get_dataset_info/config.vsh.yaml +++ b/src/common/process_task_results/get_dataset_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_method_info/config.vsh.yaml b/src/common/process_task_results/get_method_info/config.vsh.yaml index 7caf98dbcb..ee606c852e 100644 --- a/src/common/process_task_results/get_method_info/config.vsh.yaml +++ b/src/common/process_task_results/get_method_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_metric_info/config.vsh.yaml b/src/common/process_task_results/get_metric_info/config.vsh.yaml index 8ed18ad5b2..e6555bca36 100644 --- a/src/common/process_task_results/get_metric_info/config.vsh.yaml +++ b/src/common/process_task_results/get_metric_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/get_results/config.vsh.yaml b/src/common/process_task_results/get_results/config.vsh.yaml index 84cc5f27bf..5e1b716731 100644 --- a/src/common/process_task_results/get_results/config.vsh.yaml +++ b/src/common/process_task_results/get_results/config.vsh.yaml @@ -42,7 +42,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, yaml, rlang, dplyr, tidyr, readr, lubridate, dynutils, processx ] diff --git a/src/common/process_task_results/get_task_info/config.vsh.yaml b/src/common/process_task_results/get_task_info/config.vsh.yaml index 6acdc65e1b..b74c67c3e7 100644 --- a/src/common/process_task_results/get_task_info/config.vsh.yaml +++ b/src/common/process_task_results/get_task_info/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ purrr, yaml, rlang, processx ] diff --git a/src/common/process_task_results/yaml_to_json/config.vsh.yaml b/src/common/process_task_results/yaml_to_json/config.vsh.yaml index 4e24134d02..de54b44cce 100644 --- a/src/common/process_task_results/yaml_to_json/config.vsh.yaml +++ b/src/common/process_task_results/yaml_to_json/config.vsh.yaml @@ -11,6 +11,6 @@ functionality: dest: test_file.yaml platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow - type: native diff --git a/src/datasets/loaders/cellxgene_census/config.vsh.yaml b/src/datasets/loaders/cellxgene_census/config.vsh.yaml index 6593b91c1f..f59547174a 100644 --- a/src/datasets/loaders/cellxgene_census/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census/config.vsh.yaml @@ -151,7 +151,7 @@ functionality: path: test.py platforms: - type: docker - #image: ghcr.io/openproblems-bio/base_python:1.0.2 + #image: ghcr.io/openproblems-bio/base_python:1.0.4 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml index 1ccd1df18b..91fad8769f 100644 --- a/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml +++ b/src/datasets/loaders/cellxgene_census_from_source_h5ad/config.vsh.yaml @@ -114,7 +114,7 @@ functionality: path: test.py platforms: - type: docker - #image: ghcr.io/openproblems-bio/base_python:1.0.2 + #image: ghcr.io/openproblems-bio/base_python:1.0.4 image: python:3.11 setup: - type: python diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml index 345788157f..f8837cba6d 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ highmem, midcpu , midtime] \ No newline at end of file + label: [highmem, midcpu , midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_v1/config.vsh.yaml b/src/datasets/loaders/openproblems_v1/config.vsh.yaml index 584d79cd30..5a53755b82 100644 --- a/src/datasets/loaders/openproblems_v1/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1/config.vsh.yaml @@ -72,7 +72,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: apt packages: git @@ -83,4 +83,4 @@ platforms: pip install --no-cache-dir --editable /opt/openproblems - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml index ee5cbd0607..0f07dbff62 100644 --- a/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/loaders/openproblems_v1_multimodal/config.vsh.yaml @@ -80,7 +80,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: apt packages: git @@ -91,4 +91,4 @@ platforms: pip install --no-cache-dir --editable /opt/openproblems - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/datasets/normalization/atac_tfidf/config.vsh.yaml b/src/datasets/normalization/atac_tfidf/config.vsh.yaml index 83c152101a..3240fec43f 100644 --- a/src/datasets/normalization/atac_tfidf/config.vsh.yaml +++ b/src/datasets/normalization/atac_tfidf/config.vsh.yaml @@ -12,11 +12,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: - muon - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/l1_sqrt/config.vsh.yaml b/src/datasets/normalization/l1_sqrt/config.vsh.yaml index 2be09a1216..a133bdee48 100644 --- a/src/datasets/normalization/l1_sqrt/config.vsh.yaml +++ b/src/datasets/normalization/l1_sqrt/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -24,4 +24,4 @@ platforms: - numpy - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/log_cp/config.vsh.yaml b/src/datasets/normalization/log_cp/config.vsh.yaml index 21285a2c30..dd02663380 100644 --- a/src/datasets/normalization/log_cp/config.vsh.yaml +++ b/src/datasets/normalization/log_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml index 87fd346fe5..3431e8174b 100644 --- a/src/datasets/normalization/log_scran_pooling/config.vsh.yaml +++ b/src/datasets/normalization/log_scran_pooling/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ Matrix, rlang, scran, BiocParallel ] @@ -15,4 +15,4 @@ platforms: pip: scanpy - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/prot_clr/config.vsh.yaml b/src/datasets/normalization/prot_clr/config.vsh.yaml index c12c8afdbc..351cc0569a 100644 --- a/src/datasets/normalization/prot_clr/config.vsh.yaml +++ b/src/datasets/normalization/prot_clr/config.vsh.yaml @@ -16,11 +16,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: - muon - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/normalization/sqrt_cp/config.vsh.yaml b/src/datasets/normalization/sqrt_cp/config.vsh.yaml index fe001c0674..7da0165229 100644 --- a/src/datasets/normalization/sqrt_cp/config.vsh.yaml +++ b/src/datasets/normalization/sqrt_cp/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: description: "Number of counts per cell" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/datasets/processors/hvg/config.vsh.yaml b/src/datasets/processors/hvg/config.vsh.yaml index 86c7d54171..d2702d90d6 100644 --- a/src/datasets/processors/hvg/config.vsh.yaml +++ b/src/datasets/processors/hvg/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/knn/config.vsh.yaml b/src/datasets/processors/knn/config.vsh.yaml index 8084cc7791..652676ab90 100644 --- a/src/datasets/processors/knn/config.vsh.yaml +++ b/src/datasets/processors/knn/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/pca/config.vsh.yaml b/src/datasets/processors/pca/config.vsh.yaml index 8fd788a357..027faf1e08 100644 --- a/src/datasets/processors/pca/config.vsh.yaml +++ b/src/datasets/processors/pca/config.vsh.yaml @@ -11,7 +11,7 @@ functionality: # - path: "../../../resources_test/common/pancreas" platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index 76cea7cf20..e2a33ed084 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -41,11 +41,11 @@ functionality: - path: /resources_test/common/pancreas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 test_setup: - type: python packages: - viashpy - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/datasets/processors/svd/config.vsh.yaml b/src/datasets/processors/svd/config.vsh.yaml index 61546777e1..e59865da5e 100644 --- a/src/datasets/processors/svd/config.vsh.yaml +++ b/src/datasets/processors/svd/config.vsh.yaml @@ -7,10 +7,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: [scikit-learn] - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/migration/check_migration_status/config.vsh.yaml b/src/migration/check_migration_status/config.vsh.yaml index 56e2c4b1b0..a2dea51e00 100644 --- a/src/migration/check_migration_status/config.vsh.yaml +++ b/src/migration/check_migration_status/config.vsh.yaml @@ -25,6 +25,6 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow - type: native diff --git a/src/migration/list_git_shas/config.vsh.yaml b/src/migration/list_git_shas/config.vsh.yaml index 1dbbb90ae4..53fc63aabb 100644 --- a/src/migration/list_git_shas/config.vsh.yaml +++ b/src/migration/list_git_shas/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 test_setup: - type: docker run: "git clone https://github.com/openproblems-bio/openproblems-v2.git" diff --git a/src/migration/update_bibtex/config.vsh.yaml b/src/migration/update_bibtex/config.vsh.yaml index 013704966a..0df07b66c2 100644 --- a/src/migration/update_bibtex/config.vsh.yaml +++ b/src/migration/update_bibtex/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: test.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: git+https://github.com/sciunto-org/python-bibtexparser@main diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml index 1f18bb0bee..06c354f634 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -23,4 +23,4 @@ platforms: - numpy - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml index bf525fad0f..1a0f130664 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml @@ -15,11 +15,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scikit-learn - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml index d0ab554ec3..0f8bb0d0f4 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -28,4 +28,4 @@ platforms: - scipy - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml index a190913dba..b98ff82039 100644 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml @@ -15,11 +15,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - numpy - type: nextflow directives: - label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml index 60d6414a35..1d1d42aa89 100644 --- a/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/bbknn/config.vsh.yaml @@ -39,11 +39,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - bbknn - type: nextflow directives: - label: [ midtime, midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/methods/combat/config.vsh.yaml b/src/tasks/batch_integration/methods/combat/config.vsh.yaml index 5511dd769c..dbb4b042ec 100644 --- a/src/tasks/batch_integration/methods/combat/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/combat/config.vsh.yaml @@ -34,7 +34,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, lowcpu ] + label: [midtime, highmem, lowcpu] diff --git a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml index 07622a548c..1fc6910a81 100644 --- a/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_embedding/config.vsh.yaml @@ -26,11 +26,11 @@ functionality: path: ../fastmnn_feature/script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.3 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r bioc: - batchelor - type: nextflow directives: - label: [ midtime, lowcpu, highmem ] + label: [midtime, lowcpu, highmem] diff --git a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml index 5c706da9ff..4336f93c8e 100644 --- a/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/fastmnn_feature/config.vsh.yaml @@ -25,10 +25,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.3 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r bioc: batchelor - type: nextflow directives: - label: [ midtime, lowcpu, highmem ] + label: [midtime, lowcpu, highmem] diff --git a/src/tasks/batch_integration/methods/liger/config.vsh.yaml b/src/tasks/batch_integration/methods/liger/config.vsh.yaml index f43697e2e7..d0db8e2996 100644 --- a/src/tasks/batch_integration/methods/liger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/liger/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.3 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: apt packages: cmake @@ -28,4 +28,4 @@ platforms: github: welch-lab/RcppPlanc - type: nextflow directives: - label: [ lowcpu, highmem, midtime ] + label: [lowcpu, highmem, midtime] diff --git a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml index 3284514982..7a795fc759 100644 --- a/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnn_correct/config.vsh.yaml @@ -17,11 +17,11 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.3 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r bioc: - batchelor - type: nextflow directives: - label: [ midtime, lowcpu, highmem ] + label: [midtime, lowcpu, highmem] diff --git a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml index 2c5075534b..de1894ab68 100644 --- a/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml @@ -49,4 +49,4 @@ platforms: - chriscainx/mnnpy - type: nextflow directives: - label: [ midtime, lowcpu, lowmem ] + label: [midtime, lowcpu, lowmem] diff --git a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml index fd124c05ec..0d8f262620 100644 --- a/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/pyliger/config.vsh.yaml @@ -23,7 +23,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -32,4 +32,4 @@ platforms: - dask-expr - type: nextflow directives: - label: [ lowcpu, highmem, midtime ] + label: [lowcpu, highmem, midtime] diff --git a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml index 3fea89f30e..179d478412 100644 --- a/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_embed/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -36,4 +36,4 @@ platforms: - torch<2.1 - type: nextflow directives: - label: [ lowmem, lowcpu, midtime ] + label: [lowmem, lowcpu, midtime] diff --git a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml index 2cc484ab70..2d8d05a98f 100644 --- a/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scalex_feature/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -36,4 +36,4 @@ platforms: - torch<2.1 - type: nextflow directives: - label: [ lowmem, lowcpu, midtime ] + label: [lowmem, lowcpu, midtime] diff --git a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml index fda846438f..387745fc38 100644 --- a/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_embed/config.vsh.yaml @@ -29,11 +29,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scanorama - type: nextflow directives: - label: [ midtime, midmem, lowcpu ] \ No newline at end of file + label: [midtime, midmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml index 86a3fe1d72..50246875ae 100644 --- a/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanorama_feature/config.vsh.yaml @@ -29,11 +29,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scanorama - type: nextflow directives: - label: [ midtime, midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index 72e82cf7dd..f7f8cd9b24 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -46,11 +46,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python pypi: - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ midtime, lowmem, lowcpu, gpu ] + label: [midtime, lowmem, lowcpu, gpu] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index 03362da69c..bed1d9add0 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -44,11 +44,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python pypi: - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ midtime, midmem, lowcpu, gpu ] + label: [midtime, midmem, lowcpu, gpu] diff --git a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml index d9f9dff3ba..bb2f7b48c7 100644 --- a/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_batch/config.vsh.yaml @@ -38,11 +38,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml index 57ea6cd0f8..4fd0d7ac32 100644 --- a/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/asw_label/config.vsh.yaml @@ -26,11 +26,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml index de42057de1..1e8edd5ee7 100644 --- a/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/cell_cycle_conservation/config.vsh.yaml @@ -35,11 +35,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml index 60185ba12a..6fa7b9c9a9 100644 --- a/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/clustering_overlap/config.vsh.yaml @@ -49,11 +49,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml index dbc6079e84..627f480e4c 100644 --- a/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/graph_connectivity/config.vsh.yaml @@ -35,11 +35,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml index a67a5ca1c5..1076f03619 100644 --- a/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/hvg_overlap/config.vsh.yaml @@ -34,11 +34,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml index 16d2b3e2ad..cf1702fb93 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_asw/config.vsh.yaml @@ -28,11 +28,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml index 2d4fce1e75..4208e502ec 100644 --- a/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/isolated_label_f1/config.vsh.yaml @@ -40,11 +40,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml index eb4bcf9f12..39bd895680 100644 --- a/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/kbet/config.vsh.yaml @@ -40,7 +40,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r github: theislab/kBET @@ -51,4 +51,4 @@ platforms: - anndata2ri - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml index e957434bd9..1687dc5c1c 100644 --- a/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/lisi/config.vsh.yaml @@ -44,11 +44,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - git+https://github.com/theislab/scib.git@v1.1.4 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml index e1662b3ef9..8644120657 100644 --- a/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml +++ b/src/tasks/batch_integration/metrics/pcr/config.vsh.yaml @@ -32,11 +32,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/process_dataset/config.vsh.yaml b/src/tasks/batch_integration/process_dataset/config.vsh.yaml index 2b48e72359..0dbe5f3bcd 100644 --- a/src/tasks/batch_integration/process_dataset/config.vsh.yaml +++ b/src/tasks/batch_integration/process_dataset/config.vsh.yaml @@ -8,11 +8,11 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scib==1.1.5 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml index 694cd6e2b0..7f881da214 100644 --- a/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/embed_to_graph/config.vsh.yaml @@ -11,10 +11,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: scanpy - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml index 0cf8b5f002..8ec4da8170 100644 --- a/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml +++ b/src/tasks/batch_integration/transformers/feature_to_embed/config.vsh.yaml @@ -12,10 +12,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: scanpy - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml index ce6238fe0e..ec3ed2469d 100644 --- a/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/no_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml index ab4d71164e..c36581e205 100644 --- a/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml +++ b/src/tasks/denoising/control_methods/perfect_denoising/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/denoising/methods/alra/config.vsh.yaml b/src/tasks/denoising/methods/alra/config.vsh.yaml index 76eda37a29..1354b5c00c 100644 --- a/src/tasks/denoising/methods/alra/config.vsh.yaml +++ b/src/tasks/denoising/methods/alra/config.vsh.yaml @@ -33,11 +33,11 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ Matrix, rsvd ] github: KlugerLab/ALRA - type: nextflow directives: - label: [ midtime, highmem, highcpu] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/denoising/methods/dca/config.vsh.yaml b/src/tasks/denoising/methods/dca/config.vsh.yaml index 046eceb8a4..33c6079866 100644 --- a/src/tasks/denoising/methods/dca/config.vsh.yaml +++ b/src/tasks/denoising/methods/dca/config.vsh.yaml @@ -28,11 +28,18 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: python:3.9 setup: + - type: apt + packages: procps - type: python packages: + - anndata~=0.8.0 + - scanpy + - pyyaml + - requests + - jsonschema - "git+https://github.com/scottgigante-immunai/dca.git@patch-1" - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml index f84616f631..975d729990 100644 --- a/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml +++ b/src/tasks/denoising/methods/knn_smoothing/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -38,4 +38,4 @@ platforms: - scottgigante-immunai/knn-smoothing@python_package - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/denoising/methods/magic/config.vsh.yaml b/src/tasks/denoising/methods/magic/config.vsh.yaml index 261d739ee7..0d2ff14c98 100644 --- a/src/tasks/denoising/methods/magic/config.vsh.yaml +++ b/src/tasks/denoising/methods/magic/config.vsh.yaml @@ -54,7 +54,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pip: [scprep, magic-impute, scipy, scikit-learn<1.2] diff --git a/src/tasks/denoising/methods/saver/config.vsh.yaml b/src/tasks/denoising/methods/saver/config.vsh.yaml index af7fcadfc4..fcd3e4b88a 100644 --- a/src/tasks/denoising/methods/saver/config.vsh.yaml +++ b/src/tasks/denoising/methods/saver/config.vsh.yaml @@ -23,10 +23,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r github: mohuangx/SAVER - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/denoising/metrics/mse/config.vsh.yaml b/src/tasks/denoising/metrics/mse/config.vsh.yaml index ff3da70675..3260c2694a 100644 --- a/src/tasks/denoising/metrics/mse/config.vsh.yaml +++ b/src/tasks/denoising/metrics/mse/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -27,4 +27,4 @@ platforms: - scprep - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/denoising/metrics/poisson/config.vsh.yaml b/src/tasks/denoising/metrics/poisson/config.vsh.yaml index af02493367..5d239b0c92 100644 --- a/src/tasks/denoising/metrics/poisson/config.vsh.yaml +++ b/src/tasks/denoising/metrics/poisson/config.vsh.yaml @@ -19,10 +19,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pip: scprep - type: nextflow directives: - label: [ midtime, highmem, midcpu ] \ No newline at end of file + label: [midtime, highmem, midcpu] \ No newline at end of file diff --git a/src/tasks/denoising/process_dataset/config.vsh.yaml b/src/tasks/denoising/process_dataset/config.vsh.yaml index 41bea59011..6c30e6ab12 100644 --- a/src/tasks/denoising/process_dataset/config.vsh.yaml +++ b/src/tasks/denoising/process_dataset/config.vsh.yaml @@ -26,7 +26,7 @@ functionality: - path: helper.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -34,4 +34,4 @@ platforms: - scipy - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml index 8fa77a63af..cc5a4be442 100644 --- a/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/random_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] \ No newline at end of file + label: [midtime, highmem, highcpu] \ No newline at end of file diff --git a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml index 1fed7ff812..8e409f7bbc 100644 --- a/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/spectral_features/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: @@ -38,4 +38,4 @@ platforms: - numpy - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml index 3a095d12e5..43f660d34d 100644 --- a/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/control_methods/true_features/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml index 532785519e..778ee410bb 100644 --- a/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/densmap/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -42,4 +42,4 @@ platforms: - type: native - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml index 2ad6ac887f..e8ad2b1f99 100644 --- a/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/diffusion_map/config.vsh.yaml @@ -22,10 +22,10 @@ functionality: default: 3 platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r bioc: destiny - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml index bb6f88894e..9f72001546 100644 --- a/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/ivis/config.vsh.yaml @@ -33,7 +33,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -41,4 +41,4 @@ platforms: - tensorflow<2.16 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml index c6b1c4d0d3..98a7cd53a4 100644 --- a/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/lmds/config.vsh.yaml @@ -35,10 +35,10 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ Matrix, lmds ] - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml index ca802f29aa..130cd7faf2 100644 --- a/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/neuralee/config.vsh.yaml @@ -44,7 +44,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -52,4 +52,4 @@ platforms: - "git+https://github.com/michalk8/neuralee@8946abf" - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml index 5546509d1f..ec86b6725f 100644 --- a/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pca/config.vsh.yaml @@ -31,10 +31,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scanpy - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml index 36ec4d20d9..1c2dd68e2b 100644 --- a/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/phate/config.vsh.yaml @@ -46,7 +46,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -55,4 +55,4 @@ platforms: - "scikit-learn<1.2" - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml index ec3b39b402..1948fd51ea 100644 --- a/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/pymde/config.vsh.yaml @@ -32,10 +32,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: pymde - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml index 9157634498..210801ac0e 100644 --- a/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/simlr/config.vsh.yaml @@ -45,7 +45,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r packages: [ grDevices ] @@ -54,4 +54,4 @@ platforms: - type: native - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml index 81a2e0077c..9dbc917e0f 100644 --- a/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/tsne/config.vsh.yaml @@ -35,7 +35,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: apt packages: @@ -46,4 +46,4 @@ platforms: - DmitryUlyanov/Multicore-TSNE - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml index 3f43794344..6b4b222fef 100644 --- a/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/methods/umap/config.vsh.yaml @@ -39,7 +39,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -47,4 +47,4 @@ platforms: - pynndescent==0.5.11 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml index b04f8698a2..56757c0a02 100644 --- a/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/clustering_performance/config.vsh.yaml @@ -51,11 +51,11 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: [ scikit-learn, scanpy, leidenalg ] - type: native - type: nextflow directives: - label: [ midtime, midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml index 526432a99f..b7a82fe3d7 100644 --- a/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/coranking/config.vsh.yaml @@ -157,10 +157,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ coRanking ] - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml index 8993ebf383..c421f6a479 100644 --- a/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/density_preservation/config.vsh.yaml @@ -30,7 +30,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -40,4 +40,4 @@ platforms: - pynndescent~=0.5.11 - type: nextflow directives: - label: [ midtime, lowmem, midcpu ] + label: [midtime, lowmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml index cb4d0cad8e..44ff1950e5 100644 --- a/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/distance_correlation/config.vsh.yaml @@ -36,7 +36,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -47,4 +47,4 @@ platforms: - scipy - type: nextflow directives: - label: [ midtime, highmem, midcpu ] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml index b2c7311706..2e66527bd4 100644 --- a/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/metrics/trustworthiness/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -28,4 +28,4 @@ platforms: - numpy - type: nextflow directives: - label: [ midtime, highmem, lowcpu ] + label: [midtime, highmem, lowcpu] diff --git a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml index 83f10077c8..292318947d 100644 --- a/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml +++ b/src/tasks/dimensionality_reduction/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml index 5cc589db65..641cc89b71 100644 --- a/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/majority_vote/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml index 8e75645036..52f4c6a072 100644 --- a/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/random_labels/config.vsh.yaml @@ -16,10 +16,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scanpy - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml index c43152d7c1..c464a3a9dc 100644 --- a/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml +++ b/src/tasks/label_projection/control_methods/true_labels/config.vsh.yaml @@ -16,7 +16,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/label_projection/methods/knn/config.vsh.yaml b/src/tasks/label_projection/methods/knn/config.vsh.yaml index 782757f2e8..a083f1ff20 100644 --- a/src/tasks/label_projection/methods/knn/config.vsh.yaml +++ b/src/tasks/label_projection/methods/knn/config.vsh.yaml @@ -28,10 +28,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: [scikit-learn, jsonschema] - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml index 449a0757c9..2497d5c803 100644 --- a/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml +++ b/src/tasks/label_projection/methods/logistic_regression/config.vsh.yaml @@ -25,10 +25,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/label_projection/methods/mlp/config.vsh.yaml b/src/tasks/label_projection/methods/mlp/config.vsh.yaml index 580d663cf8..944ed6e4f7 100644 --- a/src/tasks/label_projection/methods/mlp/config.vsh.yaml +++ b/src/tasks/label_projection/methods/mlp/config.vsh.yaml @@ -38,10 +38,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml index 8989974c9d..2a09c7fa5d 100644 --- a/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml +++ b/src/tasks/label_projection/methods/naive_bayes/config.vsh.yaml @@ -24,10 +24,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 01e6e1ea36..0db9ec292a 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -32,7 +32,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python packages: @@ -40,4 +40,4 @@ platforms: - scvi-tools>=1.1.0 - type: nextflow directives: - label: [ midtime, midmem, highcpu, gpu ] + label: [midtime, midmem, highcpu, gpu] diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 284ab3da91..1dd2a27749 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -41,10 +41,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python pypi: scvi-tools>=1.1.0 - type: nextflow directives: - label: [ midtime, midmem, midcpu, gpu ] + label: [midtime, midmem, midcpu, gpu] diff --git a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml index 78a8e140fd..2bdac1c370 100644 --- a/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml +++ b/src/tasks/label_projection/methods/seurat_transferdata/config.vsh.yaml @@ -27,10 +27,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ Matrix>=1.5.3, Seurat, rlang ] - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml index 4d3271b571..d0892b9e8c 100644 --- a/src/tasks/label_projection/methods/xgboost/config.vsh.yaml +++ b/src/tasks/label_projection/methods/xgboost/config.vsh.yaml @@ -25,10 +25,10 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: xgboost - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml index b1b4883b8f..cad211fd77 100644 --- a/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/accuracy/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/metrics/f1/config.vsh.yaml b/src/tasks/label_projection/metrics/f1/config.vsh.yaml index 980557c8ef..d059a236bb 100644 --- a/src/tasks/label_projection/metrics/f1/config.vsh.yaml +++ b/src/tasks/label_projection/metrics/f1/config.vsh.yaml @@ -41,7 +41,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn diff --git a/src/tasks/label_projection/process_dataset/config.vsh.yaml b/src/tasks/label_projection/process_dataset/config.vsh.yaml index 28e16f3cb6..63724de9cd 100644 --- a/src/tasks/label_projection/process_dataset/config.vsh.yaml +++ b/src/tasks/label_projection/process_dataset/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml index 440184da0a..efe3dd5e42 100644 --- a/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml @@ -15,11 +15,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: - numpy - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml index 3c5f47eee8..0fefd7f49b 100644 --- a/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml +++ b/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] \ No newline at end of file + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml index 69ee306151..db343218b7 100644 --- a/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml @@ -20,10 +20,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r bioc: batchelor - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml index f45eacd319..466c26d160 100644 --- a/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml @@ -27,12 +27,12 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python github: - KrishnaswamyLab/harmonic-alignment#subdirectory=python - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml index 69f3fcda29..e0c95afcc2 100644 --- a/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml @@ -19,11 +19,11 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python pypi: - scipy - type: nextflow directives: - label: [ "midtime", midmem, midcpu ] \ No newline at end of file + label: [midtime, midmem, midcpu] \ No newline at end of file diff --git a/src/tasks/match_modalities/methods/scot/config.vsh.yaml b/src/tasks/match_modalities/methods/scot/config.vsh.yaml index e6dddc9ccb..5ea1a45164 100644 --- a/src/tasks/match_modalities/methods/scot/config.vsh.yaml +++ b/src/tasks/match_modalities/methods/scot/config.vsh.yaml @@ -19,7 +19,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: apt packages: git @@ -27,4 +27,4 @@ platforms: run: "cd /opt && git clone --depth 1 https://github.com/rsinghlab/SCOT.git && cd SCOT && pip install -r requirements.txt" - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml index a6566ffd8a..d629f20c38 100644 --- a/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/knn_auc/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -33,4 +33,4 @@ platforms: - scikit-learn - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml index add2f42335..a6fadd43f1 100644 --- a/src/tasks/match_modalities/metrics/mse/config.vsh.yaml +++ b/src/tasks/match_modalities/metrics/mse/config.vsh.yaml @@ -20,7 +20,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -29,4 +29,4 @@ platforms: - scprep - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/match_modalities/process_dataset/config.vsh.yaml b/src/tasks/match_modalities/process_dataset/config.vsh.yaml index 9785c0d9ae..4560b350b3 100644 --- a/src/tasks/match_modalities/process_dataset/config.vsh.yaml +++ b/src/tasks/match_modalities/process_dataset/config.vsh.yaml @@ -12,7 +12,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ highmem, midcpu , midtime] + label: [highmem, midcpu , midtime] diff --git a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml index 87cde8ab9c..87696bd678 100644 --- a/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/meanpergene/config.vsh.yaml @@ -10,8 +10,8 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml index ba77d5c1a5..d36e02d3c0 100644 --- a/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/random_predict/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml index 3019e1d764..64cf880a97 100644 --- a/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/solution/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml index 5e15d92fe1..d557556c32 100644 --- a/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml +++ b/src/tasks/predict_modality/control_methods/zeros/config.vsh.yaml @@ -10,7 +10,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index cfd891969a..231416caf2 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -25,7 +25,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.3 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -34,4 +34,4 @@ platforms: - numpy - type: nextflow directives: - label: [ midtime, highmem, highcpu] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 99e0a5f4be..8fb2cb5f33 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index 6a5570fa5c..226cd0a53d 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -27,10 +27,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ lmds, FNN, proxyC] - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 244137fc4f..507f27fd35 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -23,10 +23,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ lmds, RcppArmadillo, pbapply] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] + label: [midtime, highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index def16f755c..9b880d4e9d 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -31,11 +31,11 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ lmds, FNN, proxy, proxyC] bioc: [ SingleCellExperiment, NewWave ] - type: nextflow directives: - label: [ midtime, highmem, highcpu, highsharedmem ] + label: [midtime, highmem, highcpu, highsharedmem] diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index d8d5435c99..3ec12abd4d 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -27,10 +27,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ lmds, ranger, pbapply] - type: nextflow directives: - label: [ "midtime", highmem, highcpu ] \ No newline at end of file + label: [midtime, highmem, highcpu] \ No newline at end of file diff --git a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml index 08b0cb21df..c3837e990a 100644 --- a/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/correlation/config.vsh.yaml @@ -56,10 +56,10 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ proxyC, testthat, dynutils ] - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml index 3383eddc2a..a80c7a15a6 100644 --- a/src/tasks/predict_modality/metrics/mse/config.vsh.yaml +++ b/src/tasks/predict_modality/metrics/mse/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: path: script.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ "midtime", lowmem, lowcpu ] + label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index b95c2f8308..66110eaa4e 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -15,7 +15,7 @@ functionality: path: script.R platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 - type: nextflow directives: - label: [ "midtime", midmem, lowcpu ] + label: [midtime, midmem, lowcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml index e453dae5af..a0ccc70c61 100644 --- a/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/random_proportions/config.vsh.yaml @@ -15,11 +15,11 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: numpy - type: native - type: nextflow directives: - label: ["midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml index 4c5f1a05ec..7979f59c1e 100644 --- a/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/control_methods/true_proportions/config.vsh.yaml @@ -15,8 +15,8 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: native - type: nextflow directives: - label: ["midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml index 67c85181f7..a0151c8bc3 100644 --- a/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/dataset_simulator/config.vsh.yaml @@ -191,11 +191,11 @@ functionality: dest: resources_test/common/cxg_mouse_pancreas_atlas platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: [numpy, scanpy] - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] - type: native diff --git a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml index 843c6932dc..531568c372 100644 --- a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml @@ -71,7 +71,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -79,8 +79,9 @@ platforms: - cell2location - jax==0.4.23 - jaxlib==0.4.23 + - scipy<1.13 # The scipy.linalg functions tri, triu & tril are deprecated and will be removed in SciPy 1.13. - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index 2637b39668..02a9b82dd2 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python packages: @@ -38,4 +38,4 @@ platforms: - type: native - type: nextflow directives: - label: [ midtime, midmem, midcpu, gpu ] + label: [midtime, midmem, midcpu, gpu] diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml index 2509287c99..8cb45c4a4f 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -34,4 +34,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml index 07f3e73feb..537c7140cf 100644 --- a/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nnls/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -27,4 +27,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml index b80c07a308..78cb8e7846 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -27,7 +27,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [ Matrix ] @@ -35,4 +35,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml index fb947b634e..ab222f5b1e 100644 --- a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml @@ -28,7 +28,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_r:1.0.2 + image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r cran: [Matrix, Seurat] @@ -36,4 +36,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime", midmem, midcpu] + label: [midtime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index 88a1fd3faa..a1d5c0d9ae 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -29,7 +29,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.3 + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 setup: - type: python packages: @@ -37,4 +37,4 @@ platforms: - type: native - type: nextflow directives: - label: [ midtime, midmem, midcpu, gpu ] + label: [midtime, midmem, midcpu, gpu] diff --git a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml index a67596a8f4..e1320e750e 100644 --- a/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/tangram/config.vsh.yaml @@ -28,11 +28,11 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: tangram-sc - type: native - type: nextflow directives: - label: [ "midtime",midmem, midcpu] + label: [midtime,midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml index 7bfd68e5b8..7341cee6f2 100644 --- a/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/config.vsh.yaml @@ -24,7 +24,7 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: @@ -34,4 +34,4 @@ platforms: - type: native - type: nextflow directives: - label: [ "midtime",midmem, midcpu] + label: [midtime,midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml index 06a3c62db3..bc5585f2b6 100644 --- a/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/metrics/r2/config.vsh.yaml @@ -22,11 +22,11 @@ functionality: platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 setup: - type: python packages: scikit-learn - type: native - type: nextflow directives: - label: [ "midtime",midmem, midcpu] + label: [midtime,midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml index 83f10077c8..292318947d 100644 --- a/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/process_dataset/config.vsh.yaml @@ -7,7 +7,7 @@ functionality: - path: /src/common/helper_functions/subset_anndata.py platforms: - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.2 + image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [ midtime, highmem, highcpu ] + label: [midtime, highmem, highcpu] From dbb9f1544111300b510ce0c10df163e154093647 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Thu, 25 Apr 2024 12:31:34 +0530 Subject: [PATCH 1206/1233] Minor updates to fix failing processes in spatial decomposition benchmark (#435) * include more dataset info in solution file * use only log_cp10k normalized datasets for benchmark * use floor of values in count layer * increase time resources * update viash code block * use highmem * use conserve.memory for SCTransform * avoid conversion to dense matrix * don't use early stopping Former-commit-id: b5f5582eed3e5b0bcf84d35087e30e6e24b284da --- .../api/file_solution.yaml | 36 ++++++++++++++++--- .../methods/cell2location/config.vsh.yaml | 2 +- .../methods/cell2location/script.py | 2 +- .../methods/destvi/config.vsh.yaml | 2 +- .../methods/destvi/script.py | 2 +- .../methods/nmfreg/config.vsh.yaml | 2 +- .../methods/nmfreg/script.py | 2 +- .../methods/nnls/script.py | 2 +- .../methods/rctd/config.vsh.yaml | 2 +- .../methods/rctd/script.R | 6 ++-- .../methods/seurat/config.vsh.yaml | 2 +- .../methods/seurat/script.R | 8 +++-- .../methods/stereoscope/config.vsh.yaml | 2 +- .../methods/stereoscope/script.py | 6 ++-- .../methods/tangram/script.py | 2 +- .../methods/vanillanmf/script.py | 2 +- .../process_dataset/script.py | 4 +++ .../workflows/run_benchmark/main.nf | 12 +++++++ 18 files changed, 71 insertions(+), 25 deletions(-) diff --git a/src/tasks/spatial_decomposition/api/file_solution.yaml b/src/tasks/spatial_decomposition/api/file_solution.yaml index bfe20e56f5..ecd447e061 100644 --- a/src/tasks/spatial_decomposition/api/file_solution.yaml +++ b/src/tasks/spatial_decomposition/api/file_solution.yaml @@ -19,11 +19,39 @@ info: description: True cell type proportions for each spot required: true uns: - - type: string - name: cell_type_names + - name: cell_type_names + type: string description: Cell type names corresponding to columns of `proportions` required: true - - type: string - name: dataset_id + - name: dataset_id + type: string description: "A unique identifier for the dataset" + required: true + - name: dataset_name + type: string + description: Nicely formatted name. + required: true + - type: string + name: dataset_url + description: Link to the original source of the dataset. + required: false + - name: dataset_reference + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: dataset_summary + type: string + description: Short description of the dataset. + required: true + - name: dataset_description + type: string + description: Long description of the dataset. + required: true + - name: dataset_organism + type: string + description: The organism of the sample in the dataset. + required: false + - type: string + name: normalization_id + description: "Which normalization was used" required: true \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml index 531568c372..42b99b0d9e 100644 --- a/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/cell2location/config.vsh.yaml @@ -84,4 +84,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu] + label: [hightime, midmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/cell2location/script.py b/src/tasks/spatial_decomposition/methods/cell2location/script.py index ea78421bd1..3d47991691 100644 --- a/src/tasks/spatial_decomposition/methods/cell2location/script.py +++ b/src/tasks/spatial_decomposition/methods/cell2location/script.py @@ -8,7 +8,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'detection_alpha': 20.0, 'n_cells_per_location': 20, diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index 02a9b82dd2..84088afbd5 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -38,4 +38,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu, gpu] + label: [hightime, midmem, midcpu, gpu] diff --git a/src/tasks/spatial_decomposition/methods/destvi/script.py b/src/tasks/spatial_decomposition/methods/destvi/script.py index 7a3cb82034..4682e74f49 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/script.py +++ b/src/tasks/spatial_decomposition/methods/destvi/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'max_epochs_sc': 500, 'max_epochs_sp': 5000 diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml index 8cb45c4a4f..97320cb550 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/nmfreg/config.vsh.yaml @@ -34,4 +34,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/script.py b/src/tasks/spatial_decomposition/methods/nmfreg/script.py index dd3a104d8d..8854368d65 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/script.py +++ b/src/tasks/spatial_decomposition/methods/nmfreg/script.py @@ -8,7 +8,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'n_components': 30 } diff --git a/src/tasks/spatial_decomposition/methods/nnls/script.py b/src/tasks/spatial_decomposition/methods/nnls/script.py index cbe86c3d51..9fa865674a 100644 --- a/src/tasks/spatial_decomposition/methods/nnls/script.py +++ b/src/tasks/spatial_decomposition/methods/nnls/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad' } meta = { diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml index 78cb8e7846..6c633d92b8 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -35,4 +35,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/rctd/script.R b/src/tasks/spatial_decomposition/methods/rctd/script.R index 814c41e874..31ebe6369a 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/script.R +++ b/src/tasks/spatial_decomposition/methods/rctd/script.R @@ -5,7 +5,7 @@ library(Matrix) ## VIASH START par <- list( input_single_cell = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad", - input_spatial = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", + input_spatial_masked = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", output = "output.h5ad", fc_cutoff = 0.5, fc_cutoff_reg = 0.75 @@ -30,7 +30,7 @@ celltype_counts <- table(input_single_cell$obs$cell_type) input_single_cell <- input_single_cell[input_single_cell$obs$cell_type %in% names(as.table(celltype_counts[celltype_counts > 25]))] # get single cell reference counts -sc_counts <- t(as.matrix(input_single_cell$layers['counts'])) +sc_counts <- t(input_single_cell$layers['counts']) # get single cell reference labels sc_cell_types <- factor(input_single_cell$obs$cell_type) names(sc_cell_types) <- rownames(input_single_cell) @@ -38,7 +38,7 @@ names(sc_cell_types) <- rownames(input_single_cell) reference <- Reference(sc_counts, sc_cell_types) # get spatial data counts -sp_counts <- t(as.matrix(input_spatial$layers['counts'])) +sp_counts <- t(input_spatial$layers['counts']) # get spatial data coordinates sp_coords <- as.data.frame(input_spatial$obsm['coordinates']) colnames(sp_coords) <- c("x", "y") diff --git a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml index ab222f5b1e..c82a1c9a7b 100644 --- a/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/seurat/config.vsh.yaml @@ -36,4 +36,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu] + label: [midtime, highmem, midcpu] diff --git a/src/tasks/spatial_decomposition/methods/seurat/script.R b/src/tasks/spatial_decomposition/methods/seurat/script.R index df4ee0565f..77917dd92e 100644 --- a/src/tasks/spatial_decomposition/methods/seurat/script.R +++ b/src/tasks/spatial_decomposition/methods/seurat/script.R @@ -4,7 +4,7 @@ library(Seurat) ## VIASH START par <- list( input_single_cell = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad", - input_spatial = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", + input_spatial_masked = "resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad", output = "output.h5ad", n_pcs = 30, sctransform_n_cells = 500 @@ -35,7 +35,8 @@ seurat_sp <- SCTransform( seurat_sp, assay = "spatial", ncells = min(par$sctransform_n_cells, nrow(seurat_sp)), - verbose = TRUE + verbose = TRUE, + conserve.memory = TRUE ) seurat_sp <- RunPCA(seurat_sp, assay = "SCT", verbose = FALSE, n_pcs = par$n_pcs) @@ -45,7 +46,8 @@ seurat_sc <- SCTransform( seurat_sc, assay = "RNA", ncells = min(par$sctransform_n_cells, nrow(seurat_sc)), - verbose = TRUE + verbose = TRUE, + conserve.memory = TRUE ) seurat_sc <- RunPCA(seurat_sc, verbose = FALSE, n_pcs = par$n_pcs) diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index a1d5c0d9ae..647167fe72 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -37,4 +37,4 @@ platforms: - type: native - type: nextflow directives: - label: [midtime, midmem, midcpu, gpu] + label: [hightime, midmem, midcpu, gpu] diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/script.py b/src/tasks/spatial_decomposition/methods/stereoscope/script.py index 7965312e98..e69bb5f118 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/script.py +++ b/src/tasks/spatial_decomposition/methods/stereoscope/script.py @@ -5,7 +5,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'max_epochs_sc': 100, 'max_epochs_sp': 1000 @@ -29,7 +29,7 @@ sc_model.train( max_epochs=par["max_epochs_sc"], # early_stopping=True, - # early_stopping_monitor="elbo_train" + # early_stopping_monitor="elbo_validation" ) SpatialStereoscope.setup_anndata(input_spatial) @@ -37,7 +37,7 @@ st_model.train( max_epochs=par["max_epochs_sp"], # early_stopping=True, - # early_stopping_monitor="elbo_train" + # early_stopping_monitor="elbo_validation" ) input_spatial.obsm["proportions_pred"] = st_model.get_proportions().to_numpy() diff --git a/src/tasks/spatial_decomposition/methods/tangram/script.py b/src/tasks/spatial_decomposition/methods/tangram/script.py index b24bc22b5f..544664ff94 100644 --- a/src/tasks/spatial_decomposition/methods/tangram/script.py +++ b/src/tasks/spatial_decomposition/methods/tangram/script.py @@ -7,7 +7,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'num_epochs': 1000, 'n_markers': 100 diff --git a/src/tasks/spatial_decomposition/methods/vanillanmf/script.py b/src/tasks/spatial_decomposition/methods/vanillanmf/script.py index 9ca1302b55..ff550796b0 100644 --- a/src/tasks/spatial_decomposition/methods/vanillanmf/script.py +++ b/src/tasks/spatial_decomposition/methods/vanillanmf/script.py @@ -6,7 +6,7 @@ ## VIASH START par = { 'input_single_cell': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad', - 'input_spatial': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', + 'input_spatial_masked': 'resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/spatial_masked.h5ad', 'output': 'output.h5ad', 'max_iter': 4000 } diff --git a/src/tasks/spatial_decomposition/process_dataset/script.py b/src/tasks/spatial_decomposition/process_dataset/script.py index d944a99d42..6e73a17830 100644 --- a/src/tasks/spatial_decomposition/process_dataset/script.py +++ b/src/tasks/spatial_decomposition/process_dataset/script.py @@ -1,5 +1,6 @@ import anndata as ad import sys +import numpy as np ## VIASH START par = { @@ -21,6 +22,9 @@ print(">> Load dataset", flush=True) adata = ad.read_h5ad(par["input"]) +# TO DO: Non-integer values in the counts layer are detected as un-normalized data by some methods, thereby causing them to fail. +adata.layers['counts'] = adata.layers['counts'].floor() + print(">> Figuring out which data needs to be copied to which output file", flush=True) slot_info = read_config_slots_info(meta["config"]) diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf index 509a13f0de..b518bf4c54 100644 --- a/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf @@ -59,6 +59,18 @@ workflow run_wf { | runEach( components: methods, + // use the 'filter' argument to only run a method on the normalisation the component is asking for + filter: { id, state, comp -> + def norm = state.dataset_uns.normalization_id + def pref = comp.config.functionality.info.preferred_normalization + // if the preferred normalisation is none at all, + // we can pass whichever dataset we want + def norm_check = (norm == "log_cp10k" && pref == "counts") || norm == pref + def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name) + + method_check && norm_check + }, + // define a new 'id' by appending the method name to the dataset id id: { id, state, comp -> id + "." + comp.config.functionality.name From 8886fee4f539621ef6a47a86811a83e5161186a7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 25 Apr 2024 09:01:46 +0200 Subject: [PATCH 1207/1233] Bump peaceiris/actions-gh-pages from 3 to 4 (#426) Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. - [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) - [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) - [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) --- updated-dependencies: - dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Former-commit-id: e763de0a04c00655db32232afecbbc8bc46c0617 --- .github/workflows/integration-test.yml | 2 +- .github/workflows/main-build.yml | 2 +- .github/workflows/release-build.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index 9a68bfa543..dd828fddd3 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -37,7 +37,7 @@ jobs: parallel: true - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index ba1872afa8..5ddc2e3aea 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -45,7 +45,7 @@ jobs: # tools_version: 'main_build' - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 1d98b8e711..041a59ae44 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -58,7 +58,7 @@ jobs: tools_version: 'main_build' - name: Deploy to target branch - uses: peaceiris/actions-gh-pages@v3 + uses: peaceiris/actions-gh-pages@v4 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: . From bbe93846ac8712d6ff2951f113128f837783f6ac Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Apr 2024 12:15:03 +0200 Subject: [PATCH 1208/1233] update cxg census (#436) Former-commit-id: b8337001d5f1da422e273d23e94b61161be9ddf0 --- .../loaders/cellxgene_census/script.py | 46 ++++++++----------- 1 file changed, 18 insertions(+), 28 deletions(-) diff --git a/src/datasets/loaders/cellxgene_census/script.py b/src/datasets/loaders/cellxgene_census/script.py index 8c2bcc7227..49c44b6b32 100644 --- a/src/datasets/loaders/cellxgene_census/script.py +++ b/src/datasets/loaders/cellxgene_census/script.py @@ -78,33 +78,34 @@ def get_anndata(census_connection, par): # ) def filter_min_cells_per_group(adata, par): - t0 = adata.shape + n_cells_before, _ = adata.shape cell_count = adata.obs \ .groupby(par["cell_filter_grouping"])["soma_joinid"] \ .transform("count") \ adata = adata[cell_count >= par["cell_filter_minimum_count"]] - t1 = adata.shape + n_cells_after, _ = adata.shape logger.info( "Removed %s cells based on %s cell_filter_minimum_count of %s cell_filter_grouping." - % ((t0[0] - t1[0]), par["cell_filter_minimum_count"], par["cell_filter_grouping"]) + % ((n_cells_before - n_cells_after), par["cell_filter_minimum_count"], par["cell_filter_grouping"]) ) return adata def filter_by_counts(adata, par): logger.info("Remove cells with few counts and genes with few counts.") - t0 = adata.shape + n_cells_before, n_genes_before = adata.shape # remove cells with few counts and genes with few counts - if par["cell_filter_min_counts"]: - sc.pp.filter_cells(adata, min_counts=par["cell_filter_min_counts"]) - if par["cell_filter_min_genes"]: - sc.pp.filter_cells(adata, min_genes=par["cell_filter_min_genes"]) - if par["gene_filter_min_counts"]: - sc.pp.filter_genes(adata, min_counts=par["gene_filter_min_counts"]) - if par["gene_filter_min_cells"]: - sc.pp.filter_genes(adata, min_cells=par["gene_filter_min_cells"]) - t1 = adata.shape - logger.info("Removed %s cells and %s genes.", (t0[0] - t1[0]), (t0[1] - t1[1])) + scanpy_proc = { + par["cell_filter_min_counts"]: (sc.pp.filter_cells, "min_counts"), + par["cell_filter_min_genes"]: (sc.pp.filter_cells, "min_genes"), + par["gene_filter_min_counts"]: (sc.pp.filter_genes, "min_counts"), + par["gene_filter_min_cells"]: (sc.pp.filter_genes, "min_cells"), + } + for threshold, (func, arg) in scanpy_proc.items(): + if threshold: + func(adata, **{arg: threshold}) + n_cells_after, n_genes_after = adata.shape + logger.info("Removed %s cells and %s genes.", (n_cells_before - n_cells_after), (n_genes_before - n_genes_after)) def move_x_to_layers(adata): logger.info("Move .X to .layers['counts']") @@ -136,20 +137,9 @@ def print_summary(adata): logger.info(f"Resulting dataset: {adata}") logger.info("Summary of dataset:") - print_unique(adata, "assay") - print_unique(adata, "assay_ontology_term_id") - print_unique(adata, "cell_type") - print_unique(adata, "cell_type_ontology_term_id") - print_unique(adata, "dataset_id") - print_unique(adata, "development_stage") - print_unique(adata, "development_stage_ontology_term_id") - print_unique(adata, "disease") - print_unique(adata, "disease_ontology_term_id") - print_unique(adata, "tissue") - print_unique(adata, "tissue_ontology_term_id") - print_unique(adata, "tissue_general") - print_unique(adata, "tissue_general_ontology_term_id") - + obs_fields = ["assay", "assay_ontology_term_id", "cell_type", "cell_type_ontology_term_id", "dataset_id", "development_stage", "development_stage_ontology_term_id", "disease", "disease_ontology_term_id", "tissue", "tissue_ontology_term_id", "tissue_general", "tissue_general_ontology_term_id"] + for field in obs_fields: + print_unique(adata, field) def write_anndata(adata, par): logger.info("Writing AnnData object to '%s'", par["output"]) From cdf82b11973db54451cd18a6ac368ff163538a0f Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Apr 2024 12:15:15 +0200 Subject: [PATCH 1209/1233] Minor changes in PM task (#437) * allow more time for components that need it * simplify script * add guanlab submission info Former-commit-id: 030cd349d0a8efc59bd0dbdf79bc91402d86d395 --- src/tasks/predict_modality/api/task_info.yaml | 5 +++++ .../methods/guanlab_dengkw_pm/config.vsh.yaml | 10 ++++++++-- .../methods/guanlab_dengkw_pm/script.py | 6 ++---- .../predict_modality/methods/knnr_py/config.vsh.yaml | 2 +- .../predict_modality/methods/knnr_r/config.vsh.yaml | 2 +- src/tasks/predict_modality/methods/lm/config.vsh.yaml | 2 +- .../methods/newwave_knnr/config.vsh.yaml | 4 ++-- .../methods/random_forest/config.vsh.yaml | 2 +- 8 files changed, 21 insertions(+), 12 deletions(-) diff --git a/src/tasks/predict_modality/api/task_info.yaml b/src/tasks/predict_modality/api/task_info.yaml index 4d0c5596c4..ba3b567d01 100644 --- a/src/tasks/predict_modality/api/task_info.yaml +++ b/src/tasks/predict_modality/api/task_info.yaml @@ -49,3 +49,8 @@ authors: roles: [ author ] info: github: agranado + - name: Kaiwen Deng + roles: [ contributor ] + info: + email: dengkw@umich.edu + github: nonztalk \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml index 231416caf2..a81ed56cb3 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/config.vsh.yaml @@ -5,11 +5,17 @@ functionality: label: Guanlab-dengkw summary: A kernel ridge regression method with RBF kernel. description: | - This is a solution developed by Team Guanlab - dengkw in the Neurips 2021 competiton to predeict one modality from another using kernel ridge regression (KRR) with RBF kernel. Truncated SVD is applied on the combined training and test data from modality 1 followed by row-wise z-score normalization on the reduced matrix. The truncated SVD of modality 2 is predicted by training a KRR model on the normalized training matrix of modality 1. Predictions on the normalized test matrix are then re-mapped to the modality 2 feature space via the right singular vectors. + This is a solution developed by Team Guanlab - dengkw in the Neurips 2021 competition to predict one modality + from another using kernel ridge regression (KRR) with RBF kernel. Truncated SVD is applied on the combined + training and test data from modality 1 followed by row-wise z-score normalization on the reduced matrix. The + truncated SVD of modality 2 is predicted by training a KRR model on the normalized training matrix of modality 1. + Predictions on the normalized test matrix are then re-mapped to the modality 2 feature space via the right + singular vectors. preferred_normalization: log_cp10k reference: lance2022multimodal documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/Guanlab-dengkw + competition_submission_id: 170636 arguments: - name: "--distance_method" type: "string" @@ -34,4 +40,4 @@ platforms: - numpy - type: nextflow directives: - label: [midtime, highmem, highcpu] + label: [hightime, highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py index fb4d38529f..c4614f6252 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -52,10 +52,8 @@ ) print('Determine parameters by the modalities', flush=True) -mod1_type = input_train_mod1.uns["modality"] -mod1_type = mod1_type.upper() -mod2_type = input_train_mod2.uns["modality"] -mod2_type = mod2_type.upper() +mod1_type = input_train_mod1.uns["modality"].upper() +mod2_type = input_train_mod2.uns["modality"].upper() n_comp_dict = { ("GEX", "ADT"): (300, 70, 10, 0.2), ("ADT", "GEX"): (None, 50, 10, 0.2), diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 8fb2cb5f33..4a4d7a4f1b 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -30,4 +30,4 @@ platforms: image: ghcr.io/openproblems-bio/base_python:1.0.4 - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [hightime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index 226cd0a53d..ee41993962 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: cran: [ lmds, FNN, proxyC] - type: nextflow directives: - label: [midtime, lowmem, lowcpu] + label: [hightime, lowmem, lowcpu] diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 507f27fd35..3b85936563 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -29,4 +29,4 @@ platforms: cran: [ lmds, RcppArmadillo, pbapply] - type: nextflow directives: - label: [midtime, highmem, highcpu] + label: [hightime, highmem, highcpu] diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 9b880d4e9d..606d04f7d3 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -34,8 +34,8 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r - cran: [ lmds, FNN, proxy, proxyC] + cran: [ lmds, FNN, proxy, proxyC ] bioc: [ SingleCellExperiment, NewWave ] - type: nextflow directives: - label: [midtime, highmem, highcpu, highsharedmem] + label: [hightime, highmem, highcpu, highsharedmem] diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 3ec12abd4d..329fd50ddb 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -33,4 +33,4 @@ platforms: cran: [ lmds, ranger, pbapply] - type: nextflow directives: - label: [midtime, highmem, highcpu] \ No newline at end of file + label: [hightime, highmem, highcpu] \ No newline at end of file From 5d3b2046da4b40f07f4102eb4cabaf1c0479fe8b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Apr 2024 16:10:32 +0200 Subject: [PATCH 1210/1233] Update PM api (#439) * make gitignore more strict * update api files Co-authored-by: Kai Waldrant * create separate file for pretrained model --------- Co-authored-by: Kai Waldrant Former-commit-id: 6754cfc3d9bdd451b1f489c8dc7f7f1a7045e7da --- .gitignore | 12 ++++----- .../api/comp_method_predict.yaml | 27 +++++++++++++++++++ .../api/comp_method_train.yaml | 27 +++++++++++++++++++ .../api/file_common_dataset_mod1.yaml | 10 +++++++ .../api/file_common_dataset_mod2.yaml | 10 +++++++ .../api/file_pretrained_model.yaml | 4 +++ .../predict_modality/api/file_test_mod1.yaml | 10 +++++++ .../predict_modality/api/file_test_mod2.yaml | 10 +++++++ .../predict_modality/api/file_train_mod1.yaml | 10 +++++++ .../predict_modality/api/file_train_mod2.yaml | 10 +++++++ 10 files changed, 124 insertions(+), 6 deletions(-) create mode 100644 src/tasks/predict_modality/api/comp_method_predict.yaml create mode 100644 src/tasks/predict_modality/api/comp_method_train.yaml create mode 100644 src/tasks/predict_modality/api/file_pretrained_model.yaml diff --git a/.gitignore b/.gitignore index 9efeaab825..b27efa26e7 100644 --- a/.gitignore +++ b/.gitignore @@ -3,7 +3,7 @@ *.h5ad # IDE ignores -.idea/ +/.idea/ # repo specific ignores output_bash @@ -15,14 +15,14 @@ output_bash # viash specific ignores docker_output/ -target/ +/target/ check_results/ log.txt .viash* -resources/ -resources_test/ +/resources/ +/resources_test/ # nextflow specific ignores -.nextflow* -work +/.nextflow* +/work output diff --git a/src/tasks/predict_modality/api/comp_method_predict.yaml b/src/tasks/predict_modality/api/comp_method_predict.yaml new file mode 100644 index 0000000000..6c2c4bafa2 --- /dev/null +++ b/src/tasks/predict_modality/api/comp_method_predict.yaml @@ -0,0 +1,27 @@ +functionality: + namespace: "predict_modality/methods" + info: + type: method_predict + preferred_normalization: counts # there is currently only one type of normalization + type_info: + label: Predict + summary: Make predictions using a trained model. + description: | + This method makes predictions using a trained model. + arguments: + - name: "--input_test_mod1" + __merge__: file_test_mod1.yaml + direction: input + required: true + - name: "--input_train_mod2" + __merge__: file_train_mod2.yaml + direction: input + required: true + - name: "--input_model" + __merge__: file_pretrained_model.yaml + direction: input + required: true + - name: "--output" + __merge__: file_prediction.yaml + direction: output + required: true \ No newline at end of file diff --git a/src/tasks/predict_modality/api/comp_method_train.yaml b/src/tasks/predict_modality/api/comp_method_train.yaml new file mode 100644 index 0000000000..43839ca3b1 --- /dev/null +++ b/src/tasks/predict_modality/api/comp_method_train.yaml @@ -0,0 +1,27 @@ +functionality: + namespace: "predict_modality/methods" + info: + type: method_train + preferred_normalization: counts + type_info: + label: Train + summary: Train a model to predict the expression of one modality from another. + description: | + This method trains a model to predict the expression of one modality from another. + arguments: + - name: "--input_train_mod1" + __merge__: file_train_mod1.yaml + direction: input + required: true + - name: "--input_train_mod2" + __merge__: file_train_mod2.yaml + direction: input + required: true + - name: "--input_test_mod1" + __merge__: file_test_mod1.yaml + direction: input + required: false + - name: "--output" + __merge__: file_pretrained_model.yaml + direction: output + required: true \ No newline at end of file diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml index d893c0e27a..268f54b993 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml @@ -34,6 +34,16 @@ info: description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it required: true + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml index d00c0e0cdc..fc4573cda2 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml @@ -34,6 +34,16 @@ info: description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it required: true + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_pretrained_model.yaml b/src/tasks/predict_modality/api/file_pretrained_model.yaml new file mode 100644 index 0000000000..f8c4a717ac --- /dev/null +++ b/src/tasks/predict_modality/api/file_pretrained_model.yaml @@ -0,0 +1,4 @@ +type: file +info: + label: "Pretrained model" + summary: "A pretrained model for predicting the expression of one modality from another." diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml index 82925b0d49..fa67672104 100644 --- a/src/tasks/predict_modality/api/file_test_mod1.yaml +++ b/src/tasks/predict_modality/api/file_test_mod1.yaml @@ -27,6 +27,16 @@ info: name: gene_ids description: The gene identifiers (if available) required: false + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml index dcff45087e..417edf6162 100644 --- a/src/tasks/predict_modality/api/file_test_mod2.yaml +++ b/src/tasks/predict_modality/api/file_test_mod2.yaml @@ -27,6 +27,16 @@ info: name: gene_ids description: The gene identifiers (if available) required: false + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml index 393669263e..a4919ee7bd 100644 --- a/src/tasks/predict_modality/api/file_train_mod1.yaml +++ b/src/tasks/predict_modality/api/file_train_mod1.yaml @@ -27,6 +27,16 @@ info: name: gene_ids description: The gene identifiers (if available) required: false + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml index 34eeffb414..dcbfae45de 100644 --- a/src/tasks/predict_modality/api/file_train_mod2.yaml +++ b/src/tasks/predict_modality/api/file_train_mod2.yaml @@ -27,6 +27,16 @@ info: name: gene_ids description: The gene identifiers (if available) required: false + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A score for the feature indicating how highly variable it is. + required: true uns: - type: string name: dataset_id From 916bbc217fd161bfcefb1f45fd95032f804fc049 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Apr 2024 17:09:23 +0200 Subject: [PATCH 1211/1233] fix regex Former-commit-id: 5129ed619f3aa53b177052465dffe4318639705d --- .github/workflows/integration-test.yml | 2 +- .github/workflows/main-build.yml | 2 +- .github/workflows/release-build.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index dd828fddd3..b8e85c22e2 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -29,7 +29,7 @@ jobs: - name: Remove target folder from .gitignore run: | # allow publishing the target folder - sed -i '/^target.*/d' .gitignore + sed -i 's#^/target/$##g' .gitignore - uses: viash-io/viash-actions/ns-build@v5 with: diff --git a/.github/workflows/main-build.yml b/.github/workflows/main-build.yml index 5ddc2e3aea..efdf563065 100644 --- a/.github/workflows/main-build.yml +++ b/.github/workflows/main-build.yml @@ -21,7 +21,7 @@ jobs: - name: Remove target folder from .gitignore run: | # allow publishing the target folder - sed -i '/^target.*/d' .gitignore + sed -i 's#^/target/$##g' .gitignore - uses: viash-io/viash-actions/ns-build@v5 with: diff --git a/.github/workflows/release-build.yml b/.github/workflows/release-build.yml index 041a59ae44..4d4b18c2f8 100644 --- a/.github/workflows/release-build.yml +++ b/.github/workflows/release-build.yml @@ -34,7 +34,7 @@ jobs: - name: Remove target folder from .gitignore run: | # allow publishing the target folder - sed -i '/^target.*/d' .gitignore + sed -i 's#^/target/$##g' .gitignore - uses: viash-io/viash-actions/ns-build@v5 with: From 9c76f78e2552380681b55418c41c9a2edc4b221a Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Apr 2024 22:43:12 +0200 Subject: [PATCH 1212/1233] Various PM fixes (#442) * fix description * subsample evenly * fix method_predict api * let guanlab method use the normalized data * add missing columns to var * don't binarize the data * remove comment * clean up guanlab script; use comments as primary data source * disable newwave and rf * fix preferred normalization * add lmds_irlba_rf method * only process the log_cp10k datasets Former-commit-id: d7e29d729114904b3a1ff837572a5cf6677b0956 --- .../processors/subsample/config.vsh.yaml | 2 +- .../resource_test_scripts/neurips2021_bmmc.sh | 1 + .../main.nf | 1 - .../predict_modality/api/comp_method.yaml | 1 - .../api/comp_method_predict.yaml | 9 +- .../api/comp_method_train.yaml | 1 - .../methods/guanlab_dengkw_pm/script.py | 79 +++++++--------- .../methods/knnr_py/config.vsh.yaml | 2 +- .../methods/knnr_r/config.vsh.yaml | 2 +- .../methods/lm/config.vsh.yaml | 2 +- .../methods/lmds_irlba_rf/config.vsh.yaml | 37 ++++++++ .../methods/lmds_irlba_rf/script.R | 93 +++++++++++++++++++ .../methods/newwave_knnr/config.vsh.yaml | 3 +- .../methods/random_forest/config.vsh.yaml | 3 +- .../predict_modality/process_dataset/script.R | 8 +- .../resources_scripts/process_datasets.sh | 3 +- .../resources_scripts/run_benchmark.sh | 3 +- .../workflows/run_benchmark/config.vsh.yaml | 5 +- .../workflows/run_benchmark/main.nf | 5 +- 19 files changed, 190 insertions(+), 70 deletions(-) create mode 100644 src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/lmds_irlba_rf/script.R diff --git a/src/datasets/processors/subsample/config.vsh.yaml b/src/datasets/processors/subsample/config.vsh.yaml index e2a33ed084..bbfacdf832 100644 --- a/src/datasets/processors/subsample/config.vsh.yaml +++ b/src/datasets/processors/subsample/config.vsh.yaml @@ -18,7 +18,7 @@ functionality: - name: "--keep_cell_type_categories" type: "string" multiple: true - description: "Categories indexes to be selected" + description: "Cell type indexes to be selected" required: false - name: "--keep_batch_categories" type: "string" diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 189969617e..69d766cf18 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -30,6 +30,7 @@ dataset_url: "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE194122" dataset_reference: luecken2021neurips normalization_methods: [log_cp10k] do_subsample: true +even: true n_obs: 600 n_vars: 1500 output_mod1: '$id/dataset_mod1.h5ad' diff --git a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf index 1d73ab4429..5f3b9867c7 100644 --- a/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf +++ b/src/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf @@ -139,7 +139,6 @@ workflow run_wf { toState: [ "hvg_mod1": "output" ] ) - // TODO: should this only run on ATAC? or even not at all?s | hvg.run( key: "hvg_mod2", fromState: [ "input": "svd_mod2" ], diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml index 0855227a55..49ccc1e27b 100644 --- a/src/tasks/predict_modality/api/comp_method.yaml +++ b/src/tasks/predict_modality/api/comp_method.yaml @@ -2,7 +2,6 @@ functionality: namespace: "predict_modality/methods" info: type: method - preferred_normalization: counts # there is currently only one type of normalization type_info: label: Method summary: A regression method. diff --git a/src/tasks/predict_modality/api/comp_method_predict.yaml b/src/tasks/predict_modality/api/comp_method_predict.yaml index 6c2c4bafa2..ebd56aed51 100644 --- a/src/tasks/predict_modality/api/comp_method_predict.yaml +++ b/src/tasks/predict_modality/api/comp_method_predict.yaml @@ -2,21 +2,24 @@ functionality: namespace: "predict_modality/methods" info: type: method_predict - preferred_normalization: counts # there is currently only one type of normalization type_info: label: Predict summary: Make predictions using a trained model. description: | This method makes predictions using a trained model. arguments: - - name: "--input_test_mod1" - __merge__: file_test_mod1.yaml + - name: "--input_train_mod1" + __merge__: file_train_mod1.yaml direction: input required: true - name: "--input_train_mod2" __merge__: file_train_mod2.yaml direction: input required: true + - name: "--input_test_mod1" + __merge__: file_test_mod1.yaml + direction: input + required: true - name: "--input_model" __merge__: file_pretrained_model.yaml direction: input diff --git a/src/tasks/predict_modality/api/comp_method_train.yaml b/src/tasks/predict_modality/api/comp_method_train.yaml index 43839ca3b1..3f07c1efcf 100644 --- a/src/tasks/predict_modality/api/comp_method_train.yaml +++ b/src/tasks/predict_modality/api/comp_method_train.yaml @@ -2,7 +2,6 @@ functionality: namespace: "predict_modality/methods" info: type: method_train - preferred_normalization: counts type_info: label: Train summary: Train a model to predict the expression of one modality from another. diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py index c4614f6252..09ad2a4a10 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -1,6 +1,5 @@ import anndata as ad import numpy as np -import gc from scipy.sparse import csc_matrix from sklearn.decomposition import TruncatedSVD from sklearn.gaussian_process.kernels import RBF @@ -8,15 +7,15 @@ ## VIASH START par = { - 'input_train_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod1.h5ad', - 'input_train_mod2': 'resources_test/predict_modality/neurips2021_bmmc_cite/train_mod2.h5ad', - 'input_test_mod1': 'resources_test/predict_modality/neurips2021_bmmc_cite/test_mod1.h5ad', - 'output': 'output.h5ad', - 'distance_method': 'minkowski', - 'n_pcs': 50 + 'input_train_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/test_mod1.h5ad', + 'output': 'output.h5ad', + 'distance_method': 'minkowski', + 'n_pcs': 50 } meta = { - 'functionality_name': 'guanlab_dengkw_pm' + 'functionality_name': 'guanlab_dengkw_pm' } ## VIASH END @@ -27,21 +26,10 @@ input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) -dataset_id = input_train_mod1.uns['dataset_id'] - -pred_dimx = input_test_mod1.shape[0] -pred_dimy = input_train_mod2.shape[1] - -feature_obs = input_train_mod1.obs -gs_obs = input_train_mod2.obs - batches = input_train_mod1.obs.batch.unique().tolist() batch_len = len(batches) -obs = input_test_mod1.obs -var = input_train_mod2.var -dataset_id = input_train_mod1.uns['dataset_id'] - +# combine the train and test data input_train = ad.concat( {"train": input_train_mod1, "test": input_test_mod1}, axis=0, @@ -55,11 +43,11 @@ mod1_type = input_train_mod1.uns["modality"].upper() mod2_type = input_train_mod2.uns["modality"].upper() n_comp_dict = { - ("GEX", "ADT"): (300, 70, 10, 0.2), - ("ADT", "GEX"): (None, 50, 10, 0.2), - ("GEX", "ATAC"): (1000, 50, 10, 0.1), - ("ATAC", "GEX"): (100, 70, 10, 0.1) - } + ("GEX", "ADT"): (300, 70, 10, 0.2), + ("ADT", "GEX"): (None, 50, 10, 0.2), + ("GEX", "ATAC"): (1000, 50, 10, 0.1), + ("ATAC", "GEX"): (100, 70, 10, 0.1) +} print(f"{mod1_type}, {mod2_type}", flush=True) n_mod1, n_mod2, scale, alpha = n_comp_dict[(mod1_type, mod2_type)] print(f"{n_mod1}, {n_mod2}, {scale}, {alpha}", flush=True) @@ -67,20 +55,20 @@ # Perform PCA on the input data print('Models using the Truncated SVD to reduce the dimension', flush=True) -if n_mod1 is not None and n_mod1 < input_train.shape[1]: +if n_mod1 is not None and n_mod1 < input_train.n_vars: embedder_mod1 = TruncatedSVD(n_components=n_mod1) - mod1_pca = embedder_mod1.fit_transform(input_train.layers["counts"]).astype(np.float32) + mod1_pca = embedder_mod1.fit_transform(input_train.layers["normalized"]).astype(np.float32) train_matrix = mod1_pca[input_train.obs['group'] == 'train'] test_matrix = mod1_pca[input_train.obs['group'] == 'test'] else: - train_matrix = input_train_mod1.to_df(layer="counts").values.astype(np.float32) - test_matrix = input_test_mod1.to_df(layer="counts").values.astype(np.float32) + train_matrix = input_train_mod1.to_df(layer="normalized").values.astype(np.float32) + test_matrix = input_test_mod1.to_df(layer="normalized").values.astype(np.float32) -if n_mod2 is not None and n_mod2 < input_train_mod2.shape[1]: +if n_mod2 is not None and n_mod2 < input_train_mod2.n_vars: embedder_mod2 = TruncatedSVD(n_components=n_mod2) - train_gs = embedder_mod2.fit_transform(input_train_mod2.layers["counts"]).astype(np.float32) + train_gs = embedder_mod2.fit_transform(input_train_mod2.layers["normalized"]).astype(np.float32) else: - train_gs = input_train_mod2.to_df(layer="counts").values.astype(np.float32) + train_gs = input_train_mod2.to_df(layer="normalized").values.astype(np.float32) del input_train @@ -98,26 +86,23 @@ del test_matrix print('Running KRR model ...', flush=True) -y_pred = np.zeros((pred_dimx, pred_dimy), dtype=np.float32) -np.random.seed(1000) +y_pred = np.zeros((input_test_mod1.n_obs, input_train_mod2.n_vars), dtype=np.float32) for _ in range(5): - np.random.shuffle(batches) - for batch in [batches[:batch_len//2], batches[batch_len//2:]]: - # for passing the test - if not batch: - batch = [batches[0]] + np.random.shuffle(batches) + for batch in [batches[:batch_len//2], batches[batch_len//2:]]: + # for passing the test + if not batch: + batch = [batches[0]] print(batch, flush=True) kernel = RBF(length_scale = scale) krr = KernelRidge(alpha=alpha, kernel=kernel) print('Fitting KRR ... ', flush=True) - krr.fit(train_norm[feature_obs.batch.isin(batch)], train_gs[gs_obs.batch.isin(batch)]) + krr.fit(train_norm[input_train_mod1.obs.batch.isin(batch)], train_gs[input_train_mod2.obs.batch.isin(batch)]) y_pred += (krr.predict(test_norm) @ embedder_mod2.components_) np.clip(y_pred, a_min=0, a_max=None, out=y_pred) -if mod2_type == "ATAC": - np.clip(y_pred, a_min=0, a_max=1, out=y_pred) y_pred /= 10 @@ -129,13 +114,11 @@ print("Write output AnnData to file", flush=True) output = ad.AnnData( - layers = { - 'normalized': y_pred - }, - obs = obs, - var = var, + layers = { 'normalized': y_pred }, + obs = input_test_mod1.obs[[]], + var = input_train_mod2.var[[]], uns = { - 'dataset_id': dataset_id, + 'dataset_id': input_train_mod1.uns['dataset_id'], 'method_id': meta['functionality_name'] } ) diff --git a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml index 4a4d7a4f1b..4ef88dd62b 100644 --- a/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: reference: fix1989discriminatory documentation_url: https://scikit-learn.org/stable/modules/neighbors.html repository_url: https://github.com/scikit-learn/scikit-learn - preferred_normalization: counts + preferred_normalization: log_cp10k arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml index ee41993962..cda809b109 100644 --- a/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/knnr_r/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: reference: fix1989discriminatory documentation_url: https://cran.r-project.org/package=FNN repository_url: https://github.com/cran/FNN - preferred_normalization: counts + preferred_normalization: log_cp10k arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/lm/config.vsh.yaml b/src/tasks/predict_modality/methods/lm/config.vsh.yaml index 3b85936563..98d3268abd 100644 --- a/src/tasks/predict_modality/methods/lm/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/lm/config.vsh.yaml @@ -8,7 +8,7 @@ functionality: reference: wilkinson1973symbolic repository_url: https://github.com/RcppCore/RcppArmadillo documentation_url: https://cran.r-project.org/package=RcppArmadillo - preferred_normalization: counts + preferred_normalization: log_cp10k arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml new file mode 100644 index 0000000000..37906c9c96 --- /dev/null +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/config.vsh.yaml @@ -0,0 +1,37 @@ +__merge__: ../../api/comp_method.yaml +functionality: + name: lmds_irlba_rf + info: + label: LMDS + IRLBA + RF + summary: A random forest regression using LMDS of modality 1 to predict a PCA embedding of modality 2, which is then reversed to predict the original modality 2. + description: | + A random forest regression using LMDS of modality 1 to predict a PCA embedding of modality 2, which is then reversed to predict the original modality 2. + reference: lance2022multimodal + documentation_url: https://github.com/openproblems-bio/openproblems-v2/tree/main/src/tasks/predict_modality/methods #/lmds_irlba_rf + repository_url: https://github.com/openproblems-bio/openproblems-v2 + preferred_normalization: log_cp10k + arguments: + - name: "--distance_method" + type: "string" + default: "pearson" + description: The distance method to use. Possible values are euclidean, pearson, spearman and others. + - name: "--n_pcs" + type: "integer" + default: 20 + description: Number of principal components to use. + - name: "--n_trees" + type: "integer" + default: 500 + description: Number of trees to use. + resources: + - type: r_script + path: script.R +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_r:1.0.4 + setup: + - type: r + cran: [lmds, ranger, pbapply, irlba] + - type: nextflow + directives: + label: [hightime, highmem, highcpu] \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R b/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R new file mode 100644 index 0000000000..3458a55bef --- /dev/null +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R @@ -0,0 +1,93 @@ +cat("Loading dependencies\n") +requireNamespace("anndata", quietly = TRUE) +requireNamespace("pbapply", quietly = TRUE) +library(Matrix, warn.conflicts = FALSE, quietly = TRUE) + +## VIASH START +path <- "resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/" +par <- list( + input_train_mod1 = paste0(path, "train_mod1.h5ad"), + input_test_mod1 = paste0(path, "test_mod1.h5ad"), + input_train_mod2 = paste0(path, "train_mod2.h5ad"), + output = "output.h5ad", + n_pcs = 20L, + n_trees = 50L +) +meta <- list(functionality_name = "foo") +## VIASH END + +n_cores <- parallel::detectCores(all.tests = FALSE, logical = TRUE) + +cat("Reading mod1 files\n") +input_train_mod1 <- anndata::read_h5ad(par$input_train_mod1) +input_test_mod1 <- anndata::read_h5ad(par$input_test_mod1) + +dataset_id <- input_train_mod1$uns[["dataset_id"]] + +cat("Performing DR on the mod1 values\n") +dr <- lmds::lmds( + rbind(input_train_mod1$layers[["normalized"]], input_test_mod1$layers[["normalized"]]), + ndim = par$n_pcs, + distance_method = par$distance_method +) +# alternative: +# pr_out <- irlba::prcomp_irlba( +# rbind(input_train_mod1$layers[["normalized"]], input_test_mod1$layers[["normalized"]]), +# n = par$n_pcs +# ) +# dr <- pr_out$x + +# split up dr data +ix <- seq_len(nrow(input_train_mod1)) +dr_train <- as.data.frame(dr[ix, , drop = FALSE]) +dr_test <- as.data.frame(dr[-ix, , drop = FALSE]) +dr_train <- dr[ix, , drop = FALSE] +dr_test <- dr[-ix, , drop = FALSE] + +rm(input_train_mod1, input_test_mod1) +gc() + + +cat("Reading mod2 files\n") +X_mod2 <- anndata::read_h5ad(par$input_train_mod2)$layers[["normalized"]] +prcomp_mod2 <- irlba::prcomp_irlba(X_mod2, n = par$n_pcs) +dr_mod2 <- prcomp_mod2$x + +cat("Predicting for each column in modality 2\n") +pred_drs <- pbapply::pblapply( + seq_len(ncol(dr_mod2)), + function(i) { + y <- dr_mod2[, i] + uy <- unique(y) + if (length(uy) > 1) { + rf <- ranger::ranger( + x = dr_train, + y = y, + num.trees = par$n_trees, + num.threads = n_cores + ) + stats::predict(rf, dr_test)$prediction + } else { + rep(uy, nrow(dr_test)) + } + } +) + +cat("Creating outputs object\n") +pred_dr <- Matrix::Matrix(do.call(cbind, pred_drs), sparse = TRUE) +prediction <- pred_dr %*% t(prcomp_mod2$rotation) +rownames(prediction) <- rownames(dr_test) +colnames(prediction) <- colnames(X_mod2) + +out <- anndata::AnnData( + layers = list(normalized = as.matrix(prediction)), + shape = dim(prediction), + uns = list( + dataset_id = dataset_id, + method_id = meta$functionality_name + ) +) + + +cat("Writing predictions to file\n") +zzz <- out$write_h5ad(par$output, compression = "gzip") diff --git a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml index 606d04f7d3..1e01b4fc6a 100644 --- a/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/newwave_knnr/config.vsh.yaml @@ -1,6 +1,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: newwave_knnr + status: disabled # disabled due to poor performance and long execution times info: label: NewWave+KNNR summary: Perform DR with NewWave, predict modality with KNN regression. @@ -8,7 +9,7 @@ functionality: reference: agostinis2022newwave repository_url: https://github.com/fedeago/NewWave documentation_url: https://bioconductor.org/packages/release/bioc/html/NewWave.html - preferred_normalization: counts + preferred_normalization: log_cp10k arguments: - name: "--newwave_maxiter" type: "integer" diff --git a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml index 329fd50ddb..110582e07c 100644 --- a/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml +++ b/src/tasks/predict_modality/methods/random_forest/config.vsh.yaml @@ -1,6 +1,7 @@ __merge__: ../../api/comp_method.yaml functionality: name: random_forest + status: disabled # disabled due to long execution times info: label: Random Forests summary: Random forest regression. @@ -8,7 +9,7 @@ functionality: reference: breiman2001random documentation_url: https://www.stat.berkeley.edu/~breiman/RandomForests/reg_home.htm repository_url: https://github.com/cran/randomForest - preferred_normalization: counts + preferred_normalization: log_cp10k arguments: - name: "--distance_method" type: "string" diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index cbaeb161dc..2c8bbf38d3 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -55,13 +55,13 @@ ad1_uns$dataset_name <- ad2_uns$dataset_name <- new_dataset_name # determine new obsm ad1_obsm <- ad2_obsm <- list() -# determine new varm -ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids")), drop = FALSE] -ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids")), drop = FALSE] +# determine new var +ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] +ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] if (ad1_mod == "ATAC") { # binarize features - ad1$layers[["normalized"]]@x <- (ad1$layers[["normalized"]]@x > 0) + 0 + # ad1$layers[["normalized"]]@x <- (ad1$layers[["normalized"]]@x > 0) + 0 # copy gene activity in new object ad1_uns$gene_activity_var_names <- ad1$uns$gene_activity_var_names diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 11da1b6ee6..3ddacfddcf 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -1,8 +1,9 @@ #!/bin/bash +# only process the 'log_cp10k' datasets cat > /tmp/params.yaml << 'HERE' id: predict_modality_process_datasets -input_states: s3://openproblems-data/resources/datasets/**/state.yaml +input_states: s3://openproblems-data/resources/datasets/**/log_cp10k/state.yaml settings: '{"output_train_mod1": "$id/train_mod1.h5ad", "output_train_mod2": "$id/train_mod2.h5ad", "output_test_mod1": "$id/test_mod1.h5ad", "output_test_mod2": "$id/test_mod2.h5ad"}' rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' output_state: "$id/state.yaml" diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 279a579294..64901573df 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -3,9 +3,10 @@ RUN_ID="run_$(date +%Y-%m-%d_%H-%M-%S)" publish_dir="s3://openproblems-data/resources/predict_modality/results/${RUN_ID}" +# only process the 'log_cp10k' datasets cat > /tmp/params.yaml << HERE id: predict_modality -input_states: s3://openproblems-data/resources/predict_modality/datasets/**/state.yaml +input_states: s3://openproblems-data/resources/predict_modality/datasets/**/log_cp10k/state.yaml rename_keys: 'input_train_mod1:output_train_mod1,input_train_mod2:output_train_mod2,input_test_mod1:output_test_mod1,input_test_mod2:output_test_mod2' output_state: "state.yaml" publish_dir: "$publish_dir" diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index 5f9eceb2c5..f406d5f66b 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -70,8 +70,9 @@ functionality: - name: predict_modality/methods/knnr_py - name: predict_modality/methods/knnr_r - name: predict_modality/methods/lm - - name: predict_modality/methods/newwave_knnr - - name: predict_modality/methods/random_forest + - name: predict_modality/methods/lmds_irlba_rf + # - name: predict_modality/methods/newwave_knnr + # - name: predict_modality/methods/random_forest - name: predict_modality/methods/guanlab_dengkw_pm - name: predict_modality/metrics/correlation - name: predict_modality/metrics/mse diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 8839cc18d4..5f54ef29fa 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -20,8 +20,9 @@ workflow run_wf { knnr_py, knnr_r, lm, - newwave_knnr, - random_forest, + lmds_irlba_rf, + // newwave_knnr, + // random_forest, guanlab_dengkw_pm ] From 62e3a16a2837099474a61c63900b4a6a1a99fa4b Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Thu, 25 Apr 2024 23:30:21 +0200 Subject: [PATCH 1213/1233] Neurips22 dataset (#438) * neurips22 loader * NeurIPS22 dataset loader * minor tweaks to component * add neurips2022 processing wf * update bibtex and scripts --------- Co-authored-by: xlancelottx Co-authored-by: Robrecht Cannoodt Former-commit-id: 1913ae1526417c6a9c486725d32569f9d8f6b819 --- src/common/library.bib | 8 + .../config.vsh.yaml | 80 ++++++++ .../openproblems_neurips2022_pbmc/script.py | 91 +++++++++ .../openproblems_neurips2022_pbmc/test.py | 100 +++++++++ .../openproblems_neurips2022_pbmc.sh | 57 ++++++ .../resource_test_scripts/neurips2022_pbmc.sh | 54 +++++ .../config.vsh.yaml | 143 +++++++++++++ .../main.nf | 192 ++++++++++++++++++ 8 files changed, 725 insertions(+) create mode 100644 src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml create mode 100644 src/datasets/loaders/openproblems_neurips2022_pbmc/script.py create mode 100644 src/datasets/loaders/openproblems_neurips2022_pbmc/test.py create mode 100755 src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh create mode 100755 src/datasets/resource_test_scripts/neurips2022_pbmc.sh create mode 100644 src/datasets/workflows/process_openproblems_neurips2022_pbmc/config.vsh.yaml create mode 100644 src/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf diff --git a/src/common/library.bib b/src/common/library.bib index 50524c4b38..313bfff56d 100644 --- a/src/common/library.bib +++ b/src/common/library.bib @@ -776,6 +776,14 @@ @article{lance2022multimodal } +@article{lance2024predicting, + title = {Predicting cellular profiles across modalities in longitudinal single-cell data: An Open Problems competition}, + author = {...}, + year = {2024}, + journal = {In preparation}, +} + + @book{lawson1995solving, title = {Solving Least Squares Problems}, author = {Charles L. Lawson and Richard J. Hanson}, diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml new file mode 100644 index 0000000000..a6d79c701d --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/config.vsh.yaml @@ -0,0 +1,80 @@ +functionality: + name: "openproblems_neurips2022_pbmc" + namespace: "datasets/loaders" + description: "Fetch a dataset from the OpenProblems NeurIPS2022 competition" + argument_groups: + - name: Inputs + arguments: + - name: "--input_mod1" + type: file + description: "Processed RNA h5ad file" + required: true + example: cite_rna_merged.h5ad + - name: "--input_mod2" + type: file + description: "Processed ADT or ATAC h5ad file" + required: true + example: cite_prot_merged.h5ad + - name: "--mod1" + type: string + description: Name of the first modality. + required: true + example: GEX + - name: "--mod2" + type: string + description: Name of the second modality. + required: true + example: ADT + - name: Metadata + arguments: + - name: "--dataset_id" + type: string + description: "A unique identifier for the dataset" + required: true + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Outputs + arguments: + - name: "--output_mod1" + __merge__: ../../api/file_raw.yaml + direction: "output" + - name: "--output_mod2" + __merge__: ../../api/file_raw.yaml + direction: "output" + resources: + - type: python_script + path: script.py + # skip unit test until data is public + # test_resources: + # - type: python_script + # path: test.py + # - type: file + # path: /resources_test/common/openproblems_neurips2021/neurips2021_bmmc_cite.h5ad +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ highmem, midcpu, midtime] \ No newline at end of file diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py b/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py new file mode 100644 index 0000000000..cf937f3a19 --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py @@ -0,0 +1,91 @@ +import anndata as ad +from scipy import sparse + +## VIASH START +par = { + "input_mod1": "cite_rna_merged.h5ad", + "input_mod2": "cite_prot_merged.h5ad", + "mod1": "GEX", + "mod2": "ADT", + "dataset_id": "openproblems/neurips2022_pbmc", + "dataset_name": "Kaggle22 PBMC (CITE-seq)", + "dataset_url": "https://www.kaggle.com/competitions/open-problems-multimodal/data", + "dataset_reference": "Neurips22", + "dataset_summary": "Neurips22 competition dataset", + "dataset_description": "The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors.", + "dataset_organism": "homo_sapiens", + "output_mod1": "output/mod1.h5ad", + "output_mod2": "output/mod2.h5ad" +} +meta = { + "functionality_name": "openproblems_neurips2022_pbmc", +} +## VIASH END + + +def convert_matrix(adata): + for key in adata: + if isinstance(adata[key], sparse.csr_matrix): + adata[key] = sparse.csc_matrix(adata[key]) + + +print("load dataset modality 1 file", flush=True) +adata_mod1 = ad.read_h5ad(par["input_mod1"]) + +print("load dataset modality 2 file", flush=True) +adata_mod2 = ad.read_h5ad(par["input_mod2"]) + +# Convert to sparse csc_matrix +convert_matrix(adata_mod1.layers) +convert_matrix(adata_mod1.obsm) +convert_matrix(adata_mod2.layers) +convert_matrix(adata_mod2.obsm) + + +# Add is_train to obs (modality 1) +if "is_train" not in adata_mod1.obs.columns: + split_info = adata_mod1.obs["kaggle_dataset"] + train_sets = ["train", "test_public"] + adata_mod1.obs["is_train"] = [ "train" if x in train_sets else "test" for x in split_info ] + +# Add is_train to obs if it is missing (modality 2) +if "is_train" not in adata_mod2.obs.columns: + split_info = adata_mod2.obs["kaggle_dataset"] + train_sets = ["train", "test_public"] + adata_mod2.obs["is_train"] = [ "train" if x in train_sets else "test" for x in split_info ] + + +# split up index in modality 1 into feature ID and feature name +adata_mod1.var['feature_id'] = [str(s).split('_')[0] for s in adata_mod1.var.index.tolist()] +adata_mod1.var['feature_name'] = [str(s).split('_')[1] for s in adata_mod1.var.index.tolist()] +adata_mod1.var.set_index('feature_id',drop=False, inplace=True) + +# set feature_name (proteins have only partial ensmble IDs)) +adata_mod2.var['feature_name'] = adata_mod2.var.index.tolist() +adata_mod2.var.set_index('feature_name',drop=False, inplace=True) + + +# remove adata.X +del adata_mod1.X +del adata_mod2.X + + +print("Add metadata to uns", flush=True) +metadata_fields = [ + "dataset_id", "dataset_name", "dataset_url", "dataset_reference", + "dataset_summary", "dataset_description", "dataset_organism" +] +for key in metadata_fields: + if key in par: + print(f" Setting .uns['{key}']", flush=True) + adata_mod1.uns[key] = par[key] + adata_mod2.uns[key] = par[key] + + +print("Writing adata to file", flush=True) +adata_mod1.write_h5ad(par["output_mod1"], compression="gzip") +adata_mod2.write_h5ad(par["output_mod2"], compression="gzip") + + + + diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/test.py b/src/datasets/loaders/openproblems_neurips2022_pbmc/test.py new file mode 100644 index 0000000000..3bb5c677eb --- /dev/null +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/test.py @@ -0,0 +1,100 @@ +from os import path +import subprocess +import anndata as ad + +# TODO: update once data is public + +input_mod1 = "cite_rna_merged.h5ad" #change data set path after loading manually? +input_mod2 = "cite_prot_merged.h5ad" #change data set path after loading manually? +mod1 = "GEX" +mod2 = "ADT" + +output_mod1_file = "output_mod1.h5ad" +output_mod2_file = "output_mod2.h5ad" + +input_url_mod1 = "s3://openproblems-nextflow/datasets_private/neurips2022/cite_rna_merged.h5ad" +input_url_mod2 = "s3://openproblems-nextflow/datasets_private/neurips2022/cite_prot_merged.h5ad" + +# download input +# print(">> Downloading input modality 1", flush=True) +# out = subprocess.run( +# [ +# "aws s3 cp", +# "-O", input_mod1, +# input_url_mod1, +# ], +# stderr=subprocess.STDOUT +# ) + +# print(">> Downloading input modality 2", flush=True) +# out = subprocess.run( +# [ +# "aws s3 cp", +# "-O", input_mod2, +# input_url_mod2, +# ], +# stderr=subprocess.STDOUT +# ) + + +print(">> Running script", flush=True) +out = subprocess.run( + [ + meta["executable"], + "--input_mod1", input_mod1, + "--input_mod2", input_mod2, + "--mod1", mod1, + "--mod2", mod2, + "--output_mod1", output_mod1_file, + "--output_mod2", output_mod2_file, + "--dataset_id", "openproblems/neurips2021_bmmc", + "--dataset_name", "Kaggle22 PBMC (CITE-seq)", + "--dataset_url", "https://www.kaggle.com/competitions/open-problems-multimodal/data", + "--dataset_reference", "Neurips22", + "--dataset_summary", "Neurips22 competition dataset", + "--dataset_description", "The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors.", + "--dataset_organism", "homo_sapiens", + ], + stderr=subprocess.STDOUT +) + +if out.stdout: + print(out.stdout, flush=True) + +if out.returncode: + print(f"script: '{out.args}' exited with an error.", flush=True) + exit(out.returncode) + +print(">> Checking whether files exist", flush=True) +assert path.exists(output_mod1_file), "Output mod1 file does not exist" +assert path.exists(output_mod2_file), "Output mod2 file does not exist" + +print(">> Read output anndata", flush=True) +output_mod1 = ad.read_h5ad(output_mod1_file) +output_mod2 = ad.read_h5ad(output_mod2_file) + +print(f"output_mod1: {output_mod1}", flush=True) +print(f"output_mod2: {output_mod2}", flush=True) + +print(">> Check that output mod1 fits expected API", flush=True) +assert output_mod1.X is None, ".X is not None/empty in mod 1 output" +assert "counts" in output_mod1.layers, "'counts' not found in mod 1 output layers" +assert "cell_type" in output_mod1.obs.columns, "cell_type column not found in mod 1 output obs" +assert "batch" in output_mod1.obs.columns, "batch column not found in mod 1 output obs" +assert output_mod1.uns["dataset_name"] == "Kaggle22 PBMC (CITE-seq)", "Expected: Kaggle22 PBMC (CITE-seq) as value for dataset_name in mod 1 output uns" +assert output_mod1.uns["dataset_url"] == "https://www.kaggle.com/competitions/open-problems-multimodal/data", "Expected: https://www.kaggle.com/competitions/open-problems-multimodal/data as value for dataset_url in mod 1 output uns" +assert output_mod1.uns["dataset_reference"] == "Neurips22", "Expected: Neurips22 as value for dataset_reference in mod 1 output uns" +assert output_mod1.uns["dataset_summary"] == "Neurips22 competition dataset", "Expected: Neurips22 competition dataset as value for dataset_summary in mod 1 output uns" +assert output_mod1.uns["dataset_description"] == "The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors.", "Expected: The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors. as value for dataset_description in mod 1 output uns" + + +print(">> Check that output mod2 fits expected API", flush=True) +assert output_mod2.X is None, ".X is not None/empty in mod 2 output" +assert "counts" in output_mod2.layers, "'counts' not found in mod 2 output layers" +assert "cell_type" in output_mod2.obs.columns, "cell_type column not found in mod 2 output obs" +assert "batch" in output_mod2.obs.columns, "batch column not found in mod 2 output obs" +assert output_mod2.uns["dataset_name"] == "Kaggle22 PBMC (CITE-seq)", "Expected: Kaggle22 PBMC (CITE-seq) as value for dataset_name in mod 2 output uns" +assert output_mod2.uns["dataset_url"] == "https://www.kaggle.com/competitions/open-problems-multimodal/data", "Expected: https://www.kaggle.com/competitions/open-problems-multimodal/data as value for dataset_url in mod 2 output uns" +assert output_mod2.uns["dataset_reference"] == "Neurips22", "Expected: Neurips22 as value for dataset_reference in mod 2 output uns" +assert output_mod2.uns["dataset_summary"] == "Neurips22 competition dataset", "Expected: Neurips22 competition dataset as value for dataset_summary in mod 2 output uns" +assert output_mod2.uns["dataset_description"] == "The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors.", "Expected: The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors. as value for dataset_description in mod 2 output uns" \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh b/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh new file mode 100755 index 0000000000..56b61ca104 --- /dev/null +++ b/src/datasets/resource_scripts/openproblems_neurips2022_pbmc.sh @@ -0,0 +1,57 @@ +#!/bin/bash + +set -e + +params_file="/tmp/datasets_openproblems_neurips2022_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_neurips2022/pbmc_cite + input_mod1: s3://openproblems-nextflow/datasets_private/neurips2022/cite_rna_merged.h5ad + input_mod2: s3://openproblems-nextflow/datasets_private/neurips2022/cite_prot_merged.h5ad + mod1: GEX + mod2: ADT + dataset_name: OpenProblems NeurIPS2022 CITE-Seq + dataset_organism: homo_sapiens + dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2022. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + + - id: openproblems_neurips2022/pbmc_multiome + input_mod1: s3://openproblems-nextflow/datasets_private/neurips2022/multiome_rna_merged.h5ad + input_mod2: s3://openproblems-nextflow/datasets_private/neurips2022/multiome_atac_merged.h5ad + mod1: GEX + mod2: ATAC + dataset_name: OpenProblems NeurIPS2022 Multiome + dataset_organism: homo_sapiens + dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2022. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + +dataset_url: "https://www.kaggle.com/competitions/open-problems-multimodal/data" +dataset_reference: lance2024predicting +normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' +output_state: '$id/state.yaml' +publish_dir: s3://openproblems-data/resources/datasets +HERE + +cat > /tmp/nextflow.config << HERE +process { + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } +} +HERE + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ + --config /tmp/nextflow.config \ + --labels openproblems_neurips2022_pbmc,dataset_loader \ diff --git a/src/datasets/resource_test_scripts/neurips2022_pbmc.sh b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh new file mode 100755 index 0000000000..d15ad8fe16 --- /dev/null +++ b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh @@ -0,0 +1,54 @@ +#!/bin/bash + +set -e + +params_file="/tmp/datasets_openproblems_neurips2022_params.yaml" + +cat > "$params_file" << 'HERE' +param_list: + - id: openproblems_neurips2022/pbmc_cite + input_mod1: s3://openproblems-nextflow/datasets_private/neurips2022/cite_rna_merged.h5ad + input_mod2: s3://openproblems-nextflow/datasets_private/neurips2022/cite_prot_merged.h5ad + mod1: GEX + mod2: ADT + dataset_name: OpenProblems NeurIPS2022 CITE-Seq + dataset_organism: homo_sapiens + dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2022. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + + - id: openproblems_neurips2022/pbmc_multiome + input_mod1: s3://openproblems-nextflow/datasets_private/neurips2022/multiome_rna_merged.h5ad + input_mod2: s3://openproblems-nextflow/datasets_private/neurips2022/multiome_atac_merged.h5ad + mod1: GEX + mod2: ATAC + dataset_name: OpenProblems NeurIPS2022 Multiome + dataset_organism: homo_sapiens + dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. + dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2022. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." + +dataset_url: "https://www.kaggle.com/competitions/open-problems-multimodal/data" +dataset_reference: lance2024predicting +normalization_methods: [log_cp10k] +do_subsample: true +even: true +n_obs: 600 +n_vars: 1500 +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' +output_meta_mod1: '$id/dataset_metadata_mod1.yaml' +output_meta_mod2: '$id/dataset_metadata_mod2.yaml' +output_state: '$id/state.yaml' +# publish_dir: s3://openproblems-data/resources_test/common +HERE + +nextflow run . \ + -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ + -profile docker \ + -resume \ + --publish_dir resources_test/common \ + -params-file "$params_file" \ + -c src/wf_utils/labels.config + + +# run task process dataset components +# src/tasks/predict_modality/resources_test_scripts/neurips2022_pbmc.sh \ No newline at end of file diff --git a/src/datasets/workflows/process_openproblems_neurips2022_pbmc/config.vsh.yaml b/src/datasets/workflows/process_openproblems_neurips2022_pbmc/config.vsh.yaml new file mode 100644 index 0000000000..96bcc3ee2c --- /dev/null +++ b/src/datasets/workflows/process_openproblems_neurips2022_pbmc/config.vsh.yaml @@ -0,0 +1,143 @@ +functionality: + name: process_openproblems_neurips2022_pbmc + namespace: datasets/workflows + description: | + Fetch and process Neurips 2022 multimodal datasets + argument_groups: + - name: Inputs + arguments: + - name: "--id" + type: "string" + description: "The ID of the dataset" + required: true + - name: "--input_mod1" + type: file + description: "Processed RNA h5ad file" + required: true + example: cite_rna_merged.h5ad + - name: "--input_mod2" + type: file + description: "Processed ADT or ATAC h5ad file" + required: true + example: cite_prot_merged.h5ad + - name: "--mod1" + type: string + description: Name of the first modality. + required: true + example: GEX + - name: "--mod2" + type: string + description: Name of the second modality. + required: true + example: ADT + - name: Metadata + arguments: + - name: "--dataset_name" + type: string + description: Nicely formatted name. + required: true + - name: "--dataset_url" + type: string + description: Link to the original source of the dataset. + required: false + - name: "--dataset_reference" + type: string + description: Bibtex reference of the paper in which the dataset was published. + required: false + - name: "--dataset_summary" + type: string + description: Short description of the dataset. + required: true + - name: "--dataset_description" + type: string + description: Long description of the dataset. + required: true + - name: "--dataset_organism" + type: string + description: The organism of the dataset. + required: false + - name: Sampling options + arguments: + - name: "--do_subsample" + type: boolean + default: false + description: "Whether or not to subsample the dataset" + - name: "--n_obs" + type: integer + description: Maximum number of observations to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--n_vars" + type: integer + description: Maximum number of variables to be kept. It might end up being less because empty cells / genes are removed. + default: 500 + - name: "--keep_features" + type: string + multiple: true + description: A list of genes to keep. + - name: "--keep_cell_type_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--keep_batch_categories" + type: "string" + multiple: true + description: "Categories indexes to be selected" + required: false + - name: "--even" + type: "boolean_true" + description: Subsample evenly from different batches + - name: "--seed" + type: "integer" + description: "A seed for the subsampling." + example: 123 + - name: Normalization + arguments: + - name: "--normalization_methods" + type: string + multiple: true + choices: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt", "log_scran_pooling"] + default: ["log_cp10k", "log_cpm", "sqrt_cp10k", "sqrt_cpm", "l1_sqrt"] + description: "Which normalization methods to run." + - name: Outputs + arguments: + - name: "--output_mod1" + direction: "output" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml + - name: "--output_mod2" + direction: "output" + __merge__: /src/datasets/api/file_multimodal_dataset.yaml + - name: "--output_meta_mod1" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_mod1.yaml" + - name: "--output_meta_mod2" + direction: "output" + type: file + description: "Dataset metadata" + example: "dataset_metadata_mod2.yaml" + resources: + - type: nextflow_script + path: main.nf + entrypoint: run_wf + - path: /src/wf_utils/helper.nf + dependencies: + - name: datasets/loaders/openproblems_neurips2022_pbmc + - name: datasets/normalization/log_cp + - name: datasets/normalization/log_scran_pooling + - name: datasets/normalization/sqrt_cp + - name: datasets/normalization/l1_sqrt + - name: datasets/normalization/prot_clr + - name: datasets/normalization/atac_tfidf + - name: datasets/processors/subsample + - name: datasets/processors/svd + - name: datasets/processors/hvg + - name: common/extract_metadata + - name: common/decompress_gzip + # test_resources: + # - type: nextflow_script + # path: main.nf + # entrypoint: test_wf +platforms: + - type: nextflow diff --git a/src/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf b/src/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf new file mode 100644 index 0000000000..834d52bf63 --- /dev/null +++ b/src/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf @@ -0,0 +1,192 @@ +include { findArgumentSchema } from "${meta.resources_dir}/helper.nf" + +workflow run_wf { + take: + input_ch + + main: + + // create different normalization methods by overriding the defaults + normalization_methods = [ + log_cp.run( + key: "log_cp10k", + args: [normalization_id: "log_cp10k", n_cp: 10000] + ), + log_cp.run( + key: "log_cpm", + args: [normalization_id: "log_cpm", n_cp: 1000000] + ), + sqrt_cp.run( + key: "sqrt_cp10k", + args: [normalization_id: "sqrt_cp10k", n_cp: 10000] + ), + sqrt_cp.run( + key: "sqrt_cpm", + args: [normalization_id: "sqrt_cpm", n_cp: 1000000] + ), + l1_sqrt.run( + key: "l1_sqrt", + args: [normalization_id: "l1_sqrt"] + ), + log_scran_pooling.run( + key: "log_scran_pooling", + args: [normalization_id: "log_scran_pooling"] + ) + ] + + output_ch = input_ch + + // store original id for later use + | map{ id, state -> + [id, state + [_meta: [join_id: id]]] + } + + // process neurips downloaded dataset + | openproblems_neurips2022_pbmc.run( + fromState: [ + "input_mod1": "input_mod1", + "input_mod2": "input_mod2", + "mod1": "mod1", + "mod2": "mod2", + "dataset_id": "id", + "dataset_name": "dataset_name", + "dataset_url": "dataset_url", + "dataset_reference": "dataset_reference", + "dataset_summary": "dataset_summary", + "dataset_description": "dataset_description", + "dataset_organism": "dataset_organism" + ], + toState: [ + "raw_mod1": "output_mod1", + "raw_mod2": "output_mod2" + ] + ) + + // subsample if need be + | subsample.run( + runIf: { id, state -> state.do_subsample }, + fromState: [ + "input": "raw_mod1", + "input_mod2": "raw_mod2", + "n_obs": "n_obs", + "n_vars": "n_vars", + "keep_features": "keep_features", + "keep_cell_type_categories": "keep_cell_type_categories", + "keep_batch_categories": "keep_batch_categories", + "even": "even", + "seed": "seed" + ], + toState: [ + "raw_mod1": "output", + "raw_mod2": "output_mod2" + ] + ) + + // run mod1 normalization methods + | runEach( + components: normalization_methods, + id: { id, state, comp -> + if (state.normalization_methods.size() > 1) { + id + "/" + comp.name + } else { + id + } + }, + filter: { id, state, comp -> + comp.name in state.normalization_methods + }, + fromState: ["input": "raw_mod1"], + toState: { id, output, state, comp -> + state + [ + "normalization_id": comp.name, + "normalized_mod1": output.output + ] + } + ) + + // run normalization methods on second modality + // TODO: can we change this to DSB? + | prot_clr.run( + runIf: { id, state -> state.mod2 == "ADT" }, + args: [normalization_id: "prot_clr"], + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] + ) + | atac_tfidf.run( + runIf: { id, state -> state.mod2 == "ATAC" }, + args: [normalization_id: "atac_tfidf"], + fromState: ["input": "raw_mod2"], + toState: ["normalized_mod2": "output"] + ) + + | svd.run( + fromState: [ + "input": "normalized_mod1", + "input_mod2": "normalized_mod2" + ], + toState: [ + "svd_mod1": "output", + "svd_mod2": "output_mod2" + ] + ) + + | hvg.run( + fromState: [ "input": "svd_mod1" ], + toState: [ "hvg_mod1": "output" ] + ) + + | hvg.run( + key: "hvg_mod2", + fromState: [ "input": "svd_mod2" ], + toState: [ "hvg_mod2": "output" ] + ) + + // add synonyms + | map{ id, state -> + [id, state + ["output_mod1": state.hvg_mod1, "output_mod2": state.hvg_mod2]] + } + + | extract_metadata.run( + key: "extract_metadata_mod1", + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_mod1") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) + [ + "input": state.output_mod1, + "schema": schemaYaml + ] + }, + toState: ["output_meta_mod1": "output"] + ) + + | extract_metadata.run( + key: "extract_metadata_mod2", + fromState: { id, state -> + def schema = findArgumentSchema(meta.config, "output_mod2") + // workaround: convert GString to String + schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) + def schemaYaml = tempFile("schema.yaml") + writeYaml(schema, schemaYaml) + [ + "input": state.output_mod2, + "schema": schemaYaml + ] + }, + toState: ["output_meta_mod2": "output"] + ) + + // only output the files for which an output file was specified + | setState([ + "output_mod1", + "output_mod2", + "output_meta_mod1", + "output_meta_mod2", + "_meta" + ]) + + emit: + output_ch +} From a839e1d2c19b988102e41162e0791aee1bfc645b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 Apr 2024 03:50:58 +0200 Subject: [PATCH 1214/1233] More PM fixes (#443) * make sure prediction is sparse * fix regex by hardcoding normalisation * add workarounds * process on cluster Former-commit-id: f0ef558f16a94526f16ce888f246d3a3d3986e9d --- .../process_task_results/get_results/script.R | 5 ++- .../openproblems_neurips2022_pbmc/script.py | 7 +++- .../resource_test_scripts/neurips2022_pbmc.sh | 38 +++++++++++++++---- .../methods/lmds_irlba_rf/script.R | 2 +- 4 files changed, 39 insertions(+), 13 deletions(-) diff --git a/src/common/process_task_results/get_results/script.R b/src/common/process_task_results/get_results/script.R index 111eb8a2d5..822562aa18 100644 --- a/src/common/process_task_results/get_results/script.R +++ b/src/common/process_task_results/get_results/script.R @@ -9,7 +9,7 @@ library(purrr, warn.conflicts = FALSE) library(rlang, warn.conflicts = FALSE) ## VIASH START -dir <- "/home/rcannood/workspace/openproblems-bio/task-dge-perturbation-prediction/work/8f/1ee60cd1fbfddd98eadcc11f3fb1d0/_viash_par" +dir <- "work/c1/6660ea0cc6155d7e13fa341d16057b/_viash_par" par <- list( task_id = "task_1", input_scores = paste0(dir, "/input_scores_1/score_uns.yaml"), @@ -130,7 +130,8 @@ scores <- raw_scores %>% ) # read nxf log and process the task id -id_regex <- "^.*:(.*)_process \\((.*)(/[^\\.]*)?(.[^\\.]*)?\\.(.*)\\)$" +norm_methods <- "/log_cp10k|/log_cpm|/sqrt_cp10k|/sqrt_cpm|/l1_sqrt|/log_scran_pooling" +id_regex <- paste0("^.*:(.*)_process \\(([^\\.]*)(", norm_methods, ")?(.[^\\.]*)?\\.(.*)\\)$") trace <- readr::read_tsv(par$input_execution) %>% mutate( diff --git a/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py b/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py index cf937f3a19..d0dd855b55 100644 --- a/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2022_pbmc/script.py @@ -57,10 +57,13 @@ def convert_matrix(adata): # split up index in modality 1 into feature ID and feature name adata_mod1.var['feature_id'] = [str(s).split('_')[0] for s in adata_mod1.var.index.tolist()] -adata_mod1.var['feature_name'] = [str(s).split('_')[1] for s in adata_mod1.var.index.tolist()] +# TODO: index does not always contain an underscore. +if "_" in adata_mod1.var.index[0]: + adata_mod1.var['feature_name'] = [str(s).split('_')[1] for s in adata_mod1.var.index.tolist()] adata_mod1.var.set_index('feature_id',drop=False, inplace=True) -# set feature_name (proteins have only partial ensmble IDs)) +# set feature_name (proteins have only partial ensemble IDs)) +adata_mod2.var['feature_id'] = adata_mod2.var.index.tolist() # feature id needs to be filled in adata_mod2.var['feature_name'] = adata_mod2.var.index.tolist() adata_mod2.var.set_index('feature_name',drop=False, inplace=True) diff --git a/src/datasets/resource_test_scripts/neurips2022_pbmc.sh b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh index d15ad8fe16..ef2e0523e1 100755 --- a/src/datasets/resource_test_scripts/neurips2022_pbmc.sh +++ b/src/datasets/resource_test_scripts/neurips2022_pbmc.sh @@ -38,16 +38,38 @@ output_mod2: '$id/dataset_mod2.h5ad' output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' -# publish_dir: s3://openproblems-data/resources_test/common +publish_dir: s3://openproblems-data/resources_test/common HERE -nextflow run . \ - -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ - -profile docker \ - -resume \ - --publish_dir resources_test/common \ - -params-file "$params_file" \ - -c src/wf_utils/labels.config +# nextflow run . \ +# -main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ +# -profile docker \ +# -resume \ +# --publish_dir resources_test/common \ +# -params-file "$params_file" \ +# -c src/wf_utils/labels.config + + +cat > /tmp/nextflow.config << HERE +process { + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } +} +HERE + + +tw launch https://github.com/openproblems-bio/openproblems-v2.git \ + --revision main_build \ + --pull-latest \ + --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2022_pbmc/main.nf \ + --workspace 53907369739130 \ + --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --params-file "$params_file" \ + --config /tmp/nextflow.config \ + --labels openproblems_neurips2022_pbmc,dataset_loader \ + # run task process dataset components diff --git a/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R b/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R index 3458a55bef..6a5b7ed595 100644 --- a/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R +++ b/src/tasks/predict_modality/methods/lmds_irlba_rf/script.R @@ -80,7 +80,7 @@ rownames(prediction) <- rownames(dr_test) colnames(prediction) <- colnames(X_mod2) out <- anndata::AnnData( - layers = list(normalized = as.matrix(prediction)), + layers = list(normalized = as(prediction, "CsparseMatrix")), shape = dim(prediction), uns = list( dataset_id = dataset_id, From 436368e24400c79c9dc875d8bf1af0446e66565d Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 Apr 2024 10:33:57 +0200 Subject: [PATCH 1215/1233] More PM fixes (#444) * use original batch subsetting method * add print statement * use heuristic to determine modality * make feature_name optional for now * fix division Former-commit-id: f8c18d7070399a1986ddbc3715d291f4ac33f10e --- src/common/check_dataset_schema/script.py | 1 + .../api/file_common_dataset_mod1.yaml | 2 +- .../api/file_common_dataset_mod2.yaml | 2 +- .../methods/guanlab_dengkw_pm/script.py | 33 ++++++++++++------- .../predict_modality/process_dataset/script.R | 22 +++++++++++-- 5 files changed, 44 insertions(+), 16 deletions(-) diff --git a/src/common/check_dataset_schema/script.py b/src/common/check_dataset_schema/script.py index b5a1c072c0..cd84f9cdcf 100644 --- a/src/common/check_dataset_schema/script.py +++ b/src/common/check_dataset_schema/script.py @@ -48,6 +48,7 @@ def check_structure(slot, slot_info, adata_slot): print("Checking slot", slot, flush=True) missing = check_structure(slot, def_slots[slot], getattr(adata, slot)) if missing: + print(f"Dataset is missing {slot} {missing}", flush=True) out['exit_code'] = 1 out['data_schema'] = 'not ok' out['error'][slot] = missing diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml index 268f54b993..c82e0be026 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml @@ -33,7 +33,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: true + required: false - type: boolean name: hvg diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml index fc4573cda2..1a447b24c0 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml @@ -33,7 +33,7 @@ info: name: feature_name description: A human-readable name for the feature, usually a gene symbol. # TODO: make this required once the dataloader supports it - required: true + required: false - type: boolean name: hvg diff --git a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py index 09ad2a4a10..aafd2948c8 100644 --- a/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py +++ b/src/tasks/predict_modality/methods/guanlab_dengkw_pm/script.py @@ -86,25 +86,36 @@ del test_matrix print('Running KRR model ...', flush=True) -y_pred = np.zeros((input_test_mod1.n_obs, input_train_mod2.n_vars), dtype=np.float32) - -for _ in range(5): - np.random.shuffle(batches) - for batch in [batches[:batch_len//2], batches[batch_len//2:]]: - # for passing the test - if not batch: - batch = [batches[0]] +if batch_len == 1: + # just in case there is only one batch + batch_subsets = [batches] +elif mod1_type == "ADT" or mod2_type == "ADT": + # two fold consensus predictions + batch_subsets = [ + batches[:batch_len//2], + batches[batch_len//2:] + ] +else: + # leave-one-batch-out consensus predictions + batch_subsets = [ + batches[:i] + batches[i+1:] + for i in range(batch_len) + ] +y_pred = np.zeros((input_test_mod1.n_obs, input_train_mod2.n_vars), dtype=np.float32) +for batch in batch_subsets: print(batch, flush=True) kernel = RBF(length_scale = scale) krr = KernelRidge(alpha=alpha, kernel=kernel) print('Fitting KRR ... ', flush=True) - krr.fit(train_norm[input_train_mod1.obs.batch.isin(batch)], train_gs[input_train_mod2.obs.batch.isin(batch)]) + krr.fit( + train_norm[input_train_mod1.obs.batch.isin(batch)], + train_gs[input_train_mod2.obs.batch.isin(batch)] + ) y_pred += (krr.predict(test_norm) @ embedder_mod2.components_) np.clip(y_pred, a_min=0, a_max=None, out=y_pred) - -y_pred /= 10 +y_pred /= len(batch_subsets) # Store as sparse matrix to be efficient. # Note that this might require different classifiers/embedders before-hand. diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 2c8bbf38d3..d2436ea845 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -32,9 +32,25 @@ cat("Reading input data\n") ad1 <- anndata::read_h5ad(if (!par$swap) par$input_mod1 else par$input_mod2) ad2 <- anndata::read_h5ad(if (!par$swap) par$input_mod2 else par$input_mod1) -# figure out modality types -ad1_mod <- unique(ad1$var[["feature_types"]]) -ad2_mod <- unique(ad2$var[["feature_types"]]) +# use heuristic to determine modality +# TODO: should be removed once modality is stored in the uns +determine_modality <- function(ad, mod1 = TRUE) { + if ("modality" %in% names(ad$uns)) { + ad$uns[["modality"]] + } else if ("feature_types" %in% colnames(ad$var)) { + unique(ad$var[["feature_types"]]) + } else if (mod1) { + "RNA" + } else if (grepl("cite", ad$uns[["dataset_id"]])) { + "ADT" + } else if (grepl("multiome", ad$uns[["dataset_id"]])) { + "ATAC" + } else { + stop("Could not determine modality") + } +} +ad1_mod <- determine_modality(ad1, !par$swap) +ad2_mod <- determine_modality(ad2, par$swap) # determine new uns uns_vars <- c("dataset_id", "dataset_name", "dataset_url", "dataset_reference", "dataset_summary", "dataset_description", "dataset_organism", "normalization_id") From a6024bbbdec2e754c00e4c9ec07226732c2e2b04 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 Apr 2024 11:34:15 +0200 Subject: [PATCH 1216/1233] Multimodal fixes (#445) * rename ouput_dataset_mod[12] * gene_activity is not necessarily present * need more resources Former-commit-id: 84f03e11d5618377bf6bfbdae9abd802496b1855 --- src/datasets/resource_scripts/dataset_info.sh | 2 +- .../openproblems_v1_multimodal.sh | 4 ++-- .../openproblems_v1_multimodal_test.sh | 4 ++-- .../resource_test_scripts/scicar_cell_lines.sh | 4 ++-- .../config.vsh.yaml | 4 ++-- .../process_openproblems_v1_multimodal/main.nf | 16 ++++++++-------- .../resources_scripts/process_datasets.sh | 2 +- .../resources_test_scripts/scicar_cell_lines.sh | 2 +- .../process_dataset/config.vsh.yaml | 2 +- .../predict_modality/process_dataset/script.R | 16 ++++++---------- 10 files changed, 26 insertions(+), 30 deletions(-) diff --git a/src/datasets/resource_scripts/dataset_info.sh b/src/datasets/resource_scripts/dataset_info.sh index ecfa6e058a..54fa196339 100755 --- a/src/datasets/resource_scripts/dataset_info.sh +++ b/src/datasets/resource_scripts/dataset_info.sh @@ -9,7 +9,7 @@ param_list: rename_keys: 'input:output_dataset' - id: openproblems_v1_multimodal input_states: "$DATASETS_DIR/openproblems_v1_multimodal/**/log_cp10k/state.yaml" - rename_keys: 'input:output_dataset_mod1' + rename_keys: 'input:output_mod1' - id: cellxgene_census input_states: "$DATASETS_DIR/cellxgene_census/**/log_cp10k/state.yaml" rename_keys: 'input:output_dataset' diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 1fb8b2adf0..0961dcd58c 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -55,8 +55,8 @@ param_list: mod2: ATAC normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_dataset_mod1: '$id/dataset_mod1.h5ad' -output_dataset_mod2: '$id/dataset_mod2.h5ad' +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh index 5ffd3a4185..268a17cf7d 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal_test.sh @@ -28,8 +28,8 @@ param_list: layer_counts: counts normalization_methods: [log_cp10k, sqrt_cp10k, l1_sqrt] -output_dataset_mod1: '$id/dataset_mod1.h5ad' -output_dataset_mod2: '$id/dataset_mod2.h5ad' +output_mod1: '$id/dataset_mod1.h5ad' +output_mod2: '$id/dataset_mod2.h5ad' output_meta_mod1: '$id/dataset_metadata_mod1.yaml' output_meta_mod2: '$id/dataset_metadata_mod2.yaml' output_state: '$id/state.yaml' diff --git a/src/datasets/resource_test_scripts/scicar_cell_lines.sh b/src/datasets/resource_test_scripts/scicar_cell_lines.sh index 895cde58cb..f765744136 100755 --- a/src/datasets/resource_test_scripts/scicar_cell_lines.sh +++ b/src/datasets/resource_test_scripts/scicar_cell_lines.sh @@ -37,8 +37,8 @@ nextflow run . \ --n_vars 1500 \ --seed 123 \ --normalization_methods log_cp10k \ - --output_dataset_mod1 '$id/dataset_mod1.h5ad' \ - --output_dataset_mod2 '$id/dataset_mod2.h5ad' \ + --output_mod1 '$id/dataset_mod1.h5ad' \ + --output_mod2 '$id/dataset_mod2.h5ad' \ --output_meta_mod1 '$id/dataset_metadata_mod1.yaml' \ --output_meta_mod2 '$id/dataset_metadata_mod2.yaml' \ --output_state '$id/state.yaml' \ diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml index b21bb34482..58b045cc3b 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/config.vsh.yaml @@ -120,10 +120,10 @@ functionality: description: "Which normalization methods to run." - name: Outputs arguments: - - name: "--output_dataset_mod1" + - name: "--output_mod1" direction: "output" __merge__: /src/datasets/api/file_multimodal_dataset.yaml - - name: "--output_dataset_mod2" + - name: "--output_mod2" direction: "output" __merge__: /src/datasets/api/file_multimodal_dataset.yaml - name: "--output_meta_mod1" diff --git a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf index da4d34ef5f..96d37d6182 100644 --- a/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf +++ b/src/datasets/workflows/process_openproblems_v1_multimodal/main.nf @@ -153,21 +153,21 @@ workflow run_wf { // add synonyms | map{ id, state -> [id, state + [ - "output_dataset_mod1": state.hvg_mod1, - "output_dataset_mod2": state.hvg_mod2 + "output_mod1": state.hvg_mod1, + "output_mod2": state.hvg_mod2 ]] } | extract_metadata.run( key: "extract_metadata_mod1", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "output_dataset_mod1") + def schema = findArgumentSchema(meta.config, "output_mod1") // workaround: convert GString to String schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.output_dataset_mod1, + "input": state.output_mod1, "schema": schemaYaml ] }, @@ -177,13 +177,13 @@ workflow run_wf { | extract_metadata.run( key: "extract_metadata_mod2", fromState: { id, state -> - def schema = findArgumentSchema(meta.config, "output_dataset_mod2") + def schema = findArgumentSchema(meta.config, "output_mod2") // workaround: convert GString to String schema = iterateMap(schema, { it instanceof GString ? it.toString() : it }) def schemaYaml = tempFile("schema.yaml") writeYaml(schema, schemaYaml) [ - "input": state.output_dataset_mod2, + "input": state.output_mod2, "schema": schemaYaml ] }, @@ -192,8 +192,8 @@ workflow run_wf { // only output the files for which an output file was specified | setState([ - "output_dataset_mod1", - "output_dataset_mod2", + "output_mod1", + "output_mod2", "output_meta_mod1", "output_meta_mod2", "_meta" diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index 27ba91ebbe..2d46f191de 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -3,7 +3,7 @@ cat > /tmp/params.yaml << 'HERE' id: match_modalities_process_datasets input_states: s3://openproblems-data/resources/datasets/openproblems_v1_multimodal/**/state.yaml -rename_keys: 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' +rename_keys: 'input_mod1:output_mod1,input_mod2:output_mod2' settings: '{"output_mod1": "$id/output_mod1.h5ad", "output_mod2": "$id/output_mod2.h5ad", "output_solution_mod1": "$id/output_solution_mod1.h5ad", "output_solution_mod2": "$id/output_solution_mod2.h5ad"}' output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/match_modalities/datasets/openproblems_v1_multimodal diff --git a/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh index 91e90d52dd..6a35138815 100755 --- a/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh +++ b/src/tasks/match_modalities/resources_test_scripts/scicar_cell_lines.sh @@ -20,7 +20,7 @@ nextflow run . \ -profile docker \ -entry auto \ --input_states "$RAW_DATA/**/state.yaml" \ - --rename_keys 'input_mod1:output_dataset_mod1,input_mod2:output_dataset_mod2' \ + --rename_keys 'input_mod1:output_mod1,input_mod2:output_mod2' \ --settings '{"output_mod1": "$id/dataset_mod1.h5ad", "output_mod2": "$id/dataset_mod2.h5ad", "output_solution_mod1": "$id/solution_mod1.h5ad", "output_solution_mod2": "$id/solution_mod2.h5ad"}' \ --publish_dir "$DATASET_DIR" \ --output_state '$id/state.yaml' diff --git a/src/tasks/predict_modality/process_dataset/config.vsh.yaml b/src/tasks/predict_modality/process_dataset/config.vsh.yaml index 66110eaa4e..fdf7e3ab39 100644 --- a/src/tasks/predict_modality/process_dataset/config.vsh.yaml +++ b/src/tasks/predict_modality/process_dataset/config.vsh.yaml @@ -18,4 +18,4 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.4 - type: nextflow directives: - label: [midtime, midmem, lowcpu] + label: [hightime, highmem, highcpu] diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index d2436ea845..b133d16b52 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -75,10 +75,7 @@ ad1_obsm <- ad2_obsm <- list() ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] -if (ad1_mod == "ATAC") { - # binarize features - # ad1$layers[["normalized"]]@x <- (ad1$layers[["normalized"]]@x > 0) + 0 - +if (ad1_mod == "ATAC" && "gene_activity" %in% names(ad1$obsm)) { # copy gene activity in new object ad1_uns$gene_activity_var_names <- ad1$uns$gene_activity_var_names ad1_obsm$gene_activity <- as(ad1$obsm$gene_activity, "CsparseMatrix") @@ -93,12 +90,11 @@ if (ad2_mod == "ATAC") { ad2_var <- ad2_var[sel_ix, , drop = FALSE] } - # binarize features - ad2$layers[["normalized"]]@x <- (ad2$layers[["normalized"]]@x > 0) + 0 - - # copy gene activity in new object - ad2_uns$gene_activity_var_names <- ad2$uns$gene_activity_var_names - ad2_obsm$gene_activity <- as(ad2$obsm$gene_activity, "CsparseMatrix") + if ("gene_activity" %in% names(ad2$obsm)) { + # copy gene activity in new object + ad2_uns$gene_activity_var_names <- ad2$uns$gene_activity_var_names + ad2_obsm$gene_activity <- as(ad2$obsm$gene_activity, "CsparseMatrix") + } } cat("Creating train/test split\n") From 60046cc83d4389fe611bf34208b33e352b173fc0 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 26 Apr 2024 14:28:40 +0200 Subject: [PATCH 1217/1233] fix modality label in process_dataset Former-commit-id: 22ceaf05cecb3f9fdbceb63fec6b2fceba30a516 --- src/tasks/predict_modality/process_dataset/script.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index b133d16b52..4ef92b8578 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -40,7 +40,7 @@ determine_modality <- function(ad, mod1 = TRUE) { } else if ("feature_types" %in% colnames(ad$var)) { unique(ad$var[["feature_types"]]) } else if (mod1) { - "RNA" + "GEX" } else if (grepl("cite", ad$uns[["dataset_id"]])) { "ADT" } else if (grepl("multiome", ad$uns[["dataset_id"]])) { From 2ebefe8fbddca55bc9729b06aa4b955ee33172e4 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 29 Apr 2024 09:41:17 +0200 Subject: [PATCH 1218/1233] Add gpu processing (#440) * Add gpu label * activate scanvi * Change compute env * update gpu config * Add Jax * Add jaxx install * Update comp env * Update src/wf_utils/labels_tw.config Co-authored-by: Robrecht Cannoodt --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 6db04429523fc1e0056236e5c81c6f0e6d2038ba --- src/common/process_task_results/run/run_nf_tower_test.sh | 2 +- src/datasets/resource_scripts/cellxgene_census.sh | 2 +- src/datasets/resource_scripts/dataset_info.sh | 2 +- .../resource_scripts/openproblems_neurips2021_multimodal.sh | 2 +- src/datasets/resource_scripts/openproblems_v1.sh | 2 +- src/datasets/resource_scripts/openproblems_v1_multimodal.sh | 2 +- src/datasets/resource_test_scripts/neurips2021_bmmc.sh | 2 +- src/tasks/batch_integration/methods/scanvi/config.vsh.yaml | 3 +++ src/tasks/batch_integration/methods/scvi/config.vsh.yaml | 3 +++ .../batch_integration/resources_scripts/process_datasets.sh | 2 +- .../batch_integration/resources_scripts/run_benchmark.sh | 2 +- .../resources_scripts/run_benchmark_test.sh | 2 +- src/tasks/denoising/resources_scripts/process_datasets.sh | 2 +- src/tasks/denoising/resources_scripts/run_benchmark.sh | 2 +- src/tasks/denoising/resources_scripts/run_benchmark_test.sh | 2 +- .../resources_scripts/process_datasets.sh | 2 +- .../resources_scripts/run_benchmark.sh | 2 +- .../resources_scripts/run_benchmark_test.sh | 2 +- src/tasks/label_projection/methods/scanvi/config.vsh.yaml | 3 +++ .../label_projection/methods/scanvi_scarches/config.vsh.yaml | 3 +++ .../label_projection/resources_scripts/process_datasets.sh | 2 +- .../label_projection/resources_scripts/run_benchmark.sh | 3 ++- .../label_projection/resources_scripts/run_benchmark_test.sh | 2 +- .../label_projection/workflows/run_benchmark/config.vsh.yaml | 2 +- src/tasks/label_projection/workflows/run_benchmark/main.nf | 2 +- .../match_modalities/resources_scripts/process_datasets.sh | 2 +- .../match_modalities/resources_scripts/run_benchmark.sh | 2 +- .../predict_modality/resources_scripts/process_datasets.sh | 2 +- .../predict_modality/resources_scripts/run_benchmark.sh | 2 +- .../spatial_decomposition/methods/destvi/config.vsh.yaml | 4 +++- .../methods/stereoscope/config.vsh.yaml | 3 +++ .../resources_scripts/process_datasets.sh | 2 +- .../spatial_decomposition/resources_scripts/run_benchmark.sh | 2 +- src/wf_utils/labels_tw.config | 5 +++++ 34 files changed, 51 insertions(+), 28 deletions(-) diff --git a/src/common/process_task_results/run/run_nf_tower_test.sh b/src/common/process_task_results/run/run_nf_tower_test.sh index 9d9a284a76..95fa080f12 100644 --- a/src/common/process_task_results/run/run_nf_tower_test.sh +++ b/src/common/process_task_results/run/run_nf_tower_test.sh @@ -33,6 +33,6 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/common/workflows/transform_meta/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/resource_scripts/cellxgene_census.sh b/src/datasets/resource_scripts/cellxgene_census.sh index 089600b5ef..f0d93c9210 100755 --- a/src/datasets/resource_scripts/cellxgene_census.sh +++ b/src/datasets/resource_scripts/cellxgene_census.sh @@ -147,7 +147,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_cellxgene_census/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "/tmp/params.yaml" \ --config /tmp/nextflow.config \ --labels cellxgene_census,dataset_loader diff --git a/src/datasets/resource_scripts/dataset_info.sh b/src/datasets/resource_scripts/dataset_info.sh index 54fa196339..6ec2de9963 100755 --- a/src/datasets/resource_scripts/dataset_info.sh +++ b/src/datasets/resource_scripts/dataset_info.sh @@ -37,7 +37,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/datasets/workflows/extract_dataset_info/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "/tmp/params.yaml" \ --config /tmp/nextflow.config diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index 236ecf3c7c..af32b8c853 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -49,7 +49,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "$params_file" \ --config /tmp/nextflow.config \ --labels openproblems_neurips2021_bmmc,dataset_loader \ diff --git a/src/datasets/resource_scripts/openproblems_v1.sh b/src/datasets/resource_scripts/openproblems_v1.sh index cea09b2e65..1a01e2120e 100755 --- a/src/datasets/resource_scripts/openproblems_v1.sh +++ b/src/datasets/resource_scripts/openproblems_v1.sh @@ -176,7 +176,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "$params_file" \ --config /tmp/nextflow.config \ --labels openproblems_v1,dataset_loader \ No newline at end of file diff --git a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh index 0961dcd58c..3efb960c45 100755 --- a/src/datasets/resource_scripts/openproblems_v1_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_v1_multimodal.sh @@ -79,7 +79,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/datasets/workflows/process_openproblems_v1_multimodal/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "$params_file" \ --labels openproblems_v1_multimodal,dataset_loader \ --config /tmp/nextflow.config \ No newline at end of file diff --git a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh index 69d766cf18..7922f634cb 100755 --- a/src/datasets/resource_test_scripts/neurips2021_bmmc.sh +++ b/src/datasets/resource_test_scripts/neurips2021_bmmc.sh @@ -62,7 +62,7 @@ nextflow run . \ # --revision main_build \ # --main-script target/nextflow/datasets/workflows/process_openproblems_neurips2021_bmmc/main.nf \ # --workspace 53907369739130 \ -# --compute-env 1pK56PjjzeraOOC2LDZvN2 \ +# --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ # --params-file "$params_file" \ # --config /tmp/nextflow.config \ # --labels predict_modality diff --git a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml index f7f8cd9b24..3801d5bbe7 100644 --- a/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scanvi/config.vsh.yaml @@ -51,6 +51,9 @@ platforms: - type: python pypi: - scvi-tools>=1.1.0 + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: nextflow directives: label: [midtime, lowmem, lowcpu, gpu] diff --git a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml index bed1d9add0..86f9e919b2 100644 --- a/src/tasks/batch_integration/methods/scvi/config.vsh.yaml +++ b/src/tasks/batch_integration/methods/scvi/config.vsh.yaml @@ -49,6 +49,9 @@ platforms: - type: python pypi: - scvi-tools>=1.1.0 + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: nextflow directives: label: [midtime, midmem, lowcpu, gpu] diff --git a/src/tasks/batch_integration/resources_scripts/process_datasets.sh b/src/tasks/batch_integration/resources_scripts/process_datasets.sh index 139f7732b5..97e6b2c61c 100755 --- a/src/tasks/batch_integration/resources_scripts/process_datasets.sh +++ b/src/tasks/batch_integration/resources_scripts/process_datasets.sh @@ -26,7 +26,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh index c8b40cfe53..f48a5ccdd1 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark.sh @@ -15,7 +15,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh index b328bdbc78..b9b80a38ea 100755 --- a/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/batch_integration/resources_scripts/run_benchmark_test.sh @@ -18,7 +18,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/batch_integration/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/denoising/resources_scripts/process_datasets.sh b/src/tasks/denoising/resources_scripts/process_datasets.sh index d79fa70900..44060a8f66 100755 --- a/src/tasks/denoising/resources_scripts/process_datasets.sh +++ b/src/tasks/denoising/resources_scripts/process_datasets.sh @@ -27,7 +27,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/denoising/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/denoising/resources_scripts/run_benchmark.sh b/src/tasks/denoising/resources_scripts/run_benchmark.sh index 3d7e34e7b6..983c42cc56 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark.sh @@ -16,7 +16,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh index ff0f3c166e..7f3ecbd3d2 100755 --- a/src/tasks/denoising/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/denoising/resources_scripts/run_benchmark_test.sh @@ -18,7 +18,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/denoising/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh index bbb064fb26..f83056dad6 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/process_datasets.sh @@ -27,7 +27,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh index 7d42c31176..02c58d5cc5 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark.sh @@ -15,7 +15,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh index d7a21b2757..1c778d345c 100755 --- a/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/dimensionality_reduction/resources_scripts/run_benchmark_test.sh @@ -18,7 +18,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/dimensionality_reduction/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml index 0db9ec292a..b271878a5c 100644 --- a/src/tasks/label_projection/methods/scanvi/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi/config.vsh.yaml @@ -38,6 +38,9 @@ platforms: packages: - scarches - scvi-tools>=1.1.0 + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: nextflow directives: label: [midtime, midmem, highcpu, gpu] diff --git a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml index 1dd2a27749..ddd18f4e91 100644 --- a/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml +++ b/src/tasks/label_projection/methods/scanvi_scarches/config.vsh.yaml @@ -45,6 +45,9 @@ platforms: setup: - type: python pypi: scvi-tools>=1.1.0 + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: nextflow directives: label: [midtime, midmem, midcpu, gpu] diff --git a/src/tasks/label_projection/resources_scripts/process_datasets.sh b/src/tasks/label_projection/resources_scripts/process_datasets.sh index 2527c4950a..dbd284d237 100755 --- a/src/tasks/label_projection/resources_scripts/process_datasets.sh +++ b/src/tasks/label_projection/resources_scripts/process_datasets.sh @@ -27,7 +27,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark.sh b/src/tasks/label_projection/resources_scripts/run_benchmark.sh index cb859e5f56..58a16c38d3 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark.sh @@ -7,6 +7,7 @@ cat > /tmp/params.yaml << HERE input_states: s3://openproblems-data/resources/label_projection/datasets/**/state.yaml rename_keys: 'input_train:output_train,input_test:output_test,input_solution:output_solution' output_state: "state.yaml" +settings: '{"method_ids": "scanvi_scarches"}' publish_dir: "$publish_dir" HERE @@ -15,7 +16,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh index e61b82c336..5baf56f4e4 100755 --- a/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh +++ b/src/tasks/label_projection/resources_scripts/run_benchmark_test.sh @@ -18,7 +18,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/label_projection/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml index 159a7fe179..083bb47a5a 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/label_projection/workflows/run_benchmark/config.vsh.yaml @@ -68,7 +68,7 @@ functionality: - name: label_projection/methods/knn - name: label_projection/methods/logistic_regression - name: label_projection/methods/mlp - # - name: label_projection/methods/scanvi + - name: label_projection/methods/scanvi - name: label_projection/methods/scanvi_scarches - name: label_projection/methods/xgboost - name: label_projection/metrics/accuracy diff --git a/src/tasks/label_projection/workflows/run_benchmark/main.nf b/src/tasks/label_projection/workflows/run_benchmark/main.nf index 01c308575d..5dafc98d1e 100644 --- a/src/tasks/label_projection/workflows/run_benchmark/main.nf +++ b/src/tasks/label_projection/workflows/run_benchmark/main.nf @@ -19,7 +19,7 @@ workflow run_wf { knn, logistic_regression, mlp, - // scanvi, + scanvi, scanvi_scarches, // seurat_transferdata, xgboost diff --git a/src/tasks/match_modalities/resources_scripts/process_datasets.sh b/src/tasks/match_modalities/resources_scripts/process_datasets.sh index 2d46f191de..149130d0cf 100755 --- a/src/tasks/match_modalities/resources_scripts/process_datasets.sh +++ b/src/tasks/match_modalities/resources_scripts/process_datasets.sh @@ -27,7 +27,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/match_modalities/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh index 77b9e8eb0b..001ba3437b 100755 --- a/src/tasks/match_modalities/resources_scripts/run_benchmark.sh +++ b/src/tasks/match_modalities/resources_scripts/run_benchmark.sh @@ -16,7 +16,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/match_modalities/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 3ddacfddcf..22380458b0 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -25,7 +25,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/predict_modality/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh index 64901573df..6d4d35219c 100755 --- a/src/tasks/predict_modality/resources_scripts/run_benchmark.sh +++ b/src/tasks/predict_modality/resources_scripts/run_benchmark.sh @@ -17,7 +17,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/predict_modality/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml index 84088afbd5..a415bd760c 100644 --- a/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/destvi/config.vsh.yaml @@ -34,7 +34,9 @@ platforms: - type: python packages: - scvi-tools>=1.1.0 - + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: native - type: nextflow directives: diff --git a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml index 647167fe72..f9a74dd9ff 100644 --- a/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/stereoscope/config.vsh.yaml @@ -34,6 +34,9 @@ platforms: - type: python packages: - scvi-tools>=1.1.0 + - type: docker + run: | + pip install -U "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html - type: native - type: nextflow directives: diff --git a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh index b435a8eeb8..337aa34512 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/process_datasets.sh @@ -29,7 +29,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/spatial_decomposition/workflows/process_datasets/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config /tmp/nextflow.config \ diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh index a87f0c889c..010a4fce79 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh @@ -15,7 +15,7 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --pull-latest \ --main-script target/nextflow/spatial_decomposition/workflows/run_benchmark/main.nf \ --workspace 53907369739130 \ - --compute-env 1pK56PjjzeraOOC2LDZvN2 \ + --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index 161a23573e..bafda0a323 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -34,6 +34,11 @@ process { withLabel: highsharedmem { containerOptions = { workflow.containerEngine != 'singularity' ? "--shm-size ${String.format("%.0f",task.memory.mega * 0.25)}" : ""} } + withLabel: gpu { + accelerator = 1 + containerOptions = { workflow.containerEngine == "singularity" ? '--nv': + ( workflow.containerEngine == "docker" ? '--gpus all': null ) } + } } def get_memory(to_compare) { From ddc5989206fa789b4fedbb032d5fa45514fbd0df Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 29 Apr 2024 10:45:16 +0200 Subject: [PATCH 1219/1233] Update Neurips2021 dataset loader (#447) * Add validation batches to train set * Add comment Former-commit-id: b6b85a3ebd341d70a43f5a70e7e8967e263095b9 --- src/datasets/loaders/openproblems_neurips2021_bmmc/script.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py index 3a8342fbde..de62f039f6 100644 --- a/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py +++ b/src/datasets/loaders/openproblems_neurips2021_bmmc/script.py @@ -48,7 +48,8 @@ def convert_matrix(adata): if "is_train" not in adata.obs.columns: batch_info = adata.obs["batch"] batch_categories = batch_info.dtype.categories - train = ["s1d1", "s2d1", "s2d4", "s3d6", "s3d1"] + # From https://github.com/openproblems-bio/neurips2021_multimodal_viash/blob/75281c039ab98b459edbf52058a18597e710ed4d/src/common/datasets/process_inhouse_datasets/script.R#L14-L17 + train = ["s1d1", "s1d2", "s2d1", "s2d4", "s3d1", "s3d6", "s3d7"] adata.obs["is_train"] = [ "train" if x in train else "test" for x in batch_info ] # Construct Modality datasets From 1b975246f85c49dcd101807b92e90ee9ceece990 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 29 Apr 2024 15:45:49 +0200 Subject: [PATCH 1220/1233] just use labels_tw (#448) Former-commit-id: 1a1019592365d7a47e0d4afd34316cf3f66f1b6a --- .../resources_scripts/process_datasets.sh | 12 +----------- src/wf_utils/labels_tw.config | 6 ++++++ 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/src/tasks/predict_modality/resources_scripts/process_datasets.sh b/src/tasks/predict_modality/resources_scripts/process_datasets.sh index 22380458b0..69d886725f 100755 --- a/src/tasks/predict_modality/resources_scripts/process_datasets.sh +++ b/src/tasks/predict_modality/resources_scripts/process_datasets.sh @@ -10,16 +10,6 @@ output_state: "$id/state.yaml" publish_dir: s3://openproblems-data/resources/predict_modality/datasets HERE -cat > /tmp/nextflow.config << HERE -process { - executor = 'awsbatch' - withName:'.*publishStatesProc' { - memory = '16GB' - disk = '100GB' - } -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -28,5 +18,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file /tmp/params.yaml \ --entry-name auto \ - --config /tmp/nextflow.config \ + --config src/wf_utils/labels_tw.config \ --labels predict_modality,process_datasets \ No newline at end of file diff --git a/src/wf_utils/labels_tw.config b/src/wf_utils/labels_tw.config index bafda0a323..93a076367b 100644 --- a/src/wf_utils/labels_tw.config +++ b/src/wf_utils/labels_tw.config @@ -39,6 +39,12 @@ process { containerOptions = { workflow.containerEngine == "singularity" ? '--nv': ( workflow.containerEngine == "docker" ? '--gpus all': null ) } } + + // make sure publishstates gets enough disk space and memory + withName:'.*publishStatesProc' { + memory = '16GB' + disk = '100GB' + } } def get_memory(to_compare) { From f76a30c403fa4ef77988bd5388c1bb403025be76 Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Tue, 7 May 2024 12:51:59 +0530 Subject: [PATCH 1221/1233] Minor updates to spatial decomposition methods (#450) * add NNLS method to benchmark workflow * update docker setup * avoid conversion to dense matrix * don't remove rare cell types Former-commit-id: 5f3e6ca59338f04d4c3e35caa4e1d77b13c25465 --- .../methods/nmfreg/script.py | 20 +++++-------------- .../methods/nnls/script.py | 4 +--- .../methods/rctd/config.vsh.yaml | 5 +++-- .../methods/rctd/script.R | 4 ++-- .../resources_scripts/run_benchmark.sh | 2 +- .../workflows/run_benchmark/main.nf | 1 + 6 files changed, 13 insertions(+), 23 deletions(-) diff --git a/src/tasks/spatial_decomposition/methods/nmfreg/script.py b/src/tasks/spatial_decomposition/methods/nmfreg/script.py index 8854368d65..1cc0fd165a 100644 --- a/src/tasks/spatial_decomposition/methods/nmfreg/script.py +++ b/src/tasks/spatial_decomposition/methods/nmfreg/script.py @@ -24,13 +24,9 @@ n_types = input_single_cell.obs["cell_type"].cat.categories.shape[0] # Learn from reference -if issparse(input_single_cell.layers['counts']): - X = input_single_cell.layers['counts'].toarray() -else: - X = input_single_cell.layers['counts'] -X_norm = X / X.sum(1)[:, np.newaxis] +X = input_single_cell.layers['counts'] +X_norm = X / X.sum(1) X_scaled = StandardScaler(with_mean=False).fit_transform(X_norm) - model = NMF( n_components=par['n_components'], init="random", @@ -61,20 +57,14 @@ Ha_norm = StandardScaler(with_mean=False).fit_transform(Ha) sc_deconv = np.dot(Ha_norm**2, factor_to_best_celltype_matrix) - sc_deconv = sc_deconv / sc_deconv.sum(1)[:, np.newaxis] # Start run on actual spatial data -if issparse(input_spatial.layers['counts']): - X_sp = input_spatial.layers['counts'].toarray() -else: - X_sp = input_spatial.layers['counts'] -X_sp_norm = X_sp / X_sp.sum(1)[:, np.newaxis] +X_sp = input_spatial.layers['counts'] +X_sp_norm = X_sp / X_sp.sum(1) X_sp_scaled = StandardScaler(with_mean=False).fit_transform(X_sp_norm) -bead_prop_soln = np.array( - [nnls(Wa.T, X_sp_scaled[b, :])[0] for b in range(X_sp_scaled.shape[0])] -) +bead_prop_soln = np.array([nnls(Wa.T, X_sp_scaled[b, : ].toarray().reshape(-1))[0] for b in range(X_sp_scaled.shape[0])]) bead_prop_soln = StandardScaler(with_mean=False).fit_transform(bead_prop_soln) bead_prop = np.dot(bead_prop_soln, factor_to_best_celltype_matrix) diff --git a/src/tasks/spatial_decomposition/methods/nnls/script.py b/src/tasks/spatial_decomposition/methods/nnls/script.py index 9fa865674a..069ba572fa 100644 --- a/src/tasks/spatial_decomposition/methods/nnls/script.py +++ b/src/tasks/spatial_decomposition/methods/nnls/script.py @@ -32,11 +32,9 @@ X = adata_means.X.T y = input_spatial.layers['counts'].T -if issparse(y): - y = y.toarray() res = np.zeros((y.shape[1], X.shape[1])) # (voxels, cells) for i in range(y.shape[1]): - x, _ = nnls(X, y[:, i]) + x, _ = nnls(X, y[:, i].toarray().reshape(-1)) res[i] = x # Normalize coefficients to sum to 1 diff --git a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml index 6c633d92b8..2d2f82ca47 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/methods/rctd/config.vsh.yaml @@ -30,8 +30,9 @@ platforms: image: ghcr.io/openproblems-bio/base_r:1.0.4 setup: - type: r - cran: [ Matrix ] - github: [ dmcable/spacexr ] + cran: [ Matrix, pak ] + - type: r + script: 'pak::pkg_install("dmcable/spacexr")' - type: native - type: nextflow directives: diff --git a/src/tasks/spatial_decomposition/methods/rctd/script.R b/src/tasks/spatial_decomposition/methods/rctd/script.R index 31ebe6369a..f5878ae05e 100644 --- a/src/tasks/spatial_decomposition/methods/rctd/script.R +++ b/src/tasks/spatial_decomposition/methods/rctd/script.R @@ -26,8 +26,8 @@ rownames(coordinates) <- rownames(input_single_cell) input_single_cell$obsm <- list(coordinates = coordinates) # remove rare cell types to prevent RCTD error -celltype_counts <- table(input_single_cell$obs$cell_type) -input_single_cell <- input_single_cell[input_single_cell$obs$cell_type %in% names(as.table(celltype_counts[celltype_counts > 25]))] +# celltype_counts <- table(input_single_cell$obs$cell_type) +# input_single_cell <- input_single_cell[input_single_cell$obs$cell_type %in% names(as.table(celltype_counts[celltype_counts > 25]))] # get single cell reference counts sc_counts <- t(input_single_cell$layers['counts']) diff --git a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh index 010a4fce79..85d5e4fb1e 100755 --- a/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh +++ b/src/tasks/spatial_decomposition/resources_scripts/run_benchmark.sh @@ -19,4 +19,4 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --params-file /tmp/params.yaml \ --entry-name auto \ --config src/wf_utils/labels_tw.config \ - --labels spatial_decomposition,full \ No newline at end of file + # --labels spatial_decomposition,full \ No newline at end of file diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf index b518bf4c54..82a29fe136 100644 --- a/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/main.nf @@ -18,6 +18,7 @@ workflow run_wf { cell2location, destvi, nmfreg, + nnls, rctd, seurat, stereoscope, From 15aff051ad2c43f52979ba4a1544faf3d2af074f Mon Sep 17 00:00:00 2001 From: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com> Date: Tue, 7 May 2024 18:33:42 +0530 Subject: [PATCH 1222/1233] Add nnls to dependencies (#451) Former-commit-id: 4fbd8f5e81e93a8faacaedb626c1604ed53a9732 --- .../workflows/run_benchmark/config.vsh.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml b/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml index ad2ab676b1..38d97d01c1 100644 --- a/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/spatial_decomposition/workflows/run_benchmark/config.vsh.yaml @@ -58,6 +58,7 @@ functionality: - name: spatial_decomposition/methods/cell2location - name: spatial_decomposition/methods/destvi - name: spatial_decomposition/methods/nmfreg + - name: spatial_decomposition/methods/nnls - name: spatial_decomposition/methods/rctd - name: spatial_decomposition/methods/seurat - name: spatial_decomposition/methods/stereoscope From 71ee604fcbfac2a29581ca6ff85cd09cb3c186e7 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 24 May 2024 12:51:58 +0200 Subject: [PATCH 1223/1233] add more info to the json outputs (#453) Former-commit-id: 907447bc4c8073182f35850747298d05aad536d7 --- src/common/process_task_results/get_dataset_info/script.R | 5 ++++- src/common/process_task_results/get_method_info/script.R | 1 + src/common/process_task_results/get_metric_info/script.R | 3 ++- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/src/common/process_task_results/get_dataset_info/script.R b/src/common/process_task_results/get_dataset_info/script.R index 17e3fb8afd..a2c5317c05 100644 --- a/src/common/process_task_results/get_dataset_info/script.R +++ b/src/common/process_task_results/get_dataset_info/script.R @@ -24,8 +24,11 @@ outputs <- map(datasets, function(dataset) { "dataset_id" = dataset$dataset_id, "dataset_name" = dataset$dataset_name, "dataset_summary" = dataset$dataset_summary, + "dataset_description" = dataset$dataset_description %||% NA_character_, "data_reference" = dataset$dataset_reference %||% NA_character_, - "data_url" = dataset$dataset_url %||% NA_character_ + "data_url" = dataset$dataset_url %||% NA_character_, + "date_created" = dataset$date_created %||% NA_character_, + "file_size" = dataset$file_size %||% NA_character_ ) if (!is.null(dataset[["common_dataset_id"]])) { diff --git a/src/common/process_task_results/get_method_info/script.R b/src/common/process_task_results/get_method_info/script.R index a923df4f39..59cf4bd52c 100644 --- a/src/common/process_task_results/get_method_info/script.R +++ b/src/common/process_task_results/get_method_info/script.R @@ -39,6 +39,7 @@ outputs <- map(configs, function(config) { method_id = info$id, method_name = info$label, method_summary = info$summary, + method_description = info$description, is_baseline = grepl("control", info$type), paper_reference = info$reference %||% NA_character_, code_url = info$repository_url %||% NA_character_, diff --git a/src/common/process_task_results/get_metric_info/script.R b/src/common/process_task_results/get_metric_info/script.R index 9af0b6c852..c384892595 100644 --- a/src/common/process_task_results/get_metric_info/script.R +++ b/src/common/process_task_results/get_metric_info/script.R @@ -41,7 +41,8 @@ outputs <- map(configs, function(config) { task_id = info$task_id, metric_id = info$id, metric_name = info$label, - metric_summary = info$description, + metric_summary = info$summary, + metric_description = info$description, paper_reference = info$reference %||% NA_character_, implementation_url = info$implementation_url %||% NA_character_, code_version = NA_character_, From ef6659a26e75a4177ab046ca397bb20474c83d21 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Fri, 31 May 2024 15:57:57 +0200 Subject: [PATCH 1224/1233] prepare task result processors for viash 0.9 (#455) * prepare task result processors for viash 0.9 * remove assertion Former-commit-id: 2a8390cc524bcb2eba803536b02f6f083d388b9a --- .../get_method_info/script.R | 30 ++++++++++++------- .../get_metric_info/script.R | 23 +++++++++----- 2 files changed, 34 insertions(+), 19 deletions(-) diff --git a/src/common/process_task_results/get_method_info/script.R b/src/common/process_task_results/get_method_info/script.R index 59cf4bd52c..a332413b69 100644 --- a/src/common/process_task_results/get_method_info/script.R +++ b/src/common/process_task_results/get_method_info/script.R @@ -16,20 +16,28 @@ outputs <- map(configs, function(config) { if (length(config$functionality$status) > 0 && config$functionality$status == "disabled") { return(NULL) } - info <- config$functionality$info + + # prep for viash 0.9.0 + build_info <- config$build_info %||% config$info + if ("functionality" %in% names(config)) { + config[names(config$functionality)] <- config$functionality + config[["functionality"]] <- NULL + } + + info <- config$info # add extra info - info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config) - info$task_id <- gsub("/.*", "", config$functionality$namespace) - info$id <- config$functionality$name - info$namespace <- config$functionality$namespace - info$commit_sha <- config$info$git_commit %||% "missing-sha" + info$config_path <- gsub(".*/src/", "src/", build_info$config) + info$task_id <- gsub("/.*", "", config$namespace) + info$id <- config$name + info$namespace <- config$namespace + info$commit_sha <- build_info$git_commit %||% "missing-sha" info$code_version <- "missing-version" - info$implementation_url <- paste0( - "https://github.com/openproblems-bio/openproblems-v2/tree/", - info$commit_sha, "/", - info$config_path - ) + info$implementation_url <- paste0( + build_info$git_remote, "/blob/", + build_info$git_commit, "/", + info$config_path + ) # ↑ this could be used as the new format diff --git a/src/common/process_task_results/get_metric_info/script.R b/src/common/process_task_results/get_metric_info/script.R index c384892595..5ef8f6b04b 100644 --- a/src/common/process_task_results/get_metric_info/script.R +++ b/src/common/process_task_results/get_metric_info/script.R @@ -17,20 +17,27 @@ outputs <- map(configs, function(config) { return(NULL) } + # prep for viash 0.9.0 + build_info <- config$build_info %||% config$info + if ("functionality" %in% names(config)) { + config[names(config$functionality)] <- config$functionality + config[["functionality"]] <- NULL + } + map( - config$functionality$info$metrics, + config$info$metrics, function(info) { # add extra info - info$config_path <- gsub(".*openproblems-v2/src/", "src/", config$info$config) - info$task_id <- gsub("/.*", "", config$functionality$namespace) + info$config_path <- gsub(".*/src/", "src/", build_info$config) + info$task_id <- gsub("/.*", "", config$namespace) info$id <- info$name - info$component_id <- config$functionality$name - info$namespace <- config$functionality$namespace - info$commit_sha <- config$info$git_commit %||% "missing-sha" + info$component_id <- config$name + info$namespace <- config$namespace + info$commit_sha <- build_info$git_commit %||% "missing-sha" info$code_version <- "missing-version" info$implementation_url <- paste0( - "https://github.com/openproblems-bio/openproblems-v2/tree/", - info$commit_sha, "/", + build_info$git_remote, "/blob/", + build_info$git_commit, "/", info$config_path ) From c2e14c08fd951ce66cc7dae29081d47e5145c848 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 13 Jun 2024 11:21:04 +0200 Subject: [PATCH 1225/1233] add csv and parquet support to the readme generator (#458) Former-commit-id: b4817e3ce213df201ef20f373e62193deb837a2c --- src/common/helper_functions/read_api_files.R | 147 +++++++++++++------ 1 file changed, 104 insertions(+), 43 deletions(-) diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R index a2bfc35711..be602b58c4 100644 --- a/src/common/helper_functions/read_api_files.R +++ b/src/common/helper_functions/read_api_files.R @@ -1,14 +1,21 @@ anndata_struct_names <- c("obs", "var", "obsm", "obsp", "varm", "varp", "layers", "uns") -read_anndata_spec <- function(path) { +read_file_spec <- function(path) { spec <- read_and_merge_yaml(path) - list( - info = read_anndata_info(spec, path), - slots = read_anndata_slots(spec, path) + out <- list( + info = read_file_info(spec, path) ) + if (out$info$file_type == "h5ad" || "slots" %in% names(spec$info)) { + out$info$file_type <- "h5ad" + out$slots <- read_anndata_slots(spec, path) + } + if (out$info$file_type == "csv" || out$info$file_type == "tsv" || out$info$file_type == "parquet") { + out$columns <- read_tabular_columns(spec, path) + } + out } -read_anndata_info <- function(spec, path) { +read_file_info <- function(spec, path) { # TEMP: make it readable spec$info$slots <- NULL df <- list_as_tibble(spec) @@ -35,44 +42,95 @@ read_anndata_slots <- function(spec, path) { } ) } +read_tabular_columns <- function(spec, path) { + map_df( + spec$info$columns, + function(column) { + df <- list_as_tibble(column) + df$file_name <- basename(path) %>% gsub("\\.yaml", "", .) + df$required <- df$required %||% TRUE %|% TRUE + df$multiple <- df$multiple %||% FALSE %|% FALSE + as_tibble(df) + } + ) +} -format_slots <- function(spec) { - example <- spec$slots %>% - group_by(struct) %>% - summarise( - str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) - ) %>% - arrange(match(struct, anndata_struct_names)) +format_file_format <- function(spec) { + if (spec$info$file_type == "h5ad") { + example <- spec$slots %>% + group_by(struct) %>% + summarise( + str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", ")) + ) %>% + arrange(match(struct, anndata_struct_names)) + + c(" AnnData object", paste0(" ", example$str)) + } else if (spec$info$file_type == "csv" || spec$info$file_type == "tsv" || spec$info$file_type == "parquet") { + example <- spec$columns %>% + summarise( + str = paste0("'", name, "'", collapse = ", ") + ) - c(" AnnData object", paste0(" ", example$str)) + c(" Tabular data", paste0(" ", example$str)) + } else { + "" + } } -format_slots_as_kable <- function(spec) { - if (nrow(spec$slots) == 0) return("") - spec$slots %>% - mutate( - tag_str = pmap_chr(lst(required), function(required) { - out <- c() - if (!required) { - out <- c(out, "Optional") - } - if (length(out) == 0) { - "" - } else { - paste0("(_", paste(out, collapse = ", "), "_) ") - } - }) - ) %>% - transmute( - Slot = paste0("`", struct, "[\"", name, "\"]`"), - Type = paste0("`", type, "`"), - Description = paste0( - tag_str, - description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), - "." - ) - ) %>% - knitr::kable() +format_file_format_as_kable <- function(spec) { + if (spec$info$file_type == "h5ad") { + spec$slots %>% + mutate( + tag_str = pmap_chr(lst(required), function(required) { + out <- c() + if (!required) { + out <- c(out, "Optional") + } + if (length(out) == 0) { + "" + } else { + paste0("(_", paste(out, collapse = ", "), "_) ") + } + }) + ) %>% + transmute( + Slot = paste0("`", struct, "[\"", name, "\"]`"), + Type = paste0("`", type, "`"), + Description = paste0( + tag_str, + description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), + "." + ) + ) %>% + knitr::kable() + } else if (spec$info$file_type == "csv" || spec$info$file_type == "tsv" || spec$info$file_type == "parquet") { + spec$columns %>% + mutate( + tag_str = pmap_chr(lst(required), function(required) { + out <- c() + if (!required) { + out <- c(out, "Optional") + } + if (length(out) == 0) { + "" + } else { + paste0("(_", paste(out, collapse = ", "), "_) ") + } + }) + ) %>% + transmute( + Column = paste0("`", name, "`"), + Type = paste0("`", type, "`"), + Description = paste0( + tag_str, + description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), + "." + ) + ) %>% + knitr::kable() + } else { + "" + } } list_contains_tibble <- function(li) { @@ -97,6 +155,9 @@ read_comp_info <- function(spec_yaml, path) { spec_yaml$functionality$argument_groups <- NULL df <- list_as_tibble(spec_yaml$functionality) + if (nrow(df) == 0) { + df <- data.frame(a = 1)[, integer(0)] + } if (list_contains_tibble(spec_yaml$functionality$info)) { df <- dplyr::bind_cols(df, list_as_tibble(spec_yaml$functionality$info)) } @@ -187,7 +248,7 @@ render_component <- function(spec) { # path <- "src/datasets/api/file_pca.yaml" render_file <- function(spec) { if (is.character(spec)) { - spec <- read_anndata_spec(spec) + spec <- read_file_spec(spec) } if (!"label" %in% names(spec$info)) { @@ -220,13 +281,13 @@ render_file <- function(spec) { §Format: § §:::{{.small}} - §{paste(format_slots(spec), collapse = '\n')} + §{paste(format_file_format(spec), collapse = '\n')} §::: § §Slot description: § §:::{{.small}} - §{paste(format_slots_as_kable(spec), collapse = '\n')} + §{paste(format_file_format_as_kable(spec), collapse = '\n')} §::: § §"), symbol = "§") @@ -262,7 +323,7 @@ read_task_api <- function(path) { project_path = project_path, parent_path = api_dir ) - files <- map(file_yamls, read_anndata_spec) + files <- map(file_yamls, read_file_spec) names(files) <- basename(file_yamls) %>% gsub("\\..*$", "", .) file_info <- map_df(files, "info") file_slots <- map_df(files, "slots") From a2aef7e0e80cc41967169fd567be7686edc957aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michaela=20M=C3=BCller?= <51025211+mumichae@users.noreply.github.com> Date: Fri, 14 Jun 2024 13:44:39 +0200 Subject: [PATCH 1226/1233] [BI] Add control methods (#454) * move no_integration_batch to new folder structure * modify script to work with opsca-v2 API * add global no integration for embed and graph * add global no integration for feature * refactor global random integration * allow to reuse existing kNN * move utils to top-level and reuse precomputed kNN graph in no_integration graph * fix naming * add per batch random integrations * add random cell type integrations * refactor perfect cell type integrations (one-hot encoding) * update images to 1.0.4 * update Changelog * flatten control method folder structure * add control methods to nextflow workflow * fix namespaces * missing control methods from nextflow workflow * fix utils path --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: d0bc03fb05d43fb26f51c6fe6aa2e2a2f7ff5ade --- CHANGELOG.md | 8 +-- .../api/comp_control_method_feature.yaml | 26 ++++++++ .../batch_embed}/config.vsh.yaml | 10 +--- .../no_integration/batch_embed/script.py | 39 ++++++++++++ .../global_embed/config.vsh.yaml | 22 +++++++ .../no_integration/global_embed/script.py | 26 ++++++++ .../global_feature/config.vsh.yaml | 22 +++++++ .../no_integration/global_feature/script.py | 27 +++++++++ .../global_graph/config.vsh.yaml | 23 ++++++++ .../no_integration/global_graph/script.py | 35 +++++++++++ .../no_integration_batch/script.py | 38 ------------ .../celltype_embed}/config.vsh.yaml | 14 ++--- .../celltype_embed/script.py | 29 +++++++++ .../celltype_jitter_embed}/config.vsh.yaml | 14 ++--- .../celltype_jitter_embed/script.py | 33 +++++++++++ .../random_embed_cell/script.py | 31 ---------- .../random_embed_cell_jitter/script.py | 36 ----------- .../batch_embed/config.vsh.yaml | 23 ++++++++ .../random_integration/batch_embed/script.py | 34 +++++++++++ .../batch_feature/config.vsh.yaml | 23 ++++++++ .../batch_feature/script.py | 33 +++++++++++ .../batch_graph/config.vsh.yaml | 23 ++++++++ .../random_integration/batch_graph/script.py | 35 +++++++++++ .../celltype_embed/config.vsh.yaml | 23 ++++++++ .../celltype_embed/script.py | 32 ++++++++++ .../celltype_feature/config.vsh.yaml | 23 ++++++++ .../celltype_feature/script.py | 35 +++++++++++ .../celltype_graph/config.vsh.yaml | 23 ++++++++ .../celltype_graph/script.py | 35 +++++++++++ .../random_integration/config.vsh.yaml | 25 -------- .../global_embed/config.vsh.yaml | 23 ++++++++ .../random_integration/global_embed/script.py | 31 ++++++++++ .../global_feature/config.vsh.yaml | 23 ++++++++ .../global_feature/script.py | 30 ++++++++++ .../global_graph/config.vsh.yaml | 23 ++++++++ .../random_integration/global_graph/script.py | 31 ++++++++++ .../random_integration/script.py | 59 ------------------- .../control_methods/utils.py | 56 ++++++++++++++++++ .../workflows/run_benchmark/config.vsh.yaml | 34 +++++++++-- .../workflows/run_benchmark/main.nf | 19 ++++-- 40 files changed, 903 insertions(+), 226 deletions(-) create mode 100644 src/tasks/batch_integration/api/comp_control_method_feature.yaml rename src/tasks/batch_integration/control_methods/{no_integration_batch => no_integration/batch_embed}/config.vsh.yaml (79%) create mode 100644 src/tasks/batch_integration/control_methods/no_integration/batch_embed/script.py create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_embed/script.py create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_feature/script.py create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/no_integration/global_graph/script.py delete mode 100644 src/tasks/batch_integration/control_methods/no_integration_batch/script.py rename src/tasks/batch_integration/control_methods/{random_embed_cell => perfect_integration/celltype_embed}/config.vsh.yaml (63%) create mode 100644 src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/script.py rename src/tasks/batch_integration/control_methods/{random_embed_cell_jitter => perfect_integration/celltype_jitter_embed}/config.vsh.yaml (76%) create mode 100644 src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/script.py delete mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell/script.py delete mode 100644 src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_embed/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_feature/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/batch_graph/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_embed/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_feature/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/celltype_graph/script.py delete mode 100644 src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_embed/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_feature/script.py create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml create mode 100644 src/tasks/batch_integration/control_methods/random_integration/global_graph/script.py delete mode 100644 src/tasks/batch_integration/control_methods/random_integration/script.py create mode 100644 src/tasks/batch_integration/control_methods/utils.py diff --git a/CHANGELOG.md b/CHANGELOG.md index a3196f4bf9..139379d4d2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -132,13 +132,11 @@ * Removed the separate subtask specific subfolders. The "subtask" is added to the config. -* `control_methods/no_integration_batch`: Migrated from v1 embedding. +* `control_methods/no_integration`: Migrated from v1. -* `control_methods/random_embed_cell`: Migrated from v1 embedding. +* `control_methods/perfect_integration`: Migrated from v1, renaming "random embedding" to "perfect integration". -* `control_methods/random_embed_cel_jitter`: Migrated from v1 embedding. - -* `control_methods/random_integration`: Migrated from v1 graph. +* `control_methods/random_integration`: Migrated from v1. * `methods/bbknn`: Migrated from v1 graph. diff --git a/src/tasks/batch_integration/api/comp_control_method_feature.yaml b/src/tasks/batch_integration/api/comp_control_method_feature.yaml new file mode 100644 index 0000000000..3d2ac9853d --- /dev/null +++ b/src/tasks/batch_integration/api/comp_control_method_feature.yaml @@ -0,0 +1,26 @@ +functionality: + namespace: batch_integration/control_methods + info: + type: control_method + subtype: feature + type_info: + label: Control method (feature) + summary: A batch integration feature control method. + description: | + A batch integration control method which outputs a batch-corrected feature space. + arguments: + - name: --input + __merge__: file_dataset.yaml + direction: input + required: true + - name: --output + direction: output + __merge__: file_integrated_feature.yaml + required: true + test_resources: + - type: python_script + path: /src/common/comp_tests/check_method_config.py + - type: python_script + path: /src/common/comp_tests/run_and_check_adata.py + - path: /resources_test/batch_integration/pancreas + dest: resources_test/batch_integration/pancreas diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml similarity index 79% rename from src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml rename to src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml index 06c354f634..67d74ae8ab 100644 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/config.vsh.yaml @@ -1,7 +1,8 @@ # use method api spec -__merge__: ../../api/comp_control_method_embedding.yaml +__merge__: ../../../api/comp_control_method_embedding.yaml functionality: - name: no_integration_batch + name: batch_embed + namespace: batch_integration/control_methods/no_integration info: label: No integration by Batch summary: "Cells are embedded by computing PCA independently on each batch" @@ -16,11 +17,6 @@ functionality: platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.4 - setup: - - type: python - pypi: - - scanpy - - numpy - type: nextflow directives: label: [midtime, lowmem, lowcpu] diff --git a/src/tasks/batch_integration/control_methods/no_integration/batch_embed/script.py b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/script.py new file mode 100644 index 0000000000..7fbb4a537e --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/batch_embed/script.py @@ -0,0 +1,39 @@ +import scanpy as sc +import numpy as np + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) +adata.X = adata.layers["normalized"] +adata.var["highly_variable"] = adata.var["hvg"] + +print("Process dataset", flush=True) +adata.obsm["X_emb"] = np.zeros((adata.shape[0], 50), dtype=float) +for batch in adata.obs["batch"].unique(): + batch_idx = adata.obs["batch"] == batch + n_comps = min(50, np.sum(batch_idx)) + solver = "full" if n_comps == np.sum(batch_idx) else "arpack" + adata.obsm["X_emb"][batch_idx, :n_comps] = sc.tl.pca( + adata[batch_idx], + n_comps=n_comps, + use_highly_variable=True, + svd_solver=solver, + copy=True, + ).obsm["X_pca"] + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml new file mode 100644 index 0000000000..6b2f724ed9 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_embed/config.vsh.yaml @@ -0,0 +1,22 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_embedding.yaml +functionality: + name: global_embed + namespace: batch_integration/control_methods/no_integration + info: + label: No integration + summary: "Cells are embedded by PCA on the unintegrated data" + description: "Cells are embedded by PCA on the unintegrated data" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_embed/script.py b/src/tasks/batch_integration/control_methods/no_integration/global_embed/script.py new file mode 100644 index 0000000000..4b16b82525 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_embed/script.py @@ -0,0 +1,26 @@ +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("process dataset", flush=True) +adata.obsm["X_emb"] = adata.obsm["X_pca"] + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml new file mode 100644 index 0000000000..7b1013221e --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_feature/config.vsh.yaml @@ -0,0 +1,22 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_feature.yaml +functionality: + name: global_feature + namespace: batch_integration/control_methods/no_integration + info: + label: No integration + summary: "Original feature space is not modified" + description: "Original feature space is not modified" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_feature/script.py b/src/tasks/batch_integration/control_methods/no_integration/global_feature/script.py new file mode 100644 index 0000000000..9ddbab0432 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_feature/script.py @@ -0,0 +1,27 @@ +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +# no processing, subset matrix to highly variable genes +adata_hvg = adata[:, adata.var["hvg"]].copy() +adata.layers['corrected_counts'] = adata_hvg.layers["normalized"].copy() + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml new file mode 100644 index 0000000000..ead6281806 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_graph/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_graph.yaml +functionality: + name: global_graph + namespace: batch_integration/control_methods/no_integration + info: + label: No integration + summary: "kNN graph is built on the PCA of the unintegrated data" + description: "Cells are embedded by PCA on the unintegrated data. A kNN graph is built on this PCA." + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/no_integration/global_graph/script.py b/src/tasks/batch_integration/control_methods/no_integration/global_graph/script.py new file mode 100644 index 0000000000..22b39d10d5 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/no_integration/global_graph/script.py @@ -0,0 +1,35 @@ +import scanpy as sc +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _set_uns + + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("process dataset", flush=True) +neighbors_map = adata.uns['knn'] +adata.obsp['connectivities'] = adata.obsp[neighbors_map['connectivities_key']] +adata.obsp['distances'] = adata.obsp[neighbors_map['distances_key']] +_set_uns(adata, neighbors_key='knn') + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/no_integration_batch/script.py b/src/tasks/batch_integration/control_methods/no_integration_batch/script.py deleted file mode 100644 index c47dd1d8fc..0000000000 --- a/src/tasks/batch_integration/control_methods/no_integration_batch/script.py +++ /dev/null @@ -1,38 +0,0 @@ -import scanpy as sc -import numpy as np -import yaml - -## VIASH START - -par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - 'output': 'output.h5ad', -} - -meta = { - 'functionality': 'foo', - 'config': 'bar' -} - -## VIASH END - -print('Read input', flush=True) -input = sc.read_h5ad(par['input']) - -print("process dataset", flush=True) -input.obsm["X_emb"] = np.zeros((input.shape[0], 50), dtype=float) -for batch in input.obs["batch"].unique(): - batch_idx = input.obs["batch"] == batch - n_comps = min(50, np.sum(batch_idx)) - solver = "full" if n_comps == np.sum(batch_idx) else "arpack" - # input.obsm["X_emb"][batch_idx, :n_comps] = sc.tl.pca( - # input[batch_idx], - # n_comps=n_comps, - # use_highly_variable=False, - # svd_solver=solver, - # copy=True, - # ).obsm["X_pca"] - -print("Store outputs", flush=True) -input.uns['method_id'] = meta['functionality_name'] -input.write_h5ad(par['output'], compression='gzip') \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml similarity index 63% rename from src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml rename to src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml index 1a0f130664..9d50f13aaf 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/config.vsh.yaml @@ -1,25 +1,23 @@ # use method api spec -__merge__: ../../api/comp_control_method_embedding.yaml +__merge__: ../../../api/comp_control_method_embedding.yaml functionality: - name: random_embed_cell + name: celltype_embed + namespace: batch_integration/control_methods/perfect_integration info: - label: Random Embedding by Celltype + label: Perfect embedding by cell type summary: "Cells are embedded as a one-hot encoding of celltype labels" description: "Cells are embedded as a one-hot encoding of celltype labels" v1: - path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 preferred_normalization: log_cp10k resources: - type: python_script path: script.py + - path: ../../utils.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.4 - setup: - - type: python - pypi: - - scikit-learn - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/script.py b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/script.py new file mode 100644 index 0000000000..b15ce33047 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_embed/script.py @@ -0,0 +1,29 @@ +import anndata as ad +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END +sys.path.append(meta["resources_dir"]) +from utils import _perfect_embedding + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Process data...', flush=True) +adata.obsm["X_emb"] = _perfect_embedding(partition=adata.obs["label"]) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml similarity index 76% rename from src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml rename to src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml index 0f8bb0d0f4..e0af4e4a5b 100644 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/config.vsh.yaml +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/config.vsh.yaml @@ -1,9 +1,10 @@ # use method api spec -__merge__: ../../api/comp_control_method_embedding.yaml +__merge__: ../../../api/comp_control_method_embedding.yaml functionality: - name: random_embed_cell_jitter + name: celltype_jitter_embed + namespace: batch_integration/control_methods/perfect_integration info: - label: Random Embedding by Celltype with jitter + label: Perfect embedding by celltype with jitter summary: "Cells are embedded as a one-hot encoding of celltype labels, with a small amount of random noise added to the embedding" description: "Cells are embedded as a one-hot encoding of celltype labels, with a small amount of random noise added to the embedding" v1: @@ -17,15 +18,10 @@ functionality: resources: - type: python_script path: script.py + - path: ../../utils.py platforms: - type: docker image: ghcr.io/openproblems-bio/base_python:1.0.4 - setup: - - type: python - pypi: - - scikit-learn - - numpy - - scipy - type: nextflow directives: label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/script.py b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/script.py new file mode 100644 index 0000000000..75f5889f8d --- /dev/null +++ b/src/tasks/batch_integration/control_methods/perfect_integration/celltype_jitter_embed/script.py @@ -0,0 +1,33 @@ +import anndata as ad +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', + 'jitter': 0.01, +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END +sys.path.append(meta["resources_dir"]) +from utils import _perfect_embedding + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Process data...', flush=True) +adata.obsm["X_emb"] = _perfect_embedding( + partition=adata.obs["label"], + jitter=par["jitter"] +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell/script.py deleted file mode 100644 index 5c7c87da87..0000000000 --- a/src/tasks/batch_integration/control_methods/random_embed_cell/script.py +++ /dev/null @@ -1,31 +0,0 @@ -from sklearn.preprocessing import LabelEncoder -from sklearn.preprocessing import OneHotEncoder -import anndata as ad -import yaml - -## VIASH START - -par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - 'output': 'output.h5ad', -} - -meta = { - 'functionality': 'foo', - 'config': 'bar' -} - -## VIASH END - -print('Read input', flush=True) -input = ad.read_h5ad(par['input']) - - -print('processing data', flush=True) -input.obsm['X_emb'] = OneHotEncoder().fit_transform( - LabelEncoder().fit_transform(input.obs["label"])[:, None] -) - -print("Store outputs", flush=True) -input.uns['method_id'] = meta['functionality_name'] -input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py b/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py deleted file mode 100644 index a99f5c14cd..0000000000 --- a/src/tasks/batch_integration/control_methods/random_embed_cell_jitter/script.py +++ /dev/null @@ -1,36 +0,0 @@ -from sklearn.preprocessing import LabelEncoder -from sklearn.preprocessing import OneHotEncoder -import numpy as np -import anndata as ad -import yaml -from scipy.sparse import csr_matrix - -## VIASH START - -par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - 'output': 'output.h5ad', - 'jitter': 0.01 -} - -meta = { - 'functionality': 'foo', - 'config': 'bar' -} - -## VIASH END - -print('Read input', flush=True) -input = ad.read_h5ad(par['input']) - - -print('processing data', flush=True) -embedding = OneHotEncoder().fit_transform( - LabelEncoder().fit_transform(input.obs["label"])[:, None] -) - -input.obsm['X_emb'] = csr_matrix(embedding + np.random.uniform(-1 * par['jitter'], par['jitter'], embedding.shape)) - -print("Store outputs", flush=True) -input.uns['method_id'] = meta['functionality_name'] -input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml new file mode 100644 index 0000000000..717d14ab42 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_embedding.yaml +functionality: + name: batch_embed + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration by batch + summary: "Embedding coordinates are randomly permuted within each batch" + description: "Embedding coordinates are randomly permuted within each batch" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_embed/script.py b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/script.py new file mode 100644 index 0000000000..3cc476b863 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_embed/script.py @@ -0,0 +1,34 @@ +import sys +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("process dataset", flush=True) +adata.obsm["X_emb"] = _randomize_features( + adata.obsm["X_pca"], + partition=adata.obs["batch"], +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml new file mode 100644 index 0000000000..ad1957b070 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_feature.yaml +functionality: + name: batch_feature + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration by batch + summary: "Feature values are randomly permuted within each batch" + description: "Feature values are randomly permuted within each batch" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: acf5c95a7306b819c4a13972783433d0a48f769b + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_feature/script.py b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/script.py new file mode 100644 index 0000000000..755f4782f9 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_feature/script.py @@ -0,0 +1,33 @@ +import anndata as ad +import sys + + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar', +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +adata.layers['corrected_counts'] = _randomize_features( + adata.layers["normalized"], + partition=adata.obs["batch"], +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml new file mode 100644 index 0000000000..553e7431a8 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_graph.yaml +functionality: + name: batch_graph + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration + summary: "Graph connectivity values are randomly permuted within each batch" + description: "Graph connectivity values are randomly permuted within each batch" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/batch_graph/script.py b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/script.py new file mode 100644 index 0000000000..d07e3b339e --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/batch_graph/script.py @@ -0,0 +1,35 @@ +import anndata as ad +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar', +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_graph + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Randomize graph...', flush=True) +adata = _randomize_graph( + adata, + neighbors_key="knn", + partition=adata.obs["batch"], +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml new file mode 100644 index 0000000000..d591b2a1df --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_embedding.yaml +functionality: + name: celltype_embed + namespace: batch_integration/control_methods/random_integration + info: + label: Random embedding by cell type + summary: "Embedding coordinates are randomized within celltype labels" + description: "Embedding coordinates are randomized within celltype labels" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/script.py b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/script.py new file mode 100644 index 0000000000..bf793fad75 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_embed/script.py @@ -0,0 +1,32 @@ +import anndata as ad +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar' +} + +## VIASH END +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Process data...', flush=True) +adata.obsm["X_emb"] = _randomize_features( + adata.obsm["X_pca"], + partition=adata.obs["label"] +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml new file mode 100644 index 0000000000..2719a68d87 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_feature.yaml +functionality: + name: celltype_feature + namespace: batch_integration/control_methods/random_integration + info: + label: Random feature by cell type + summary: "Features are randomized within celltype labels" + description: "Features are randomized within celltype labels" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/script.py b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/script.py new file mode 100644 index 0000000000..a06e6c1ab7 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_feature/script.py @@ -0,0 +1,35 @@ +import sys +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("Process data...", flush=True) +adata.layers['corrected_counts'] = _randomize_features( + adata.layers["normalized"], + partition=adata.obs["label"] +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml new file mode 100644 index 0000000000..948bcacf29 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_graph.yaml +functionality: + name: celltype_graph + namespace: batch_integration/control_methods/random_integration + info: + label: Random graph by cell type + summary: "Graph connectivities are randomized within celltype labels" + description: "Graph connectivities are randomized within celltype labels" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/script.py b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/script.py new file mode 100644 index 0000000000..7b02353ed4 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/celltype_graph/script.py @@ -0,0 +1,35 @@ +import sys +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_graph + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("Process data...", flush=True) +adata = _randomize_graph( + adata, + neighbors_key="knn", + partition=adata.obs["label"], +) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml deleted file mode 100644 index b98ff82039..0000000000 --- a/src/tasks/batch_integration/control_methods/random_integration/config.vsh.yaml +++ /dev/null @@ -1,25 +0,0 @@ -# use method api spec -__merge__: ../../api/comp_control_method_graph.yaml -functionality: - name: random_integration - info: - label: Random integration - summary: "Feature values, embedding coordinates, and graph connectivity are all randomly permuted." - description: "Feature values, embedding coordinates, and graph connectivity are all randomly permuted." - v1: - path: openproblems/tasks/_batch_integration/batch_integration_embed/methods/baseline.py - commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 - preferred_normalization: log_cp10k - resources: - - type: python_script - path: script.py -platforms: - - type: docker - image: ghcr.io/openproblems-bio/base_python:1.0.4 - setup: - - type: python - pypi: - - numpy - - type: nextflow - directives: - label: [midtime, lowmem, lowcpu] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml new file mode 100644 index 0000000000..b17174744f --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_embed/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_embedding.yaml +functionality: + name: global_embed + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration + summary: "Embedding coordinates are randomly permuted" + description: "Embedding coordinates are randomly permuted" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_embed/script.py b/src/tasks/batch_integration/control_methods/random_integration/global_embed/script.py new file mode 100644 index 0000000000..fc7ba6cee5 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_embed/script.py @@ -0,0 +1,31 @@ +import sys +import scanpy as sc + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad', +} + +meta = { + 'functionality': 'foo', + 'config': 'bar', + "resources_dir": "src/tasks/batch_integration/control_methods/" +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + +print('Read input', flush=True) +adata = sc.read_h5ad(par['input']) + +print("process dataset", flush=True) +adata.obsm["X_emb"] = _randomize_features(adata.obsm["X_pca"]) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml new file mode 100644 index 0000000000..8dd71aec93 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_feature/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_feature.yaml +functionality: + name: global_feature + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration + summary: "Feature values are randomly permuted" + description: "Feature values are randomly permuted" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: acf5c95a7306b819c4a13972783433d0a48f769b + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] \ No newline at end of file diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_feature/script.py b/src/tasks/batch_integration/control_methods/random_integration/global_feature/script.py new file mode 100644 index 0000000000..1c7c838b6e --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_feature/script.py @@ -0,0 +1,30 @@ +import anndata as ad +import sys + + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar', +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_features + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +adata.layers['corrected_counts'] = _randomize_features(adata.layers["normalized"]) + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml new file mode 100644 index 0000000000..9780485e92 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_graph/config.vsh.yaml @@ -0,0 +1,23 @@ +# use method api spec +__merge__: ../../../api/comp_control_method_graph.yaml +functionality: + name: global_graph + namespace: batch_integration/control_methods/random_integration + info: + label: Random integration + summary: "Graph connectivity values are randomly permuted" + description: "Graph connectivity values are randomly permuted" + v1: + path: openproblems/tasks/_batch_integration/_common/methods/baseline.py + commit: b3456fd73c04c28516f6df34c57e6e3e8b0dab32 + preferred_normalization: log_cp10k + resources: + - type: python_script + path: script.py + - path: ../../utils.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_python:1.0.4 + - type: nextflow + directives: + label: [ "midtime", "lowmem", "lowcpu"] diff --git a/src/tasks/batch_integration/control_methods/random_integration/global_graph/script.py b/src/tasks/batch_integration/control_methods/random_integration/global_graph/script.py new file mode 100644 index 0000000000..c0277c74b7 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/random_integration/global_graph/script.py @@ -0,0 +1,31 @@ +import anndata as ad +import sys + +## VIASH START + +par = { + 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', + 'output': 'output.h5ad' +} + +meta = { + 'functionality_name': 'foo', + 'config': 'bar', +} + +## VIASH END + +# add helper scripts to path +sys.path.append(meta["resources_dir"]) +from utils import _randomize_graph + + +print('Read input', flush=True) +adata = ad.read_h5ad(par['input']) + +print('Randomize graph...', flush=True) +adata = _randomize_graph(adata, neighbors_key="knn") + +print("Store outputs", flush=True) +adata.uns['method_id'] = meta['functionality_name'] +adata.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/random_integration/script.py b/src/tasks/batch_integration/control_methods/random_integration/script.py deleted file mode 100644 index 7b7cf45e69..0000000000 --- a/src/tasks/batch_integration/control_methods/random_integration/script.py +++ /dev/null @@ -1,59 +0,0 @@ -import anndata as ad -import numpy as np -import yaml - - -## VIASH START - -par = { - 'input': 'resources_test/batch_integration/pancreas/unintegrated.h5ad', - 'output': 'output.h5ad' -} - -meta = { - 'functionality_name': 'foo', - 'config': 'bar', -} - -## VIASH END - -def _set_uns(adata): - adata.uns["neighbors"] = adata.uns["knn"] - adata.uns["neighbors"]["connectivities_key"] = "connectivities" - adata.uns["neighbors"]["distances_key"] = "distances" - -def _randomize_features(X, partition=None): - X_out = X.copy() - if partition is None: - partition = np.full(X.shape[0], 0) - else: - partition = np.asarray(partition) - for partition_name in np.unique(partition): - partition_idx = np.argwhere(partition == partition_name).flatten() - X_out[partition_idx] = X[np.random.permutation(partition_idx)] - return X_out - -def _randomize_graph(adata, partition=None): - distances, connectivities = ( - adata.obsp["knn_distances"], - adata.obsp["knn_connectivities"], - ) - new_idx = _randomize_features(np.arange(distances.shape[0]), partition=partition) - adata.obsp["distances"] = distances[new_idx][:, new_idx] - adata.obsp["connectivities"] = connectivities[new_idx][:, new_idx] - _set_uns(adata) - return adata - -print('Read input', flush=True) -input = ad.read_h5ad(par['input']) -input.X = input.layers["normalized"] - -input.X = _randomize_features(input.X) -input.obsm["X_emb"] = _randomize_features(input.obsm["X_pca"]) -input = _randomize_graph(input) -del input.X - -print("Store outputs", flush=True) -input.uns['method_id'] = meta['functionality_name'] - -input.write_h5ad(par['output'], compression='gzip') diff --git a/src/tasks/batch_integration/control_methods/utils.py b/src/tasks/batch_integration/control_methods/utils.py new file mode 100644 index 0000000000..954e24af26 --- /dev/null +++ b/src/tasks/batch_integration/control_methods/utils.py @@ -0,0 +1,56 @@ +import numpy as np + + +def _set_uns(adata, neighbors_key): + adata.uns["neighbors"] = adata.uns[neighbors_key] + adata.uns["neighbors"]["connectivities_key"] = "connectivities" + adata.uns["neighbors"]["distances_key"] = "distances" + + +def _randomize_features(X, partition=None): + """ + Taken and adapted from opsca-v1: + https://github.com/openproblems-bio/openproblems/blob/acf5c95a7306b819c4a13972783433d0a48f769b/openproblems/tasks/_batch_integration/_common/methods/baseline.py#L13 + """ + X_out = X.copy() + if partition is None: + partition = np.full(X.shape[0], 0) + else: + partition = np.asarray(partition) + for partition_name in np.unique(partition): + partition_idx = np.argwhere(partition == partition_name).flatten() + X_out[partition_idx] = X[np.random.permutation(partition_idx)] + return X_out + + +def _randomize_graph(adata, partition=None, neighbors_key="neighbors"): + """ + Taken and adapted from opsca-v1: + https://github.com/openproblems-bio/openproblems/blob/acf5c95a7306b819c4a13972783433d0a48f769b/openproblems/tasks/_batch_integration/_common/methods/baseline.py#L25 + """ + knn_map = adata.uns[neighbors_key] + distances, connectivities = ( + adata.obsp[knn_map["distances_key"]], + adata.obsp[knn_map["connectivities_key"]], + ) + new_idx = _randomize_features(np.arange(distances.shape[0]), partition=partition) + adata.obsp["distances"] = distances[new_idx][:, new_idx] + adata.obsp["connectivities"] = connectivities[new_idx][:, new_idx] + _set_uns(adata, neighbors_key) + return adata + + +def _perfect_embedding(partition, jitter=0.01): + """ + Taken and adapted from opsca-v1: + https://github.com/openproblems-bio/openproblems/blob/acf5c95a7306b819c4a13972783433d0a48f769b/openproblems/tasks/_batch_integration/_common/methods/baseline.py#L37 + """ + from sklearn.preprocessing import LabelEncoder + from sklearn.preprocessing import OneHotEncoder + + embedding = OneHotEncoder().fit_transform( + LabelEncoder().fit_transform(partition)[:, None] + ) + if jitter is not None: + embedding = embedding + np.random.uniform(-1 * jitter, jitter, embedding.shape) + return np.asarray(embedding) diff --git a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml index b430734e22..fd6f6811d2 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/batch_integration/workflows/run_benchmark/config.vsh.yaml @@ -69,10 +69,36 @@ functionality: - name: batch_integration/methods/scanorama_feature - name: batch_integration/methods/scanvi - name: batch_integration/methods/scvi - - name: batch_integration/control_methods/no_integration_batch - - name: batch_integration/control_methods/random_embed_cell - - name: batch_integration/control_methods/random_embed_cell_jitter - - name: batch_integration/control_methods/random_integration + - name: batch_integration/control_methods/no_integration/batch_embed + alias: no_integration_batch_embed + - name: batch_integration/control_methods/no_integration/global_embed + alias: no_integration_global_embed + - name: batch_integration/control_methods/no_integration/global_feature + alias: no_integration_global_feature + - name: batch_integration/control_methods/no_integration/global_graph + alias: no_integration_global_graph + - name: batch_integration/control_methods/perfect_integration/celltype_embed + alias: perfect_integration_celltype_embed + - name: batch_integration/control_methods/perfect_integration/celltype_jitter_embed + alias: perfect_integration_celltype_jitter_embed + - name: batch_integration/control_methods/random_integration/batch_embed + alias: random_integration_batch_embed + - name: batch_integration/control_methods/random_integration/batch_feature + alias: random_integration_batch_feature + - name: batch_integration/control_methods/random_integration/batch_graph + alias: random_integration_batch_graph + - name: batch_integration/control_methods/random_integration/celltype_embed + alias: random_integration_celltype_embed + - name: batch_integration/control_methods/random_integration/celltype_feature + alias: random_integration_celltype_feature + - name: batch_integration/control_methods/random_integration/celltype_graph + alias: random_integration_celltype_graph + - name: batch_integration/control_methods/random_integration/global_embed + alias: random_integration_global_embed + - name: batch_integration/control_methods/random_integration/global_feature + alias: random_integration_global_feature + - name: batch_integration/control_methods/random_integration/global_graph + alias: random_integration_global_graph - name: batch_integration/transformers/feature_to_embed - name: batch_integration/transformers/embed_to_graph - name: batch_integration/metrics/asw_batch diff --git a/src/tasks/batch_integration/workflows/run_benchmark/main.nf b/src/tasks/batch_integration/workflows/run_benchmark/main.nf index 5543ac91cd..d86293f2a5 100644 --- a/src/tasks/batch_integration/workflows/run_benchmark/main.nf +++ b/src/tasks/batch_integration/workflows/run_benchmark/main.nf @@ -27,10 +27,21 @@ workflow run_wf { scanorama_feature, scanvi, scvi, - no_integration_batch, - random_embed_cell, - random_embed_cell_jitter, - random_integration + no_integration_batch_embed, + no_integration_global_embed, + no_integration_global_feature, + no_integration_global_graph, + perfect_integration_celltype_embed, + perfect_integration_celltype_jitter_embed, + random_integration_batch_embed, + random_integration_batch_feature, + random_integration_batch_graph, + random_integration_celltype_embed, + random_integration_celltype_feature, + random_integration_celltype_graph, + random_integration_global_embed, + random_integration_global_feature, + random_integration_global_graph, ] // construct list of metrics From 2749958dcd9cc2dd9fd5cc1f7575076b9f663bcc Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Mon, 26 Aug 2024 23:33:30 +0200 Subject: [PATCH 1227/1233] Add novel method to predict modality task (#339) * WIP integral copy * WIP update * split method in train and run comp * fix errors * update train model * refactor method comp * rename method_predict and method_train api files * refactor novel components (WIP) * WIP refactor novel * refactor train_test split novel method * Add scritpt to test all test files * Make dim a variable * add hvg * Remove unused code * update train image * Update predict part * Update novel wf * Add novel to benchmark * update directives * Update test scripts * update train output * fix config predict * Update run config * add submission info * update lib ref * Add batches to train data * update subworkflow * set output defaults * reorder helper functions * update directives * fix directives * set to hightime * fix run config * remove views * Fix config * Add pref norm * Update directives * Update predict config * Remove setState * Apply suggestion Co-authored-by: Robrecht Cannoodt * add back setstate * Add fix for test * prevent divide by zero * Add workaround for nextflow error * Fix if variable is empty * Update dataset_name for neurips 2021 --------- Co-authored-by: Robrecht Cannoodt Former-commit-id: 7cea6a5c7ded1d32cd13dce63322b1ca0f23deb8 --- .../openproblems_neurips2021_multimodal.sh | 17 +- .../api/comp_method_predict.yaml | 4 +- .../api/file_common_dataset_mod1.yaml | 10 + .../api/file_common_dataset_mod2.yaml | 10 + .../methods/novel/helper_functions.py | 247 ++++++++++++++++++ .../methods/novel/predict/config.vsh.yaml | 25 ++ .../methods/novel/predict/run_test.sh | 8 + .../methods/novel/predict/script.py | 119 +++++++++ .../methods/novel/run/config.vsh.yaml | 21 ++ .../methods/novel/run/main.nf | 25 ++ .../methods/novel/run/run_test.sh | 15 ++ .../methods/novel/train/config.vsh.yaml | 31 +++ .../methods/novel/train/run_test.sh | 29 ++ .../methods/novel/train/script.py | 148 +++++++++++ .../predict_modality/process_dataset/script.R | 2 +- .../workflows/run_benchmark/config.vsh.yaml | 1 + .../workflows/run_benchmark/main.nf | 3 +- 17 files changed, 698 insertions(+), 17 deletions(-) create mode 100644 src/tasks/predict_modality/methods/novel/helper_functions.py create mode 100644 src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/novel/predict/run_test.sh create mode 100644 src/tasks/predict_modality/methods/novel/predict/script.py create mode 100644 src/tasks/predict_modality/methods/novel/run/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/novel/run/main.nf create mode 100644 src/tasks/predict_modality/methods/novel/run/run_test.sh create mode 100644 src/tasks/predict_modality/methods/novel/train/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/novel/train/run_test.sh create mode 100644 src/tasks/predict_modality/methods/novel/train/script.py diff --git a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh index af32b8c853..8fd7e3a72d 100755 --- a/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh +++ b/src/datasets/resource_scripts/openproblems_neurips2021_multimodal.sh @@ -9,7 +9,7 @@ param_list: input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fcite%5FBMMC%5Fprocessed%2Eh5ad%2Egz" mod1: GEX mod2: ADT - dataset_name: OpenProblems NeurIPS2021 CITE-Seq + dataset_name: NeurIPS2021 CITE-Seq dataset_organism: homo_sapiens dataset_summary: Single-cell CITE-Seq (GEX+ADT) data collected from bone marrow mononuclear cells of 12 healthy human donors. dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X 3 prime Single-Cell Gene Expression kit with Feature Barcoding in combination with the BioLegend TotalSeq B Universal Human Panel v1.0. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." @@ -19,7 +19,7 @@ param_list: input: "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE194nnn/GSE194122/suppl/GSE194122%5Fopenproblems%5Fneurips2021%5Fmultiome%5FBMMC%5Fprocessed%2Eh5ad%2Egz" mod1: GEX mod2: ATAC - dataset_name: OpenProblems NeurIPS2021 Multiome + dataset_name: NeurIPS2021 Multiome dataset_organism: homo_sapiens dataset_summary: Single-cell Multiome (GEX+ATAC) data collected from bone marrow mononuclear cells of 12 healthy human donors. dataset_description: "Single-cell CITE-Seq data collected from bone marrow mononuclear cells of 12 healthy human donors using the 10X Multiome Gene Expression and Chromatin Accessibility kit. The dataset was generated to support Multimodal Single-Cell Data Integration Challenge at NeurIPS 2021. Samples were prepared using a standard protocol at four sites. The resulting data was then annotated to identify cell types and remove doublets. The dataset was designed with a nested batch layout such that some donor samples were measured at multiple sites with some donors measured at a single site." @@ -35,15 +35,6 @@ output_state: '$id/state.yaml' publish_dir: s3://openproblems-data/resources/datasets HERE -cat > /tmp/nextflow.config << HERE -process { - withName:'.*publishStatesProc' { - memory = '16GB' - disk = '100GB' - } -} -HERE - tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --revision main_build \ --pull-latest \ @@ -51,5 +42,5 @@ tw launch https://github.com/openproblems-bio/openproblems-v2.git \ --workspace 53907369739130 \ --compute-env 6TeIFgV5OY4pJCk8I0bfOh \ --params-file "$params_file" \ - --config /tmp/nextflow.config \ - --labels openproblems_neurips2021_bmmc,dataset_loader \ + --config src/wf_utils/labels_tw.config \ + --labels neurips2021,dataset_loader \ diff --git a/src/tasks/predict_modality/api/comp_method_predict.yaml b/src/tasks/predict_modality/api/comp_method_predict.yaml index ebd56aed51..a43cd1e5c5 100644 --- a/src/tasks/predict_modality/api/comp_method_predict.yaml +++ b/src/tasks/predict_modality/api/comp_method_predict.yaml @@ -11,11 +11,11 @@ functionality: - name: "--input_train_mod1" __merge__: file_train_mod1.yaml direction: input - required: true + required: false - name: "--input_train_mod2" __merge__: file_train_mod2.yaml direction: input - required: true + required: false - name: "--input_test_mod1" __merge__: file_test_mod1.yaml direction: input diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml index c82e0be026..4824a05c46 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod1.yaml @@ -44,6 +44,16 @@ info: name: hvg_score description: A score for the feature indicating how highly variable it is. required: true + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A ranking of the features by hvg. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml index 1a447b24c0..e0b1b3bae9 100644 --- a/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml +++ b/src/tasks/predict_modality/api/file_common_dataset_mod2.yaml @@ -44,6 +44,16 @@ info: name: hvg_score description: A score for the feature indicating how highly variable it is. required: true + + - type: boolean + name: hvg + description: Whether or not the feature is considered to be a 'highly variable gene' + required: true + + - type: double + name: hvg_score + description: A ranking of the features by hvg. + required: true uns: - type: string name: dataset_id diff --git a/src/tasks/predict_modality/methods/novel/helper_functions.py b/src/tasks/predict_modality/methods/novel/helper_functions.py new file mode 100644 index 0000000000..17c57c9b3b --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/helper_functions.py @@ -0,0 +1,247 @@ +import torch + +from torch import nn +import torch.nn.functional as F + +from torch.utils.data import Dataset + +from typing import Optional + +import anndata +import numpy as np +import pandas as pd +import scipy.sparse +import sklearn.decomposition +import sklearn.feature_extraction.text +import sklearn.preprocessing +import sklearn.neighbors +import sklearn.utils.extmath + +class tfidfTransformer(): + def __init__(self): + self.idf = None + self.fitted = False + + def fit(self, X): + self.idf = X.shape[0] / X.sum(axis=0) + self.fitted = True + + def transform(self, X): + if not self.fitted: + raise RuntimeError('Transformer was not fitted on any data') + if scipy.sparse.issparse(X): + tf = X.multiply(1 / X.sum(axis=1)) + return tf.multiply(self.idf) + else: + tf = X / X.sum(axis=1, keepdims=True) + return tf * self.idf + + def fit_transform(self, X): + self.fit(X) + return self.transform(X) + +class lsiTransformer(): + def __init__(self, + n_components: int = 20, + use_highly_variable = None + ): + self.n_components = n_components + self.use_highly_variable = use_highly_variable + self.tfidfTransformer = tfidfTransformer() + self.normalizer = sklearn.preprocessing.Normalizer(norm="l1") + self.pcaTransformer = sklearn.decomposition.TruncatedSVD(n_components = self.n_components, random_state=777) + # self.lsi_mean = None + # self.lsi_std = None + self.fitted = None + + def fit(self, adata: anndata.AnnData): + if self.use_highly_variable is None: + self.use_highly_variable = "hvg" in adata.var + adata_use = adata[:, adata.var["hvg"]] if self.use_highly_variable else adata + X = self.tfidfTransformer.fit_transform(adata_use.X) + X_norm = self.normalizer.fit_transform(X) + X_norm = np.log1p(X_norm * 1e4) + X_lsi = self.pcaTransformer.fit_transform(X_norm) + # self.lsi_mean = X_lsi.mean(axis=1, keepdims=True) + # self.lsi_std = X_lsi.std(axis=1, ddof=1, keepdims=True) + self.fitted = True + + def transform(self, adata): + if not self.fitted: + raise RuntimeError('Transformer was not fitted on any data') + adata_use = adata[:, adata.var["hvg"]] if self.use_highly_variable else adata + X = self.tfidfTransformer.transform(adata_use.X) + X_norm = self.normalizer.transform(X) + X_norm = np.log1p(X_norm * 1e4) + X_lsi = self.pcaTransformer.transform(X_norm) + X_lsi -= X_lsi.mean(axis=1, keepdims=True) + X_lsi /= X_lsi.std(axis=1, ddof=1, keepdims=True) + lsi_df = pd.DataFrame(X_lsi, index = adata_use.obs_names) + return lsi_df + + def fit_transform(self, adata): + self.fit(adata) + return self.transform(adata) + +class ModalityMatchingDataset(Dataset): + def __init__( + self, df_modality1, df_modality2, is_train=True + ): + super().__init__() + self.df_modality1 = df_modality1 + self.df_modality2 = df_modality2 + self.is_train = is_train + def __len__(self): + return self.df_modality1.shape[0] + + def __getitem__(self, index: int): + if self.is_train == True: + x = self.df_modality1.iloc[index].values + y = self.df_modality2.iloc[index].values + return x, y + else: + x = self.df_modality1.iloc[index].values + return x + +class Swish(torch.autograd.Function): + @staticmethod + def forward(ctx, i): + result = i * sigmoid(i) + ctx.save_for_backward(i) + return result + @staticmethod + def backward(ctx, grad_output): + i = ctx.saved_variables[0] + sigmoid_i = sigmoid(i) + return grad_output * (sigmoid_i * (1 + i * (1 - sigmoid_i))) + +class Swish_module(nn.Module): + def forward(self, x): + return Swish.apply(x) + +sigmoid = torch.nn.Sigmoid() + +class ModelRegressionGex2Atac(nn.Module): + def __init__(self, dim_mod1, dim_mod2): + super(ModelRegressionGex2Atac, self).__init__() + #self.bn = torch.nn.BatchNorm1d(1024) + self.input_ = nn.Linear(dim_mod1, 1024) + self.fc = nn.Linear(1024, 256) + self.fc1 = nn.Linear(256, 2048) + self.dropout1 = nn.Dropout(p=0.298885630228993) + self.dropout2 = nn.Dropout(p=0.11289717442776658) + self.dropout3 = nn.Dropout(p=0.13523634924414762) + self.output = nn.Linear(2048, dim_mod2) + def forward(self, x): + x = F.gelu(self.input_(x)) + x = self.dropout1(x) + x = F.gelu(self.fc(x)) + x = self.dropout2(x) + x = F.gelu(self.fc1(x)) + x = self.dropout3(x) + x = F.gelu(self.output(x)) + return x + +class ModelRegressionAtac2Gex(nn.Module): # + def __init__(self, dim_mod1, dim_mod2): + super(ModelRegressionAtac2Gex, self).__init__() + self.input_ = nn.Linear(dim_mod1, 2048) + self.fc = nn.Linear(2048, 2048) + self.fc1 = nn.Linear(2048, 512) + self.dropout1 = nn.Dropout(p=0.2649138776004753) + self.dropout2 = nn.Dropout(p=0.1769628308148758) + self.dropout3 = nn.Dropout(p=0.2516791883012817) + self.output = nn.Linear(512, dim_mod2) + def forward(self, x): + x = F.gelu(self.input_(x)) + x = self.dropout1(x) + x = F.gelu(self.fc(x)) + x = self.dropout2(x) + x = F.gelu(self.fc1(x)) + x = self.dropout3(x) + x = F.gelu(self.output(x)) + return x + +class ModelRegressionAdt2Gex(nn.Module): + def __init__(self, dim_mod1, dim_mod2): + super(ModelRegressionAdt2Gex, self).__init__() + self.input_ = nn.Linear(dim_mod1, 512) + self.dropout1 = nn.Dropout(p=0.0) + self.swish = Swish_module() + self.fc = nn.Linear(512, 512) + self.fc1 = nn.Linear(512, 512) + self.fc2 = nn.Linear(512, 512) + self.output = nn.Linear(512, dim_mod2) + def forward(self, x): + x = F.gelu(self.input_(x)) + x = F.gelu(self.fc(x)) + x = F.gelu(self.fc1(x)) + x = F.gelu(self.fc2(x)) + x = F.gelu(self.output(x)) + return x + +class ModelRegressionGex2Adt(nn.Module): + def __init__(self, dim_mod1, dim_mod2): + super(ModelRegressionGex2Adt, self).__init__() + self.input_ = nn.Linear(dim_mod1, 512) + self.dropout1 = nn.Dropout(p=0.20335661386636347) + self.dropout2 = nn.Dropout(p=0.15395289261127876) + self.dropout3 = nn.Dropout(p=0.16902655078832815) + self.fc = nn.Linear(512, 512) + self.fc1 = nn.Linear(512, 2048) + self.output = nn.Linear(2048, dim_mod2) + def forward(self, x): + # x = self.batchswap_noise(x) + x = F.gelu(self.input_(x)) + x = self.dropout1(x) + x = F.gelu(self.fc(x)) + x = self.dropout2(x) + x = F.gelu(self.fc1(x)) + x = self.dropout3(x) + x = F.gelu(self.output(x)) + return x + +def rmse(y, y_pred): + return np.sqrt(np.mean(np.square(y - y_pred))) + +def train_and_valid(model, optimizer, loss_fn, dataloader_train, dataloader_test, name_model, device): + best_score = 100000 + for i in range(100): + train_losses = [] + test_losses = [] + model.train() + + for x, y in dataloader_train: + optimizer.zero_grad() + output = model(x.float().to(device)) + loss = torch.sqrt(loss_fn(output, y.float().to(device))) + loss.backward() + train_losses.append(loss.item()) + optimizer.step() + + model.eval() + with torch.no_grad(): + for x, y in dataloader_test: + output = model(x.float().to(device)) + output[output<0] = 0.0 + loss = torch.sqrt(loss_fn(output, y.float().to(device))) + test_losses.append(loss.item()) + + outputs = [] + targets = [] + model.eval() + with torch.no_grad(): + for x, y in dataloader_test: + output = model(x.float().to(device)) + + outputs.append(output.detach().cpu().numpy()) + targets.append(y.float().detach().cpu().numpy()) + cat_outputs = np.concatenate(outputs) + cat_targets = np.concatenate(targets) + cat_outputs[cat_outputs<0.0] = 0 + + if best_score > rmse(cat_targets,cat_outputs): + torch.save(model.state_dict(), name_model) + best_score = rmse(cat_targets,cat_outputs) + print("best rmse: ", best_score) + diff --git a/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml new file mode 100644 index 0000000000..2efc42a59f --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml @@ -0,0 +1,25 @@ +__merge__: ../../../api/comp_method_predict.yaml +functionality: + name: novel_predict + arguments: + - name: "--input_transform" + type: file + direction: input + required: false + example: "lsi_transformer.pickle" + resources: + - type: python_script + path: script.py + - path: ../helper_functions.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + setup: + - type: python + packages: + - scikit-learn + - networkx + - type: nextflow + directives: + label: [highmem, hightime, midcpu, highsharedmem, gpu] + diff --git a/src/tasks/predict_modality/methods/novel/predict/run_test.sh b/src/tasks/predict_modality/methods/novel/predict/run_test.sh new file mode 100644 index 0000000000..af5550e5d7 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/predict/run_test.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +viash run src/tasks/predict_modality/methods/novel/predict/config.vsh.yaml -- \ + --input_train_mod2 'resources/predict_modality/datasets/openproblems_neurips2021/bmmc_cite/normal/log_cp10k/train_mod2.h5ad' \ + --input_test_mod1 'resources/predict_modality/datasets/openproblems_neurips2021/bmmc_cite/normal/log_cp10k/test_mod1.h5ad' \ + --input_model output/novel/model.pt \ + --input_transform output/novel/lsi_transform.pickle \ + --output 'output/novel/novel_test.h5ad' \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/novel/predict/script.py b/src/tasks/predict_modality/methods/novel/predict/script.py new file mode 100644 index 0000000000..5f336ce7b0 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/predict/script.py @@ -0,0 +1,119 @@ +import sys +import torch +from torch.utils.data import DataLoader + +import anndata as ad +import pickle +import numpy as np +from scipy.sparse import csc_matrix + +#check gpu available +if (torch.cuda.is_available()): + device = 'cuda:0' #switch to current device + print('current device: gpu', flush=True) +else: + device = 'cpu' + print('current device: cpu', flush=True) + + +## VIASH START + +par = { + 'input_train_mod2': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/test_mod1.h5ad', + 'input_model': 'resources_test/predict_modality/neurips2021_bmmc_cite/model.pt', + 'input_transform': 'transformer.pickle' +} +meta = { + 'resources_dir': 'src/tasks/predict_modality/methods/novel', + 'functionality_name': '171129' +} +## VIASH END + +sys.path.append(meta['resources_dir']) +from helper_functions import ModelRegressionAtac2Gex, ModelRegressionAdt2Gex, ModelRegressionGex2Adt, ModelRegressionGex2Atac, ModalityMatchingDataset + +print("Load data", flush=True) + +input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) +input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) + +mod1 = input_test_mod1.uns['modality'] +mod2 = input_train_mod2.uns['modality'] + +n_vars_mod1 = input_train_mod2.uns["model_dim"]["mod1"] +n_vars_mod2 = input_train_mod2.uns["model_dim"]["mod2"] + +input_test_mod1.X = input_test_mod1.layers['normalized'].tocsr() + +# Remove vars that were removed from training set. Mostlyy only applicable for testing. +if input_train_mod2.uns.get("removed_vars"): + rem_var = input_train_mod2.uns["removed_vars"] + input_test_mod1 = input_test_mod1[:, ~input_test_mod1.var_names.isin(rem_var)] + +del input_train_mod2 + + +model_fp = par['input_model'] + +print("Start predict", flush=True) + +if mod1 == 'GEX' and mod2 == 'ADT': + model = ModelRegressionGex2Adt(n_vars_mod1,n_vars_mod2) + weight = torch.load(model_fp, map_location='cpu') + with open(par['input_transform'], 'rb') as f: + lsi_transformer_gex = pickle.load(f) + + model.load_state_dict(weight) + input_test_mod1_ = lsi_transformer_gex.transform(input_test_mod1) + +elif mod1 == 'GEX' and mod2 == 'ATAC': + model = ModelRegressionGex2Atac(n_vars_mod1,n_vars_mod2) + weight = torch.load(model_fp, map_location='cpu') + with open(par['input_transform'], 'rb') as f: + lsi_transformer_gex = pickle.load(f) + + model.load_state_dict(weight) + input_test_mod1_ = lsi_transformer_gex.transform(input_test_mod1) + +elif mod1 == 'ATAC' and mod2 == 'GEX': + model = ModelRegressionAtac2Gex(n_vars_mod1,n_vars_mod2) + weight = torch.load(model_fp, map_location='cpu') + with open(par['input_transform'], 'rb') as f: + lsi_transformer_gex = pickle.load(f) + + model.load_state_dict(weight) + input_test_mod1_ = lsi_transformer_gex.transform(input_test_mod1) + +elif mod1 == 'ADT' and mod2 == 'GEX': + model = ModelRegressionAdt2Gex(n_vars_mod1,n_vars_mod2) + weight = torch.load(model_fp, map_location='cpu') + + model.load_state_dict(weight) + input_test_mod1_ = input_test_mod1.to_df() + +dataset_test = ModalityMatchingDataset(input_test_mod1_, None, is_train=False) +dataloader_test = DataLoader(dataset_test, 32, shuffle = False, num_workers = 4) + +outputs = [] +model.eval() +with torch.no_grad(): + for x in dataloader_test: + output = model(x.float()) + outputs.append(output.detach().cpu().numpy()) + +outputs = np.concatenate(outputs) +outputs[outputs<0] = 0 +outputs = csc_matrix(outputs) + +adata = ad.AnnData( + layers={"normalized": outputs}, + shape=outputs.shape, + uns={ + 'dataset_id': input_test_mod1.uns['dataset_id'], + 'method_id': meta['functionality_name'], + }, +) +adata.write_h5ad(par['output'], compression = "gzip") + + diff --git a/src/tasks/predict_modality/methods/novel/run/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/run/config.vsh.yaml new file mode 100644 index 0000000000..682782e059 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/run/config.vsh.yaml @@ -0,0 +1,21 @@ +__merge__: ../../../api/comp_method.yaml +functionality: + name: novel + info: + label: Novel + summary: A method using encoder-decoder MLP model + description: This method trains an encoder-decoder MLP model with one output neuron per component in the target. As an input, the encoders use representations obtained from ATAC and GEX data via LSI transform and raw ADT data. The hyperparameters of the models were found via broad hyperparameter search using the Optuna framework. + documentation_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/novel#readme + repository_url: https://github.com/openproblems-bio/neurips2021_multimodal_topmethods/tree/main/src/predict_modality/methods/novel + reference: pmlr-v176-lance2022multimodal + submission_id: "169769" + preferred_normalization: log_cp10k + resources: + - path: main.nf + type: nextflow_script + entrypoint: run_wf + dependencies: + - name: predict_modality/methods/novel_train + - name: predict_modality/methods/novel_predict +platforms: + - type: nextflow \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/novel/run/main.nf b/src/tasks/predict_modality/methods/novel/run/main.nf new file mode 100644 index 0000000000..59111194cb --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/run/main.nf @@ -0,0 +1,25 @@ +workflow run_wf { + take: input_ch + main: + output_ch = input_ch + | novel_train.run( + fromState: ["input_train_mod1", "input_train_mod2"], + toState: ["input_model": "output", "input_transform": "output_transform", "output_train_mod2": "output_train_mod2"] + ) + | novel_predict.run( + fromState: { id, state -> + [ + "input_train_mod2": state.output_train_mod2, + "input_test_mod1": state.input_test_mod1, + "input_model": state.input_model, + "input_transform": state.input_transform, + "output": state.output]}, + toState: ["output": "output"] + ) + + | map { tup -> + [tup[0], [output: tup[1].output]] + } + + emit: output_ch +} \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/novel/run/run_test.sh b/src/tasks/predict_modality/methods/novel/run/run_test.sh new file mode 100644 index 0000000000..f6da6b0863 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/run/run_test.sh @@ -0,0 +1,15 @@ +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +set -e + +nextflow run . \ + -main-script target/nextflow/predict_modality/methods/novel/main.nf \ + -profile docker \ + -c src/wf_utils/labels_ci.config \ + --input_train_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod1.h5ad \ + --input_train_mod2 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod2.h5ad \ + --input_test_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/test_mod1.h5ad \ + --publish_dir output/novel/nextflow diff --git a/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml new file mode 100644 index 0000000000..a6ae6a4bb8 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/train/config.vsh.yaml @@ -0,0 +1,31 @@ +__merge__: ../../../api/comp_method_train.yaml +functionality: + name: novel_train + arguments: + - name: --output_transform + type: file + description: "The output transform file" + required: false + default: "lsi_transformer.pickle" + direction: output + - name: --output_train_mod2 + type: file + description: copy of the input with model dim in `.uns` + direction: output + default: "train_mod2.h5ad" + required: false + resources: + - path: script.py + type: python_script + - path: ../helper_functions.py +platforms: + - type: docker + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + setup: + - type: python + packages: + - scikit-learn + - networkx + - type: nextflow + directives: + label: [highmem, hightime, midcpu, highsharedmem, gpu] \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/novel/train/run_test.sh b/src/tasks/predict_modality/methods/novel/train/run_test.sh new file mode 100644 index 0000000000..08630b1ac0 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/train/run_test.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +# Run script for all test resources + +echo "GEX2ADT" +viash run src/tasks/predict_modality/methods/novel/train/config.vsh.yaml -- \ + --input_train_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod1.h5ad \ + --input_train_mod2 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod2.h5ad \ + --output output/model.pt + +# echo "ADT2GEX" +# viash run src/tasks/predict_modality/methods/novel/train/config.vsh.yaml -- \ +# --input_train_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod1.h5ad \ +# --input_train_mod2 resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/swap/train_mod2.h5ad \ +# --output output/model.pt + +# echo "GEX2ATAC" +# viash run src/tasks/predict_modality/methods/novel/train/config.vsh.yaml -- \ +# --input_train_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/train_mod1.h5ad \ +# --input_train_mod2 resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/normal/train_mod2.h5ad \ +# --output output/model.pt + +# echo "ATAC2GEX" +# viash run src/tasks/predict_modality/methods/novel/train/config.vsh.yaml -- \ +# --input_train_mod1 resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/swap/train_mod1.h5ad \ +# --input_train_mod2 resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/swap/train_mod2.h5ad \ +# --output output/model.pt + + diff --git a/src/tasks/predict_modality/methods/novel/train/script.py b/src/tasks/predict_modality/methods/novel/train/script.py new file mode 100644 index 0000000000..39ea8b4778 --- /dev/null +++ b/src/tasks/predict_modality/methods/novel/train/script.py @@ -0,0 +1,148 @@ +import sys + +import torch +from torch.utils.data import DataLoader +# from sklearn.model_selection import train_test_split + +import anndata as ad +import pickle + +#check gpu available +if (torch.cuda.is_available()): + device = 'cuda:0' #switch to current device + print('current device: gpu', flush=True) +else: + device = 'cpu' + print('current device: cpu', flush=True) + + +## VIASH START + +par = { + 'input_train_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/normal/train_mod2.h5ad', + 'output_train_mod2': 'train_mod2.h5ad', + 'output': 'model.pt' +} + +meta = { + 'resources_dir': 'src/tasks/predict_modality/methods/novel', +} +## VIASH END + + +sys.path.append(meta['resources_dir']) +from helper_functions import train_and_valid, lsiTransformer, ModalityMatchingDataset +from helper_functions import ModelRegressionAtac2Gex, ModelRegressionAdt2Gex, ModelRegressionGex2Adt, ModelRegressionGex2Atac + +print('Load data', flush=True) + +input_train_mod1 = ad.read_h5ad(par['input_train_mod1']) +input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) + +adata = input_train_mod2.copy() + +mod1 = input_train_mod1.uns['modality'] +mod2 = input_train_mod2.uns['modality'] + +input_train_mod1.X = input_train_mod1.layers['normalized'] +input_train_mod2.X = input_train_mod2.layers['normalized'] + +input_train_mod2_df = input_train_mod2.to_df() + +del input_train_mod2 + +print('Start train', flush=True) + + +# Check for zero divide +zero_row = input_train_mod1.X.sum(axis=0) == 0 + +rem_var = None +if True in zero_row: + rem_var = input_train_mod1[:, zero_row].var_names + input_train_mod1 = input_train_mod1[:, ~zero_row] + + +# select number of variables for LSI +n_comp = input_train_mod1.n_vars -1 if input_train_mod1.n_vars < 256 else 256 + +if mod1 != 'ADT': + lsi_transformer_gex = lsiTransformer(n_components=n_comp) + input_train_mod1_df = lsi_transformer_gex.fit_transform(input_train_mod1) +else: + input_train_mod1_df = input_train_mod1.to_df() + +# reproduce train/test split from phase 1 +batch = input_train_mod1.obs["batch"] +train_ix = [ k for k,v in enumerate(batch) if v not in {'s1d2', 's3d7'} ] +test_ix = [ k for k,v in enumerate(batch) if v in {'s1d2', 's3d7'} ] + +train_mod1 = input_train_mod1_df.iloc[train_ix, :] +train_mod2 = input_train_mod2_df.iloc[train_ix, :] +test_mod1 = input_train_mod1_df.iloc[test_ix, :] +test_mod2 = input_train_mod2_df.iloc[test_ix, :] + +n_vars_train_mod1 = train_mod1.shape[1] +n_vars_train_mod2 = train_mod2.shape[1] +n_vars_test_mod1 = test_mod1.shape[1] +n_vars_test_mod2 = test_mod2.shape[1] + +n_vars_mod1 = input_train_mod1_df.shape[1] +n_vars_mod2 = input_train_mod2_df.shape[1] + +if mod1 == 'ATAC' and mod2 == 'GEX': + dataset_train = ModalityMatchingDataset(train_mod1, train_mod2) + dataloader_train = DataLoader(dataset_train, 256, shuffle = True, num_workers = 8) + + dataset_test = ModalityMatchingDataset(test_mod1, test_mod2) + dataloader_test = DataLoader(dataset_test, 64, shuffle = False, num_workers = 8) + + model = ModelRegressionAtac2Gex(n_vars_mod1,n_vars_mod2).to(device) + optimizer = torch.optim.AdamW(model.parameters(), lr=0.00008386597445284492,weight_decay=0.000684887347727808) + +elif mod1 == 'ADT' and mod2 == 'GEX': + dataset_train = ModalityMatchingDataset(train_mod1, train_mod2) + dataloader_train = DataLoader(dataset_train, 64, shuffle = True, num_workers = 4) + + dataset_test = ModalityMatchingDataset(test_mod1, test_mod2) + dataloader_test = DataLoader(dataset_test, 32, shuffle = False, num_workers = 4) + + model = ModelRegressionAdt2Gex(n_vars_mod1,n_vars_mod2).to(device) + optimizer = torch.optim.Adam(model.parameters(), lr=0.00041, weight_decay=0.0000139) + + +elif mod1 == 'GEX' and mod2 == 'ADT': + dataset_train = ModalityMatchingDataset(train_mod1, train_mod2) + dataloader_train = DataLoader(dataset_train, 32, shuffle = True, num_workers = 8) + + dataset_test = ModalityMatchingDataset(test_mod1, test_mod2) + dataloader_test = DataLoader(dataset_test, 64, shuffle = False, num_workers = 8) + + model = ModelRegressionGex2Adt(n_vars_mod1,n_vars_mod2).to(device) + optimizer = torch.optim.AdamW(model.parameters(), lr=0.000034609210829678734, weight_decay=0.0009965881574697426) + + +elif mod1 == 'GEX' and mod2 == 'ATAC': + dataset_train = ModalityMatchingDataset(train_mod1, train_mod2) + dataloader_train = DataLoader(dataset_train, 64, shuffle = True, num_workers = 8) + + dataset_test = ModalityMatchingDataset(test_mod1, test_mod2) + dataloader_test = DataLoader(dataset_test, 64, shuffle = False, num_workers = 8) + + model = ModelRegressionGex2Atac(n_vars_mod1,n_vars_mod2).to(device) + optimizer = torch.optim.AdamW(model.parameters(), lr=0.00001806762345275399, weight_decay=0.0004084171379280058) + +loss_fn = torch.nn.MSELoss() +train_and_valid(model, optimizer, loss_fn, dataloader_train, dataloader_test, par['output'], device) + +# Add model dim for use in predict part +adata.uns["model_dim"] = {"mod1": n_vars_mod1, "mod2": n_vars_mod2} +if rem_var: + adata.uns["removed_vars"] = [rem_var[0]] +adata.write_h5ad(par['output_train_mod2'], compression="gzip") + +if mod1 != 'ADT': + with open(par['output_transform'], 'wb') as f: + pickle.dump(lsi_transformer_gex, f) + diff --git a/src/tasks/predict_modality/process_dataset/script.R b/src/tasks/predict_modality/process_dataset/script.R index 4ef92b8578..f45559ebed 100644 --- a/src/tasks/predict_modality/process_dataset/script.R +++ b/src/tasks/predict_modality/process_dataset/script.R @@ -71,7 +71,7 @@ ad1_uns$dataset_name <- ad2_uns$dataset_name <- new_dataset_name # determine new obsm ad1_obsm <- ad2_obsm <- list() -# determine new var +# determine new varm ad1_var <- ad1$var[, intersect(colnames(ad1$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] ad2_var <- ad2$var[, intersect(colnames(ad2$var), c("gene_ids", "hvg", "hvg_score")), drop = FALSE] diff --git a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml index f406d5f66b..c2340a31db 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml +++ b/src/tasks/predict_modality/workflows/run_benchmark/config.vsh.yaml @@ -74,6 +74,7 @@ functionality: # - name: predict_modality/methods/newwave_knnr # - name: predict_modality/methods/random_forest - name: predict_modality/methods/guanlab_dengkw_pm + - name: predict_modality/methods/novel - name: predict_modality/metrics/correlation - name: predict_modality/metrics/mse platforms: diff --git a/src/tasks/predict_modality/workflows/run_benchmark/main.nf b/src/tasks/predict_modality/workflows/run_benchmark/main.nf index 5f54ef29fa..2b20059f2f 100644 --- a/src/tasks/predict_modality/workflows/run_benchmark/main.nf +++ b/src/tasks/predict_modality/workflows/run_benchmark/main.nf @@ -23,7 +23,8 @@ workflow run_wf { lmds_irlba_rf, // newwave_knnr, // random_forest, - guanlab_dengkw_pm + guanlab_dengkw_pm, + novel ] // construct list of metrics From 36cff3bd84fc451305edc5561bada988d233863e Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Mon, 26 Aug 2024 23:41:38 +0200 Subject: [PATCH 1228/1233] Simple MLP attempt #2 (#441) * make gitignore more strict * update api files Co-authored-by: Kai Waldrant * create separate file for pretrained model * add train component * clean up resources * wip components * wip refactor * fix issues with training component * make input_train optional in prediction methods * clean up predict method * fix wf * clean up train * add helper test script * update configs * add to wf * always store ymean.npy * add shmsize to simplemlp * Update src/tasks/predict_modality/methods/simple_mlp/train/script.py * bigger shm * Add nextflow workaround * lower cpu label --------- Co-authored-by: Kai Waldrant Former-commit-id: 41fc02751dc001bc76c8c3e073f93df9fcb4234d --- src/tasks/predict_modality/api/task_info.yaml | 13 +- .../simple_mlp/predict/config.vsh.yaml | 21 +++ .../methods/simple_mlp/predict/script.py | 104 ++++++++++++ .../methods/simple_mlp/resources/models.py | 68 ++++++++ .../methods/simple_mlp/resources/utils.py | 37 +++++ .../resources/yaml/mlp_ADT2GEX.yaml | 28 ++++ .../resources/yaml/mlp_ATAC2GEX.yaml | 28 ++++ .../resources/yaml/mlp_GEX2ADT.yaml | 28 ++++ .../methods/simple_mlp/run/config.vsh.yaml | 26 +++ .../methods/simple_mlp/run/main.nf | 21 +++ .../methods/simple_mlp/run/run_test.sh | 15 ++ .../methods/simple_mlp/test.sh | 14 ++ .../methods/simple_mlp/train/config.vsh.yaml | 21 +++ .../methods/simple_mlp/train/script.py | 155 ++++++++++++++++++ .../workflows/run_benchmark/config.vsh.yaml | 1 + .../workflows/run_benchmark/main.nf | 1 + 16 files changed, 580 insertions(+), 1 deletion(-) create mode 100644 src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/predict/script.py create mode 100644 src/tasks/predict_modality/methods/simple_mlp/resources/models.py create mode 100644 src/tasks/predict_modality/methods/simple_mlp/resources/utils.py create mode 100644 src/tasks/predict_modality/methods/simple_mlp/resources/yaml/mlp_ADT2GEX.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/resources/yaml/mlp_ATAC2GEX.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/resources/yaml/mlp_GEX2ADT.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/run/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/run/main.nf create mode 100644 src/tasks/predict_modality/methods/simple_mlp/run/run_test.sh create mode 100755 src/tasks/predict_modality/methods/simple_mlp/test.sh create mode 100644 src/tasks/predict_modality/methods/simple_mlp/train/config.vsh.yaml create mode 100644 src/tasks/predict_modality/methods/simple_mlp/train/script.py diff --git a/src/tasks/predict_modality/api/task_info.yaml b/src/tasks/predict_modality/api/task_info.yaml index ba3b567d01..e0d1ed9da7 100644 --- a/src/tasks/predict_modality/api/task_info.yaml +++ b/src/tasks/predict_modality/api/task_info.yaml @@ -53,4 +53,15 @@ authors: roles: [ contributor ] info: email: dengkw@umich.edu - github: nonztalk \ No newline at end of file + github: nonztalk + - name: Xueer Chen + roles: [ contributor ] + info: + github: xuerchen + email: xc2579@columbia.edu + - name: Jiwei Liu + roles: [ contributor ] + info: + github: daxiongshu + email: jiweil@nvidia.com + orcid: "0000-0002-8799-9763" diff --git a/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml new file mode 100644 index 0000000000..e5806b395c --- /dev/null +++ b/src/tasks/predict_modality/methods/simple_mlp/predict/config.vsh.yaml @@ -0,0 +1,21 @@ +__merge__: ../../../api/comp_method_predict.yaml +functionality: + name: simplemlp_predict + resources: + - type: python_script + path: script.py + - path: ../resources/ +platforms: + - type: docker + # image: pytorch/pytorch:1.9.0-cuda11.1-cudnn8-runtime + image: ghcr.io/openproblems-bio/base_pytorch_nvidia:1.0.4 + # run_args: ["--gpus all --ipc=host"] + setup: + - type: python + pypi: + - scikit-learn + - scanpy + - pytorch-lightning + - type: nextflow + directives: + label: [highmem, hightime, midcpu, gpu, highsharedmem] \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/simple_mlp/predict/script.py b/src/tasks/predict_modality/methods/simple_mlp/predict/script.py new file mode 100644 index 0000000000..b67284e348 --- /dev/null +++ b/src/tasks/predict_modality/methods/simple_mlp/predict/script.py @@ -0,0 +1,104 @@ +from glob import glob +import sys +import numpy as np +from scipy.sparse import csc_matrix +import anndata as ad +import torch +from torch.utils.data import TensorDataset,DataLoader + +## VIASH START +par = { + 'input_train_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/swap/train_mod1.h5ad', + 'input_train_mod2': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/swap/train_mod2.h5ad', + 'input_test_mod1': 'resources_test/predict_modality/openproblems_neurips2021/bmmc_multiome/swap/test_mod1.h5ad', + 'input_model': 'output/model', + 'output': 'output/prediction' +} +meta = { + 'resources_dir': 'src/tasks/predict_modality/methods/simple_mlp', + 'cpus': 10 +} +## VIASH END + +resources_dir = f"{meta['resources_dir']}/resources" +sys.path.append(resources_dir) +from models import MLP +import utils + +def _predict(model,dl): + model = model.cuda() + model.eval() + yps = [] + for x in dl: + with torch.no_grad(): + yp = model(x[0].cuda()) + yps.append(yp.detach().cpu().numpy()) + yp = np.vstack(yps) + return yp + + +print('Load data', flush=True) +input_train_mod2 = ad.read_h5ad(par['input_train_mod2']) +input_test_mod1 = ad.read_h5ad(par['input_test_mod1']) + +# determine variables +mod_1 = input_test_mod1.uns['modality'] +mod_2 = input_train_mod2.uns['modality'] + +task = f'{mod_1}2{mod_2}' + +print('Load ymean', flush=True) +ymean_path = f"{par['input_model']}/{task}_ymean.npy" +ymean = np.load(ymean_path) + +print('Start predict', flush=True) +if task == 'GEX2ATAC': + y_pred = ymean*np.ones([input_test_mod1.n_obs, input_test_mod1.n_vars]) +else: + folds = [0, 1, 2] + + ymean = torch.from_numpy(ymean).float() + yaml_path=f"{resources_dir}/yaml/mlp_{task}.yaml" + config = utils.load_yaml(yaml_path) + X = input_test_mod1.layers["normalized"].toarray() + X = torch.from_numpy(X).float() + + te_ds = TensorDataset(X) + + yp = 0 + for fold in folds: + # load_path = f"{par['input_model']}/{task}_fold_{fold}/version_0/checkpoints/*" + load_path = f"{par['input_model']}/{task}_fold_{fold}/**.ckpt" + print(load_path) + ckpt = glob(load_path)[0] + model_inf = MLP.load_from_checkpoint( + ckpt, + in_dim=X.shape[1], + out_dim=input_test_mod1.n_vars, + ymean=ymean, + config=config + ) + te_loader = DataLoader( + te_ds, + batch_size=config.batch_size, + num_workers=0, + shuffle=False, + drop_last=False + ) + yp = yp + _predict(model_inf, te_loader) + + y_pred = yp/len(folds) + +y_pred = csc_matrix(y_pred) + +adata = ad.AnnData( + layers={"normalized": y_pred}, + shape=y_pred.shape, + uns={ + 'dataset_id': input_test_mod1.uns['dataset_id'], + 'method_id': meta['functionality_name'], + }, +) + +print('Write data', flush=True) +adata.write_h5ad(par['output'], compression = "gzip") \ No newline at end of file diff --git a/src/tasks/predict_modality/methods/simple_mlp/resources/models.py b/src/tasks/predict_modality/methods/simple_mlp/resources/models.py new file mode 100644 index 0000000000..25ce9b2995 --- /dev/null +++ b/src/tasks/predict_modality/methods/simple_mlp/resources/models.py @@ -0,0 +1,68 @@ +import torch +import pytorch_lightning as pl +import torch.nn as nn +import torch.nn.functional as F + +class MLP(pl.LightningModule): + def __init__(self,in_dim,out_dim,ymean,config): + super(MLP, self).__init__() + self.ymean = ymean.cuda() + H1 = config.H1 + H2 = config.H2 + p = config.dropout + self.config = config + self.fc1 = nn.Linear(in_dim, H1) + self.fc2 = nn.Linear(H1,H2) + self.fc3 = nn.Linear(H1+H2, out_dim) + self.dp2 = nn.Dropout(p=p) + + def forward(self, x): + x0 = x + x1 = F.relu(self.fc1(x)) + x1 = self.dp2(x1) + x = F.relu(self.fc2(x1)) + x = torch.cat([x,x1],dim=1) + x = self.fc3(x) + x = self.apply_mask(x) + return x + + def apply_mask(self,yp): + tmp = torch.ones_like(yp).float()*self.ymean + mask = tmp

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zxtb?KC!&YlX`wGT<>>LG{js~|{aWXFzRvr5jccYaY<-|{y*2Jd9e-*^*RVzB@t)Ry zr~Oyxe$e#@J-p5~jnj|hde`$#)cx(J<9(!Y+jQL1^>(sA&+~Xa4-abGFM6J)XgQ+! z=xdfc_4v^Bw5N4qZ|Hu%rty@QPGeuSmySTX=Z|M@bSGSIHhXC=_oZFk5lDVM(cKdC wG9a&uR`>r?m0s#{=mknAnEYJgg6gJTCw}g8uNmI;+A$kwB Date: Tue, 20 Jul 2021 12:37:45 +0200 Subject: [PATCH 0136/1233] remove log normalisation for pancreas data Former-commit-id: 834c77a97191cdabe4ef2c479a58f55924c6d579 --- .../datasets/pancreas/script.py | 21 +++++++++---------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/src/batch_integration/datasets/pancreas/script.py b/src/batch_integration/datasets/pancreas/script.py index 22352ade27..48c1df190a 100644 --- a/src/batch_integration/datasets/pancreas/script.py +++ b/src/batch_integration/datasets/pancreas/script.py @@ -3,21 +3,21 @@ print(os.getcwd()) par = { - 'adata': './src/batch_integration/resources/data_loader_pancreas.h5ad', + 'adata': './src/batch_integration/datasets/resources/data_loader_pancreas.h5ad', 'label': 'celltype', 'batch': 'tech', 'hvgs': 2000, - 'output': 'adata_out.h5ad', + 'output': './src/batch_integration/datasets/resources/datasets_pancreas.h5ad', 'debug': True } -resources_dir = '../' +resources_dir = './src/batch_integration/datasets' ## VIASH END print('Importing libraries') import scanpy as sc -import sys -sys.path.append(resources_dir) -from utils import log_scran_pooling +# import sys +# sys.path.append(resources_dir) +# from utils import log_scran_pooling if par['debug']: import pprint @@ -34,17 +34,16 @@ adata = sc.read(adata_file) # Rename columns -adata.obs['label'] = adata.obs[label] -adata.obs['batch'] = adata.obs[batch] +adata.obs.rename(columns={label: 'label', batch: 'batch'}, inplace=True) adata.layers['counts'] = adata.X print(f'Select {hvgs} highly variable genes') if adata.n_obs > hvgs: sc.pp.subsample(adata, n_obs=hvgs) -print('Normalisation with scran') -log_scran_pooling(adata) -adata.layers['logcounts'] = adata.X +#print('Normalisation with scran') +#log_scran_pooling(adata) +#adata.layers['logcounts'] = adata.X print('Transformation: PCA') sc.tl.pca( From 17e502d65aa2a2c60e4ec4f56266d96bf69f657e Mon Sep 17 00:00:00 2001 From: Michaela Mueller Date: Tue, 20 Jul 2021 22:05:26 +0200 Subject: [PATCH 0137/1233] adapted ari, nmi, asw_batch to API Former-commit-id: 07ad78fc283c7d615a7d4895774272d5b62174ec --- .../metrics/asw_batch/config.vsh.yaml | 6 +--- .../embedding/metrics/asw_batch/script.py | 26 ++++-------------- .../embedding/metrics/asw_batch/test.py | 7 ++--- .../graph/metrics/ari/config.vsh.yaml | 6 +--- .../graph/metrics/ari/script.py | 25 ++++------------- .../graph/metrics/ari/test.py | 7 ++--- .../graph/metrics/nmi/config.vsh.yaml | 6 +--- .../graph/metrics/nmi/script.py | 24 ++++------------ .../graph/metrics/nmi/test.py | 7 ++--- .../resources/pancreas_mnn.h5ad | Bin 0 -> 3438982 bytes 10 files changed, 28 insertions(+), 86 deletions(-) create mode 100644 src/batch_integration/resources/pancreas_mnn.h5ad diff --git a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml index acf284256d..b2503be2e6 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml +++ b/src/batch_integration/embedding/metrics/asw_batch/config.vsh.yaml @@ -18,10 +18,6 @@ functionality: type: file description: Anndata HDF5 file before integration required: true - - name: --hvgs - type: integer - description: Number of highly variable genes - default: 2000 - name: --debug type: boolean description: Verbose output for debugging @@ -33,7 +29,7 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/mnn.h5ad' + - path: '../../../resources/pancreas_mnn.h5ad' platforms: - type: docker image: mumichae/scib-base:0.1 diff --git a/src/batch_integration/embedding/metrics/asw_batch/script.py b/src/batch_integration/embedding/metrics/asw_batch/script.py index 90e74f5380..8ab202df57 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/script.py +++ b/src/batch_integration/embedding/metrics/asw_batch/script.py @@ -1,8 +1,7 @@ ## VIASH START par = { - 'adata': '../resources/mnn.h5ad', - 'hvgs': 2000, - 'output': 'asw_batch.tsv', + 'adata': './src/batch_integration/embedding/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/embedding/resources/asw_batch_pancreas_mnn.tsv', 'debug': True } ## VIASH END @@ -10,35 +9,22 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.preprocessing import reduce_data from scIB.metrics import silhouette_batch if par['debug']: pprint.pprint(par) +OUTPUT_TYPE = 'embedding' METRIC = 'asw_batch' -EMBEDDING = 'X_pca' +EMBEDDING = 'X_emb' adata_file = par['adata'] -n_hvgs = par['hvgs'] -n_hvgs = n_hvgs if n_hvgs > 0 else None output = par['output'] print('Read adata') adata = sc.read(adata_file) name = adata.uns['name'] -# preprocess adata object -print('preprocess adata') -reduce_data( - adata, - n_top_genes=n_hvgs, - pca=True, - neighbors=False, - use_rep=EMBEDDING, - umap=False -) - print('compute score') _, sil_clus = silhouette_batch( adata, @@ -50,7 +36,7 @@ score = sil_clus['silhouette_score'].mean() with open(output, 'w') as file: - header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] - entry = [name, 'feature', n_hvgs, METRIC, score] + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] file.write('\t'.join(header) + '\n') file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/embedding/metrics/asw_batch/test.py b/src/batch_integration/embedding/metrics/asw_batch/test.py index 16104dce0b..0fe5bb4c4e 100644 --- a/src/batch_integration/embedding/metrics/asw_batch/test.py +++ b/src/batch_integration/embedding/metrics/asw_batch/test.py @@ -11,8 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'mnn.h5ad', - '--hvgs', '2000', + "--adata", 'pancreas_mnn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -21,11 +20,11 @@ print(">> Check that score makes sense") result = pd.read_table(metric_file) -assert result.shape == (1, 5) +assert result.shape == (1, 4) score = result.loc[0, 'value'] print(score) assert 0 < score < 1 -assert score == 0.8778942688412869 +assert score == 0.9035066414882263 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/ari/config.vsh.yaml b/src/batch_integration/graph/metrics/ari/config.vsh.yaml index c95c0cab8f..b5c8f2f418 100644 --- a/src/batch_integration/graph/metrics/ari/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/ari/config.vsh.yaml @@ -18,10 +18,6 @@ functionality: type: file description: Anndata HDF5 file required: true - - name: --hvgs - type: integer - description: Number of highly variable genes - default: 2000 - name: --debug type: boolean description: Verbose output for debugging @@ -33,7 +29,7 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/mnn.h5ad' + - path: '../../../resources/pancreas_mnn.h5ad' platforms: - type: docker image: mumichae/scib-base:0.1 diff --git a/src/batch_integration/graph/metrics/ari/script.py b/src/batch_integration/graph/metrics/ari/script.py index f51e3ed539..39d5add64f 100644 --- a/src/batch_integration/graph/metrics/ari/script.py +++ b/src/batch_integration/graph/metrics/ari/script.py @@ -1,8 +1,7 @@ ## VIASH START par = { - 'adata': '../resources/mnn.h5ad', - 'hvgs': 2000, - 'output': 'metrics.tsv', + 'adata': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/graph/resources/ari_pancreas_mnn.tsv', 'debug': True } ## VIASH END @@ -10,36 +9,22 @@ print('Importing libraries') import pprint import scanpy as sc -from scIB.preprocessing import reduce_data from scIB.clustering import opt_louvain from scIB.metrics import ari if par['debug']: pprint.pprint(par) +OUTPUT_TYPE = 'graph' METRIC = 'ari' -EMBEDDING = 'X_pca' adata_file = par['adata'] -n_hvgs = par['hvgs'] -n_hvgs = n_hvgs if n_hvgs > 0 else None output = par['output'] print('Read adata') adata = sc.read(adata_file) name = adata.uns['name'] -# preprocess adata object -print('preprocess adata') -reduce_data( - adata, - n_top_genes=n_hvgs, - neighbors=True, - use_rep=EMBEDDING, - pca=True, - umap=False -) - print('clustering') opt_louvain( adata, @@ -54,7 +39,7 @@ score = ari(adata, group1='cluster', group2='label') with open(output, 'w') as file: - header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] - entry = [name, 'feature', n_hvgs, METRIC, score] + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] file.write('\t'.join(header) + '\n') file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/graph/metrics/ari/test.py b/src/batch_integration/graph/metrics/ari/test.py index ecd125e95a..bdb3053201 100644 --- a/src/batch_integration/graph/metrics/ari/test.py +++ b/src/batch_integration/graph/metrics/ari/test.py @@ -11,8 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'mnn.h5ad', - '--hvgs', '100', + "--adata", 'pancreas_mnn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -21,11 +20,11 @@ result = pd.read_table(metric_file) print(">> Check that score makes sense") -assert result.shape == (1, 5) +assert result.shape == (1, 4) score = result.loc[0, 'value'] print(score) assert 0 < score < 1 -assert score == 0.2459195865045752 +assert score == 0.9341303589103552 print(">> All tests passed successfully") diff --git a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml index afae13cb93..158668d019 100644 --- a/src/batch_integration/graph/metrics/nmi/config.vsh.yaml +++ b/src/batch_integration/graph/metrics/nmi/config.vsh.yaml @@ -18,10 +18,6 @@ functionality: type: file description: Anndata HDF5 file required: true - - name: --hvgs - type: integer - description: Number of highly variable genes - default: 2000 - name: --debug type: boolean description: Verbose output for debugging @@ -33,7 +29,7 @@ functionality: tests: - type: python_script path: test.py - - path: '../../../resources/mnn.h5ad' + - path: '../../../resources/pancreas_mnn.h5ad' platforms: - type: docker image: mumichae/scib-base:0.1 diff --git a/src/batch_integration/graph/metrics/nmi/script.py b/src/batch_integration/graph/metrics/nmi/script.py index a46344ae2e..8f05831734 100644 --- a/src/batch_integration/graph/metrics/nmi/script.py +++ b/src/batch_integration/graph/metrics/nmi/script.py @@ -1,8 +1,7 @@ ## VIASH START par = { - 'adata': '../resources/mnn.h5ad', - 'hvgs': 2000, - 'output': 'nmi.tsv', + 'adata': './src/batch_integration/graph/resources/mnn_pancreas.h5ad', + 'output': './src/batch_integration/graph/resources/nmi_pancreas_mnn.tsv', 'debug': True } ## VIASH END @@ -17,29 +16,16 @@ if par['debug']: pprint.pprint(par) +OUTPUT_TYPE = 'graph' METRIC = 'nmi' -EMBEDDING = 'X_pca' adata_file = par['adata'] -n_hvgs = par['hvgs'] -n_hvgs = n_hvgs if n_hvgs > 0 else None output = par['output'] print('Read adata') adata = sc.read(adata_file) name = adata.uns['name'] -# preprocess adata object -print('preprocess adata') -reduce_data( - adata, - n_top_genes=n_hvgs, - neighbors=True, - use_rep=EMBEDDING, - pca=True, - umap=False -) - print('clustering') opt_louvain( adata, @@ -54,7 +40,7 @@ score = nmi(adata, group1='cluster', group2='label') with open(output, 'w') as file: - header = ['dataset', 'output_type', 'hvg', 'metric', 'value'] - entry = [name, 'feature', n_hvgs, METRIC, score] + header = ['dataset', 'output_type', 'metric', 'value'] + entry = [name, OUTPUT_TYPE, METRIC, score] file.write('\t'.join(header) + '\n') file.write('\t'.join([str(x) for x in entry])) diff --git a/src/batch_integration/graph/metrics/nmi/test.py b/src/batch_integration/graph/metrics/nmi/test.py index da47719a10..91a17338c8 100644 --- a/src/batch_integration/graph/metrics/nmi/test.py +++ b/src/batch_integration/graph/metrics/nmi/test.py @@ -11,8 +11,7 @@ print(">> Running script") out = subprocess.check_output([ "./" + metric, - "--adata", 'mnn.h5ad', - '--hvgs', '2000', + "--adata", 'pancreas_mnn.h5ad', "--output", metric_file ]).decode("utf-8") @@ -21,11 +20,11 @@ print(">> Check that score makes sense") result = pd.read_table(metric_file) -assert result.shape == (1, 5) +assert result.shape == (1, 4) score = result.loc[0, 'value'] print(score) assert 0 < score < 1 -assert score == 0.4871368591999889 +assert score == 0.8589185688918367 print(">> All tests passed successfully") diff --git a/src/batch_integration/resources/pancreas_mnn.h5ad b/src/batch_integration/resources/pancreas_mnn.h5ad new file mode 100644 index 0000000000000000000000000000000000000000..78ad89ce8da53e5c96da5b28da064826c7efdb43 GIT binary patch literal 3438982 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